@article {pmid30427935,
year = {2018},
author = {Schneider, P and Greischar, MA and Birget, PLG and Repton, C and Mideo, N and Reece, SE},
title = {Adaptive plasticity in the gametocyte conversion rate of malaria parasites.},
journal = {PLoS pathogens},
volume = {14},
number = {11},
pages = {e1007371},
doi = {10.1371/journal.ppat.1007371},
pmid = {30427935},
issn = {1553-7374},
support = {NE/K006029/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 202769/Z/16/Z//Wellcome Trust/United Kingdom ; },
mesh = {Adaptation, Biological/physiology ; Adaptation, Physiological/*physiology ; Animals ; Biological Evolution ; Computer Simulation ; Erythrocytes/parasitology ; Host-Parasite Interactions ; Malaria/*parasitology ; Models, Theoretical ; Parasites ; Plasmodium/*physiology ; Plasmodium chabaudi/physiology ; Reproduction/physiology ; Reproduction, Asexual/physiology ; },
abstract = {Sexually reproducing parasites, such as malaria parasites, experience a trade-off between the allocation of resources to asexual replication and the production of sexual forms. Allocation by malaria parasites to sexual forms (the conversion rate) is variable but the evolutionary drivers of this plasticity are poorly understood. We use evolutionary theory for life histories to combine a mathematical model and experiments to reveal that parasites adjust conversion rate according to the dynamics of asexual densities in the blood of the host. Our model predicts the direction of change in conversion rates that returns the greatest fitness after perturbation of asexual densities by different doses of antimalarial drugs. The loss of a high proportion of asexuals is predicted to elicit increased conversion (terminal investment), while smaller losses are managed by reducing conversion (reproductive restraint) to facilitate within-host survival and future transmission. This non-linear pattern of allocation is consistent with adaptive reproductive strategies observed in multicellular organisms. We then empirically estimate conversion rates of the rodent malaria parasite Plasmodium chabaudi in response to the killing of asexual stages by different doses of antimalarial drugs and forecast the short-term fitness consequences of these responses. Our data reveal the predicted non-linear pattern, and this is further supported by analyses of previous experiments that perturb asexual stage densities using drugs or within-host competition, across multiple parasite genotypes. Whilst conversion rates, across all datasets, are most strongly influenced by changes in asexual density, parasites also modulate conversion according to the availability of red blood cell resources. In summary, increasing conversion maximises short-term transmission and reducing conversion facilitates in-host survival and thus, future transmission. Understanding patterns of parasite allocation to reproduction matters because within-host replication is responsible for disease symptoms and between-host transmission determines disease spread.},
}
@article {pmid27870211,
year = {2016},
author = {Cunningham, JA and Vargas, K and Marone, F and Bengtson, S and Donoghue, PC},
title = {A multicellular organism with embedded cell clusters from the Ediacaran Weng'an biota (Doushantuo Formation, South China).},
journal = {Evolution & development},
volume = {18},
number = {5-6},
pages = {308-316},
doi = {10.1111/ede.12210},
pmid = {27870211},
issn = {1525-142X},
mesh = {*Biological Evolution ; China ; Eukaryota/ultrastructure ; Fossils/*anatomy & histology/ultrastructure ; Microscopy, Electron, Scanning ; },
abstract = {Three-dimensional analyses of the early Ediacaran microfossils from the Weng'an biota (Doushantuo Formation) have focused predominantly on multicellular forms that have been interpreted as embryos, and yet they have defied phylogenetic interpretation principally because of absence of evidence from other stages in their life cycle. It is therefore unfortunate that the affinities of the various other Doushantuo microfossils have been neglected. A new conical fossil that is preserved at a cellular level is described here. The fossil contains distinct cell clusters that are characterized and analysed in three dimensions. These clusters are often exposed at the specimen surface, and the fossil preserves many hemispherical craters that are interpreted as positions where clusters have left the organism. The cell clusters may be either reproductive propagules or infesting organisms. Similar clusters are found in a variety of Doushantuo organisms including putative animal embryos and algae.},
}
@article {pmid27549405,
year = {2016},
author = {Rödelsperger, C and Menden, K and Serobyan, V and Witte, H and Baskaran, P},
title = {First insights into the nature and evolution of antisense transcription in nematodes.},
journal = {BMC evolutionary biology},
volume = {16},
number = {1},
pages = {165},
pmid = {27549405},
issn = {1471-2148},
mesh = {Animals ; Biological Evolution ; Evolution, Molecular ; Gene Expression Regulation ; Gene Library ; Genes, Helminth ; *Introns ; Nematoda/*genetics ; Proteomics ; RNA, Antisense/*genetics ; Synteny ; Transcription, Genetic ; },
abstract = {BACKGROUND: The development of multicellular organisms is coordinated by various gene regulatory mechanisms that ensure correct spatio-temporal patterns of gene expression. Recently, the role of antisense transcription in gene regulation has moved into focus of research. To characterize genome-wide patterns of antisense transcription and to study their evolutionary conservation, we sequenced a strand-specific RNA-seq library of the nematode Pristionchus pacificus.<br><br>RESULTS: We identified 1112 antisense configurations of which the largest group represents 465 antisense transcripts (ASTs) that are fully embedded in introns of their host genes. We find that most ASTs show homology to protein-coding genes and are overrepresented in proteomic data. Together with the finding, that expression levels of ASTs and host genes are uncorrelated, this indicates that most ASTs in P. pacificus do not represent non-coding RNAs and do not exhibit regulatory functions on their host genes. We studied the evolution of antisense gene pairs across 20 nematode genomes, showing that the majority of pairs is lineage-specific and even the highly conserved vps-4, ddx-27, and sel-2 loci show abundant structural changes including duplications, deletions, intron gains and loss of antisense transcription. In contrast, host genes in general, are remarkably conserved and encode exceptionally long introns leading to unusually large blocks of conserved synteny.<br><br>CONCLUSIONS: Our study has shown that in P. pacificus antisense transcription as such does not define non-coding RNAs but is rather a feature of highly conserved genes with long introns. We hypothesize that the presence of regulatory elements imposes evolutionary constraint on the intron length, but simultaneously, their large size makes them a likely target for translocation of genomic elements including protein-coding genes that eventually end up as ASTs.},
}
@article {pmid30886348,
year = {2019},
author = {Talbert, PB and Meers, MP and Henikoff, S},
title = {Old cogs, new tricks: the evolution of gene expression in a chromatin context.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41576-019-0105-7},
pmid = {30886348},
issn = {1471-0064},
abstract = {Sophisticated gene-regulatory mechanisms probably evolved in prokaryotes billions of years before the emergence of modern eukaryotes, which inherited the same basic enzymatic machineries. However, the epigenomic landscapes of eukaryotes are dominated by nucleosomes, which have acquired roles in genome packaging, mitotic condensation and silencing parasitic genomic elements. Although the molecular mechanisms by which nucleosomes are displaced and modified have been described, just how transcription factors, histone variants and modifications and chromatin regulators act on nucleosomes to regulate transcription is the subject of considerable ongoing study. We explore the extent to which these transcriptional regulatory components function in the context of the evolutionarily ancient role of chromatin as a barrier to processes acting on DNA and how chromatin proteins have diversified to carry out evolutionarily recent functions that accompanied the emergence of differentiation and development in multicellular eukaryotes.},
}
@article {pmid30886148,
year = {2019},
author = {Xu, S and Stapley, J and Gablenz, S and Boyer, J and Appenroth, KJ and Sree, KS and Gershenzon, J and Widmer, A and Huber, M},
title = {Low genetic variation is associated with low mutation rate in the giant duckweed.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1243},
doi = {10.1038/s41467-019-09235-5},
pmid = {30886148},
issn = {2041-1723},
abstract = {Mutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. Here we investigate genetic diversity, spontaneous mutation rate and Ne in the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals reveals extremely low intraspecific genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereas Ne is large. These results demonstrate that low genetic diversity can be associated with large-Ne species, where selection can reduce mutation rates to very low levels. This study also highlights that accurate estimates of mutation rate can help to explain seemingly unexpected patterns of genome-wide variation.},
}
@article {pmid29575407,
year = {2018},
author = {Radzvilavicius, AL and Blackstone, NW},
title = {The evolution of individuality revisited.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {93},
number = {3},
pages = {1620-1633},
doi = {10.1111/brv.12412},
pmid = {29575407},
issn = {1469-185X},
mesh = {Animals ; *Biological Evolution ; Eukaryota ; Genetic Variation ; *Individuality ; *Models, Biological ; },
abstract = {Evolutionary theory is formulated in terms of individuals that carry heritable information and are subject to selective pressures. However, individuality itself is a trait that had to evolve - an individual is not an indivisible entity, but a result of evolutionary processes that necessarily begin at the lower level of hierarchical organisation. Traditional approaches to biological individuality focus on cooperation and relatedness within a group, division of labour, policing mechanisms and strong selection at the higher level. Nevertheless, despite considerable theoretical progress in these areas, a full dynamical first-principles account of how new types of individuals arise is missing. To the extent that individuality is an emergent trait, the problem can be approached by recognising the importance of individuating mechanisms that are present from the very beginning of the transition, when only lower-level selection is acting. Here we review some of the most influential theoretical work on the role of individuating mechanisms in these transitions, and demonstrate how a lower-level, bottom-up evolutionary framework can be used to understand biological complexity involved in the origin of cellular life, early eukaryotic evolution, sexual life cycles and multicellular development. Some of these mechanisms inevitably stem from environmental constraints, population structure and ancestral life cycles. Others are unique to specific transitions - features of the natural history and biochemistry that are co-opted into conflict mediation. Identifying mechanisms of individuation that provide a coarse-grained description of the system's evolutionary dynamics is an important step towards understanding how biological complexity and hierarchical organisation evolves. In this way, individuality can be reconceptualised as an approximate model that with varying degrees of precision applies to a wide range of biological systems.},
}
@article {pmid29597064,
year = {2018},
author = {Presting, GG},
title = {Centromeric retrotransposons and centromere function.},
journal = {Current opinion in genetics &amp; development},
volume = {49},
number = {},
pages = {79-84},
doi = {10.1016/j.gde.2018.03.004},
pmid = {29597064},
issn = {1879-0380},
mesh = {Centromere/*genetics ; DNA Breaks, Double-Stranded ; Eukaryota/genetics ; *Evolution, Molecular ; Retroelements/*genetics ; Tandem Repeat Sequences/*genetics ; },
abstract = {The centromeric DNA of most multicellular eukaryotes consists of tandem repeats (TR) that bind centromere-specific proteins and act as a substrate for the efficient repair of frequent double-stranded DNA breaks. Some retrotransposons target active centromeres during integration with such specificity that they can be used to deduce current and historic centromere positions. The roles of transposons in centromere function remain incompletely understood but appear to include maintaining centromere size and increasing the repeat content of neocentromeres that lack TR. Retrotransposons are known to give rise to TR. Centromere-targeting elements thus have the potential to replace centromeric TR essentially in situ, providing a mechanism to explain the centromere paradox, that is, the presence of unrelated centromeric TRs in closely related species.},
}
@article {pmid30763317,
year = {2019},
author = {Raza, Q and Choi, JY and Li, Y and O'Dowd, RM and Watkins, SC and Chikina, M and Hong, Y and Clark, NL and Kwiatkowski, AV},
title = {Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila.},
journal = {PLoS genetics},
volume = {15},
number = {2},
pages = {e1007720},
doi = {10.1371/journal.pgen.1007720},
pmid = {30763317},
issn = {1553-7404},
support = {R01 HL127711/HL/NHLBI NIH HHS/United States ; R01 HG009299/HG/NHGRI NIH HHS/United States ; R01 GM086423/GM/NIGMS NIH HHS/United States ; },
mesh = {Actin Cytoskeleton/metabolism ; Actins/*metabolism ; Adherens Junctions/metabolism ; Animals ; Cadherins/*metabolism ; Cell Adhesion/*physiology ; Cell Membrane/metabolism ; Cell Movement/physiology ; Circadian Rhythm Signaling Peptides and Proteins/*metabolism ; Drosophila/*metabolism ; Drosophila Proteins/*metabolism ; Signal Transduction/physiology ; },
abstract = {The adherens junction couples the actin cytoskeletons of neighboring cells to provide the foundation for multicellular organization. The core of the adherens junction is the cadherin-catenin complex that arose early in the evolution of multicellularity to link actin to intercellular adhesions. Over time, evolutionary pressures have shaped the signaling and mechanical functions of the adherens junction to meet specific developmental and physiological demands. Evolutionary rate covariation (ERC) identifies proteins with correlated fluctuations in evolutionary rate that can reflect shared selective pressures and functions. Here we use ERC to identify proteins with evolutionary histories similar to the Drosophila E-cadherin (DE-cad) ortholog. Core adherens junction components α-catenin and p120-catenin displayed positive ERC correlations with DE-cad, indicating that they evolved under similar selective pressures during evolution between Drosophila species. Further analysis of the DE-cad ERC profile revealed a collection of proteins not previously associated with DE-cad function or cadherin-mediated adhesion. We then analyzed the function of a subset of ERC-identified candidates by RNAi during border cell (BC) migration and identified novel genes that function to regulate DE-cad. Among these, we found that the gene CG42684, which encodes a putative GTPase activating protein (GAP), regulates BC migration and adhesion. We named CG42684 raskol (&quot;to split&quot; in Russian) and show that it regulates DE-cad levels and actin protrusions in BCs. We propose that Raskol functions with DE-cad to restrict Ras/Rho signaling and help guide BC migration. Our results demonstrate that a coordinated selective pressure has shaped the adherens junction and this can be leveraged to identify novel components of the complexes and signaling pathways that regulate cadherin-mediated adhesion.},
}
@article {pmid29632261,
year = {2018},
author = {Halatek, J and Brauns, F and Frey, E},
title = {Self-organization principles of intracellular pattern formation.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {373},
number = {1747},
pages = {},
pmid = {29632261},
issn = {1471-2970},
mesh = {Animals ; Caenorhabditis elegans/*genetics ; Caenorhabditis elegans Proteins/genetics ; Escherichia coli/*genetics ; Escherichia coli Proteins/genetics ; *Evolution, Molecular ; Models, Genetic ; Saccharomyces cerevisiae/*genetics ; cdc42 GTP-Binding Protein, Saccharomyces cerevisiae/genetics ; },
abstract = {Dynamic patterning of specific proteins is essential for the spatio-temporal regulation of many important intracellular processes in prokaryotes, eukaryotes and multicellular organisms. The emergence of patterns generated by interactions of diffusing proteins is a paradigmatic example for self-organization. In this article, we review quantitative models for intracellular Min protein patterns in Escherichia coli, Cdc42 polarization in Saccharomyces cerevisiae and the bipolar PAR protein patterns found in Caenorhabditis elegans By analysing the molecular processes driving these systems we derive a theoretical perspective on general principles underlying self-organized pattern formation. We argue that intracellular pattern formation is not captured by concepts such as 'activators', 'inhibitors' or 'substrate depletion'. Instead, intracellular pattern formation is based on the redistribution of proteins by cytosolic diffusion, and the cycling of proteins between distinct conformational states. Therefore, mass-conserving reaction-diffusion equations provide the most appropriate framework to study intracellular pattern formation. We conclude that directed transport, e.g. cytosolic diffusion along an actively maintained cytosolic gradient, is the key process underlying pattern formation. Thus the basic principle of self-organization is the establishment and maintenance of directed transport by intracellular protein dynamics.This article is part of the theme issue 'Self-organization in cell biology'.},
}
@article {pmid29373067,
year = {2017},
author = {Lindström, JB and Pierce, NT and Latz, MI},
title = {Role of TRP Channels in Dinoflagellate Mechanotransduction.},
journal = {The Biological bulletin},
volume = {233},
number = {2},
pages = {151-167},
doi = {10.1086/695421},
pmid = {29373067},
issn = {1939-8697},
mesh = {Biological Evolution ; Dinoflagellida/classification/genetics/*physiology ; Signal Transduction/genetics ; Transient Receptor Potential Channels/genetics/*metabolism ; },
abstract = {Transient receptor potential (TRP) ion channels are common components of mechanosensing pathways, mainly described in mammals and other multicellular organisms. To gain insight into the evolutionary origins of eukaryotic mechanosensory proteins, we investigated the involvement of TRP channels in mechanosensing in a unicellular eukaryotic protist, the dinoflagellate Lingulodinium polyedra. BLASTP analysis of the protein sequences predicted from the L. polyedra transcriptome revealed six sequences with high similarity to human TRPM2, TRPM8, TRPML2, TRPP1, and TRPP2; and characteristic TRP domains were identified in all sequences. In a phylogenetic tree including all mammalian TRP subfamilies and TRP channel sequences from unicellular and multicellular organisms, the L. polyedra sequences grouped with the TRPM, TPPML, and TRPP clades. In pharmacological experiments, we used the intrinsic bioluminescence of L. polyedra as a reporter of mechanoresponsivity. Capsaicin and RN1734, agonists of mammalian TRPV, and arachidonic acid, an agonist of mammalian TRPV, TRPA, TRPM, and Drosophila TRP, all stimulated bioluminescence in L. polyedra. Mechanical stimulation of bioluminescence, but not capsaicin-stimulated bioluminescence, was inhibited by gadolinium (Gd3+), a general inhibitor of mechanosensitive ion channels, and the phospholipase C (PLC) inhibitor U73122. These pharmacological results are consistent with the involvement of TRP-like channels in mechanosensing by L. polyedra. The TRP channels do not appear to be mechanoreceptors but rather are components of the mechanotransduction signaling pathway and may be activated via a PLC-dependent mechanism. The presence and function of TRP channels in a dinoflagellate emphasize the evolutionary conservation of both the channel structures and their functions.},
}
@article {pmid29294063,
year = {2018},
author = {Featherston, J and Arakaki, Y and Hanschen, ER and Ferris, PJ and Michod, RE and Olson, BJSC and Nozaki, H and Durand, PM},
title = {The 4-Celled Tetrabaena socialis Nuclear Genome Reveals the Essential Components for Genetic Control of Cell Number at the Origin of Multicellularity in the Volvocine Lineage.},
journal = {Molecular biology and evolution},
volume = {35},
number = {4},
pages = {855-870},
doi = {10.1093/molbev/msx332},
pmid = {29294063},
issn = {1537-1719},
mesh = {*Biological Evolution ; Chlorophyta/*genetics ; Cyclins/genetics ; Genes, Retinoblastoma ; *Genes, cdc ; *Genome Components ; Multigene Family ; Proteasome Endopeptidase Complex/genetics ; Selection, Genetic ; Transcriptome ; Ubiquitin/genetics ; },
abstract = {Multicellularity is the premier example of a major evolutionary transition in individuality and was a foundational event in the evolution of macroscopic biodiversity. The volvocine chlorophyte lineage is well suited for studying this process. Extant members span unicellular, simple colonial, and obligate multicellular taxa with germ-soma differentiation. Here, we report the nuclear genome sequence of one of the most morphologically simple organisms in this lineage-the 4-celled colonial Tetrabaena socialis and compare this to the three other complete volvocine nuclear genomes. Using conservative estimates of gene family expansions a minimal set of expanded gene families was identified that associate with the origin of multicellularity. These families are rich in genes related to developmental processes. A subset of these families is lineage specific, which suggests that at a genomic level the evolution of multicellularity also includes lineage-specific molecular developments. Multiple points of evidence associate modifications to the ubiquitin proteasomal pathway (UPP) with the beginning of coloniality. Genes undergoing positive or accelerating selection in the multicellular volvocines were found to be enriched in components of the UPP and gene families gained at the origin of multicellularity include components of the UPP. A defining feature of colonial/multicellular life cycles is the genetic control of cell number. The genomic data presented here, which includes diversification of cell cycle genes and modifications to the UPP, align the genetic components with the evolution of this trait.},
}
@article {pmid30410727,
year = {2018},
author = {Morris, JJ},
title = {What is the hologenome concept of evolution?.},
journal = {F1000Research},
volume = {7},
number = {},
pages = {},
pmid = {30410727},
issn = {2046-1402},
mesh = {Animals ; *Biological Evolution ; Biota ; Genome ; Humans ; Microbiota/*genetics ; Phenotype ; Selection, Genetic ; },
abstract = {All multicellular organisms are colonized by microbes, but a gestalt study of the composition of microbiome communities and their influence on the ecology and evolution of their macroscopic hosts has only recently become possible. One approach to thinking about the topic is to view the host-microbiome ecosystem as a &quot;holobiont&quot;. Because natural selection acts on an organism's realized phenotype, and the phenotype of a holobiont is the result of the integrated activities of both the host and all of its microbiome inhabitants, it is reasonable to think that evolution can act at the level of the holobiont and cause changes in the &quot;hologenome&quot;, or the collective genomic content of all the individual bionts within the holobiont. This relatively simple assertion has nevertheless been controversial within the microbiome community. Here, I provide a review of recent work on the hologenome concept of evolution. I attempt to provide a clear definition of the concept and its implications and to clarify common points of disagreement.},
}
@article {pmid30826447,
year = {2019},
author = {Fillinger, RJ and Anderson, MZ},
title = {Seasons of change: Mechanisms of genome evolution in human fungal pathogens.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.meegid.2019.02.031},
pmid = {30826447},
issn = {1567-7257},
abstract = {Fungi are a diverse kingdom of organisms capable of thriving in various niches across the world including those in close association with multicellular eukaryotes. Fungal pathogens that contribute to human disease reside both within the host as commensal organisms of the microbiota and the environment. Their niche of origin dictates how infection initiates but also places specific selective pressures on the fungal pathogen that contributes to its genome organization and genetic repertoire. Recent efforts to catalogue genomic variation among major human fungal pathogens have unveiled evolutionary themes that shape the fungal genome. Mechanisms ranging from large scale changes such as aneuploidy and ploidy cycling as well as more targeted mutations like base substitutions and gene copy number variations contribute to the evolution of these species, which are often under multiple competing selective pressures with their host, environment, and other microbes. Here, we provide an overview of the major selective pressures and mechanisms acting to evolve the genome of clinically important fungal pathogens of humans.},
}
@article {pmid30824779,
year = {2019},
author = {Kabir, M and Wenlock, S and Doig, AJ and Hentges, KE},
title = {The Essentiality Status of Mouse Duplicate Gene Pairs Correlates with Developmental Co-Expression Patterns.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {3224},
doi = {10.1038/s41598-019-39894-9},
pmid = {30824779},
issn = {2045-2322},
support = {BB/L018276/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/L018276/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
abstract = {During the evolution of multicellular eukaryotes, gene duplication occurs frequently to generate new genes and/or functions. A duplicated gene may have a similar function to its ancestral gene. Therefore, it may be expected that duplicated genes are less likely to be critical for the survival of an organism, since there are multiple copies of the gene rendering each individual copy redundant. In this study, we explored the developmental expression patterns of duplicate gene pairs and the relationship between development co-expression and phenotypes resulting from the knockout of duplicate genes in the mouse. We define genes that generate lethal phenotypes in single gene knockout experiments as essential genes. We found that duplicate gene pairs comprised of two essential genes tend to be expressed at different stages of development, compared to duplicate gene pairs with at least one non-essential member, showing that the timing of developmental expression affects the ability of one paralogue to compensate for the loss of the other. Gene essentiality, developmental expression and gene duplication are thus closely linked.},
}
@article {pmid29789717,
year = {2018},
author = {Al Habyan, S and Kalos, C and Szymborski, J and McCaffrey, L},
title = {Multicellular detachment generates metastatic spheroids during intra-abdominal dissemination in epithelial ovarian cancer.},
journal = {Oncogene},
volume = {37},
number = {37},
pages = {5127-5135},
pmid = {29789717},
issn = {1476-5594},
mesh = {Abdomen/*pathology ; Anoikis/physiology ; Ascites/pathology ; Carcinoma, Ovarian Epithelial/*pathology ; Cell Line, Tumor ; Drug Resistance, Neoplasm/physiology ; Female ; Humans ; Neoplasm Recurrence, Local/pathology ; Ovarian Neoplasms/*pathology ; Spheroids, Cellular/*pathology ; },
abstract = {Ovarian cancer is the most lethal gynecological cancer, where survival rates have had modest improvement over the last 30 years. Metastasis of cancer cells is a major clinical problem, and patient mortality occurs when ovarian cancer cells spread beyond the confinement of ovaries. Disseminated ovarian cancer cells typically spread within the abdomen, where ascites accumulation aids in their transit. Metastatic ascites contain multicellular spheroids, which promote chemo-resistance and recurrence. However, little is known about the origin and mechanisms through which spheroids arise. Using live-imaging of 3D culture models and animal models, we report that epithelial ovarian cancer (EOC) cells, the most common type of ovarian cancer, can spontaneously detach as either single cells or clusters. We report that clusters are more resistant to anoikis and have a potent survival advantage over single cells. Using in vivo lineage tracing, we found that multicellular spheroids arise preferentially from collective detachment, rather than aggregation in the abdomen. Finally, we report that multicellular spheroids from collective detachment are capable of seeding intra-abdominal metastases that retain intra-tumoral heterogeneity from the primary tumor.},
}
@article {pmid29425731,
year = {2018},
author = {Israel, MR and Morgan, M and Tay, B and Deuis, JR},
title = {Toxins as tools: Fingerprinting neuronal pharmacology.},
journal = {Neuroscience letters},
volume = {679},
number = {},
pages = {4-14},
doi = {10.1016/j.neulet.2018.02.001},
pmid = {29425731},
issn = {1872-7972},
mesh = {Animals ; Behavior Rating Scale ; Electrophysiology/methods ; Humans ; Ion Channel Gating/drug effects ; Ion Channels/chemistry/metabolism/pharmacology ; Models, Animal ; Neurons/*drug effects/physiology ; Neuropharmacology/*methods ; Neurotoxins/*pharmacology/*therapeutic use ; Sensory Receptor Cells/chemistry/*metabolism ; },
abstract = {Toxins have been used as tools for decades to study the structure and function of neuronal ion channels and receptors. The biological origin of these toxins varies from single cell organisms, including bacteria and algae, to complex multicellular organisms, including a wide variety of plants and venomous animals. Toxins are a structurally and functionally diverse group of compounds that often modulate neuronal function by interacting with an ion channel or receptor. Many of these toxins display high affinity and exquisite selectivity, making them valuable tools to probe the structure and function of neuronal ion channels and receptors. This review article provides an overview of the experimental techniques used to assess the effects that toxins have on neuronal function, as well as discussion on toxins that have been used as tools, with a focus on toxins that target voltage-gated and ligand-gated ion channels.},
}
@article {pmid30787193,
year = {2019},
author = {Dunning, LT and Olofsson, JK and Parisod, C and Choudhury, RR and Moreno-Villena, JJ and Yang, Y and Dionora, J and Quick, WP and Park, M and Bennetzen, JL and Besnard, G and Nosil, P and Osborne, CP and Christin, PA},
title = {Lateral transfers of large DNA fragments spread functional genes among grasses.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1810031116},
pmid = {30787193},
issn = {1091-6490},
abstract = {A fundamental tenet of multicellular eukaryotic evolution is that vertical inheritance is paramount, with natural selection acting on genetic variants transferred from parents to offspring. This lineal process means that an organism's adaptive potential can be restricted by its evolutionary history, the amount of standing genetic variation, and its mutation rate. Lateral gene transfer (LGT) theoretically provides a mechanism to bypass many of these limitations, but the evolutionary importance and frequency of this process in multicellular eukaryotes, such as plants, remains debated. We address this issue by assembling a chromosome-level genome for the grass Alloteropsis semialata, a species surmised to exhibit two LGTs, and screen it for other grass-to-grass LGTs using genomic data from 146 other grass species. Through stringent phylogenomic analyses, we discovered 57 additional LGTs in the A. semialata nuclear genome, involving at least nine different donor species. The LGTs are clustered in 23 laterally acquired genomic fragments that are up to 170 kb long and have accumulated during the diversification of Alloteropsis. The majority of the 59 LGTs in A. semialata are expressed, and we show that they have added functions to the recipient genome. Functional LGTs were further detected in the genomes of five other grass species, demonstrating that this process is likely widespread in this globally important group of plants. LGT therefore appears to represent a potent evolutionary force capable of spreading functional genes among distantly related grass species.},
}
@article {pmid30764885,
year = {2019},
author = {Lipinska, AP and Serrano-Serrano, ML and Cormier, A and Peters, AF and Kogame, K and Cock, JM and Coelho, SM},
title = {Rapid turnover of life-cycle-related genes in the brown algae.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {35},
doi = {10.1186/s13059-019-1630-6},
pmid = {30764885},
issn = {1474-760X},
support = {638240//FP7 Ideas: European Research Council/ ; },
abstract = {BACKGROUND: Sexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, many plants and algae alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. In many algae, gametophytes and sporophytes are independent and free-living and may present dramatic phenotypic differences. The same shared genome can therefore be subject to different, even conflicting, selection pressures during each of the life cycle generations. Here, we analyze the nature and extent of genome-wide, generation-biased gene expression in four species of brown algae with contrasting levels of dimorphism between life cycle generations.<br><br>RESULTS: We show that the proportion of the transcriptome that is generation-specific is broadly associated with the level of phenotypic dimorphism between the life cycle stages. Importantly, our data reveals a remarkably high turnover rate for life-cycle-related gene sets across the brown algae and highlights the importance not only of co-option of regulatory programs from one generation to the other but also of a role for newly emerged, lineage-specific gene expression patterns in the evolution of the gametophyte and sporophyte developmental programs in this major eukaryotic group. Moreover, we show that generation-biased genes display distinct evolutionary modes, with gametophyte-biased genes evolving rapidly at the coding sequence level whereas sporophyte-biased genes tend to exhibit changes in their patterns of expression.<br><br>CONCLUSION: Our analysis uncovers the characteristics, expression patterns, and evolution of generation-biased genes and underlines the selective forces that shape this previously underappreciated source of phenotypic diversity.},
}
@article {pmid29069493,
year = {2018},
author = {Gao, D and Chu, Y and Xia, H and Xu, C and Heyduk, K and Abernathy, B and Ozias-Akins, P and Leebens-Mack, JH and Jackson, SA},
title = {Horizontal Transfer of Non-LTR Retrotransposons from Arthropods to Flowering Plants.},
journal = {Molecular biology and evolution},
volume = {35},
number = {2},
pages = {354-364},
pmid = {29069493},
issn = {1537-1719},
mesh = {Animals ; Arachis/*genetics ; Arthropods/*genetics ; Base Sequence ; *Gene Transfer, Horizontal ; Genome, Plant ; Phylogeny ; *Retroelements ; Sequence Homology, Nucleic Acid ; },
abstract = {Even though lateral movements of transposons across families and even phyla within multicellular eukaryotic kingdoms have been found, little is known about transposon transfer between the kingdoms Animalia and Plantae. We discovered a novel non-LTR retrotransposon, AdLINE3, in a wild peanut species. Sequence comparisons and phylogenetic analyses indicated that AdLINE3 is a member of the RTE clade, originally identified in a nematode and rarely reported in plants. We identified RTE elements in 82 plants, spanning angiosperms to algae, including recently active elements in some flowering plants. RTE elements in flowering plants were likely derived from a single family we refer to as An-RTE. Interestingly, An-RTEs show significant DNA sequence identity with non-LTR retroelements from 42 animals belonging to four phyla. Moreover, the sequence identity of RTEs between two arthropods and two plants was higher than that of homologous genes. Phylogenetic and evolutionary analyses of RTEs from both animals and plants suggest that the An-RTE family was likely transferred horizontally into angiosperms from an ancient aphid(s) or ancestral arthropod(s). Notably, some An-RTEs were recruited as coding sequences of functional genes participating in metabolic or other biochemical processes in plants. This is the first potential example of horizontal transfer of transposons between animals and flowering plants. Our findings help to understand exchanges of genetic material between the kingdom Animalia and Plantae and suggest arthropods likely impacted on plant genome evolution.},
}
@article {pmid30760850,
year = {2019},
author = {Junqueira Alves, C and Yotoko, K and Zou, H and Friedel, RH},
title = {Origin and evolution of plexins, semaphorins, and Met receptor tyrosine kinases.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {1970},
doi = {10.1038/s41598-019-38512-y},
pmid = {30760850},
issn = {2045-2322},
support = {R01 NS092735//U.S. Department of Health &amp; Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; },
abstract = {The transition from unicellular to multicellular organisms poses the question as to when genes that regulate cell-cell interactions emerged during evolution. The receptor and ligand pairing of plexins and semaphorins regulates cellular interactions in a wide range of developmental and physiological contexts. We surveyed here genomes of unicellular eukaryotes and of non-bilaterian and bilaterian Metazoa and performed phylogenetic analyses to gain insight into the evolution of plexin and semaphorin families. Remarkably, we detected plexins and semaphorins in unicellular choanoflagellates, indicating their evolutionary origin in a common ancestor of Choanoflagellida and Metazoa. The plexin domain structure is conserved throughout all clades; in contrast, semaphorins are structurally diverse. Choanoflagellate semaphorins are transmembrane proteins with multiple fibronectin type III domains following the N-terminal Sema domain (termed Sema-FN). Other previously not yet described semaphorin classes include semaphorins of Ctenophora with tandem immunoglobulin domains (Sema-IG) and secreted semaphorins of Echinoderamata (Sema-SP, Sema-SI). Our study also identified Met receptor tyrosine kinases (RTKs), which carry a truncated plexin extracellular domain, in several bilaterian clades, indicating evolutionary origin in a common ancestor of Bilateria. In addition, a novel type of Met-like RTK with a complete plexin extracellular domain was detected in Lophotrochozoa and Echinodermata (termed Met-LP RTK). Our findings are consistent with an ancient function of plexins and semaphorins in regulating cytoskeletal dynamics and cell adhesion that predates their role as axon guidance molecules.},
}
@article {pmid30760717,
year = {2019},
author = {Ferrari, C and Proost, S and Janowski, M and Becker, J and Nikoloski, Z and Bhattacharya, D and Price, D and Tohge, T and Bar-Even, A and Fernie, A and Stitt, M and Mutwil, M},
title = {Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {737},
doi = {10.1038/s41467-019-08703-2},
pmid = {30760717},
issn = {2041-1723},
abstract = {Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.},
}
@article {pmid29880641,
year = {2018},
author = {Miller, PW and Pokutta, S and Mitchell, JM and Chodaparambil, JV and Clarke, DN and Nelson, WJ and Weis, WI and Nichols, SA},
title = {Analysis of a vinculin homolog in a sponge (phylum Porifera) reveals that vertebrate-like cell adhesions emerged early in animal evolution.},
journal = {The Journal of biological chemistry},
volume = {293},
number = {30},
pages = {11674-11686},
pmid = {29880641},
issn = {1083-351X},
support = {P41 GM103393/GM/NIGMS NIH HHS/United States ; R01 GM114462/GM/NIGMS NIH HHS/United States ; R35 GM118064/GM/NIGMS NIH HHS/United States ; },
mesh = {Actins/analysis/metabolism ; Animals ; Cell Adhesion ; Focal Adhesions/metabolism ; Models, Molecular ; Porifera/*cytology/metabolism/ultrastructure ; Protein Binding ; Protein Conformation ; Pseudopodia/metabolism/ultrastructure ; Talin/analysis/metabolism ; Vinculin/analysis/*metabolism ; },
abstract = {The evolution of cell-adhesion mechanisms in animals facilitated the assembly of organized multicellular tissues. Studies in traditional animal models have revealed two predominant adhesion structures, the adherens junction (AJ) and focal adhesions (FAs), which are involved in the attachment of neighboring cells to each other and to the secreted extracellular matrix (ECM), respectively. The AJ (containing cadherins and catenins) and FAs (comprising integrins, talin, and paxillin) differ in protein composition, but both junctions contain the actin-binding protein vinculin. The near ubiquity of these structures in animals suggests that AJ and FAs evolved early, possibly coincident with multicellularity. However, a challenge to this perspective is that previous studies of sponges-a divergent animal lineage-indicate that their tissues are organized primarily by an alternative, sponge-specific cell-adhesion mechanism called &quot;aggregation factor.&quot; In this study, we examined the structure, biochemical properties, and tissue localization of a vinculin ortholog in the sponge Oscarella pearsei (Op). Our results indicate that Op vinculin localizes to both cell-cell and cell-ECM contacts and has biochemical and structural properties similar to those of vertebrate vinculin. We propose that Op vinculin played a role in cell adhesion and tissue organization in the last common ancestor of sponges and other animals. These findings provide compelling evidence that sponge tissues are indeed organized like epithelia in other animals and support the notion that AJ- and FA-like structures extend to the earliest periods of animal evolution.},
}
@article {pmid30532226,
year = {2018},
author = {Shan, M and Dai, D and Vudem, A and Varner, JD and Stroock, AD},
title = {Multi-scale computational study of the Warburg effect, reverse Warburg effect and glutamine addiction in solid tumors.},
journal = {PLoS computational biology},
volume = {14},
number = {12},
pages = {e1006584},
doi = {10.1371/journal.pcbi.1006584},
pmid = {30532226},
issn = {1553-7358},
mesh = {Cell Line, Tumor ; Cell Proliferation ; Citric Acid Cycle/physiology ; Glucose/metabolism ; Glutamine/*metabolism ; Glycolysis/*physiology ; Humans ; Kinetics ; Lactic Acid/metabolism ; Metabolic Networks and Pathways/physiology ; Metabolome ; Neoplasms/metabolism ; Oxygen/metabolism ; Tumor Microenvironment/*physiology ; },
abstract = {Cancer metabolism has received renewed interest as a potential target for cancer therapy. In this study, we use a multi-scale modeling approach to interrogate the implications of three metabolic scenarios of potential clinical relevance: the Warburg effect, the reverse Warburg effect and glutamine addiction. At the intracellular level, we construct a network of central metabolism and perform flux balance analysis (FBA) to estimate metabolic fluxes; at the cellular level, we exploit this metabolic network to calculate parameters for a coarse-grained description of cellular growth kinetics; and at the multicellular level, we incorporate these kinetic schemes into the cellular automata of an agent-based model (ABM), iDynoMiCS. This ABM evaluates the reaction-diffusion of the metabolites, cellular division and motion over a simulation domain. Our multi-scale simulations suggest that the Warburg effect provides a growth advantage to the tumor cells under resource limitation. However, we identify a non-monotonic dependence of growth rate on the strength of glycolytic pathway. On the other hand, the reverse Warburg scenario provides an initial growth advantage in tumors that originate deeper in the tissue. The metabolic profile of stromal cells considered in this scenario allows more oxygen to reach the tumor cells in the deeper tissue and thus promotes tumor growth at earlier stages. Lastly, we suggest that glutamine addiction does not confer a selective advantage to tumor growth with glutamine acting as a carbon source in the tricarboxylic acid (TCA) cycle, any advantage of glutamine uptake must come through other pathways not included in our model (e.g., as a nitrogen donor). Our analysis illustrates the importance of accounting explicitly for spatial and temporal evolution of tumor microenvironment in the interpretation of metabolic scenarios and hence provides a basis for further studies, including evaluation of specific therapeutic strategies that target metabolism.},
}
@article {pmid29381236,
year = {2018},
author = {Li, Y and Zuo, S and Zhang, Z and Li, Z and Han, J and Chu, Z and Hasterok, R and Wang, K},
title = {Centromeric DNA characterization in the model grass Brachypodium distachyon provides insights on the evolution of the genus.},
journal = {The Plant journal : for cell and molecular biology},
volume = {93},
number = {6},
pages = {1088-1101},
doi = {10.1111/tpj.13832},
pmid = {29381236},
issn = {1365-313X},
mesh = {Amino Acid Sequence ; Brachypodium/classification/*genetics/metabolism ; Centromere/*genetics/metabolism ; Chromosomes, Plant/genetics/metabolism ; DNA, Plant/*genetics/metabolism ; Evolution, Molecular ; Genome, Plant/*genetics ; Histones/genetics/metabolism ; In Situ Hybridization, Fluorescence ; Nucleosomes/genetics/metabolism ; Phylogeny ; Plant Proteins/genetics/metabolism ; Polyploidy ; Protein Binding ; Sequence Homology, Amino Acid ; },
abstract = {Brachypodium distachyon is a well-established model monocot plant, and its small and compact genome has been used as an accurate reference for the much larger and often polyploid genomes of cereals such as Avena sativa (oats), Hordeum vulgare (barley) and Triticum aestivum (wheat). Centromeres are indispensable functional units of chromosomes and they play a core role in genome polyploidization events during evolution. As the Brachypodium genus contains about 20 species that differ significantly in terms of their basic chromosome numbers, genome size, ploidy levels and life strategies, studying their centromeres may provide important insight into the structure and evolution of the genome in this interesting and important genus. In this study, we isolated the centromeric DNA of the B. distachyon reference line Bd21 and characterized its composition via the chromatin immunoprecipitation of the nucleosomes that contain the centromere-specific histone CENH3. We revealed that the centromeres of Bd21 have the features of typical multicellular eukaryotic centromeres. Strikingly, these centromeres contain relatively few centromeric satellite DNAs; in particular, the centromere of chromosome 5 (Bd5) consists of only ~40 kb. Moreover, the centromeric retrotransposons in B. distachyon (CRBds) are evolutionarily young. These transposable elements are located both within and adjacent to the CENH3 binding domains, and have similar compositions. Moreover, based on the presence of CRBds in the centromeres, the species in this study can be grouped into two distinct lineages. This may provide new evidence regarding the phylogenetic relationships within the Brachypodium genus.},
}
@article {pmid29738987,
year = {2018},
author = {Tasic, B},
title = {Single cell transcriptomics in neuroscience: cell classification and beyond.},
journal = {Current opinion in neurobiology},
volume = {50},
number = {},
pages = {242-249},
doi = {10.1016/j.conb.2018.04.021},
pmid = {29738987},
issn = {1873-6882},
mesh = {Animals ; Biological Evolution ; Humans ; Neurons/classification/*metabolism ; *Neurosciences ; Single-Cell Analysis/methods ; Transcriptome/*physiology ; },
abstract = {Biology has been facing a daunting problem since the cell was understood to be the building block of metazoans: how do we study multicellular systems, when a universal approach to characterize their building blocks and classify them does not exist? Metazoan diversity has not helped: there are many model and non-model organisms, developmental and adult stages, healthy and diseased states. Here, I review the application of single cell transcriptomics to cell classification in neuroscience and its corollaries: the differentially expressed genes discovered in this process are a treasure trove for understanding cell type function and enabling specific access to those types. The advancements and widespread adoption of single-cell transcriptomics are bound to transform our understanding of neural system development, function, pathology and evolution.},
}
@article {pmid30500812,
year = {2018},
author = {Medina-Castellanos, E and Villalobos-Escobedo, JM and Riquelme, M and Read, ND and Abreu-Goodger, C and Herrera-Estrella, A},
title = {Danger signals activate a putative innate immune system during regeneration in a filamentous fungus.},
journal = {PLoS genetics},
volume = {14},
number = {11},
pages = {e1007390},
doi = {10.1371/journal.pgen.1007390},
pmid = {30500812},
issn = {1553-7404},
mesh = {Adenosine Triphosphate/metabolism ; Animals ; Biomarkers ; Calcium/metabolism ; Gene Expression Regulation, Fungal ; *Host-Pathogen Interactions ; Hyphae ; *Immunity, Innate ; Mycoses/immunology/*microbiology ; *Regeneration ; *Signal Transduction ; Trichoderma/*physiology ; },
abstract = {The ability to respond to injury is a biological process shared by organisms of different kingdoms that can even result in complete regeneration of a part or structure that was lost. Due to their immobility, multicellular fungi are prey to various predators and are therefore constantly exposed to mechanical damage. Nevertheless, our current knowledge of how fungi respond to injury is scarce. Here we show that activation of injury responses and hyphal regeneration in the filamentous fungus Trichoderma atroviride relies on the detection of two danger or alarm signals. As an early response to injury, we detected a transient increase in cytosolic free calcium ([Ca2+]c) that was promoted by extracellular ATP, and which is likely regulated by a mechanism of calcium-induced calcium-release. In addition, we demonstrate that the mitogen activated protein kinase Tmk1 plays a key role in hyphal regeneration. Calcium- and Tmk1-mediated signaling cascades activated major transcriptional changes early following injury, including induction of a set of regeneration associated genes related to cell signaling, stress responses, transcription regulation, ribosome biogenesis/translation, replication and DNA repair. Interestingly, we uncovered the activation of a putative fungal innate immune response, including the involvement of HET domain genes, known to participate in programmed cell death. Our work shows that fungi and animals share danger-signals, signaling cascades, and the activation of the expression of genes related to immunity after injury, which are likely the result of convergent evolution.},
}
@article {pmid30362942,
year = {2018},
author = {Castiglione, GM and Chang, BS},
title = {Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
pmid = {30362942},
issn = {2050-084X},
support = {Discovery grant//Natural Sciences and Engineering Research Council of Canada/International ; },
mesh = {*Adaptation, Biological ; Animals ; *Biological Evolution ; Epistasis, Genetic ; Light ; Rhodopsin/genetics ; Selection, Genetic ; *Vertebrates ; Vision, Ocular/*physiology ; },
abstract = {Trade-offs between protein stability and activity can restrict access to evolutionary trajectories, but widespread epistasis may facilitate indirect routes to adaptation. This may be enhanced by natural environmental variation, but in multicellular organisms this process is poorly understood. We investigated a paradoxical trajectory taken during the evolution of tetrapod dim-light vision, where in the rod visual pigment rhodopsin, E122 was fixed 350 million years ago, a residue associated with increased active-state (MII) stability but greatly diminished rod photosensitivity. Here, we demonstrate that high MII stability could have likely evolved without E122, but instead, selection appears to have entrenched E122 in tetrapods via epistatic interactions with nearby coevolving sites. In fishes by contrast, selection may have exploited these epistatic effects to explore alternative trajectories, but via indirect routes with low MII stability. Our results suggest that within tetrapods, E122 and high MII stability cannot be sacrificed-not even for improvements to rod photosensitivity.},
}
@article {pmid30102347,
year = {2018},
author = {Gaouda, H and Hamaji, T and Yamamoto, K and Kawai-Toyooka, H and Suzuki, M and Noguchi, H and Minakuchi, Y and Toyoda, A and Fujiyama, A and Nozaki, H and Smith, DR},
title = {Exploring the Limits and Causes of Plastid Genome Expansion in Volvocine Green Algae.},
journal = {Genome biology and evolution},
volume = {10},
number = {9},
pages = {2248-2254},
pmid = {30102347},
issn = {1759-6653},
mesh = {Chlorophyta/genetics ; DNA, Algal/*genetics ; Evolution, Molecular ; *Genome, Plastid ; Plastids/genetics ; Sequence Analysis, DNA ; Volvox/*genetics ; },
abstract = {Plastid genomes are not normally celebrated for being large. But researchers are steadily uncovering algal lineages with big and, in rare cases, enormous plastid DNAs (ptDNAs), such as volvocine green algae. Plastome sequencing of five different volvocine species has revealed some of the largest, most repeat-dense plastomes on record, including that of Volvox carteri (∼525 kb). Volvocine algae have also been used as models for testing leading hypotheses on organelle genome evolution (e.g., the mutational hazard hypothesis), and it has been suggested that ptDNA inflation within this group might be a consequence of low mutation rates and/or the transition from a unicellular to multicellular existence. Here, we further our understanding of plastome size variation in the volvocine line by examining the ptDNA sequences of the colonial species Yamagishiella unicocca and Eudorina sp. NIES-3984 and the multicellular Volvox africanus, which are phylogenetically situated between species with known ptDNA sizes. Although V. africanus is closely related and similar in multicellular organization to V. carteri, its ptDNA was much less inflated than that of V. carteri. Synonymous- and noncoding-site nucleotide substitution rate analyses of these two Volvox ptDNAs suggest that there are drastically different plastid mutation rates operating in the coding versus intergenic regions, supporting the idea that error-prone DNA repair in repeat-rich intergenic spacers is contributing to genome expansion. Our results reinforce the idea that the volvocine line harbors extremes in plastome size but ultimately shed doubt on some of the previously proposed hypotheses for ptDNA inflation within the lineage.},
}
@article {pmid30473004,
year = {2018},
author = {Gruenheit, N and Parkinson, K and Brimson, CA and Kuwana, S and Johnson, EJ and Nagayama, K and Llewellyn, J and Salvidge, WM and Stewart, B and Keller, T and van Zon, W and Cotter, SL and Thompson, CRL},
title = {Cell Cycle Heterogeneity Can Generate Robust Cell Type Proportioning.},
journal = {Developmental cell},
volume = {47},
number = {4},
pages = {494-508.e4},
pmid = {30473004},
issn = {1878-1551},
support = {//Wellcome Trust/United Kingdom ; 095643/A/11/Z//Wellcome Trust/United Kingdom ; 101582/Z/13/Z//Wellcome Trust/United Kingdom ; 105610/Z/14/Z//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Cell Cycle/*physiology ; Cell Differentiation/*physiology ; Cell Division/*physiology ; Cell Lineage/physiology ; Dictyostelium/*metabolism ; Spores, Fungal/metabolism ; },
abstract = {Cell-cell heterogeneity can facilitate lineage choice during embryonic development because it primes cells to respond to differentiation cues. However, remarkably little is known about the origin of heterogeneity or whether intrinsic and extrinsic variation can be controlled to generate reproducible cell type proportioning seen in vivo. Here, we use experimentation and modeling in D. discoideum to demonstrate that population-level cell cycle heterogeneity can be optimized to generate robust cell fate proportioning. First, cell cycle position is quantitatively linked to responsiveness to differentiation-inducing signals. Second, intrinsic variation in cell cycle length ensures cells are randomly distributed throughout the cell cycle at the onset of multicellular development. Finally, extrinsic perturbation of optimal cell cycle heterogeneity is buffered by compensatory changes in global signal responsiveness. These studies thus illustrate key regulatory principles underlying cell-cell heterogeneity optimization and the generation of robust and reproducible fate choice in development.},
}
@article {pmid30089142,
year = {2018},
author = {Tverskoi, D and Makarenkov, V and Aleskerov, F},
title = {Modeling functional specialization of a cell colony under different fecundity and viability rates and resource constraint.},
journal = {PloS one},
volume = {13},
number = {8},
pages = {e0201446},
pmid = {30089142},
issn = {1932-6203},
mesh = {Biological Evolution ; Cell Communication/*physiology ; Cell Differentiation/*physiology ; Cell Survival/physiology ; Chlorophyta/cytology/*physiology ; Fertility/*physiology ; Germ Cells, Plant/physiology ; *Models, Biological ; },
abstract = {The emergence of functional specialization is a core problem in biology. In this work we focus on the emergence of reproductive (germ) and vegetative viability-enhancing (soma) cell functions (or germ-soma specialization). We consider a group of cells and assume that they contribute to two different evolutionary tasks, fecundity and viability. The potential of cells to contribute to fitness components is traded off. As embodied in current models, the curvature of the trade-off between fecundity and viability is concave in small-sized organisms and convex in large-sized multicellular organisms. We present a general mathematical model that explores how the division of labor in a cell colony depends on the trade-off curvatures, a resource constraint and different fecundity and viability rates. Moreover, we consider the case of different trade-off functions for different cells. We describe the set of all possible solutions of the formulated mathematical programming problem and show some interesting examples of optimal specialization strategies found for our objective fitness function. Our results suggest that the transition to specialized organisms can be achieved in several ways. The evolution of Volvocalean green algae is considered to illustrate the application of our model. The proposed model can be generalized to address a number of important biological issues, including the evolution of specialized enzymes and the emergence of complex organs.},
}
@article {pmid29512128,
year = {2018},
author = {Flamier, A and Singh, S and Rasmussen, TP},
title = {Use of Human Embryoid Bodies for Teratology.},
journal = {Current protocols in toxicology},
volume = {75},
number = {},
pages = {13.13.1-13.13.14},
doi = {10.1002/cptx.38},
pmid = {29512128},
issn = {1934-9262},
mesh = {Embryoid Bodies/*drug effects ; Embryonic Stem Cells/drug effects ; Humans ; Pluripotent Stem Cells/drug effects ; Teratology/*methods ; Toxicity Tests/methods ; },
abstract = {Human birth defects are relatively common and can be caused by exposure to environmental teratogens or to pharmaceuticals with teratogenic activities. Human embryonic stem cells (hESCs), by virtue of their pluripotent nature, provide an excellent cellular platform for teratogen detection and risk assessment. This unit describes detailed protocols for the preparation and validation of highly pluripotent hESCs, the production of large quantities of aggregated multicellular spheroids composed of hESCs, and these spheroids' differentiation into embryoid bodies (EBs). EBs contain a variety of cells of endodermal, ectodermal, and mesodermal origin and can be subjected to compound exposure in vitro. Hence, they are useful for the detection of chemicals with teratogenic activities. Beyond describing protocols to assemble and culture EBs, this unit details methods to exploit the EB system for teratological assessment. In addition, strategies to distinguish compounds with bona fide teratogenic activity versus simple toxicity are discussed. © 2018 by John Wiley &amp; Sons, Inc.},
}
@article {pmid30667071,
year = {2019},
author = {Coelho, SM and Mignerot, L and Cock, JM},
title = {Origin and evolution of sex-determination systems in the brown algae.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.15694},
pmid = {30667071},
issn = {1469-8137},
abstract = {Sexual reproduction is a nearly universal feature of eukaryotic organisms. Meiosis appears to have had a single ancient origin but the mechanisms underlying male or female sex determination are diverse and have emerged repeatedly and independently in the different eukaryotic groups. The brown algae are a group of multicellular photosynthetic eukaryotes that have a distinct evolutionary history compared with animals and plants, as they have been evolving independently for over a billion years. Here, we review recent work using the brown alga Ectocarpus as a model organism to study haploid sex chromosomes, and highlight how the diversity of reproductive and life cycle features of the brown algae offer unique opportunities to characterise the evolutionary forces and the mechanisms underlying the evolution of sex determination. This article is protected by copyright. All rights reserved.},
}
@article {pmid29337961,
year = {2018},
author = {Trigos, AS and Pearson, RB and Papenfuss, AT and Goode, DL},
title = {How the evolution of multicellularity set the stage for cancer.},
journal = {British journal of cancer},
volume = {118},
number = {2},
pages = {145-152},
pmid = {29337961},
issn = {1532-1827},
mesh = {Animals ; Biological Evolution ; Gene Regulatory Networks ; Humans ; Neoplasms/*genetics/*pathology ; },
abstract = {Neoplastic growth and many of the hallmark properties of cancer are driven by the disruption of molecular networks established during the emergence of multicellularity. Regulatory pathways and molecules that evolved to impose regulatory constraints upon networks established in earlier unicellular organisms enabled greater communication and coordination between the diverse cell types required for multicellularity, but also created liabilities in the form of points of vulnerability in the network that when mutated or dysregulated facilitate the development of cancer. These factors are usually overlooked in genomic analyses of cancer, but understanding where vulnerabilities to cancer lie in the networks of multicellular species would provide important new insights into how core molecular processes and gene regulation change during tumourigenesis. We describe how the evolutionary origins of genes influence their roles in cancer, and how connections formed between unicellular and multicellular genes that act as key regulatory hubs for normal tissue homeostasis can also contribute to malignant transformation when disrupted. Tumours in general are characterised by increased dependence on unicellular processes for survival, and major dysregulation of the control structures imposed on these processes during the evolution of multicellularity. Mounting molecular evidence suggests altered interactions at the interface between unicellular and multicellular genes play key roles in the initiation and progression of cancer. Furthermore, unicellular network regions activated in cancer show high degrees of robustness and plasticity, conferring increased adaptability to tumour cells by supporting effective responses to environmental pressures such as drug exposure. Examining how the links between multicellular and unicellular regions get disrupted in tumours has great potential to identify novel drivers of cancer, and to guide improvements to cancer treatment by identifying more effective therapeutic strategies. Recent successes in targeting unicellular processes by novel compounds underscore the logic of such approaches. Further gains could come from identifying genes at the interface between unicellular and multicellular processes and manipulating the communication between network regions of different evolutionary ages.},
}
@article {pmid30649338,
year = {2019},
author = {Russell, SL},
title = {Transmission mode is associated with environment type and taxa across bacteria-eukaryote symbioses: a systematic review and meta-analysis.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnz013},
pmid = {30649338},
issn = {1574-6968},
abstract = {Symbiotic associations between bacteria and eukaryotes exhibit a range of transmission strategies. The rates and distributions of transmission modes have not been thoroughly investigated across associations, despite their consequences on symbiont and host evolution. To address this empirically, I compiled data from the literature on bacteria-multicellular eukaryote associations for which transmission mode data was available. Of the total 528 analyzed symbioses, 21.2% were strictly horizontally transmitted, 36.0% exhibited some form of mixed mode transmission, and 42.8% were strictly vertically transmitted. Controlling for phylogenetically independent symbiosis events revealed modes were approximately equally distributed among the 113 independent associations, at 32.1 + /-0.57% horizontal, 37.8 + /-1.4% mixed mode, and 31.1 + /-1.3% vertical transmission. Binning symbioses by environment revealed an abundance of vertical transmission on land and a lack of it in aquatic environments. The naturally-occurring uneven distribution of taxa among environments prevented controlling for host/symbiont phylogeny. However, the results were robust over a large number of independently evolved associations, suggesting that many vertically transmitted bacteria are capable of horizontal transmission and barriers exist that reduce the rate of these events. Thus, both the environment type and host/symbiont taxa influence symbiont transmission mode evolution.},
}
@article {pmid29175233,
year = {2018},
author = {Miller, WB},
title = {Biological information systems: Evolution as cognition-based information management.},
journal = {Progress in biophysics and molecular biology},
volume = {134},
number = {},
pages = {1-26},
doi = {10.1016/j.pbiomolbio.2017.11.005},
pmid = {29175233},
issn = {1873-1732},
mesh = {Animals ; *Biological Evolution ; Cells/cytology/metabolism ; Cognition ; Humans ; },
abstract = {An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses.},
}
@article {pmid29340409,
year = {2018},
author = {Ray, A and Morford, RK and Ghaderi, N and Odde, DJ and Provenzano, PP},
title = {Dynamics of 3D carcinoma cell invasion into aligned collagen.},
journal = {Integrative biology : quantitative biosciences from nano to macro},
volume = {10},
number = {2},
pages = {100-112},
pmid = {29340409},
issn = {1757-9708},
support = {R01 CA172986/CA/NCI NIH HHS/United States ; R01 CA181385/CA/NCI NIH HHS/United States ; U54 CA210190/CA/NCI NIH HHS/United States ; },
mesh = {Breast Neoplasms/metabolism/pathology ; Carcinoma/metabolism/*pathology ; Cell Line, Tumor ; Cell Movement/physiology ; Collagen/metabolism ; Extracellular Matrix/metabolism/pathology ; Female ; Humans ; Imaging, Three-Dimensional ; Microscopy, Fluorescence, Multiphoton ; Models, Biological ; Neoplasm Invasiveness/*pathology/physiopathology ; Systems Biology ; },
abstract = {Carcinoma cells frequently expand and invade from a confined lesion, or multicellular clusters, into and through the stroma on the path to metastasis, often with an efficiency dictated by the architecture and composition of the microenvironment. Specifically, in desmoplastic carcinomas such as those of the breast, aligned collagen tracks provide contact guidance cues for directed cancer cell invasion. Yet, the evolving dynamics of this process of invasion remains poorly understood, in part due to difficulties in continuously capturing both spatial and temporal heterogeneity and progression to invasion in experimental systems. Therefore, to study the local invasion process from cell dense clusters into aligned collagen architectures found in solid tumors, we developed a novel engineered 3D invasion platform that integrates an aligned collagen matrix with a cell dense tumor-like plug. Using multiphoton microscopy and quantitative analysis of cell motility, we track the invasion of cancer cells from cell-dense bulk clusters into the pre-aligned 3D matrix, and define the temporal evolution of the advancing invasion fronts over several days. This enables us to identify and probe cell dynamics in key regions of interest: behind, at, and beyond the edge of the invading lesion at distinct time points. Analysis of single cell migration identifies significant spatial heterogeneity in migration behavior between cells in the highly cell-dense region behind the leading edge of the invasion front and cells at and beyond the leading edge. Moreover, temporal variations in motility and directionality are also observed between cells within the cell-dense tumor-like plug and the leading invasive edge as its boundary extends into the anisotropic collagen over time. Furthermore, experimental results combined with mathematical modeling demonstrate that in addition to contact guidance, physical crowding of cells is a key regulating factor orchestrating variability in single cell migration during invasion into anisotropic ECM. Thus, our novel platform enables us to capture spatio-temporal dynamics of cell behavior behind, at, and beyond the invasive front and reveals heterogeneous, local interactions that lead to the emergence and maintenance of the advancing front.},
}
@article {pmid30404915,
year = {2018},
author = {Gao, A and Shrinivas, K and Lepeudry, P and Suzuki, HI and Sharp, PA and Chakraborty, AK},
title = {Evolution of weak cooperative interactions for biological specificity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {47},
pages = {E11053-E11060},
pmid = {30404915},
issn = {1091-6490},
support = {P01 CA042063/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Biological Evolution ; *Cell Physiological Phenomena ; *Computer Simulation ; Humans ; *Models, Biological ; Protein Domains/physiology ; Proteins/metabolism ; },
abstract = {A hallmark of biological systems is that particular functions and outcomes are realized in specific contexts, such as when particular signals are received. One mechanism for mediating specificity is described by Fisher's &quot;lock and key&quot; metaphor, exemplified by enzymes that bind selectively to a particular substrate via specific finely tuned interactions. Another mechanism, more prevalent in multicellular organisms, relies on multivalent weak cooperative interactions. Its importance has recently been illustrated by the recognition that liquid-liquid phase transitions underlie the formation of membraneless condensates that perform specific cellular functions. Based on computer simulations of an evolutionary model, we report that the latter mechanism likely became evolutionarily prominent when a large number of tasks had to be performed specifically for organisms to function properly. We find that the emergence of weak cooperative interactions for mediating specificity results in organisms that can evolve to accomplish new tasks with fewer, and likely less lethal, mutations. We argue that this makes the system more capable of undergoing evolutionary changes robustly, and thus this mechanism has been repeatedly positively selected in increasingly complex organisms. Specificity mediated by weak cooperative interactions results in some useful cross-reactivity for related tasks, but at the same time increases susceptibility to misregulation that might lead to pathologies.},
}
@article {pmid30066215,
year = {2018},
author = {Stencel, A and Wloch-Salamon, DM},
title = {Some theoretical insights into the hologenome theory of evolution and the role of microbes in speciation.},
journal = {Theory in biosciences = Theorie in den Biowissenschaften},
volume = {137},
number = {2},
pages = {197-206},
pmid = {30066215},
issn = {1611-7530},
support = {2018/28/T/HS1/00201//Narodowe Centrum Nauki/ ; Opus 2017/25/B/NZ8/01035//Narodowe Centrum Nauki/ ; DS/762 - K/ZDS/007338//Uniwersytet Jagielloński w Krakowie/ ; },
mesh = {*Adaptation, Biological ; Adaptation, Physiological/genetics ; Animals ; *Genetic Speciation ; Host-Parasite Interactions/genetics ; Microbiota ; Philosophy ; Plants ; Species Specificity ; *Symbiosis ; },
abstract = {Research on symbiotic communities (microbiomes) of multicellular organisms seems to be changing our understanding of how species of plants and animals have evolved over millions of years. The quintessence of these discoveries is the emergence of the hologenome theory of evolution, founded on the concept that a holobiont (a host along with all of its associated symbiotic microorganisms) acts a single unit of selection in the process of evolution. Although the hologenome theory has become very popular among certain scientific circles, its principles are still being debated. In this paper, we argue, firstly, that only a very small number of symbiotic microorganisms are sufficiently integrated into multicellular organisms to act in concert with them as units of selection, thus rendering claims that holobionts are units of selection invalid. Secondly, even though holobionts are not units of selection, they can still constitute genuine units from an evolutionary perspective, provided we accept certain constraints: mainly, they should be considered units of co-operation. Thirdly, we propose a reconciliation of the role of symbiotic microorganisms with the theory of speciation through the use of a developed framework. Mainly, we will argue that, in order to understand the role of microorganisms in the speciation of multicellular organisms, it is not necessary to consider holobionts units of selection; it is sufficient to consider them units of co-operation.},
}
@article {pmid30498215,
year = {2018},
author = {Billerbeck, S and Brisbois, J and Agmon, N and Jimenez, M and Temple, J and Shen, M and Boeke, JD and Cornish, VW},
title = {A scalable peptide-GPCR language for engineering multicellular communication.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {5057},
pmid = {30498215},
issn = {2041-1723},
support = {R01 AI110794/AI/NIAID NIH HHS/United States ; S10 RR027050/RR/NCRR NIH HHS/United States ; T32 GM066704/GM/NIGMS NIH HHS/United States ; },
mesh = {Computational Biology/methods ; Peptides/genetics/*metabolism ; Protein Binding ; Receptors, G-Protein-Coupled/genetics/*metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Signal Transduction ; Synthetic Biology/methods ; },
abstract = {Engineering multicellularity is one of the next breakthroughs for Synthetic Biology. A key bottleneck to building multicellular systems is the lack of a scalable signaling language with a large number of interfaces that can be used simultaneously. Here, we present a modular, scalable, intercellular signaling language in yeast based on fungal mating peptide/G-protein-coupled receptor (GPCR) pairs harnessed from nature. First, through genome-mining, we assemble 32 functional peptide-GPCR signaling interfaces with a range of dose-response characteristics. Next, we demonstrate that these interfaces can be combined into two-cell communication links, which serve as assembly units for higher-order communication topologies. Finally, we show 56 functional, two-cell links, which we use to assemble three- to six-member communication topologies and a three-member interdependent community. Importantly, our peptide-GPCR language is scalable and tunable by genetic encoding, requires minimal component engineering, and should be massively scalable by further application of our genome mining pipeline or directed evolution.},
}
@article {pmid30590727,
year = {2018},
author = {Tsitsekian, D and Daras, G and Alatzas, A and Templalexis, D and Hatzopoulos, P and Rigas, S},
title = {Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/ery440},
pmid = {30590727},
issn = {1460-2431},
abstract = {The degradation of damaged proteins is essential for cell viability. Lon is a highly conserved ATP-dependent serine-lysine protease that maintains proteostasis. We performed a comparative genome-wide analysis to determine the evolutionary history of Lon proteases. Prokaryotes and unicellular eukaryotes retained a single Lon copy, whereas multicellular eukaryotes acquired a peroxisomal copy, in addition to the mitochondrial gene, to sustain the evolution of higher order organ structures. Land plants developed small Lon gene families. Despite the Lon2 peroxisomal paralog, Lon genes triplicated in the Arabidopsis lineage through sequential evolutionary events including whole-genome and tandem duplications. The retention of Lon1, Lon4, and Lon3 triplicates relied on their differential and even contrasting expression patterns, distinct subcellular targeting mechanisms, and functional divergence. Lon1 seems similar to the pre-duplication ancestral gene unit, whereas the duplication of Lon3 and Lon4 is evolutionarily recent. In the wider context of plant evolution, papaya is the only genome with a single ancestral Lon1-type gene. The evolutionary trend among plants is to acquire Lon copies with ambiguous pre-sequences for dual-targeting to mitochondria and chloroplasts, and a substrate recognition domain that deviates from the ancestral Lon1 type. Lon genes constitute a paradigm of dynamic evolution contributing to understanding the functional fate of gene duplicates.},
}
@article {pmid29422410,
year = {2018},
author = {Potjewyd, G and Moxon, S and Wang, T and Domingos, M and Hooper, NM},
title = {Tissue Engineering 3D Neurovascular Units: A Biomaterials and Bioprinting Perspective.},
journal = {Trends in biotechnology},
volume = {36},
number = {4},
pages = {457-472},
doi = {10.1016/j.tibtech.2018.01.003},
pmid = {29422410},
issn = {1879-3096},
mesh = {Animals ; Biocompatible Materials/*chemistry ; *Bioprinting ; Brain Diseases/therapy ; Extracellular Matrix/chemistry ; Humans ; Hydrogels/chemistry ; Models, Animal ; Neuroglia/chemistry ; Neurons/chemistry ; *Printing, Three-Dimensional ; *Tissue Engineering ; },
abstract = {Neurovascular dysfunction is a central process in the pathogenesis of stroke and most neurodegenerative diseases, including Alzheimer's disease. The multicellular neurovascular unit (NVU) combines the neural, vascular and extracellular matrix (ECM) components in an important interface whose correct functioning is critical to maintain brain health. Tissue engineering is now offering new tools and insights to advance our understanding of NVU function. Here, we review how the use of novel biomaterials to mimic the mechanical and functional cues of the ECM, coupled with precisely layered deposition of the different cells of the NVU through 3D bioprinting, is revolutionising the study of neurovascular function and dysfunction.},
}
@article {pmid28592899,
year = {2017},
author = {Nan, F and Feng, J and Lv, J and Liu, Q and Fang, K and Gong, C and Xie, S},
title = {Origin and evolutionary history of freshwater Rhodophyta: further insights based on phylogenomic evidence.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2934},
pmid = {28592899},
issn = {2045-2322},
mesh = {*Biological Evolution ; Evolution, Molecular ; *Fresh Water ; Genes, Plant ; Genetic Variation ; Genome, Chloroplast ; Genome, Mitochondrial ; Genomics/methods ; Phylogeny ; Rhodophyta/*classification/*genetics ; },
abstract = {Freshwater representatives of Rhodophyta were sampled and the complete chloroplast and mitochondrial genomes were determined. Characteristics of the chloroplast and mitochondrial genomes were analyzed and phylogenetic relationship of marine and freshwater Rhodophyta were reconstructed based on the organelle genomes. The freshwater member Compsopogon caeruleus was determined for the largest chloroplast genome among multicellular Rhodophyta up to now. Expansion and subsequent reduction of both the genome size and GC content were observed in the Rhodophyta except for the freshwater Compsopogon caeruleus. It was inferred that the freshwater members of Rhodophyta occurred through diverse origins based on evidence of genome size, GC-content, phylogenomic analysis and divergence time estimation. The freshwater species Compsopogon caeruleus and Hildenbrandia rivularis originated and evolved independently at the inland water, whereas the Bangia atropurpurea, Batrachospermum arcuatum and Thorea hispida are derived from the marine relatives. The typical freshwater representatives Thoreales and Batrachospermales are probably derived from the marine relative Palmaria palmata at approximately 415-484 MYA. The origin and evolutionary history of freshwater Rhodophyta needs to be testified with more organelle genome sequences and wider global sampling.},
}
@article {pmid28588313,
year = {2017},
author = {Salmeán, AA and Duffieux, D and Harholt, J and Qin, F and Michel, G and Czjzek, M and Willats, WGT and Hervé, C},
title = {Insoluble (1 → 3), (1 → 4)-β-D-glucan is a component of cell walls in brown algae (Phaeophyceae) and is masked by alginates in tissues.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {2880},
pmid = {28588313},
issn = {2045-2322},
mesh = {Alginates/*metabolism ; Cell Wall/*chemistry/*metabolism ; Chromatography, High Pressure Liquid ; Fluorescent Antibody Technique ; Glucans/*chemistry/*metabolism ; Immunohistochemistry ; Organ Specificity ; Phaeophyta/classification/genetics/*metabolism ; Solubility ; },
abstract = {Brown algae are photosynthetic multicellular marine organisms. They belong to the phylum of Stramenopiles, which are not closely related to land plants and green algae. Brown algae share common evolutionary features with other photosynthetic and multicellular organisms, including a carbohydrate-rich cell-wall. Brown algal cell walls are composed predominantly of the polyanionic polysaccharides alginates and fucose-containing sulfated polysaccharides. These polymers are prevalent over neutral and crystalline components, which are believed to be mostly, if not exclusively, cellulose. In an attempt to better understand brown algal cell walls, we performed an extensive glycan array analysis of a wide range of brown algal species. Here we provide the first demonstration that mixed-linkage (1 → 3), (1 → 4)-β-D-glucan (MLG) is common in brown algal cell walls. Ultra-Performance Liquid Chromatography analyses indicate that MLG in brown algae solely consists of trisaccharide units of contiguous (1 → 4)-β-linked glucose residues joined by (1 → 3)-β-linkages. This regular conformation may allow long stretches of the molecule to align and to form well-structured microfibrils. At the tissue level, immunofluorescence studies indicate that MLG epitopes in brown algae are unmasked by a pre-treatment with alginate lyases to remove alginates. These findings are further discussed in terms of the origin and evolution of MLG in the Stramenopile lineage.},
}
@article {pmid30553725,
year = {2018},
author = {Taggart, JC and Li, GW},
title = {Production of Protein-Complex Components Is Stoichiometric and Lacks General Feedback Regulation in Eukaryotes.},
journal = {Cell systems},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cels.2018.11.003},
pmid = {30553725},
issn = {2405-4712},
abstract = {Constituents of multiprotein complexes are required at well-defined levels relative to each other. However, it remains unknown whether eukaryotic cells typically produce precise amounts of subunits, or instead rely on degradation to mitigate imprecise production. Here, we quantified the production rates of multiprotein complexes in unicellular and multicellular eukaryotes using ribosome profiling. By resolving read-mapping ambiguities, which occur for a large fraction of ribosome footprints and distort quantitation accuracy in eukaryotes, we found that obligate components of multiprotein complexes are produced in proportion to their stoichiometry, indicating that their abundances are already precisely tuned at the synthesis level. By systematically interrogating the impact of gene dosage variations in budding yeast, we found a general lack of negative feedback regulation protecting the normally precise rates of subunit synthesis. These results reveal a core principle of proteome homeostasis and highlight the evolution toward quantitative control at every step in the central dogma.},
}
@article {pmid30348074,
year = {2018},
author = {Kin, K and Forbes, G and Cassidy, A and Schaap, P},
title = {Cell-type specific RNA-Seq reveals novel roles and regulatory programs for terminally differentiated Dictyostelium cells.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {764},
pmid = {30348074},
issn = {1471-2164},
support = {742288//H2020 European Research Council/ ; ALTF 295-2015//European Molecular Biology Organization/ ; H28-1002//Japan Society for the Promotion of Science/ ; },
mesh = {Dictyostelium/*cytology/*genetics/metabolism ; Gene Expression Regulation ; Gene Ontology ; Metabolic Networks and Pathways/genetics ; RNA, Protozoan/*genetics ; *Sequence Analysis, RNA ; Transcription Factors/genetics ; },
abstract = {BACKGROUND: A major hallmark of multicellular evolution is increasing complexity by the evolution of new specialized cell types. During Dictyostelid evolution novel specialization occurred within taxon group 4. We here aim to retrace the nature and ancestry of the novel &quot;cup&quot; cells by comparing their transcriptome to that of other cell types.<br><br>RESULTS: RNA-Seq was performed on purified mature spore, stalk and cup cells and on vegetative amoebas. Clustering and phylogenetic analyses showed that cup cells were most similar to stalk cells, suggesting that they share a common ancestor. The affinity between cup and stalk cells was also evident from promoter-reporter studies of newly identified cell-type genes, which revealed late expression in cups of many stalk genes. However, GO enrichment analysis reveal the unexpected prominence of GTPase mediated signalling in cup cells, in contrast to enrichment of autophagy and cell wall synthesis related transcripts in stalk cells. Combining the cell type RNA-Seq data with developmental expression profiles revealed complex expression dynamics in each cell type as well as genes exclusively expressed during terminal differentiation. Most notable were nine related hssA-like genes that were highly and exclusively expressed in cup cells.<br><br>CONCLUSIONS: This study reveals the unique transcriptomes of the mature cup, stalk and spore cells of D. discoideum and provides insight into the ancestry of cup cells and roles in signalling that were not previously realized. The data presented in this study will serve as an important resource for future studies into the regulation and evolution of cell type specialization.},
}
@article {pmid29966484,
year = {2018},
author = {Liao, Z and Kjellin, J and Hoeppner, MP and Grabherr, M and Söderbom, F},
title = {Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.},
journal = {RNA biology},
volume = {15},
number = {7},
pages = {937-954},
pmid = {29966484},
issn = {1555-8584},
mesh = {Adaptation, Biological ; Biological Evolution ; Dictyostelium/genetics/*metabolism ; Gene Knockout Techniques ; Genome, Protozoan/genetics ; High-Throughput Nucleotide Sequencing ; MicroRNAs/analysis/*biosynthesis/genetics ; Oligonucleotide Probes/analysis/genetics/metabolism ; Promoter Regions, Genetic/genetics ; Protozoan Proteins/genetics/*metabolism ; RNA, Protozoan/analysis/*biosynthesis/genetics ; Ribonuclease III/genetics/*metabolism ; Transcription, Genetic ; },
abstract = {Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3'-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.},
}
@article {pmid30538242,
year = {2018},
author = {Higo, A and Kawashima, T and Borg, M and Zhao, M and López-Vidriero, I and Sakayama, H and Montgomery, SA and Sekimoto, H and Hackenberg, D and Shimamura, M and Nishiyama, T and Sakakibara, K and Tomita, Y and Togawa, T and Kunimoto, K and Osakabe, A and Suzuki, Y and Yamato, KT and Ishizaki, K and Nishihama, R and Kohchi, T and Franco-Zorrilla, JM and Twell, D and Berger, F and Araki, T},
title = {Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {5283},
doi = {10.1038/s41467-018-07728-3},
pmid = {30538242},
issn = {2041-1723},
abstract = {Evolutionary mechanisms underlying innovation of cell types have remained largely unclear. In multicellular eukaryotes, the evolutionary molecular origin of sperm differentiation is unknown in most lineages. Here, we report that in algal ancestors of land plants, changes in the DNA-binding domain of the ancestor of the MYB transcription factor DUO1 enabled the recognition of a new cis-regulatory element. This event led to the differentiation of motile sperm. After neo-functionalization, DUO1 acquired sperm lineage-specific expression in the common ancestor of land plants. Subsequently the downstream network of DUO1 was rewired leading to sperm with distinct morphologies. Conjugating green algae, a sister group of land plants, accumulated mutations in the DNA-binding domain of DUO1 and lost sperm differentiation. Our findings suggest that the emergence of DUO1 was the defining event in the evolution of sperm differentiation and the varied modes of sexual reproduction in the land plant lineage.},
}
@article {pmid29545531,
year = {2018},
author = {Moroni, M and Servin-Vences, MR and Fleischer, R and Sánchez-Carranza, O and Lewin, GR},
title = {Voltage gating of mechanosensitive PIEZO channels.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {1096},
pmid = {29545531},
issn = {2041-1723},
mesh = {Animals ; Cell Line ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster ; Evolution, Molecular ; Humans ; Ion Channels/genetics/*metabolism ; *Mechanotransduction, Cellular ; Mice ; Mutation, Missense ; Patch-Clamp Techniques ; Zebrafish ; Zebrafish Proteins/genetics/*metabolism ; },
abstract = {Mechanosensitive PIEZO ion channels are evolutionarily conserved proteins whose presence is critical for normal physiology in multicellular organisms. Here we show that, in addition to mechanical stimuli, PIEZO channels are also powerfully modulated by voltage and can even switch to a purely voltage-gated mode. Mutations that cause human diseases, such as xerocytosis, profoundly shift voltage sensitivity of PIEZO1 channels toward the resting membrane potential and strongly promote voltage gating. Voltage modulation may be explained by the presence of an inactivation gate in the pore, the opening of which is promoted by outward permeation. Older invertebrate (fly) and vertebrate (fish) PIEZO proteins are also voltage sensitive, but voltage gating is a much more prominent feature of these older channels. We propose that the voltage sensitivity of PIEZO channels is a deep property co-opted to add a regulatory mechanism for PIEZO activation in widely different cellular contexts.},
}
@article {pmid29427837,
year = {2018},
author = {Baldauf, SL and Romeralo, M and Fiz-Palacios, O and Heidari, N},
title = {A Deep Hidden Diversity of Dictyostelia.},
journal = {Protist},
volume = {169},
number = {1},
pages = {64-78},
doi = {10.1016/j.protis.2017.12.005},
pmid = {29427837},
issn = {1618-0941},
mesh = {*Biodiversity ; DNA Primers/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Dictyostelium/classification/*genetics/isolation &amp; purification ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Dictyostelia is a monophyletic group of transiently multicellular (sorocarpic) amoebae, whose study is currently limited to laboratory culture. This tends to favour faster growing species with robust sorocarps, while species with smaller more delicate sorocarps constitute most of the group's taxonomic breadth. The number of known species is also small (∼150) given Dictyostelia's molecular depth and apparent antiquity (>600 myr). Nonetheless, dictyostelid sequences are rarely recovered in culture independent sampling (ciPCR) surveys. We developed ciPCR primers to specifically target dictyostelid small subunit (SSU or 18S) rDNA and tested them on total DNAs extracted from a wide range of soils from five continents. The resulting clone libraries show mostly dictyostelid sequences (∼90%), and phylogenetic analyses of these sequences indicate novel lineages in all four dictyostelid families and most genera. This is especially true for the species-rich Heterostelium and Dictyosteliaceae but also the less species-rich Raperosteliaceae. However, the most novel deep branches are found in two very species-poor taxa, including the deepest branch yet seen in the highly divergent Cavenderiaceae. These results confirm a deep hidden diversity of Dictyostelia, potentially including novel morphologies and developmental schemes. The primers and protocols presented here should also enable more comprehensive studies of dictyostelid ecology.},
}
@article {pmid30478288,
year = {2018},
author = {Pollier, J and Vancaester, E and Kuzhiumparambil, U and Vickers, CE and Vandepoele, K and Goossens, A and Fabris, M},
title = {A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-018-0305-5},
pmid = {30478288},
issn = {2058-5276},
abstract = {Steroids are essential triterpenoid molecules that are present in all eukaryotes and modulate the fluidity and flexibility of cell membranes. Steroids also serve as signalling molecules that are crucial for growth, development and differentiation of multicellular organisms1-3. The steroid biosynthetic pathway is highly conserved and is key in eukaryote evolution4-7. The flavoprotein squalene epoxidase (SQE) catalyses the first oxygenation reaction in this pathway and is rate limiting. However, despite its conservation in animals, plants and fungi, several phylogenetically widely distributed eukaryote genomes lack an SQE-encoding gene7,8. Here, we discovered and characterized an alternative SQE (AltSQE) belonging to the fatty acid hydroxylase superfamily. AltSQE was identified through screening of a gene library of the diatom Phaeodactylum tricornutum in a SQE-deficient yeast. In accordance with its divergent protein structure and need for cofactors, we found that AltSQE is insensitive to the conventional SQE inhibitor terbinafine. AltSQE is present in many eukaryotic lineages but is mutually exclusive with SQE and shows a patchy distribution within monophyletic clades. Our discovery provides an alternative element for the conserved steroid biosynthesis pathway, raises questions about eukaryote metabolic evolution and opens routes to develop selective SQE inhibitors to control hazardous organisms.},
}
@article {pmid29687830,
year = {2017},
author = {Cazzolla Gatti, R},
title = {Adaptation, Evolution And Reproduction Of Gaia By The Means Of Our Species.},
journal = {Theoretical biology forum},
volume = {110},
number = {1-2},
pages = {25-45},
doi = {10.19272/201711402003},
pmid = {29687830},
issn = {0035-6050},
mesh = {*Adaptation, Physiological ; Animals ; Atmosphere ; *Biological Evolution ; *Earth (Planet) ; *Ecosystem ; *Evolution, Planetary ; Humans ; *Models, Biological ; *Reproduction ; Symbiosis ; },
abstract = {Nowadays, the idea that life affects the development of the planetary environment, and can, in turn, affect the future evolution of itself (in a coevolutionary way) is well-accepted. However, since the proposal of the Gaia hypothesis, there has been widespread criticism. Most of it is related to teleology, the absence of natural selection at a universal scale, and the lack of planetary reproduction. Some of the problems concerning the 'internal' logic of the idea have been resolved. Nevertheless, it is not sure whether Earth can be considered a unit of selection and (therefore) Gaia can adapt according to Darwinian evolution. After Lovelock and Margulis, Gaia has been considered a symbiotic planet composed of biotic (the biosphere) and abiotic (the geosphere-atmosphere) interacting with and coevolving elements. Here I propose why and suggest how a Gaian system should be considered alive in any evolutionary sense. I take into consideration the three principal criticisms and I analyse them following a logic-inductive reasoning. I use thought experiments and analogical arguments to analyse the rationale and the mechanisms by which Gaia evolves and may reproduce. This reasoning could allow rejecting the aforementioned criticisms as outdated and insufficient to discredit the main idea. I argue that without invoking teleology - so without any foresight or planning - a Gaian planet can be considered a coevolutionary system analogous to a multicellular body: a super-unit of selection. I describe different situations according to which Gaia is able to reproduce and transfer her planetary genome to other uninhabited or inhabited planets. Then I suggest that Gaia can face exclusion- competition-coexistence states depending on the fitness of her biota compared to those of the other reproducing biospheres. This demonstrates that Gaia can reproduce and evolve in competition-cooperation with other planets. Some deep implications arise from this evidence, also in light of the recent discovery of a new solar system with Earth-like planets by NASA.},
}
@article {pmid28580966,
year = {2017},
author = {Driscoll, WW and Travisano, M},
title = {Synergistic cooperation promotes multicellular performance and unicellular free-rider persistence.},
journal = {Nature communications},
volume = {8},
number = {},
pages = {15707},
doi = {10.1038/ncomms15707},
pmid = {28580966},
issn = {2041-1723},
mesh = {Biological Evolution ; Cluster Analysis ; *Ecology ; Flocculation ; Genotype ; Green Fluorescent Proteins/metabolism ; Kluyveromyces/genetics/*physiology ; Microscopy, Confocal ; Phenotype ; Saccharomyces cerevisiae/genetics/*physiology ; Species Specificity ; Video Recording ; },
abstract = {The evolution of multicellular life requires cooperation among cells, which can be undermined by intra-group selection for selfishness. Theory predicts that selection to avoid non-cooperators limits social interactions among non-relatives, yet previous evolution experiments suggest that intra-group conflict is an outcome, rather than a driver, of incipient multicellular life cycles. Here we report the evolution of multicellularity via two distinct mechanisms of group formation in the unicellular budding yeast Kluyveromyces lactis. Cells remain permanently attached following mitosis, giving rise to clonal clusters (staying together); clusters then reversibly assemble into social groups (coming together). Coming together amplifies the benefits of multicellularity and allows social clusters to collectively outperform solitary clusters. However, cooperation among non-relatives also permits fast-growing unicellular lineages to 'free-ride' during selection for increased size. Cooperation and competition for the benefits of multicellularity promote the stable coexistence of unicellular and multicellular genotypes, underscoring the importance of social and ecological context during the transition to multicellularity.},
}
@article {pmid29475741,
year = {2018},
author = {Thomas, F and Kareva, I and Raven, N and Hamede, R and Pujol, P and Roche, B and Ujvari, B},
title = {Evolved Dependence in Response to Cancer.},
journal = {Trends in ecology &amp; evolution},
volume = {33},
number = {4},
pages = {269-276},
doi = {10.1016/j.tree.2018.01.012},
pmid = {29475741},
issn = {1872-8383},
mesh = {*Biological Evolution ; Eukaryota/*genetics ; Evolution, Molecular ; Neoplasms/*genetics/prevention &amp; control/therapy ; *Selection, Genetic ; },
abstract = {Evolved dependence is a process through which one species becomes 'dependent' on another following a long evolutionary history of interaction. This happens when adaptations selected in the first species for interacting lead to fitness costs when the second species is not encountered. Evolved dependence is frequent in host-parasite interactions, where hosts may achieve a higher fitness in the presence of the parasite than in its absence. Since oncogenic manifestations are (i) ubiquitous across multicellular life, (ii) involved in parasitic-like interactions with their hosts, and (iii) have effectively driven the selection of numerous adaptations, it is possible that multicellular organisms display evolved dependence in response to oncogenic processes. We provide a comprehensive overview of the topic, including the implications for cancer prevention and treatment.},
}
@article {pmid28485371,
year = {2017},
author = {Milholland, B and Dong, X and Zhang, L and Hao, X and Suh, Y and Vijg, J},
title = {Differences between germline and somatic mutation rates in humans and mice.},
journal = {Nature communications},
volume = {8},
number = {},
pages = {15183},
doi = {10.1038/ncomms15183},
pmid = {28485371},
issn = {2041-1723},
support = {P01 AG017242/AG/NIA NIH HHS/United States ; P01 AG047200/AG/NIA NIH HHS/United States ; },
mesh = {Animals ; Child ; Genome ; Germ-Line Mutation/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Mice, Inbred C57BL ; *Mutation Rate ; },
abstract = {The germline mutation rate has been extensively studied and has been found to vary greatly between species, but much less is known about the somatic mutation rate in multicellular organisms, which remains very difficult to determine. Here, we present data on somatic mutation rates in mice and humans, obtained by sequencing single cells and clones derived from primary fibroblasts, which allows us to make the first direct comparison with germline mutation rates in these two species. The results indicate that the somatic mutation rate is almost two orders of magnitude higher than the germline mutation rate and that both mutation rates are significantly higher in mice than in humans. Our findings demonstrate both the privileged status of germline genome integrity and species-specific differences in genome maintenance.},
}
@article {pmid28961459,
year = {2018},
author = {Deb, J and Bland, HM and Østergaard, L},
title = {Developmental cartography: coordination via hormonal and genetic interactions during gynoecium formation.},
journal = {Current opinion in plant biology},
volume = {41},
number = {},
pages = {54-60},
doi = {10.1016/j.pbi.2017.09.004},
pmid = {28961459},
issn = {1879-0356},
support = {BBS/E/J/00000613//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M004112/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004588/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P013511/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Arabidopsis/genetics/growth &amp; development/*physiology ; Cytokinins/metabolism ; Evolution, Molecular ; Flowers/genetics/growth &amp; development/*physiology ; Indoleacetic Acids/metabolism ; Plant Growth Regulators/*metabolism ; Plant Leaves/genetics/growth &amp; development/physiology ; },
abstract = {Development in multicellular organisms requires the establishment of tissue identity through polarity cues. The Arabidopsis gynoecium presents an excellent model to study this coordination, as it comprises a complex tissue structure which is established through multiple polarity systems. The gynoecium is derived from the fusion of two carpels and forms in the centre of the flower. Many regulators of carpel development also have roles in leaf development, emphasizing the evolutionary origin of carpels as modified leaves. The gynoecium can therefore be considered as having evolved from a simple setup followed by adjustment in tissue polarity to facilitate efficient reproduction. Here, we discuss concepts to understand how hormonal and genetic systems interact to pattern the gynoecium.},
}
@article {pmid29225309,
year = {2017},
author = {Jong, LW and Fujiwara, T and Nozaki, H and Miyagishima, SY},
title = {Cell size for commitment to cell division and number of successive cell divisions in multicellular volvocine green algae Tetrabaena socialis and Gonium pectorale.},
journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences},
volume = {93},
number = {10},
pages = {832-840},
doi = {10.2183/pjab.93.052},
pmid = {29225309},
issn = {1349-2896},
mesh = {Cell Count/methods ; Cell Culture Techniques/methods ; Cell Division ; Cell Size ; Chlorophyta/*cytology ; Electrophoresis, Polyacrylamide Gel/methods ; },
abstract = {Volvocine algae constitute a green algal lineage comprising unicellular Chlamydomonas, four-celled Tetrabaena, eight to 32-celled Gonium, and others up to Volvox spp., which consist of up to 50,000 cells. These algae proliferate by multiple fissions with cellular growth up to several fold in size and subsequent successive cell divisions. Chlamydomonas reinhardtii cells produce two to 32 daughter cells by one to five divisions, depending on cellular growth in the G1 phase. By contrast, in this study, we found that Tetrabaena socialis and Gonium pectorale cells mostly produced four and eight daughter cells by two and three successive divisions, respectively. In contrast to C. reinhardtii, which is committed to cell division when the cell has grown two-fold, T. socialis and G. pectorale are committed only when the cells have grown four- and eight-fold, respectively. Thus, our results suggest that evolutionary changes in cellular size for commitment largely contributes to the emergence and evolution of multicellularity in volvocine algae.},
}
@article {pmid30396330,
year = {2018},
author = {Joo, S and Wang, MH and Lui, G and Lee, J and Barnas, A and Kim, E and Sudek, S and Worden, AZ and Lee, JH},
title = {Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida.},
journal = {BMC biology},
volume = {16},
number = {1},
pages = {136},
doi = {10.1186/s12915-018-0605-5},
pmid = {30396330},
issn = {1741-7007},
support = {Discovery Grant 418471-12//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; KCRC 2016M1A8A1925345//Ministry of Education, Science and Technology/ ; 0843119//Division of Integrative Organismal Systems/ ; 0843506//Division of Integrative Organismal Systems/ ; GBMF 3788//Gordon and Betty Moore Foundation/ ; CAREER-1453639//Directorate for Biological Sciences/ ; },
abstract = {BACKGROUND: Complex multicellularity requires elaborate developmental mechanisms, often based on the versatility of heterodimeric transcription factor (TF) interactions. Homeobox TFs in the TALE superclass are deeply embedded in the gene regulatory networks that orchestrate embryogenesis. Knotted-like homeobox (KNOX) TFs, homologous to animal MEIS, have been found to drive the haploid-to-diploid transition in both unicellular green algae and land plants via heterodimerization with other TALE superclass TFs, demonstrating remarkable functional conservation of a developmental TF across lineages that diverged one billion years ago. Here, we sought to delineate whether TALE-TALE heterodimerization is ancestral to eukaryotes.<br><br>RESULTS: We analyzed TALE endowment in the algal radiations of Archaeplastida, ancestral to land plants. Homeodomain phylogeny and bioinformatics analysis partitioned TALEs into two broad groups, KNOX and non-KNOX. Each group shares previously defined heterodimerization domains, plant KNOX-homology in the KNOX group and animal PBC-homology in the non-KNOX group, indicating their deep ancestry. Protein-protein interaction experiments showed that the TALEs in the two groups all participated in heterodimerization.<br><br>CONCLUSIONS: Our study indicates that the TF dyads consisting of KNOX/MEIS and PBC-containing TALEs must have evolved early in eukaryotic evolution. Based on our results, we hypothesize that in early eukaryotes, the TALE heterodimeric configuration provided transcription-on switches via dimerization-dependent subcellular localization, ensuring execution of the haploid-to-diploid transition only when the gamete fusion is correctly executed between appropriate partner gametes. The TALE switch then diversified in the several lineages that engage in a complex multicellular organization.},
}
@article {pmid29892951,
year = {2018},
author = {Gao, Q and Xu, S and Zhu, X and Wang, L and Yang, Z and Zhao, X},
title = {Genome-wide identification and characterization of the RIO atypical kinase family in plants.},
journal = {Genes &amp; genomics},
volume = {40},
number = {6},
pages = {669-683},
doi = {10.1007/s13258-018-0658-4},
pmid = {29892951},
issn = {2092-9293},
support = {31601385//National Natural Science Foundation of China/International ; 2016ZX08012-002//National Science and Technology Major Project/International ; 2014AA10A601-5//National High-tech R&amp;D Program/International ; BK20160429//Natural Science Foundation of Jiangsu Province/International ; 16KJB210001//Natural Science Research Project in Universities of Jiangsu Province/International ; PPZY2015A018//Top-notch Academic Programs Project of Jiangsu Higher Education Institutions/International ; },
mesh = {Amino Acid Sequence/genetics ; Arabidopsis/genetics ; Gene Expression Regulation, Plant/genetics ; Genes, Plant/genetics ; Multigene Family ; Oryza/genetics ; Phylogeny ; Plant Proteins/genetics ; Plants/genetics ; Protein-Serine-Threonine Kinases/*genetics/metabolism ; Sequence Alignment/methods ; Transcriptome/genetics ; Viridiplantae/*genetics ; Zea mays/genetics ; },
abstract = {Members of the right open reading frame (RIO) atypical kinase family are present in all three domains of life. In eukaryotes, three subfamilies have been identified: RIO1, RIO2, and RIO3. Studies have shown that the yeast and human RIO1 and RIO2 kinases are essential for the biogenesis of small ribosomal subunits. Thus far, RIO3 has been found only in multicellular eukaryotes. In this study, we systematically identified members of the RIO gene family in 37 species representing the major evolutionary lineages in Viridiplantae. A total of 84 RIO genes were identified; among them, 41 were classified as RIO1 and 43 as RIO2. However, no RIO3 gene was found in any of the species examined. Phylogenetic trees constructed for plant RIO1 and RIO2 proteins were generally congruent with the species phylogeny. Subcellular localization analyses showed that the plant RIO proteins were localized mainly in the nucleus and/or cytoplasm. Expression profile analysis of rice, maize, and Arabidopsis RIO genes in different tissues revealed similar expression patterns between RIO1 and RIO2 genes, and their expression levels were high in certain tissues. In addition, the expressions of plant RIO genes were regulated by two drugs: mycophenolic acid and actinomycin D. Function prediction using genome-wide coexpression analysis revealed that most plant RIO genes may be involved in ribosome biogenesis. Our results will be useful for the evolutionary analysis of the ancient RIO kinase family and provide a basis for further functional characterization of RIO genes in plants.},
}
@article {pmid29850801,
year = {2018},
author = {Nishiyama, E and Ohshima, K},
title = {Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons.},
journal = {Genome biology and evolution},
volume = {10},
number = {6},
pages = {1471-1483},
doi = {10.1093/gbe/evy098},
pmid = {29850801},
issn = {1759-6653},
mesh = {Animals ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Plant/genetics ; Lizards/genetics ; Long Interspersed Nucleotide Elements/genetics ; Magnoliopsida/genetics ; Mammals/genetics ; Microsatellite Repeats/genetics ; Mutagenesis, Insertional/methods ; Phylogeny ; Retroelements/*genetics ; Reverse Transcription/genetics ; Short Interspersed Nucleotide Elements/genetics ; },
abstract = {In multicellular organisms, such as vertebrates and flowering plants, horizontal transfer (HT) of genetic information is thought to be a rare event. However, recent findings unveiled unexpectedly frequent HT of RTE-clade LINEs. To elucidate the molecular footprints of the genomic integration machinery of RTE-related retroposons, the sequence patterns surrounding the insertion sites of plant Au-like SINE families were analyzed in the genomes of a wide variety of flowering plants. A novel and remarkable finding regarding target site duplications (TSDs) for SINEs was they start with thymine approximately one helical pitch (ten nucleotides) downstream of a thymine stretch. This TSD pattern was found in RTE-clade LINEs, which share the 3'-end sequence of these SINEs, in the genome of leguminous plants. These results demonstrably show that Au-like SINEs were mobilized by the enzymatic machinery of RTE-clade LINEs. Further, we discovered the same TSD pattern in animal SINEs from lizard and mammals, in which the RTE-clade LINEs sharing the 3'-end sequence with these animal SINEs showed a distinct TSD pattern. Moreover, a significant correlation was observed between the first nucleotide of TSDs and microsatellite-like sequences found at the 3'-ends of SINEs and LINEs. We propose that RTE-encoded protein could preferentially bind to a DNA region that contains a thymine stretch to cleave a phosphodiester bond downstream of the stretch. Further, determination of cleavage sites and/or efficiency of primer sites for reverse transcription may depend on microsatellite-like repeats in the RNA template. Such a unique mechanism may have enabled retroposons to successfully expand in frontier genomes after HT.},
}
@article {pmid29788279,
year = {2018},
author = {Tarver, JE and Taylor, RS and Puttick, MN and Lloyd, GT and Pett, W and Fromm, B and Schirrmeister, BE and Pisani, D and Peterson, KJ and Donoghue, PCJ},
title = {Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss.},
journal = {Genome biology and evolution},
volume = {10},
number = {6},
pages = {1457-1470},
doi = {10.1093/gbe/evy096},
pmid = {29788279},
issn = {1759-6653},
mesh = {Animals ; Conserved Sequence/genetics ; Evolution, Molecular ; MicroRNAs/*genetics ; Molecular Sequence Annotation/methods ; Phenotype ; Phylogeny ; },
abstract = {microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.},
}
@article {pmid30288746,
year = {2018},
author = {Stiller, JW and Yang, C and Collén, J and Kowalczyk, N and Thompson, BE},
title = {Evolution and expression of core SWI/SNF genes in red algae.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.12795},
pmid = {30288746},
issn = {1529-8817},
support = {0741907//NSF Research Collaboration Network/ ; DE-AC02-05CH11231//U.S. Department of Energy Joint Genome Institute/ ; },
abstract = {Red algae are the oldest identifiable multicellular eukaryotes, with a fossil record dating back more than a billion years. During that time two major rhodophyte lineages, bangiophytes and florideophytes, have evolved varied levels of morphological complexity. These two groups are distinguished, in part, by different patterns of multicellular development, with florideophytes exhibiting a far greater diversity of morphologies. Interestingly, during their long evolutionary history, there is no record of a rhodophyte achieving the kinds of cellular and tissue-specific differentiation present in other multicellular algal lineages. To date, the genetic underpinnings of unique aspects of red algal development are largely unexplored; however, they must reflect the complements and patterns of expression of key regulatory genes. Here we report comparative evolutionary and gene expression analyses of core subunits of the SWI/SNF chromatin-remodeling complex, which is implicated in cell differentiation and developmental regulation in more well studied multicellular groups. Our results suggest that a single, canonical SWI/SNF complex was present in the rhodophyte ancestor, with gene duplications and evolutionary diversification of SWI/SNF subunits accompanying the evolution of multicellularity in the common ancestor of bangiophytes and florideophytes. Differences in how SWI/SNF chromatin remodeling evolved subsequently, in particular gene losses and more rapid divergence of SWI3 and SNF5 in bangiophytes, could help to explain why they exhibit a more limited range of morphological complexity than their florideophyte cousins.},
}
@article {pmid30171399,
year = {2018},
author = {Liu, Y and Liu, D and Khan, AR and Liu, B and Wu, M and Huang, L and Wu, J and Song, G and Ni, H and Ying, H and Yu, H and Gan, Y},
title = {NbGIS regulates glandular trichome initiation through GA signaling in tobacco.},
journal = {Plant molecular biology},
volume = {98},
number = {1-2},
pages = {153-167},
doi = {10.1007/s11103-018-0772-3},
pmid = {30171399},
issn = {1573-5028},
support = {31570183; 31529001; 31661143004//National Natural Science Foundation of China/ ; LZ15C020001//Zhejiang Provincial Natural Science Foundation of China/ ; 2015CB150200//Major State Basic Research Development Program/ ; 2016YFD0100701//the National Key R &amp; D Program of China/ ; },
mesh = {Amino Acid Sequence ; Biosynthetic Pathways/genetics ; Gene Expression Regulation, Plant ; Genes, Plant ; Gibberellins/biosynthesis/*metabolism ; Phenotype ; Phylogeny ; Plant Development/genetics ; Plant Proteins/chemistry/*metabolism ; Plant Shoots/physiology ; Plants, Genetically Modified ; *Signal Transduction ; Tobacco/genetics/growth &amp; development/*metabolism ; Trichomes/*growth &amp; development/*metabolism/ultrastructure ; },
abstract = {KEY MESSAGE: A novel gene NbGIS positively regulates glandular trichome initiation through GA Signaling in tobacco. NbMYB123-like regulates glandular trichome initiation by acting downstream of NbGIS in tobacco. Glandular trichome is a specialized multicellular structure which has capability to synthesize and secrete secondary metabolites and protects plants from biotic and abiotic stresses. Our previous results revealed that a C2H2 zinc-finger transcription factor GIS and its sub-family genes act upstream of GL3/EGL3-GL1-TTG1 transcriptional activator complex to regulate trichome initiation in Arabidopsis. In this present study, we found that NbGIS could positively regulate glandular trichome development in Nicotiana benthamiana (tobacco). Our result demonstrated that 35S:NbGIS lines exhibited much higher densities of trichome on leaves, main stems, lateral branches and sepals than WT plants, while NbGIS:RNAi lines had the opposite phenotypes. Furthermore, our results also showed that NbGIS was required in response to GA signal to control glandular trichome initiation in Nicotiana benthamiana. In addition, our results also showed that NbGIS significantly influenced GA accumulation and expressions of marker genes of the GA biosynthesis, might result in the changes of growth and maturation in tobacco. Lastly, our results also showed that NbMYB123-like regulated glandular trichome initiation in tobacco by acting downstream of NbGIS. These findings provide new insights to discover the molecular mechanism by which C2H2 transcriptional factors regulates glandular trichome initiation through GA signaling pathway in tobacco.},
}
@article {pmid30078827,
year = {2018},
author = {Oka, M and Yoneda, Y},
title = {Importin α: functions as a nuclear transport factor and beyond.},
journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences},
volume = {94},
number = {7},
pages = {259-274},
doi = {10.2183/pjab.94.018},
pmid = {30078827},
issn = {1349-2896},
mesh = {Active Transport, Cell Nucleus ; Animals ; Cell Nucleus/*metabolism ; Humans ; Neurons/cytology/metabolism ; Nuclear Pore/metabolism ; alpha Karyopherins/*metabolism ; },
abstract = {Nucleocytoplasmic transport is an essential process in eukaryotes. The molecular mechanisms underlying nuclear transport that involve the nuclear transport receptor, small GTPase Ran, and the nuclear pore complex are highly conserved from yeast to humans. On the other hand, it has become clear that the nuclear transport system diverged during evolution to achieve various physiological functions in multicellular eukaryotes. In this review, we first summarize the molecular mechanisms of nuclear transport and how these were elucidated. Then, we focus on the diverse functions of importin α, which acts not merely an import factor but also as a multi-functional protein contributing to a variety of cellular functions in higher eukaryotes.},
}
@article {pmid30068565,
year = {2018},
author = {Bornens, M},
title = {Cell polarity: having and making sense of direction-on the evolutionary significance of the primary cilium/centrosome organ in Metazoa.},
journal = {Open biology},
volume = {8},
number = {8},
pages = {},
doi = {10.1098/rsob.180052},
pmid = {30068565},
issn = {2046-2441},
abstract = {Cell-autonomous polarity in Metazoans is evolutionarily conserved. I assume that permanent polarity in unicellular eukaryotes is required for cell motion and sensory reception, integration of these two activities being an evolutionarily constrained function. Metazoans are unique in making cohesive multicellular organisms through complete cell divisions. They evolved a primary cilium/centrosome (PC/C) organ, ensuring similar functions to the basal body/flagellum of unicellular eukaryotes, but in different cells, or in the same cell at different moments. The possibility that this innovation contributed to the evolution of individuality, in being instrumental in the early specification of the germ line during development, is further discussed. Then, using the example of highly regenerative organisms like planarians, which have lost PC/C organ in dividing cells, I discuss the possibility that part of the remodelling necessary to reach a new higher-level unit of selection in multi-cellular organisms has been triggered by conflicts among individual cell polarities to reach an organismic polarity. Finally, I briefly consider organisms with a sensorimotor organ like the brain that requires exceedingly elongated polarized cells for its activity. I conclude that beyond critical consequences for embryo development, the conservation of cell-autonomous polarity in Metazoans had far-reaching implications for the evolution of individuality.},
}
@article {pmid30059538,
year = {2018},
author = {Waldron, FM and Stone, GN and Obbard, DJ},
title = {Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes.},
journal = {PLoS genetics},
volume = {14},
number = {7},
pages = {e1007533},
doi = {10.1371/journal.pgen.1007533},
pmid = {30059538},
issn = {1553-7404},
abstract = {RNA interference (RNAi)-related pathways target viruses and transposable element (TE) transcripts in plants, fungi, and ecdysozoans (nematodes and arthropods), giving protection against infection and transmission. In each case, this produces abundant TE and virus-derived 20-30nt small RNAs, which provide a characteristic signature of RNAi-mediated defence. The broad phylogenetic distribution of the Argonaute and Dicer-family genes that mediate these pathways suggests that defensive RNAi is ancient, and probably shared by most animal (metazoan) phyla. Indeed, while vertebrates had been thought an exception, it has recently been argued that mammals also possess an antiviral RNAi pathway, although its immunological relevance is currently uncertain and the viral small RNAs (viRNAs) are not easily detectable. Here we use a metagenomic approach to test for the presence of viRNAs in five species from divergent animal phyla (Porifera, Cnidaria, Echinodermata, Mollusca, and Annelida), and in a brown alga-which represents an independent origin of multicellularity from plants, fungi, and animals. We use metagenomic RNA sequencing to identify around 80 virus-like contigs in these lineages, and small RNA sequencing to identify viRNAs derived from those viruses. We identified 21U small RNAs derived from an RNA virus in the brown alga, reminiscent of plant and fungal viRNAs, despite the deep divergence between these lineages. However, contrary to our expectations, we were unable to identify canonical (i.e. Drosophila- or nematode-like) viRNAs in any of the animals, despite the widespread presence of abundant micro-RNAs, and somatic transposon-derived piwi-interacting RNAs. We did identify a distinctive group of small RNAs derived from RNA viruses in the mollusc. However, unlike ecdysozoan viRNAs, these had a piRNA-like length distribution but lacked key signatures of piRNA biogenesis. We also identified primary piRNAs derived from putatively endogenous copies of DNA viruses in the cnidarian and the echinoderm, and an endogenous RNA virus in the mollusc. The absence of canonical virus-derived small RNAs from our samples may suggest that the majority of animal phyla lack an antiviral RNAi response. Alternatively, these phyla could possess an antiviral RNAi response resembling that reported for vertebrates, with cryptic viRNAs not detectable through simple metagenomic sequencing of wild-type individuals. In either case, our findings show that the antiviral RNAi responses of arthropods and nematodes, which are highly divergent from each other and from that of plants and fungi, are also highly diverged from the most likely ancestral metazoan state.},
}
@article {pmid29914363,
year = {2018},
author = {Dunning Hotopp, JC},
title = {Grafting or pruning in the animal tree: lateral gene transfer and gene loss?.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {470},
doi = {10.1186/s12864-018-4832-5},
pmid = {29914363},
issn = {1471-2164},
support = {R01 CA206188/CA/NCI NIH HHS/United States ; ABI-1457957//National Science Foundation/ ; 1-R01-CA206188//National Cancer Institute/ ; },
abstract = {BACKGROUND: Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted LGTs in vertebrates/chordates than invertebrates, but there is still evidence of LGT into chordates, including humans. More recently, a reanalysis of a subset of these putative LGTs into vertebrates concluded that there is not horizontal gene transfer in the human genome. One of the genes in dispute is an N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which encodes ACY3. This gene was initially identified as a putative bacteria-chordate LGT but was later debunked as it has a significant BLAST match to a more recently deposited genome of Saccoglossus kowalevskii, a flatworm, Metazoan, and hemichordate.<br><br>RESULTS: Using BLAST searches, HMM searches, and phylogenetics to assess the evidence for LGT, gene loss, and rate variation in ACY3/ASPA homologues, the most parsimonious explanation for the distribution of ACY3/ASPA genes in eukaryotes involves both gene loss and bacteria-animal LGT, albeit LGT that occurred hundreds of millions of years ago prior to the divergence of gnathostomes.<br><br>CONCLUSIONS: ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these time scales in the ancestors of humans are not unexpected given the many known, well-characterized, and adaptive LGTs from bacteria to insects and nematodes.},
}
@article {pmid29891718,
year = {2018},
author = {Smith, CCR and Tittes, S and Mendieta, JP and Collier-Zans, E and Rowe, HC and Rieseberg, LH and Kane, NC},
title = {Genetics of alternative splicing evolution during sunflower domestication.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {26},
pages = {6768-6773},
doi = {10.1073/pnas.1803361115},
pmid = {29891718},
issn = {1091-6490},
mesh = {*Alternative Splicing ; Domestication ; *Evolution, Molecular ; Helianthus/*genetics ; Plant Breeding ; Plant Proteins/genetics/metabolism ; Protein Isoforms/genetics/metabolism ; Quantitative Trait Loci ; RNA, Plant/*genetics ; Spliceosomes ; Transcriptome ; },
abstract = {Alternative splicing enables organisms to produce the diversity of proteins necessary for multicellular life by using relatively few protein-coding genes. Although differences in splicing have been identified among divergent taxa, the shorter-term evolution of splicing is understudied. The origins of novel splice forms, and the contributions of alternative splicing to major evolutionary transitions, are largely unknown. This study used transcriptomes of wild and domesticated sunflowers to examine splice differentiation and regulation during domestication. We identified substantial splicing divergence between wild and domesticated sunflowers, mainly in the form of intron retention. Transcripts with divergent splicing were enriched for seed-development functions, suggesting that artificial selection impacted splicing patterns. Mapping of quantitative trait loci (QTLs) associated with 144 differential splicing cases revealed primarily trans-acting variation affecting splicing patterns. A large proportion of identified QTLs contain known spliceosome proteins and are associated with splicing variation in multiple genes. Examining a broader set of wild and domesticated sunflower genotypes revealed that most differential splicing patterns in domesticated sunflowers likely arose from standing variation in wild Helianthus annuus and gained frequency during the domestication process. However, several domesticate-associated splicing patterns appear to be introgressed from other Helianthus species. These results suggest that sunflower domestication involved selection on pleiotropic regulatory alleles. More generally, our findings indicate that substantial differences in isoform abundances arose rapidly during a recent evolutionary transition and appear to contribute to adaptation and population divergence.},
}
@article {pmid29875290,
year = {2018},
author = {Ye, AY and Dou, Y and Yang, X and Wang, S and Huang, AY and Wei, L},
title = {A model for postzygotic mosaicisms quantifies the allele fraction drift, mutation rate, and contribution to de novo mutations.},
journal = {Genome research},
volume = {28},
number = {7},
pages = {943-951},
doi = {10.1101/gr.230003.117},
pmid = {29875290},
issn = {1549-5469},
mesh = {Alleles ; Child ; Female ; Genome, Human/genetics ; Humans ; Male ; Mosaicism ; Mutation/*genetics ; Mutation Rate ; Pedigree ; Polymorphism, Single Nucleotide/*genetics ; },
abstract = {The allele fraction (AF) distribution, occurrence rate, and evolutionary contribution of postzygotic single-nucleotide mosaicisms (pSNMs) remain largely unknown. In this study, we developed a mathematical model to describe the accumulation and AF drift of pSNMs during the development of multicellular organisms. By applying the model, we quantitatively analyzed two large-scale data sets of pSNMs identified from human genomes. We found that the postzygotic mutation rate per cell division during early embryogenesis, especially during the first cell division, was higher than the average mutation rate in either male or female gametes. We estimated that the stochastic cell death rate per cell cleavage during human embryogenesis was ∼5%, and parental pSNMs occurring during the first three cell divisions contributed to ∼10% of the de novo mutations observed in children. We further demonstrated that the genomic profiles of pSNMs could be used to measure the divergence distance between tissues. Our results highlight the importance of pSNMs in estimating recurrence risk and clarified the quantitative relationship between postzygotic and de novo mutations.},
}
@article {pmid29860723,
year = {2018},
author = {Mustafin, RN and Khusnutdinova, EK},
title = {[Epigenetic hypothesis of the role of peptides in aging.].},
journal = {Advances in gerontology = Uspekhi gerontologii},
volume = {31},
number = {1},
pages = {10-20},
pmid = {29860723},
issn = {1561-9125},
abstract = {In regulation of gene expression in the ontogenesis of multicellular eukaryotes, in addition to transcription factors, an important role is played by epigenetic factors that control the release of genetic information in each cell division. Many binding sites for the transcription factors were derived from transposons sequences. Mobile elements are also important sources of non-coding RNA. Due to this, transposons have an indirect effect on gene expression and genome methylation. In evolution, transposons serve as important sources for the origin of new protein and proteins domains. A number of studies have identified that long non-coding RNAs and microRNAs can be translated into functional peptides. At the same time, transposons remain active in the hypothalamus of adult humans, which is consistent with the transcription of non-coding RNAs in these structures, which may be key in aging.},
}
@article {pmid29797026,
year = {2018},
author = {Hauser, CJ and Otterbein, LE},
title = {Danger signals from mitochondrial DAMPS in trauma and post-injury sepsis.},
journal = {European journal of trauma and emergency surgery : official publication of the European Trauma Society},
volume = {44},
number = {3},
pages = {317-324},
doi = {10.1007/s00068-018-0963-2},
pmid = {29797026},
issn = {1863-9941},
support = {W81XWH-16-1-0464//U.S. Department of Defense/ ; },
mesh = {Alarmins/*immunology ; Animals ; Humans ; Immunity, Innate ; Inflammation/*immunology ; Mitochondria/*immunology ; Signal Transduction/immunology ; Wounds and Injuries/*immunology ; },
abstract = {In all multicellular organisms, immediate host responses to both sterile and infective threat are initiated by very primitive systems now grouped together under the general term 'danger responses'. Danger signals are generated when primitive 'pattern recognition receptors' (PRR) encounter activating 'alarmins'. These molecular species may be of pathogenic infective origin (pathogen-associated molecular patterns) or of sterile endogenous origin (danger-associated molecular patterns). There are many sterile and infective alarmins and there is considerable overlap in their ability to activate PRR, but in all cases the end result is inflammation. It is the overlap between sterile and infective signals acting via a relatively limited number of PRR that generally underlies the great clinical similarity we see between sterile and infective systemic inflammatory responses. Mitochondria (MT) are evolutionarily derived from bacteria, and thus they sit at the crossroads between sterile and infective danger signal pathways. Many of the molecular species in mitochondria are alarmins, and so the release of MT from injured cells results in a wide variety of inflammatory events. This paper discusses the known participation of MT in inflammation and reviews what is known about how the major.},
}
@article {pmid29735660,
year = {2018},
author = {Elsner, D and Meusemann, K and Korb, J},
title = {Longevity and transposon defense, the case of termite reproductives.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {21},
pages = {5504-5509},
doi = {10.1073/pnas.1804046115},
pmid = {29735660},
issn = {1091-6490},
mesh = {Animals ; *DNA Transposable Elements ; *Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Isoptera/*genetics ; *Longevity ; RNA, Small Interfering/*genetics ; *Reproduction ; },
abstract = {Social insects are promising new models in aging research. Within single colonies, longevity differences of several magnitudes exist that can be found elsewhere only between different species. Reproducing queens (and, in termites, also kings) can live for several decades, whereas sterile workers often have a lifespan of a few weeks only. We studied aging in the wild in a highly social insect, the termite Macrotermes bellicosus, which has one of the most pronounced longevity differences between reproductives and workers. We show that gene-expression patterns differed little between young and old reproductives, implying negligible aging. By contrast, old major workers had many genes up-regulated that are related to transposable elements (TEs), which can cause aging. Strikingly, genes from the PIWI-interacting RNA (piRNA) pathway, which are generally known to silence TEs in the germline of multicellular animals, were down-regulated only in old major workers but not in reproductives. Continued up-regulation of the piRNA defense commonly found in the germline of animals can explain the long life of termite reproductives, implying somatic cooption of germline defense during social evolution. This presents a striking germline/soma analogy as envisioned by the superorganism concept: the reproductives and workers of a colony reflect the germline and soma of multicellular animals, respectively. Our results provide support for the disposable soma theory of aging.},
}
@article {pmid29731304,
year = {2018},
author = {Maclean, AE and Hertle, AP and Ligas, J and Bock, R and Balk, J and Meyer, EH},
title = {Absence of Complex I Is Associated with Diminished Respiratory Chain Function in European Mistletoe.},
journal = {Current biology : CB},
volume = {28},
number = {10},
pages = {1614-1619.e3},
doi = {10.1016/j.cub.2018.03.036},
pmid = {29731304},
issn = {1879-0445},
abstract = {Parasitism is a life history strategy found across all domains of life whereby nutrition is obtained from a host. It is often associated with reductive evolution of the genome, including loss of genes from the organellar genomes [1, 2]. In some unicellular parasites, the mitochondrial genome (mitogenome) has been lost entirely, with far-reaching consequences for the physiology of the organism [3, 4]. Recently, mitogenome sequences of several species of the hemiparasitic plant mistletoe (Viscum sp.) have been reported [5, 6], revealing a striking loss of genes not seen in any other multicellular eukaryotes. In particular, the nad genes encoding subunits of respiratory complex I are all absent and other protein-coding genes are also lost or highly diverged in sequence, raising the question what remains of the respiratory complexes and mitochondrial functions. Here we show that oxidative phosphorylation (OXPHOS) in European mistletoe, Viscum album, is highly diminished. Complex I activity and protein subunits of complex I could not be detected. The levels of complex IV and ATP synthase were at least 5-fold lower than in the non-parasitic model plant Arabidopsis thaliana, whereas alternative dehydrogenases and oxidases were higher in abundance. Carbon flux analysis indicates that cytosolic reactions including glycolysis are greater contributors to ATP synthesis than the mitochondrial tricarboxylic acid (TCA) cycle. Our results describe the extreme adjustments in mitochondrial functions of the first reported multicellular eukaryote without complex I.},
}
@article {pmid29730580,
year = {2018},
author = {Vijay, K},
title = {Toll-like receptors in immunity and inflammatory diseases: Past, present, and future.},
journal = {International immunopharmacology},
volume = {59},
number = {},
pages = {391-412},
doi = {10.1016/j.intimp.2018.03.002},
pmid = {29730580},
issn = {1878-1705},
mesh = {Animals ; Genetic Predisposition to Disease ; Humans ; *Immunity, Innate ; Infection/genetics/immunology ; Inflammation/genetics/*immunology ; Polymorphism, Genetic ; Toll-Like Receptors/genetics/*immunology ; },
abstract = {The immune system is a very diverse system of the host that evolved during evolution to cope with various pathogens present in the vicinity of environmental surroundings inhabited by multicellular organisms ranging from achordates to chordates (including humans). For example, cells of immune system express various pattern recognition receptors (PRRs) that detect danger via recognizing specific pathogen-associated molecular patterns (PAMPs) and mount a specific immune response. Toll-like receptors (TLRs) are one of these PRRs expressed by various immune cells. However, they were first discovered in the Drosophila melanogaster (common fruit fly) as genes/proteins important in embryonic development and dorso-ventral body patterning/polarity. Till date, 13 different types of TLRs (TLR1-TLR13) have been discovered and described in mammals since the first discovery of TLR4 in humans in late 1997. This discovery of TLR4 in humans revolutionized the field of innate immunity and thus the immunology and host-pathogen interaction. Since then TLRs are found to be expressed on various immune cells and have been targeted for therapeutic drug development for various infectious and inflammatory diseases including cancer. Even, Single nucleotide polymorphisms (SNPs) among various TLR genes have been identified among the different human population and their association with susceptibility/resistance to certain infections and other inflammatory diseases. Thus, in the present review the current and future importance of TLRs in immunity, their pattern of expression among various immune cells along with TLR based therapeutic approach is reviewed.},
}
@article {pmid29688518,
year = {2018},
author = {Lee, J and Yang, EC and Graf, L and Yang, JH and Qiu, H and Zelzion, U and Chan, CX and Stephens, TG and Weber, APM and Boo, GH and Boo, SM and Kim, KM and Shin, Y and Jung, M and Lee, SJ and Yim, HS and Lee, JH and Bhattacharya, D and Yoon, HS},
title = {Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta.},
journal = {Molecular biology and evolution},
volume = {35},
number = {8},
pages = {1869-1886},
doi = {10.1093/molbev/msy081},
pmid = {29688518},
issn = {1537-1719},
abstract = {Red algae (Rhodophyta) underwent two phases of large-scale genome reduction during their early evolution. The red seaweeds did not attain genome sizes or gene inventories typical of other multicellular eukaryotes. We generated a high-quality 92.1 Mb draft genome assembly from the red seaweed Gracilariopsis chorda, including methylation and small (s)RNA data. We analyzed these and other Archaeplastida genomes to address three questions: 1) What is the role of repeats and transposable elements (TEs) in explaining Rhodophyta genome size variation, 2) what is the history of genome duplication and gene family expansion/reduction in these taxa, and 3) is there evidence for TE suppression in red algae? We find that the number of predicted genes in red algae is relatively small (4,803-13,125 genes), particularly when compared with land plants, with no evidence of polyploidization. Genome size variation is primarily explained by TE expansion with the red seaweeds having the largest genomes. Long terminal repeat elements and DNA repeats are the major contributors to genome size growth. About 8.3% of the G. chorda genome undergoes cytosine methylation among gene bodies, promoters, and TEs, and 71.5% of TEs contain methylated-DNA with 57% of these regions associated with sRNAs. These latter results suggest a role for TE-associated sRNAs in RNA-dependent DNA methylation to facilitate silencing. We postulate that the evolution of genome size in red algae is the result of the combined action of TE spread and the concomitant emergence of its epigenetic suppression, together with other important factors such as changes in population size.},
}
@article {pmid29685747,
year = {2018},
author = {Miller, WB and Torday, JS},
title = {Four domains: The fundamental unicell and Post-Darwinian Cognition-Based Evolution.},
journal = {Progress in biophysics and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pbiomolbio.2018.04.006},
pmid = {29685747},
issn = {1873-1732},
abstract = {Contemporary research supports the viewpoint that self-referential cognition is the proper definition of life. From that initiating platform, a cohesive alternative evolutionary narrative distinct from standard Neodarwinism can be presented. Cognition-Based Evolution contends that biological variation is a product of a self-reinforcing information cycle that derives from self-referential attachment to biological information space-time with its attendant ambiguities. That information cycle is embodied through obligatory linkages among energy, biological information, and communication. Successive reiterations of the information cycle enact the informational architectures of the basic unicellular forms. From that base, inter-domain and cell-cell communications enable genetic and cellular variations through self-referential natural informational engineering and cellular niche construction. Holobionts are the exclusive endpoints of that self-referential cellular engineering as obligatory multicellular combinations of the essential Four Domains: Prokaryota, Archaea, Eukaryota and the Virome. Therefore, it is advocated that these Four Domains represent the perpetual object of the living circumstance rather than the visible macroorganic forms. In consequence, biology and its evolutionary development can be appraised as the continual defense of instantiated cellular self-reference. As the survival of cells is as dependent upon limitations and boundaries as upon any freedom of action, it is proposed that selection represents only one of many forms of cellular constraint that sustain self-referential integrity.},
}
@article {pmid29675831,
year = {2018},
author = {Kauko, A and Lehto, K},
title = {Eukaryote specific folds: Part of the whole.},
journal = {Proteins},
volume = {86},
number = {8},
pages = {868-881},
doi = {10.1002/prot.25517},
pmid = {29675831},
issn = {1097-0134},
abstract = {The origin of eukaryotes is one of the central transitions in the history of life; without eukaryotes there would be no complex multicellular life. The most accepted scenarios suggest the endosymbiosis of a mitochondrial ancestor with a complex archaeon, even though the details regarding the host and the triggering factors are still being discussed. Accordingly, phylogenetic analyses have demonstrated archaeal affiliations with key informational systems, while metabolic genes are often related to bacteria, mostly to the mitochondrial ancestor. Despite of this, there exists a large number of protein families and folds found only in eukaryotes. In this study, we have analyzed structural superfamilies and folds that probably appeared during eukaryogenesis. These folds typically represent relatively small binding domains of larger multidomain proteins. They are commonly involved in biological processes that are particularly complex in eukaryotes, such as signaling, trafficking/cytoskeleton, ubiquitination, transcription and RNA processing, but according to recent studies, these processes also have prokaryotic roots. Thus the folds originating from an eukaryotic stem seem to represent accessory parts that have contributed in the expansion of several prokaryotic processes to a new level of complexity. This might have taken place as a co-evolutionary process where increasing complexity and fold innovations have supported each other.},
}
@article {pmid29641448,
year = {2018},
author = {Zheng, S and Long, J and Liu, Z and Tao, W and Wang, D},
title = {Identification and Evolution of TGF-β Signaling Pathway Members in Twenty-Four Animal Species and Expression in Tilapia.},
journal = {International journal of molecular sciences},
volume = {19},
number = {4},
pages = {},
doi = {10.3390/ijms19041154},
pmid = {29641448},
issn = {1422-0067},
mesh = {Activin Receptors, Type I/genetics/metabolism ; Animals ; *Evolution, Molecular ; Fish Proteins/*genetics/metabolism ; Phylogeny ; Receptors, Transforming Growth Factor beta/genetics/metabolism ; *Signal Transduction ; Smad4 Protein/genetics/metabolism ; Tilapia/classification/*genetics/metabolism ; Transforming Growth Factor beta/*genetics/metabolism ; },
abstract = {Transforming growth factor β (TGF-β) signaling controls diverse cellular processes during embryogenesis as well as in mature tissues of multicellular animals. Here we carried out a comprehensive analysis of TGF-β pathway members in 24 representative animal species. The appearance of the TGF-β pathway was intrinsically linked to the emergence of metazoan. The total number of TGF-β ligands, receptors, and smads changed slightly in all invertebrates and jawless vertebrates analyzed. In contrast, expansion of the pathway members, especially ligands, was observed in jawed vertebrates most likely due to the second round of whole genome duplication (2R) and additional rounds in teleosts. Duplications of TGFB2, TGFBR2, ACVR1, SMAD4 and SMAD6, which were resulted from 2R, were first isolated. Type II receptors may be originated from the ACVR2-like ancestor. Interestingly, AMHR2 was not identified in Chimaeriformes and Cypriniformes even though they had the ligand AMH. Based on transcriptome data, TGF-β ligands exhibited a tissue-specific expression especially in the heart and gonads. However, most receptors and smads were expressed in multiple tissues indicating they were shared by different ligands. Spatial and temporal expression profiles of 8 genes in gonads of different developmental stages provided a fundamental clue for understanding their important roles in sex determination and reproduction. Taken together, our findings provided a global insight into the phylogeny and expression patterns of the TGF-β pathway genes, and hence contribute to the greater understanding of their biological roles in the organism especially in teleosts.},
}
@article {pmid29625658,
year = {2018},
author = {Padder, SA and Prasad, R and Shah, AH},
title = {Quorum sensing: A less known mode of communication among fungi.},
journal = {Microbiological research},
volume = {210},
number = {},
pages = {51-58},
doi = {10.1016/j.micres.2018.03.007},
pmid = {29625658},
issn = {1618-0623},
mesh = {Anti-Infective Agents/pharmacology ; Bacteria/drug effects/genetics ; Bacterial Physiological Phenomena ; Candida albicans/physiology ; Drug Resistance, Multiple/genetics ; Farnesol/metabolism ; Fungi/*drug effects/*physiology ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Fungal ; Phenylethyl Alcohol/analogs &amp; derivatives/metabolism ; Pheromones/metabolism ; Quorum Sensing/*drug effects/genetics/*physiology ; Virulence/genetics ; Volatile Organic Compounds/metabolism ; },
abstract = {Quorum sensing (QS), a density-dependent signaling mechanism of microbial cells, involves an exchange and sense of low molecular weight signaling compounds called autoinducers. With the increase in population density, the autoinducers accumulate in the extracellular environment and once their concentration reaches a threshold, many genes are either expressed or repressed. This cell density-dependent signaling mechanism enables single cells to behave as multicellular organisms and regulates different microbial behaviors like morphogenesis, pathogenesis, competence, biofilm formation, bioluminescence, etc guided by environmental cues. Initially, QS was regarded to be a specialized system of certain bacteria. The discovery of filamentation control in pathogenic polymorphic fungus Candida albicans by farnesol revealed the phenomenon of QS in fungi as well. Pathogenic microorganisms primarily regulate the expression of virulence genes using QS systems. The indirect role of QS in the emergence of multiple drug resistance (MDR) in microbial pathogens necessitates the finding of alternative antimicrobial therapies that target QS and inhibit the same. A related phenomenon of quorum sensing inhibition (QSI) performed by small inhibitor molecules called quorum sensing inhibitors (QSIs) has an ability for efficient reduction of gene expression regulated by quorum sensing. In the present review, recent advancements in the study of different fungal quorum sensing molecules (QSMs) and quorum sensing inhibitors (QSIs) of fungal origin along with their mechanism of action and/or role/s are discussed.},
}
@article {pmid29614268,
year = {2018},
author = {Park, B and Kim, H and Jeon, TJ},
title = {Loss of RapC causes defects in cytokinesis, cell migration, and multicellular development of Dictyostelium.},
journal = {Biochemical and biophysical research communications},
volume = {499},
number = {4},
pages = {783-789},
doi = {10.1016/j.bbrc.2018.03.223},
pmid = {29614268},
issn = {1090-2104},
mesh = {Cell Adhesion ; *Cell Movement ; Cell Shape ; *Cytokinesis ; Dictyostelium/*cytology/*growth &amp; development/metabolism ; Phenotype ; Phylogeny ; Protozoan Proteins/chemistry/*metabolism ; Sequence Homology, Amino Acid ; rap1 GTP-Binding Proteins/chemistry ; },
abstract = {The small GTPase Ras proteins are involved in diverse cellular processes. We investigated the functions of RapC, one of 15 Ras subfamily GTPases in Dictyostelium. Loss of RapC resulted in a spread shape of cells; severe defects in cytokinesis leading to multinucleation; decrease of migration speed in chemoattractant-mediated cell migration, likely through increased cell adhesion; and aberrations in multicellular development producing abnormal multiple tips from one mound and multi-branched developmental structures. Defects in cells lacking RapC were rescued by expressing GFP-RapC in rapC null cells. Our results demonstrate that RapC, despite its high sequence homology with Rap1, plays a negative role in cell spreading and cell adhesion, in contrast to Rap1, which is a key regulator of cell adhesion and cytoskeleton rearrangement. In addition, RapC appears to have a unique function in multicellular development and is involved in tip formation from mounds. This study contributes to the understanding of Ras-mediated cellular processes.},
}
@article {pmid29608173,
year = {2018},
author = {Clarke, EK and Rivera Gomez, KA and Mustachi, Z and Murph, MC and Schvarzstein, M},
title = {Manipulation of Ploidy in Caenorhabditis elegans.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {133},
pages = {},
doi = {10.3791/57296},
pmid = {29608173},
issn = {1940-087X},
support = {P40 OD010440/OD/NIH HHS/United States ; //CIHR/Canada ; },
mesh = {Animals ; Caenorhabditis elegans/*genetics ; Male ; *Ploidies ; },
abstract = {Mechanisms that involve whole genome polyploidy play important roles in development and evolution; also, an abnormal generation of tetraploid cells has been associated with both the progression of cancer and the development of drug resistance. Until now, it has not been feasible to easily manipulate the ploidy of a multicellular animal without generating mostly sterile progeny. Presented here is a simple and rapid protocol for generating tetraploid Caenorhabditis elegans animals from any diploid strain. This method allows the user to create a bias in chromosome segregation during meiosis, ultimately increasing ploidy in C. elegans. This strategy relies on the transient reduction of expression of the rec-8 gene to generate diploid gametes. A rec-8 mutant produces diploid gametes that can potentially produce tetraploids upon fertilization. This tractable scheme has been used to generate tetraploid strains carrying mutations and chromosome rearrangements to gain insight into chromosomal dynamics and interactions during pairing and synapsis in meiosis. This method is efficient for generating stable tetraploid strains without genetic markers, can be applied to any diploid strain, and can be used to derive triploid C. elegans. This straightforward method is useful for investigating other fundamental biological questions relevant to genome instability, gene dosage, biological scaling, extracellular signaling, adaptation to stress, development of resistance to drugs, and mechanisms of speciation.},
}
@article {pmid29606595,
year = {2018},
author = {Lherminier, P},
title = {[Informative predation: Towards a new species concept].},
journal = {Comptes rendus biologies},
volume = {341},
number = {4},
pages = {209-218},
doi = {10.1016/j.crvi.2018.02.004},
pmid = {29606595},
issn = {1768-3238},
mesh = {*Adaptation, Physiological ; Animals ; Biological Evolution ; Child ; Courtship ; Diploidy ; Female ; Fertility ; Genome ; Humans ; Male ; *Predatory Behavior ; Pregnancy ; Reproduction/genetics ; *Selection, Genetic ; },
abstract = {We distinguish two types of predations: the predation of matter-energy equals the food chain, and the informative predation is the capture of the information brought by the sexual partners. The cell or parent consumes energy and matter to grow, multiply and produce offspring. A fixed amount of resources is divided by the number of organisms, so individual growth and numerical multiplication are limited by depletion resources of the environment. Inversely, fertilization does not destroy information, but instead produces news. The information is multiplied by the number of partners and children, since each fertilization gives rise to a new genome following a combinatorial process that continues without exhaustion. The egg does not swallow the sperm to feed, but exchange good food for quality information. With the discovery of sex, that is, 1.5 Ga ago, life added soft predation to hard predation, i.e. information production within each species to matter-energy flow between species. Replicative and informative structures are subject to two competing biological constraints: replicative fidelity promotes proliferation, but limits adaptive evolution. On the contrary, the offspring of a couple obviously cannot be a copy of both partners, they are a new production, a re-production. Sexual recombination allows the exponential enrichment of the genetic diversity, thus promoting indefinite adaptive and evolutionary capacities. Evolutionary history illustrates this: the bacteria proliferate but have remained at the first purely nutritive stage in which most of the sensory functions, mobility, defense, and feeding have experienced almost no significant novelty in three billion years. Another world appeared with the sexual management of information. Sexual reproduction actually combines two functions: multiplicative by &quot;vertical transfer&quot; and informative by &quot;horizontal transfer&quot;. This distinction is very common: polypus - medusa alternations, parasite multiplication cycles, the lytochal and deuterotochal parthenogenesis of aphids, and the innumerable para- and pseudo-sexual strategies of plants opportunistically combine the two modes of asexual replication and sexual combination. However, for the majority of animals and multicellular plants that produce many gametes, numerical proliferation by descendants and informative diversity by sexuality are mutually implicated, for example in the seed. The true discovery of eukaryotes may not be the &quot;true nucleus&quot;, as their name implies, but an orderly informative function. The field of recombinations circumscribes a class of partners genetically compatible with each other, each simultaneously prey and predator of the DNA of the other. The mythical Maxwell demon capable of tracing entropy by sorting molecules according to their state does exist: each mate is the other's Maxwell's demon. While a sexless bacterium is simply divided into two cells, two sexual parents work together to produce a single offspring a time. Added to this are the burdens involved in meiosis and crossing-over, cellular diploidy, and mating. Sex produces an information gain that is paid for by a cost of energy-material, and this barter must be fair to survive. The domains of sexual intercourse are very diverse: uniparental reproduction, alternation of asexual proliferation and sexual information, self-fertilization, endogamy, exogamy, panmixis, diffuse or structured polymorphism, fertile or sterile hybridization, horizontal transfers. Each species is a recombination field between two domains, cloning and hybridization. Multiplicative descent and informative fertilization are organically distinct, but selectively associated: the information produced by the parents' sexuality favors the predation of matter-energy and therefore the proliferation of offspring, and this proliferation in turn favors the sexed producers of information. The equation specific to each species is: enough energy to proliferate, enough information to diversify. Alternatively, two other reproductive modes obtain or transmit less information at lower cost: not enough recombinations=repetitive clonal proliferation, and too many recombinations=disordered hybridization. But these marginal modes have poor prospects, as the model of the species is successfully attractive. Better discriminate to better inform. In bacteria, the exchanged and incorporated DNA segments are directly identified by the parity of the complementary strands, which determines simultaneously the similarity, the offspring, and the pairing. In eukaryotes, on the contrary, somatic growth and germinal information are segregated. During speciation, adaptive information is compacted, delocalized, codified and published to inform the species about its own state: the prezygotic relationship governs viable mating. Under the effect of sexual selection, the runaway and the reinforcement of the characters related to courtship testifies to their identifying function, which explains the paradox of the singularity and luxuriance of the sexual hypertrophies. The speciation discretizes a balanced recombination field and validates the informative relations. The species is without degree. Mates of a species recognize each other quickly and well because the logic of coding disengages from the ecological game of adaptations. The system of mate recognition has a function of cohesion and its regularity allows the adaptations of the less regular being, it is neither elitist nor normative, it is subjected neither to a level of aptitudes, nor to sexual performances, but permissive; it protects the variability and polymorphism. Two mutually irreducible relationships triggered the debate between the taxonomists who support the phyletic definition of the species by the descendance, and the proponents of the definition by interfertility. Such a taxonomic disagreement is not insurmountable, but the issue is deeper than taxonomic concepts, because these concepts relate to two different modes of evolution. According to the phyletic model, each species is a lineage passively isolated by external circumstances; on the contrary, in the sexual model each species is actively produced by an internal process of adjustment between replicative costs and informative gains. Each species develops a solution of the equation that matches material-energy expenditures with informative gains. A species concept based on a lasting relationship between these two quantities or on the limits of certain values or their equilibrium is therefore legitimate. It is this equilibrium that all couples resolve, without our formulation being as clearly as biology desires and as physics demands. Energy expenditures and informative gains in sexuality are almost impossible to measure, yet observation and experience allow an approximate ranking of the energy/information ratio. For example, endogamy is more economical, but less diversifying than exogamy, polymorphism increases information, the reinforcement of sexual isolation limits the rate of unproductive fertilization, between neighboring species hybridization allows certain genetic contributions, etc. A closed species evolves naturally towards another just as closed. On the contrary, the artificial transfer of DNA opens the species. The natural boundaries that isolate the species are easily trespassed as energy costs and constraints of sexual recognition are easily controlled; and the perspectives of manipulations are visible, whereas natural selection never anticipates and thus works blindly. Informative, artificially directed predation stimulates the evolution of species.},
}
@article {pmid29599012,
year = {2018},
author = {Bang, C and Dagan, T and Deines, P and Dubilier, N and Duschl, WJ and Fraune, S and Hentschel, U and Hirt, H and Hülter, N and Lachnit, T and Picazo, D and Pita, L and Pogoreutz, C and Rädecker, N and Saad, MM and Schmitz, RA and Schulenburg, H and Voolstra, CR and Weiland-Bräuer, N and Ziegler, M and Bosch, TCG},
title = {Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?.},
journal = {Zoology (Jena, Germany)},
volume = {127},
number = {},
pages = {1-19},
doi = {10.1016/j.zool.2018.02.004},
pmid = {29599012},
issn = {1873-2720},
mesh = {*Adaptation, Physiological/physiology ; Animals ; Ecosystem ; *Extreme Environments ; Microbiota/genetics/*physiology ; Phylogeny ; Symbiosis/physiology ; },
abstract = {From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forming a metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms. Research on host-microbe interactions has become an emerging cross-disciplinary field. In both vertebrates and invertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, its disturbance can contribute to the development of disease states. However, the molecular and cellular mechanisms controlling the interactions within a metaorganism are poorly understood and many key interactions between the associated organisms remain unknown. In this perspective article, we outline some of the issues in interspecies interactions and in particular address the question of how metaorganisms react and adapt to inputs from extreme environments such as deserts, the intertidal zone, oligothrophic seas, and hydrothermal vents.},
}
@article {pmid29590089,
year = {2018},
author = {Alemany, A and Florescu, M and Baron, CS and Peterson-Maduro, J and van Oudenaarden, A},
title = {Whole-organism clone tracing using single-cell sequencing.},
journal = {Nature},
volume = {556},
number = {7699},
pages = {108-112},
doi = {10.1038/nature25969},
pmid = {29590089},
issn = {1476-4687},
mesh = {Animal Fins/cytology ; Animals ; Brain/cytology ; CRISPR-Cas Systems/genetics ; *Cell Lineage/genetics ; Cell Tracking/*methods ; Clone Cells/*cytology/*metabolism ; Embryonic Stem Cells/cytology/metabolism ; Eye/cytology ; Female ; Genes, Reporter/genetics ; Hematopoietic Stem Cells/cytology/metabolism ; Male ; Multipotent Stem Cells/cytology/metabolism ; Organ Specificity ; Regeneration ; Sequence Analysis/*methods ; *Single-Cell Analysis ; Transcriptome ; Whole Body Imaging ; Zebrafish/*anatomy &amp; histology/embryology/genetics ; },
abstract = {Embryonic development is a crucial period in the life of a multicellular organism, during which limited sets of embryonic progenitors produce all cells in the adult body. Determining which fate these progenitors acquire in adult tissues requires the simultaneous measurement of clonal history and cell identity at single-cell resolution, which has been a major challenge. Clonal history has traditionally been investigated by microscopically tracking cells during development, monitoring the heritable expression of genetically encoded fluorescent proteins and, more recently, using next-generation sequencing technologies that exploit somatic mutations, microsatellite instability, transposon tagging, viral barcoding, CRISPR-Cas9 genome editing and Cre-loxP recombination. Single-cell transcriptomics provides a powerful platform for unbiased cell-type classification. Here we present ScarTrace, a single-cell sequencing strategy that enables the simultaneous quantification of clonal history and cell type for thousands of cells obtained from different organs of the adult zebrafish. Using ScarTrace, we show that a small set of multipotent embryonic progenitors generate all haematopoietic cells in the kidney marrow, and that many progenitors produce specific cell types in the eyes and brain. In addition, we study when embryonic progenitors commit to the left or right eye. ScarTrace reveals that epidermal and mesenchymal cells in the caudal fin arise from the same progenitors, and that osteoblast-restricted precursors can produce mesenchymal cells during regeneration. Furthermore, we identify resident immune cells in the fin with a distinct clonal origin from other blood cell types. We envision that similar approaches will have major applications in other experimental systems, in which the matching of embryonic clonal origin to adult cell type will ultimately allow reconstruction of how the adult body is built from a single cell.},
}
@article {pmid29587819,
year = {2018},
author = {Dickson, LB and Ghozlane, A and Volant, S and Bouchier, C and Ma, L and Vega-Rúa, A and Dusfour, I and Jiolle, D and Paupy, C and Mayanja, MN and Kohl, A and Lutwama, JJ and Duong, V and Lambrechts, L},
title = {Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {207},
doi = {10.1186/s13071-018-2780-1},
pmid = {29587819},
issn = {1756-3305},
support = {ANR-16-CE35-0004-01//Agence Nationale de la Recherche/International ; ANR-17-ERC2-0016-01//Agence Nationale de la Recherche/International ; ANR-10-LABX-62-IBEID//Investissement d'Avenir program Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases/International ; 734584//European Union's Horizon 2020 research and innovation programme under ZikaPLAN/International ; 2015-FED-192//Programme Opérationnel FEDER-Guadeloupe-Conseil Régional/International ; MC_UU_12014//Medical Research Council/United Kingdom ; ANR10-INBS-09-08//France Génomique consortium/International ; },
mesh = {Aedes/*microbiology ; Animals ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Host-associated microbes, collectively known as the microbiota, play an important role in the biology of multicellular organisms. In mosquito vectors of human pathogens, the gut bacterial microbiota influences vectorial capacity and has become the subject of intense study. In laboratory studies of vector biology, genetic effects are often inferred from differences between geographically and genetically diverse colonies of mosquitoes that are reared in the same insectary. It is unclear, however, to what extent genetic effects can be confounded by uncontrolled differences in the microbiota composition among mosquito colonies. To address this question, we used 16S metagenomics to compare the midgut bacterial microbiome of six laboratory colonies of Aedes aegypti recently derived from wild populations representing the geographical range and genetic diversity of the species.<br><br>RESULTS: We found that the diversity, abundance, and community structure of the midgut bacterial microbiome was remarkably similar among the six different colonies of Ae. aegypti, regardless of their geographical origin. We also confirmed the relatively low complexity of bacterial communities inhabiting the mosquito midgut.<br><br>CONCLUSIONS: Our finding that geographically diverse colonies of Ae. aegypti reared in the same insectary harbor a similar gut bacterial microbiome supports the conclusion that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype. Thus, uncontrolled differences in microbiota composition are unlikely to represent a significant confounding factor in genetic studies of vector biology.},
}
@article {pmid29579574,
year = {2018},
author = {Lower, SS and McGurk, MP and Clark, AG and Barbash, DA},
title = {Satellite DNA evolution: old ideas, new approaches.},
journal = {Current opinion in genetics &amp; development},
volume = {49},
number = {},
pages = {70-78},
doi = {10.1016/j.gde.2018.03.003},
pmid = {29579574},
issn = {1879-0380},
support = {F32 GM126736/GM/NIGMS NIH HHS/United States ; R01 GM119125/GM/NIGMS NIH HHS/United States ; },
abstract = {A substantial portion of the genomes of most multicellular eukaryotes consists of large arrays of tandemly repeated sequence, collectively called satellite DNA. The processes generating and maintaining different satellite DNA abundances across lineages are important to understand as satellites have been linked to chromosome mis-segregation, disease phenotypes, and reproductive isolation between species. While much theory has been developed to describe satellite evolution, empirical tests of these models have fallen short because of the challenges in assessing satellite repeat regions of the genome. Advances in computational tools and sequencing technologies now enable identification and quantification of satellite sequences genome-wide. Here, we describe some of these tools and how their applications are furthering our knowledge of satellite evolution and function.},
}
@article {pmid29547664,
year = {2018},
author = {Zielich, J and Tzima, E and Schröder, EA and Jemel, F and Conradt, B and Lambie, EJ},
title = {Overlapping expression patterns and functions of three paralogous P5B ATPases in Caenorhabditis elegans.},
journal = {PloS one},
volume = {13},
number = {3},
pages = {e0194451},
doi = {10.1371/journal.pone.0194451},
pmid = {29547664},
issn = {1932-6203},
support = {P40 OD010440/OD/NIH HHS/United States ; },
mesh = {Adenosine Triphosphatases/classification/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Caenorhabditis elegans/cytology/enzymology/*genetics ; Caenorhabditis elegans Proteins/*genetics/metabolism ; Cell Movement/genetics ; *Gene Expression Profiling ; *Gene Expression Regulation, Enzymologic ; Luminescent Proteins/genetics/metabolism ; Membrane Proteins/genetics/metabolism ; Mutation ; Organelles/enzymology ; Phylogeny ; Sequence Homology, Amino Acid ; },
abstract = {P5B ATPases are present in the genomes of diverse unicellular and multicellular eukaryotes, indicating that they have an ancient origin, and that they are important for cellular fitness. Inactivation of ATP13A2, one of the four human P5B ATPases, leads to early-onset Parkinson's disease (Kufor-Rakeb Syndrome). The presence of an invariant PPALP motif within the putative substrate interaction pocket of transmembrane segment M4 suggests that all P5B ATPases might have similar transport specificity; however, the identity of the transport substrate(s) remains unknown. Nematodes of the genus Caenorhabditis possess three paralogous P5B ATPase genes, catp-5, catp-6 and catp-7, which probably originated from a single ancestral gene around the time of origin of the Caenorhabditid clade. By using CRISPR/Cas9, we have systematically investigated the expression patterns, subcellular localization and biological functions of each of the P5B ATPases of C. elegans. We find that each gene has a unique expression pattern, and that some tissues express more than one P5B. In some tissues where their expression patterns overlap, different P5Bs are targeted to different subcellular compartments (e.g., early endosomes vs. plasma membrane), whereas in other tissues they localize to the same compartment (plasma membrane). We observed lysosomal co-localization between CATP-6::GFP and LMP-1::RFP in transgenic animals; however, this was an artifact of the tagged LMP-1 protein, since anti-LMP-1 antibody staining of native protein revealed that LMP-1 and CATP-6::GFP occupy different compartments. The nematode P5Bs are at least partially redundant, since we observed synthetic sterility in catp-5(0); catp-6(0) and catp-6(0) catp-7(0) double mutants. The double mutants exhibit defects in distal tip cell migration that resemble those of ina-1 (alpha integrin ortholog) and vab-3 (Pax6 ortholog) mutants, suggesting that the nematode P5Bs are required for ina-1and/or vab-3 function. This is potentially a conserved regulatory interaction, since mammalian ATP13A2, alpha integrin and Pax6 are all required for proper dopaminergic neuron function.},
}
@article {pmid29546391,
year = {2018},
author = {Kritzer, JA and Freyzon, Y and Lindquist, S},
title = {Yeast can accommodate phosphotyrosine: v-Src toxicity in yeast arises from a single disrupted pathway.},
journal = {FEMS yeast research},
volume = {18},
number = {3},
pages = {},
doi = {10.1093/femsyr/foy027},
pmid = {29546391},
issn = {1567-1364},
abstract = {Tyrosine phosphorylation is a key biochemical signal that controls growth and differentiation in multicellular organisms. Saccharomyces cerevisiae and nearly all other unicellular eukaryotes lack intact phosphotyrosine signaling pathways. However, many of these organisms have primitive phosphotyrosine-binding proteins and tyrosine phosphatases, leading to the assumption that the major barrier for emergence of phosphotyrosine signaling was the negative consequences of promiscuous tyrosine kinase activity. In this work, we reveal that the classic oncogene v-Src, which phosphorylates many dozens of proteins in yeast, is toxic because it disrupts a specific spore wall remodeling pathway. Using genetic selections, we find that expression of a specific cyclic peptide, or overexpression of SMK1, a MAP kinase that controls spore wall assembly, both lead to robust growth despite a continuous high level of phosphotyrosine in the yeast proteome. Thus, minimal genetic manipulations allow yeast to tolerate high levels of phosphotyrosine. These results indicate that the introduction of tyrosine kinases within single-celled organisms may not have been a major obstacle to the evolution of phosphotyrosine signaling.},
}
@article {pmid29545511,
year = {2018},
author = {Rosenberg, AB and Roco, CM and Muscat, RA and Kuchina, A and Sample, P and Yao, Z and Graybuck, LT and Peeler, DJ and Mukherjee, S and Chen, W and Pun, SH and Sellers, DL and Tasic, B and Seelig, G},
title = {Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.},
journal = {Science (New York, N.Y.)},
volume = {360},
number = {6385},
pages = {176-182},
doi = {10.1126/science.aam8999},
pmid = {29545511},
issn = {1095-9203},
support = {R01 CA207029/CA/NCI NIH HHS/United States ; R01 NS064404/NS/NINDS NIH HHS/United States ; R21 NS086500/NS/NINDS NIH HHS/United States ; TL1 TR002318/TR/NCATS NIH HHS/United States ; },
mesh = {Animals ; Brain/*growth &amp; development ; Cell Nucleus/genetics ; Gene Expression Profiling/*methods ; *Gene Expression Regulation, Developmental ; HEK293 Cells ; Humans ; Mice ; NIH 3T3 Cells ; Neurons/metabolism ; Sequence Analysis, RNA ; Single-Cell Analysis/*methods ; Spinal Cord/*growth &amp; development ; *Transcriptome ; },
abstract = {To facilitate scalable profiling of single cells, we developed split-pool ligation-based transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing, and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. More than 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation. Pseudotime analysis revealed transcriptional programs driving four developmental lineages, providing a snapshot of early postnatal development in the murine central nervous system. SPLiT-seq provides a path toward comprehensive single-cell transcriptomic analysis of other similarly complex multicellular systems.},
}
@article {pmid29461501,
year = {2018},
author = {Żółtowska-Aksamitowska, S and Shaala, LA and Youssef, DTA and Elhady, SS and Tsurkan, MV and Petrenko, I and Wysokowski, M and Tabachnick, K and Meissner, H and Ivanenko, VN and Bechmann, N and Joseph, Y and Jesionowski, T and Ehrlich, H},
title = {First Report on Chitin in a Non-Verongiid Marine Demosponge: The Mycale euplectellioides Case.},
journal = {Marine drugs},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/md16020068},
pmid = {29461501},
issn = {1660-3397},
mesh = {Animals ; Aquatic Organisms/chemistry/*metabolism ; Biocompatible Materials/chemistry ; Biomimetics/methods ; Chitin/*chemistry/*metabolism ; Chitinases/metabolism ; Microscopy, Electron, Scanning/methods ; Porifera/*chemistry/*metabolism ; Skeleton/chemistry/metabolism ; Spectroscopy, Fourier Transform Infrared/methods ; Spectrum Analysis, Raman/methods ; Tissue Engineering/methods ; },
abstract = {Sponges (Porifera) are recognized as aquatic multicellular organisms which developed an effective biochemical pathway over millions of years of evolution to produce both biologically active secondary metabolites and biopolymer-based skeletal structures. Among marine demosponges, only representatives of the Verongiida order are known to synthetize biologically active substances as well as skeletons made of structural polysaccharide chitin. The unique three-dimensional (3D) architecture of such chitinous skeletons opens the widow for their recent applications as adsorbents, as well as scaffolds for tissue engineering and biomimetics. This study has the ambitious goal of monitoring other orders beyond Verongiida demosponges and finding alternative sources of naturally prestructured chitinous scaffolds; especially in those demosponge species which can be cultivated at large scales using marine farming conditions. Special attention has been paid to the demosponge Mycale euplectellioides(Heteroscleromorpha: Poecilosclerida: Mycalidae) collected in the Red Sea. For the first time, we present here a detailed study of the isolation of chitin from the skeleton of this sponge, as well as its identification using diverse bioanalytical tools. Calcofluor white staining, Fourier-transform Infrared Spcetcroscopy (FTIR), electrospray ionization mass spectrometry (ESI-MS), scanning electron microscopy (SEM), and fluorescence microscopy, as well as a chitinase digestion assay were applied in order to confirm with strong evidence the finding of a-chitin in the skeleton of M. euplectellioides. We suggest that the discovery of chitin within representatives of the Mycale genus is a promising step in their evaluation of these globally distributed sponges as new renewable sources for both biologically active metabolites and chitin, which are of prospective use for pharmacology and biomaterials oriented biomedicine, respectively.},
}
@article {pmid29442314,
year = {2018},
author = {Aruga, J and Hatayama, M},
title = {Comparative Genomics of the Zic Family Genes.},
journal = {Advances in experimental medicine and biology},
volume = {1046},
number = {},
pages = {3-26},
doi = {10.1007/978-981-10-7311-3_1},
pmid = {29442314},
issn = {0065-2598},
mesh = {Animals ; *Evolution, Molecular ; Humans ; Multigene Family/*physiology ; *Phylogeny ; Protein Domains ; Species Specificity ; *Transcription Factors/genetics/metabolism ; Zinc Fingers/*physiology ; },
abstract = {Zic family genes encode five C2H2-type zinc finger domain-containing proteins that have many roles in animal development and maintenance. Recent phylogenetic analyses showed that Zic family genes are distributed in metazoans (multicellular animals), except Porifera (sponges) and Ctenophora (comb jellies). The sequence comparisons revealed that the zinc finger domains were absolutely conserved among the Zic family genes. Zic zinc finger domains are similar to, but distinct from those of the Gli, Glis, and Nkl gene family, and these zinc finger protein families are proposed to have been derived from a common ancestor gene. The Gli-Glis-Nkl-Zic superfamily and some other eukaryotic zinc finger proteins share a tandem CWCH2 (tCWCH2) motif, a hallmark for inter-zinc finger interaction between two adjacent C2H2 zinc fingers. In Zic family proteins, there exist additional evolutionally conserved domains known as ZOC and ZFNC, both of which may have appeared before cnidarian-bilaterian divergence. Comparison of the exon-intron boundaries in the Zic zinc finger domains revealed an intron (A-intron) that was absolutely conserved in bilaterians (metazoans with bilateral symmetry) and a placozoan (a simple nonparasitic metazoan). In vertebrates, there are five to seven Zic paralogs among which Zic1, Zic2, and Zic3 are generated through a tandem gene duplication and carboxy-terminal truncation in a vertebrate common ancestor, sharing a conserved carboxy-terminal sequence. Several hypotheses have been proposed to explain the Zic family phylogeny, including their origin, unique features in the first and second zinc finger motif, evolution of the nuclear localization signal, significance of the animal taxa-selective degeneration, gene multiplication in the vertebrate lineage, and involvement in the evolutionary alteration of the animal body plan.},
}
@article {pmid29440299,
year = {2018},
author = {Simonini, S and Stephenson, P and Østergaard, L},
title = {A molecular framework controlling style morphology in Brassicaceae.},
journal = {Development (Cambridge, England)},
volume = {145},
number = {5},
pages = {},
doi = {10.1242/dev.158105},
pmid = {29440299},
issn = {1477-9129},
support = {BBS/E/J/00000613//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M004112/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004588/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P013511/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Brassicaceae/*genetics/*growth &amp; development ; Flowers/anatomy &amp; histology/*genetics/*growth &amp; development ; Gene Expression Regulation, Developmental/drug effects ; Gene Expression Regulation, Plant/drug effects ; Indoleacetic Acids/pharmacology ; Phenotype ; Plant Development/drug effects/*genetics ; Plant Growth Regulators/pharmacology ; Plants, Genetically Modified ; Transcription Factors/physiology ; },
abstract = {Organ formation in multicellular organisms depends on the coordinated activities of regulatory components that integrate developmental and hormonal cues to control gene expression and mediate cell-type specification. For example, development of the Arabidopsis gynoecium is tightly controlled by distribution and synthesis of the plant hormone auxin. The functions of several transcription factors (TFs) have been linked with auxin dynamics during gynoecium development; yet how their activities are coordinated is not known. Here, we show that five such TFs function together to ensure polarity establishment at the gynoecium apex. The auxin response factor ETTIN (ARF3; herein, ETT) is a central component of this framework. Interaction of ETT with TF partners is sensitive to the presence of auxin and our results suggest that ETT forms part of a repressive gene-regulatory complex. We show that this function is conserved between members of the Brassicaceae family and that variation in an ETT subdomain affects interaction strengths and gynoecium morphology. These results suggest that variation in affinities between conserved TFs can lead to morphological differences and thus contribute to the evolution of diverse organ shapes.},
}
@article {pmid29436502,
year = {2018},
author = {Hörandl, E and Speijer, D},
title = {How oxygen gave rise to eukaryotic sex.},
journal = {Proceedings. Biological sciences},
volume = {285},
number = {1872},
pages = {},
doi = {10.1098/rspb.2017.2706},
pmid = {29436502},
issn = {1471-2954},
abstract = {How did full meiotic eukaryotic sex evolve and what was the immediate advantage allowing it to develop? We propose that the crucial determinant can be found in internal reactive oxygen species (ROS) formation at the start of eukaryotic evolution approximately 2 × 109 years ago. The large amount of ROS coming from a bacterial endosymbiont gave rise to DNA damage and vast increases in host genome mutation rates. Eukaryogenesis and chromosome evolution represent adaptations to oxidative stress. The host, an archaeon, most probably already had repair mechanisms based on DNA pairing and recombination, and possibly some kind of primitive cell fusion mechanism. The detrimental effects of internal ROS formation on host genome integrity set the stage allowing evolution of meiotic sex from these humble beginnings. Basic meiotic mechanisms thus probably evolved in response to endogenous ROS production by the 'pre-mitochondrion'. This alternative to mitosis is crucial under novel, ROS-producing stress situations, like extensive motility or phagotrophy in heterotrophs and endosymbiontic photosynthesis in autotrophs. In multicellular eukaryotes with a germline-soma differentiation, meiotic sex with diploid-haploid cycles improved efficient purging of deleterious mutations. Constant pressure of endogenous ROS explains the ubiquitous maintenance of meiotic sex in practically all eukaryotic kingdoms. Here, we discuss the relevant observations underpinning this model.},
}
@article {pmid29432421,
year = {2018},
author = {Exposito-Alonso, M and Becker, C and Schuenemann, VJ and Reiter, E and Setzer, C and Slovak, R and Brachi, B and Hagmann, J and Grimm, DG and Chen, J and Busch, W and Bergelson, J and Ness, RW and Krause, J and Burbano, HA and Weigel, D},
title = {The rate and potential relevance of new mutations in a colonizing plant lineage.},
journal = {PLoS genetics},
volume = {14},
number = {2},
pages = {e1007155},
doi = {10.1371/journal.pgen.1007155},
pmid = {29432421},
issn = {1553-7404},
mesh = {Arabidopsis/genetics/growth &amp; development ; Crosses, Genetic ; Directed Molecular Evolution ; Evolution, Molecular ; Gene Flow/physiology ; *Genome, Plant ; Introduced Species ; Mutation/*physiology ; *Mutation Rate ; Phenotype ; Phylogeny ; Plant Development/*genetics ; Plant Weeds/genetics/growth &amp; development ; Selection, Genetic ; Sequence Analysis, DNA ; },
abstract = {By following the evolution of populations that are initially genetically homogeneous, much can be learned about core biological principles. For example, it allows for detailed studies of the rate of emergence of de novo mutations and their change in frequency due to drift and selection. Unfortunately, in multicellular organisms with generation times of months or years, it is difficult to set up and carry out such experiments over many generations. An alternative is provided by &quot;natural evolution experiments&quot; that started from colonizations or invasions of new habitats by selfing lineages. With limited or missing gene flow from other lineages, new mutations and their effects can be easily detected. North America has been colonized in historic times by the plant Arabidopsis thaliana, and although multiple intercrossing lineages are found today, many of the individuals belong to a single lineage, HPG1. To determine in this lineage the rate of substitutions-the subset of mutations that survived natural selection and drift-, we have sequenced genomes from plants collected between 1863 and 2006. We identified 73 modern and 27 herbarium specimens that belonged to HPG1. Using the estimated substitution rate, we infer that the last common HPG1 ancestor lived in the early 17th century, when it was most likely introduced by chance from Europe. Mutations in coding regions are depleted in frequency compared to those in other portions of the genome, consistent with purifying selection. Nevertheless, a handful of mutations is found at high frequency in present-day populations. We link these to detectable phenotypic variance in traits of known ecological importance, life history and growth, which could reflect their adaptive value. Our work showcases how, by applying genomics methods to a combination of modern and historic samples from colonizing lineages, we can directly study new mutations and their potential evolutionary relevance.},
}
@article {pmid29424391,
year = {2018},
author = {Cipriano, JLD and Cruz, ACF and Mancini, KC and Schmildt, ER and Lopes, JC and Otoni, WC and Alexandre, RS},
title = {Somatic embryogenesis in Carica papaya as affected by auxins and explants, and morphoanatomical-related aspects.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {90},
number = {1},
pages = {385-400},
doi = {10.1590/0001-3765201820160252},
pmid = {29424391},
issn = {1678-2690},
mesh = {Abscisic Acid/pharmacology ; Carica/anatomy &amp; histology/drug effects/*embryology/*physiology ; Culture Media ; Germination/drug effects/physiology ; Indoleacetic Acids/*analysis ; Microscopy, Electron, Scanning ; Plant Growth Regulators/pharmacology ; Plant Leaves/drug effects/physiology ; Plant Shoots/drug effects/*physiology ; Plant Somatic Embryogenesis Techniques/*methods ; Reference Values ; Reproducibility of Results ; Time Factors ; },
abstract = {The aim of this study was to evaluate somatic embryogenesis in juvenile explants of the THB papaya cultivar. Apical shoots and cotyledonary leaves were inoculated in an induction medium composed of different concentrations of 2,4-D (6, 9, 12, 15 and 18 µM) or 4-CPA (19, 22, 25, 28 and 31 µM). The embryogenic calluses were transferred to a maturation medium for 30 days. Histological analysis were done during the induction and scanning electron microscopy after maturing. For both types of auxin, embryogenesis was achieved at higher frequencies with cotyledonary leaves incubated in induction medium than with apical shoots; except for callogenesis. The early-stage embryos (e.g., globular or heart-shape) predominated. Among the auxins, best results were observed in cotyledonary leaves induced with 4-CPA (25 µM). Histological analyses of the cotyledonary leaf-derived calluses confirmed that the somatic embryos (SEs) formed from parenchyma cells, predominantly differentiated via indirect and multicellular origin and infrequently via synchronized embryogenesis. The secondary embryogenesis was observed during induction and maturation phases in papaya THB cultivar. The combination of ABA (0.5 µM) and AC (15 g L-1) in maturation medium resulted in the highest somatic embryogenesis induction frequency (70 SEs callus-1) and the lowest percentage of early germination (4%).},
}
@article {pmid29415511,
year = {2018},
author = {Henderson, SW and Wege, S and Gilliham, M},
title = {Plant Cation-Chloride Cotransporters (CCC): Evolutionary Origins and Functional Insights.},
journal = {International journal of molecular sciences},
volume = {19},
number = {2},
pages = {},
doi = {10.3390/ijms19020492},
pmid = {29415511},
issn = {1422-0067},
mesh = {Biological Evolution ; Gene Expression ; Homeostasis ; Ions/metabolism ; Phenotype ; Plant Development/genetics ; Plant Proteins/genetics/*metabolism ; Plants/classification/drug effects/genetics/*metabolism ; Sodium-Potassium-Chloride Symporters/genetics/*metabolism ; Water/metabolism ; },
abstract = {Genomes of unicellular and multicellular green algae, mosses, grasses and dicots harbor genes encoding cation-chloride cotransporters (CCC). CCC proteins from the plant kingdom have been comparatively less well investigated than their animal counterparts, but proteins from both plants and animals have been shown to mediate ion fluxes, and are involved in regulation of osmotic processes. In this review, we show that CCC proteins from plants form two distinct phylogenetic clades (CCC1 and CCC2). Some lycophytes and bryophytes possess members from each clade, most land plants only have members of the CCC1 clade, and green algae possess only the CCC2 clade. It is currently unknown whether CCC1 and CCC2 proteins have similar or distinct functions, however they are both more closely related to animal KCC proteins compared to NKCCs. Existing heterologous expression systems that have been used to functionally characterize plant CCC proteins, namely yeast and Xenopus laevis oocytes, have limitations that are discussed. Studies from plants exposed to chemical inhibitors of animal CCC protein function are reviewed for their potential to discern CCC function in planta. Thus far, mutations in plant CCC genes have been evaluated only in two species of angiosperms, and such mutations cause a diverse array of phenotypes-seemingly more than could simply be explained by localized disruption of ion transport alone. We evaluate the putative roles of plant CCC proteins and suggest areas for future investigation.},
}
@article {pmid29405978,
year = {2018},
author = {Wechman, SL and Pradhan, AK and DeSalle, R and Das, SK and Emdad, L and Sarkar, D and Fisher, PB},
title = {New Insights Into Beclin-1: Evolution and Pan-Malignancy Inhibitor Activity.},
journal = {Advances in cancer research},
volume = {137},
number = {},
pages = {77-114},
doi = {10.1016/bs.acr.2017.11.002},
pmid = {29405978},
issn = {2162-5557},
abstract = {Autophagy is a functionally conserved self-degradation process that facilitates the survival of eukaryotic life via the management of cellular bioenergetics and maintenance of the fidelity of genomic DNA. The first known autophagy inducer was Beclin-1. Beclin-1 is expressed in multicellular eukaryotes ranging throughout plants to animals, comprising a nonmonophyllic group, as shown in this report via aggressive BLAST searches. In humans, Beclin-1 is a haploinsuffient tumor suppressor as biallelic deletions have not been observed in patient tumors clinically. Therefore, Beclin-1 fails the Knudson hypothesis, implicating expression of at least one Beclin-1 allele is essential for cancer cell survival. However, Beclin-1 is frequently monoallelically deleted in advanced human cancers and the expression of two Beclin-1 allelles is associated with greater anticancer effects. Overall, experimental evidence suggests that Beclin-1 inhibits tumor formation, angiogenesis, and metastasis alone and in cooperation with the tumor suppressive molecules UVRAG, Bif-1, Ambra1, and MDA-7/IL-24 via diverse mechanisms of action. Conversely, Beclin-1 is upregulated in cancer stem cells (CSCs), portending a role in cancer recurrence, and highlighting this molecule as an intriguing molecular target for the treatment of CSCs. Many aspects of Beclin-1's biological effects remain to be studied. The consequences of these BLAST searches on the molecular evolution of Beclin-1, and the eukaryotic branches of the tree of life, are discussed here in greater detail with future inquiry focused upon protist taxa. Also in this review, the effects of Beclin-1 on tumor suppression and cancer malignancy are discussed. Beclin-1 holds significant promise for the development of novel targeted cancer therapeutics and is anticipated to lead to a many advances in our understanding of eukaryotic evolution, multicellularity, and even the treatment of CSCs in the coming decades.},
}
@article {pmid29385672,
year = {2018},
author = {Park, B and Shin, DY and Jeon, TJ},
title = {CBP7 Interferes with the Multicellular Development of Dictyostelium Cells by Inhibiting Chemoattractant-Mediated Cell Aggregation.},
journal = {Molecules and cells},
volume = {41},
number = {2},
pages = {103-109},
doi = {10.14348/molcells.2018.2170},
pmid = {29385672},
issn = {0219-1032},
mesh = {Calcium/metabolism ; Calcium-Binding Proteins/classification/genetics/*metabolism ; Chemotactic Factors/genetics/metabolism ; *Chemotaxis ; Cyclic AMP/metabolism ; Dictyostelium/cytology/genetics/*metabolism ; Movement ; Phylogeny ; *Signal Transduction ; },
abstract = {Calcium ions are involved in the regulation of diverse cellular processes. Fourteen genes encoding calcium binding proteins have been identified in Dictyostelium. CBP7, one of the 14 CBPs, is composed of 169 amino acids and contains four EF-hand motifs. Here, we investigated the roles of CBP7 in the development and cell migration of Dictyostelium cells and found that high levels of CBP7 exerted a negative effect on cells aggregation during development, possibly by inhibiting chemoattractant-directed cell migration. While cells lacking CBP7 exhibited normal development and chemotaxis similar that of wild-type cells, CBP7 overexpressing cells completely lost their chemotactic abilities to move toward increasing cAMP concentrations. This resulted in inhibition of cellular aggregation, a process required for forming multicellular organisms during development. Low levels of cytosolic free calcium were observed in CBP7 overexpressing cells, which was likely the underlying cause of their lack of chemotaxis. Our results demonstrate that CBP7 plays an important role in cell spreading and cell-substrate adhesion. cbp7 null cells showed decreased cell size and cell-substrate adhesion. The present study contributes to further understanding the role of calcium signaling in regulation of cell migration and development.},
}
@article {pmid29381766,
year = {2018},
author = {Boyd, M and Rosenzweig, F and Herron, MD},
title = {Analysis of motility in multicellular Chlamydomonas reinhardtii evolved under predation.},
journal = {PloS one},
volume = {13},
number = {1},
pages = {e0192184},
doi = {10.1371/journal.pone.0192184},
pmid = {29381766},
issn = {1932-6203},
mesh = {Animals ; *Biological Evolution ; Chlamydomonas reinhardtii/*physiology ; *Predatory Behavior ; },
abstract = {The advent of multicellularity was a watershed event in the history of life, yet the transition from unicellularity to multicellularity is not well understood. Multicellularity opens up opportunities for innovations in intercellular communication, cooperation, and specialization, which can provide selective advantages under certain ecological conditions. The unicellular alga Chlamydomonas reinhardtii has never had a multicellular ancestor yet it is closely related to the volvocine algae, a clade containing taxa that range from simple unicells to large, specialized multicellular colonies. Simple multicellular structures have been observed to evolve in C. reinhardtii in response to predation or to settling rate-based selection. Structures formed in response to predation consist of individual cells confined within a shared transparent extracellular matrix. Evolved isolates form such structures obligately under culture conditions in which their wild type ancestors do not, indicating that newly-evolved multicellularity is heritable. C. reinhardtii is capable of photosynthesis, and possesses an eyespot and two flagella with which it moves towards or away from light in order to optimize input of radiant energy. Motility contributes to C. reinhardtii fitness because it allows cells or colonies to achieve this optimum. Utilizing phototaxis to assay motility, we determined that newly evolved multicellular strains do not exhibit significant directional movement, even though the flagellae of their constituent unicells are present and active. In C. reinhardtii the first steps towards multicellularity in response to predation appear to result in a trade-off between motility and differential survivorship, a trade-off that must be overcome by further genetic change to ensure long-term success of the new multicellular organism.},
}
@article {pmid29378020,
year = {2018},
author = {Hillmann, F and Forbes, G and Novohradská, S and Ferling, I and Riege, K and Groth, M and Westermann, M and Marz, M and Spaller, T and Winckler, T and Schaap, P and Glöckner, G},
title = {Multiple Roots of Fruiting Body Formation in Amoebozoa.},
journal = {Genome biology and evolution},
volume = {10},
number = {2},
pages = {591-606},
doi = {10.1093/gbe/evy011},
pmid = {29378020},
issn = {1759-6653},
mesh = {Amoebozoa/cytology/*genetics/*growth &amp; development ; Cell Communication ; Dictyostelium/cytology/genetics/growth &amp; development ; Evolution, Molecular ; *Gene Expression Regulation, Developmental ; Phylogeny ; Protozoan Proteins/genetics ; Transcriptome ; },
abstract = {Establishment of multicellularity represents a major transition in eukaryote evolution. A subgroup of Amoebozoa, the dictyosteliids, has evolved a relatively simple aggregative multicellular stage resulting in a fruiting body supported by a stalk. Protosteloid amoeba, which are scattered throughout the amoebozoan tree, differ by producing only one or few single stalked spores. Thus, one obvious difference in the developmental cycle of protosteliids and dictyosteliids seems to be the establishment of multicellularity. To separate spore development from multicellular interactions, we compared the genome and transcriptome of a Protostelium species (Protostelium aurantium var. fungivorum) with those of social and solitary members of the Amoebozoa. During fruiting body formation nearly 4,000 genes, corresponding to specific pathways required for differentiation processes, are upregulated. A comparison with genes involved in the development of dictyosteliids revealed conservation of >500 genes, but most of them are also present in Acanthamoeba castellanii for which fruiting bodies have not been documented. Moreover, expression regulation of those genes differs between P. aurantium and Dictyostelium discoideum. Within Amoebozoa differentiation to fruiting bodies is common, but our current genome analysis suggests that protosteliids and dictyosteliids used different routes to achieve this. Most remarkable is both the large repertoire and diversity between species in genes that mediate environmental sensing and signal processing. This likely reflects an immense adaptability of the single cell stage to varying environmental conditions. We surmise that this signaling repertoire provided sufficient building blocks to accommodate the relatively simple demands for cell-cell communication in the early multicellular forms.},
}
@article {pmid29361519,
year = {2018},
author = {Cocorocchio, M and Baldwin, AJ and Stewart, B and Kim, L and Harwood, AJ and Thompson, CRL and Andrews, PLR and Williams, RSB},
title = {Curcumin and derivatives function through protein phosphatase 2A and presenilin orthologues in Dictyostelium discoideum.},
journal = {Disease models &amp; mechanisms},
volume = {11},
number = {1},
pages = {},
doi = {10.1242/dmm.032375},
pmid = {29361519},
issn = {1754-8411},
support = {101582Z/13/Z//Wellcome Trust/United Kingdom ; },
mesh = {Antioxidants/pharmacology ; Curcumin/analogs &amp; derivatives/chemistry/*pharmacology ; Dictyostelium/drug effects/growth &amp; development/*metabolism ; Ligands ; Molecular Docking Simulation ; Presenilin-1/*metabolism ; Protein Phosphatase 2/*metabolism ; *Sequence Homology, Amino Acid ; },
abstract = {Natural compounds often have complex molecular structures and unknown molecular targets. These characteristics make them difficult to analyse using a classical pharmacological approach. Curcumin, the main curcuminoid of turmeric, is a complex molecule possessing wide-ranging biological activities, cellular mechanisms and roles in potential therapeutic treatment, including Alzheimer's disease and cancer. Here, we investigate the physiological effects and molecular targets of curcumin in Dictyostelium discoideum We show that curcumin exerts acute effects on cell behaviour, reduces cell growth and slows multicellular development. We employed a range of structurally related compounds to show the distinct role of different structural groups in curcumin's effects on cell behaviour, growth and development, highlighting active moieties in cell function, and showing that these cellular effects are unrelated to the well-known antioxidant activity of curcumin. Molecular mechanisms underlying the effect of curcumin and one synthetic analogue (EF24) were then investigated to identify a curcumin-resistant mutant lacking the protein phosphatase 2A regulatory subunit (PsrA) and an EF24-resistant mutant lacking the presenilin 1 orthologue (PsenB). Using in silico docking analysis, we then showed that curcumin might function through direct binding to a key regulatory region of PsrA. These findings reveal novel cellular and molecular mechanisms for the function of curcumin and related compounds.},
}
@article {pmid29322818,
year = {2018},
author = {Baig, AM and Zohaib, R and Tariq, S and Ahmad, HR},
title = {Evolution of pH buffers and water homeostasis in eukaryotes: homology between humans and Acanthamoeba proteins.},
journal = {Future microbiology},
volume = {13},
number = {},
pages = {195-207},
doi = {10.2217/fmb-2017-0116},
pmid = {29322818},
issn = {1746-0921},
abstract = {AIM: This study intended to trace the evolution of acid-base buffers and water homeostasis in eukaryotes. Acanthamoeba castellanii was selected as a model unicellular eukaryote for this purpose. Homologies of proteins involved in pH and water regulatory mechanisms at cellular levels were compared between humans and A. castellanii.<br><br>MATERIALS &amp; METHODS: Amino acid sequence homology, structural homology, 3D modeling and docking prediction were done to show the extent of similarities between carbonic anhydrase 1 (CA1), aquaporin (AQP), band-3 protein and H+ pump. Experimental assays were done with acetazolamide (AZM), brinzolamide and mannitol to observe their effects on the trophozoites of A. castellanii.<br><br>RESULTS: The human CA1, AQP, band-3 protein and H+-transport proteins revealed similar proteins in Acanthamoeba. Docking showed the binding of AZM on amoebal AQP-like proteins. Acanthamoeba showed transient shape changes and encystation at differential doses of brinzolamide, mannitol and AZM. Conclusion: Water and pH regulating adapter proteins in Acanthamoeba and humans show significant homology, these mechanisms evolved early in the primitive unicellular eukaryotes and have remained conserved in multicellular eukaryotes.},
}
@article {pmid29320478,
year = {2018},
author = {Smakowska-Luzan, E and Mott, GA and Parys, K and Stegmann, M and Howton, TC and Layeghifard, M and Neuhold, J and Lehner, A and Kong, J and Grünwald, K and Weinberger, N and Satbhai, SB and Mayer, D and Busch, W and Madalinski, M and Stolt-Bergner, P and Provart, NJ and Mukhtar, MS and Zipfel, C and Desveaux, D and Guttman, DS and Belkhadir, Y},
title = {An extracellular network of Arabidopsis leucine-rich repeat receptor kinases.},
journal = {Nature},
volume = {553},
number = {7688},
pages = {342-346},
doi = {10.1038/nature25184},
pmid = {29320478},
issn = {1476-4687},
mesh = {Arabidopsis/cytology/*enzymology/immunology/microbiology ; Arabidopsis Proteins/*chemistry/*metabolism ; Leucine/*metabolism ; Protein Binding ; Protein Domains ; Protein Kinases/*chemistry/*metabolism ; Protein-Serine-Threonine Kinases/chemistry/metabolism ; Receptors, Cell Surface/chemistry/metabolism ; Reproducibility of Results ; Signal Transduction ; },
abstract = {The cells of multicellular organisms receive extracellular signals using surface receptors. The extracellular domains (ECDs) of cell surface receptors function as interaction platforms, and as regulatory modules of receptor activation. Understanding how interactions between ECDs produce signal-competent receptor complexes is challenging because of their low biochemical tractability. In plants, the discovery of ECD interactions is complicated by the massive expansion of receptor families, which creates tremendous potential for changeover in receptor interactions. The largest of these families in Arabidopsis thaliana consists of 225 evolutionarily related leucine-rich repeat receptor kinases (LRR-RKs), which function in the sensing of microorganisms, cell expansion, stomata development and stem-cell maintenance. Although the principles that govern LRR-RK signalling activation are emerging, the systems-level organization of this family of proteins is unknown. Here, to address this, we investigated 40,000 potential ECD interactions using a sensitized high-throughput interaction assay, and produced an LRR-based cell surface interaction network (CSILRR) that consists of 567 interactions. To demonstrate the power of CSILRR for detecting biologically relevant interactions, we predicted and validated the functions of uncharacterized LRR-RKs in plant growth and immunity. In addition, we show that CSILRR operates as a unified regulatory network in which the LRR-RKs most crucial for its overall structure are required to prevent the aberrant signalling of receptors that are several network-steps away. Thus, plants have evolved LRR-RK networks to process extracellular signals into carefully balanced responses.},
}
@article {pmid29320389,
year = {2018},
author = {Ćetković, H and Halasz, M and Herak Bosnar, M},
title = {Sponges: A Reservoir of Genes Implicated in Human Cancer.},
journal = {Marine drugs},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/md16010020},
pmid = {29320389},
issn = {1660-3397},
mesh = {Animals ; Evolution, Molecular ; Genome/genetics ; Humans ; Neoplasms/*genetics ; Porifera/*genetics ; Proteome/genetics ; Signal Transduction/genetics ; },
abstract = {Recently, it was shown that the majority of genes linked to human diseases, such as cancer genes, evolved in two major evolutionary transitions-the emergence of unicellular organisms and the transition to multicellularity. Therefore, it has been widely accepted that the majority of disease-related genes has already been present in species distantly related to humans. An original way of studying human diseases relies on analyzing genes and proteins that cause a certain disease using model organisms that belong to the evolutionary level at which these genes have emerged. This kind of approach is supported by the simplicity of the genome/proteome, body plan, and physiology of such model organisms. It has been established for quite some time that sponges are an ideal model system for such studies, having a vast variety of genes known to be engaged in sophisticated processes and signalling pathways associated with higher animals. Sponges are considered to be the simplest multicellular animals and have changed little during evolution. Therefore, they provide an insight into the metazoan ancestor genome/proteome features. This review compiles current knowledge of cancer-related genes/proteins in marine sponges.},
}
@article {pmid29301490,
year = {2018},
author = {Strader, ME and Aglyamova, GV and Matz, MV},
title = {Molecular characterization of larval development from fertilization to metamorphosis in a reef-building coral.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {17},
doi = {10.1186/s12864-017-4392-0},
pmid = {29301490},
issn = {1471-2164},
support = {DEB-1501463//National Science Foundation/International ; },
mesh = {Animals ; Anthozoa/anatomy &amp; histology/embryology/*genetics/*growth &amp; development ; Behavior, Animal/drug effects ; Fertilization ; Larva/genetics/growth &amp; development/metabolism ; Luminescent Proteins/metabolism ; Metamorphosis, Biological/genetics ; Transcriptome ; },
abstract = {BACKGROUND: Molecular mechanisms underlying coral larval competence, the ability of larvae to respond to settlement cues, determine their dispersal potential and are potential targets of natural selection. Here, we profiled competence, fluorescence and genome-wide gene expression in embryos and larvae of the reef-building coral Acropora millepora daily throughout 12 days post-fertilization.<br><br>RESULTS: Gene expression associated with competence was positively correlated with transcriptomic response to the natural settlement cue, confirming that mature coral larvae are &quot;primed&quot; for settlement. Rise of competence through development was accompanied by up-regulation of sensory and signal transduction genes such as ion channels, genes involved in neuropeptide signaling, and G-protein coupled receptor (GPCRs). A drug screen targeting components of GPCR signaling pathways confirmed a role in larval settlement behavior and metamorphosis.<br><br>CONCLUSIONS: These results gives insight into the molecular complexity underlying these transitions and reveals receptors and pathways that, if altered by changing environments, could affect dispersal capabilities of reef-building corals. In addition, this dataset provides a toolkit for asking broad questions about sensory capacity in multicellular animals and the evolution of development.},
}
@article {pmid29292130,
year = {2018},
author = {López, JL and Alvarez, F and Príncipe, A and Salas, ME and Lozano, MJ and Draghi, WO and Jofré, E and Lagares, A},
title = {Isolation, taxonomic analysis, and phenotypic characterization of bacterial endophytes present in alfalfa (Medicago sativa) seeds.},
journal = {Journal of biotechnology},
volume = {267},
number = {},
pages = {55-62},
doi = {10.1016/j.jbiotec.2017.12.020},
pmid = {29292130},
issn = {1873-4863},
mesh = {Actinobacteria/genetics/isolation &amp; purification ; Bacteroidetes/genetics/isolation &amp; purification ; Endophytes/classification/*genetics ; Firmicutes/genetics/isolation &amp; purification ; Medicago sativa/genetics/*microbiology ; Microbiota/*genetics ; *Phylogeny ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seedlings/microbiology ; Seeds/microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {A growing body of evidence has reinforced the central role of microbiomes in the life of sound multicellular eukaryotes, thus more properly described as true holobionts. Though soil was considered a main source of plant microbiomes, seeds have been shown to be endophytically colonized by microorganisms thus representing natural carriers of a selected microbial inoculum to the young seedlings. In this work we have investigated the type of culturable endophytic bacteria that are carried within surface-sterilized alfalfa seeds. MALDI-TOF analysis revealed the presence of bacteria that belonged to 40 separate genera, distributed within four taxa (Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes). Nonsymbiotic members of the Rhizobiaceae family were also found. The evaluation of nine different in-vitro biochemical activities demonstrated isolates with complex combinations of traits that, upon a Principal-Component-Analysis, could be classified into four phenotypic groups. That isolates from nearly half of the genera identified had been able to colonize alfalfa plants grown under axenic conditions was remarkable. Further analyses should be addressed to investigating the colonization mechanisms of the alfalfa seeds, the evolutionary significance of the alfalfa-seed endophytes, and also how after germination the seed microbiome competes with spermospheric and rhizospheric soil bacteria to colonize newly emerging seedlings.},
}
@article {pmid29245010,
year = {2017},
author = {Kundu, P and Blacher, E and Elinav, E and Pettersson, S},
title = {Our Gut Microbiome: The Evolving Inner Self.},
journal = {Cell},
volume = {171},
number = {7},
pages = {1481-1493},
doi = {10.1016/j.cell.2017.11.024},
pmid = {29245010},
issn = {1097-4172},
mesh = {Aging ; Animals ; Bacteria/classification/*growth &amp; development/metabolism ; Biological Evolution ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Organ Specificity ; Puberty ; Symbiosis ; },
abstract = {The &quot;holobiont&quot; concept, defined as the collective contribution of the eukaryotic and prokaryotic counterparts to the multicellular organism, introduces a complex definition of individuality enabling a new comprehensive view of human evolution and personalized characteristics. Here, we provide snapshots of the evolving microbial-host associations and relations during distinct milestones across the lifespan of a human being. We discuss the current knowledge of biological symbiosis between the microbiome and its host and portray the challenges in understanding these interactions and their potential effects on human physiology, including microbiome-nervous system inter-relationship and its relevance to human variation and individuality.},
}
@article {pmid29212441,
year = {2017},
author = {Arakaki, Y and Fujiwara, T and Kawai-Toyooka, H and Kawafune, K and Featherston, J and Durand, PM and Miyagishima, SY and Nozaki, H},
title = {Evolution of cytokinesis-related protein localization during the emergence of multicellularity in volvocine green algae.},
journal = {BMC evolutionary biology},
volume = {17},
number = {1},
pages = {243},
doi = {10.1186/s12862-017-1091-z},
pmid = {29212441},
issn = {1471-2148},
support = {2016-B//NIG-JOINT/International ; 25-9234//Japan Society for the Promotion of Science/International ; 16H02518//Japan Society for the Promotion of Science/International ; RA151217156515//National Research Foundation/International ; },
mesh = {Algal Proteins/*genetics ; Cytokinesis/*genetics ; *Evolution, Molecular ; Likelihood Functions ; Models, Biological ; Phylogeny ; Protein Transport ; Species Specificity ; Subcellular Fractions/metabolism ; Volvox/*cytology/*genetics ; },
abstract = {BACKGROUND: The volvocine lineage, containing unicellular Chlamydomonas reinhardtii and differentiated multicellular Volvox carteri, is a powerful model for comparative studies aiming at understanding emergence of multicellularity. Tetrabaena socialis is the simplest multicellular volvocine alga and belongs to the family Tetrabaenaceae that is sister to more complex multicellular volvocine families, Goniaceae and Volvocaceae. Thus, T. socialis is a key species to elucidate the initial steps in the evolution of multicellularity. In the asexual life cycle of C. reinhardtii and multicellular volvocine species, reproductive cells form daughter cells/colonies by multiple fission. In embryogenesis of the multicellular species, daughter protoplasts are connected to one another by cytoplasmic bridges formed by incomplete cytokinesis during multiple fission. These bridges are important for arranging the daughter protoplasts in appropriate positions such that species-specific integrated multicellular individuals are shaped. Detailed comparative studies of cytokinesis between unicellular and simple multicellular volvocine species will help to elucidate the emergence of multicellularity from the unicellular ancestor. However, the cytokinesis-related genes between closely related unicellular and multicellular species have not been subjected to a comparative analysis.<br><br>RESULTS: Here we focused on dynamin-related protein 1 (DRP1), which is known for its role in cytokinesis in land plants. Immunofluorescence microscopy using an antibody against T. socialis DRP1 revealed that volvocine DRP1 was localized to division planes during cytokinesis in unicellular C. reinhardtii and two simple multicellular volvocine species T. socialis and Gonium pectorale. DRP1 signals were mainly observed in the newly formed division planes of unicellular C. reinhardtii during multiple fission, whereas in multicellular T. socialis and G. pectorale, DRP1 signals were observed in all division planes during embryogenesis.<br><br>CONCLUSIONS: These results indicate that the molecular mechanisms of cytokinesis may be different in unicellular and multicellular volvocine algae. The localization of DRP1 during multiple fission might have been modified in the common ancestor of multicellular volvocine algae. This modification may have been essential for the re-orientation of cells and shaping colonies during the emergence of multicellularity in this lineage.},
}
@article {pmid29208647,
year = {2018},
author = {Matt, GY and Umen, JG},
title = {Cell-Type Transcriptomes of the Multicellular Green Alga Volvox carteri Yield Insights into the Evolutionary Origins of Germ and Somatic Differentiation Programs.},
journal = {G3 (Bethesda, Md.)},
volume = {8},
number = {2},
pages = {531-550},
doi = {10.1534/g3.117.300253},
pmid = {29208647},
issn = {2160-1836},
support = {P30 CA091842/CA/NCI NIH HHS/United States ; R01 GM078376/GM/NIGMS NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; },
mesh = {Algal Proteins/classification/genetics ; Cell Differentiation/*genetics ; Energy Metabolism/genetics ; *Evolution, Molecular ; *Gene Expression Profiling ; Gene Ontology ; Light-Harvesting Protein Complexes/classification/genetics ; Phylogeny ; Volvox/cytology/*genetics/metabolism ; },
abstract = {Germ-soma differentiation is a hallmark of complex multicellular organisms, yet its origins are not well understood. Volvox carteri is a simple multicellular green alga that has recently evolved a simple germ-soma dichotomy with only two cell-types: large germ cells called gonidia and small terminally differentiated somatic cells. Here, we provide a comprehensive characterization of the gonidial and somatic transcriptomes of V. carteri to uncover fundamental differences between the molecular and metabolic programming of these cell-types. We found extensive transcriptome differentiation between cell-types, with somatic cells expressing a more specialized program overrepresented in younger, lineage-specific genes, and gonidial cells expressing a more generalist program overrepresented in more ancient genes that shared striking overlap with stem cell-specific genes from animals and land plants. Directed analyses of different pathways revealed a strong dichotomy between cell-types with gonidial cells expressing growth-related genes and somatic cells expressing an altruistic metabolic program geared toward the assembly of flagella, which support organismal motility, and the conversion of storage carbon to sugars, which act as donors for production of extracellular matrix (ECM) glycoproteins whose secretion enables massive organismal expansion. V. carteri orthologs of diurnally controlled genes from C. reinhardtii, a single-celled relative, were analyzed for cell-type distribution and found to be strongly partitioned, with expression of dark-phase genes overrepresented in somatic cells and light-phase genes overrepresented in gonidial cells- a result that is consistent with cell-type programs in V. carteri arising by cooption of temporal regulons in a unicellular ancestor. Together, our findings reveal fundamental molecular, metabolic, and evolutionary mechanisms that underlie the origins of germ-soma differentiation in V. carteri and provide a template for understanding the acquisition of germ-soma differentiation in other multicellular lineages.},
}
@article {pmid29198427,
year = {2018},
author = {Kenny, NJ and de Goeij, JM and de Bakker, DM and Whalen, CG and Berezikov, E and Riesgo, A},
title = {Towards the identification of ancestrally shared regenerative mechanisms across the Metazoa: A Transcriptomic case study in the Demosponge Halisarca caerulea.},
journal = {Marine genomics},
volume = {37},
number = {},
pages = {135-147},
doi = {10.1016/j.margen.2017.11.001},
pmid = {29198427},
issn = {1876-7478},
mesh = {Animals ; *Evolution, Molecular ; Porifera/genetics/*physiology ; Regeneration/*genetics ; Time Factors ; *Transcriptome ; },
abstract = {Regeneration is an essential process for all multicellular organisms, allowing them to recover effectively from internal and external injury. This process has been studied extensively in a medical context in vertebrates, with pathways often investigated mechanistically, both to derive increased understanding and as potential drug targets for therapy. Several species from other parts of the metazoan tree of life, including Hydra, planarians and echinoderms, noted for their regenerative capabilities, have previously been targeted for study. Less well-documented for their regenerative abilities are sponges. This is surprising, as they are both one of the earliest-branching extant metazoan phyla on Earth, and are rapidly able to respond to injury. Their sessile lifestyle, lack of an external protective layer, inability to respond to predation and filter-feeding strategy all mean that regeneration is often required. In particular the demosponge genus Halisarca has been noted for its fast cell turnover and ability to quickly adjust its cell kinetic properties to repair damage through regeneration. However, while the rate and structure of regeneration in sponges has begun to be investigated, the molecular mechanisms behind this ability are yet to be catalogued. Here we describe the assembly of a reference transcriptome for Halisarca caerulea, along with additional transcriptomes noting response to injury before, shortly following (2h post-), and 12h after trauma. RNAseq reads were assembled using Trinity, annotated, and samples compared, to allow initial insight into the transcriptomic basis of sponge regenerative processes. These resources are deep, with our reference assembly containing >92.6% of the BUSCO Metazoa set of genes, and well-assembled (N50s of 836, 957, 1688 and 2032 for untreated, 2h, 12h and reference transcriptomes respectively), and therefore represent excellent qualitative resources as a bedrock for future study. The generation of transcriptomic resources from sponges before and following deliberate damage has allowed us to study particular pathways within this species responsible for repairing damage. We note particularly the involvement of the Wnt cascades in this process in this species, and detail the contents of this cascade, along with cell cycle, extracellular matrix and apoptosis-linked genes in this work. This resource represents an initial starting point for the continued development of this knowledge, given H. caerulea's ability to regenerate and position as an outgroup for comparing the process of regeneration across metazoan lineages. With this resource in place, we can begin to infer the regenerative capacity of the common ancestor of all extant animal life, and unravel the elements of regeneration in an often-overlooked clade.},
}
@article {pmid29191225,
year = {2017},
author = {Sanfilippo, P and Wen, J and Lai, EC},
title = {Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species.},
journal = {Genome biology},
volume = {18},
number = {1},
pages = {229},
doi = {10.1186/s13059-017-1358-0},
pmid = {29191225},
issn = {1474-760X},
support = {R01-GM083300//National Institute of General Medical Sciences/ ; P30-CA008748//National Cancer Institute/ ; R01-NS083833//National Institute of Neurological Disorders and Stroke/ ; P30 CA008748/CA/NCI NIH HHS/United States ; R01 NS083833/NS/NINDS NIH HHS/United States ; R01 GM083300/GM/NIGMS NIH HHS/United States ; },
mesh = {*3' Untranslated Regions ; Animals ; Cell Line ; Computational Biology/methods ; Drosophila/embryology/*genetics ; Drosophila melanogaster/genetics ; *Evolution, Molecular ; Molecular Sequence Annotation ; Organ Specificity/genetics ; *Poly A ; Polyadenylation ; RNA Isoforms ; RNA-Binding Proteins/metabolism ; Species Specificity ; *Transcription, Genetic ; },
abstract = {BACKGROUND: Drosophila melanogaster has one of best-described transcriptomes of any multicellular organism. Nevertheless, the paucity of 3'-sequencing data in this species precludes comprehensive assessment of alternative polyadenylation (APA), which is subject to broad tissue-specific control.<br><br>RESULTS: Here, we generate deep 3'-sequencing data from 23 developmental stages, tissues, and cell lines of D. melanogaster, yielding a comprehensive atlas of ~ 62,000 polyadenylated ends. These data broadly extend the annotated transcriptome, identify ~ 40,000 novel 3' termini, and reveal that two-thirds of Drosophila genes are subject to APA. Furthermore, we dramatically expand the numbers of genes known to be subject to tissue-specific APA, such as 3' untranslated region (UTR) lengthening in head and 3' UTR shortening in testis, and characterize new tissue and developmental 3' UTR patterns. Our thorough 3' UTR annotations permit reassessment of post-transcriptional regulatory networks, via conserved miRNA and RNA binding protein sites. To evaluate the evolutionary conservation and divergence of APA patterns, we generate developmental and tissue-specific 3'-seq libraries from Drosophila yakuba and Drosophila virilis. We document broadly analogous tissue-specific APA trends in these species, but also observe significant alterations in 3' end usage across orthologs. We exploit the population of functionally evolving poly(A) sites to gain clear evidence that evolutionary divergence in core polyadenylation signal (PAS) and downstream sequence element (DSE) motifs drive broad alterations in 3' UTR isoform expression across the Drosophila phylogeny.<br><br>CONCLUSIONS: These data provide a critical resource for the Drosophila community and offer many insights into the complex control of alternative tissue-specific 3' UTR formation and its consequences for post-transcriptional regulatory networks.},
}
@article {pmid29179763,
year = {2017},
author = {Klein, B and Wibberg, D and Hallmann, A},
title = {Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri.},
journal = {BMC biology},
volume = {15},
number = {1},
pages = {111},
doi = {10.1186/s12915-017-0450-y},
pmid = {29179763},
issn = {1741-7007},
mesh = {*Biological Evolution ; Computational Biology ; Gene Expression Profiling ; *Genome ; Sequence Analysis, RNA ; *Transcriptome ; Volvox/*genetics ; },
abstract = {BACKGROUND: One of evolution's most important achievements is the development and radiation of multicellular organisms with different types of cells. Complex multicellularity has evolved several times in eukaryotes; yet, in most lineages, an investigation of its molecular background is considerably challenging since the transition occurred too far in the past and, in addition, these lineages evolved a large number of cell types. However, for volvocine green algae, such as Volvox carteri, multicellularity is a relatively recent innovation. Furthermore, V. carteri shows a complete division of labor between only two cell types - small, flagellated somatic cells and large, immotile reproductive cells. Thus, V. carteri provides a unique opportunity to study multicellularity and cellular differentiation at the molecular level.<br><br>RESULTS: This study provides a whole transcriptome RNA-Seq analysis of separated cell types of the multicellular green alga V. carteri f. nagariensis to reveal cell type-specific components and functions. To this end, 246 million quality filtered reads were mapped to the genome and valid expression data were obtained for 93% of the 14,247 gene loci. In the subsequent search for protein domains with assigned molecular function, we identified 9435 previously classified domains in 44% of all gene loci. Furthermore, in 43% of all gene loci we identified 15,254 domains that are involved in biological processes. All identified domains were investigated regarding cell type-specific expression. Moreover, we provide further insight into the expression pattern of previously described gene families (e.g., pherophorin, extracellular matrix metalloprotease, and VARL families). Our results demonstrate an extensive compartmentalization of the transcriptome between cell types: More than half of all genes show a clear difference in expression between somatic and reproductive cells.<br><br>CONCLUSIONS: This study constitutes the first transcriptome-wide RNA-Seq analysis of separated cell types of V. carteri focusing on gene expression. The high degree of differential expression indicates a strong differentiation of cell types despite the fact that V. carteri diverged relatively recently from its unicellular relatives. Our expression dataset and the bioinformatic analyses provide the opportunity to further investigate and understand the mechanisms of cell type-specific expression and its transcriptional regulation.},
}
@article {pmid29166656,
year = {2017},
author = {Pichugin, Y and Peña, J and Rainey, PB and Traulsen, A},
title = {Fragmentation modes and the evolution of life cycles.},
journal = {PLoS computational biology},
volume = {13},
number = {11},
pages = {e1005860},
doi = {10.1371/journal.pcbi.1005860},
pmid = {29166656},
issn = {1553-7358},
mesh = {Animals ; Bacteria/cytology ; *Biological Evolution ; Cell Physiological Phenomena/*physiology ; Computational Biology ; Life Cycle Stages/*physiology ; *Models, Biological ; Reproduction/physiology ; },
abstract = {Reproduction is a defining feature of living systems. To reproduce, aggregates of biological units (e.g., multicellular organisms or colonial bacteria) must fragment into smaller parts. Fragmentation modes in nature range from binary fission in bacteria to collective-level fragmentation and the production of unicellular propagules in multicellular organisms. Despite this apparent ubiquity, the adaptive significance of fragmentation modes has received little attention. Here, we develop a model in which groups arise from the division of single cells that do not separate but stay together until the moment of group fragmentation. We allow for all possible fragmentation patterns and calculate the population growth rate of each associated life cycle. Fragmentation modes that maximise growth rate comprise a restrictive set of patterns that include production of unicellular propagules and division into two similar size groups. Life cycles marked by single-cell bottlenecks maximise population growth rate under a wide range of conditions. This surprising result offers a new evolutionary explanation for the widespread occurrence of this mode of reproduction. All in all, our model provides a framework for exploring the adaptive significance of fragmentation modes and their associated life cycles.},
}
@article {pmid29141015,
year = {2017},
author = {Bozler, J and Kacsoh, BZ and Bosco, G},
title = {Nematocytes: Discovery and characterization of a novel anculeate hemocyte in Drosophila falleni and Drosophila phalerata.},
journal = {PloS one},
volume = {12},
number = {11},
pages = {e0188133},
doi = {10.1371/journal.pone.0188133},
pmid = {29141015},
issn = {1932-6203},
support = {DP1 MH110234/MH/NIMH NIH HHS/United States ; P30 CA023108/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Drosophila/*classification/immunology ; *Hemocytes ; Immunity, Innate ; Microscopy, Fluorescence ; Phylogeny ; Species Specificity ; },
abstract = {Immune challenges, such as parasitism, can be so pervasive and deleterious that they constitute an existential threat to a species' survival. In response to these ecological pressures, organisms have developed a wide array of novel behavioral, cellular, and molecular adaptations. Research into these immune defenses in model systems has resulted in a revolutionary understanding of evolution and functional biology. As the field has expanded beyond the limited number of model organisms our appreciation of evolutionary innovation and unique biology has widened as well. With this in mind, we have surveyed the hemolymph of several non-model species of Drosophila. Here we identify and describe a novel hemocyte, type-II nematocytes, found in larval stages of numerous Drosophila species. Examined in detail in Drosophila falleni and Drosophila phalerata, we find that these remarkable cells are distinct from previously described hemocytes due to their anucleate state (lacking a nucleus) and unusual morphology. Type-II nematocytes are long, narrow cells with spindle-like projections extending from a cell body with high densities of mitochondria and microtubules, and exhibit the ability to synthesize proteins. These properties are unexpected for enucleated cells, and together with our additional characterization, we demonstrate that these type-II nematocytes represent a biological novelty. Surprisingly, despite the absence of a nucleus, we observe through live cell imaging that these cells remain motile with a highly dynamic cellular shape. Furthermore, these cells demonstrate the ability to form multicellular structures, which we suggest may be a component of the innate immune response to macro-parasites. In addition, live cell imaging points to a large nucleated hemocyte, type-I nematocyte, as the progenitor cell, leading to enucleation through a budding or asymmetrical division process rather than nuclear ejection: This study is the first to report such a process of enucleation. Here we describe these cells in detail for the first time and examine their evolutionary history in Drosophila.},
}
@article {pmid29133443,
year = {2017},
author = {Kempes, CP and Wolpert, D and Cohen, Z and Pérez-Mercader, J},
title = {The thermodynamic efficiency of computations made in cells across the range of life.},
journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
volume = {375},
number = {2109},
pages = {},
doi = {10.1098/rsta.2016.0343},
pmid = {29133443},
issn = {1471-2962},
abstract = {Biological organisms must perform computation as they grow, reproduce and evolve. Moreover, ever since Landauer's bound was proposed, it has been known that all computation has some thermodynamic cost-and that the same computation can be achieved with greater or smaller thermodynamic cost depending on how it is implemented. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting both from the perspective of how close life has come to maximally efficient computation (presumably under the pressure of natural selection), and from the practical perspective of what efficiencies we might hope that engineered biological computers might achieve, especially in comparison with current computational systems. Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude, and is only about an order of magnitude worse than the Landauer bound. However, this efficiency depends strongly on the size and architecture of the cell in question. In particular, we show that the useful efficiency of an amino acid operation, defined as the bulk energy per amino acid polymerization, decreases for increasing bacterial size and converges to the polymerization cost of the ribosome. This cost of the largest bacteria does not change in cells as we progress through the major evolutionary shifts to both single- and multicellular eukaryotes. However, the rates of total computation per unit mass are non-monotonic in bacteria with increasing cell size, and also change across different biological architectures, including the shift from unicellular to multicellular eukaryotes.This article is part of the themed issue 'Reconceptualizing the origins of life'.},
}
@article {pmid29129605,
year = {2018},
author = {Pogozheva, ID and Lomize, AL},
title = {Evolution and adaptation of single-pass transmembrane proteins.},
journal = {Biochimica et biophysica acta. Biomembranes},
volume = {1860},
number = {2},
pages = {364-377},
doi = {10.1016/j.bbamem.2017.11.002},
pmid = {29129605},
issn = {0005-2736},
mesh = {*Adaptation, Physiological ; Arabidopsis/genetics/metabolism ; Cell Membrane/*metabolism ; Databases, Protein ; Dictyostelium/genetics/metabolism ; Escherichia coli/genetics/metabolism ; *Evolution, Molecular ; Humans ; Membrane Proteins/chemistry/genetics/*metabolism ; Methanocaldococcus/genetics/metabolism ; Protein Conformation, alpha-Helical ; Protein Multimerization ; Proteome/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Species Specificity ; },
abstract = {A comparative analysis of 6039 single-pass (bitopic) membrane proteins from six evolutionarily distant organisms was performed based on data from the Membranome database. The observed repertoire of bitopic proteins is significantly enlarged in eukaryotic cells and especially in multicellular organisms due to the diversification of enzymes, emergence of proteins involved in vesicular trafficking, and expansion of receptors, structural, and adhesion proteins. The majority of bitopic proteins in multicellular organisms are located in the plasma membrane (PM) and involved in cell communication. Bitopic proteins from different membranes significantly diverge in terms of their biological functions, size, topology, domain architecture, physical properties of transmembrane (TM) helices and propensity to form homodimers. Most proteins from eukaryotic PM and endoplasmic reticulum (ER) have the N-out topology. The predicted lengths of TM helices and hydrophobic thicknesses, stabilities and hydrophobicities of TM α-helices are the highest for proteins from eukaryotic PM, intermediate for proteins from prokaryotic cells, ER and Golgi apparatus, and lowest for proteins from mitochondria, chloroplasts, and peroxisomes. Tyr and Phe residues accumulate at the cytoplasmic leaflet of PM and at the outer leaflet of membranes of bacteria, Golgi apparatus, and nucleus. The propensity for dimerization increases from unicellular to multicellular eukaryotes, from enzymes to receptors, and from intracellular membrane proteins to PM proteins. More than half of PM proteins form homodimers with a 2:1 ratio of right-handed to left-handed helix packing arrangements. The inverse ratio (1:2) was observed for dimers from the ER, Golgi and vesicles.},
}
@article {pmid29121339,
year = {2017},
author = {Polychronopoulos, D and King, JWD and Nash, AJ and Tan, G and Lenhard, B},
title = {Conserved non-coding elements: developmental gene regulation meets genome organization.},
journal = {Nucleic acids research},
volume = {45},
number = {22},
pages = {12611-12624},
doi = {10.1093/nar/gkx1074},
pmid = {29121339},
issn = {1362-4962},
support = {MC_UP_1102/1//Medical Research Council/United Kingdom ; },
mesh = {Animals ; Base Sequence ; Conserved Sequence/*genetics ; Evolution, Molecular ; *Gene Expression Regulation, Developmental ; Genes, Developmental/genetics ; Genome/*genetics ; Humans ; Regulatory Sequences, Nucleic Acid/*genetics ; Sequence Homology, Nucleic Acid ; },
abstract = {Comparative genomics has revealed a class of non-protein-coding genomic sequences that display an extraordinary degree of conservation between two or more organisms, regularly exceeding that found within protein-coding exons. These elements, collectively referred to as conserved non-coding elements (CNEs), are non-randomly distributed across chromosomes and tend to cluster in the vicinity of genes with regulatory roles in multicellular development and differentiation. CNEs are organized into functional ensembles called genomic regulatory blocks-dense clusters of elements that collectively coordinate the expression of shared target genes, and whose span in many cases coincides with topologically associated domains. CNEs display sequence properties that set them apart from other sequences under constraint, and have recently been proposed as useful markers for the reconstruction of the evolutionary history of organisms. Disruption of several of these elements is known to contribute to diseases linked with development, and cancer. The emergence, evolutionary dynamics and functions of CNEs still remain poorly understood, and new approaches are required to enable comprehensive CNE identification and characterization. Here, we review current knowledge and identify challenges that need to be tackled to resolve the impasse in understanding extreme non-coding conservation.},
}
@article {pmid29119267,
year = {2018},
author = {Li, L and Aslam, M and Rabbi, F and Vanderwel, MC and Ashton, NW and Suh, DY},
title = {PpORS, an ancient type III polyketide synthase, is required for integrity of leaf cuticle and resistance to dehydration in the moss, Physcomitrella patens.},
journal = {Planta},
volume = {247},
number = {2},
pages = {527-541},
doi = {10.1007/s00425-017-2806-5},
pmid = {29119267},
issn = {1432-2048},
support = {262038-2013//Natural Sciences and Engineering Research Council of Canada/ ; 2982-2008//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Acyltransferases/genetics/*metabolism ; Biological Evolution ; Bryopsida/*enzymology/genetics/physiology ; Dehydration ; Gene Knockout Techniques ; Mutation ; Phenotype ; Phylogeny ; Plant Leaves/enzymology/genetics/physiology ; Plant Proteins/genetics/metabolism ; Water/physiology ; },
abstract = {MAIN CONCLUSION: PpORS knockout mutants produced abnormal leaves with increased dye permeability and were more susceptible to dehydration, consistent with PpORS products being constituents of a cuticular structure in the moss. Type III polyketide synthases (PKSs) have co-evolved with terrestrial plants such that each taxon can generate a characteristic collection of polyketides, fine-tuned to its needs. 2'-Oxoalkylresorcinol synthase from Physcomitrella patens (PpORS) is basal to all plant type III PKSs in phylogenetic trees and may closely resemble their most recent common ancestor. To gain insight into the roles that ancestral plant type III PKSs might have played during early land plant evolution, we constructed and phenotypically characterized targeted knockouts of PpORS. Ors gametophores, unless submerged in water while they were developing, displayed various leaf malformations that included grossly misshapen leaves, missing or abnormal midribs, multicellular protuberances and localized necrosis. Ors leaves, particularly abnormal ones, showed increased permeability to the hydrophilic dye, toluidine blue. Ors gametophores lost water faster and were more susceptible to dehydration than those of the control strain. Our findings are consistent with ors leaves possessing a partially defective cuticle and implicate PpORS in synthesis of the intact cuticle. PpORS orthologs are present in a few moss species but have not been found in other plants. However, conceivably an ancestral ORS in early land plants may have contributed to their protection from dehydration.},
}
@article {pmid29118134,
year = {2017},
author = {Berger, D and Stångberg, J and Grieshop, K and Martinossi-Allibert, I and Arnqvist, G},
title = {Temperature effects on life-history trade-offs, germline maintenance and mutation rate under simulated climate warming.},
journal = {Proceedings. Biological sciences},
volume = {284},
number = {1866},
pages = {},
doi = {10.1098/rspb.2017.1721},
pmid = {29118134},
issn = {1471-2954},
mesh = {Acclimatization ; Animals ; Climate Change ; Coleoptera/*physiology ; Female ; *Germ-Line Mutation ; *Life History Traits ; Longevity ; Male ; *Mutation Rate ; Reproduction ; },
abstract = {Mutation has a fundamental influence over evolutionary processes, but how evolutionary processes shape mutation rate remains less clear. In asexual unicellular organism, increased mutation rates have been observed in stressful environments and the reigning paradigm ascribes this increase to selection for evolvability. However, this explanation does not apply in sexually reproducing species, where little is known about how the environment affects mutation rate. Here we challenged experimental lines of seed beetle, evolved at ancestral temperature or under simulated climate warming, to repair induced mutations at ancestral and stressful temperature. Results show that temperature stress causes individuals to pass on a greater mutation load to their grand-offspring. This suggests that stress-induced mutation rates, in unicellular and multicellular organisms alike, can result from compromised germline DNA repair in low condition individuals. Moreover, lines adapted to simulated climate warming had evolved increased longevity at the cost of reproduction, and this allocation decision improved germline repair. These results suggest that mutation rates can be modulated by resource allocation trade-offs encompassing life-history traits and the germline and have important implications for rates of adaptation and extinction as well as our understanding of genetic diversity in multicellular organisms.},
}
@article {pmid29109219,
year = {2017},
author = {Stapley, J and Feulner, PGD and Johnston, SE and Santure, AW and Smadja, CM},
title = {Variation in recombination frequency and distribution across eukaryotes: patterns and processes.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {372},
number = {1736},
pages = {},
doi = {10.1098/rstb.2016.0455},
pmid = {29109219},
issn = {1471-2970},
mesh = {Chromosome Mapping ; Eukaryota/*genetics ; *Genetic Linkage ; *Genome ; Recombination, Genetic/*genetics ; },
abstract = {Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is an essential feature of sexual reproduction in nearly all multicellular organisms. While the role of recombination in the evolution of sex has received theoretical and empirical attention, less is known about how recombination rate itself evolves and what influence this has on evolutionary processes within sexually reproducing organisms. Here, we explore the patterns of, and processes governing recombination in eukaryotes. We summarize patterns of variation, integrating current knowledge with an analysis of linkage map data in 353 organisms. We then discuss proximate and ultimate processes governing recombination rate variation and consider how these influence evolutionary processes. Genome-wide recombination rates (cM/Mb) can vary more than tenfold across eukaryotes, and there is large variation in the distribution of recombination events across closely related taxa, populations and individuals. We discuss how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures. There has been great progress in determining the molecular mechanisms governing recombination, and with the continued development of new modelling and empirical approaches, there is now also great opportunity to further our understanding of how and why recombination rate varies.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.},
}
@article {pmid29101312,
year = {2017},
author = {Björnfot Holmström, S and Clark, R and Zwicker, S and Bureik, D and Kvedaraite, E and Bernasconi, E and Nguyen Hoang, AT and Johannsen, G and Marsland, BJ and Boström, EA and Svensson, M},
title = {Gingival Tissue Inflammation Promotes Increased Matrix Metalloproteinase-12 Production by CD200Rlow Monocyte-Derived Cells in Periodontitis.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {199},
number = {12},
pages = {4023-4035},
doi = {10.4049/jimmunol.1700672},
pmid = {29101312},
issn = {1550-6606},
mesh = {Adult ; Antigens, Surface/biosynthesis/genetics/*physiology ; Cell Division ; Cells, Cultured ; Coculture Techniques ; Cyclooxygenase Inhibitors/pharmacology ; Epithelial Cells/metabolism ; Fibroblasts/metabolism ; Flow Cytometry ; Gene Expression Regulation ; Gingiva/*enzymology/pathology ; Granulocyte-Macrophage Colony-Stimulating Factor/pharmacology ; Humans ; Inflammation ; Keratinocytes/metabolism ; Matrix Metalloproteinase 12/biosynthesis/genetics/*physiology ; Monocytes/*enzymology/pathology ; Periodontitis/*enzymology/pathology ; Pyrazoles/pharmacology ; Real-Time Polymerase Chain Reaction ; Receptors, Cell Surface/biosynthesis/genetics/*physiology ; },
abstract = {Irreversible tissue recession in chronic inflammatory diseases is associated with dysregulated immune activation and production of tissue degradative enzymes. In this study, we identified elevated levels of matrix metalloproteinase (MMP)-12 in gingival tissue of patients with the chronic inflammatory disease periodontitis (PD). The source of MMP12 was cells of monocyte origin as determined by the expression of CD14, CD68, and CD64. These MMP12-producing cells showed reduced surface levels of the coinhibitory molecule CD200R. Similarly, establishing a multicellular three-dimensional model of human oral mucosa with induced inflammation promoted MMP12 production and reduced CD200R surface expression by monocyte-derived cells. MMP12 production by monocyte-derived cells was induced by CSF2 rather than the cyclooxygenase-2 pathway, and treatment of monocyte-derived cells with a CD200R ligand reduced CSF2-induced MMP12 production. Further, MMP12-mediated degradation of the extracellular matrix proteins tropoelastin and fibronectin in the tissue model coincided with a loss of Ki-67, a protein strictly associated with cell proliferation. Reduced amounts of tropoelastin were confirmed in gingival tissue from PD patients. Thus, this novel association of the CD200/CD200R pathway with MMP12 production by monocyte-derived cells may play a key role in PD progression and will be important to take into consideration in the development of future strategies to diagnose, treat, and prevent PD.},
}
@article {pmid29099481,
year = {2018},
author = {Strasser, A and Vaux, DL},
title = {Viewing BCL2 and cell death control from an evolutionary perspective.},
journal = {Cell death and differentiation},
volume = {25},
number = {1},
pages = {13-20},
doi = {10.1038/cdd.2017.145},
pmid = {29099481},
issn = {1476-5403},
mesh = {Animals ; *Apoptosis ; Biological Evolution ; Caenorhabditis elegans/genetics ; Humans ; Inflammation ; Neoplasms/drug therapy ; Proto-Oncogene Proteins c-bcl-2/genetics/*physiology ; Stress, Physiological ; },
abstract = {The last 30 years of studying BCL2 have brought cell death research into the molecular era, and revealed its relevance to human pathophysiology. Most, if not all metazoans use an evolutionarily conserved process for cellular self destruction that is controlled and implemented by proteins related to BCL2. We propose the anti-apoptotic BCL2-like and pro-apoptotic BH3-only members of the family arose through duplication and modification of genes for the pro-apoptotic multi-BH domain family members, such as BAX and BAK1. In that way, a cell suicide process that initially evolved as a mechanism for defense against intracellular parasites was then also used in multicellular organisms for morphogenesis and to maintain the correct number of cells in adults by balancing cell production by mitosis.},
}
@article {pmid29085064,
year = {2017},
author = {Sipos, G and Prasanna, AN and Walter, MC and O'Connor, E and Bálint, B and Krizsán, K and Kiss, B and Hess, J and Varga, T and Slot, J and Riley, R and Bóka, B and Rigling, D and Barry, K and Lee, J and Mihaltcheva, S and LaButti, K and Lipzen, A and Waldron, R and Moloney, NM and Sperisen, C and Kredics, L and Vágvölgyi, C and Patrignani, A and Fitzpatrick, D and Nagy, I and Doyle, S and Anderson, JB and Grigoriev, IV and Güldener, U and Münsterkötter, M and Nagy, LG},
title = {Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria.},
journal = {Nature ecology &amp; evolution},
volume = {1},
number = {12},
pages = {1931-1941},
doi = {10.1038/s41559-017-0347-8},
pmid = {29085064},
issn = {2397-334X},
mesh = {Armillaria/*genetics ; Fungal Proteins/*genetics ; *Genome, Fungal ; Proteomics ; Sequence Analysis, RNA ; Species Specificity ; Transcriptome ; },
abstract = {Armillaria species are both devastating forest pathogens and some of the largest terrestrial organisms on Earth. They forage for hosts and achieve immense colony sizes via rhizomorphs, root-like multicellular structures of clonal dispersal. Here, we sequenced and analysed the genomes of four Armillaria species and performed RNA sequencing and quantitative proteomic analysis on the invasive and reproductive developmental stages of A. ostoyae. Comparison with 22 related fungi revealed a significant genome expansion in Armillaria, affecting several pathogenicity-related genes, lignocellulose-degrading enzymes and lineage-specific genes expressed during rhizomorph development. Rhizomorphs express an evolutionarily young transcriptome that shares features with the transcriptomes of both fruiting bodies and vegetative mycelia. Several genes show concomitant upregulation in rhizomorphs and fruiting bodies and share cis-regulatory signatures in their promoters, providing genetic and regulatory insights into complex multicellularity in fungi. Our results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria might have drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity.},
}
@article {pmid29070590,
year = {2017},
author = {de Wiljes, OO and van Elburg, RAJ and Keijzer, FA},
title = {Modelling the effects of short and random proto-neural elongations.},
journal = {Journal of the Royal Society, Interface},
volume = {14},
number = {135},
pages = {},
doi = {10.1098/rsif.2017.0399},
pmid = {29070590},
issn = {1742-5662},
mesh = {Animals ; Axons/*physiology ; *Computer Simulation ; Dendrites/*physiology ; *Models, Biological ; },
abstract = {To understand how neurons and nervous systems first evolved, we need an account of the origins of neural elongations: why did neural elongations (axons and dendrites) first originate, such that they could become the central component of both neurons and nervous systems? Two contrasting conceptual accounts provide different answers to this question. Braitenberg's vehicles provide the iconic illustration of the dominant input-output (IO) view. Here, the basic role of neural elongations is to connect sensors to effectors, both situated at different positions within the body. For this function, neural elongations are thought of as comparatively long and specific connections, which require an articulated body involving substantial developmental processes to build. Internal coordination (IC) models stress a different function for early nervous systems. Here, the coordination of activity across extended parts of a multicellular body is held central, in particular, for the contractions of (muscle) tissue. An IC perspective allows the hypothesis that the earliest proto-neural elongations could have been functional even when they were initially simple, short and random connections, as long as they enhanced the patterning of contractile activity across a multicellular surface. The present computational study provides a proof of concept that such short and random neural elongations can play this role. While an excitable epithelium can generate basic forms of patterning for small body configurations, adding elongations allows such patterning to scale up to larger bodies. This result supports a new, more gradual evolutionary route towards the origins of the very first neurons and nervous systems.},
}
@article {pmid29061894,
year = {2017},
author = {Aktipis, A and Maley, CC},
title = {Cooperation and cheating as innovation: insights from cellular societies.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {372},
number = {1735},
pages = {},
doi = {10.1098/rstb.2016.0421},
pmid = {29061894},
issn = {1471-2970},
support = {P01 CA091955/CA/NCI NIH HHS/United States ; R01 CA140657/CA/NCI NIH HHS/United States ; R01 CA185138/CA/NCI NIH HHS/United States ; },
mesh = {*Biological Evolution ; Cooperative Behavior ; *Eukaryota ; Microbial Interactions ; *Microbiota ; Models, Biological ; },
abstract = {The capacity to innovate is often considered a defining feature of human societies, but it is not a capacity that is unique to human societies: innovation occurs in cellular societies as well. Cellular societies such as multicellular bodies and microbial communities, including the human microbiome, are capable of innovation in response to novel opportunities and threats. Multicellularity represents a suite of innovations for cellular cooperation, but multicellularity also opened up novel opportunities for cells to cheat, exploiting the infrastructure and resources of the body. Multicellular bodies evolve less quickly than the cells within them, leaving them vulnerable to cellular innovations that can lead to cancer and infections. In order to counter these threats, multicellular bodies deploy additional innovations including the adaptive immune system and the development of partnerships with preferred microbial partners. What can we learn from examining these innovations in cooperation and cheating in cellular societies? First, innovation in social systems involves a constant tension between novel mechanisms that enable greater size and complexity of cooperative entities and novel ways of cheating. Second, cultivating cooperation with partners who can rapidly and effectively innovate (such as microbes) is important for large entities including multicellular bodies. And third, multicellularity enabled cells to manage risk socially, allowing organisms to survive in challenging environments where life would otherwise be impossible. Throughout, we ask how insights from cellular societies might be translated into new innovations in human health and medicine, promoting and protecting the cellular cooperation that makes us viable multicellular organisms.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.},
}
@article {pmid29061893,
year = {2017},
author = {Ratcliff, WC and Herron, M and Conlin, PL and Libby, E},
title = {Nascent life cycles and the emergence of higher-level individuality.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {372},
number = {1735},
pages = {},
doi = {10.1098/rstb.2016.0420},
pmid = {29061893},
issn = {1471-2970},
mesh = {Animals ; *Biological Evolution ; Individuality ; *Life Cycle Stages ; *Life History Traits ; Models, Genetic ; Mutation ; },
abstract = {Evolutionary transitions in individuality (ETIs) occur when formerly autonomous organisms evolve to become parts of a new, 'higher-level' organism. One of the first major hurdles that must be overcome during an ETI is the emergence of Darwinian evolvability in the higher-level entity (e.g. a multicellular group), and the loss of Darwinian autonomy in the lower-level units (e.g. individual cells). Here, we examine how simple higher-level life cycles are a key innovation during an ETI, allowing this transfer of fitness to occur 'for free'. Specifically, we show how novel life cycles can arise and lead to the origin of higher-level individuals by (i) mitigating conflicts between levels of selection, (ii) engendering the expression of heritable higher-level traits and (iii) allowing selection to efficiently act on these emergent higher-level traits. Further, we compute how canonical early life cycles vary in their ability to fix beneficial mutations via mathematical modelling. Life cycles that lack a persistent lower-level stage and develop clonally are far more likely to fix 'ratcheting' mutations that limit evolutionary reversion to the pre-ETI state. By stabilizing the fragile first steps of an evolutionary transition in individuality, nascent higher-level life cycles may play a crucial role in the origin of complex life.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.},
}
@article {pmid29050666,
year = {2017},
author = {Fortier, LC},
title = {The Contribution of Bacteriophages to the Biology and Virulence of Pathogenic Clostridia.},
journal = {Advances in applied microbiology},
volume = {101},
number = {},
pages = {169-200},
doi = {10.1016/bs.aambs.2017.05.002},
pmid = {29050666},
issn = {0065-2164},
mesh = {Bacteriophages/*physiology ; Clostridium difficile/pathogenicity/physiology/*virology ; Humans ; Prophages ; Virulence ; },
abstract = {Bacteriophages are key players in the evolution of most bacteria. Temperate phages have been associated with virulence of some of the deadliest pathogenic bacteria. Among the most notorious cases, the genes encoding the botulinum neurotoxin produced by Clostridium botulinum types C and D and the α-toxin (TcnA) produced by Clostridium novyi are both encoded within prophage genomes. Clostridium difficile is another important human pathogen and the recent identification of a complete binary toxin locus (CdtLoc) carried on a C. difficile prophage raises the potential for horizontal transfer of toxin genes by mobile genetic elements. Although the TcdA and TcdB toxins produced by C. difficile have never been found outside the pathogenicity locus (PaLoc), some prophages can still influence their production. Prophages can alter the expression of several metabolic and regulatory genes in C. difficile, as well as cell surface proteins such as CwpV, which confers phage resistance. Homologs of an Agr-like quorum sensing system have been identified in a C. difficile prophage, suggesting that it could possibly participate in cell-cell communication. Yet, other C. difficile prophages contain riboswitches predicted to recognize the secondary messenger molecule c-di-GMP involved in bacterial multicellular behaviors. Altogether, recent findings on clostridial phages underline the diversity of mechanisms and intricate relationship linking phages with their host. Here, milestone discoveries linking phages and virulence of some of the most pathogenic clostridial species will be retraced, with a focus on C. botulinum, C. novyi, C. difficile, and Clostridium perfringens phages, for which evidences are mostly available.},
}
@article {pmid29046735,
year = {2017},
author = {Luebeck, EG and Curtius, K and Hazelton, WD and Maden, S and Yu, M and Thota, PN and Patil, DT and Chak, A and Willis, JE and Grady, WM},
title = {Identification of a key role of widespread epigenetic drift in Barrett's esophagus and esophageal adenocarcinoma.},
journal = {Clinical epigenetics},
volume = {9},
number = {},
pages = {113},
doi = {10.1186/s13148-017-0409-4},
pmid = {29046735},
issn = {1868-7083},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; P50 CA150964/CA/NCI NIH HHS/United States ; U01 CA086402/CA/NCI NIH HHS/United States ; U01 CA182940/CA/NCI NIH HHS/United States ; P30 CA043703/CA/NCI NIH HHS/United States ; U01 CA152756/CA/NCI NIH HHS/United States ; U54 CA163060/CA/NCI NIH HHS/United States ; },
mesh = {Adenocarcinoma/*genetics ; Aged ; Barrett Esophagus/*genetics ; CpG Islands ; *DNA Methylation ; Databases, Genetic ; Disease Progression ; Epigenesis, Genetic ; Esophageal Neoplasms/*genetics ; Female ; Gene Expression Regulation, Neoplastic ; *Genetic Drift ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Models, Genetic ; },
abstract = {BACKGROUND: Recent studies have identified age-related changes in DNA methylation patterns in normal and cancer tissues in a process that is called epigenetic drift. However, the evolving patterns, functional consequences, and dynamics of epigenetic drift during carcinogenesis remain largely unexplored. Here we analyze the evolution of epigenetic drift patterns during progression from normal squamous esophagus tissue to Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) using 173 tissue samples from 100 (nonfamilial) BE patients, along with publically available datasets including The Cancer Genome Atlas (TCGA).<br><br>RESULTS: Our analysis reveals extensive methylomic drift between normal squamous esophagus and BE tissues in nonprogressed BE patients, with differential drift affecting 4024 (24%) of 16,984 normally hypomethylated cytosine-guanine dinucleotides (CpGs) occurring in CpG islands. The majority (63%) of islands that include drift CpGs are associated with gene promoter regions. Island CpGs that drift have stronger pairwise correlations than static islands, reflecting collective drift consistent with processive DNA methylation maintenance. Individual BE tissues are extremely heterogeneous in their distribution of methylomic drift and encompass unimodal low-drift to bimodal high-drift patterns, reflective of differences in BE tissue age. Further analysis of longitudinally collected biopsy samples from 20 BE patients confirm the time-dependent evolution of these drift patterns. Drift patterns in EAC are similar to those in BE, but frequently exhibit enhanced bimodality and advanced mode drift. To better understand the observed drift patterns, we developed a multicellular stochastic model at the CpG island level. Importantly, we find that nonlinear feedback in the model between mean island methylation and CpG methylation rates is able to explain the widely heterogeneous collective drift patterns. Using matched gene expression and DNA methylation data in EAC from TCGA and other publically available data, we also find that advanced methylomic drift is correlated with significant transcriptional repression of ~ 200 genes in important regulatory and developmental pathways, including several checkpoint and tumor suppressor-like genes.<br><br>CONCLUSIONS: Taken together, our findings suggest that epigenetic drift evolution acts to significantly reduce the expression of developmental genes that may alter tissue characteristics and improve functional adaptation during BE to EAC progression.},
}
@article {pmid29021161,
year = {2017},
author = {Jackson, MDB and Duran-Nebreda, S and Bassel, GW},
title = {Network-based approaches to quantify multicellular development.},
journal = {Journal of the Royal Society, Interface},
volume = {14},
number = {135},
pages = {},
doi = {10.1098/rsif.2017.0484},
pmid = {29021161},
issn = {1742-5662},
mesh = {Animals ; Humans ; *Models, Biological ; },
abstract = {Multicellularity and cellular cooperation confer novel functions on organs following a structure-function relationship. How regulated cell migration, division and differentiation events generate cellular arrangements has been investigated, providing insight into the regulation of genetically encoded patterning processes. Much less is known about the higher-order properties of cellular organization within organs, and how their functional coordination through global spatial relations shape and constrain organ function. Key questions to be addressed include: why are cells organized in the way they are? What is the significance of the patterns of cellular organization selected for by evolution? What other configurations are possible? These may be addressed through a combination of global cellular interaction mapping and network science to uncover the relationship between organ structure and function. Using this approach, global cellular organization can be discretized and analysed, providing a quantitative framework to explore developmental processes. Each of the local and global properties of integrated multicellular systems can be analysed and compared across different tissues and models in discrete terms. Advances in high-resolution microscopy and image analysis continue to make cellular interaction mapping possible in an increasing variety of biological systems and tissues, broadening the further potential application of this approach. Understanding the higher-order properties of complex cellular assemblies provides the opportunity to explore the evolution and constraints of cell organization, establishing structure-function relationships that can guide future organ design.},
}
@article {pmid28988859,
year = {2017},
author = {Vermeij, GJ},
title = {How the Land Became the Locus of Major Evolutionary Innovations.},
journal = {Current biology : CB},
volume = {27},
number = {20},
pages = {3178-3182.e1},
doi = {10.1016/j.cub.2017.08.076},
pmid = {28988859},
issn = {1879-0445},
mesh = {Animals ; *Biological Evolution ; *Embryophyta/anatomy &amp; histology/physiology ; *Environment ; *Invertebrates/anatomy &amp; histology/physiology ; *Vertebrates/anatomy &amp; histology/physiology ; },
abstract = {Life originated in the sea and evolved its early metabolic pathways in water [1, 2]. Nevertheless, activities of organisms on land have influenced and enriched marine ecosystems with oxygen and nutrients for billions of years [3-7]. In contrast to the history of species diversity in the sea and on land [8-10] and the flows of resources within and between these two realms [11], little is known about the times and places of origin of major metabolic and ecological innovations during the Phanerozoic. Many innovations among multicellular organisms originated in the sea during or before the Cambrian, including predation and most of its variations, biomineralization, colonial or clonal growth, bioerosion, deposit feeding, bioturbation by animals, communication at a distance by vision and olfaction, photosymbiosis, chemosymbiosis, suspension feeding, osmotrophy, internal fertilization, jet propulsion, undulatory locomotion, and appendages for movement. Activity is less constrained in air than in the denser, more viscous medium of water [9, 12-14]. I therefore predict that high-performance metabolic and ecological innovations should predominantly originate on land after the Ordovician once organisms had conquered the challenges of life away from water and later appeared in the sea, either in marine-colonizing clades or by arising separately in clades that never left the sea. In support of this hypothesis, I show that 11 of 13 major post-Ordovician innovations appeared first or only on land. This terrestrial locus of innovation cannot be explained by the Cretaceous to recent expansion of diversity on land. It reveals one of several irreversible shifts in the history of life.},
}
@article {pmid28985561,
year = {2017},
author = {Bowman, JL and Kohchi, T and Yamato, KT and Jenkins, J and Shu, S and Ishizaki, K and Yamaoka, S and Nishihama, R and Nakamura, Y and Berger, F and Adam, C and Aki, SS and Althoff, F and Araki, T and Arteaga-Vazquez, MA and Balasubrmanian, S and Barry, K and Bauer, D and Boehm, CR and Briginshaw, L and Caballero-Perez, J and Catarino, B and Chen, F and Chiyoda, S and Chovatia, M and Davies, KM and Delmans, M and Demura, T and Dierschke, T and Dolan, L and Dorantes-Acosta, AE and Eklund, DM and Florent, SN and Flores-Sandoval, E and Fujiyama, A and Fukuzawa, H and Galik, B and Grimanelli, D and Grimwood, J and Grossniklaus, U and Hamada, T and Haseloff, J and Hetherington, AJ and Higo, A and Hirakawa, Y and Hundley, HN and Ikeda, Y and Inoue, K and Inoue, SI and Ishida, S and Jia, Q and Kakita, M and Kanazawa, T and Kawai, Y and Kawashima, T and Kennedy, M and Kinose, K and Kinoshita, T and Kohara, Y and Koide, E and Komatsu, K and Kopischke, S and Kubo, M and Kyozuka, J and Lagercrantz, U and Lin, SS and Lindquist, E and Lipzen, AM and Lu, CW and De Luna, E and Martienssen, RA and Minamino, N and Mizutani, M and Mizutani, M and Mochizuki, N and Monte, I and Mosher, R and Nagasaki, H and Nakagami, H and Naramoto, S and Nishitani, K and Ohtani, M and Okamoto, T and Okumura, M and Phillips, J and Pollak, B and Reinders, A and Rövekamp, M and Sano, R and Sawa, S and Schmid, MW and Shirakawa, M and Solano, R and Spunde, A and Suetsugu, N and Sugano, S and Sugiyama, A and Sun, R and Suzuki, Y and Takenaka, M and Takezawa, D and Tomogane, H and Tsuzuki, M and Ueda, T and Umeda, M and Ward, JM and Watanabe, Y and Yazaki, K and Yokoyama, R and Yoshitake, Y and Yotsui, I and Zachgo, S and Schmutz, J},
title = {Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.},
journal = {Cell},
volume = {171},
number = {2},
pages = {287-304.e15},
doi = {10.1016/j.cell.2017.09.030},
pmid = {28985561},
issn = {1097-4172},
mesh = {Adaptation, Biological ; *Biological Evolution ; Embryophyta/*genetics/physiology ; Gene Expression Regulation, Plant ; *Genome, Plant ; Marchantia/*genetics/physiology ; Molecular Sequence Annotation ; Signal Transduction ; Transcription, Genetic ; },
abstract = {The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.},
}
@article {pmid28938124,
year = {2017},
author = {Hinshaw, SM and Makrantoni, V and Harrison, SC and Marston, AL},
title = {The Kinetochore Receptor for the Cohesin Loading Complex.},
journal = {Cell},
volume = {171},
number = {1},
pages = {72-84.e13},
doi = {10.1016/j.cell.2017.08.017},
pmid = {28938124},
issn = {1097-4172},
support = {107827//Wellcome Trust/United Kingdom ; },
mesh = {Cell Cycle Proteins/*metabolism ; Centromere/metabolism ; Chromosomal Proteins, Non-Histone/*metabolism ; Cytoskeletal Proteins/metabolism ; Kinetochores/*metabolism ; Multiprotein Complexes/metabolism ; Phosphorylation ; Phylogeny ; Saccharomyces cerevisiae/cytology/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; X-Ray Diffraction ; },
abstract = {The ring-shaped cohesin complex brings together distant DNA domains to maintain, express, and segregate the genome. Establishing specific chromosomal linkages depends on cohesin recruitment to defined loci. One such locus is the budding yeast centromere, which is a paradigm for targeted cohesin loading. The kinetochore, a multiprotein complex that connects centromeres to microtubules, drives the recruitment of high levels of cohesin to link sister chromatids together. We have exploited this system to determine the mechanism of specific cohesin recruitment. We show that phosphorylation of the Ctf19 kinetochore protein by a conserved kinase, DDK, provides a binding site for the Scc2/4 cohesin loading complex, thereby directing cohesin loading to centromeres. A similar mechanism targets cohesin to chromosomes in vertebrates. These findings represent a complete molecular description of targeted cohesin loading, a phenomenon with wide-ranging importance in chromosome segregation and, in multicellular organisms, transcription regulation.},
}
@article {pmid28936730,
year = {2017},
author = {Conigliaro, A and Fontana, S and Raimondo, S and Alessandro, R},
title = {Exosomes: Nanocarriers of Biological Messages.},
journal = {Advances in experimental medicine and biology},
volume = {998},
number = {},
pages = {23-43},
doi = {10.1007/978-981-10-4397-0_2},
pmid = {28936730},
issn = {0065-2598},
mesh = {Animals ; Exosomes/genetics/*metabolism/ultrastructure ; Humans ; Intracellular Signaling Peptides and Proteins/*metabolism ; *Lipid Metabolism ; *Nanoparticles ; Nucleic Acids/*metabolism ; Organelle Size ; Protein Transport ; *Signal Transduction ; },
abstract = {Cell-cell communication is crucial to maintain homeostasis in multicellular organism. Cells communicate each other by direct contact or by releasing factors that, soluble or packaged in membrane vesicles, can reach different regions of the organism. To date numerous studies highlighted the existence of several types of extracellular vesicles that, differing for dimension, origin and contents, play a role in physiological and/or pathological processes. Among extracellular vesicles, exosomes are emerging as efficient players to modulate target cells phenotype and as new non-invasive diagnostic and prognostic tools in multiple diseases. They, in fact, strictly reflect the type and functional status of the producing cells and are able to deliver their contents even over a long distance. The results accumulated in the last two decades and collected in this chapter, indicated that exosomes, can carry RNAs, microRNAs, long non-coding RNAs, DNA, lipids, metabolites and proteins; a deeper understanding of their contents is therefore needed to get the most from this incredible cell product.},
}
@article {pmid28923586,
year = {2017},
author = {Dennis, JW},
title = {Genetic code asymmetry supports diversity through experimentation with posttranslational modifications.},
journal = {Current opinion in chemical biology},
volume = {41},
number = {},
pages = {1-11},
doi = {10.1016/j.cbpa.2017.08.012},
pmid = {28923586},
issn = {1879-0402},
mesh = {Animals ; Evolution, Molecular ; *Genetic Code ; Humans ; Protein Processing, Post-Translational/*genetics ; Proteins/*genetics/*metabolism ; Selection, Genetic ; },
abstract = {Protein N-glycosylation has been identified in all three domains of life presumably conserved for its early role in glycoprotein folding. However, the N-glycans added to proteins in the secretory pathway of multicellular organisms are remodeling in the Golgi, increasing structural diversity exponentially and adding new layers of functionality in immunity, metabolism and other systems. The branching and elongation of N-glycan chains found on cell surface receptors generates a gradation of affinities for carbohydrate-binding proteins, the galectin, selectin and siglec families. These interactions adapt cellular responsiveness to environmental conditions, but their complexity presents a daunting challenge to drug design. To gain further insight, I review how N-glycans biosynthesis and biophysical properties provide a selective advantage in the form of tunable and ultrasensitive stimulus-response relationships. In addition, the N-glycosylation motif favors step-wise mutational experimentation with sites. Glycoproteins display accelerated evolution during vertebrate radiation, and the encoding asymmetry of NXS/T(X≠P) has left behind phylogenetic evidence suggesting that the genetic code may have been selected to optimize diversity in part through emerging posttranslational modifications.},
}
@article {pmid28916376,
year = {2017},
author = {Peng, L and Wang, L and Yang, YF and Zou, MM and He, WY and Wang, Y and Wang, Q and Vasseur, L and You, MS},
title = {Transcriptome profiling of the Plutella xylostella (Lepidoptera: Plutellidae) ovary reveals genes involved in oogenesis.},
journal = {Gene},
volume = {637},
number = {},
pages = {90-99},
doi = {10.1016/j.gene.2017.09.020},
pmid = {28916376},
issn = {1879-0038},
mesh = {Animals ; Female ; Gene Expression Profiling/*methods ; Gene Regulatory Networks ; Insect Proteins/*genetics/metabolism ; Insecticide Resistance/*genetics ; Moths/*genetics/growth &amp; development/metabolism ; *Oogenesis ; Ovary/growth &amp; development/*metabolism ; Phylogeny ; Reproduction ; *Transcriptome ; },
abstract = {BACKGROUND: As a specialized organ, the insect ovary performs valuable functions by ensuring fecundity and population survival. Oogenesis is the complex physiological process resulting in the production of mature eggs, which are involved in epigenetic programming, germ cell behavior, cell cycle regulation, etc. Identification of the genes involved in ovary development and oogenesis is critical to better understand the reproductive biology and screening for the potential molecular targets in Plutella xylostella, a worldwide destructive pest of economically major crops.<br><br>RESULTS: Based on transcriptome sequencing, a total of 7.88Gb clean nucleotides was obtained, with 19,934 genes and 1861 new transcripts being identified. Expression profiling indicated that 61.7% of the genes were expressed (FPKM≥1) in the P. xylostella ovary. GO annotation showed that the pathways of multicellular organism reproduction and multicellular organism reproduction process, as well as gamete generation and chorion were significantly enriched. Processes that were most likely relevant to reproduction included the spliceosome, ubiquitin mediated proteolysis, endocytosis, PI3K-Akt signaling pathway, insulin signaling pathway, cAMP signaling pathway, and focal adhesion were identified in the top 20 'highly represented' KEGG pathways. Functional genes involved in oogenesis were further analyzed and validated by qRT-PCR to show their potential predominant roles in P. xylostella reproduction.<br><br>CONCLUSIONS: Our newly developed P. xylostella ovary transcriptome provides an overview of the gene expression profiling in this specialized tissue and the functional gene network closely related to the ovary development and oogenesis. This is the first genome-wide transcriptome dataset of P. xylostella ovary that includes a subset of functionally activated genes. This global approach will be the basis for further studies on molecular mechanisms of P. xylostella reproduction aimed at screening potential molecular targets for integrated pest management.},
}
@article {pmid28904210,
year = {2017},
author = {Willy, NM and Ferguson, JP and Huber, SD and Heidotting, SP and Aygün, E and Wurm, SA and Johnston-Halperin, E and Poirier, MG and Kural, C},
title = {Membrane mechanics govern spatiotemporal heterogeneity of endocytic clathrin coat dynamics.},
journal = {Molecular biology of the cell},
volume = {28},
number = {24},
pages = {3480-3488},
doi = {10.1091/mbc.E17-05-0282},
pmid = {28904210},
issn = {1939-4586},
support = {R01 AI121124/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Biomechanical Phenomena ; Cell Line, Tumor ; Cell Membrane/metabolism/physiology ; Cells, Cultured ; Cercopithecus aethiops ; Clathrin/metabolism ; Clathrin-Coated Vesicles/metabolism/*physiology ; Coated Pits, Cell-Membrane/metabolism/physiology ; Cytoplasm/metabolism ; Drosophila ; Endocytosis/physiology ; Humans ; Spatio-Temporal Analysis ; },
abstract = {Dynamics of endocytic clathrin-coated structures can be remarkably divergent across different cell types, cells within the same culture, or even distinct surfaces of the same cell. The origin of this astounding heterogeneity remains to be elucidated. Here we show that cellular processes associated with changes in effective plasma membrane tension induce significant spatiotemporal alterations in endocytic clathrin coat dynamics. Spatiotemporal heterogeneity of clathrin coat dynamics is also observed during morphological changes taking place within developing multicellular organisms. These findings suggest that tension gradients can lead to patterning and differentiation of tissues through mechanoregulation of clathrin-mediated endocytosis.},
}
@article {pmid28899581,
year = {2017},
author = {Kennedy, P and Baron, G and Qiu, B and Freitak, D and Helanterä, H and Hunt, ER and Manfredini, F and O'Shea-Wheller, T and Patalano, S and Pull, CD and Sasaki, T and Taylor, D and Wyatt, CDR and Sumner, S},
title = {Deconstructing Superorganisms and Societies to Address Big Questions in Biology.},
journal = {Trends in ecology &amp; evolution},
volume = {32},
number = {11},
pages = {861-872},
doi = {10.1016/j.tree.2017.08.004},
pmid = {28899581},
issn = {1872-8383},
mesh = {Animals ; *Behavior, Animal ; Biological Evolution ; Hymenoptera/*physiology ; Isoptera/*physiology ; *Social Behavior ; },
abstract = {Social insect societies are long-standing models for understanding social behaviour and evolution. Unlike other advanced biological societies (such as the multicellular body), the component parts of social insect societies can be easily deconstructed and manipulated. Recent methodological and theoretical innovations have exploited this trait to address an expanded range of biological questions. We illustrate the broadening range of biological insight coming from social insect biology with four examples. These new frontiers promote open-minded, interdisciplinary exploration of one of the richest and most complex of biological phenomena: sociality.},
}
@article {pmid28889015,
year = {2017},
author = {He, HH and Chi, YM and Yuan, K and Li, XY and Weng, SP and He, JG and Chen, YH},
title = {Functional characterization of a reactive oxygen species modulator 1 gene in Litopenaeus vannamei.},
journal = {Fish &amp; shellfish immunology},
volume = {70},
number = {},
pages = {270-279},
doi = {10.1016/j.fsi.2017.09.024},
pmid = {28889015},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/*genetics/*immunology ; Base Sequence ; Cell Line ; Drosophila melanogaster ; Gene Expression Regulation ; *Immunity, Innate ; Penaeidae/*genetics/*immunology ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Sequence Alignment ; Vibrio alginolyticus/physiology ; White spot syndrome virus 1/physiology ; },
abstract = {Reactive oxygen species (ROS) imparts a dual effect on multicellular organisms, wherein high levels are usually harmful, and low levels could facilitate in combating pathogenic microorganisms; therefore, the regulation of ROS production is critical. Previous studies have suggested that ROS contributes to resistance to the white spot syndrome virus (WSSV) or Vibrio alginolyticus in Litopenaeus vannamei. However, the regulation of ROS metabolism in L. vannamei remains elusive. In the present study, we proved that the overexpression of L. vannamei reactive oxygen species modulator 1 (LvROMO1) increases ROS production in Drosophila Schneider 2 (S2) cells. Real-time RT-PCR analysis indicated that LvROMO1 is induced by WSSV or V. alginolyticus infection and β-glucan or microcystin (MC-LR) injection. Further investigation showed that LvROMO1 responding to MC-LR, thereby inducing hemocytes to undergo apoptosis, and ultimately resulting in hepatopancreatic damage. And LvROMO1 downregulation induced an increase in the cumulative mortality of WSSV-infected shrimp by reducing ROS production and suppressing the expression of antimicrobial peptides genes. The findings of present study suggest that LvROMO1 plays an important role in ROS production in L. vannamei and is involved in innate immunity.},
}
@article {pmid28866006,
year = {2017},
author = {Witting, L},
title = {The natural selection of metabolism and mass selects allometric transitions from prokaryotes to mammals.},
journal = {Theoretical population biology},
volume = {117},
number = {},
pages = {23-42},
doi = {10.1016/j.tpb.2017.08.005},
pmid = {28866006},
issn = {1096-0325},
mesh = {Animals ; Basal Metabolism ; Biological Evolution ; Body Size ; Ecology ; Mammals/*metabolism ; Models, Biological ; Prokaryotic Cells/*metabolism ; Selection, Genetic/*physiology ; },
abstract = {The exponents of inter-specific allometries for several life history (metabolism, lifespan, reproductive rate, survival) and ecological (population density, home range) traits may evolve from the spatial dimensionality (d) of the intra-specific interactive competition that selects net assimilated energy into mass, with 1∕4 exponents being the two-dimensional (2D) case of the more general 1∕2d (Witting, 1995). While the exponents for mass-specific metabolism cluster around the predicted -1/4 and -1/6 in terrestrial and pelagic vertebrates, the allometries of mobile organisms are more diverse than the prediction. An exponent around zero has been reported for protists and protozoa (Makarieva et al., 2005, 2008), and the exponent appears to be strongly positive in prokaryotes with a value of about 5/6 (DeLong et al., 2010). I show that the natural selection of metabolism and mass is sufficient to explain exponents for mass-specific metabolism that decline from 5/6 over zero to -1∕6 in 3D, and from 3/4 over zero to -1∕4 in 2D. These results suggest that mass-specific metabolism is selected as the pace of the resource handling that generates net energy for self-replication and the selection of mass, with the decline in the metabolic exponent following from a decline in the importance of mass-specific metabolism for the selection of mass. The body mass variation in prokaryotes is found to be selected from primary variation in mass-specific metabolism, while the variation in multicellular animals is selected from primary variation in the handling and/or densities of the underlying resources, with protists and protozoa being selected as an intermediate lifeform.},
}
@article {pmid28864113,
year = {2017},
author = {Li, DD and Luo, Z and Chen, GH and Song, YF and Wei, CC and Pan, YX},
title = {Identification of apoptosis-related genes Bcl2 and Bax from yellow catfish Pelteobagrus fulvidraco and their transcriptional responses to waterborne and dietborne zinc exposure.},
journal = {Gene},
volume = {633},
number = {},
pages = {1-8},
doi = {10.1016/j.gene.2017.08.029},
pmid = {28864113},
issn = {1879-0038},
mesh = {Animals ; Apoptosis/*genetics/physiology ; Catfishes/*genetics/metabolism ; DNA, Complementary/genetics ; Down-Regulation ; Environmental Exposure ; Fish Proteins/classification/*genetics/physiology ; Lipid Metabolism/genetics ; Liver/metabolism ; Phylogeny ; RNA, Messenger/genetics/metabolism ; *Transcription, Genetic ; Up-Regulation ; Water/chemistry ; Zinc/analysis/*metabolism ; bcl-2-Associated X Protein/classification/*genetics/physiology ; bcl-Associated Death Protein/classification/*genetics/physiology ; },
abstract = {Apoptosis plays a key role in the physiology of multicellular organisms, and has been well studied in mammals, but not in teleosts. Zinc (Zn) has been shown to be an important regulator of apoptosis and apoptosis involves in the regulation of lipid metabolism. Moreover, our recent study indicated that waterborne and dietborne Zn exposure differently influenced lipid metabolism in Pelteobagrus fulvidraco, but further mechanism remained unknown. The hypothesis of the present study is that apoptosis mediated the Zn-induced changes of lipid metabolism of P. fulvidraco subjected to different exposure pathways. To this end, we cloned full-length cDNA sequences of Bcl2 and three Bax subtypes involved in apoptosis in P. fulvidraco, explored their mRNA expressions in responses to different Zn exposure pathways. Bcl2 and three Bax subtypes shared similar domain structure as typical pro- and anti-apoptotic Bcl2 family members. Their mRNAs were widely expressed among various tissues, but at variable levels. Waterborne Zn exposure down-regulated mRNA levels of Baxg and ratios of Baxa/Bcl2, and Baxg/Bcl2, but showed no significant effects on mRNA abundances of Bcl2, Baxa and Baxb, and the ratio of Baxb/Bcl2. In contrast, dietborne Zn exposure up-regulated mRNA levels of Bcl2, Baxa, Baxb and Baxg, but reduced the ratios of Baxa/Bcl2, Baxb/Bcl2, and Baxg/Bcl2. Considering their important roles of these genes in apoptosis induced by Zn, apoptosis may mediate the Zn-induced changes of hepatic lipid metabolism of Pelteobagrus fulvidraco under different Zn exposure pathways. For the first time, we characterized the full-length cDNA sequences of Bcl2 and three Bax subtypes, determined their expression profiles and transcriptional responses to different Zn exposure pathways, which would contribute to our understanding of the molecular basis of apoptosis, and also provide new insights into physiological responses to different Zn exposure pathways.},
}
@article {pmid28859501,
year = {2017},
author = {Csaba, G},
title = {Is there a hormonal regulation of phagocytosis at unicellular and multicellular levels? A critical review.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {64},
number = {4},
pages = {357-372},
doi = {10.1556/030.64.2017.024},
pmid = {28859501},
issn = {1217-8950},
mesh = {Animals ; Hormones/*immunology ; Humans ; Macrophages/cytology/*immunology ; *Phagocytosis ; },
abstract = {Phagocytosis is an ancient cell function, which is similar at unicellular and multicellular levels. Unicells synthesize, store, and secrete multicellular (mammalian) hormones, which influence their phagocytosis. Amino acid hormones, such as histamine, serotonin, epinephrine, and melatonin stimulate phagocytosis, whereas peptide hormones, such as adrenocorticotropic hormone (ACTH), insulin, opioids, arginine vasopressin, and atrial natriuretic peptide decreased it, independently on their chemical structure or function in multicellulars. Macrophage phagocytosis of multicellulars is also stimulated by amino acid hormones, such as histamine, epinephrine, melatonin, and thyroid hormones, however, the effect of peptide hormones is not uniform: prolactin, insulin, glucagon, somatostatin, and leptin have positive effects, whereas ACTH, human chorionic gonadotropin, opioids, and ghrelin have negative ones. Steroid hormones, such as estrogen, hydrocortisone, and dexamethasone are stimulating macrophage phagocytosis, whereas progesterone, aldosterone, and testosterone are depressing it. Considering the data and observations there is not a specific phagocytosis hormone, or a hormonal regulation of phagocytosis neither unicellular, nor multicellular level, however, hormones having specific functions in multicellulars also influence phagocytosis at both levels universally (in unicellulars) or individually (in macrophages). Nevertheless, the hormonal influence cannot be neglected, as phagocytosis (as a function) is rather sensitive to minute dose of hormones and endocrine disruptors. The hormonal influence of phagocytosis by macrophages can be deduced to the events at unicellular level.},
}
@article {pmid28856734,
year = {2017},
author = {Deines, P and Lachnit, T and Bosch, TCG},
title = {Competing forces maintain the Hydra metaorganism.},
journal = {Immunological reviews},
volume = {279},
number = {1},
pages = {123-136},
doi = {10.1111/imr.12564},
pmid = {28856734},
issn = {1600-065X},
mesh = {Animals ; *Biological Evolution ; Homeostasis ; Host-Pathogen Interactions ; Humans ; Hydra/*physiology ; *Immunity, Innate ; Symbiosis ; },
abstract = {Our conventional view of multicellular organisms often overlooks the fact that they are metaorganisms. They consist of a host, which is comprised of both a community of self-replicating cells that can compete as well as cooperate and a community of associated microorganisms. This newly discovered complexity raises a profound challenge: How to maintain such a multicellular association that includes independently replicating units and even different genotypes? Here, we identify competing forces acting at the host tissue level, the host-microbe interface, and within the microbial community as key factors to maintain the metaorganism Hydra. Maintenance of host tissue integrity, as well as proper regulation and management of the multiorganismic interactions are fundamental to organismal survival and health. Findings derived from the in vivo context of the Hydra model may provide one of the simplest possible systems to address questions on how a metaorganism is established and remains in balance over time.},
}
@article {pmid28846170,
year = {2017},
author = {Votaw, HR and Ostrowski, EA},
title = {Stalk size and altruism investment within and among populations of the social amoeba.},
journal = {Journal of evolutionary biology},
volume = {30},
number = {11},
pages = {2017-2030},
doi = {10.1111/jeb.13172},
pmid = {28846170},
issn = {1420-9101},
mesh = {Altruism ; Dictyostelium/*cytology/genetics/*physiology ; Epistasis, Genetic ; Genotype ; Reproduction ; },
abstract = {Reproductive division of labour is common in many societies, including those of eusocial insects, cooperatively breeding vertebrates, and most forms of multicellularity. However, conflict over what is best for the individual vs. the group can prevent an optimal division of labour from being achieved. In the social amoeba Dictyostelium discoideum, cells aggregate to become multicellular and a fraction behaves altruistically, forming a dead stalk that supports the rest. Theory suggests that intra-organismal conflict over spore-stalk cell fate can drive rapid evolutionary change in allocation traits, leading to polymorphisms within populations or rapid divergence between them. Here, we assess several proxies for stalk size and spore-stalk allocation as metrics of altruism investment among strains and across geographic regions. We observe geographic divergence in stalk height that can be partly explained by differences in multicellular size, as well as variation among strains in clonal spore-stalk allocation, suggesting within-population variation in altruism investment. Analyses of chimeras comprised of strains from the same vs. different populations indicated genotype-by-genotype epistasis, where the morphology of the chimeras deviated significantly from the average morphology of the strains developed clonally. The significantly negative epistasis observed for allopatric pairings suggests that populations are diverging in their spore-stalk allocation behaviours, generating incompatibilities when they encounter one another. Our results demonstrate divergence in microbial social traits across geographically separated populations and demonstrate how quantification of genotype-by-genotype interactions can elucidate the trajectory of social trait evolution in nature.},
}
@article {pmid28839913,
year = {2017},
author = {Shapiro, JA},
title = {Biological action in Read-Write genome evolution.},
journal = {Interface focus},
volume = {7},
number = {5},
pages = {20160115},
doi = {10.1098/rsfs.2016.0115},
pmid = {28839913},
issn = {2042-8898},
abstract = {Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with 'non-coding' DNA content rather than with protein-coding capacity in the genome. Coincidentally, 'non-coding' RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.},
}
@article {pmid28827358,
year = {2017},
author = {Larsen, NB and Liberti, SE and Vogel, I and Jørgensen, SW and Hickson, ID and Mankouri, HW},
title = {Stalled replication forks generate a distinct mutational signature in yeast.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {114},
number = {36},
pages = {9665-9670},
doi = {10.1073/pnas.1706640114},
pmid = {28827358},
issn = {1091-6490},
mesh = {DNA Replication/*genetics ; DNA, Fungal/genetics/metabolism ; DNA, Single-Stranded/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Exodeoxyribonucleases/genetics/metabolism ; Genes, Reporter ; Genetic Engineering ; Humans ; Models, Biological ; Mutagenesis ; Mutation ; Nuclear Proteins/genetics/metabolism ; RecQ Helicases/genetics/metabolism ; Recombinant Proteins/genetics/metabolism ; Recombinational DNA Repair ; Replication Origin ; Saccharomyces cerevisiae/*genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; },
abstract = {Proliferating cells acquire genome alterations during the act of DNA replication. This leads to mutation accumulation and somatic cell mosaicism in multicellular organisms, and is also implicated as an underlying cause of aging and tumorigenesis. The molecular mechanisms of DNA replication-associated genome rearrangements are poorly understood, largely due to methodological difficulties in analyzing specific replication forks in vivo. To provide an insight into this process, we analyzed the mutagenic consequences of replication fork stalling at a single, site-specific replication barrier (the Escherichia coli Tus/Ter complex) engineered into the yeast genome. We demonstrate that transient stalling at this barrier induces a distinct pattern of genome rearrangements in the newly replicated region behind the stalled fork, which primarily consist of localized losses and duplications of DNA sequences. These genetic alterations arise through the aberrant repair of a single-stranded DNA gap, in a process that is dependent on Exo1- and Shu1-dependent homologous recombination repair (HRR). Furthermore, aberrant processing of HRR intermediates, and elevated HRR-associated mutagenesis, is detectable in a yeast model of the human cancer predisposition disorder, Bloom's syndrome. Our data reveal a mechanism by which cellular responses to stalled replication forks can actively generate genomic alterations and genetic diversity in normal proliferating cells.},
}
@article {pmid28825126,
year = {2018},
author = {Chi, S and Liu, T and Wang, X and Wang, R and Wang, S and Wang, G and Shan, G and Liu, C},
title = {Functional genomics analysis reveals the biosynthesis pathways of important cellular components (alginate and fucoidan) of Saccharina.},
journal = {Current genetics},
volume = {64},
number = {1},
pages = {259-273},
doi = {10.1007/s00294-017-0733-4},
pmid = {28825126},
issn = {1432-0983},
support = {41376143//National Natural Science Foundation of China/ ; 14-2-4-104-jch//Qingdao applied basic research project/ ; },
mesh = {Alginates/*metabolism ; *Biosynthetic Pathways/genetics ; Computational Biology/methods ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Transfer, Horizontal ; *Genome ; *Genomics/methods ; Glucuronic Acid/metabolism ; Hexuronic Acids/metabolism ; High-Throughput Nucleotide Sequencing ; Phaeophyta/classification/*genetics/*metabolism ; Phylogeny ; Polysaccharides/*metabolism ; Symbiosis/genetics ; Transcriptome ; },
abstract = {Although alginate and fucoidan are unique cellular components and have important biological significance in brown algae, and many possible involved genes are present in brown algal genomes, their functions and regulatory mechanisms have not been fully revealed. Both polysaccharides may play important roles in the evolution of multicellular brown algae, but specific and in-depth studies are still limited. In this study, a functional genomics analysis of alginate and fucoidan biosynthesis routes was conducted in Saccharina, and the key events in these pathways in brown algae were identified. First, genes from different sources, including eukaryotic hosts via endosymbiotic gene transfer and bacteria via horizontal gene transfer, were combined to build a complete pathway framework. Then, a critical event occurred to drive these pathways to have real function: one of the mannose-6-phosphate isomerase homologs that arose by gene duplication subsequently adopted the function of the mannose-1-phosphate guanylyltransferase (MGP) gene, which was absent in algal genomes. Further, downstream pathway genes proceeded with gene expansions and complex transcriptional mechanisms, which may be conducive to the synthesis of alginate and fucoidan with diverse structures and contents depending on the developmental stage, tissue structure, and environmental conditions. This study revealed the alginate and fucoidan synthesis pathways and all included genes from separate phylogenetic sources in brown algae. Enzyme assays confirmed the function of key genes and led to the determination of a substitute for the missing MPG. All gene families had constitutively expressed member(s) to maintain the basic synthesis; and the gene function differentiation, enzyme characterization and gene expression regulation differences separated brown algae from other algae lineages and were considered to be the major driving forces for sophisticated system evolution of brown algae.},
}
@article {pmid28820125,
year = {2017},
author = {Stajich, JE},
title = {Fungal Genomes and Insights into the Evolution of the Kingdom.},
journal = {Microbiology spectrum},
volume = {5},
number = {4},
pages = {},
doi = {10.1128/microbiolspec.FUNK-0055-2016},
pmid = {28820125},
issn = {2165-0497},
support = {S10 OD016290/OD/NIH HHS/United States ; },
mesh = {Evolution, Molecular ; Fungi/*genetics ; Genes, Fungal/*genetics ; Genome, Fungal/*genetics ; },
abstract = {The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute's Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.},
}
@article {pmid28820115,
year = {2017},
author = {Nagy, LG and Tóth, R and Kiss, E and Slot, J and Gácser, A and Kovács, GM},
title = {Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases.},
journal = {Microbiology spectrum},
volume = {5},
number = {4},
pages = {},
doi = {10.1128/microbiolspec.FUNK-0036-2016},
pmid = {28820115},
issn = {2165-0497},
mesh = {*Biological Evolution ; Cell Lineage/genetics ; Evolution, Molecular ; Fruiting Bodies, Fungal/*growth &amp; development ; Fungi/*genetics/*growth &amp; development ; Hyphae/*growth &amp; development ; Mycorrhizae/physiology ; Phylogeny ; Plants/microbiology ; },
abstract = {The fungal lineage is one of the three large eukaryotic lineages that dominate terrestrial ecosystems. They share a common ancestor with animals in the eukaryotic supergroup Opisthokonta and have a deeper common ancestry with plants, yet several phenotypes, such as morphological, physiological, or nutritional traits, make them unique among all living organisms. This article provides an overview of some of the most important fungal traits, how they evolve, and what major genes and gene families contribute to their development. The traits highlighted here represent just a sample of the characteristics that have evolved in fungi, including polarized multicellular growth, fruiting body development, dimorphism, secondary metabolism, wood decay, and mycorrhizae. However, a great number of other important traits also underlie the evolution of the taxonomically and phenotypically hyperdiverse fungal kingdom, which could fill up a volume on its own. After reviewing the evolution of these six well-studied traits in fungi, we discuss how the recurrent evolution of phenotypic similarity, that is, convergent evolution in the broad sense, has shaped their phylogenetic distribution in extant species.},
}
@article {pmid28819830,
year = {2017},
author = {Liu, A and He, F and Gu, X},
title = {Identification and characterization of tyrosine kinases in anole lizard indicate the conserved tyrosine kinase repertoire in vertebrates.},
journal = {Molecular genetics and genomics : MGG},
volume = {292},
number = {6},
pages = {1405-1418},
doi = {10.1007/s00438-017-1356-7},
pmid = {28819830},
issn = {1617-4623},
mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; Lizards/classification/genetics/*metabolism ; Phylogeny ; Protein-Tyrosine Kinases/chemistry/*genetics ; },
abstract = {The tyrosine kinases (TKs) play principal roles in regulation of multicellular aspects of the organism and are implicated in many cancer types and congenital disorders. The anole lizard has recently been introduced as a model organism for laboratory-based studies of organismal function and field studies of ecology and evolution. However, the TK family of anole lizard has not been systematically identified and characterized yet. In this study, we identified 82 TK-encoding genes in the anole lizard genome and classified them into 28 subfamilies through phylogenetic analysis, with no member from ROS and STYK1 subfamilies identified. Although TK domain sequences and domain organization in each subfamily were conserved, the total number of TKs in different species was much variable. In addition, extensive evolutionary analysis in metazoans indicated that TK repertoire in vertebrates tends to be remarkably stable. Phylogenetic analysis of Eph subfamily indicated that the divergence of EphA and EphB occurred prior to the whole genome duplication (WGD) but after the split of Urochordates and vertebrates. Moreover, the expression pattern analysis of lizard TK genes among 9 different tissues showed that 14 TK genes exhibited tissue-specific expression and 6 TK genes were widely expressed. Comparative analysis of TK expression suggested that the tissue specifically expressed genes showed different expression pattern but the widely expressed genes showed similar pattern between anole lizard and human. These results may provide insights into the evolutionary diversification of animal TK genes and would aid future studies on TK protein regulation of key growth and developmental processes.},
}
@article {pmid28804953,
year = {2017},
author = {Gyoja, F},
title = {Basic helix-loop-helix transcription factors in evolution: Roles in development of mesoderm and neural tissues.},
journal = {Genesis (New York, N.Y. : 2000)},
volume = {55},
number = {9},
pages = {},
doi = {10.1002/dvg.23051},
pmid = {28804953},
issn = {1526-968X},
mesh = {Animals ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/chemistry/*genetics/metabolism ; *Evolution, Molecular ; *Gene Expression Regulation, Developmental ; Mesoderm/growth &amp; development/*metabolism ; Nervous System/growth &amp; development/*metabolism ; },
abstract = {Basic helix-loop-helix (bHLH) transcription factors have attracted the attention of developmental and evolutionary biologists for decades because of their conserved functions in mesodermal and neural tissue formation in both vertebrates and fruit flies. Their evolutionary history is of special interest because it will likely provide insights into developmental processes and refinement of metazoan-specific traits. This review briefly considers advances in developmental biological studies on bHLHs/HLHs. I also discuss recent genome-wide surveys and molecular phylogenetic analyses of these factors in a wide range of metazoans. I hypothesize that interactions between metazoan-specific Group A, D, and E bHLH/HLH factors enabled a sophisticated transition system from cell proliferation to differentiation in multicellular development. This control mechanism probably emerged initially to organize a multicellular animal body and was subsequently recruited to form evolutionarily novel tissues, which differentiated during a later ontogenetic phase.},
}
@article {pmid28802203,
year = {2017},
author = {Campbell, S and Aswad, A and Katzourakis, A},
title = {Disentangling the origins of virophages and polintons.},
journal = {Current opinion in virology},
volume = {25},
number = {},
pages = {59-65},
doi = {10.1016/j.coviro.2017.07.011},
pmid = {28802203},
issn = {1879-6265},
mesh = {DNA Transposable Elements/*genetics ; DNA, Viral/genetics ; Eukaryota/*virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Viral ; Giant Viruses/*genetics/physiology ; Phylogeny ; Virophages/*genetics ; Virus Diseases/genetics/transmission ; },
abstract = {Virophages and polintons are part of a complex system that also involves eukaryotes, giant viruses, as well as other viruses and transposable elements. Virophages are cosmopolitan, being found in environments ranging from the Amazon River to Antarctic hypersaline lakes, while polintons are found in many single celled and multicellular eukaryotes. Virophages and polintons have a shared ancestry, but their exact origins are unknown and obscured by antiquity and extensive horizontal gene transfer (HGT). Paleovirology can help disentangle the complicated gene flow between these two, as well as their giant viral and eukaryotic hosts. We outline the evidence and theoretical support for polintons being descended from viruses and not vice versa. In order to disentangle the natural history of polintons and virophages, we suggest that there is much to be gained by embracing rigorous metagenomics and evolutionary analyses. Methods from paleovirology will play a pivotal role in unravelling ancient relationships, HGT and patterns of cross-species transmission.},
}
@article {pmid28774341,
year = {2017},
author = {Riffle, S and Hegde, RS},
title = {Modeling tumor cell adaptations to hypoxia in multicellular tumor spheroids.},
journal = {Journal of experimental &amp; clinical cancer research : CR},
volume = {36},
number = {1},
pages = {102},
doi = {10.1186/s13046-017-0570-9},
pmid = {28774341},
issn = {1756-9966},
support = {R01 CA207068/CA/NCI NIH HHS/United States ; },
mesh = {Cell Line, Tumor ; Cell Proliferation/*drug effects ; Humans ; Spheroids, Cellular/*metabolism ; },
abstract = {Under hypoxic conditions, tumor cells undergo a series of adaptations that promote evolution of a more aggressive tumor phenotype including the activation of DNA damage repair proteins, altered metabolism, and decreased proliferation. Together these changes mitigate the negative impact of oxygen deprivation and allow preservation of genomic integrity and proliferative capacity, thus contributing to tumor growth and metastasis. As a result the presence of a hypoxic microenvironment is considered a negative clinical feature of many solid tumors. Hypoxic niches in tumors also represent a therapeutically privileged environment in which chemo- and radiation therapy is less effective. Although the negative impact of tumor hypoxia has been well established, the precise effect of oxygen deprivation on tumor cell behavior, and the molecular signals that allow a tumor cell to survive in vivo are poorly understood. Multicellular tumor spheroids (MCTS) have been used as an in vitro model for the avascular tumor niche, capable of more accurately recreating tumor genomic profiles and predicting therapeutic response. However, relatively few studies have used MCTS to study the molecular mechanisms driving tumor cell adaptations within the hypoxic tumor environment. Here we will review what is known about cell proliferation, DNA damage repair, and metabolic pathways as modeled in MCTS in comparison to observations made in solid tumors. A more precise definition of the cell populations present within 3D tumor models in vitro could better inform our understanding of the heterogeneity within tumors as well as provide a more representative platform for the testing of therapeutic strategies.},
}
@article {pmid28768887,
year = {2017},
author = {Tong, K and Wang, Y and Su, Z},
title = {Phosphotyrosine signalling and the origin of animal multicellularity.},
journal = {Proceedings. Biological sciences},
volume = {284},
number = {1860},
pages = {},
doi = {10.1098/rspb.2017.0681},
pmid = {28768887},
issn = {1471-2954},
mesh = {Animals ; *Biological Evolution ; *Cell Communication ; Eukaryota/enzymology/*genetics ; Phosphotyrosine/*metabolism ; Protein-Tyrosine Kinases/*metabolism ; *Signal Transduction ; },
abstract = {The evolution of multicellular animals (i.e. metazoans) from a unicellular ancestor is one of the most important yet least understood evolutionary transitions. Historically, given its indispensable functions in intercellular communication and exclusive presence in metazoans, phosphotyrosine (pTyr) signalling was considered a metazoan-specific evolutionary innovation that might have contributed to the origin of metazoan multicellularity. However, recent studies have led to a new understanding of pTyr signalling evolution and its role in the metazoan origin. Sequence analyses have unravelled a much earlier emergence of pTyr signalling in eukaryotic evolution. Even so, several distinct properties of holozoan pTyr signalling may have paved the way for a hypothesized functional transition of pTyr signalling at the multicellular origin, from environmental sensing to intercellular communication, and for it to evolve as a powerful intercellular signalling system for multicellularity. Biochemical analyses of premetazoan pTyr signalling components have further revealed the premetazoan origin of many key features of metazoan pTyr signalling, and the metazoan establishment of others, including the Csk-mediated negative regulation of the activity of Src, a conserved tyrosine kinase in the Holozoa. Finally, potential future directions are discussed, with a stress on the biological functions of premetazoan pTyr signalling via newly developed gene manipulation tools in non-animal holozoans.},
}
@article {pmid28762573,
year = {2017},
author = {Zanchi, C and Johnston, PR and Rolff, J},
title = {Evolution of defence cocktails: Antimicrobial peptide combinations reduce mortality and persistent infection.},
journal = {Molecular ecology},
volume = {26},
number = {19},
pages = {5334-5343},
doi = {10.1111/mec.14267},
pmid = {28762573},
issn = {1365-294X},
mesh = {Animals ; Bacterial Load ; Gene Knockdown Techniques ; Host-Pathogen Interactions ; *Immunity, Innate ; Insect Proteins/genetics/*immunology ; RNA Interference ; Staphylococcal Infections/*immunology ; Staphylococcus aureus ; Tenebrio/*immunology ; },
abstract = {The simultaneous expression of costly immune effectors such as multiple antimicrobial peptides is a hallmark of innate immunity of multicellular organisms, yet the adaptive advantage remains unresolved. Here, we test current hypotheses on the evolution of such defence cocktails. We use RNAi gene knock-down to explore, the effects of three highly expressed antimicrobial peptides, displaying different degrees of activity in vitro against Staphylococcus aureus, during an infection in the beetle Tenebrio molitor. We find that a defensin confers no survival benefit but reduces bacterial loads. A coleoptericin contributes to host survival without affecting bacterial loads. An attacin has no individual effect. Simultaneous knock-down of the defensin with the other AMPs results in increased mortality and elevated bacterial loads. Contrary to common expectations, the effects on host survival and bacterial load can be independent. The expression of multiple AMPs increases host survival and contributes to the control of persisting infections and tolerance. This is an emerging property that explains the adaptive benefit of defence cocktails.},
}
@article {pmid28761011,
year = {2017},
author = {Borges, RM},
title = {Co-niche construction between hosts and symbionts: ideas and evidence.},
journal = {Journal of genetics},
volume = {96},
number = {3},
pages = {483-489},
pmid = {28761011},
issn = {0973-7731},
mesh = {Animals ; Biological Evolution ; *Ecosystem ; Gene Transfer, Horizontal ; Genome/genetics ; Host Specificity/*genetics ; *Inheritance Patterns ; Phenotype ; Symbiosis/*genetics ; },
abstract = {Symbiosis is a process that can generate evolutionary novelties and can extend the phenotypic niche space of organisms. Symbionts can act together with their hosts to co-construct host organs, within which symbionts are housed. Once established within hosts, symbionts can also influence various aspects of host phenotype, such as resource acquisition, protection from predation by acquisition of toxicity, as well as behaviour. Once symbiosis is established, its fidelity between generations must be ensured. Hosts evolve various mechanisms to screen unwanted symbionts and to facilitate faithful transmission of mutualistic partners between generations. Microbes are the most important symbionts that have influenced plant and animal phenotypes; multicellular organisms engage in developmental symbioses with microbes at many stages in ontogeny. The co-construction of niches may result in composite organisms that are physically nested within each other. While it has been advocated that these composite organisms need new evolutionary theories and perspectives to describe their properties and evolutionary trajectories, it appears that standard evolutionary theories are adequate to explore selection pressures on their composite or individual traits. Recent advances in our understanding of composite organisms open up many important questions regarding the stability and transmission of these units.},
}
@article {pmid28755343,
year = {2017},
author = {Abdelbar, OH},
title = {Histological Analysis of the Developmental Stages of Direct Somatic Embryogenesis Induced from In Vitro Leaf Explants of Date Palm.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1637},
number = {},
pages = {145-162},
doi = {10.1007/978-1-4939-7156-5_13},
pmid = {28755343},
issn = {1940-6029},
mesh = {Culture Media/chemistry ; Germination ; In Vitro Techniques ; Inflorescence/*cytology ; Phoeniceae/cytology/*growth &amp; development ; Plant Leaves/growth &amp; development ; Plant Somatic Embryogenesis Techniques/*methods ; Regeneration ; Seeds/growth &amp; development ; },
abstract = {Somatic embryogenesis is an ideal technique for the micropropagation of date palm using different explant tissue; however, histological studies describing the ontogenesis of plant regeneration are limited. This chapter provides a simple protocol for the histological analysis of the successive developmental stages of direct somatic embryogenesis induced from in vitro leaf explants. Direct somatic embryos are obtained from Murashige and Skoog (MS) medium containing 2 mg/L 6-benzylaminopurine. In order to observe the different developmental stages, histological analysis is carried out on samples at 15-day intervals for 60 days. Samples are fixed in formalin acetic alcohol and embedded in paraffin wax. Stain serial transverse and longitudinal sections, 8 μm thick, are stained with safranin-Fast Green. After 15 days on the induction medium, somatic embryos exhibit multicellular origin directly from the procambium cells, whereas the mesophyll and the epidermal cells are not involved in this process. After 2 months, several developmental stages (pre-globular, globular, early bipolar, bipolar, and cotyledonary-shaped) are observed. These embryos germinate after transferring to MS medium without plant growth regulators and rooting on 2 mg/L NAA-containing medium resulting in complete plantlets.},
}
@article {pmid28749982,
year = {2017},
author = {Yoshida, Y and Koutsovoulos, G and Laetsch, DR and Stevens, L and Kumar, S and Horikawa, DD and Ishino, K and Komine, S and Kunieda, T and Tomita, M and Blaxter, M and Arakawa, K},
title = {Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus.},
journal = {PLoS biology},
volume = {15},
number = {7},
pages = {e2002266},
doi = {10.1371/journal.pbio.2002266},
pmid = {28749982},
issn = {1545-7885},
mesh = {Animals ; Base Sequence ; Chromosome Mapping/veterinary ; DNA/chemistry/metabolism ; Desiccation ; Extremophiles/*genetics/growth &amp; development/physiology ; Gene Expression Profiling/veterinary ; *Gene Expression Regulation ; Gene Transfer, Horizontal ; Genetic Linkage ; Genome Size ; Genome-Wide Association Study/veterinary ; Genomic Library ; High-Throughput Nucleotide Sequencing/veterinary ; Multigene Family ; Phylogeny ; Proteome/genetics/*metabolism ; Reproducibility of Results ; Species Specificity ; Tardigrada/*genetics/growth &amp; development/physiology ; },
abstract = {Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.},
}
@article {pmid28741966,
year = {2017},
author = {Bryja, V and Červenka, I and Čajánek, L},
title = {The connections of Wnt pathway components with cell cycle and centrosome: side effects or a hidden logic?.},
journal = {Critical reviews in biochemistry and molecular biology},
volume = {52},
number = {6},
pages = {614-637},
doi = {10.1080/10409238.2017.1350135},
pmid = {28741966},
issn = {1549-7798},
support = {166533//Swiss National Science Foundation/Switzerland ; },
mesh = {Animals ; Cell Communication ; *Cell Cycle ; Cell Polarity ; Centrosome/*metabolism ; Humans ; *Wnt Signaling Pathway ; },
abstract = {Wnt signaling cascade has developed together with multicellularity to orchestrate the development and homeostasis of complex structures. Wnt pathway components - such as β-catenin, Dishevelled (DVL), Lrp6, and Axin-- are often dedicated proteins that emerged in evolution together with the Wnt signaling cascade and are believed to function primarily in the Wnt cascade. It is interesting to see that in recent literature many of these proteins are connected with cellular functions that are more ancient and not limited to multicellular organisms - such as cell cycle regulation, centrosome biology, or cell division. In this review, we summarize the recent literature describing this crosstalk. Specifically, we attempt to find the answers to the following questions: Is the response to Wnt ligands regulated by the cell cycle? Is the centrosome and/or cilium required to activate the Wnt pathway? How do Wnt pathway components regulate the centrosomal cycle and cilia formation and function? We critically review the evidence that describes how these connections are regulated and how they help to integrate cell-to-cell communication with the cell and the centrosomal cycle in order to achieve a fine-tuned, physiological response.},
}
@article {pmid28726632,
year = {2017},
author = {Grau-Bové, X and Torruella, G and Donachie, S and Suga, H and Leonard, G and Richards, TA and Ruiz-Trillo, I},
title = {Dynamics of genomic innovation in the unicellular ancestry of animals.},
journal = {eLife},
volume = {6},
number = {},
pages = {},
doi = {10.7554/eLife.26036},
pmid = {28726632},
issn = {2050-084X},
support = {616960//European Research Council/International ; },
mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; *Genome, Protozoan ; Genomics ; },
abstract = {Which genomic innovations underpinned the origin of multicellular animals is still an open debate. Here, we investigate this question by reconstructing the genome architecture and gene family diversity of ancestral premetazoans, aiming to date the emergence of animal-like traits. Our comparative analysis involves genomes from animals and their closest unicellular relatives (the Holozoa), including four new genomes: three Ichthyosporea and Corallochytrium limacisporum. Here, we show that the earliest animals were shaped by dynamic changes in genome architecture before the emergence of multicellularity: an early burst of gene diversity in the ancestor of Holozoa, enriched in transcription factors and cell adhesion machinery, was followed by multiple and differently-timed episodes of synteny disruption, intron gain and genome expansions. Thus, the foundations of animal genome architecture were laid before the origin of complex multicellularity - highlighting the necessity of a unicellular perspective to understand early animal evolution.},
}
@article {pmid28716924,
year = {2017},
author = {Brawley, SH and Blouin, NA and Ficko-Blean, E and Wheeler, GL and Lohr, M and Goodson, HV and Jenkins, JW and Blaby-Haas, CE and Helliwell, KE and Chan, CX and Marriage, TN and Bhattacharya, D and Klein, AS and Badis, Y and Brodie, J and Cao, Y and Collén, J and Dittami, SM and Gachon, CMM and Green, BR and Karpowicz, SJ and Kim, JW and Kudahl, UJ and Lin, S and Michel, G and Mittag, M and Olson, BJSC and Pangilinan, JL and Peng, Y and Qiu, H and Shu, S and Singer, JT and Smith, AG and Sprecher, BN and Wagner, V and Wang, W and Wang, ZY and Yan, J and Yarish, C and Zäuner-Riek, S and Zhuang, Y and Zou, Y and Lindquist, EA and Grimwood, J and Barry, KW and Rokhsar, DS and Schmutz, J and Stiller, JW and Grossman, AR and Prochnik, SE},
title = {Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta).},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {114},
number = {31},
pages = {E6361-E6370},
doi = {10.1073/pnas.1703088114},
pmid = {28716924},
issn = {1091-6490},
support = {P20 GM103418/GM/NIGMS NIH HHS/United States ; P20 GM103638/GM/NIGMS NIH HHS/United States ; BB/1013164/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Actins/genetics ; Calcium Signaling/genetics ; Cell Cycle/genetics ; Cell Wall/genetics/metabolism ; Chromatin/genetics ; Cytoskeleton/*genetics ; *Evolution, Molecular ; Genome, Plant/*genetics ; Kinesin/genetics ; Phylogeny ; Porphyra/*cytology/*genetics ; },
abstract = {Porphyra umbilicalis (laver) belongs to an ancient group of red algae (Bangiophyceae), is harvested for human food, and thrives in the harsh conditions of the upper intertidal zone. Here we present the 87.7-Mbp haploid Porphyra genome (65.8% G + C content, 13,125 gene loci) and elucidate traits that inform our understanding of the biology of red algae as one of the few multicellular eukaryotic lineages. Novel features of the Porphyra genome shared by other red algae relate to the cytoskeleton, calcium signaling, the cell cycle, and stress-tolerance mechanisms including photoprotection. Cytoskeletal motor proteins in Porphyra are restricted to a small set of kinesins that appear to be the only universal cytoskeletal motors within the red algae. Dynein motors are absent, and most red algae, including Porphyra, lack myosin. This surprisingly minimal cytoskeleton offers a potential explanation for why red algal cells and multicellular structures are more limited in size than in most multicellular lineages. Additional discoveries further relating to the stress tolerance of bangiophytes include ancestral enzymes for sulfation of the hydrophilic galactan-rich cell wall, evidence for mannan synthesis that originated before the divergence of green and red algae, and a high capacity for nutrient uptake. Our analyses provide a comprehensive understanding of the red algae, which are both commercially important and have played a major role in the evolution of other algal groups through secondary endosymbioses.},
}
@article {pmid28714591,
year = {2017},
author = {Kloesener, MH and Bose, J and Schulte, RD},
title = {Experimental evolution with a multicellular host causes diversification within and between microbial parasite populations-Differences in emerging phenotypes of two different parasite strains.},
journal = {Evolution; international journal of organic evolution},
volume = {71},
number = {9},
pages = {2194-2205},
doi = {10.1111/evo.13306},
pmid = {28714591},
issn = {1558-5646},
mesh = {Animals ; *Bacillus thuringiensis ; Biological Evolution ; Caenorhabditis elegans/parasitology ; Genotype ; *Host-Parasite Interactions ; Parasites ; Phenotype ; Selection, Genetic ; },
abstract = {Host-parasite coevolution is predicted to have complex evolutionary consequences, potentially leading to the emergence of genetic and phenotypic diversity for both antagonists. However, little is known about variation in phenotypic responses to coevolution between different parasite strains exposed to the same experimental conditions. We infected Caenorhabditis elegans with one of two strains of Bacillus thuringiensis and either allowed the host and the parasite to experimentally coevolve (coevolution treatment) or allowed only the parasite to adapt to the host (one-sided parasite adaptation). By isolating single parasite clones from evolved populations, we found phenotypic diversification of the ancestral strain into distinct clones, which varied in virulence toward ancestral hosts and competitive ability against other parasite genotypes. Parasite phenotypes differed remarkably not only between the two strains, but also between and within different replicate populations, indicating diversification of the clonal population caused by selection. This study highlights that the evolutionary selection pressure mediated by a multicellular host causes phenotypic diversification, but not necessarily with the same phenotypic outcome for different parasite strains.},
}
@article {pmid28704372,
year = {2017},
author = {Trail, F and Wang, Z and Stefanko, K and Cubba, C and Townsend, JP},
title = {The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi.},
journal = {PLoS genetics},
volume = {13},
number = {7},
pages = {e1006867},
doi = {10.1371/journal.pgen.1006867},
pmid = {28704372},
issn = {1553-7404},
mesh = {Bayes Theorem ; *Biological Evolution ; Fruiting Bodies, Fungal/genetics ; Fungi/genetics ; Gene Expression Regulation, Fungal/genetics ; Gene Knockout Techniques ; Genome, Fungal/*genetics ; Neurospora crassa/genetics ; Phenotype ; Phylogeny ; Sex Differentiation/*genetics ; Sordariales/genetics/growth &amp; development ; Transcriptome/*genetics ; },
abstract = {Changes in gene expression have been hypothesized to play an important role in the evolution of divergent morphologies. To test this hypothesis in a model system, we examined differences in fruiting body morphology of five filamentous fungi in the Sordariomycetes, culturing them in a common garden environment and profiling genome-wide gene expression at five developmental stages. We reconstructed ancestral gene expression phenotypes, identifying genes with the largest evolved increases in gene expression across development. Conducting knockouts and performing phenotypic analysis in two divergent species typically demonstrated altered fruiting body development in the species that had evolved increased expression. Our evolutionary approach to finding relevant genes proved far more efficient than other gene deletion studies targeting whole genomes or gene families. Combining gene expression measurements with knockout phenotypes facilitated the refinement of Bayesian networks of the genes underlying fruiting body development, regulation of which is one of the least understood processes of multicellular development.},
}
@article {pmid28700638,
year = {2017},
author = {Ashrafi, S and Helaly, S and Schroers, HJ and Stadler, M and Richert-Poeggeler, KR and Dababat, AA and Maier, W},
title = {Ijuhya vitellina sp. nov., a novel source for chaetoglobosin A, is a destructive parasite of the cereal cyst nematode Heterodera filipjevi.},
journal = {PloS one},
volume = {12},
number = {7},
pages = {e0180032},
doi = {10.1371/journal.pone.0180032},
pmid = {28700638},
issn = {1932-6203},
mesh = {Animals ; Hyphae/growth &amp; development ; Hypocreales/classification/genetics/metabolism/*pathogenicity ; Indole Alkaloids/*metabolism ; Oocytes/microbiology ; Phylogeny ; Tylenchoidea/growth &amp; development/microbiology ; },
abstract = {Cyst nematodes are globally important pathogens in agriculture. Their sedentary lifestyle and long-term association with the roots of host plants render cyst nematodes especially good targets for attack by parasitic fungi. In this context fungi were specifically isolated from nematode eggs of the cereal cyst nematode Heterodera filipjevi. Here, Ijuhya vitellina (Ascomycota, Hypocreales, Bionectriaceae), encountered in wheat fields in Turkey, is newly described on the basis of phylogenetic analyses, morphological characters and life-style related inferences. The species destructively parasitises eggs inside cysts of H. filipjevi. The parasitism was reproduced in in vitro studies. Infected eggs were found to harbour microsclerotia produced by I. vitellina that resemble long-term survival structures also known from other ascomycetes. Microsclerotia were also formed by this species in pure cultures obtained from both, solitarily isolated infected eggs obtained from fields and artificially infected eggs. Hyphae penetrating the eggshell colonised the interior of eggs and became transformed into multicellular, chlamydospore-like structures that developed into microsclerotia. When isolated on artificial media, microsclerotia germinated to produce multiple emerging hyphae. The specific nature of morphological structures produced by I. vitellina inside nematode eggs is interpreted as a unique mode of interaction allowing long-term survival of the fungus inside nematode cysts that are known to survive periods of drought or other harsh environmental conditions. Generic classification of the new species is based on molecular phylogenetic inferences using five different gene regions. I. vitellina is the only species of the genus known to parasitise nematodes and produce microsclerotia. Metabolomic analyses revealed that within the Ijuhya species studied here, only I. vitellina produces chaetoglobosin A and its derivate 19-O-acetylchaetoglobosin A. Nematicidal and nematode-inhibiting activities of these compounds have been demonstrated suggesting that the production of these compounds may represent an adaptation to nematode parasitism.},
}
@article {pmid28683136,
year = {2017},
author = {Ballinger, MJ and Perlman, SJ},
title = {Generality of toxins in defensive symbiosis: Ribosome-inactivating proteins and defense against parasitic wasps in Drosophila.},
journal = {PLoS pathogens},
volume = {13},
number = {7},
pages = {e1006431},
doi = {10.1371/journal.ppat.1006431},
pmid = {28683136},
issn = {1553-7374},
mesh = {Animals ; Bacterial Proteins/genetics/metabolism/*toxicity ; Bacterial Toxins/genetics/metabolism/*toxicity ; Biological Evolution ; Drosophila/genetics/*microbiology/*parasitology/physiology ; Larva/genetics/microbiology/parasitology/physiology ; Ribosome Inactivating Proteins/genetics/metabolism/*toxicity ; Spiroplasma/genetics/*metabolism ; *Symbiosis ; Wasps/*drug effects/physiology ; },
abstract = {While it has become increasingly clear that multicellular organisms often harbor microbial symbionts that protect their hosts against natural enemies, the mechanistic underpinnings underlying most defensive symbioses are largely unknown. Spiroplasma bacteria are widespread associates of terrestrial arthropods, and include strains that protect diverse Drosophila flies against parasitic wasps and nematodes. Recent work implicated a ribosome-inactivating protein (RIP) encoded by Spiroplasma, and related to Shiga-like toxins in enterohemorrhagic Escherichia coli, in defense against a virulent parasitic nematode in the woodland fly, Drosophila neotestacea. Here we test the generality of RIP-mediated protection by examining whether Spiroplasma RIPs also play a role in wasp protection, in D. melanogaster and D. neotestacea. We find strong evidence for a major role of RIPs, with ribosomal RNA (rRNA) from the larval endoparasitic wasps, Leptopilina heterotoma and Leptopilina boulardi, exhibiting the hallmarks of RIP activity. In Spiroplasma-containing hosts, parasitic wasp ribosomes show abundant site-specific depurination in the α-sarcin/ricin loop of the 28S rRNA, with depurination occurring soon after wasp eggs hatch inside fly larvae. Interestingly, we found that the pupal ectoparasitic wasp, Pachycrepoideus vindemmiae, escapes protection by Spiroplasma, and its ribosomes do not show high levels of depurination. We also show that fly ribosomes show little evidence of targeting by RIPs. Finally, we find that the genome of D. neotestacea's defensive Spiroplasma encodes a diverse repertoire of RIP genes, which are differ in abundance. This work suggests that specificity of defensive symbionts against different natural enemies may be driven by the evolution of toxin repertoires, and that toxin diversity may play a role in shaping host-symbiont-enemy interactions.},
}
@article {pmid28682226,
year = {2017},
author = {El Kafsi, H and Gorochov, G and Larsen, M},
title = {.},
journal = {Biologie aujourd'hui},
volume = {211},
number = {1},
pages = {39-49},
doi = {10.1051/jbio/2017010},
pmid = {28682226},
issn = {2105-0686},
mesh = {Animals ; Gastrointestinal Microbiome/*genetics/*immunology ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Immune System/metabolism/*physiology ; Immunity, Cellular/physiology ; Immunity, Humoral/physiology ; Immunoglobulin A, Secretory/physiology ; Inheritance Patterns ; Symbiosis/*genetics/*immunology ; },
abstract = {Genetic evolution of multicellular organisms occurred as a response to environmental challenges, in particular competition for nutrients, climatic change, physical and chemical stressors and pathogens. However organism fitness depends on both the efficiency of its defences and its capacities for benefiting from its symbiotic organisms. Indeed microbes not only engender pathogenies, but enable efficient uptake of host non-self biodegradable nutriments. Furthermore, microbes play an important role in the development of host immunity. We shall review here the associations between some specific genes of the host, microbiota and the immune system. Recent genome-wide association studies disclose that symbiosis between host and microbiota results from a stringent genetic co-evolution. On the other hand, a microbe subset isolated from murine and human microbiotes has been identified on the basis of its interaction with both the host genetics and immunity. Remarkably, microbes which have two such connections are taxonomically related. The best performing bacterial genuses in these two perspectives are Bifidobacterium, Lactobacillus and Akkermansia. We conclude that future therapies targeting microbiota within the framework of chronic inflammatory diseases must consider together host immune and genetic characters associated with microbiota homeostasis.},
}
@article {pmid28681487,
year = {2017},
author = {Wloch-Salamon, DM and Fisher, RM and Regenberg, B},
title = {Division of labour in the yeast: Saccharomyces cerevisiae.},
journal = {Yeast (Chichester, England)},
volume = {34},
number = {10},
pages = {399-406},
doi = {10.1002/yea.3241},
pmid = {28681487},
issn = {1097-0061},
mesh = {Adaptation, Physiological ; Apoptosis ; Biofilms/growth &amp; development ; Biological Evolution ; Phenotype ; Resting Phase, Cell Cycle ; Saccharomyces cerevisiae/genetics/*physiology ; },
abstract = {Division of labour between different specialized cell types is a central part of how we describe complexity in multicellular organisms. However, it is increasingly being recognized that division of labour also plays an important role in the lives of predominantly unicellular organisms. Saccharomyces cerevisiae displays several phenotypes that could be considered a division of labour, including quiescence, apoptosis and biofilm formation, but they have not been explicitly treated as such. We discuss each of these examples, using a definition of division of labour that involves phenotypic variation between cells within a population, cooperation between cells performing different tasks and maximization of the inclusive fitness of all cells involved. We then propose future research directions and possible experimental tests using S. cerevisiae as a model organism for understanding the genetic mechanisms and selective pressures that can lead to the evolution of the very first stages of a division of labour. Copyright © 2017 John Wiley &amp; Sons, Ltd.},
}
@article {pmid28673540,
year = {2017},
author = {Song, Y and Botvinnik, OB and Lovci, MT and Kakaradov, B and Liu, P and Xu, JL and Yeo, GW},
title = {Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation.},
journal = {Molecular cell},
volume = {67},
number = {1},
pages = {148-161.e5},
doi = {10.1016/j.molcel.2017.06.003},
pmid = {28673540},
issn = {1097-4164},
support = {R01 AI095277/AI/NIAID NIH HHS/United States ; R01 AI123202/AI/NIAID NIH HHS/United States ; P30 NS047101/NS/NINDS NIH HHS/United States ; R01 HG004659/HG/NHGRI NIH HHS/United States ; U19 MH107367/MH/NIMH NIH HHS/United States ; R01 HD085902/HD/NICHD NIH HHS/United States ; R01 NS075449/NS/NINDS NIH HHS/United States ; },
mesh = {Algorithms ; *Alternative Splicing ; Bayes Theorem ; Cell Line ; Computer Simulation ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Humans ; Kinetics ; Male ; Models, Genetic ; Nerve Tissue Proteins/*biosynthesis/genetics ; Neural Stem Cells/*metabolism ; *Neurogenesis ; Neurons/*metabolism ; Phenotype ; Pluripotent Stem Cells/*metabolism ; RNA, Messenger/genetics/*metabolism ; *Single-Cell Analysis ; },
abstract = {Alternative splicing (AS) generates isoform diversity for cellular identity and homeostasis in multicellular life. Although AS variation has been observed among single cells, little is known about the biological or evolutionary significance of such variation. We developed Expedition, a computational framework consisting of outrigger, a de novo splice graph transversal algorithm to detect AS; anchor, a Bayesian approach to assign modalities; and bonvoyage, a visualization tool using non-negative matrix factorization to display modality changes. Applying Expedition to single pluripotent stem cells undergoing neuronal differentiation, we discover that up to 20% of AS exons exhibit bimodality. Bimodal exons are flanked by more conserved intronic sequences harboring distinct cis-regulatory motifs, constitute much of cell-type-specific splicing, are highly dynamic during cellular transitions, preserve reading frame, and reveal intricacy of cell states invisible to conventional gene expression analysis. Systematic AS characterization in single cells redefines our understanding of AS complexity in cell biology.},
}
@article {pmid28669817,
year = {2017},
author = {Timoshevskiy, VA and Lampman, RT and Hess, JE and Porter, LL and Smith, JJ},
title = {Deep ancestry of programmed genome rearrangement in lampreys.},
journal = {Developmental biology},
volume = {429},
number = {1},
pages = {31-34},
doi = {10.1016/j.ydbio.2017.06.032},
pmid = {28669817},
issn = {1095-564X},
support = {R01 GM104123/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; DNA/metabolism ; Gene Rearrangement/*genetics ; *Genome ; Germ Cells/metabolism ; Lampreys/*genetics ; *Phylogeny ; },
abstract = {In most multicellular organisms, the structure and content of the genome is rigorously maintained over the course of development. However some species have evolved genome biologies that permit, or require, developmentally regulated changes in the physical structure and content of the genome (programmed genome rearrangement: PGR). Relatively few vertebrates are known to undergo PGR, although all agnathans surveyed to date (several hagfish and one lamprey: Petromyzon marinus) show evidence of large scale PGR. To further resolve the ancestry of PGR within vertebrates, we developed probes that allow simultaneous tracking of nearly all sequences eliminated by PGR in P. marinus and a second lamprey species (Entosphenus tridentatus). These comparative analyses reveal conserved subcellular structures (lagging chromatin and micronuclei) associated with PGR and provide the first comparative embryological evidence in support of the idea that PGR represents an ancient and evolutionarily stable strategy for regulating inherent developmental/genetic conflicts between germline and soma.},
}
@article {pmid28663071,
year = {2017},
author = {Rosa-Fernandes, L and Maselli, LMF and Maeda, NY and Palmisano, G and Bydlowski, SP},
title = {Outside-in, inside-out: Proteomic analysis of endothelial stress mediated by 7-ketocholesterol.},
journal = {Chemistry and physics of lipids},
volume = {207},
number = {Pt B},
pages = {231-238},
doi = {10.1016/j.chemphyslip.2017.06.008},
pmid = {28663071},
issn = {1873-2941},
mesh = {Cell Survival/drug effects ; Cells, Cultured ; Computational Biology ; Dose-Response Relationship, Drug ; Human Umbilical Vein Endothelial Cells/*drug effects ; Humans ; Ketocholesterols/*pharmacology ; Mass Spectrometry ; Oxidative Stress/*drug effects ; Platelet Aggregation/drug effects ; *Proteomics ; Structure-Activity Relationship ; },
abstract = {Oxysterols are cholesterol oxidation products formed through enzymatic or autoxidation mechanisms. 7-ketocholeterol (7KC) is one of most abundant oxysterols found in atherosclerotic lesions. Its role in atherosclerosis pathogenesis has been broadly studied in a variety of models. The arterial microenvironment is a multicellular dynamic compartment that, among other systemic factors, is continuously stimulated by 7KC. Endothelial cells have a key role on that environment, being in intimate contact with both the blood stream and the vessel wall, the site of disease origin. 7KC has been shown to promote endothelial cell death and/or dysfunction, depending on its concentration. However, its contribution to the cell microenvironment through cell stimulation has not received much attention. Here we applied mass spectrometry-based proteomics followed by bioinformatics workflow to analyze the effect of a non-toxic 7KC concentration on endothelial cell protein expression and secretion in vitro. Trypsin digests were prepared from the secretome of the endothelial cells and from the total cell pellet after 24h exposure to 7KC. All samples were analyzed by high resolution and accurate mass nano-LC MS/MS. After database search and statistical analysis, differentially expressed proteins were selected for further studies. Our workflow identified 1805 secreted proteins and 2203 intracellular proteins, and of these, 48 and 53, respectively, were regulated. Regulated proteins upon 7KC exposure are involved in unfolded protein response, vascular homeostasis, and reduced control of angiogenesis. Moreover, blood coagulation was another main pathway regulated through Tissue Factor Pathway Inhibitor (TFPI), an antithrombotic agent associated with coronary disease that we found to be more than 2 times downregulated. Taken together, these data show differential endothelial protein regulation and secretion upon 7KC exposure for short time periods under non-toxic conditions. Herewith, these data support the role of 7KC in atherosclerosis pathophysiology and thus reinforce the deleterious effect of endothelial cells stress in the arterial microenvironment.},
}
@article {pmid28648822,
year = {2017},
author = {Hehenberger, E and Tikhonenkov, DV and Kolisko, M and Del Campo, J and Esaulov, AS and Mylnikov, AP and Keeling, PJ},
title = {Novel Predators Reshape Holozoan Phylogeny and Reveal the Presence of a Two-Component Signaling System in the Ancestor of Animals.},
journal = {Current biology : CB},
volume = {27},
number = {13},
pages = {2043-2050.e6},
doi = {10.1016/j.cub.2017.06.006},
pmid = {28648822},
issn = {1879-0445},
mesh = {Animals ; *Biological Evolution ; Eukaryota/*classification/genetics/*physiology ; Evolution, Molecular ; Fetal Proteins/genetics/metabolism ; *Predatory Behavior ; RNA, Ribosomal, 18S/genetics ; *Signal Transduction ; T-Box Domain Proteins/genetics/metabolism ; },
abstract = {Our understanding of the origin of animals has been transformed by characterizing their most closely related, unicellular sisters: the choanoflagellates, filastereans, and ichthyosporeans. Together with animals, these lineages make up the Holozoa [1, 2]. Many traits previously considered &quot;animal specific&quot; were subsequently found in other holozoans [3, 4], showing that they evolved before animals, although exactly when is currently uncertain because several key relationships remain unresolved [2, 5]. Here we report the morphology and transcriptome sequencing from three novel unicellular holozoans: Pigoraptor vietnamica and Pigoraptor chileana, which are related to filastereans, and Syssomonas multiformis, which forms a new lineage with Corallochytrium in phylogenomic analyses. All three species are predatory flagellates that feed on large eukaryotic prey, and all three also appear to exhibit complex life histories with several distinct stages, including multicellular clusters. Examination of genes associated with multicellularity in animals showed that the new filastereans contain a cell-adhesion gene repertoire similar to those of other species in this group. Syssomonas multiformis possessed a smaller complement overall but does encode genes absent from the earlier-branching ichthyosporeans. Analysis of the T-box transcription factor domain showed expansion of T-box transcription factors based on combination with a non-T-box domain (a receiver domain), which has not been described outside of vertebrates. This domain and other domains we identified in all unicellular holozoans are part of the two-component signaling system that has been lost in animals, suggesting the continued use of this system in the closest relatives of animals and emphasizing the importance of studying loss of function as well as gain in major evolutionary transitions.},
}
@article {pmid28637850,
year = {2017},
author = {Heim, NA and Payne, JL and Finnegan, S and Knope, ML and Kowalewski, M and Lyons, SK and McShea, DW and Novack-Gottshall, PM and Smith, FA and Wang, SC},
title = {Hierarchical complexity and the size limits of life.},
journal = {Proceedings. Biological sciences},
volume = {284},
number = {1857},
pages = {},
doi = {10.1098/rspb.2017.1039},
pmid = {28637850},
issn = {1471-2954},
mesh = {*Biological Evolution ; Earth (Planet) ; *Eukaryota ; *Prokaryotic Cells ; },
abstract = {Over the past 3.8 billion years, the maximum size of life has increased by approximately 18 orders of magnitude. Much of this increase is associated with two major evolutionary innovations: the evolution of eukaryotes from prokaryotic cells approximately 1.9 billion years ago (Ga), and multicellular life diversifying from unicellular ancestors approximately 0.6 Ga. However, the quantitative relationship between organismal size and structural complexity remains poorly documented. We assessed this relationship using a comprehensive dataset that includes organismal size and level of biological complexity for 11 172 extant genera. We find that the distributions of sizes within complexity levels are unimodal, whereas the aggregate distribution is multimodal. Moreover, both the mean size and the range of size occupied increases with each additional level of complexity. Increases in size range are non-symmetric: the maximum organismal size increases more than the minimum. The majority of the observed increase in organismal size over the history of life on the Earth is accounted for by two discrete jumps in complexity rather than evolutionary trends within levels of complexity. Our results provide quantitative support for an evolutionary expansion away from a minimal size constraint and suggest a fundamental rescaling of the constraints on minimal and maximal size as biological complexity increases.},
}
@article {pmid28637420,
year = {2017},
author = {Baig, AM and Rana, Z and Tariq, SS and Ahmad, HR},
title = {Bioinformatic Insights on Target Receptors of Amiodarone in Human and Acanthamoeba castellanii.},
journal = {Infectious disorders drug targets},
volume = {17},
number = {3},
pages = {160-177},
doi = {10.2174/1871526517666170622075154},
pmid = {28637420},
issn = {2212-3989},
mesh = {Acanthamoeba castellanii/chemistry/*drug effects/metabolism ; Amiodarone/*metabolism/*pharmacology ; Calcium Channels/*chemistry/genetics ; *Computational Biology ; Cytochrome P-450 CYP3A/*chemistry/genetics ; Humans ; Intramolecular Transferases/chemistry/genetics ; Ligands ; Models, Molecular ; Protein Binding ; Protozoan Proteins/*chemistry/metabolism ; Sequence Homology, Amino Acid ; Trypanosoma cruzi/chemistry/drug effects/genetics ; },
abstract = {BACKGROUND: Amiodarone is prescribed for certain cardiac arrhythmias in current medical practice. The drug targets and inhibits voltage dependent sodium (Na+ v), calcium (Ca+2 v), potassium (K+ v) channels, enzymes like cytochrome P450 and oxidosqualene cyclase. Past studies have shown that amiodarone exerts antiparasitic effects against Trypanosoma cruzi and Acanthamoeba castellanii.<br><br>OBJECTIVES: The presence of aforementioned targets and the type of cell death induced by amiodarone in pathogenic eukaryotes like Acanthamoeba castellanii remains to be established. We inferred the presence of homologous targets of amiodarone in A. castellanii compared with humans.<br><br>METHODS: This study used bioinformatics exploration for amino acid sequence homology, ligand binding attribute predictions, 3D structural model development, and experimental assays that highlight similarity between certain target proteins in Acanthamoeba as compared to humans.<br><br>RESULTS: The sequence identity scores for amino acids and 3D models show that A. castellanii expresses similar types of targets of amiodarone like Na+ v - K+1 v channels, cytochrome P450 3A4, and lanosterol synthase (oxidosqualene cyclase). We show that even though human like L-type and two pore Ca+2 channels are present in A. castellanii, there was no evidence of the expression of T-type voltage dependent Ca+2 channels. Growth assays showed amoebicidal and amoebistatic effects at doses of 40-80μg/ml.<br><br>CONCLUSION: The existing bioinformatics tools, ligand binding attribute prediction, and model building offer a specific method to establish homology of proteins, discover drug targets, and facilitate the investigation of the evolution of several types of cardinal ion channels from unicellular eukaryotes to multicellular species as humans.},
}
@article {pmid28631149,
year = {2017},
author = {Krsmanovic, P},
title = {Vigor of survival determinism: subtle evolutionary gradualism interspersed with robust phylogenetic leaping.},
journal = {Theory in biosciences = Theorie in den Biowissenschaften},
volume = {136},
number = {3-4},
pages = {141-151},
doi = {10.1007/s12064-017-0251-4},
pmid = {28631149},
issn = {1611-7530},
mesh = {Animals ; *Biological Evolution ; Caenorhabditis elegans ; Cell Lineage ; Drosophila melanogaster ; Female ; Genetic Drift ; Genetic Variation ; Genetics, Population ; Genomics ; Male ; Models, Genetic ; Mutagenesis ; Mutation ; *Phylogeny ; Saccharomyces cerevisiae ; *Selection, Genetic ; Stochastic Processes ; },
abstract = {Discussions of the survival determinism concept have previously focused on its primary role in the evolution of early unicellular organisms in the light of findings which have been reported on a number of diseases. The rationale for such parallel was in the view according to which multicellular organisms could be regarded as sophisticated colonies of semi-autonomous, single-celled entities, whereby various diseases were described as conditions arising upon the activation of the respective survival mechanisms in a milieu unsuitable for such robust stress response. The cellular mechanisms that were discussed in these contexts have been known to play various roles in other biological processes. The proposed notion could thereby be further extended to discussion on mechanisms for the implementation of the respective survival pathways in the development of metazoa, considering that they would have been propagated in their evolution for so long. This manuscript first presents a concise overview of the model previously discussed, followed by the discussion on the role of respective mechanism(s) in origins and development of metazoa. Finally, a reflection on the concept in relation to the prominent evolutionary models is put forward to illustrate a broader context of what is being discussed.},
}
@article {pmid28630027,
year = {2017},
author = {Sapir, L and Tzlil, S},
title = {Talking over the extracellular matrix: How do cells communicate mechanically?.},
journal = {Seminars in cell &amp; developmental biology},
volume = {71},
number = {},
pages = {99-105},
doi = {10.1016/j.semcdb.2017.06.010},
pmid = {28630027},
issn = {1096-3634},
mesh = {Animals ; Biomechanical Phenomena ; Cell Communication ; Cell Movement ; *Extracellular Matrix ; Humans ; Myocardium/cytology ; },
abstract = {Communication between cells enables them to coordinate their activity and is crucial for the differentiation, development, and function of tissues and multicellular organisms. Cell-cell communication is discussed almost exclusively as having a chemical or electrical origin. Only recently, a new mode of cell communication was elucidated: mechanical communication through the extracellular matrix (ECM). Cells can communicate mechanically by responding either to mechanical deformations generated by their neighbors or to a change in the mechanical properties of the ECM induced by a neighboring cell. This newly resolved mode of communication possesses unique features that complement the cellular ability to receive and share information, and to consequently act in a cooperative way with surrounding cells. Herein, we review several examples of mechanical communication, discuss their unique properties, and comment on the major challenges facing the field.},
}
@article {pmid28629791,
year = {2017},
author = {Xie, N and Ruprich-Robert, G and Chapeland-Leclerc, F and Coppin, E and Lalucque, H and Brun, S and Debuchy, R and Silar, P},
title = {Inositol-phosphate signaling as mediator for growth and sexual reproduction in Podospora anserina.},
journal = {Developmental biology},
volume = {429},
number = {1},
pages = {285-305},
doi = {10.1016/j.ydbio.2017.06.017},
pmid = {28629791},
issn = {1095-564X},
mesh = {Amino Acid Sequence ; Cell Nucleus/metabolism ; Fertility ; Fruiting Bodies, Fungal/metabolism ; Fungal Proteins/chemistry/metabolism ; Genes, Fungal ; Green Fluorescent Proteins/metabolism ; Inositol/metabolism ; Inositol Phosphates/*metabolism ; MAP Kinase Signaling System ; Mosaicism ; Mutation/genetics ; Phenotype ; Pigments, Biological/metabolism ; Podospora/enzymology/genetics/*growth &amp; development/*metabolism ; Protein Transport ; Reproduction ; *Signal Transduction ; Sordariales/metabolism ; Spores, Fungal/metabolism ; Temperature ; Zygote/metabolism ; },
abstract = {The molecular pathways involved in the development of multicellular fruiting bodies in fungi are still not well known. Especially, the interplay between the mycelium, the female tissues and the zygotic tissues of the fruiting bodies is poorly documented. Here, we describe PM154, a new strain of the model ascomycetes Podospora anserina able to mate with itself and that enabled the easy recovery of new mutants affected in fruiting body development. By complete genome sequencing of spod1, one of the new mutants, we identified an inositol phosphate polykinase gene as essential, especially for fruiting body development. A factor present in the wild type and diffusible in mutant hyphae was able to induce the development of the maternal tissues of the fruiting body in spod1, but failed to promote complete development of the zygotic ones. Addition of myo-inositol in the growth medium was able to increase the number of developing fruiting bodies in the wild type, but not in spod1. Overall, the data indicated that inositol and inositol polyphosphates were involved in promoting fruiting body maturation, but also in regulating the number of fruiting bodies that developed after fertilization. The same effect of inositol was seen in two other fungi, Sordaria macrospora and Chaetomium globosum. Key role of the inositol polyphosphate pathway during fruiting body maturation appears thus conserved during the evolution of Sordariales fungi.},
}
@article {pmid28627239,
year = {2017},
author = {Csaba, G},
title = {Complex multicellular functions at a unicellular eukaryote level: Learning, memory, and immunity.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {64},
number = {2},
pages = {105-120},
doi = {10.1556/030.64.2017.013},
pmid = {28627239},
issn = {1217-8950},
mesh = {Animals ; Eukaryota/genetics/*immunology/*physiology ; Humans ; Learning ; Memory ; },
abstract = {According to experimental data, eukaryote unicellulars are able to learn, have immunity and memory. Learning is carried out in a very primitive form, and the memory is not neural but an epigenetic one. However, this epigenetic memory, which is well justified by the presence and manifestation of hormonal imprinting, is strong and permanent in the life of cell and also in its progenies. This memory is epigenetically executed by the alteration and fixation of methylation pattern of genes without changes in base sequences. The immunity of unicellulars is based on self/non-self discrimination, which leads to the destruction of non-self invaders and utilization of them as nourishment (by phagocytosis). The tools of learning, memory, and immunity of unicellulars are uniformly found in plasma membrane receptors, which formed under the effect of dynamic receptor pattern generation, suggested by Koch et al., and this is the basis of hormonal imprinting, by which the encounter between a chemical substance and the cell is specifically memorized. The receptors and imprinting are also used in the later steps of evolution up to mammals (including man) in each mentioned functions. This means that learning, memory, and immunity can be deduced to a unicellular eukaryote level.},
}
@article {pmid28605523,
year = {2017},
author = {Vergara, Z and Sequeira-Mendes, J and Morata, J and Peiró, R and Hénaff, E and Costas, C and Casacuberta, JM and Gutierrez, C},
title = {Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin.},
journal = {Nucleic acids research},
volume = {45},
number = {14},
pages = {8358-8368},
doi = {10.1093/nar/gkx524},
pmid = {28605523},
issn = {1362-4962},
mesh = {Arabidopsis/cytology/*genetics/metabolism ; Cell Line ; Chromatin/genetics/metabolism ; Chromosome Mapping ; *DNA Replication ; DNA, Plant/genetics/metabolism ; GC Rich Sequence/genetics ; Genome, Plant/genetics ; Heterochromatin/*genetics/metabolism ; Histones/metabolism ; Lysine/metabolism ; Methylation ; Microscopy, Confocal ; Replication Origin/*genetics ; Retroelements/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic ; },
abstract = {Genomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands of DNA replication origins (ORIs) scattered throughout the genome. The DNA and chromatin features determining ORI specification are not presently known. We have generated a high-resolution genome-wide map of 3230 ORIs in cultured Arabidopsis thaliana cells. Here, we focused on defining the features associated with ORIs in heterochromatin. In pericentromeric gene-poor domains ORIs associate almost exclusively with the retrotransposon class of transposable elements (TEs), in particular of the Gypsy family. ORI activity in retrotransposons occurs independently of TE expression and while maintaining high levels of H3K9me2 and H3K27me1, typical marks of repressed heterochromatin. ORI-TEs largely colocalize with chromatin signatures defining GC-rich heterochromatin. Importantly, TEs with active ORIs contain a local GC content higher than the TEs lacking them. Our results lead us to conclude that ORI colocalization with retrotransposons is determined by their transposition mechanism based on transcription, and a specific chromatin landscape. Our detailed analysis of ORIs responsible for heterochromatin replication has implications on the mechanisms of ORI specification in other multicellular organisms in which retrotransposons are major components of heterochromatin and of the entire genome.},
}
@article {pmid28584082,
year = {2017},
author = {Vergara, HM and Bertucci, PY and Hantz, P and Tosches, MA and Achim, K and Vopalensky, P and Arendt, D},
title = {Whole-organism cellular gene-expression atlas reveals conserved cell types in the ventral nerve cord of Platynereis dumerilii.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {114},
number = {23},
pages = {5878-5885},
doi = {10.1073/pnas.1610602114},
pmid = {28584082},
issn = {1091-6490},
mesh = {Algorithms ; Animals ; *Biological Evolution ; Body Patterning/genetics ; Cell Differentiation ; Gene Expression Profiling/methods ; Gene Expression Regulation, Developmental ; Models, Biological ; Neurons/cytology ; Polychaeta/cytology/*genetics ; },
abstract = {The comparative study of cell types is a powerful approach toward deciphering animal evolution. To avoid selection biases, however, comparisons ideally involve all cell types present in a multicellular organism. Here, we use image registration and a newly developed &quot;Profiling by Signal Probability Mapping&quot; algorithm to generate a cellular resolution 3D expression atlas for an entire animal. We investigate three-segmented young worms of the marine annelid Platynereis dumerilii, with a rich diversity of differentiated cells present in relatively low number. Starting from whole-mount expression images for close to 100 neural specification and differentiation genes, our atlas identifies and molecularly characterizes 605 bilateral pairs of neurons at specific locations in the ventral nerve cord. Among these pairs, we identify sets of neurons expressing similar combinations of transcription factors, located at spatially coherent anterior-posterior, dorsal-ventral, and medial-lateral coordinates that we interpret as cell types. Comparison with motor and interneuron types in the vertebrate neural tube indicates conserved combinations, for example, of cell types cospecified by Gata1/2/3 and Tal transcription factors. These include V2b interneurons and the central spinal fluid-contacting Kolmer-Agduhr cells in the vertebrates, and several neuron types in the intermediate ventral ganglionic mass in the annelid. We propose that Kolmer-Agduhr cell-like mechanosensory neurons formed part of the mucociliary sole in protostome-deuterostome ancestors and diversified independently into several neuron types in annelid and vertebrate descendants.},
}
@article {pmid28571799,
year = {2017},
author = {Salerian, AJ},
title = {Human body may produce bacteria.},
journal = {Medical hypotheses},
volume = {103},
number = {},
pages = {131-132},
doi = {10.1016/j.mehy.2017.05.005},
pmid = {28571799},
issn = {1532-2777},
mesh = {Animals ; *Bacteria ; *Bacterial Physiological Phenomena ; Fermentation ; *Human Body ; Humans ; Models, Theoretical ; Muscles/physiology ; Origin of Life ; },
abstract = {&quot;Human body may produce bacteria&quot; proposes that human body may produce bacteria and represent an independent source of infections contrary to the current paradigm of infectious disorders proposed by Louis Pasteur in 1880. The following observations are consistent with this hypothesis: A. Bidirectional transformations of both living and nonliving things have been commonly observed in nature. B. Complex multicellular organisms harbor the necessary properties to produce bacteria (water, nitrogen and oxygen). C. Physical laws suggest any previously observed phenomenon or action will occur again (life began on earth; a non living thing). D. Animal muscle cells may generate energy (fermentation). E. Sterilized food products (i.e. boiled eggs), may produce bacteria and fungus under special conditions and without any exposure to foreign living cells. &quot;Human body may produce bacteria&quot; may challenge the current medical paradigm that views human infectious disorders as the exclusive causative byproducts of invading foreign cells. It may also introduce new avenues to treat infectious disorders.},
}
@article {pmid28560344,
year = {2017},
author = {Knoll, AH and Nowak, MA},
title = {The timetable of evolution.},
journal = {Science advances},
volume = {3},
number = {5},
pages = {e1603076},
doi = {10.1126/sciadv.1603076},
pmid = {28560344},
issn = {2375-2548},
mesh = {*Biological Evolution ; *Ecosystem ; *Models, Biological ; },
abstract = {The integration of fossils, phylogeny, and geochronology has resulted in an increasingly well-resolved timetable of evolution. Life appears to have taken root before the earliest known minimally metamorphosed sedimentary rocks were deposited, but for a billion years or more, evolution played out beneath an essentially anoxic atmosphere. Oxygen concentrations in the atmosphere and surface oceans first rose in the Great Oxygenation Event (GOE) 2.4 billion years ago, and a second increase beginning in the later Neoproterozoic Era [Neoproterozoic Oxygenation Event (NOE)] established the redox profile of modern oceans. The GOE facilitated the emergence of eukaryotes, whereas the NOE is associated with large and complex multicellular organisms. Thus, the GOE and NOE are fundamental pacemakers for evolution. On the time scale of Earth's entire 4 billion-year history, the evolutionary dynamics of the planet's biosphere appears to be fast, and the pace of evolution is largely determined by physical changes of the planet. However, in Phanerozoic ecosystems, interactions between new functions enabled by the accumulation of characters in a complex regulatory environment and changing biological components of effective environments appear to have an important influence on the timing of evolutionary innovations. On the much shorter time scale of transient environmental perturbations, such as those associated with mass extinctions, rates of genetic accommodation may have been limiting for life.},
}
@article {pmid28550046,
year = {2017},
author = {Vijg, J and Dong, X and Milholland, B and Zhang, L},
title = {Genome instability: a conserved mechanism of ageing?.},
journal = {Essays in biochemistry},
volume = {61},
number = {3},
pages = {305-315},
doi = {10.1042/EBC20160082},
pmid = {28550046},
issn = {1744-1358},
support = {P01 AG017242/AG/NIA NIH HHS/United States ; P01 AG047200/AG/NIA NIH HHS/United States ; P30 AG038072/AG/NIA NIH HHS/United States ; R01 CA180126/CA/NCI NIH HHS/United States ; },
mesh = {Aging/genetics/*physiology ; Animals ; DNA Repair/genetics/physiology ; Genomic Instability/genetics/*physiology ; Humans ; Mutation/genetics ; },
abstract = {DNA is the carrier of genetic information and the primary template from which all cellular information is ultimately derived. Changes in the DNA information content through mutation generate diversity for evolution through natural selection but are also a source of deleterious effects. It has since long been hypothesized that mutation accumulation in somatic cells of multicellular organisms could causally contribute to age-related cellular degeneration and death. Assays to detect different types of mutations, from base substitutions to large chromosomal aberrations, have been developed and show unequivocally that mutations accumulate in different tissues and cell types of ageing humans and animals. More recently, next-generation sequencing-based methods have been developed to accurately determine the complete landscape of base substitution mutations in single cells. The first results show that the somatic mutation rate is much higher than the germline mutation rate and that base substitution loads in somatic cells are high enough to potentially affect cellular function.},
}
@article {pmid28525299,
year = {2017},
author = {Berbee, ML and James, TY and Strullu-Derrien, C},
title = {Early Diverging Fungi: Diversity and Impact at the Dawn of Terrestrial Life.},
journal = {Annual review of microbiology},
volume = {71},
number = {},
pages = {41-60},
doi = {10.1146/annurev-micro-030117-020324},
pmid = {28525299},
issn = {1545-3251},
mesh = {*Evolution, Molecular ; Fungi/*classification/*genetics ; *Genetic Variation ; },
abstract = {As decomposers or plant pathogens, fungi deploy invasive growth and powerful carbohydrate active enzymes to reduce multicellular plant tissues to humus and simple sugars. Fungi are perhaps also the most important mutualistic symbionts in modern ecosystems, transporting poorly soluble mineral nutrients to plants and thus enhancing the growth of vegetation. However, at their origin over a billion years ago, fungi, like plants and animals, were unicellular marine microbes. Like the other multicellular kingdoms, Fungi evolved increased size, complexity, and metabolic functioning. Interactions of fungi with plants changed terrestrial ecology and geology and modified the Earth's atmosphere. In this review, we discuss the diversification and ecological roles of the fungi over their first 600 million years, from their origin through their colonization of land, drawing on phylogenomic evidence for their relationships and metabolic capabilities and on molecular dating, fossils, and modeling of Earth's paleoclimate.},
}
@article {pmid28509401,
year = {2017},
author = {Dittami, SM and Heesch, S and Olsen, JL and Collén, J},
title = {Transitions between marine and freshwater environments provide new clues about the origins of multicellular plants and algae.},
journal = {Journal of phycology},
volume = {53},
number = {4},
pages = {731-745},
doi = {10.1111/jpy.12547},
pmid = {28509401},
issn = {1529-8817},
mesh = {Adaptation, Biological ; *Biological Evolution ; *Ecosystem ; Fresh Water ; *Phaeophyta ; *Plants ; Seawater ; },
abstract = {Marine-freshwater and freshwater-marine transitions have been key events in the evolution of life, and most major groups of organisms have independently undergone such events at least once in their history. Here, we first compile an inventory of bidirectional freshwater and marine transitions in multicellular photosynthetic eukaryotes. While green and red algae have mastered multiple transitions in both directions, brown algae have colonized freshwater on a maximum of six known occasions, and angiosperms have made the transition to marine environments only two or three times. Next, we review the early evolutionary events leading to the colonization of current habitats. It is commonly assumed that the conquest of land proceeded in a sequence from marine to freshwater habitats. However, recent evidence suggests that early photosynthetic eukaryotes may have arisen in subaerial or freshwater environments and only later colonized marine environments as hypersaline oceans were diluted to the contemporary level. Although this hypothesis remains speculative, it is important to keep these alternative scenarios in mind when interpreting the current habitat distribution of plants and algae. Finally, we discuss the roles of structural and functional adaptations of the cell wall, reactive oxygen species scavengers, osmoregulation, and reproduction. These are central for acclimatization to freshwater or to marine environments. We observe that successful transitions appear to have occurred more frequently in morphologically simple forms and conclude that, in addition to physiological studies of euryhaline species, comparative studies of closely related species fully adapted to one or the other environment are necessary to better understand the adaptive processes.},
}
@article {pmid28508537,
year = {2018},
author = {Boomsma, JJ and Gawne, R},
title = {Superorganismality and caste differentiation as points of no return: how the major evolutionary transitions were lost in translation.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {93},
number = {1},
pages = {28-54},
doi = {10.1111/brv.12330},
pmid = {28508537},
issn = {1469-185X},
abstract = {More than a century ago, William Morton Wheeler proposed that social insect colonies can be regarded as superorganisms when they have morphologically differentiated reproductive and nursing castes that are analogous to the metazoan germ-line and soma. Following the rise of sociobiology in the 1970s, Wheeler's insights were largely neglected, and we were left with multiple new superorganism concepts that are mutually inconsistent and uninformative on how superorganismality originated. These difficulties can be traced to the broadened sociobiological concept of eusociality, which denies that physical queen-worker caste differentiation is a universal hallmark of superorganismal colonies. Unlike early evolutionary naturalists and geneticists such as Weismann, Huxley, Fisher and Haldane, who set out to explain the acquisition of an unmated worker caste, the goal of sociobiology was to understand the evolution of eusociality, a broad-brush convenience category that covers most forms of cooperative breeding. By lumping a diverse spectrum of social systems into a single category, and drawing attention away from the evolution of distinct quantifiable traits, the sociobiological tradition has impeded straightforward connections between inclusive fitness theory and the major evolutionary transitions paradigm for understanding irreversible shifts to higher organizational complexity. We evaluate the history by which these inconsistencies accumulated, develop a common-cause approach for understanding the origins of all major transitions in eukaryote hierarchical complexity, and use Hamilton's rule to argue that they are directly comparable. We show that only Wheeler's original definition of superorganismality can be unambiguously linked to irreversible evolutionary transitions from context-dependent reproductive altruism to unconditional differentiation of permanently unmated castes in the ants, corbiculate bees, vespine wasps and higher termites. We argue that strictly monogamous parents were a necessary, albeit not sufficient condition for all transitions to superorganismality, analogous to single-zygote bottlenecking being a necessary but not sufficient condition for the convergent origins of complex soma across multicellular eukaryotes. We infer that conflict reduction was not a necessary condition for the origin of any of these major transitions, and conclude that controversies over the status of inclusive fitness theory primarily emanate from the arbitrarily defined sociobiological concepts of superorganismality and eusociality, not from the theory itself.},
}
@article {pmid28506208,
year = {2017},
author = {Labocha, MK and Yuan, W and Aleman-Meza, B and Zhong, W},
title = {A strategy to apply quantitative epistasis analysis on developmental traits.},
journal = {BMC genetics},
volume = {18},
number = {1},
pages = {42},
doi = {10.1186/s12863-017-0508-4},
pmid = {28506208},
issn = {1471-2156},
support = {K99 HG004724/HG/NHGRI NIH HHS/United States ; R00 HG004724/HG/NHGRI NIH HHS/United States ; R01 DA018341/DA/NIDA NIH HHS/United States ; },
mesh = {Animals ; Caenorhabditis elegans/*genetics/*growth &amp; development ; Caenorhabditis elegans Proteins/genetics ; *Epistasis, Genetic ; High-Throughput Nucleotide Sequencing/methods ; Models, Genetic ; *Quantitative Trait Loci ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits.<br><br>METHODS: In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement.<br><br>RESULTS: Using two different C. elegans developmental phenotypes, body length and sex ratio, as examples, we showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. For example, several sex-ratio genes were found to interact with brc-1 and brd-1, the orthologs of the human breast cancer genes BRCA1 and BARD1, respectively. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1, him-3 (ortholog of HORMAD1, HORMAD2), sdc-1, and set-2 (ortholog of SETD1A, SETD1B, KMT2C, KMT2D), validating the effectiveness of our method in detecting genetic interactions.<br><br>CONCLUSIONS: We developed a reliable, high-throughput method for quantitative epistasis analysis of developmental phenotypes.},
}
@article {pmid28505429,
year = {2017},
author = {Siu, KH and Chen, W},
title = {Control of the Yeast Mating Pathway by Reconstitution of Functional α-Factor Using Split Intein-Catalyzed Reactions.},
journal = {ACS synthetic biology},
volume = {6},
number = {8},
pages = {1453-1460},
doi = {10.1021/acssynbio.7b00078},
pmid = {28505429},
issn = {2161-5063},
mesh = {Catalysis ; Gene Expression Regulation, Fungal/*genetics ; Genes, Mating Type, Fungal/*genetics ; Inteins/*genetics ; Metabolic Engineering/*methods ; Metabolic Networks and Pathways/*genetics ; Models, Genetic ; Pheromones/*genetics ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; Signal Transduction/genetics ; },
abstract = {Synthetic control strategies using signaling peptides to regulate and coordinate cellular behaviors in multicellular organisms and synthetic consortia remain largely underdeveloped because of the complexities necessitated by heterologous peptide expression. Using recombinant proteins that exploit split intein-mediated reactions, we presented here a new strategy for reconstituting functional signaling peptides capable of eliciting desired cellular responses in S. cerevisiae. These designs can potentially be tailored to any signaling peptides to be reconstituted, as the split inteins are promiscuous and both the peptides and the reactions are amenable to changes by directed evolution and other protein engineering tools, thereby offering a general strategy to implement synthetic control strategies in a large variety of applications.},
}
@article {pmid28484005,
year = {2017},
author = {Trigos, AS and Pearson, RB and Papenfuss, AT and Goode, DL},
title = {Altered interactions between unicellular and multicellular genes drive hallmarks of transformation in a diverse range of solid tumors.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {114},
number = {24},
pages = {6406-6411},
doi = {10.1073/pnas.1617743114},
pmid = {28484005},
issn = {1091-6490},
mesh = {Animals ; Carcinogenesis/genetics ; Cell Transformation, Neoplastic/genetics ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Genome, Human ; Humans ; Models, Genetic ; Neoplasms/etiology/*genetics ; Oncogenes ; Phenotype ; Stress, Physiological/genetics ; Systems Biology ; },
abstract = {Tumors of distinct tissues of origin and genetic makeup display common hallmark cellular phenotypes, including sustained proliferation, suppression of cell death, and altered metabolism. These phenotypic commonalities have been proposed to stem from disruption of conserved regulatory mechanisms evolved during the transition to multicellularity to control fundamental cellular processes such as growth and replication. Dating the evolutionary emergence of human genes through phylostratigraphy uncovered close association between gene age and expression level in RNA sequencing data from The Cancer Genome Atlas for seven solid cancers. Genes conserved with unicellular organisms were strongly up-regulated, whereas genes of metazoan origin were primarily inactivated. These patterns were most consistent for processes known to be important in cancer, implicating both selection and active regulation during malignant transformation. The coordinated expression of strongly interacting multicellularity and unicellularity processes was lost in tumors. This separation of unicellular and multicellular functions appeared to be mediated by 12 highly connected genes, marking them as important general drivers of tumorigenesis. Our findings suggest common principles closely tied to the evolutionary history of genes underlie convergent changes at the cellular process level across a range of solid cancers. We propose altered activity of genes at the interfaces between multicellular and unicellular regions of human gene regulatory networks activate primitive transcriptional programs, driving common hallmark features of cancer. Manipulation of cross-talk between biological processes of different evolutionary origins may thus present powerful and broadly applicable treatment strategies for cancer.},
}
@article {pmid28481398,
year = {2017},
author = {Lei, Y and Anders, HJ},
title = {Evolutionary trade-offs in kidney injury and repair.},
journal = {Histology and histopathology},
volume = {32},
number = {11},
pages = {1099-1113},
doi = {10.14670/HH-11-900},
pmid = {28481398},
issn = {1699-5848},
mesh = {Animals ; *Biological Evolution ; Humans ; Kidney/*injuries ; *Regeneration ; },
abstract = {Evolutionary medicine has proven helpful to understand the origin of human disease, e.g. in identifying causal roles of recent environmental changes impacting on human physiology (environment-phenotype mismatch). In contrast, diseases affecting only a limited number of members of a species often originate from evolutionary trade-offs for usually physiologic adaptations assuring reproductive success in the context of extrinsic threats. For example, the G1 and G2 variants of the APOL1 gene supporting control of Trypanosoma infection come with the trade-off that they promote the progression of kidney disease. In this review we extend the concept of evolutionary nephrology by discussing how the physiologic adaptations (danger responses) to tissue injury create evolutionary trade-offs that drive histopathological changes underlying acute and chronic kidney diseases. The evolution of multicellular organisms positively selected a number of danger response programs for their overwhelming benefits in assuring survival such as clotting, inflammation, epithelial healing and mesenchymal healing, i.e. fibrosis and sclerosis. Upon kidney injury these danger programs often present as pathomechanisms driving persistent nephron loss and renal failure. We explore how classic kidney disease entities involve insufficient or overshooting activation of these danger response programs for which the underlying genetic basis remains largely to be defined. Dissecting the causative and hierarchical relationships between danger programs should help to identify molecular targets to control kidney injury and to improve disease outcomes.},
}
@article {pmid28459980,
year = {2017},
author = {Fares, MA and Sabater-Muñoz, B and Toft, C},
title = {Genome Mutational and Transcriptional Hotspots Are Traps for Duplicated Genes and Sources of Adaptations.},
journal = {Genome biology and evolution},
volume = {9},
number = {5},
pages = {1229-1240},
doi = {10.1093/gbe/evx085},
pmid = {28459980},
issn = {1759-6653},
mesh = {Adaptation, Biological ; *Gene Duplication ; *Mutation ; Mutation Rate ; Promoter Regions, Genetic ; Saccharomyces cerevisiae/*genetics/*physiology ; Stress, Physiological ; *Transcription, Genetic ; },
abstract = {Gene duplication generates new genetic material, which has been shown to lead to major innovations in unicellular and multicellular organisms. A whole-genome duplication occurred in the ancestor of Saccharomyces yeast species but 92% of duplicates returned to single-copy genes shortly after duplication. The persisting duplicated genes in Saccharomyces led to the origin of major metabolic innovations, which have been the source of the unique biotechnological capabilities in the Baker's yeast Saccharomyces cerevisiae. What factors have determined the fate of duplicated genes remains unknown. Here, we report the first demonstration that the local genome mutation and transcription rates determine the fate of duplicates. We show, for the first time, a preferential location of duplicated genes in the mutational and transcriptional hotspots of S. cerevisiae genome. The mechanism of duplication matters, with whole-genome duplicates exhibiting different preservation trends compared to small-scale duplicates. Genome mutational and transcriptional hotspots are rich in duplicates with large repetitive promoter elements. Saccharomyces cerevisiae shows more tolerance to deleterious mutations in duplicates with repetitive promoter elements, which in turn exhibit higher transcriptional plasticity against environmental perturbations. Our data demonstrate that the genome traps duplicates through the accelerated regulatory and functional divergence of their gene copies providing a source of novel adaptations in yeast.},
}
@article {pmid28457024,
year = {2017},
author = {Golstein, P},
title = {Conserved nucleolar stress at the onset of cell death.},
journal = {The FEBS journal},
volume = {284},
number = {22},
pages = {3791-3800},
doi = {10.1111/febs.14095},
pmid = {28457024},
issn = {1742-4658},
mesh = {Animals ; *Cell Death ; Cell Nucleolus/metabolism/*pathology ; Humans ; Nuclear Proteins/*metabolism ; *Stress, Physiological ; },
abstract = {Cell death pervasiveness among multicellular eukaryotes suggested that some core steps of cell death may be conserved. This could be addressed by comparing the course of cell death in organisms belonging to distinct eukaryotic kingdoms. A search for early cell death events in a protist revealed nucleolar disorganization similar to the nucleolar stress often reported in dying animal cells. This indicated a conserved role for the nucleolus at the onset of eukaryotic cell death and leads one to consider the course of cell death as a succession of unequally conserved modules.},
}
@article {pmid28453786,
year = {2017},
author = {Porath, HT and Schaffer, AA and Kaniewska, P and Alon, S and Eisenberg, E and Rosenthal, J and Levanon, EY and Levy, O},
title = {A-to-I RNA Editing in the Earliest-Diverging Eumetazoan Phyla.},
journal = {Molecular biology and evolution},
volume = {34},
number = {8},
pages = {1890-1901},
doi = {10.1093/molbev/msx125},
pmid = {28453786},
issn = {1537-1719},
support = {311257//European Research Council/International ; },
mesh = {Adenosine Deaminase/*genetics/metabolism ; Animals ; Anthozoa/*genetics/metabolism ; Base Sequence ; Evolution, Molecular ; Genome ; Genomics ; Humans ; Mammals/genetics ; Phylogeny ; RNA ; RNA Editing/*genetics ; RNA, Messenger/genetics ; RNA-Binding Proteins/genetics ; },
abstract = {The highly conserved ADAR enzymes, found in all multicellular metazoans, catalyze the editing of mRNA transcripts by the deamination of adenosines to inosines. This type of editing has two general outcomes: site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.},
}
@article {pmid28441401,
year = {2017},
author = {Cisneros, L and Bussey, KJ and Orr, AJ and Miočević, M and Lineweaver, CH and Davies, P},
title = {Ancient genes establish stress-induced mutation as a hallmark of cancer.},
journal = {PloS one},
volume = {12},
number = {4},
pages = {e0176258},
doi = {10.1371/journal.pone.0176258},
pmid = {28441401},
issn = {1932-6203},
mesh = {Animals ; Cell Cycle/genetics ; DNA Repair/genetics ; Databases, Genetic ; Humans ; *Mutation ; Neoplasms/*genetics ; *Oncogenes ; Phenotype ; Phylogeny ; },
abstract = {Cancer is sometimes depicted as a reversion to single cell behavior in cells adapted to live in a multicellular assembly. If this is the case, one would expect that mutation in cancer disrupts functional mechanisms that suppress cell-level traits detrimental to multicellularity. Such mechanisms should have evolved with or after the emergence of multicellularity. This leads to two related, but distinct hypotheses: 1) Somatic mutations in cancer will occur in genes that are younger than the emergence of multicellularity (1000 million years [MY]); and 2) genes that are frequently mutated in cancer and whose mutations are functionally important for the emergence of the cancer phenotype evolved within the past 1000 million years, and thus would exhibit an age distribution that is skewed to younger genes. In order to investigate these hypotheses we estimated the evolutionary ages of all human genes and then studied the probability of mutation and their biological function in relation to their age and genomic location for both normal germline and cancer contexts. We observed that under a model of uniform random mutation across the genome, controlled for gene size, genes less than 500 MY were more frequently mutated in both cases. Paradoxically, causal genes, defined in the COSMIC Cancer Gene Census, were depleted in this age group. When we used functional enrichment analysis to explain this unexpected result we discovered that COSMIC genes with recessive disease phenotypes were enriched for DNA repair and cell cycle control. The non-mutated genes in these pathways are orthologous to those underlying stress-induced mutation in bacteria, which results in the clustering of single nucleotide variations. COSMIC genes were less common in regions where the probability of observing mutational clusters is high, although they are approximately 2-fold more likely to harbor mutational clusters compared to other human genes. Our results suggest this ancient mutational response to stress that evolved among prokaryotes was co-opted to maintain diversity in the germline and immune system, while the original phenotype is restored in cancer. Reversion to a stress-induced mutational response is a hallmark of cancer that allows for effectively searching &quot;protected&quot; genome space where genes causally implicated in cancer are located and underlies the high adaptive potential and concomitant therapeutic resistance that is characteristic of cancer.},
}
@article {pmid28427949,
year = {2017},
author = {Freese, JM and Lane, CE},
title = {Parasitism finds many solutions to the same problems in red algae (Florideophyceae, Rhodophyta).},
journal = {Molecular and biochemical parasitology},
volume = {214},
number = {},
pages = {105-111},
doi = {10.1016/j.molbiopara.2017.04.006},
pmid = {28427949},
issn = {1872-9428},
mesh = {*Biological Evolution ; *Host-Parasite Interactions ; Microscopy ; Phylogeny ; Rhodophyta/classification/cytology/*genetics/*physiology ; },
abstract = {Parasitic red algae evolve from a common ancestor with their hosts, parasitizing cousins using familiar cellular mechanisms. They have independently evolved over one hundred times within the exclusively multicellular red algal class Florideophyceae. Reduced morphology, a lack of pigmentation, and direct cell-cell connections with their hosts are markers of red algal parasitism. With so many potential evolutionary pathways, red algal parasite diversity offers a unique test case to understand the earliest stages of this lifestyle transition. Molecular and morphological investigations led to the categorization of these parasites based on their relationship to their host. &quot;Adelphoparasites&quot; are phylogenetically close to their hosts, often infecting a sister species, whereas &quot;alloparasites&quot; are more distantly related to their hosts. The differentiation of these parasites, based on their phylogenetic relationship to their host, has resulted in a simplified classification of these parasites that may not reflect the many evolutionary pathways they take to arrive at a similar endpoint. Accordingly, many parasites fall into a gray area between adelphoparasite and alloparasite definitions, challenging the established features we use to classify them. Molecular phylogenetic research has been essential in identifying gaps in knowledge, but microscopy needs to be reincorporated in order to address red algal parasite developmental variation to establish a new paradigm. The joint utilization of molecular and microscopic methods will be critical in identifying the genomic and physiological traits of both nascent and well-established parasites.},
}
@article {pmid28427501,
year = {2017},
author = {Fonseca, NA and Cruz, AF and Moura, V and Simões, S and Moreira, JN},
title = {The cancer stem cell phenotype as a determinant factor of the heterotypic nature of breast tumors.},
journal = {Critical reviews in oncology/hematology},
volume = {113},
number = {},
pages = {111-121},
doi = {10.1016/j.critrevonc.2017.03.016},
pmid = {28427501},
issn = {1879-0461},
mesh = {Breast Neoplasms/metabolism/pathology/*physiopathology ; Epithelial-Mesenchymal Transition ; Female ; Humans ; Neoplastic Stem Cells/*metabolism/physiology ; Neovascularization, Pathologic ; *Phosphoproteins ; *RNA-Binding Proteins ; *Signal Transduction ; *Tumor Microenvironment ; },
abstract = {Gathering evidence supports the existence of a population of cells with stem-like characteristics, named cancer stem cells (CSC), which is involved not only in tumor recurrence but also in tumorigenicity, metastization and drug resistance. Several markers have been used to identify putative CSC sub-populations in different cancers. Notwithstanding, it has been acknowledged that breast CSC may originate from non-stem cancer cells (non-SCC), interconverting through an epithelial-to-mesenchymal transition-mediated process, and presenting several deregulated canonical and developmental signaling pathways. These support the heterogeneity that, directly or indirectly, influences fundamental biological features supporting breast tumor development. Accordingly, CSC have increasingly become highly relevant cellular targets. In this review, we will address the stemness concept in cancer, setting the perspective on CSC and their origin, by exploring their relation and regulation within the tumor microenvironment, in the context of emerging therapeutic targets. Within this framework, we will discuss nucleolin, a protein that has been associated with angiogenesis and, more recently, with the stemness phenotype, becoming a common denominator between CSC and non-SCC for multicellular targeting.},
}
@article {pmid28425150,
year = {2017},
author = {Grochau-Wright, ZI and Hanschen, ER and Ferris, PJ and Hamaji, T and Nozaki, H and Olson, BJSC and Michod, RE},
title = {Genetic basis for soma is present in undifferentiated volvocine green algae.},
journal = {Journal of evolutionary biology},
volume = {30},
number = {6},
pages = {1205-1218},
doi = {10.1111/jeb.13100},
pmid = {28425150},
issn = {1420-9101},
support = {NNX13AH41G//NASA/ ; T32 GM084905/GM/NIGMS NIH HHS/United States ; },
mesh = {Adaptation, Physiological ; *Biological Evolution ; Chlorophyta ; *Phylogeny ; Stress, Physiological ; *Volvox ; },
abstract = {Somatic cellular differentiation plays a critical role in the transition from unicellular to multicellular life, but the evolution of its genetic basis remains poorly understood. By definition, somatic cells do not reproduce to pass on genes and so constitute an extreme form of altruistic behaviour. The volvocine green algae provide an excellent model system to study the evolution of multicellularity and somatic differentiation. In Volvox carteri, somatic cell differentiation is controlled by the regA gene, which is part of a tandem duplication of genes known as the reg cluster. Although previous work found the reg cluster in divergent Volvox species, its origin and distribution in the broader group of volvocine algae has not been known. Here, we show that the reg cluster is present in many species without somatic cells and determine that the genetic basis for soma arose before the phenotype at the origin of the family Volvocaceae approximately 200 million years ago. We hypothesize that the ancestral function was involved in regulating reproduction in response to stress and that this function was later co-opted to produce soma. Determining that the reg cluster was co-opted to control somatic cell development provides insight into how cellular differentiation, and with it greater levels of complexity and individuality, evolves.},
}
@article {pmid28424311,
year = {2017},
author = {Deora, T and Gundiah, N and Sane, SP},
title = {Mechanics of the thorax in flies.},
journal = {The Journal of experimental biology},
volume = {220},
number = {Pt 8},
pages = {1382-1395},
doi = {10.1242/jeb.128363},
pmid = {28424311},
issn = {1477-9145},
mesh = {Animals ; Biomechanical Phenomena ; Body Size ; Diptera/anatomy &amp; histology/*physiology ; *Flight, Animal ; Wings, Animal/anatomy &amp; histology/*physiology ; },
abstract = {Insects represent more than 60% of all multicellular life forms, and are easily among the most diverse and abundant organisms on earth. They evolved functional wings and the ability to fly, which enabled them to occupy diverse niches. Insects of the hyper-diverse orders show extreme miniaturization of their body size. The reduced body size, however, imposes steep constraints on flight ability, as their wings must flap faster to generate sufficient forces to stay aloft. Here, we discuss the various physiological and biomechanical adaptations of the thorax in flies which enabled them to overcome the myriad constraints of small body size, while ensuring very precise control of their wing motion. One such adaptation is the evolution of specialized myogenic or asynchronous muscles that power the high-frequency wing motion, in combination with neurogenic or synchronous steering muscles that control higher-order wing kinematic patterns. Additionally, passive cuticular linkages within the thorax coordinate fast and yet precise bilateral wing movement, in combination with an actively controlled clutch and gear system that enables flexible flight patterns. Thus, the study of thoracic biomechanics, along with the underlying sensory-motor processing, is central in understanding how the insect body form is adapted for flight.},
}
@article {pmid28418331,
year = {2017},
author = {Fidler, AL and Darris, CE and Chetyrkin, SV and Pedchenko, VK and Boudko, SP and Brown, KL and Gray Jerome, W and Hudson, JK and Rokas, A and Hudson, BG},
title = {Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues.},
journal = {eLife},
volume = {6},
number = {},
pages = {},
doi = {10.7554/eLife.24176},
pmid = {28418331},
issn = {2050-084X},
support = {P60 DK020593/DK/NIDDK NIH HHS/United States ; R24 DK103067/DK/NIDDK NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 DK018381/DK/NIDDK NIH HHS/United States ; U2C DK059637/DK/NIDDK NIH HHS/United States ; P30 EY008126/EY/NEI NIH HHS/United States ; P30 DK020593/DK/NIDDK NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; U24 DK059637/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Basement Membrane/*chemistry ; Collagen Type IV/*analysis/*genetics ; Ctenophora/cytology/genetics/metabolism/*physiology ; Evolution, Molecular ; Extracellular Matrix/*chemistry ; },
abstract = {The role of the cellular microenvironment in enabling metazoan tissue genesis remains obscure. Ctenophora has recently emerged as one of the earliest-branching extant animal phyla, providing a unique opportunity to explore the evolutionary role of the cellular microenvironment in tissue genesis. Here, we characterized the extracellular matrix (ECM), with a focus on collagen IV and its variant, spongin short-chain collagens, of non-bilaterian animal phyla. We identified basement membrane (BM) and collagen IV in Ctenophora, and show that the structural and genomic features of collagen IV are homologous to those of non-bilaterian animal phyla and Bilateria. Yet, ctenophore features are more diverse and distinct, expressing up to twenty genes compared to six in vertebrates. Moreover, collagen IV is absent in unicellular sister-groups. Collectively, we conclude that collagen IV and its variant, spongin, are primordial components of the extracellular microenvironment, and as a component of BM, collagen IV enabled the assembly of a fundamental architectural unit for multicellular tissue genesis.},
}
@article {pmid28409312,
year = {2017},
author = {Garcin, CL and Habib, SJ},
title = {A Comparative Perspective on Wnt/β-Catenin Signalling in Cell Fate Determination.},
journal = {Results and problems in cell differentiation},
volume = {61},
number = {},
pages = {323-350},
doi = {10.1007/978-3-319-53150-2_15},
pmid = {28409312},
issn = {0080-1844},
mesh = {Animals ; Body Patterning/physiology ; Cell Differentiation/*physiology ; Embryonic Development/*physiology ; Humans ; Wnt Signaling Pathway/*physiology ; },
abstract = {The Wnt/β-catenin pathway is an ancient and highly conserved signalling pathway that plays fundamental roles in the regulation of embryonic development and adult homeostasis. This pathway has been implicated in numerous cellular processes, including cell proliferation, differentiation, migration, morphological changes and apoptosis. In this chapter, we aim to illustrate with specific examples the involvement of Wnt/β-catenin signalling in cell fate determination. We discuss the roles of the Wnt/β-catenin pathway in specifying cell fate throughout evolution, how its function in patterning during development is often reactivated during regeneration and how perturbation of this pathway has negative consequences for the control of cell fate.The origin of all life was a single cell that had the capacity to respond to cues from the environment. With evolution, multicellular organisms emerged, and as a result, subsets of cells arose to form tissues able to respond to specific instructive signals and perform specialised functions. This complexity and specialisation required two types of messages to direct cell fate: intra- and intercellular. A fundamental question in developmental biology is to understand the underlying mechanisms of cell fate choice. Amongst the numerous external cues involved in the generation of cellular diversity, a prominent pathway is the Wnt signalling pathway in all its forms.},
}
@article {pmid28406446,
year = {2017},
author = {Breviario, D},
title = {Is There any Alternative to Canonical DNA Barcoding of Multicellular Eukaryotic Species? A Case for the Tubulin Gene Family.},
journal = {International journal of molecular sciences},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/ijms18040827},
pmid = {28406446},
issn = {1422-0067},
mesh = {DNA/chemistry/metabolism ; *DNA Barcoding, Taxonomic ; Eukaryota/*genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Tubulin/*genetics ; },
abstract = {Modern taxonomy is largely relying on DNA barcoding, a nucleotide sequence-based approach that provides automated species identification using short orthologous DNA regions, mainly of organellar origin when applied to multicellular Eukaryotic species. Target DNA loci have been selected that contain a minimal amount of nucleotide sequence variation within species while diverging among species. This strategy is quite effective for the identification of vertebrates and other animal lineages but poses a problem in plants where different combinations of two or three loci are constantly used. Even so, species discrimination in such plant categories as ornamentals and herbals remain problematic as well as the confident identification of subspecies, ecotypes, and closely related or recently evolved species. All these limitations may be successfully solved by the application of a different strategy, based on the use of a multi-locus, ubiquitous, nuclear marker, that is tubulin. In fact, the tubulin-based polymorphism method can release specific genomic profiles to any plant species independently from its taxonomic group. This offers the rare possibility of an effective yet generic genomic fingerprint. In a more general context, the issue is raised about the possibility that approaches alternative to systematic DNA sequencing may still provide useful and simple solutions.},
}
@article {pmid28405374,
year = {2017},
author = {Pratlong, M and Haguenauer, A and Chenesseau, S and Brener, K and Mitta, G and Toulza, E and Bonabaud, M and Rialle, S and Aurelle, D and Pontarotti, P},
title = {Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral (Corallium rubrum).},
journal = {Royal Society open science},
volume = {4},
number = {3},
pages = {160880},
doi = {10.1098/rsos.160880},
pmid = {28405374},
issn = {2054-5703},
abstract = {Sexual reproduction is widespread among eukaryotes, and the sex-determining processes vary greatly among species. While genetic sex determination (GSD) has been intensively described in bilaterian species, no example has yet been recorded among non-bilaterians. However, the quasi-ubiquitous repartition of GSD among multicellular species suggests that similar evolutionary forces can promote this system, and that these forces could occur also in non-bilaterians. Studying sex determination across the range of Metazoan diversity is indeed important to understand better the evolution of this mechanism and its lability. We tested the existence of sex-linked genes in the gonochoric red coral (Corallium rubrum, Cnidaria) using restriction site-associated DNA sequencing. We analysed 27 461 single nucleotide polymorphisms (SNPs) in 354 individuals from 12 populations including 53 that were morphologically sexed. We found a strong association between the allele frequencies of 472 SNPs and the sex of individuals, suggesting an XX/XY sex-determination system. This result was confirmed by the identification of 435 male-specific loci. An independent test confirmed that the amplification of these loci enabled us to identify males with absolute certainty. This is the first demonstration of a GSD system among non-bilaterian species and a new example of its convergence in multicellular eukaryotes.},
}
@article {pmid28398223,
year = {2017},
author = {Cao, TJ and Huang, XQ and Qu, YY and Zhuang, Z and Deng, YY and Lu, S},
title = {Cloning and Functional Characterization of a Lycopene β-Cyclase from Macrophytic Red Alga Bangia fuscopurpurea.},
journal = {Marine drugs},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/md15040116},
pmid = {28398223},
issn = {1660-3397},
mesh = {Amino Acid Sequence ; Base Sequence ; Carotenoids/*genetics/*metabolism ; Cloning, Molecular/methods ; Escherichia coli/genetics ; Intramolecular Lyases/*genetics/*metabolism ; Photosynthesis/physiology ; Phylogeny ; Rhodophyta/*genetics/*metabolism ; Zeaxanthins/genetics/metabolism ; beta Carotene/genetics/metabolism ; },
abstract = {Lycopene cyclases cyclize the open ends of acyclic lycopene (ψ,ψ-carotene) into β- or ε-ionone rings in the crucial bifurcation step of carotenoid biosynthesis. Among all carotenoid constituents, β-carotene (β,β-carotene) is found in all photosynthetic organisms, except for purple bacteria and heliobacteria, suggesting a ubiquitous distribution of lycopene β-cyclase activity in these organisms. In this work, we isolated a gene (BfLCYB) encoding a lycopene β-cyclase from Bangia fuscopurpurea, a red alga that is considered to be one of the primitive multicellular eukaryotic photosynthetic organisms and accumulates carotenoid constituents with both β- and ε-rings, including β-carotene, zeaxanthin, α-carotene (β,ε-carotene) and lutein. Functional complementation in Escherichia coli demonstrated that BfLCYB is able to catalyze cyclization of lycopene into monocyclic γ-carotene (β,ψ-carotene) and bicyclic β-carotene, and cyclization of the open end of monocyclic δ-carotene (ε,ψ-carotene) to produce α-carotene. No ε-cyclization activity was identified for BfLCYB. Sequence comparison showed that BfLCYB shares conserved domains with other functionally characterized lycopene cyclases from different organisms and belongs to a group of ancient lycopene cyclases. Although B. fuscopurpurea also synthesizes α-carotene and lutein, its enzyme-catalyzing ε-cyclization is still unknown.},
}
@article {pmid28392224,
year = {2017},
author = {Schiffmann, Y},
title = {The non-equilibrium basis of Turing Instability and localised biological work.},
journal = {Progress in biophysics and molecular biology},
volume = {127},
number = {},
pages = {12-32},
doi = {10.1016/j.pbiomolbio.2017.04.002},
pmid = {28392224},
issn = {1873-1732},
mesh = {Adenosine Triphosphate/metabolism ; Animals ; *Biological Evolution ; Humans ; Hydrolysis ; *Models, Biological ; },
abstract = {Turing's theory for biological pattern formation is based on the instability of the homogeneous state, which occurs if certain key criteria are met. The problem of how chemical energy is converted to localised biological work requires one to understand not only the basis of localised power generation, but also the age-old puzzle of how organisms decrease their entropy; these problems can only be solved by the identification of the Turing Instability. At the heart of this is how natural selection, not chemistry, has fashioned the large non-equilibrium overall affinity (ΔG is a large negative quantity) for the oxidation of the fuel molecules. Natural selection has also resulted in the homeostasis at non-equilibrium values of the hydrolysis of molecules like ATP, GTP, which are the energy links between the overall oxidation of the fuel and biological work. The conditions for such homeostasis are central requirements for the Turing Instability and are the essence of being alive. The Turing-Child (TC) patterns are the spontaneous primary spatial cause not only of localised biological work in multicellular systems (especially those in patterning and development) but also of intracellular patterns including the mitotic spindle and the contractile ring. The Turing picture comprises the nonuniform distribution of the concentrations of the Turing morphogens, cAMP and ATP, and the Child picture is the resulting nonuniform distribution of the metabolic rate and of power. The TC pattern is shaped as the dominant eigenfunction in the combination of eigenfunctions which provides the spatial pattern of the Turing morphogens. The TC patterns and the bifurcation parameter manifest quantisation and symmetry as in music and in applications of quantum mechanics. The notion of correlation diagrams is also introduced.},
}
@article {pmid28384293,
year = {2017},
author = {Olariu, V and Nilsson, J and Jönsson, H and Peterson, C},
title = {Different reprogramming propensities in plants and mammals: Are small variations in the core network wirings responsible?.},
journal = {PloS one},
volume = {12},
number = {4},
pages = {e0175251},
doi = {10.1371/journal.pone.0175251},
pmid = {28384293},
issn = {1932-6203},
mesh = {Animals ; Mammals/*physiology ; Mice ; *Plant Physiological Phenomena ; },
abstract = {Although the plant and animal kingdoms were separated more than 1,6 billion years ago, multicellular development is for both guided by similar transcriptional, epigenetic and posttranscriptional machinery. One may ask to what extent there are similarities and differences in the gene regulation circuits and their dynamics when it comes to important processes like stem cell regulation. The key players in mouse embryonic stem cells governing pluripotency versus differentiation are Oct4, Sox2 and Nanog. Correspondingly, the WUSCHEL and CLAVATA3 genes represent a core in the Shoot Apical Meristem regulation for plants. In addition, both systems have designated genes that turn on differentiation. There is very little molecular homology between mammals and plants for these core regulators. Here, we focus on functional homologies by performing a comparison between the circuitry connecting these players in plants and animals and find striking similarities, suggesting that comparable regulatory logics have been evolved for stem cell regulation in both kingdoms. From in silico simulations we find similar differentiation dynamics. Further when in the differentiated state, the cells are capable of regaining the stem cell state. We find that the propensity for this is higher for plants as compared to mammalians. Our investigation suggests that, despite similarity in core regulatory networks, the dynamics of these can contribute to plant cells being more plastic than mammalian cells, i.e. capable to reorganize from single differentiated cells to whole plants-reprogramming. The presence of an incoherent feed-forward loop in the mammalian core circuitry could be the origin of the different reprogramming behaviour.},
}
@article {pmid28383827,
year = {2017},
author = {Palazzo, L and Mikoč, A and Ahel, I},
title = {ADP-ribosylation: new facets of an ancient modification.},
journal = {The FEBS journal},
volume = {284},
number = {18},
pages = {2932-2946},
doi = {10.1111/febs.14078},
pmid = {28383827},
issn = {1742-4658},
support = {101794//Wellcome Trust/United Kingdom ; C35050/A22284//Cancer Research UK/United Kingdom ; },
mesh = {ADP Ribose Transferases/*genetics/metabolism ; Aging/genetics/*metabolism ; Animals ; Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Biological Evolution ; DNA Damage ; *DNA Repair ; DNA Replication ; Gene Expression ; Humans ; Isoenzymes/genetics/metabolism ; Phosphoric Diester Hydrolases/genetics/metabolism ; Poly Adenosine Diphosphate Ribose/*metabolism ; *Protein Processing, Post-Translational ; Pyrophosphatases/genetics/metabolism ; Signal Transduction ; Viruses/genetics/metabolism ; },
abstract = {Rapid response to environmental changes is achieved by uni- and multicellular organisms through a series of molecular events, often involving modification of macromolecules, including proteins, nucleic acids and lipids. Amongst these, ADP-ribosylation is of emerging interest because of its ability to modify different macromolecules in the cells, and its association with many key biological processes, such as DNA-damage repair, DNA replication, transcription, cell division, signal transduction, stress and infection responses, microbial pathogenicity and aging. In this review, we provide an update on novel pathways and mechanisms regulated by ADP-ribosylation in organisms coming from all kingdoms of life.},
}
@article {pmid28368386,
year = {2017},
author = {Barber, J},
title = {A mechanism for water splitting and oxygen production in photosynthesis.},
journal = {Nature plants},
volume = {3},
number = {},
pages = {17041},
doi = {10.1038/nplants.2017.41},
pmid = {28368386},
issn = {2055-0278},
mesh = {Biological Evolution ; Models, Biological ; Oxidation-Reduction ; Oxygen/*metabolism ; *Photosynthesis ; Photosystem II Protein Complex/*chemistry ; Plants/*metabolism ; Water/*metabolism ; },
abstract = {Sunlight is absorbed and converted to chemical energy by photosynthetic organisms. At the heart of this process is the most fundamental reaction on Earth, the light-driven splitting of water into its elemental constituents. In this way molecular oxygen is released, maintaining an aerobic atmosphere and creating the ozone layer. The hydrogen that is released is used to convert carbon dioxide into the organic molecules that constitute life and were the origin of fossil fuels. Oxidation of these organic molecules, either by respiration or combustion, leads to the recombination of the stored hydrogen with oxygen, releasing energy and reforming water. This water splitting is achieved by the enzyme photosystem II (PSII). Its appearance at least 3 billion years ago, and linkage through an electron transfer chain to photosystem I, directly led to the emergence of eukaryotic and multicellular organisms. Before this, biological organisms had been dependent on hydrogen/electron donors, such as H2S, NH3, organic acids and Fe2+, that were in limited supply compared with the oceans of liquid water. However, it is likely that water was also used as a hydrogen source before the emergence of PSII, as found today in anaerobic prokaryotic organisms that use carbon monoxide as an energy source to split water. The enzyme that catalyses this reaction is carbon monoxide dehydrogenase (CODH). Similarities between PSII and the iron- and nickel-containing form of this enzyme (Fe-Ni CODH) suggest a possible mechanism for the photosynthetic O-O bond formation.},
}
@article {pmid28359330,
year = {2017},
author = {Szafranski, P},
title = {Evolutionarily recent, insertional fission of mitochondrial cox2 into complementary genes in bilaterian Metazoa.},
journal = {BMC genomics},
volume = {18},
number = {1},
pages = {269},
doi = {10.1186/s12864-017-3626-5},
pmid = {28359330},
issn = {1471-2164},
mesh = {Animals ; Electron Transport Complex IV/chemistry/*genetics ; *Evolution, Molecular ; Gene Expression Regulation ; *Genes, Mitochondrial ; Genome, Mitochondrial ; Hydrophobic and Hydrophilic Interactions ; Mitochondrial Dynamics/*genetics ; *Mutagenesis, Insertional ; Phylogeny ; Polyadenylation ; },
abstract = {BACKGROUND: Mitochondrial genomes (mtDNA) of multicellular animals (Metazoa) with bilateral symmetry (Bilateria) are compact and usually carry 13 protein-coding genes for subunits of three respiratory complexes and ATP synthase. However, occasionally reported exceptions to this typical mtDNA organization prompted speculation that, as in protists and plants, some bilaterian mitogenomes may continue to lose their canonical genes, or may even acquire new genes. To shed more light on this phenomenon, a PCR-based screen was conducted to assess fast-evolving mtDNAs of apocritan Hymenoptera (Arthropoda, Insecta) for genomic rearrangements that might be associated with the modification of mitochondrial gene content.<br><br>RESULTS: Sequencing of segmental inversions, identified in the screen, revealed that the cytochrome oxidase subunit II gene (cox2) of Campsomeris (Dielis) (Scoliidae) was split into two genes coding for COXIIA and COXIIB. The COXII-derived complementary polypeptides apparently form a heterodimer, have reduced hydrophobicity compared with the majority of mitogenome-encoded COX subunits, and one of them, COXIIB, features increased content of Cys residues. Analogous cox2 fragmentation is known only in two clades of protists (chlorophycean algae and alveolates), where it has been associated with piecewise relocation of this gene into the nucleus. In Campsomeris mtDNA, cox2a and cox2b loci are separated by a 3-kb large cluster of several antiparallel overlapping ORFs, one of which, qnu, seems to encode a nuclease that may have played a role in cox2 fission.<br><br>CONCLUSIONS: Although discontinuous mitochondrial protein genes encoding fragmented, complementary polypeptides are known in protists and some plants, split cox2 of Campsomeris is the first case of such a gene arrangement found in animals. The reported data also indicate that bilaterian animal mitogenomes may be carrying lineage-specific genes more often than previously thought, and suggest a homing endonuclease-based mechanism for insertional mitochondrial gene fission.},
}
@article {pmid28357395,
year = {2017},
author = {Mignot, T and Nöllmann, M},
title = {New insights into the function of a versatile class of membrane molecular motors from studies of Myxococcus xanthus surface (gliding) motility.},
journal = {Microbial cell (Graz, Austria)},
volume = {4},
number = {3},
pages = {98-100},
doi = {10.15698/mic2017.03.563},
pmid = {28357395},
issn = {2311-2638},
abstract = {Cell motility is a central function of living cells, as it empowers colonization of new environmental niches, cooperation, and development of multicellular organisms. This process is achieved by complex yet precise energy-consuming machineries in both eukaryotes and bacteria. Bacteria move on surfaces using extracellular appendages such as flagella and pili but also by a less-understood process called gliding motility. During this process, rod-shaped bacteria move smoothly along their long axis without any visible morphological changes besides occasional bending. For this reason, the molecular mechanism of gliding motility and its origin have long remained a complete mystery. An important breakthrough in the understanding of gliding motility came from single cell and genetic studies in the delta-proteobacterium Myxococcus xanthus. These early studies revealed, for the first time, the existence of bacterial Focal Adhesion complexes (FA). FAs are formed at the bacterial pole and rapidly move towards the opposite cell pole. Their attachment to the underlying surface is linked to cell propulsion, in a process similar to the rearward translocation of actomyosin complexes in Apicomplexans. The protein machinery that forms at FAs was shown to contain up to seventeen proteins predicted to localize in all layers of the bacterial cell envelope, the cytosolic face, the inner membrane (IM), the periplasmic space and the outer membrane (OM). Among these proteins, a proton-gated channel at the inner membrane was identified as the molecular motor. Thus, thrust generation requires the transduction of traction forces generated at the inner membrane through the cell envelope beyond the rigid barrier of the bacterial peptidoglycan.},
}
@article {pmid28355288,
year = {2017},
author = {Werfel, J and Ingber, DE and Bar-Yam, Y},
title = {Theory and associated phenomenology for intrinsic mortality arising from natural selection.},
journal = {PloS one},
volume = {12},
number = {3},
pages = {e0173677},
doi = {10.1371/journal.pone.0173677},
pmid = {28355288},
issn = {1932-6203},
mesh = {Aging/*physiology ; Animals ; Biological Evolution ; Herbivory/physiology ; Host-Pathogen Interactions ; Longevity/*physiology ; *Models, Biological ; *Models, Statistical ; Plants ; Poaceae/physiology ; Predatory Behavior/physiology ; Reproduction/physiology ; Selection, Genetic/*physiology ; },
abstract = {Standard evolutionary theories of aging and mortality, implicitly based on assumptions of spatial averaging, hold that natural selection cannot favor shorter lifespan without direct compensating benefit to individual reproductive success. However, a number of empirical observations appear as exceptions to or are difficult to reconcile with this view, suggesting explicit lifespan control or programmed death mechanisms inconsistent with the classic understanding. Moreover, evolutionary models that take into account the spatial distributions of populations have been shown to exhibit a variety of self-limiting behaviors, maintained through environmental feedback. Here we extend recent work on spatial modeling of lifespan evolution, showing that both theory and phenomenology are consistent with programmed death. Spatial models show that self-limited lifespan robustly results in long-term benefit to a lineage; longer-lived variants may have a reproductive advantage for many generations, but shorter lifespan ultimately confers long-term reproductive advantage through environmental feedback acting on much longer time scales. Numerous model variations produce the same qualitative result, demonstrating insensitivity to detailed assumptions; the key conditions under which self-limited lifespan is favored are spatial extent and locally exhaustible resources. Factors including lower resource availability, higher consumption, and lower dispersal range are associated with evolution of shorter lifespan. A variety of empirical observations can parsimoniously be explained in terms of long-term selective advantage for intrinsic mortality. Classically anomalous empirical data on natural lifespans and intrinsic mortality, including observations of longer lifespan associated with increased predation, and evidence of programmed death in both unicellular and multicellular organisms, are consistent with specific model predictions. The generic nature of the spatial model conditions under which intrinsic mortality is favored suggests a firm theoretical basis for the idea that evolution can quite generally select for shorter lifespan directly.},
}
@article {pmid28342854,
year = {2017},
author = {Holzer, G and Roux, N and Laudet, V},
title = {Evolution of ligands, receptors and metabolizing enzymes of thyroid signaling.},
journal = {Molecular and cellular endocrinology},
volume = {459},
number = {},
pages = {5-13},
doi = {10.1016/j.mce.2017.03.021},
pmid = {28342854},
issn = {1872-8057},
mesh = {Animals ; Biological Evolution ; Cnidaria/anatomy &amp; histology/physiology ; Gene Expression Regulation, Developmental ; Humans ; Insecta/anatomy &amp; histology/physiology ; Iodide Peroxidase/genetics/*metabolism ; Ligands ; Phylogeny ; Receptors, Thyroid Hormone/genetics/*metabolism ; Signal Transduction/*physiology ; Species Specificity ; Thyroid Gland/*physiology ; Thyroxine/genetics/*metabolism ; Triiodothyronine/analogs &amp; derivatives/genetics/*metabolism ; },
abstract = {Thyroid hormones (THs) play important roles in vertebrates such as the control of the metabolism, development and seasonality. Given the pleiotropic effects of thyroid disorders (developmental delay, mood disorder, tachycardia, etc), THs signaling is highly investigated, specially using mammalian models. In addition, the critical role of TH in controlling frog metamorphosis has led to the use of Xenopus as another prominent model to study THs action. Nevertheless, animals regarded as non-model species can also improve our understanding of THs signaling. For instance, studies in amphioxus highlighted the role of Triac as a bona fide thyroid hormone receptor (TR) ligand. In this review, we discuss our current understanding of the THs signaling in the different taxa forming the metazoans (multicellular animals) group. We mainly focus on three actors of the THs signaling: the ligand, the receptor and the deiodinases, enzymes playing a critical role in THs metabolism. By doing so, we also pinpoint many key questions that remain unanswered. How can THs accelerate metamorphosis in tunicates and echinoderms while their TRs have not been yet demonstrated as functional THs receptors in these species? Do THs have a biological effect in insects and cnidarians even though they do not have any TR? What is the basic function of THs in invertebrate protostomia? These questions can appear disconnected from pharmacological issues and human applications, but the investigation of THs signaling at the metazoans scale can greatly improve our understanding of this major endocrinological pathway.},
}
@article {pmid28317949,
year = {2017},
author = {Rudd, TR and Preston, MD and Yates, EA},
title = {The nature of the conserved basic amino acid sequences found among 437 heparin binding proteins determined by network analysis.},
journal = {Molecular bioSystems},
volume = {13},
number = {5},
pages = {852-865},
doi = {10.1039/c6mb00857g},
pmid = {28317949},
issn = {1742-2051},
mesh = {Amino Acid Sequence ; Binding Sites ; Computational Biology/methods ; Conserved Sequence ; Heparin/*metabolism ; Heparitin Sulfate/*metabolism ; Humans ; Models, Molecular ; Protein Binding ; Protein Interaction Maps ; Proteins/*chemistry/*metabolism ; },
abstract = {In multicellular organisms, a large number of proteins interact with the polyanionic polysaccharides heparan sulphate (HS) and heparin. These interactions are usually assumed to be dominated by charge-charge interactions between the anionic carboxylate and/or sulfate groups of the polysaccharide and cationic amino acids of the protein. A major question is whether there exist conserved amino acid sequences for HS/heparin binding among these diverse proteins. Potentially conserved HS/heparin binding sequences were sought amongst 437 HS/heparin binding proteins. Amino acid sequences were extracted and compared using a Levenshtein distance metric. The resultant similarity matrices were visualised as graphs, enabling extraction of strongly conserved sequences from highly variable primary sequences while excluding short, core regions. This approach did not reveal extensive, conserved HS/heparin binding sequences, rather a number of shorter, more widely spaced sequences that may work in unison to form heparin-binding sites on protein surfaces, arguing for convergent evolution. Thus, it is the three-dimensional arrangement of these conserved motifs on the protein surface, rather than the primary sequence per se, which are the evolutionary elements.},
}
@article {pmid28294448,
year = {2017},
author = {Inglis, RF and Ryu, E and Asikhia, O and Strassmann, JE and Queller, DC},
title = {Does high relatedness promote cheater-free multicellularity in synthetic lifecycles?.},
journal = {Journal of evolutionary biology},
volume = {30},
number = {5},
pages = {985-993},
doi = {10.1111/jeb.13067},
pmid = {28294448},
issn = {1420-9101},
mesh = {*Biological Evolution ; Dictyostelium/*growth &amp; development ; *Life Cycle Stages ; },
abstract = {The evolution of multicellularity is one of the key transitions in evolution and requires extreme levels of cooperation between cells. However, even when cells are genetically identical, noncooperative cheating mutants can arise that cause a breakdown in cooperation. How then, do multicellular organisms maintain cooperation between cells? A number of mechanisms that increase relatedness amongst cooperative cells have been implicated in the maintenance of cooperative multicellularity including single-cell bottlenecks and kin recognition. In this study, we explore how relatively simple biological processes such as growth and dispersal can act to increase relatedness and promote multicellular cooperation. Using experimental populations of pseudo-organisms, we found that manipulating growth and dispersal of clones of a social amoeba to create high levels of relatedness was sufficient to prevent the spread of cheating mutants. By contrast, cheaters were able to spread under low-relatedness conditions. Most surprisingly, we saw the largest increase in cheating mutants under an experimental treatment that should create intermediate levels of relatedness. This is because one of the factors raising relatedness, structured growth, also causes high vulnerability to growth rate cheaters.},
}
@article {pmid28291791,
year = {2017},
author = {Bengtson, S and Sallstedt, T and Belivanova, V and Whitehouse, M},
title = {Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae.},
journal = {PLoS biology},
volume = {15},
number = {3},
pages = {e2000735},
doi = {10.1371/journal.pbio.2000735},
pmid = {28291791},
issn = {1545-7885},
mesh = {*Fossils ; Geologic Sediments ; *Geological Phenomena ; India ; Phylogeny ; Radiometry ; Rhodophyta/*cytology/ultrastructure ; Subcellular Fractions/metabolism ; Time Factors ; },
abstract = {The ~1.6 Ga Tirohan Dolomite of the Lower Vindhyan in central India contains phosphatized stromatolitic microbialites. We report from there uniquely well-preserved fossils interpreted as probable crown-group rhodophytes (red algae). The filamentous form Rafatazmia chitrakootensis n. gen, n. sp. has uniserial rows of large cells and grows through diffusely distributed septation. Each cell has a centrally suspended, conspicuous rhomboidal disk interpreted as a pyrenoid. The septa between the cells have central structures that may represent pit connections and pit plugs. Another filamentous form, Denaricion mendax n. gen., n. sp., has coin-like cells reminiscent of those in large sulfur-oxidizing bacteria but much more recalcitrant than the liquid-vacuole-filled cells of the latter. There are also resemblances with oscillatoriacean cyanobacteria, although cell volumes in the latter are much smaller. The wider affinities of Denaricion are uncertain. Ramathallus lobatus n. gen., n. sp. is a lobate sessile alga with pseudoparenchymatous thallus, &quot;cell fountains,&quot; and apical growth, suggesting florideophycean affinity. If these inferences are correct, Rafatazmia and Ramathallus represent crown-group multicellular rhodophytes, antedating the oldest previously accepted red alga in the fossil record by about 400 million years.},
}
@article {pmid28284906,
year = {2017},
author = {Lochab, AK and Extavour, CG},
title = {Bone Morphogenetic Protein (BMP) signaling in animal reproductive system development and function.},
journal = {Developmental biology},
volume = {427},
number = {2},
pages = {258-269},
doi = {10.1016/j.ydbio.2017.03.002},
pmid = {28284906},
issn = {1095-564X},
mesh = {Animals ; *Biological Evolution ; Bone Morphogenetic Proteins/*metabolism ; Cell Lineage ; Genitalia/embryology/*metabolism ; *Germ Cells/metabolism ; Humans ; Reproduction ; Signal Transduction ; },
abstract = {In multicellular organisms, the specification, maintenance, and transmission of the germ cell lineage to subsequent generations are critical processes that ensure species survival. A number of studies suggest that the Bone Morphogenetic Protein (BMP) pathway plays multiple roles in this cell lineage. We wished to use a comparative framework to examine the role of BMP signaling in regulating these processes, to determine if patterns would emerge that might shed light on the evolution of molecular mechanisms that may play germ cell-specific or other reproductive roles across species. To this end, here we review evidence to date from the literature supporting a role for BMP signaling in reproductive processes across Metazoa. We focus on germ line-specific processes, and separately consider somatic reproductive processes. We find that from primordial germ cell (PGC) induction to maintenance of PGC identity and gametogenesis, BMP signaling regulates these processes throughout embryonic development and adult life in multiple deuterostome and protostome clades. In well-studied model organisms, functional genetic evidence suggests that BMP signaling is required in the germ line across all life stages, with the exception of PGC specification in species that do not use inductive signaling to induce germ cell formation. The current evidence is consistent with the hypothesis that BMP signaling is ancestral in bilaterian inductive PGC specification. While BMP4 appears to be the most broadly employed ligand for the reproductive processes considered herein, we also noted evidence for sex-specific usage of different BMP ligands. In gametogenesis, BMP6 and BMP15 seem to have roles restricted to oogenesis, while BMP8 is restricted to spermatogenesis. We hypothesize that a BMP-based mechanism may have been recruited early in metazoan evolution to specify the germ line, and was subsequently co-opted for use in other germ line-specific and somatic reproductive processes. We suggest that if future studies assessing the function of the BMP pathway across extant species were to include a reproductive focus, that we would be likely to find continued evidence in favor of an ancient association between BMP signaling and the reproductive cell lineage in animals.},
}
@article {pmid28258564,
year = {2017},
author = {Ishibashi, K and Morishita, Y and Tanaka, Y},
title = {The Evolutionary Aspects of Aquaporin Family.},
journal = {Advances in experimental medicine and biology},
volume = {969},
number = {},
pages = {35-50},
doi = {10.1007/978-94-024-1057-0_2},
pmid = {28258564},
issn = {0065-2598},
mesh = {Amino Acid Sequence ; Animals ; Aquaporins/chemistry/classification/*genetics/metabolism ; Biological Evolution ; Biological Transport ; Conserved Sequence ; Fungi/classification/*genetics/metabolism ; Gene Duplication ; Gene Expression ; Gene Transfer, Horizontal ; Invertebrates/classification/*genetics/metabolism ; Phylogeny ; Plants/classification/*genetics/metabolism ; Prokaryotic Cells/classification/*metabolism ; Protein Domains ; Vertebrates/classification/*genetics/metabolism ; },
abstract = {Aquaporins (AQPs) are a family of transmembrane proteins present in almost all species including virus. They are grossly divided into three subfamilies based on the sequence around a highly conserved pore-forming NPA motif: (1) classical water -selective AQP (CAQP), (2) glycerol -permeable aquaglyceroporin (AQGP) and (3) AQP super-gene channel, superaquaporin (SAQP). AQP is composed of two tandem repeats of conserved three transmembrane domains and a NPA motif. AQP ancestors probably started in prokaryotes by the duplication of half AQP genes to be diversified into CAQPs or AQGPs by evolving a subfamily-specific carboxyl-terminal NPA motif. Both AQP subfamilies may have been carried over to unicellular eukaryotic ancestors, protists and further to multicellular organisms. Although fungus lineage has kept both AQP subfamilies, the plant lineage has lost AQGP after algal ancestors with extensive diversifications of CAQPs into PIP, TIP, SIP, XIP, HIP and LIP with a possible horizontal transfer of NIP from bacteria. Interestingly, the animal lineage has obtained new SAQP subfamily with highly deviated NPA motifs, especially at the amino-terminal halves in both prostomial and deuterostomial animals. The prostomial lineage has lost AQGP after hymenoptera, while the deuterostomial lineage has kept all three subfamilies up to the vertebrate with diversified CAQPs (AQP0, 1, 2, 4, 5, 6, 8) and AQGPs (AQP3, 7, 9, 10) with limited SAQPs (AQP11, 12) in mammals. Whole-genome duplications, local gene duplications and horizontal gene transfers may have produced the AQP diversity with adaptive selections and functional alternations in response to environment changes. With the above evolutionary perspective in mind, the function of each AQP could be speculated by comparison among species to get new insights into physiological roles of AQPs . This evolutionary guidance in AQP research will lead to deeper understandings of water and solute homeostasis.},
}
@article {pmid28253955,
year = {2017},
author = {López-Otín, C and Mariño, G},
title = {Tagged ATG8-Coding Constructs for the In Vitro and In Vivo Assessment of ATG4 Activity.},
journal = {Methods in enzymology},
volume = {587},
number = {},
pages = {189-205},
doi = {10.1016/bs.mie.2016.11.001},
pmid = {28253955},
issn = {1557-7988},
mesh = {Animals ; Autophagy ; Autophagy-Related Protein 8 Family/*genetics/metabolism ; Autophagy-Related Proteins/genetics/metabolism ; Cells, Cultured ; Cysteine Endopeptidases/analysis/genetics/*metabolism ; Genetic Vectors ; Humans ; Mammals/genetics ; Mice ; Molecular Biology/*methods ; Recombinant Proteins/genetics/metabolism ; Transfection ; },
abstract = {Autophagy is a catabolic pathway, which mediates the degradation of cytoplasmic components and sustains many essential cellular functions. More than 30 genes have been involved in different aspects of this essential process in simple eukaryotes as yeast. Among these genes, those coding for members of the Atg4-Atg8 proteolytic system have acquired a high degree of complexity throughout evolution. Contrasting with the situation in unicellular eukaryotes, in which the system is composed by just a single protease (Atg4) and a single substrate (Atg8), evolution has led to the presence of several members for both Atg4 and Atg8 families in multicellular organisms. In human cells, there are four Atg4 proteases and six Atg8 substrates, which have probably evolved to cope with specific requirements for autophagic pathway in more complex scenarios. Despite these considerations, the reasons for the evolutionarily acquired complexity of this proteolytic system are still not completely understood. In this work, we describe two different applications of a relatively simple but useful technique to analyze protease-substrate specificity of this system in mammalian cells. By using the described technique, it is possible to determine the cellular efficiency in the initial cleavage for each of the Atg8 family members in diverse experimental settings both in cultured cells and live laboratory mice.},
}
@article {pmid28250339,
year = {2017},
author = {Cahill, MA},
title = {The evolutionary appearance of signaling motifs in PGRMC1.},
journal = {Bioscience trends},
volume = {11},
number = {2},
pages = {179-192},
doi = {10.5582/bst.2017.01009},
pmid = {28250339},
issn = {1881-7823},
mesh = {Animals ; Humans ; Membrane Proteins/genetics/*metabolism ; Receptors, Progesterone/genetics/*metabolism ; Signal Transduction/genetics/physiology ; },
abstract = {A complex PGRMC1-centred regulatory system controls multiple cell functions. Although PGRMC1 is phosphorylated at several positions, we do not understand the mechanisms regulating its function. PGRMC1 is the archetypal member of the membrane associated progesterone receptor (MAPR) family. Phylogentic comparison of MAPR proteins suggests that the ancestral metazoan &quot;PGRMC-like&quot; MAPR gene resembled PGRMC1/PGRMC2, containing the equivalents of PGRMC1 Y139 and Y180 SH2 target motifs. It later acquired a CK2 site with phosphoacceptor at S181. Separate PGRMC1 and PGRMC2 genes with this &quot;PGRMC-like&quot; structure diverged after the separation of vertebrates from protochordates. Terrestrial tetrapods possess a novel proline-rich PGRMC1 SH3 target motif centred on P64 which in mammals is augmented by a phosphoacceptor at PGRMC1 S54, and in primates by an additional S57 CK2 site. All of these phosphoacceptors are phosphorylated in vivo. This study suggests that an increasingly sophisticated system of PGRMC1-modulated multicellular functional regulation has characterised animal evolution since Precambrian times.},
}
@article {pmid28241893,
year = {2017},
author = {Zemková, M and Zahradník, D and Mokrejš, M and Flegr, J},
title = {Parasitism as the main factor shaping peptide vocabularies in current organisms.},
journal = {Parasitology},
volume = {144},
number = {7},
pages = {975-983},
doi = {10.1017/S0031182017000191},
pmid = {28241893},
issn = {1469-8161},
mesh = {Animals ; *Biological Evolution ; Helminth Proteins/*analysis ; *Host-Parasite Interactions ; Peptides/*analysis ; *Proteome ; Protozoan Proteins/*analysis ; },
abstract = {Self/non-self-discrimination by vertebrate immune systems is based on the recognition of the presence of peptides in proteins of a parasite that are not contained in the proteins of a host. Therefore, a reduction of the number of 'words' in its own peptide vocabulary could be an efficient evolutionary strategy of parasites for escaping recognition. Here, we compared peptide vocabularies of 30 endoparasitic and 17 free-living unicellular organisms and also eight multicellular parasitic and 16 multicellular free-living organisms. We found that both unicellular and multicellular parasites used a significantly lower number of different pentapeptides than free-living controls. Impoverished pentapeptide vocabularies in parasites were observed across all five clades that contain both the parasitic and free-living species. The effect of parasitism on a number of peptides used in an organism's proteins is larger than effects of all other studied factors, including the size of a proteome, the number of encoded proteins, etc. This decrease of pentapeptide diversity was partly compensated for by an increased number of hexapeptides. Our results support the hypothesis of parasitism-associated reduction of peptide vocabulary and suggest that T-cell receptors mostly recognize the five amino acids-long part of peptides that are presented in the groove of major histocompatibility complex molecules.},
}
@article {pmid28222679,
year = {2017},
author = {Skippington, E and Barkman, TJ and Rice, DW and Palmer, JD},
title = {Comparative mitogenomics indicates respiratory competence in parasitic Viscum despite loss of complex I and extreme sequence divergence, and reveals horizontal gene transfer and remarkable variation in genome size.},
journal = {BMC plant biology},
volume = {17},
number = {1},
pages = {49},
doi = {10.1186/s12870-017-0992-8},
pmid = {28222679},
issn = {1471-2229},
mesh = {DNA, Plant ; Electron Transport Chain Complex Proteins/genetics ; Electron Transport Complex I/*genetics/metabolism ; *Evolution, Molecular ; Gene Deletion ; *Gene Transfer, Horizontal ; Genes, Plant ; *Genetic Variation ; Genome, Mitochondrial ; *Genome, Plant ; Molecular Sequence Annotation ; Plant Proteins/genetics ; RNA, Plant ; RNA, Ribosomal ; Sequence Analysis, DNA ; Species Specificity ; Viscum/*genetics/metabolism ; Viscum album/genetics/metabolism ; },
abstract = {BACKGROUND: Aerobically respiring eukaryotes usually contain four respiratory-chain complexes (complexes I-IV) and an ATP synthase (complex V). In several lineages of aerobic microbial eukaryotes, complex I has been lost, with an alternative, nuclear-encoded NADH dehydrogenase shown in certain cases to bypass complex I and oxidize NADH without proton translocation. The first loss of complex I in any multicellular eukaryote was recently reported in two studies; one sequenced the complete mitogenome of the hemiparasitic aerial mistletoe, Viscum scurruloideum, and the other sequenced the V. album mitogenome. The V. scurruloideum study reported no significant additional loss of mitochondrial genes or genetic function, but the V. album study postulated that mitochondrial genes encoding all ribosomal RNAs and proteins of all respiratory complexes are either absent or pseudogenes, thus raising questions as to whether the mitogenome and oxidative respiration are functional in this plant.<br><br>RESULTS: To determine whether these opposing conclusions about the two Viscum mitogenomes reflect a greater degree of reductive/degenerative evolution in V. album or instead result from interpretative and analytical differences, we reannotated and reanalyzed the V. album mitogenome and compared it with the V. scurruloideum mitogenome. We find that the two genomes share a complete complement of mitochondrial rRNA genes and a typical complement of genes encoding respiratory complexes II-V. Most Viscum mitochondrial protein genes exhibit very high levels of divergence yet are evolving under purifying, albeit relaxed selection. We discover two cases of horizontal gene transfer in V. album and show that the two Viscum mitogenomes differ by 8.6-fold in size (66 kb in V. scurruloideum; 565 kb in V. album).<br><br>CONCLUSIONS: Viscum mitogenomes are extraordinary compared to other plant mitogenomes in terms of their wide size range, high rates of synonymous substitutions, degree of relaxed selection, and unprecedented loss of respiratory complex I. However, contrary to the initial conclusions regarding V. album, both Viscum mitogenomes possess conventional sets of rRNA and, excepting complex I, respiratory genes. Both plants should therefore be able to carry out aerobic respiration. Moreover, with respect to size, the V. scurruloideum mitogenome has experienced a greater level of reductive evolution.},
}
@article {pmid28214944,
year = {2017},
author = {Basile, A and Fambrini, M and Pugliesi, C},
title = {The vascular plants: open system of growth.},
journal = {Development genes and evolution},
volume = {227},
number = {2},
pages = {129-157},
doi = {10.1007/s00427-016-0572-1},
pmid = {28214944},
issn = {1432-041X},
mesh = {*Evolution, Molecular ; Magnoliopsida/*genetics/growth &amp; development/metabolism ; Meristem/*genetics/growth &amp; development/metabolism ; Plant Growth Regulators/metabolism ; Plant Proteins/genetics/metabolism ; },
abstract = {What is fascinating in plants (true also in sessile animals such as corals and hydroids) is definitely their open and indeterminate growth, as a result of meristematic activity. Plants as well as animals are characterized by a multicellular organization, with which they share a common set of genes inherited from a common eukaryotic ancestor; nevertheless, circa 1.5 billion years of evolutionary history made the two kingdoms very different in their own developmental biology. Flowering plants, also known as angiosperms, arose during the Cretaceous Period (145-65 million years ago), and up to date, they count around 235,000 species, representing the largest and most diverse group within the plant kingdom. One of the foundations of their success relies on the plant-pollinator relationship, essentially unique to angiosperms that pushed large speciation in both plants and insects and on the presence of the carpel, the structure devoted to seed enclosure. A seed represents the main organ preserving the genetic information of a plant; during embryogenesis, the primary axis of development is established by two groups of pluripotent cells: the shoot apical meristem (SAM), responsible for gene rating all aboveground organs, and the root apical meristem (RAM), responsible for producing all underground organs. During postembryonic shoot development, axillary meristem (AM) initiation and outgrowth are responsible for producing all secondary axes of growth including inflorescence branches or flowers. The production of AMs is tightly linked to the production of leaves and their separation from SAM. As leaf primordia are formed on the flanks of the SAM, a region between the apex and the developing organ is established and referred to as boundary zone. Interaction between hormones and the gene network in the boundary zone is fundamental for AM initiation. AMs only develop at the adaxial base of the leaf; thus, AM initiation is also strictly associated with leaf polarity. AMs function as new SAMs: form axillary buds with a few leaves and then the buds can either stay dormant or develop into shoot branches to define a plant architecture, which in turn affects assimilate production and reproductive efficiency. Therefore, the radiation of angiosperms was accompanied by a huge diversification in growth forms that determine an enormous morphological plasticity helping plants to environmental changes. In this review, we focused on the developmental processes of AM initiation and outgrowth. In particular, we summarized the primary growth of SAM, the key role of positional signals for AM initiation, and the dissection of molecular players involved in AM initiation and outgrowth. Finally, the interaction between phytohormone signals and gene regulatory network controlling AM development was discussed.},
}
@article {pmid28207760,
year = {2017},
author = {Neeb, ZT and Hogan, DJ and Katzman, S and Zahler, AM},
title = {Preferential expression of scores of functionally and evolutionarily diverse DNA and RNA-binding proteins during Oxytricha trifallax macronuclear development.},
journal = {PloS one},
volume = {12},
number = {2},
pages = {e0170870},
doi = {10.1371/journal.pone.0170870},
pmid = {28207760},
issn = {1932-6203},
support = {T32 GM008646/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; DNA, Protozoan/*genetics ; *Evolution, Molecular ; *Gene Expression Profiling ; Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Macronucleus/genetics/*metabolism ; Oxytricha/genetics/growth &amp; development/*metabolism ; Phylogeny ; Protozoan Proteins/genetics/*metabolism ; RNA-Binding Proteins/genetics/*metabolism ; },
abstract = {During its sexual reproduction, the stichotrichous ciliate Oxytricha trifallax orchestrates a remarkable transformation of one of the newly formed germline micronuclear genomes. Hundreds of thousands of gene pieces are stitched together, excised from chromosomes, and replicated dozens of times to yield a functional somatic macronuclear genome composed of ~16,000 distinct DNA molecules that typically encode a single gene. Little is known about the proteins that carry out this process. We profiled mRNA expression as a function of macronuclear development and identified hundreds of mRNAs preferentially expressed at specific times during the program. We find that a disproportionate number of these mRNAs encode proteins that are involved in DNA and RNA functions. Many mRNAs preferentially expressed during macronuclear development have paralogs that are either expressed constitutively or are expressed at different times during macronuclear development, including many components of the RNA polymerase II machinery and homologous recombination complexes. Hundreds of macronuclear development-specific genes encode proteins that are well-conserved among multicellular eukaryotes, including many with links to germline functions or development. Our work implicates dozens of DNA and RNA-binding proteins with diverse evolutionary trajectories in macronuclear development in O. trifallax. It suggests functional connections between the process of macronuclear development in unicellular ciliates and germline specialization and differentiation in multicellular organisms, and argues that gene duplication is a key source of evolutionary innovation in this process.},
}
@article {pmid28204813,
year = {2017},
author = {Agnati, LF and Marcoli, M and Leo, G and Maura, G and Guidolin, D},
title = {Homeostasis and the concept of 'interstitial fluids hierarchy': Relevance of cerebrospinal fluid sodium concentrations and brain temperature control (Review).},
journal = {International journal of molecular medicine},
volume = {39},
number = {3},
pages = {487-497},
doi = {10.3892/ijmm.2017.2874},
pmid = {28204813},
issn = {1791-244X},
mesh = {Animals ; Biological Evolution ; Body Temperature Regulation ; Brain/*physiology ; Cerebrospinal Fluid/metabolism ; Extracellular Fluid/*metabolism ; Feedback, Physiological ; *Homeostasis ; Humans ; Kidney/physiology ; Sodium/metabolism ; },
abstract = {In this review, the aspects and further developments of the concept of homeostasis are discussed also in the perspective of their possible impact in the clinical practice, particularly as far as psychic homeostasis is concerned. A brief historical survey and comments on the concept of homeostasis and allostasis are presented to introduce our proposal that is based on the classical assumption of the interstitial fluid (ISF) as the internal medium for multicellular organisms. However, the new concept of a hierarchic role of ISF of the various organs is introduced. Additionally, it is suggested that particularly for some chemico‑physical parameters, oscillatory rhythms within their proper set‑ranges should be considered a fundamental component of homeostasis. Against this background, we propose that the brain ISF has the highest hierarchic role in human beings, providing the optimal environment, not simply for brain cell survival, but also for brain complex functions and the oscillatory rhythms of some parameters, such as cerebrospinal fluid sodium and brain ISF pressure waves, which may play a crucial role in brain physio‑pathological states. Thus, according to this proposal, the brain ISF represents the real internal medium since the maintenance of its dynamic intra-set-range homeostasis is the main factor for a free and independent life of higher vertebrates. Furthermore, the evolutionary links between brain and kidney and their synergistic role in H2O/Na balance and brain temperature control are discussed. Finally, it is surmised that these two interrelated parameters have deep effects on the Central Nervous System (CNS) higher integrative actions such those linked to psychic homeostasis.},
}
@article {pmid28189637,
year = {2017},
author = {Sieber, KB and Bromley, RE and Dunning Hotopp, JC},
title = {Lateral gene transfer between prokaryotes and eukaryotes.},
journal = {Experimental cell research},
volume = {358},
number = {2},
pages = {421-426},
doi = {10.1016/j.yexcr.2017.02.009},
pmid = {28189637},
issn = {1090-2422},
support = {DP2 OD007372/OD/NIH HHS/United States ; R01 CA206188/CA/NCI NIH HHS/United States ; T32 DK067872/DK/NIDDK NIH HHS/United States ; 1-R01-CA206188/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Bacteria/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics/physiology ; Humans ; Mitochondria/metabolism ; Prokaryotic Cells/*cytology ; },
abstract = {Lateral gene transfer (LGT) is an all-encompassing term for the movement of DNA between diverse organisms. LGT is synonymous with horizontal gene transfer, and the terms are used interchangeably throughout the scientific literature. While LGT has been recognized within the bacteria domain of life for decades, inter-domain LGTs are being increasingly described. LGTs between bacteria and complex multicellular organisms are of interest because they challenge the long-held dogma that such transfers could only occur in closely-related, single-celled organisms. Scientists will continue to challenge our understanding of LGT as we sequence more, diverse organisms, as we sequence more endosymbiont-colonized arthropods, and as we continue to appreciate LGT events, both young and old.},
}
@article {pmid28188480,
year = {2017},
author = {Sekimoto, H},
title = {Sexual reproduction and sex determination in green algae.},
journal = {Journal of plant research},
volume = {130},
number = {3},
pages = {423-431},
doi = {10.1007/s10265-017-0908-6},
pmid = {28188480},
issn = {1618-0860},
mesh = {Biological Evolution ; Cell Adhesion/physiology ; Cell Fusion ; Chlamydomonas reinhardtii/genetics/growth &amp; development ; Chlorophyta/*genetics/growth &amp; development/*physiology ; Closterium/genetics/growth &amp; development ; Fresh Water ; Life Cycle Stages/genetics/physiology ; Membrane Fusion/physiology ; Reproduction/*genetics/*physiology ; Sex Determination Processes/*genetics/*physiology ; Volvox/genetics/growth &amp; development ; },
abstract = {The sexual reproductive processes of some representative freshwater green algae are reviewed. Chlamydomonas reinhardtii is a unicellular volvocine alga having two mating types: mating type plus (mt+) and mating type minus (mt-), which are controlled by a single, complex mating-type locus. Sexual adhesion between the gametes is mediated by sex-specific agglutinin molecules on their flagellar membranes. Cell fusion is initiated by an adhesive interaction between the mt+ and mt- mating structures, followed by localized membrane fusion. The loci of sex-limited genes and the conformation of sex-determining regions have been rearranged during the evolution of volvocine algae; however, the essential function of the sex-determining genes of the isogamous unicellular Chlamydomonas reinhardtii is conserved in the multicellular oogamous Volvox carteri. The sexual reproduction of the unicellular charophycean alga, Closterium peracerosum-strigosum-littorale complex, is also focused on here. The sexual reproductive processes of heterothallic strains are controlled by two multifunctional sex pheromones, PR-IP and PR-IP Inducer, which independently promote multiple steps in conjugation at the appropriate times through different induction mechanisms. The molecules involved in sexual reproduction and sex determination have also been characterized.},
}
@article {pmid28188197,
year = {2017},
author = {Drumm, BT and Baker, SA},
title = {Teaching a changing paradigm in physiology: a historical perspective on gut interstitial cells.},
journal = {Advances in physiology education},
volume = {41},
number = {1},
pages = {100-109},
doi = {10.1152/advan.00154.2016},
pmid = {28188197},
issn = {1522-1229},
mesh = {Animals ; Gastrointestinal Motility/*physiology ; Gastrointestinal Tract/*cytology/*physiology ; Humans ; Muscle, Smooth/cytology/physiology ; Physiology/*education ; Teaching/*trends ; },
abstract = {The study and teaching of gastrointestinal (GI) physiology necessitates an understanding of the cellular basis of contractile and electrical coupling behaviors in the muscle layers that comprise the gut wall. Our knowledge of the cellular origin of GI motility has drastically changed over the last 100 yr. While the pacing and coordination of GI contraction was once thought to be solely attributable to smooth muscle cells, it is now widely accepted that the motility patterns observed in the GI tract exist as a result of a multicellular system, consisting of not only smooth muscle cells but also enteric neurons and distinct populations of specialized interstitial cells that all work in concert to ensure proper GI functions. In this historical perspective, we focus on the emerging role of interstitial cells in GI motility and examine the key discoveries and experiments that led to a major shift in a paradigm of GI physiology regarding the role of interstitial cells in modulating GI contractile patterns. A review of these now classic experiments and papers will enable students and educators to fully appreciate the complex, multicellular nature of GI muscles as well as impart lessons on how shifting paradigms in physiology are fueled by new technologies that lead to new emerging discoveries.},
}
@article {pmid28179656,
year = {2017},
author = {Hotamisligil, GS},
title = {Inflammation, metaflammation and immunometabolic disorders.},
journal = {Nature},
volume = {542},
number = {7640},
pages = {177-185},
doi = {10.1038/nature21363},
pmid = {28179656},
issn = {1476-4687},
support = {R01 DK052539/DK/NIDDK NIH HHS/United States ; R01 HL125753/HL/NHLBI NIH HHS/United States ; R01 AI116901/AI/NIAID NIH HHS/United States ; },
mesh = {Adaptive Immunity/genetics ; Animals ; Clinical Trials as Topic ; Cytokines/metabolism ; Evolution, Molecular ; Genome-Wide Association Study ; Hormones/metabolism ; Humans ; Inflammation/complications/genetics/*immunology/*metabolism ; Invertebrates/immunology/metabolism ; Metabolic Diseases/complications/genetics/*immunology/*metabolism ; Obesity/complications/genetics/immunology/metabolism ; Organelles/metabolism ; Signal Transduction ; },
abstract = {Proper regulation and management of energy, substrate diversity and quantity, as well as macromolecular synthesis and breakdown processes, are fundamental to cellular and organismal survival and are paramount to health. Cellular and multicellular organization are defended by the immune response, a robust and critical system through which self is distinguished from non-self, pathogenic signals are recognized and eliminated, and tissue homeostasis is safeguarded. Many layers of evolutionarily conserved interactions occur between immune response and metabolism. Proper maintenance of this delicate balance is crucial for health and has important implications for many pathological states such as obesity, diabetes, and other chronic non-communicable diseases.},
}
@article {pmid28174248,
year = {2017},
author = {Jones, VA and Dolan, L},
title = {MpWIP regulates air pore complex development in the liverwort Marchantia polymorpha.},
journal = {Development (Cambridge, England)},
volume = {144},
number = {8},
pages = {1472-1476},
doi = {10.1242/dev.144287},
pmid = {28174248},
issn = {1477-9129},
mesh = {Marchantia/anatomy &amp; histology/*embryology/*metabolism/ultrastructure ; Mutation/genetics ; Plant Epidermis/cytology/*embryology/ultrastructure ; Plant Proteins/genetics/*metabolism ; Promoter Regions, Genetic/genetics ; Repressor Proteins/metabolism ; Transcription, Genetic ; },
abstract = {The colonisation of the land by plants was accompanied by the evolution of complex tissues and multicellular structures comprising different cell types as morphological adaptations to the terrestrial environment. Here, we show that the single WIP protein in the early-diverging land plant Marchantia polymorpha L. is required for the development of the multicellular gas exchange structure: the air pore complex. This 16-cell barrel-shaped structure surrounds an opening between epidermal cells that facilitates the exchange of gases between the chamber containing the photosynthetic cells inside the plant and the air outside. MpWIP is expressed in cells of the developing air pore complex and the morphogenesis of the complex is defective in plants with reduced MpWIP function. The role of WIP proteins in the control of different multicellular structures in M. polymorpha and the flowering plant Arabidopsis thaliana suggests that these proteins controlled the development of multicellular structures in the common ancestor of land plants. We hypothesise that WIP genes were subsequently co-opted in the control of morphogenesis of novel multicellular structures that evolved during the diversification of land plants.},
}
@article {pmid28173090,
year = {2017},
author = {Gallagher, MD and Macqueen, DJ},
title = {Evolution and Expression of Tissue Globins in Ray-Finned Fishes.},
journal = {Genome biology and evolution},
volume = {9},
number = {1},
pages = {32-47},
doi = {10.1093/gbe/evw266},
pmid = {28173090},
issn = {1759-6653},
support = {BB/J01446X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Biological Evolution ; *Evolution, Molecular ; Fish Proteins/*genetics ; Fishes/*classification/*genetics ; Globins/*genetics ; Phylogeny ; },
abstract = {The globin gene family encodes oxygen-binding hemeproteins conserved across the major branches of multicellular life. The origins and evolutionary histories of complete globin repertoires have been established for many vertebrates, but there remain major knowledge gaps for ray-finned fish. Therefore, we used phylogenetic, comparative genomic and gene expression analyses to discover and characterize canonical “non-blood” globin family members (i.e., myoglobin, cytoglobin, neuroglobin, globin-X, and globin-Y) across multiple ray-finned fish lineages, revealing novel gene duplicates (paralogs) conserved from whole genome duplication (WGD) and small-scale duplication events. Our key findings were that: (1) globin-X paralogs in teleosts have been retained from the teleost-specific WGD, (2) functional paralogs of cytoglobin, neuroglobin, and globin-X, but not myoglobin, have been conserved from the salmonid-specific WGD, (3) triplicate lineage-specific myoglobin paralogs are conserved in arowanas (Osteoglossiformes), which arose by tandem duplication and diverged under positive selection, (4) globin-Y is retained in multiple early branching fish lineages that diverged before teleosts, and (5) marked variation in tissue-specific expression of globin gene repertoires exists across ray-finned fish evolution, including several previously uncharacterized sites of expression. In this respect, our data provide an interesting link between myoglobin expression and the evolution of air breathing in teleosts. Together, our findings demonstrate great-unrecognized diversity in the repertoire and expression of nonblood globins that has arisen during ray-finned fish evolution.},
}
@article {pmid28168289,
year = {2017},
author = {Paulet, D and David, A and Rivals, E},
title = {Ribo-seq enlightens codon usage bias.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {24},
number = {3},
pages = {303-210},
doi = {10.1093/dnares/dsw062},
pmid = {28168289},
issn = {1756-1663},
mesh = {Animals ; Codon/analysis/*genetics ; Eukaryota/genetics ; Evolution, Molecular ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; *Protein Biosynthesis ; RNA, Messenger ; Ribosomes ; Sequence Analysis, RNA ; *Transcriptome ; },
abstract = {Codon usage is biased between lowly and highly expressed genes in a genome-specific manner. This universal bias has been well assessed in some unicellular species, but remains problematic to assess in more complex species. We propose a new method to compute codon usage bias based on genome wide translational data. A new technique based on sequencing of ribosome protected mRNA fragments (Ribo-seq) allowed us to rank genes and compute codon usage bias with high precision for a great variety of species, including mammals. Genes ranking using Ribo-Seq data confirms the influence of the tRNA pool on codon usage bias and shows a decreasing bias in multicellular species. Ribo-Seq analysis also makes possible to detect preferred codons without information on genes function.},
}
@article {pmid28161621,
year = {2017},
author = {Tollis, M and Schiffman, JD and Boddy, AM},
title = {Evolution of cancer suppression as revealed by mammalian comparative genomics.},
journal = {Current opinion in genetics &amp; development},
volume = {42},
number = {},
pages = {40-47},
doi = {10.1016/j.gde.2016.12.004},
pmid = {28161621},
issn = {1879-0380},
mesh = {Animals ; Carcinogenesis/*genetics ; Conserved Sequence/genetics ; DNA Damage/genetics ; DNA Repair/genetics ; *Evolution, Molecular ; *Genomics ; Humans ; Mammals ; Neoplasms/*genetics/pathology ; },
abstract = {Cancer suppression is an important feature in the evolution of large and long-lived animals. While some tumor suppression pathways are conserved among all multicellular organisms, others mechanisms of cancer resistance are uniquely lineage specific. Comparative genomics has become a powerful tool to discover these unique and shared molecular adaptations in respect to cancer suppression. These findings may one day be translated to human patients through evolutionary medicine. Here, we will review theory and methods of comparative cancer genomics and highlight major findings of cancer suppression across mammals. Our current knowledge of cancer genomics suggests that more efficient DNA repair and higher sensitivity to DNA damage may be the key to tumor suppression in large or long-lived mammals.},
}
@article {pmid28148211,
year = {2017},
author = {Buonanno, F and Anesi, A and Giuseppe, GD and Guella, G and Ortenzi, C},
title = {Chemical Defense by Erythrolactones in the Euryhaline Ciliated Protist, Pseudokeronopsis erythrina.},
journal = {Zoological science},
volume = {34},
number = {1},
pages = {42-51},
doi = {10.2108/zs160123},
pmid = {28148211},
issn = {0289-0003},
mesh = {Animals ; Ciliophora/genetics/*metabolism ; Invertebrates ; Lactones/*chemistry/metabolism/*toxicity ; Molecular Structure ; Phylogeny ; Predatory Behavior ; },
abstract = {Pseudokeronopsis erythrina produces three new secondary metabolites, erythrolactones A2, B2 and C2, and their respective sulfate esters (A1, B1, C1), the structures of which have been recently elucidated on the basis of NMR spectroscopic data coupled to high resolution mass measurements (HR-MALDI-TOF). An analysis of the discharge of the protozoan pigment granules revealed that the non-sulfonated erythrolactones are exclusively stored in these cortical organelles, which are commonly used by a number of ciliates as chemical weapons in offense/defense interactions with prey and predators. We evaluated the toxic activity of pigment granule discharge on a panel of free-living ciliates and micro-invertebrates, and the activity of each single purified erythrolactone on three ciliate species. We also observed predator-prey interactions of P. erythrina with unicellular and multicellular predators. Experimental results confirm that only P. erythrina cells with discharged pigment granules were preferentially or exclusively hunted and eaten by at least some of its predators, whereas almost all intact (fully pigmented) cells remained alive. Our results indicate that erythrolactones are very effective as a chemical defense in P. erythrina.},
}
@article {pmid28131316,
year = {2017},
author = {Tompitak, M and Vaillant, C and Schiessel, H},
title = {Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions.},
journal = {Biophysical journal},
volume = {112},
number = {3},
pages = {505-511},
doi = {10.1016/j.bpj.2016.12.041},
pmid = {28131316},
issn = {1542-0086},
mesh = {Animals ; Base Sequence ; DNA/genetics/metabolism ; *Evolution, Molecular ; Genome, Human/*genetics ; Humans ; Nucleosomes/genetics/*metabolism ; *Promoter Regions, Genetic ; Saccharomyces cerevisiae/genetics ; },
abstract = {Sequences that influence nucleosome positioning in promoter regions, and their relation to gene regulation, have been the topic of much research over the last decade. In yeast, significant nucleosome-depleted regions are found, which facilitate transcription. With the arrival of nucleosome positioning maps for the human genome, it was discovered that in our genome, unlike in that of yeast, promoters encode for high nucleosome occupancy. In this work, we look at the genomes of a range of different organisms, to provide a catalog of nucleosome positioning signals in promoters across the tree of life. We utilize a computational model of the nucleosome, based on crystallographic analyses of the structure and elasticity of the nucleosome, to predict the nucleosome positioning signals in promoter regions. To be able to apply our model to large genomic datasets, we introduce an approximative scheme that makes use of the limited range of correlations in nucleosomal sequence preferences to create a computationally efficient approximation of the full biophysical model. Our predictions show that a clear distinction between unicellular and multicellular life is visible in the intrinsically encoded nucleosome affinity. Furthermore, the strength of the nucleosome positioning signals correlates with the complexity of the organism. We conclude that encoding for high nucleosome occupancy, as in the human genome, is in fact a universal feature of multicellular life.},
}
@article {pmid28115992,
year = {2017},
author = {Navratilova, P and Danks, GB and Long, A and Butcher, S and Manak, JR and Thompson, EM},
title = {Sex-specific chromatin landscapes in an ultra-compact chordate genome.},
journal = {Epigenetics &amp; chromatin},
volume = {10},
number = {},
pages = {3},
doi = {10.1186/s13072-016-0110-4},
pmid = {28115992},
issn = {1756-8935},
mesh = {Animals ; Chromatin/genetics/*metabolism ; Chromatin Immunoprecipitation ; DNA Methylation ; DNA Transposable Elements/genetics ; Female ; *Genome ; Histones/chemistry/genetics/metabolism ; Male ; Ovary/metabolism ; Promoter Regions, Genetic ; Protein Processing, Post-Translational ; RNA Polymerase II/genetics/metabolism ; Testis/metabolism ; Urochordata/*genetics ; },
abstract = {BACKGROUND: In multicellular organisms, epigenome dynamics are associated with transitions in the cell cycle, development, germline specification, gametogenesis and inheritance. Evolutionarily, regulatory space has increased in complex metazoans to accommodate these functions. In tunicates, the sister lineage to vertebrates, we examine epigenome adaptations to strong secondary genome compaction, sex chromosome evolution and cell cycle modes.<br><br>RESULTS: Across the 70 MB Oikopleura dioica genome, we profiled 19 histone modifications, and RNA polymerase II, CTCF and p300 occupancies, to define chromatin states within two homogeneous tissues with distinct cell cycle modes: ovarian endocycling nurse nuclei and mitotically proliferating germ nuclei in testes. Nurse nuclei had active chromatin states similar to other metazoan epigenomes, with large domains of operon-associated transcription, a general lack of heterochromatin, and a possible role of Polycomb PRC2 in dosage compensation. Testis chromatin states reflected transcriptional activity linked to spermatogenesis and epigenetic marks that have been associated with establishment of transgenerational inheritance in other organisms. We also uncovered an unusual chromatin state specific to the Y-chromosome, which combined active and heterochromatic histone modifications on specific transposable elements classes, perhaps involved in regulating their activity.<br><br>CONCLUSIONS: Compacted regulatory space in this tunicate genome is accompanied by reduced heterochromatin and chromatin state domain widths. Enhancers, promoters and protein-coding genes have conserved epigenomic features, with adaptations to the organization of a proportion of genes in operon units. We further identified features specific to sex chromosomes, cell cycle modes, germline identity and dosage compensation, and unusual combinations of histone PTMs with opposing consensus functions.},
}
@article {pmid28112403,
year = {2018},
author = {Torday, JS and Miller, WB},
title = {A systems approach to physiologic evolution: From micelles to consciousness.},
journal = {Journal of cellular physiology},
volume = {233},
number = {1},
pages = {162-167},
doi = {10.1002/jcp.25820},
pmid = {28112403},
issn = {1097-4652},
mesh = {Adaptation, Physiological ; Animals ; *Biological Evolution ; Body Temperature Regulation ; Homeostasis ; Humans ; Lung/physiology ; Physiology/*methods ; Pulmonary Ventilation ; *Systems Biology ; *Systems Integration ; Time Factors ; },
abstract = {A systems approach to evolutionary biology offers the promise of an improved understanding of the fundamental principles of life through the effective integration of many biologic disciplines. It is presented that any critical integrative approach to evolutionary development involves a paradigmatic shift in perspective, more than just the engagement of a large number of disciplines. Critical to this differing viewpoint is the recognition that all biological processes originate from the unicellular state and remain permanently anchored to that phase throughout evolutionary development despite their macroscopic appearances. Multicellular eukaryotic development can, therefore, be viewed as a series of connected responses to epiphenomena that proceeds from that base in continuous iterative maintenance of collective cellular homeostatic equipoise juxtaposed against an ever-changing and challenging environment. By following this trajectory of multicellular eukaryotic evolution from within unicellular First Principles of Physiology forward, the mechanistic nature of complex physiology can be identified through a step-wise analysis of a continuous arc of vertebrate evolution based upon serial exaptations.},
}
@article {pmid28106309,
year = {2017},
author = {Wang, D and Qu, Z and Yang, L and Zhang, Q and Liu, ZH and Do, T and Adelson, DL and Wang, ZY and Searle, I and Zhu, JK},
title = {Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants.},
journal = {The Plant journal : for cell and molecular biology},
volume = {90},
number = {1},
pages = {133-146},
doi = {10.1111/tpj.13481},
pmid = {28106309},
issn = {1365-313X},
support = {R01 GM059138/GM/NIGMS NIH HHS/United States ; R01 GM070795/GM/NIGMS NIH HHS/United States ; },
mesh = {Abscisic Acid/pharmacology ; Arabidopsis/drug effects/genetics ; Cold Temperature ; DNA Transposable Elements/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant/drug effects/genetics ; Oryza/drug effects/genetics ; RNA, Long Noncoding/*genetics ; RNA, Plant/*genetics ; Sodium Chloride/pharmacology ; Zea mays/drug effects/genetics ; },
abstract = {Noncoding RNAs have been extensively described in plant and animal transcriptomes by using high-throughput sequencing technology. Of these noncoding RNAs, a growing number of long intergenic noncoding RNAs (lincRNAs) have been described in multicellular organisms, however the origins and functions of many lincRNAs remain to be explored. In many eukaryotic genomes, transposable elements (TEs) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TEs to lincRNAs is largely unknown. By using strand-specific RNA-sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified 47 611 and 398 TE-associated lincRNAs (TE-lincRNAs), respectively. TE-lincRNAs were more often derived from retrotransposons than DNA transposons and as retrotransposon copy number in both rice and maize genomes so did TE-lincRNAs. We validated the expression of these TE-lincRNAs by strand-specific RT-PCR and also demonstrated tissue-specific transcription and stress-induced TE-lincRNAs either after salt, abscisic acid (ABA) or cold treatments. For Arabidopsis TE-lincRNA11195, mutants had reduced sensitivity to ABA as demonstrated by longer roots and higher shoot biomass when compared to wild-type. Finally, by altering the chromatin state in the Arabidopsis chromatin remodelling mutant ddm1, unique lincRNAs including TE-lincRNAs were generated from the preceding untranscribed regions and interestingly inherited in a wild-type background in subsequent generations. Our findings not only demonstrate that TE-associated lincRNAs play important roles in plant abiotic stress responses but lincRNAs and TE-lincRNAs might act as an adaptive reservoir in eukaryotes.},
}
@article {pmid28096354,
year = {2017},
author = {Xing, S and Mehlhorn, DG and Wallmeroth, N and Asseck, LY and Kar, R and Voss, A and Denninger, P and Schmidt, VA and Schwarzländer, M and Stierhof, YD and Grossmann, G and Grefen, C},
title = {Loss of GET pathway orthologs in Arabidopsis thaliana causes root hair growth defects and affects SNARE abundance.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {114},
number = {8},
pages = {E1544-E1553},
doi = {10.1073/pnas.1619525114},
pmid = {28096354},
issn = {1091-6490},
mesh = {Adenosine Triphosphatases/metabolism ; Animals ; Arabidopsis/*physiology ; Arabidopsis Proteins/*metabolism ; Cell Membrane/*metabolism ; Cytosol/metabolism ; Endoplasmic Reticulum/metabolism ; Guanine Nucleotide Exchange Factors/metabolism ; Homeostasis/physiology ; Mammals/physiology ; Membrane Fusion/physiology ; Molecular Chaperones/metabolism ; Phylogeny ; Plant Roots/*growth &amp; development/metabolism ; Plants, Genetically Modified ; SNARE Proteins/genetics/*metabolism ; Saccharomyces cerevisiae/physiology ; Saccharomyces cerevisiae Proteins/metabolism ; Signal Transduction/*physiology ; Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins ; },
abstract = {Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins are key players in cellular trafficking and coordinate vital cellular processes, such as cytokinesis, pathogen defense, and ion transport regulation. With few exceptions, SNAREs are tail-anchored (TA) proteins, bearing a C-terminal hydrophobic domain that is essential for their membrane integration. Recently, the Guided Entry of Tail-anchored proteins (GET) pathway was described in mammalian and yeast cells that serve as a blueprint of TA protein insertion [Schuldiner M, et al. (2008) Cell 134(4):634-645; Stefanovic S, Hegde RS (2007) Cell 128(6):1147-1159]. This pathway consists of six proteins, with the cytosolic ATPase GET3 chaperoning the newly synthesized TA protein posttranslationally from the ribosome to the endoplasmic reticulum (ER) membrane. Structural and biochemical insights confirmed the potential of pathway components to facilitate membrane insertion, but the physiological significance in multicellular organisms remains to be resolved. Our phylogenetic analysis of 37 GET3 orthologs from 18 different species revealed the presence of two different GET3 clades. We identified and analyzed GET pathway components in Arabidopsis thaliana and found reduced root hair elongation in Atget lines, possibly as a result of reduced SNARE biogenesis. Overexpression of AtGET3a in a receptor knockout (KO) results in severe growth defects, suggesting presence of alternative insertion pathways while highlighting an intricate involvement for the GET pathway in cellular homeostasis of plants.},
}
@article {pmid28094816,
year = {2017},
author = {Cramer, JM and Pohlmann, D and Gomez, F and Mark, L and Kornegay, B and Hall, C and Siraliev-Perez, E and Walavalkar, NM and Sperlazza, MJ and Bilinovich, S and Prokop, JW and Hill, AL and Williams, DC},
title = {Methylation specific targeting of a chromatin remodeling complex from sponges to humans.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {40674},
doi = {10.1038/srep40674},
pmid = {28094816},
issn = {2045-2322},
support = {K01 ES025435/ES/NIEHS NIH HHS/United States ; T32 GM008570/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P30 CA016086/CA/NCI NIH HHS/United States ; R01 GM098264/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; *Chromatin Assembly and Disassembly ; DNA/chemistry/metabolism ; *DNA Methylation ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Gene Knockdown Techniques ; Humans ; Models, Molecular ; Nucleic Acid Conformation ; Phenotype ; Porifera/*genetics/metabolism ; Protein Conformation ; },
abstract = {DNA cytosine methylation and methyl-cytosine binding domain (MBD) containing proteins are found throughout all vertebrate species studied to date. However, both the presence of DNA methylation and pattern of methylation varies among invertebrate species. Invertebrates generally have only a single MBD protein, MBD2/3, that does not always contain appropriate residues for selectively binding methylated DNA. Therefore, we sought to determine whether sponges, one of the most ancient extant metazoan lineages, possess an MBD2/3 capable of recognizing methylated DNA and recruiting the associated nucleosome remodeling and deacetylase (NuRD) complex. We find that Ephydatia muelleri has genes for each of the NuRD core components including an EmMBD2/3 that selectively binds methylated DNA. NMR analyses reveal a remarkably conserved binding mode, showing almost identical chemical shift changes between binding to methylated and unmethylated CpG dinucleotides. In addition, we find that EmMBD2/3 and EmGATAD2A/B proteins form a coiled-coil interaction known to be critical for the formation of NuRD. Finally, we show that knockdown of EmMBD2/3 expression disrupts normal cellular architecture and development of E. muelleri. These data support a model in which the MBD2/3 methylation-dependent functional role emerged with the earliest multicellular organisms and has been maintained to varying degrees across animal evolution.},
}
@article {pmid28088333,
year = {2017},
author = {Baffy, G},
title = {Mitochondrial uncoupling in cancer cells: Liabilities and opportunities.},
journal = {Biochimica et biophysica acta. Bioenergetics},
volume = {1858},
number = {8},
pages = {655-664},
doi = {10.1016/j.bbabio.2017.01.005},
pmid = {28088333},
issn = {0005-2728},
mesh = {Animals ; Antineoplastic Agents/pharmacokinetics ; Cell Hypoxia ; Cell Line, Tumor ; Cellular Reprogramming ; Drug Resistance, Neoplasm/physiology ; Drug Synergism ; Energy Metabolism ; Humans ; Mitochondria/drug effects/*metabolism ; Mitochondrial Uncoupling Proteins/*physiology ; Models, Biological ; Neoplasm Proteins/physiology ; Neoplasms/drug therapy/*metabolism ; Oxidative Phosphorylation/drug effects ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Symbiosis ; Uncoupling Agents/pharmacology/therapeutic use ; },
abstract = {Acquisition of the endosymbiotic ancestor of mitochondria was a critical event in eukaryote evolution. Mitochondria offered an unparalleled source of metabolic energy through oxidative phosphorylation and allowed the development of multicellular life. However, as molecular oxygen had become the terminal electron acceptor in most eukaryotic cells, the electron transport chain proved to be the largest intracellular source of superoxide, contributing to macromolecular injury, aging, and cancer. Hence, the 'contract of endosymbiosis' represents a compromise between the possibilities and perils of multicellular life. Uncoupling proteins (UCPs), a group of the solute carrier family of transporters, may remove some of the physiologic constraints that link mitochondrial respiration and ATP synthesis by mediating inducible proton leak and limiting oxidative cell injury. This important property makes UCPs an ancient partner in the metabolic adaptation of cancer cells. Efforts are underway to explore the therapeutic opportunities stemming from the intriguing relationship of UCPs and cancer. This article is part of a Special Issue entitled Mitochondria in Cancer, edited by Giuseppe Gasparre, Rodrigue Rossignol and Pierre Sonveaux.},
}
@article {pmid28078674,
year = {2017},
author = {Bustamante, DE and Won, BY and Miller, KA and Cho, TO},
title = {Wilsonosiphonia gen. nov. (Rhodomelaceae, Rhodophyta) based on molecular and morpho-anatomical characters.},
journal = {Journal of phycology},
volume = {53},
number = {2},
pages = {368-380},
doi = {10.1111/jpy.12512},
pmid = {28078674},
issn = {1529-8817},
mesh = {DNA, Ribosomal ; Phylogeny ; Rhodophyta/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {Morphological, anatomical, and molecular sequence data were used to assess the establishment and phylogenetic position of the genus Wilsonosiphonia gen. nov. Phylogenies based on rbcL and concatenated rbcL and cox1 loci support recognition of Wilsonosiphonia gen. nov., sister to Herposiphonia. Diagnostic features for Wilsonosiphonia are rhizoids located at distal ends of pericentral cells and taproot-shaped multicellular tips of rhizoids. Wilsonosiphonia includes three species with diagnostic rbcL and cox1 sequences, Wilsonosiphonia fujiae sp. nov. (the generitype), W. howei comb. nov., and W. indica sp. nov. These three species resemble each other in external morphology, but W. fujiae is distinguished by having two tetrasporangia per segment rather than one, W. indica by having abundant and persistent trichoblasts, and W. howei by having few and deciduous trichoblasts.},
}
@article {pmid28063828,
year = {2017},
author = {Terauchi, M and Yamagishi, T and Hanyuda, T and Kawai, H},
title = {Genome-wide computational analysis of the secretome of brown algae (Phaeophyceae).},
journal = {Marine genomics},
volume = {32},
number = {},
pages = {49-59},
doi = {10.1016/j.margen.2016.12.002},
pmid = {28063828},
issn = {1876-7478},
mesh = {Amino Acid Sequence ; *Genome ; Genome-Wide Association Study ; Phaeophyta/*genetics ; Sequence Alignment ; },
abstract = {Brown algae have evolved complex multicellularity in the heterokont lineage. They are phylogenetically distant to land plants, fungi and animals. Especially, the members of Laminariales (so-called kelps) have developed highly differentiated tissues. Extracellular matrix (ECM) plays pivotal roles in a number of essential processes in multicellular organisms, such as cell adhesion, cell and tissue differentiations, cell-to-cell communication, and responses to environmental stimuli. In these processes, a set of extracellular secreted proteins called the secretome operates remodeling of the physicochemical nature of ECM and signal transduction by interacting with cell surface proteins and signaling molecules. Characterization of the secretome is a critical step to clarify the contributions of ECM to the multicellularity of brown algae. However, the identity of the brown algal secretome has been poorly understood. In order to reveal the repertory of the brown algal secretome and its involvement in the evolution of Laminariales, we conducted a genome-wide analysis of the brown algal secretome utilizing the published complete genome data of Ectocarpus siliculosus and Saccharina japonica as well as newly obtained RNA-seq data of seven laminarialean species (Agarum clathratum, Alaria crassifolia, Aureophycus aleuticus, Costaria costata, Pseudochorda nagaii, Saccharina angustata and Undaria pinnatifida) largely covering the laminarialean families. We established the in silico pipeline to systematically and accurately detect the secretome by combining multiple prediction algorithms for the N-terminal signal peptide and transmembrane domain within the protein sequence. From 16,189 proteins of E. siliculosus and 18,733 proteins of S. japonica, 552 and 964 proteins respectively were predicted to be classified as the secretome. Conserved domain analysis showed that the domain repertory were very similar to each other, and that of the brown algal secretome was partially common with that of the secretome of other multicellular organisms (land plants, fungi and animals). In the laminarialean species, it was estimated that the gene abundance and the domain architecture of putative ECM remodeling-related proteins were altered compared with those of E. siliculosus, and that the alteration started from the basal group of Laminariales. These results suggested that brown algae have developed their own secretome, and its functions became more elaborated in the more derived members in Laminariales.},
}
@article {pmid28058671,
year = {2017},
author = {Sommese, L and Zullo, A and Schiano, C and Mancini, FP and Napoli, C},
title = {Possible Muscle Repair in the Human Cardiovascular System.},
journal = {Stem cell reviews},
volume = {13},
number = {2},
pages = {170-191},
doi = {10.1007/s12015-016-9711-3},
pmid = {28058671},
issn = {1558-6804},
mesh = {Animals ; Cardiovascular Diseases/genetics/physiopathology/therapy ; Cardiovascular System/injuries/*metabolism/*physiopathology ; Cell Differentiation/genetics ; Cell Proliferation/genetics ; *Cellular Reprogramming ; Humans ; Myocardium/*metabolism/pathology ; Regeneration/genetics ; Regenerative Medicine/methods ; },
abstract = {The regenerative potential of tissues and organs could promote survival, extended lifespan and healthy life in multicellular organisms. Niches of adult stemness are widely distributed and lead to the anatomical and functional regeneration of the damaged organ. Conversely, muscular regeneration in mammals, and humans in particular, is very limited and not a single piece of muscle can fully regrow after a severe injury. Therefore, muscle repair after myocardial infarction is still a chimera. Recently, it has been recognized that epigenetics could play a role in tissue regrowth since it guarantees the maintenance of cellular identity in differentiated cells and, therefore, the stability of organs and tissues. The removal of these locks can shift a specific cell identity back to the stem-like one. Given the gradual loss of tissue renewal potential in the course of evolution, in the last few years many different attempts to retrieve such potential by means of cell therapy approaches have been performed in experimental models. Here we review pathways and mechanisms involved in the in vivo repair of cardiovascular muscle tissues in humans. Moreover, we address the ongoing research on mammalian cardiac muscle repair based on adult stem cell transplantation and pro-regenerative factor delivery. This latter issue, involving genetic manipulations of adult cells, paves the way for developing possible therapeutic strategies in the field of cardiovascular muscle repair.},
}
@article {pmid28049657,
year = {2017},
author = {Macaisne, N and Liu, F and Scornet, D and Peters, AF and Lipinska, A and Perrineau, MM and Henry, A and Strittmatter, M and Coelho, SM and Cock, JM},
title = {The Ectocarpus IMMEDIATE UPRIGHT gene encodes a member of a novel family of cysteine-rich proteins with an unusual distribution across the eukaryotes.},
journal = {Development (Cambridge, England)},
volume = {144},
number = {3},
pages = {409-418},
doi = {10.1242/dev.141523},
pmid = {28049657},
issn = {1477-9129},
support = {638240//European Research Council/International ; },
mesh = {Algal Proteins/antagonists &amp; inhibitors/chemistry/*genetics ; Amino Acid Sequence ; Cloning, Molecular ; Cysteine/chemistry ; Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Models, Genetic ; Multigene Family ; Mutation ; Phaeophyta/*genetics/growth &amp; development/virology ; Phylogeny ; RNA Interference ; Sequence Homology, Amino Acid ; Viral Proteins/chemistry/genetics ; },
abstract = {The sporophyte generation of the brown alga Ectocarpus sp. exhibits an unusual pattern of development compared with the majority of brown algae. The first cell division is symmetrical and the apical-basal axis is established late in development. In the immediate upright (imm) mutant, the initial cell undergoes an asymmetric division to immediately establish the apical-basal axis. We provide evidence which suggests that this phenotype corresponds to the ancestral state of the sporophyte. The IMM gene encodes a protein of unknown function that contains a repeated motif also found in the EsV-1-7 gene of the Ectocarpus virus EsV-1. Brown algae possess large families of EsV-1-7 domain genes but these genes are rare in other stramenopiles, suggesting that the expansion of this family might have been linked with the emergence of multicellular complexity. EsV-1-7 domain genes have a patchy distribution across eukaryotic supergroups and occur in several viral genomes, suggesting possible horizontal transfer during eukaryote evolution.},
}
@article {pmid28048969,
year = {2017},
author = {Veloso, FA},
title = {On the developmental self-regulatory dynamics and evolution of individuated multicellular organisms.},
journal = {Journal of theoretical biology},
volume = {417},
number = {},
pages = {84-99},
doi = {10.1016/j.jtbi.2016.12.025},
pmid = {28048969},
issn = {1095-8541},
mesh = {Animals ; *Biological Evolution ; Cell Differentiation/*genetics ; Cell Line ; Computational Biology ; Drosophila melanogaster ; *Epigenesis, Genetic ; *Gene Expression Regulation ; Histones/metabolism ; Humans ; Mice ; Protein Processing, Post-Translational ; RNA, Messenger/analysis ; Transcription Initiation Site ; },
abstract = {Changes in gene expression are thought to regulate the cell differentiation process intrinsically through complex epigenetic mechanisms. In fundamental terms, however, this assumed regulation refers only to the intricate propagation of changes in gene expression or else leads to non-explanatory regresses. The developmental self-regulatory dynamics and evolution of individuated multicellular organisms also lack a unified and falsifiable description. To fill this gap, I computationally analyzed publicly available high-throughput data of histone H3 post-translational modifications and mRNA abundance for different Homo sapiens, Mus musculus, and Drosophila melanogaster cell-type/developmental-period samples. My analysis of genomic regions adjacent to transcription start sites generated a profile from pairwise partial correlations between histone modifications controlling for the respective mRNA levels for each cell-type/developmental-period dataset. I found that these profiles, while explicitly uncorrelated with the respective transcriptional &quot;identities&quot; by construction, associate strongly with cell differentiation states. This association is not expected if cell differentiation is, in effect, regulated by epigenetic mechanisms. Based on these results, I propose a general, falsifiable theory of individuated multicellularity, which relies on the synergistic coupling across the extracellular space of two explicitly uncorrelated &quot;self-organizing&quot; systems constraining histone modification states at the same sites. This theory describes how the simplest multicellular individual-understood as an intrinsic, higher-order constraint-emerges from proliferating undifferentiated cells, and could explain the intrinsic regulation of gene transcriptional changes for cell differentiation and the evolution of individuated multicellular organisms.},
}
@article {pmid28036012,
year = {2016},
author = {Pauzaite, T and Thacker, U and Tollitt, J and Copeland, NA},
title = {Emerging Roles for Ciz1 in Cell Cycle Regulation and as a Driver of Tumorigenesis.},
journal = {Biomolecules},
volume = {7},
number = {1},
pages = {},
doi = {10.3390/biom7010001},
pmid = {28036012},
issn = {2218-273X},
mesh = {Animals ; Antineoplastic Agents/therapeutic use ; Carcinogenesis/*drug effects ; Cell Cycle ; *Cell Cycle Checkpoints ; Cell Transformation, Neoplastic ; Chromatin/metabolism ; Cyclin-Dependent Kinase 2/metabolism ; Cyclin-Dependent Kinase Inhibitor p21/metabolism ; *DNA Replication ; Humans ; Mice ; Nuclear Proteins/*metabolism ; },
abstract = {Precise duplication of the genome is a prerequisite for the health and longevity of multicellular organisms. The temporal regulation of origin specification, replication licensing, and firing at replication origins is mediated by the cyclin-dependent kinases. Here the role of Cip1 interacting Zinc finger protein 1 (Ciz1) in regulation of cell cycle progression is discussed. Ciz1 contributes to regulation of the G1/S transition in mammalian cells. Ciz1 contacts the pre-replication complex (pre-RC) through cell division cycle 6 (Cdc6) interactions and aids localization of cyclin A- cyclin-dependent kinase 2 (CDK2) activity to chromatin and the nuclear matrix during initiation of DNA replication. We discuss evidence that Ciz1 serves as a kinase sensor that regulates both initiation of DNA replication and prevention of re-replication. Finally, the emerging role for Ciz1 in cancer biology is discussed. Ciz1 is overexpressed in common tumors and tumor growth is dependent on Ciz1 expression, suggesting that Ciz1 is a driver of tumor growth. We present evidence that Ciz1 may contribute to deregulation of the cell cycle due to its ability to alter the CDK activity thresholds that are permissive for initiation of DNA replication. We propose that Ciz1 may contribute to oncogenesis by induction of DNA replication stress and that Ciz1 may be a multifaceted target in cancer therapy.},
}
@article {pmid28013230,
year = {2017},
author = {Ohtani, M and Akiyoshi, N and Takenaka, Y and Sano, R and Demura, T},
title = {Evolution of plant conducting cells: perspectives from key regulators of vascular cell differentiation.},
journal = {Journal of experimental botany},
volume = {68},
number = {1},
pages = {17-26},
doi = {10.1093/jxb/erw473},
pmid = {28013230},
issn = {1460-2431},
mesh = {Biological Evolution ; Cell Differentiation/*physiology ; Embryophyta/cytology/growth &amp; development/physiology ; Gene Expression Regulation, Developmental/physiology ; Gene Expression Regulation, Plant/physiology ; Phloem/*cytology/growth &amp; development/physiology ; Xylem/*cytology/growth &amp; development/physiology ; },
abstract = {One crucial problem that plants faced during their evolution, particularly during the transition to growth on land, was how to transport water, nutrients, metabolites, and small signaling molecules within a large, multicellular body. As a solution to this problem, land plants developed specific tissues for conducting molecules, called water-conducting cells (WCCs) and food-conducting cells (FCCs). The well-developed WCCs and FCCs in extant plants are the tracheary elements and sieve elements, respectively, which are found in vascular plants. Recent molecular genetic studies revealed that transcriptional networks regulate the differentiation of tracheary and sieve elements, and that the networks governing WCC differentiation are largely conserved among land plant species. In this review, we discuss the molecular evolution of plant conducting cells. By focusing on the evolution of the key transcription factors that regulate vascular cell differentiation, the NAC transcription factor VASCULAR-RELATED NAC-DOMAIN for WCCs and the MYB-coiled-coil (CC)-type transcription factor ALTERED PHLOEM DEVELOPMENT for sieve elements, we describe how land plants evolved molecular systems to produce the specialized cells that function as WCCs and FCCs.},
}
@article {pmid28007886,
year = {2017},
author = {Cleard, F and Wolle, D and Taverner, AM and Aoki, T and Deshpande, G and Andolfatto, P and Karch, F and Schedl, P},
title = {Different Evolutionary Strategies To Conserve Chromatin Boundary Function in the Bithorax Complex.},
journal = {Genetics},
volume = {205},
number = {2},
pages = {589-603},
doi = {10.1534/genetics.116.195586},
pmid = {28007886},
issn = {1943-2631},
support = {R01 GM043432/GM/NIGMS NIH HHS/United States ; R01 GM083228/GM/NIGMS NIH HHS/United States ; R56 GM043432/GM/NIGMS NIH HHS/United States ; T32 HG003284/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Chromatin/*genetics ; Conserved Sequence ; Drosophila/*genetics ; Drosophila Proteins/genetics/metabolism ; *Evolution, Molecular ; *Insulator Elements ; Transcription Factors/genetics/metabolism ; },
abstract = {Chromatin boundary elements subdivide chromosomes in multicellular organisms into physically independent domains. In addition to this architectural function, these elements also play a critical role in gene regulation. Here we investigated the evolution of a Drosophila Bithorax complex boundary element called Fab-7, which is required for the proper parasegment specific expression of the homeotic Abd-B gene. Using a &quot;gene&quot; replacement strategy, we show that Fab-7 boundaries from two closely related species, D. erecta and D. yakuba, and a more distant species, D. pseudoobscura, are able to substitute for the melanogaster boundary. Consistent with this functional conservation, the two known Fab-7 boundary factors, Elba and LBC, have recognition sequences in the boundaries from all species. However, the strategies used for maintaining binding and function in the face of sequence divergence is different. The first is conventional, and depends upon conservation of the 8 bp Elba recognition sequence. The second is unconventional, and takes advantage of the unusually large and flexible sequence recognition properties of the LBC boundary factor, and the deployment of multiple LBC recognition elements in each boundary. In the former case, binding is lost when the recognition sequence is altered. In the latter case, sequence divergence is accompanied by changes in the number, relative affinity, and location of the LBC recognition elements.},
}
@article {pmid27998811,
year = {2016},
author = {Ramírez-Sánchez, O and Pérez-Rodríguez, P and Delaye, L and Tiessen, A},
title = {Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {14},
number = {6},
pages = {357-370},
doi = {10.1016/j.gpb.2016.06.003},
pmid = {27998811},
issn = {2210-3244},
mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Eukaryota/classification/genetics/metabolism ; Evolution, Molecular ; Exons ; Genes, Plant ; Humans ; Linear Models ; Phylogeny ; Plant Proteins/*chemistry/genetics/metabolism ; Plants/classification/genetics/*metabolism ; Proteins/*chemistry/genetics/metabolism ; Symbiosis ; },
abstract = {Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa), average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ∼10 exons of small size [∼176 nucleotides (nt)]. Streptophyta have on average only ∼5.7 exons of medium size (∼230nt). Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400nt). Among subcellular compartments, membrane proteins are the largest (∼520aa), whereas the smallest proteins correspond to the gene ontology group of ribosome (∼240aa). Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ∼34% more but ∼20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes.},
}
@article {pmid27994131,
year = {2017},
author = {Jill Harrison, C},
title = {Development and genetics in the evolution of land plant body plans.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {372},
number = {1713},
pages = {},
doi = {10.1098/rstb.2015.0490},
pmid = {27994131},
issn = {1471-2970},
support = {BB/L00224811//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Biological Evolution ; Embryophyta/*genetics/*growth &amp; development ; *Genes, Plant ; Germ Cells, Plant/growth &amp; development ; },
abstract = {The colonization of land by plants shaped the terrestrial biosphere, the geosphere and global climates. The nature of morphological and molecular innovation driving land plant evolution has been an enigma for over 200 years. Recent phylogenetic and palaeobotanical advances jointly demonstrate that land plants evolved from freshwater algae and pinpoint key morphological innovations in plant evolution. In the haploid gametophyte phase of the plant life cycle, these include the innovation of mulitcellular forms with apical growth and multiple growth axes. In the diploid phase of the life cycle, multicellular axial sporophytes were an early innovation priming subsequent diversification of indeterminate branched forms with leaves and roots. Reverse and forward genetic approaches in newly emerging model systems are starting to identify the genetic basis of such innovations. The data place plant evo-devo research at the cusp of discovering the developmental and genetic changes driving the radiation of land plant body plans.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.},
}
@article {pmid27994117,
year = {2017},
author = {Bush, SJ and Chen, L and Tovar-Corona, JM and Urrutia, AO},
title = {Alternative splicing and the evolution of phenotypic novelty.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {372},
number = {1713},
pages = {},
doi = {10.1098/rstb.2015.0474},
pmid = {27994117},
issn = {1471-2970},
mesh = {*Alternative Splicing ; Animals ; *Biological Evolution ; Evolution, Molecular ; Gene Duplication ; *Phenotype ; Transcriptome ; },
abstract = {Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.},
}
@article {pmid27984033,
year = {2017},
author = {Malagoli, D and Ottaviani, E},
title = {Cross-talk among immune and neuroendocrine systems in molluscs and other invertebrate models.},
journal = {Hormones and behavior},
volume = {88},
number = {},
pages = {41-44},
doi = {10.1016/j.yhbeh.2016.10.015},
pmid = {27984033},
issn = {1095-6867},
mesh = {Animals ; *Biological Evolution ; Cell Transdifferentiation/physiology ; Homeostasis/physiology ; Immune System/immunology/*metabolism ; Invertebrates/immunology/*metabolism ; Mollusca/immunology/*metabolism ; Neurosecretory Systems/immunology/*metabolism ; },
abstract = {The comparison between immune and neuroendocrine systems in vertebrates and invertebrates suggest an ancient origin and a high degree of conservation for the mechanisms underlying the integration between immune and stress responses. This suggests that in both vertebrates and invertebrates the stress response involves the integrated network of soluble mediators (e.g., neurotransmitters, hormones and cytokines) and cell functions (e.g., chemotaxis and phagocytosis), that interact with a common objective, i.e., the maintenance of body homeostasis. During evolution, several changes observed in the stress response of more complex taxa could be the result of new roles of ancestral molecules, such as ancient immune mediators may have been recruited as neurotransmitters and hormones, or vice versa. We review older and recent evidence suggesting that immune and neuro-endocrine functions during the stress response were deeply intertwined already at the dawn of multicellular organisms. These observations found relevant reflections in the demonstration that immune cells can transdifferentiate in olfactory neurons in crayfish and the recently re-proposed neural transdifferentiation in humans.},
}
@article {pmid27980068,
year = {2017},
author = {Ihara, S and Nakayama, S and Murakami, Y and Suzuki, E and Asakawa, M and Kinoshita, T and Sawa, H},
title = {PIGN prevents protein aggregation in the endoplasmic reticulum independently of its function in the GPI synthesis.},
journal = {Journal of cell science},
volume = {130},
number = {3},
pages = {602-613},
doi = {10.1242/jcs.196717},
pmid = {27980068},
issn = {1477-9137},
mesh = {Animals ; Caenorhabditis elegans/cytology/*metabolism/ultrastructure ; Caenorhabditis elegans Proteins/*metabolism ; Conserved Sequence ; Endoplasmic Reticulum/*metabolism/ultrastructure ; Evolution, Molecular ; Glycosylphosphatidylinositols/*metabolism ; HEK293 Cells ; Humans ; Intracellular Membranes/metabolism ; Intracellular Space/metabolism ; Mutation/genetics ; Phosphotransferases/chemistry/*metabolism ; *Protein Aggregates ; Sequence Homology, Amino Acid ; },
abstract = {Quality control of proteins in the endoplasmic reticulum (ER) is essential for ensuring the integrity of secretory proteins before their release into the extracellular space. Secretory proteins that fail to pass quality control form aggregates. Here we show the PIGN-1/PIGN is required for quality control in Caenorhabditis elegans and in mammalian cells. In C. elegans pign-1 mutants, several proteins fail to be secreted and instead form abnormal aggregation. PIGN-knockout HEK293 cells also showed similar protein aggregation. Although PIGN-1/PIGN is responsible for glycosylphosphatidylinositol (GPI)-anchor biosynthesis in the ER, certain mutations in C. elegans pign-1 caused protein aggregation in the ER without affecting GPI-anchor biosynthesis. These results show that PIGN-1/PIGN has a conserved and non-canonical function to prevent deleterious protein aggregation in the ER independently of the GPI-anchor biosynthesis. PIGN is a causative gene for some human diseases including multiple congenital seizure-related syndrome (MCAHS1). Two pign-1 mutations created by CRISPR/Cas9 that correspond to MCAHS1 also cause protein aggregation in the ER, implying that the dysfunction of the PIGN non-canonical function might affect symptoms of MCAHS1 and potentially those of other diseases.},
}
@article {pmid27979655,
year = {2017},
author = {Lalucque, H and Malagnac, F and Green, K and Gautier, V and Grognet, P and Chan Ho Tong, L and Scott, B and Silar, P},
title = {IDC2 and IDC3, two genes involved in cell non-autonomous signaling of fruiting body development in the model fungus Podospora anserina.},
journal = {Developmental biology},
volume = {421},
number = {2},
pages = {126-138},
doi = {10.1016/j.ydbio.2016.12.016},
pmid = {27979655},
issn = {1095-564X},
mesh = {Amino Acid Sequence ; Blotting, Western ; Cellulose/pharmacology ; Conserved Sequence ; Cysteine/metabolism ; Evolution, Molecular ; Fruiting Bodies, Fungal/*genetics/*growth &amp; development ; Fungal Proteins/chemistry/*genetics/metabolism ; Gene Deletion ; *Genes, Fungal ; Genetic Complementation Test ; Green Fluorescent Proteins/metabolism ; Mosaicism ; Mycelium/metabolism ; Phenotype ; Phosphorylation/drug effects ; Podospora/*genetics/*growth &amp; development ; Signal Transduction/*genetics ; Subcellular Fractions/metabolism ; Vacuoles/metabolism ; },
abstract = {Filamentous ascomycetes produce complex multicellular structures during sexual reproduction. Little is known about the genetic pathways enabling the construction of such structures. Here, with a combination of classical and reverse genetic methods, as well as genetic mosaic and graft analyses, we identify and provide evidence for key roles for two genes during the formation of perithecia, the sexual fruiting bodies, of the filamentous fungus Podospora anserina. Data indicate that the proteins coded by these two genes function cell-non-autonomously and that their activity depends upon conserved cysteines, making them good candidate for being involved in the transmission of a reactive oxygen species (ROS) signal generated by the PaNox1 NADPH oxidase inside the maturing fruiting body towards the PaMpk1 MAP kinase, which is located inside the underlying mycelium, in which nutrients are stored. These data provide important new insights to our understanding of how fungi build multicellular structures.},
}
@article {pmid27965457,
year = {2017},
author = {Däster, S and Amatruda, N and Calabrese, D and Ivanek, R and Turrini, E and Droeser, RA and Zajac, P and Fimognari, C and Spagnoli, GC and Iezzi, G and Mele, V and Muraro, MG},
title = {Induction of hypoxia and necrosis in multicellular tumor spheroids is associated with resistance to chemotherapy treatment.},
journal = {Oncotarget},
volume = {8},
number = {1},
pages = {1725-1736},
doi = {10.18632/oncotarget.13857},
pmid = {27965457},
issn = {1949-2553},
mesh = {Animals ; Antimetabolites, Antineoplastic/*pharmacology ; Cell Hypoxia/*physiology ; Colorectal Neoplasms/drug therapy/*pathology ; Drug Resistance, Neoplasm/*physiology ; Fluorouracil/*pharmacology ; Gene Expression Profiling ; HCT116 Cells ; HT29 Cells ; Humans ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Necrosis/*pathology ; Oxygen/metabolism ; Spheroids, Cellular/*physiology ; Tumor Cells, Cultured ; Xenograft Model Antitumor Assays ; },
abstract = {Culture of cancerous cells in standard monolayer conditions poorly mirrors growth in three-dimensional architectures typically observed in a wide majority of cancers of different histological origin. Multicellular tumor spheroid (MCTS) culture models were developed to mimic these features. However, in vivo tumor growth is also characterized by the presence of ischemic and necrotic areas generated by oxygenation gradients and differential access to nutrients. Hypoxia and necrosis play key roles in tumor progression and resistance to treatment. To provide in vitro models recapitulating these events in highly controlled and standardized conditions, we have generated colorectal cancer (CRC) cell spheroids of different sizes and analyzed their gene expression profiles and sensitivity to treatment with 5FU, currently used in therapeutic protocols. Here we identify three MCTS stages, corresponding to defined spheroid sizes, characterized by normoxia, hypoxia, and hypoxia plus necrosis, respectively. Importantly, we show that MCTS including both hypoxic and necrotic areas most closely mimic gene expression profiles of in vivo-developing tumors and display the highest resistance to 5FU. Taken together, our data indicate that MCTS may mimic in vitro generation of ischemic and necrotic areas in highly standardized and controlled conditions, thereby qualifying as relevant models for drug screening purposes.},
}
@article {pmid27936291,
year = {2017},
author = {Hughes, KA and Leips, J},
title = {Pleiotropy, constraint, and modularity in the evolution of life histories: insights from genomic analyses.},
journal = {Annals of the New York Academy of Sciences},
volume = {1389},
number = {1},
pages = {76-91},
doi = {10.1111/nyas.13256},
pmid = {27936291},
issn = {1749-6632},
support = {F32 GM016990/GM/NIGMS NIH HHS/United States ; R01 DK084219/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Biological Evolution ; Drosophila melanogaster ; *Genetic Pleiotropy ; *Genetic Variation ; *Genetics, Population ; Genome ; Genome-Wide Association Study ; *Genomics ; Humans ; Plants ; Quantitative Trait Loci ; Selection, Genetic ; },
abstract = {Multicellular organisms display an enormous range of life history (LH) strategies and present an evolutionary conundrum; despite strong natural selection, LH traits are characterized by high levels of genetic variation. To understand the evolution of life histories and maintenance of this variation, the specific phenotypic effects of segregating alleles and the genetic networks in which they act need to be elucidated. In particular, the extent to which LH evolution is constrained by the pleiotropy of alleles contributing to LH variation is generally unknown. Here, we review recent empirical results that shed light on this question, with an emphasis on studies employing genomic analyses. While genome-scale analyses are increasingly practical and affordable, they face limitations of genetic resolution and statistical power. We describe new research approaches that we believe can produce new insights and evaluate their promise and applicability to different kinds of organisms. Two approaches seem particularly promising: experiments that manipulate selection in multiple dimensions and measure phenotypic and genomic response and analytical approaches that take into account genome-wide associations between markers and phenotypes, rather than applying a traditional marker-by-marker approach.},
}
@article {pmid27934708,
year = {2016},
author = {Jones, JD and Vance, RE and Dangl, JL},
title = {Intracellular innate immune surveillance devices in plants and animals.},
journal = {Science (New York, N.Y.)},
volume = {354},
number = {6316},
pages = {},
doi = {10.1126/science.aaf6395},
pmid = {27934708},
issn = {1095-9203},
mesh = {Animals ; Evolution, Molecular ; Host-Pathogen Interactions ; *Immunity, Innate ; *Immunologic Surveillance ; NLR Proteins/chemistry/genetics/*immunology ; Plant Diseases/immunology/microbiology ; Plants/*immunology/*microbiology ; Protein Domains ; },
abstract = {Multicellular eukaryotes coevolve with microbial pathogens, which exert strong selective pressure on the immune systems of their hosts. Plants and animals use intracellular proteins of the nucleotide-binding domain, leucine-rich repeat (NLR) superfamily to detect many types of microbial pathogens. The NLR domain architecture likely evolved independently and convergently in each kingdom, and the molecular mechanisms of pathogen detection by plant and animal NLRs have long been considered to be distinct. However, microbial recognition mechanisms overlap, and it is now possible to discern important key trans-kingdom principles of NLR-dependent immune function. Here, we attempt to articulate these principles. We propose that the NLR architecture has evolved for pathogen-sensing in diverse organisms because of its utility as a tightly folded &quot;hair trigger&quot; device into which a virtually limitless number of microbial detection platforms can be integrated. Recent findings suggest means to rationally design novel recognition capabilities to counter disease.},
}
@article {pmid27913751,
year = {2017},
author = {Wu, Y and Gao, B and Zhu, S},
title = {New fungal defensin-like peptides provide evidence for fold change of proteins in evolution.},
journal = {Bioscience reports},
volume = {37},
number = {1},
pages = {},
doi = {10.1042/BSR20160438},
pmid = {27913751},
issn = {1573-4935},
mesh = {Amino Acid Sequence ; Ascomycota/*chemistry/genetics ; Cysteine/chemistry/genetics ; Defensins/*chemistry/genetics ; Evolution, Molecular ; Fungal Proteins/*chemistry/genetics ; Genes, Fungal ; Models, Molecular ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Folding ; Sequence Alignment ; },
abstract = {Defensins containing a consensus cystine framework, Cys[1]…Cys[2]X3Cys[3]…Cys[4]… Cys[5]X1Cys[6] (X, any amino acid except Cys; …, variable residue numbers), are extensively distributed in a variety of multicellular organisms (plants, fungi and invertebrates) and essentially involved in immunity as microbicidal agents. This framework is a prerequisite for forming the cysteine-stabilized α-helix and β-sheet (CSαβ) fold, in which the two invariant motifs, Cys[2]X3Cys[3]/Cys[5]X1Cys[6], are key determinants of fold formation. By using a computational genomics approach, we identified a large superfamily of fungal defensin-like peptides (fDLPs) in the phytopathogenic fungal genus - Zymoseptoria, which includes 132 structurally typical and 63 atypical members. These atypical fDLPs exhibit an altered cystine framework and accompanying fold change associated with their secondary structure elements and disulfide bridge patterns, as identified by protein structure modelling. Despite this, they definitely are homologous with the typical fDLPs in view of their precise gene structure conservation and identical precursor organization. Sequence and structural analyses combined with functional data suggest that most of Zymoseptoria fDLPs might have lost their antimicrobial activity. The present study provides a clear example of fold change in the evolution of proteins and is valuable in establishing remote homology among peptide superfamily members with different folds.},
}
@article {pmid27903631,
year = {2017},
author = {Dettman, JR and Rodrigue, N and Schoustra, SE and Kassen, R},
title = {Genomics of Compensatory Adaptation in Experimental Populations of Aspergillus nidulans.},
journal = {G3 (Bethesda, Md.)},
volume = {7},
number = {2},
pages = {427-436},
doi = {10.1534/g3.116.036152},
pmid = {27903631},
issn = {2160-1836},
support = {//CIHR/Canada ; },
mesh = {Adaptation, Physiological/*genetics ; Aspergillus nidulans/drug effects/*genetics/growth &amp; development ; Dioxoles/pharmacology ; Drug Resistance, Fungal ; *Evolution, Molecular ; *Genetic Fitness ; Genome, Fungal ; Genomics ; Osmotic Pressure/physiology ; Pyrroles/pharmacology ; },
abstract = {Knowledge of the number and nature of genetic changes responsible for adaptation is essential for understanding and predicting evolutionary trajectories. Here, we study the genomic basis of compensatory adaptation to the fitness cost of fungicide resistance in experimentally evolved strains of the filamentous fungus Aspergillus nidulans The original selection experiment tracked the fitness recovery of lines founded by an ancestral strain that was resistant to fludioxonil, but paid a fitness cost in the absence of the fungicide. We obtained whole-genome sequence data for the ancestral A. nidulans strain and eight experimentally evolved strains. We find that fludioxonil resistance in the ancestor was likely conferred by a mutation in histidine kinase nikA, part of the two-component signal transduction system of the high-osmolarity glycerol (HOG) stress response pathway. To compensate for the pleiotropic negative effects of the resistance mutation, the subsequent fitness gains observed in the evolved lines were likely caused by secondary modification of HOG pathway activity. Candidate genes for the compensatory fitness increases were significantly overrepresented by stress response functions, and some were specifically associated with the HOG pathway itself. Parallel evolution at the gene level was rare among evolved lines. There was a positive relationship between the predicted number of adaptive steps, estimated from fitness data, and the number of genomic mutations, determined by whole-genome sequencing. However, the number of genomic mutations was, on average, 8.45 times greater than the number of adaptive steps inferred from fitness data. This research expands our understanding of the genetic basis of adaptation in multicellular eukaryotes and lays out a framework for future work on the genomics of compensatory adaptation in A. nidulans.},
}
@article {pmid27888167,
year = {2017},
author = {Liao, BK and Oates, AC},
title = {Delta-Notch signalling in segmentation.},
journal = {Arthropod structure &amp; development},
volume = {46},
number = {3},
pages = {429-447},
doi = {10.1016/j.asd.2016.11.007},
pmid = {27888167},
issn = {1873-5495},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Body Patterning/genetics/*physiology ; Gene Expression Regulation, Developmental ; Phylogeny ; Receptors, Notch/genetics/*metabolism ; *Signal Transduction ; },
abstract = {Modular body organization is found widely across multicellular organisms, and some of them form repetitive modular structures via the process of segmentation. It's vastly interesting to understand how these regularly repeated structures are robustly generated from the underlying noise in biomolecular interactions. Recent studies from arthropods reveal similarities in segmentation mechanisms with vertebrates, and raise the possibility that the three phylogenetic clades, annelids, arthropods and chordates, might share homology in this process from a bilaterian ancestor. Here, we discuss vertebrate segmentation with particular emphasis on the role of the Notch intercellular signalling pathway. We introduce vertebrate segmentation and Notch signalling, pointing out historical milestones, then describe existing models for the Notch pathway in the synchronization of noisy neighbouring oscillators, and a new role in the modulation of gene expression wave patterns. We ask what functions Notch signalling may have in arthropod segmentation and explore the relationship between Notch-mediated lateral inhibition and synchronization. Finally, we propose open questions and technical challenges to guide future investigations into Notch signalling in segmentation.},
}
@article {pmid27886385,
year = {2017},
author = {Frangedakis, E and Saint-Marcoux, D and Moody, LA and Rabbinowitsch, E and Langdale, JA},
title = {Nonreciprocal complementation of KNOX gene function in land plants.},
journal = {The New phytologist},
volume = {216},
number = {2},
pages = {591-604},
doi = {10.1111/nph.14318},
pmid = {27886385},
issn = {1469-8137},
mesh = {Bayes Theorem ; Embryophyta/*genetics ; Evolution, Molecular ; Gene Duplication ; *Genes, Plant ; *Genetic Complementation Test ; Likelihood Functions ; Loss of Function Mutation/genetics ; Phylogeny ; Plant Proteins/genetics/metabolism ; Plants, Genetically Modified ; Species Specificity ; Transgenes ; },
abstract = {Class I KNOTTED-LIKE HOMEOBOX (KNOX) proteins regulate development of the multicellular diploid sporophyte in both mosses and flowering plants; however, the morphological context in which they function differs. In order to determine how Class I KNOX function was modified as land plants evolved, phylogenetic analyses and cross-species complementation assays were performed. Our data reveal that a duplication within the charophyte sister group to land plants led to distinct Class I and Class II KNOX gene families. Subsequently, Class I sequences diverged substantially in the nonvascular bryophyte groups (liverworts, mosses and hornworts), with moss sequences being most similar to those in vascular plants. Despite this similarity, moss mutants were not complemented by vascular plant KNOX genes. Conversely, the Arabidopsis brevipedicellus (bp-9) mutant was complemented by the PpMKN2 gene from the moss Physcomitrella patens. Lycophyte KNOX genes also complemented bp-9 whereas fern genes only partially complemented the mutant. This lycophyte/fern distinction is mirrored in the phylogeny of KNOX-interacting BELL proteins, in that a gene duplication occurred after divergence of the two groups. Together, our results imply that the moss MKN2 protein can function in a broader developmental context than vascular plant KNOX proteins, the narrower scope having evolved progressively as lycophytes, ferns and flowering plants diverged.},
}
@article {pmid27882869,
year = {2016},
author = {Kirkegaard, JB and Bouillant, A and Marron, AO and Leptos, KC and Goldstein, RE},
title = {Aerotaxis in the closest relatives of animals.},
journal = {eLife},
volume = {5},
number = {},
pages = {},
doi = {10.7554/eLife.18109},
pmid = {27882869},
issn = {2050-084X},
support = {097855//Wellcome Trust/United Kingdom ; },
mesh = {*Chemotaxis ; Choanoflagellata/*drug effects/*physiology ; Lab-On-A-Chip Devices ; Oxygen/*metabolism ; },
abstract = {As the closest unicellular relatives of animals, choanoflagellates serve as useful model organisms for understanding the evolution of animal multicellularity. An important factor in animal evolution was the increasing ocean oxygen levels in the Precambrian, which are thought to have influenced the emergence of complex multicellular life. As a first step in addressing these conditions, we study here the response of the colony-forming choanoflagellate Salpingoeca rosetta to oxygen gradients. Using a microfluidic device that allows spatio-temporal variations in oxygen concentrations, we report the discovery that S. rosetta displays positive aerotaxis. Analysis of the spatial population distributions provides evidence for logarithmic sensing of oxygen, which enhances sensing in low oxygen neighborhoods. Analysis of search strategy models on the experimental colony trajectories finds that choanoflagellate aerotaxis is consistent with stochastic navigation, the statistics of which are captured using an effective continuous version based on classical run-and-tumble chemotaxis.},
}
@article {pmid27880891,
year = {2017},
author = {Guzman, A and Sánchez Alemany, V and Nguyen, Y and Zhang, CR and Kaufman, LJ},
title = {A novel 3D in vitro metastasis model elucidates differential invasive strategies during and after breaching basement membrane.},
journal = {Biomaterials},
volume = {115},
number = {},
pages = {19-29},
doi = {10.1016/j.biomaterials.2016.11.014},
pmid = {27880891},
issn = {1878-5905},
mesh = {Batch Cell Culture Techniques/*methods ; Cell Line, Tumor ; Cell Membrane/metabolism/*pathology ; Extracellular Matrix/metabolism/pathology ; Humans ; Neoplasm Invasiveness ; Neoplasm Metastasis ; Neoplasms, Experimental/metabolism/*pathology/*secondary ; *Printing, Three-Dimensional ; *Tissue Scaffolds ; },
abstract = {Invasive breast cancer and other tumors of epithelial origin must breach a layer of basement membrane (BM) that surrounds the primary tumor before invading into the adjacent extracellular matrix. To analyze invasive strategies of breast cancer cells during BM breaching and subsequent invasion into a collagen I-rich extracellular matrix (ECM), we developed a physiologically relevant 3D in vitro model that recreates the architecture of a solid tumor with an intact, degradable, cell-assembled BM layer embedded in a collagen I environment. Using this model we demonstrate that while the BM layer fully prevents dissemination of non-malignant cells, cancer cells are capable of breaching it and invading into the surrounding collagen, indicating that the developed system recreates a hallmark of invasive disease. We demonstrate that cancer cells exhibiting individual invasion in collagen matrices preferentially adopt a specific mode of collective invasion when transmigrating a cell-assembled BM that is not observed in any other tested fibrillar, non-fibrillar, or composite ECM. Matrix-degrading enzymes are found to be crucial during BM breaching but not during subsequent invasion in the collagen matrix. It is further shown that multicellular transmigration of the BM is less susceptible to pharmacological MMP inhibition than multicellular invasion in composite collagen/basement membrane extract matrices. The newly developed in vitro model of metastasis allows 3D cancer cell invasion to be studied not only as a function of a particular tumor's genetics but also as a function of its heterogeneous environment and the different stages of invasion. As such, this model is a valuable new tool with which to dissect basic mechanisms of invasion and metastasis and develop new therapeutic approaches in a physiologically relevant, yet inexpensive and highly tunable, in vitro setting.},
}
@article {pmid27880868,
year = {2017},
author = {Gaiti, F and Calcino, AD and Tanurdžić, M and Degnan, BM},
title = {Origin and evolution of the metazoan non-coding regulatory genome.},
journal = {Developmental biology},
volume = {427},
number = {2},
pages = {193-202},
doi = {10.1016/j.ydbio.2016.11.013},
pmid = {27880868},
issn = {1095-564X},
mesh = {Animals ; *Biological Evolution ; *Gene Expression Regulation ; *Genome ; Humans ; Regulatory Sequences, Nucleic Acid ; },
abstract = {Animals rely on genomic regulatory systems to direct the dynamic spatiotemporal and cell-type specific gene expression that is essential for the development and maintenance of a multicellular lifestyle. Although it is widely appreciated that these systems ultimately evolved from genomic regulatory mechanisms present in single-celled stem metazoans, it remains unclear how this occurred. Here, we focus on the contribution of the non-coding portion of the genome to the evolution of animal gene regulation, specifically on recent insights from non-bilaterian metazoan lineages, and unicellular and colonial holozoan sister taxa. High-throughput next-generation sequencing, largely in bilaterian model species, has led to the discovery of tens of thousands of non-coding RNA genes (ncRNAs), including short, long and circular forms, and uncovered the central roles they play in development. Based on the analysis of non-bilaterian metazoan, unicellular holozoan and fungal genomes, the evolution of some ncRNAs, such as Piwi-interacting RNAs, correlates with the emergence of metazoan multicellularity, while others, including microRNAs, long non-coding RNAs and circular RNAs, appear to be more ancient. Analysis of non-coding regulatory DNA and histone post-translational modifications have revealed that some cis-regulatory mechanisms, such as those associated with proximal promoters, are present in non-animal holozoans, while others appear to be metazoan innovations, most notably distal enhancers. In contrast, the cohesin-CTCF system for regulating higher-order chromatin structure and enhancer-promoter long-range interactions appears to be restricted to bilaterians. Taken together, most bilaterian non-coding regulatory mechanisms appear to have originated before the divergence of crown metazoans. However, differential expansion of non-coding RNA and cis-regulatory DNA repertoires in bilaterians may account for their increased regulatory and morphological complexity relative to non-bilaterians.},
}
@article {pmid27876853,
year = {2016},
author = {Rodriguez-Pascual, F and Slatter, DA},
title = {Collagen cross-linking: insights on the evolution of metazoan extracellular matrix.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {37374},
doi = {10.1038/srep37374},
pmid = {27876853},
issn = {2045-2322},
mesh = {Amino Acid Sequence ; Animals ; Collagen/classification/genetics/*metabolism ; Evolution, Molecular ; Extracellular Matrix/*metabolism ; Fibrillar Collagens/chemistry/genetics/*metabolism ; Humans ; Invertebrates/genetics/metabolism ; Models, Molecular ; Phylogeny ; Protein Structure, Secondary ; Protein-Lysine 6-Oxidase/*metabolism ; Sequence Homology, Amino Acid ; Vertebrates/genetics/metabolism ; },
abstract = {Collagens constitute a large family of extracellular matrix (ECM) proteins that play a fundamental role in supporting the structure of various tissues in multicellular animals. The mechanical strength of fibrillar collagens is highly dependent on the formation of covalent cross-links between individual fibrils, a process initiated by the enzymatic action of members of the lysyl oxidase (LOX) family. Fibrillar collagens are present in a wide variety of animals, therefore often being associated with metazoan evolution, where the emergence of an ancestral collagen chain has been proposed to lead to the formation of different clades. While LOX-generated collagen cross-linking metabolites have been detected in different metazoan families, there is limited information about when and how collagen acquired this particular modification. By analyzing telopeptide and helical sequences, we identified highly conserved, potential cross-linking sites throughout the metazoan tree of life. Based on this analysis, we propose that they have importantly contributed to the formation and further expansion of fibrillar collagens.},
}
@article {pmid27871856,
year = {2017},
author = {Pianca, N and Zaglia, T and Mongillo, M},
title = {Will cardiac optogenetics find the way through the obscure angles of heart physiology?.},
journal = {Biochemical and biophysical research communications},
volume = {482},
number = {4},
pages = {515-523},
doi = {10.1016/j.bbrc.2016.11.104},
pmid = {27871856},
issn = {1090-2104},
mesh = {Animals ; Arrhythmias, Cardiac/genetics/pathology/physiopathology/therapy ; Channelrhodopsins ; Equipment Design ; Heart/*physiology/physiopathology ; Humans ; Myocardium/metabolism/pathology ; Optogenetics/instrumentation/*methods ; },
abstract = {Optogenetics is a technique exploded in the last 10 years, which revolutionized several areas of biological research. The brightest side of this technology is the use of light to modulate non-invasively, with high spatial resolution and millisecond time scale, excitable cells genetically modified to express light-sensitive microbial ion channels (opsins). Neuroscience has first benefited from such fascinating strategy, in intact organisms. By shining light to specific neuronal subpopulations, optogenetics allowed unearth the mechanisms involved in cell-to-cell communication within the context of intact organs, such as the brain, formed by complex neuronal circuits. More recently, scientists looked at optogenetics as a tool to answer some of the questions, remained in the dark, of cardiovascular physiology. In this review, we focus on the application of optogenetics in the study of the heart, a complex multicellular organ, homing different populations of excitable cells, spatially and functionally interconnected. Moving from the first proof-of-principle works, published in 2010, to the present time, we discuss the in vitro and in vivo applications of optogenetics for the study of electrophysiology of the different cardiac cell types, and for the dissection of cellular mechanisms underlying arrhythmias. We also present how molecular biology and technology foster the evolution of cardiac optogenetics, with the aim to further our understanding of fundamental questions in cardiac physiology and pathology. Finally, we confer about the therapeutic potential of such biotechnological strategy for the treatment of heart rhythm disturbances (e.g. cardiac pacing, cardioversion).},
}
@article {pmid27863931,
year = {2016},
author = {Filyk, HA and Osborne, LC},
title = {The Multibiome: The Intestinal Ecosystem's Influence on Immune Homeostasis, Health, and Disease.},
journal = {EBioMedicine},
volume = {13},
number = {},
pages = {46-54},
doi = {10.1016/j.ebiom.2016.10.007},
pmid = {27863931},
issn = {2352-3964},
mesh = {Animals ; Disease Susceptibility ; Ecosystem ; *Gastrointestinal Microbiome ; *Homeostasis ; Host-Parasite Interactions/genetics/immunology ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Immunity, Mucosal ; Immunomodulation ; Intestinal Mucosa/immunology/metabolism/microbiology ; Intestines/*physiology ; },
abstract = {Mammalian evolution has occurred in the presence of mutualistic, commensal, and pathogenic micro- and macro-organisms for millennia. The presence of these organisms during mammalian evolution has allowed for intimate crosstalk between these colonizing species and the host immune system. In this review, we introduce the concept of the 'multibiome' to holistically refer to the biodiverse collection of bacteria, viruses, fungi and multicellular helminthic worms colonizing the mammalian intestine. Furthermore, we discuss new insights into multibiome-host interactions in the context of host-protective immunity and immune-mediated diseases, including inflammatory bowel disease and multiple sclerosis. Finally, we provide reasons to account for the multibiome in experimental design, analysis and in therapeutic applications.},
}
@article {pmid27829356,
year = {2016},
author = {Yamashita, S and Arakaki, Y and Kawai-Toyooka, H and Noga, A and Hirono, M and Nozaki, H},
title = {Alternative evolution of a spheroidal colony in volvocine algae: developmental analysis of embryogenesis in Astrephomene (Volvocales, Chlorophyta).},
journal = {BMC evolutionary biology},
volume = {16},
number = {1},
pages = {243},
doi = {10.1186/s12862-016-0794-x},
pmid = {27829356},
issn = {1471-2148},
mesh = {Basal Bodies/metabolism ; *Biological Evolution ; Cell Division ; Cell Lineage ; Cell Nucleus/metabolism ; Chlorophyta/*embryology/*genetics ; Fluorescent Antibody Technique, Indirect ; Phylogeny ; Protoplasts/metabolism ; Time-Lapse Imaging ; },
abstract = {BACKGROUND: Volvocine algae, which range from the unicellular Chlamydomonas to the multicellular Volvox with a germ-soma division of labor, are a model for the evolution of multicellularity. Within this group, the spheroidal colony might have evolved in two independent lineages: Volvocaceae and the goniacean Astrephomene. Astrephomene produces spheroidal colonies with posterior somatic cells. The feature that distinguishes Astrephomene from the volvocacean algae is lack of inversion during embryogenesis; the volvocacean embryo undergoes inversion after successive divisions to orient flagella toward the outside. The mechanisms of inversion at the molecular and cellular levels in volvocacean algae have been assessed in detail, particularly in Volvox carteri. However, embryogenesis in Astrephomene has not been subjected to such investigations.<br><br>RESULTS: This study relied on light microscopy time-lapse imaging using an actively growing culture of a newly established strain to conduct a developmental analysis of Astrephomene as well as to perform a comparison with the similar spheroidal volvocacean Eudorina. During the successive divisions involved in Astrephomene embryogenesis, gradual rotation of daughter protoplasts resulted in movement of their apical portions toward the embryonic posterior, forming a convex-to-spheroidal cell sheet with the apical ends of protoplasts on the outside. Differentiation of the posterior somatic cells from the embryo periphery was traced based on cell lineages during embryogenesis. In contrast, in Eudorina, the rotation of daughter protoplasts did not occur during successive cell divisions; however, inversion occurred after such divisions, and a spheroidal embryo was formed. Indirect immunofluorescence microscopy of basal bodies and nuclei verified this difference between Astrephomene and Eudorina in the movement of embryonic protoplasts.<br><br>CONCLUSIONS: These results suggest different tactics for spheroidal colony formation between the two lineages: rotation of daughter protoplasts during successive cell divisions in Astrephomene, and inversion after cell divisions in Eudorina. This study will facilitate further research into the molecular and genetic mechanisms of the parallel evolution of the spheroidal colony in volvocine algae.},
}
@article {pmid27818507,
year = {2016},
author = {Arendt, D and Musser, JM and Baker, CVH and Bergman, A and Cepko, C and Erwin, DH and Pavlicev, M and Schlosser, G and Widder, S and Laubichler, MD and Wagner, GP},
title = {The origin and evolution of cell types.},
journal = {Nature reviews. Genetics},
volume = {17},
number = {12},
pages = {744-757},
doi = {10.1038/nrg.2016.127},
pmid = {27818507},
issn = {1471-0064},
mesh = {Animals ; *Biological Evolution ; *Cell Differentiation ; *Cell Lineage ; Cells/classification/*cytology ; *Gene Regulatory Networks ; Humans ; Phylogeny ; },
abstract = {Cell types are the basic building blocks of multicellular organisms and are extensively diversified in animals. Despite recent advances in characterizing cell types, classification schemes remain ambiguous. We propose an evolutionary definition of a cell type that allows cell types to be delineated and compared within and between species. Key to cell type identity are evolutionary changes in the 'core regulatory complex' (CoRC) of transcription factors, that make emergent sister cell types distinct, enable their independent evolution and regulate cell type-specific traits termed apomeres. We discuss the distinction between developmental and evolutionary lineages, and present a roadmap for future research.},
}
@article {pmid27818249,
year = {2017},
author = {Currais, A},
title = {The origin of life at the origin of ageing?.},
journal = {Ageing research reviews},
volume = {35},
number = {},
pages = {297-300},
doi = {10.1016/j.arr.2016.10.007},
pmid = {27818249},
issn = {1872-9649},
mesh = {Aging/*physiology ; Animals ; Cell Survival/physiology ; Humans ; *Origin of Life ; },
abstract = {At first glance, the ageing of unicellular organisms would appear to be different from the ageing of complex, multicellular organisms. In an attempt to describe the nature of ageing in diverse organisms, the intimate links between the origins of life and ageing are examined. Departing from Leslie Orgel's initial ideas on why organisms age, it is then discussed how the potentially detrimental events characteristic of ageing are continuous, cell-autonomous and universal to all organisms. The manifestation of these alterations relies on the balance between their production and cellular renewal. Renewal is achieved not only by repair and maintenance mechanisms but, importantly, by the process of cell division such that every time cells divide ageing-associated effects are diluted.},
}
@article {pmid27815194,
year = {2017},
author = {Fletcher, E and Feizi, A and Bisschops, MMM and Hallström, BM and Khoomrung, S and Siewers, V and Nielsen, J},
title = {Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.},
journal = {Metabolic engineering},
volume = {39},
number = {},
pages = {19-28},
doi = {10.1016/j.ymben.2016.10.010},
pmid = {27815194},
issn = {1096-7184},
mesh = {Acids/*chemistry ; Adaptation, Physiological/*genetics ; Directed Molecular Evolution/*methods ; Gene Expression Regulation, Fungal/genetics ; Genetic Enhancement/methods ; *Hydrogen-Ion Concentration ; Saccharomyces cerevisiae/*chemistry/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; Stress, Physiological/*genetics ; },
abstract = {Tolerance of yeast to acid stress is important for many industrial processes including organic acid production. Therefore, elucidating the molecular basis of long term adaptation to acidic environments will be beneficial for engineering production strains to thrive under such harsh conditions. Previous studies using gene expression analysis have suggested that both organic and inorganic acids display similar responses during short term exposure to acidic conditions. However, biological mechanisms that will lead to long term adaptation of yeast to acidic conditions remains unknown and whether these mechanisms will be similar for tolerance to both organic and inorganic acids is yet to be explored. We therefore evolved Saccharomyces cerevisiae to acquire tolerance to HCl (inorganic acid) and to 0.3M L-lactic acid (organic acid) at pH 2.8 and then isolated several low pH tolerant strains. Whole genome sequencing and RNA-seq analysis of the evolved strains revealed different sets of genome alterations suggesting a divergence in adaptation to these two acids. An altered sterol composition and impaired iron uptake contributed to HCl tolerance whereas the formation of a multicellular morphology and rapid lactate degradation was crucial for tolerance to high concentrations of lactic acid. Our findings highlight the contribution of both the selection pressure and nature of the acid as a driver for directing the evolutionary path towards tolerance to low pH. The choice of carbon source was also an important factor in the evolutionary process since cells evolved on two different carbon sources (raffinose and glucose) generated a different set of mutations in response to the presence of lactic acid. Therefore, different strategies are required for a rational design of low pH tolerant strains depending on the acid of interest.},
}
@article {pmid27814692,
year = {2016},
author = {Schilde, C and Lawal, HM and Noegel, AA and Eichinger, L and Schaap, P and Glöckner, G},
title = {A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae.},
journal = {BMC genomics},
volume = {17},
number = {1},
pages = {871},
doi = {10.1186/s12864-016-3223-z},
pmid = {27814692},
issn = {1471-2164},
mesh = {Amoeba/classification/*genetics ; Conserved Sequence ; *Evolution, Molecular ; *Gene Expression ; Gene Expression Profiling ; Gene Knockout Techniques ; Gene Ontology ; Genome ; Mutation ; Phylogeny ; },
abstract = {BACKGROUND: The developmental cycle of Dictyostelid amoebae represents an early form of multicellularity with cell type differentiation. Mutant studies in the model Dictyostelium discoideum revealed that its developmental program integrates the actions of genes involved in signal transduction, adhesion, motility, autophagy and cell wall and matrix biosynthesis. However, due to functional redundancy and fail safe options not required in the laboratory, this single organism approach cannot capture all essential genes. To understand how multicellular organisms evolved, it is essential to recognize both the conserved core features of their developmental programs and the gene modifications that instigated phenotypic innovation. For complex organisms, such as animals, this is not within easy reach, but it is feasible for less complex forms, such as the Dictyostelid social amoebas.<br><br>RESULTS: We compared global profiles of gene expression during the development of four social amoebae species that represent 600 mya of Dictyostelia evolution, and identified orthologous conserved genes with similar developmental up-regulation of expression using three different methods. For validation, we disrupted five genes of this core set and examined the phenotypic consequences.<br><br>CONCLUSION: At least 71 of the developmentally regulated genes that were identified with all methods were likely to be already present in the last ancestor of all Dictyostelia. The lack of phenotypic changes in null mutants indicates that even highly conserved genes either participate in functionally redundant pathways or are necessary for developmental progression under adverse, non-standard laboratory conditions. Both mechanisms provide robustness to the developmental program, but impose a limit on the information that can be obtained from deleting single genes.},
}
@article {pmid27809776,
year = {2016},
author = {Liu, Z and Ji, Z and Wang, G and Chao, T and Hou, L and Wang, J},
title = {Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions.},
journal = {BMC genomics},
volume = {17},
number = {1},
pages = {863},
doi = {10.1186/s12864-016-3212-2},
pmid = {27809776},
issn = {1471-2164},
mesh = {Animals ; Breeding ; Evolution, Molecular ; Gene Ontology ; Genetics, Population ; *Genome ; *Genome-Wide Association Study ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Mutation ; Phenotype ; Polymorphism, Single Nucleotide ; *Quantitative Trait, Heritable ; Reproduction/genetics ; *Selection, Genetic ; Sheep, Domestic/*genetics ; },
abstract = {BACKGROUND: Throughout a long period of adaptation and selection, sheep have thrived in a diverse range of ecological environments. Mongolian sheep is the common ancestor of the Chinese short fat-tailed sheep. Migration to different ecoregions leads to changes in selection pressures and results in microevolution. Mongolian sheep and its subspecies differ in a number of important traits, especially reproductive traits. Genome-wide intraspecific variation is required to dissect the genetic basis of these traits.<br><br>RESULTS: This research resequenced 3 short fat-tailed sheep breeds with a 43.2-fold coverage of the sheep genome. We report more than 17 million single nucleotide polymorphisms and 2.9 million indels and identify 143 genomic regions with reduced pooled heterozygosity or increased genetic distance to each other breed that represent likely targets for selection during the migration. These regions harbor genes related to developmental processes, cellular processes, multicellular organismal processes, biological regulation, metabolic processes, reproduction, localization, growth and various components of the stress responses. Furthermore, we examined the haplotype diversity of 3 genomic regions involved in reproduction and found significant differences in TSHR and PRL gene regions among 8 sheep breeds.<br><br>CONCLUSIONS: Our results provide useful genomic information for identifying genes or causal mutations associated with important economic traits in sheep and for understanding the genetic basis of adaptation to different ecological environments.},
}
@article {pmid27807261,
year = {2016},
author = {Regenberg, B and Hanghøj, KE and Andersen, KS and Boomsma, JJ},
title = {Clonal yeast biofilms can reap competitive advantages through cell differentiation without being obligatorily multicellular.},
journal = {Proceedings. Biological sciences},
volume = {283},
number = {1842},
pages = {},
doi = {10.1098/rspb.2016.1303},
pmid = {27807261},
issn = {1471-2954},
mesh = {*Biofilms ; *Cell Differentiation ; Membrane Glycoproteins/*physiology ; Saccharomyces cerevisiae/*cytology/growth &amp; development ; Saccharomyces cerevisiae Proteins/*physiology ; },
abstract = {How differentiation between cell types evolved is a fundamental question in biology, but few studies have explored single-gene phenotypes that mediate first steps towards division of labour with selective advantage for groups of cells. Here, we show that differential expression of the FLO11 gene produces stable fractions of Flo11+ and Flo11- cells in clonal Saccharomyces cerevisiae biofilm colonies on medium with intermediate viscosity. Differentiated Flo11+/- colonies, consisting of adhesive and non-adhesive cells, obtain a fourfold growth advantage over undifferentiated colonies by overgrowing glucose resources before depleting them, rather than depleting them while they grow as undifferentiated Flo11- colonies do. Flo11+/- colonies maintain their structure and differentiated state by switching non-adhesive cells to adhesive cells with predictable probability. Mixtures of Flo11+ and Flo11- cells from mutant strains that are unable to use this epigenetic switch mechanism produced neither integrated colonies nor growth advantages, so the condition-dependent selective advantages of differentiated FLO11 expression can only be reaped by clone-mate cells. Our results show that selection for cell differentiation in clonal eukaryotes can evolve before the establishment of obligate undifferentiated multicellularity, and without necessarily leading to more advanced organizational complexity.},
}
@article {pmid27806710,
year = {2016},
author = {Dueck, A and Evers, M and Henz, SR and Unger, K and Eichner, N and Merkl, R and Berezikov, E and Engelmann, JC and Weigel, D and Wenzl, S and Meister, G},
title = {Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants.},
journal = {BMC genomics},
volume = {17},
number = {1},
pages = {853},
doi = {10.1186/s12864-016-3202-4},
pmid = {27806710},
issn = {1471-2164},
mesh = {Argonaute Proteins/metabolism ; Base Sequence ; Binding Sites ; Computational Biology/methods ; DNA Transposable Elements ; *Evolution, Molecular ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Gene Silencing ; MicroRNAs/genetics ; Molecular Sequence Annotation ; Nucleotide Motifs ; Protein Binding ; RNA, Small Untranslated/*genetics ; Reproducibility of Results ; Transcriptome ; Volvox/*genetics ; },
abstract = {BACKGROUND: Volvox carteri (V. carteri) is a multicellular green alga used as model system for the evolution of multicellularity. So far, the contribution of small RNA pathways to these phenomena is not understood. Thus, we have sequenced V. carteri Argonaute 3 (VcAGO3)-associated small RNAs from different developmental stages.<br><br>RESULTS: Using this functional approach, we define the Volvox microRNA (miRNA) repertoire and show that miRNAs are not conserved in the closely related unicellular alga Chlamydomonas reinhardtii. Furthermore, we find that miRNAs are differentially expressed during different life stages of V. carteri. In addition to miRNAs, transposon-associated small RNAs or phased siRNA loci, which are common in higher land plants, are highly abundant in Volvox as well. Transposons not only give rise to miRNAs and other small RNAs, they are also targets of small RNAs.<br><br>CONCLUSION: Our analyses reveal a surprisingly complex small RNA network in Volvox as elaborate as in higher land plants. At least the identified VcAGO3-associated miRNAs are not conserved in C. reinhardtii suggesting fast evolution of small RNA systems. Thus, distinct small RNAs may contribute to multicellularity and also division of labor in reproductive and somatic cells.},
}
@article {pmid27796199,
year = {2016},
author = {Trecartin, A and Danopoulos, S and Spurrier, R and Knaneh-Monem, H and Hiatt, M and Driscoll, B and Hochstim, C and Al-Alam, D and Grikscheit, TC},
title = {Establishing Proximal and Distal Regional Identities in Murine and Human Tissue-Engineered Lung and Trachea.},
journal = {Tissue engineering. Part C, Methods},
volume = {22},
number = {11},
pages = {1049-1057},
doi = {10.1089/ten.TEC.2016.0261},
pmid = {27796199},
issn = {1937-3392},
mesh = {Animals ; *Cell Lineage ; *Cell Proliferation ; Cells, Cultured ; Humans ; Lung/*cytology/physiology ; Lung Transplantation ; Mice ; Mice, Inbred C57BL ; Mice, Inbred NOD ; Mice, SCID ; Tissue Engineering/*methods ; Trachea/cytology/*metabolism ; *Wound Healing ; },
abstract = {The cellular and molecular mechanisms that underpin regeneration of the human lung are unknown, and the study of lung repair has been impeded by the necessity for reductionist models that may exclude key components. We hypothesized that multicellular epithelial and mesenchymal cell clusters or lung organoid units (LuOU) could be transplanted to recapitulate proximal and distal cellular structures of the native lung and airways. Transplantation of LuOU resulted in the growth of tissue-engineered lung (TELu) that contained the necessary cell types consistent with native adult lung tissue and demonstrated proliferative cells at 2 and 4 weeks. This technique recapitulated important elements of both mouse and human lungs featuring key components of both the proximal and distal lung regions. When LuOU were generated from whole lung, TELu contained key epithelial and mesenchymal cell types, and the origin of the cells was traced from both ActinGFP and SPCGFP donors to indicate that the cells in TELu were derived from the transplanted LuOU. Alveolar epithelial type 2 cells (AEC2s), club cells, ciliated cells marked by beta-tubulin IV, alveolar epithelial type I cells, Sox-2-positive proximal airway progenitors, p63-positive basal cells, and CGRP-positive pulmonary neuroendocrine cells were identified in the TELu. The mesenchymal components of peribronchial smooth muscle and nerve were identified with a CD31-positive donor endothelial cell contribution to TELu vasculature. TELu successfully grew from postnatal tissues from whole murine and human lung, distal murine lung, as well as murine and human trachea. These data support a model of postnatal lung regeneration containing the diverse cell types present in the entirety of the respiratory tract.},
}
@article {pmid27790999,
year = {2016},
author = {Chen, X and Köllner, TG and Jia, Q and Norris, A and Santhanam, B and Rabe, P and Dickschat, JS and Shaulsky, G and Gershenzon, J and Chen, F},
title = {Terpene synthase genes in eukaryotes beyond plants and fungi: Occurrence in social amoebae.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {113},
number = {43},
pages = {12132-12137},
doi = {10.1073/pnas.1610379113},
pmid = {27790999},
issn = {1091-6490},
support = {P01 HD039691/HD/NICHD NIH HHS/United States ; },
mesh = {Adaptation, Physiological ; Alkyl and Aryl Transferases/classification/*genetics/metabolism ; Biological Evolution ; Cloning, Molecular ; Dictyostelium/classification/enzymology/*genetics ; Escherichia coli/genetics/metabolism ; Gene Expression ; Gene Expression Regulation, Developmental ; *Genome, Protozoan ; Isoenzymes/classification/genetics/metabolism ; Multigene Family ; *Phylogeny ; Protozoan Proteins/classification/*genetics/metabolism ; Recombinant Proteins/genetics/metabolism ; Terpenes/*metabolism ; Volatilization ; },
abstract = {Terpenes are structurally diverse natural products involved in many ecological interactions. The pivotal enzymes for terpene biosynthesis, terpene synthases (TPSs), had been described only in plants and fungi in the eukaryotic domain. In this report, we systematically analyzed the genome sequences of a broad range of nonplant/nonfungus eukaryotes and identified putative TPS genes in six species of amoebae, five of which are multicellular social amoebae from the order of Dictyosteliida. A phylogenetic analysis revealed that amoebal TPSs are evolutionarily more closely related to fungal TPSs than to bacterial TPSs. The social amoeba Dictyostelium discoideum was selected for functional study of the identified TPSs. D. discoideum grows as a unicellular organism when food is abundant and switches from vegetative growth to multicellular development upon starvation. We found that expression of most D. discoideum TPS genes was induced during development. Upon heterologous expression, all nine TPSs from D. discoideum showed sesquiterpene synthase activities. Some also exhibited monoterpene and/or diterpene synthase activities. Direct measurement of volatile terpenes in cultures of D. discoideum revealed essentially no emission at an early stage of development. In contrast, a bouquet of terpenes, dominated by sesquiterpenes including β-barbatene and (E,E)-α-farnesene, was detected at the middle and late stages of development, suggesting a development-specific function of volatile terpenes in D. discoideum. The patchy distribution of TPS genes in the eukaryotic domain and the evidence for TPS function in D. discoideum indicate that the TPS genes mediate lineage-specific adaptations.},
}
@article {pmid27782144,
year = {2016},
author = {Balla, KM and Luallen, RJ and Bakowski, MA and Troemel, ER},
title = {Cell-to-cell spread of microsporidia causes Caenorhabditis elegans organs to form syncytia.},
journal = {Nature microbiology},
volume = {1},
number = {11},
pages = {16144},
doi = {10.1038/nmicrobiol.2016.144},
pmid = {27782144},
issn = {2058-5276},
support = {R01 GM114139/GM/NIGMS NIH HHS/United States ; T32 GM007240/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Caenorhabditis elegans/cytology/*microbiology/physiology ; Cytoplasm/microbiology ; Giant Cells/*microbiology ; *Host-Pathogen Interactions ; Intestines/microbiology ; Microsporidia/classification/growth &amp; development/*physiology ; Muscles/microbiology ; Phylogeny ; },
abstract = {The growth of pathogens is dictated by their interactions with the host environment1. Obligate intracellular pathogens undergo several cellular decisions as they progress through their life cycles inside host cells2. We have studied this process for microsporidian species in the genus Nematocida as they grew and developed inside their co-evolved animal host, Caenorhabditis elegans3-5. We found that microsporidia can restructure multicellular host tissues into a single contiguous multinucleate cell. In particular, we found that all three Nematocida species we studied were able to spread across the cells of C. elegans tissues before forming spores, with two species causing syncytial formation in the intestine and one species causing syncytial formation in the muscle. We also found that the decision to switch from replication to differentiation in Nematocida parisii was altered by the density of infection, suggesting that environmental cues influence the dynamics of the pathogen life cycle. These findings show how microsporidia can maximize the use of host space for growth and that environmental cues in the host can regulate a developmental switch in the pathogen.},
}
@article {pmid27775817,
year = {2017},
author = {Goldring, C and Antoine, DJ and Bonner, F and Crozier, J and Denning, C and Fontana, RJ and Hanley, NA and Hay, DC and Ingelman-Sundberg, M and Juhila, S and Kitteringham, N and Silva-Lima, B and Norris, A and Pridgeon, C and Ross, JA and Young, RS and Tagle, D and Tornesi, B and van de Water, B and Weaver, RJ and Zhang, F and Park, BK},
title = {Stem cell-derived models to improve mechanistic understanding and prediction of human drug-induced liver injury.},
journal = {Hepatology (Baltimore, Md.)},
volume = {65},
number = {2},
pages = {710-721},
doi = {10.1002/hep.28886},
pmid = {27775817},
issn = {1527-3350},
support = {BB/G021821/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; PG/09/027/27141//British Heart Foundation/United Kingdom ; MR/L006758/1//Medical Research Council/United Kingdom ; NC/K000225/1//National Centre for the Replacement, Refinement and Reduction of Animals in Research/International ; SP/15/9/31605//British Heart Foundation/United Kingdom ; G0801098//Medical Research Council/United Kingdom ; MR/K026666/1//Medical Research Council/United Kingdom ; G0700654//Medical Research Council/United Kingdom ; PG/14/59/31000//British Heart Foundation/United Kingdom ; G113/30//Medical Research Council/United Kingdom ; BBS/B/06164//Biotechnology and Biological Sciences Research Council/United Kingdom ; U01 DK065184/DK/NIDDK NIH HHS/United States ; BB/E006159/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L022974/1//Medical Research Council/United Kingdom ; },
mesh = {Cells, Cultured/drug effects ; Chemical and Drug Induced Liver Injury/*diagnosis ; Drug-Related Side Effects and Adverse Reactions/*diagnosis ; Hepatocytes/*drug effects/metabolism ; Humans ; In Vitro Techniques ; Pluripotent Stem Cells/*drug effects/metabolism ; Predictive Value of Tests ; Sensitivity and Specificity ; *Toxicity Tests ; },
abstract = {Current preclinical drug testing does not predict some forms of adverse drug reactions in humans. Efforts at improving predictability of drug-induced tissue injury in humans include using stem cell technology to generate human cells for screening for adverse effects of drugs in humans. The advent of induced pluripotent stem cells means that it may ultimately be possible to develop personalized toxicology to determine interindividual susceptibility to adverse drug reactions. However, the complexity of idiosyncratic drug-induced liver injury means that no current single-cell model, whether of primary liver tissue origin, from liver cell lines, or derived from stem cells, adequately emulates what is believed to occur during human drug-induced liver injury. Nevertheless, a single-cell model of a human hepatocyte which emulates key features of a hepatocyte is likely to be valuable in assessing potential chemical risk; furthermore, understanding how to generate a relevant hepatocyte will also be critical to efforts to build complex multicellular models of the liver. Currently, hepatocyte-like cells differentiated from stem cells still fall short of recapitulating the full mature hepatocellular phenotype. Therefore, we convened a number of experts from the areas of preclinical and clinical hepatotoxicity and safety assessment, from industry, academia, and regulatory bodies, to specifically explore the application of stem cells in hepatotoxicity safety assessment and to make recommendations for the way forward. In this short review, we particularly discuss the importance of benchmarking stem cell-derived hepatocyte-like cells to their terminally differentiated human counterparts using defined phenotyping, to make sure the cells are relevant and comparable between labs, and outline why this process is essential before the cells are introduced into chemical safety assessment. (Hepatology 2017;65:710-721).},
}
@article {pmid27751905,
year = {2017},
author = {Woyda-Ploszczyca, AM and Jarmuszkiewicz, W},
title = {The conserved regulation of mitochondrial uncoupling proteins: From unicellular eukaryotes to mammals.},
journal = {Biochimica et biophysica acta. Bioenergetics},
volume = {1858},
number = {1},
pages = {21-33},
doi = {10.1016/j.bbabio.2016.10.003},
pmid = {27751905},
issn = {0005-2728},
mesh = {Aldehydes/*metabolism ; Animals ; Eukaryota/*metabolism ; Fatty Acids, Nonesterified/*metabolism ; Mammals/*metabolism ; Mitochondrial Uncoupling Proteins/*metabolism ; Purine Nucleotides/*metabolism ; Ubiquinone/*metabolism ; },
abstract = {Uncoupling proteins (UCPs) belong to the mitochondrial anion carrier protein family and mediate regulated proton leak across the inner mitochondrial membrane. Free fatty acids, aldehydes such as hydroxynonenal, and retinoids activate UCPs. However, there are some controversies about the effective action of retinoids and aldehydes alone; thus, only free fatty acids are commonly accepted positive effectors of UCPs. Purine nucleotides such as GTP inhibit UCP-mediated mitochondrial proton leak. In turn, membranous coenzyme Q may play a role as a redox state-dependent metabolic sensor that modulates the complete activation/inhibition of UCPs. Such regulation has been observed for UCPs in microorganisms, plant and animal UCP1 homologues, and UCP1 in mammalian brown adipose tissue. The origin of UCPs is still under debate, but UCP homologues have been identified in all systematic groups of eukaryotes. Despite the differing levels of amino acid/DNA sequence similarities, functional studies in unicellular and multicellular organisms, from amoebae to mammals, suggest that the mechanistic regulation of UCP activity is evolutionarily well conserved. This review focuses on the regulatory feedback loops of UCPs involving free fatty acids, aldehydes, retinoids, purine nucleotides, and coenzyme Q (particularly its reduction level), which may derive from the early stages of evolution as UCP first emerged.},
}
@article {pmid27718356,
year = {2016},
author = {Carmell, MA and Dokshin, GA and Skaletsky, H and Hu, YC and van Wolfswinkel, JC and Igarashi, KJ and Bellott, DW and Nefedov, M and Reddien, PW and Enders, GC and Uversky, VN and Mello, CC and Page, DC},
title = {A widely employed germ cell marker is an ancient disordered protein with reproductive functions in diverse eukaryotes.},
journal = {eLife},
volume = {5},
number = {},
pages = {},
doi = {10.7554/eLife.19993},
pmid = {27718356},
issn = {2050-084X},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Antigens, Nuclear/*genetics/metabolism ; Caenorhabditis elegans/genetics/growth &amp; development ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Expression Regulation/genetics ; Genome/genetics ; Genomics ; Germ Cells/growth &amp; development/*metabolism ; Meiosis/genetics ; Phylogeny ; Reproduction/*genetics ; },
abstract = {The advent of sexual reproduction and the evolution of a dedicated germline in multicellular organisms are critical landmarks in eukaryotic evolution. We report an ancient family of GCNA (germ cell nuclear antigen) proteins that arose in the earliest eukaryotes, and feature a rapidly evolving intrinsically disordered region (IDR). Phylogenetic analysis reveals that GCNA proteins emerged before the major eukaryotic lineages diverged; GCNA predates the origin of a dedicated germline by a billion years. Gcna gene expression is enriched in reproductive cells across eukarya - either just prior to or during meiosis in single-celled eukaryotes, and in stem cells and germ cells of diverse multicellular animals. Studies of Gcna-mutant C. elegans and mice indicate that GCNA has functioned in reproduction for at least 600 million years. Homology to IDR-containing proteins implicated in DNA damage repair suggests that GCNA proteins may protect the genomic integrity of cells carrying a heritable genome.},
}
@article {pmid27751769,
year = {2016},
author = {Gadahi, JA and Ehsan, M and Wang, S and Zhang, Z and Wang, Y and Yan, R and Song, X and Xu, L and Li, X},
title = {Recombinant protein of Haemonchus contortus 14-3-3 isoform 2 (rHcftt-2) decreased the production of IL-4 and suppressed the proliferation of goat PBMCs in vitro.},
journal = {Experimental parasitology},
volume = {171},
number = {},
pages = {57-66},
doi = {10.1016/j.exppara.2016.10.014},
pmid = {27751769},
issn = {1090-2449},
mesh = {Amino Acid Sequence ; Animals ; Antibodies, Helminth/biosynthesis ; Cell Proliferation/drug effects ; Cloning, Molecular ; DNA, Complementary/metabolism ; DNA, Helminth/metabolism ; Dose-Response Relationship, Drug ; Female ; Goats ; Haemonchus/chemistry/genetics/*immunology ; Helminth Proteins/chemistry/*immunology/pharmacology ; Interleukin-4/*immunology/metabolism ; Neutrophils/*immunology/metabolism ; Nitric Oxide/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Protein Isoforms/immunology/pharmacology ; RNA, Helminth/genetics/isolation &amp; purification ; Rats ; Rats, Sprague-Dawley ; Recombinant Proteins/*immunology/pharmacology ; Sequence Alignment ; },
abstract = {14-3-3 proteins have been found to be an excreted/secreted antigen and assumed to be released into the host-parasite interface and described in several unicellular and multicellular parasites. However, little is known about the immunomodulatory effects of H. controtus 14-3-3 protein on host cell. In present study, 14-3-3 isoform 2 gene, designated as Hcftt-2, was amplified by reverse transcription-polymerase chain reaction (RT-PCR) from the adult H. contortus cDNA and cloned into expression plasmid pET32a (+) and expression of the recombinant protein (rHcftt-2) was induced by IPTG. Binding activity of rHcftt-2 to goat peripheral blood mononuclear cells (PBMCs) was confirmed by immunofluorescence assay (IFA) and modulatory effects on cytokine production, cell proliferation, cell migration and nitric oxide (NO) production were observed by co-incubation of rHcftt-2 with goat PBMCs. Sequence analysis showed that it had significant homology with the known 14-3-3 protein isoform 2. Results of IFA revealed that, the rHcftt-2 was bound to the cell surface. We found that, the productions of IL10, IL-17, IFN-γ and cell migration of PBMCs were increased after the cells were incubated with rHCftt-2. However, the productions of IL-4, NO and cell proliferation of the PBMCs were significantly decreased in dose depended manner. Our results showed that the Hcftt-2 played important suppressive regulatory effects on the goat PBMCs.},
}
@article {pmid27738200,
year = {2016},
author = {Spatafora, JW and Chang, Y and Benny, GL and Lazarus, K and Smith, ME and Berbee, ML and Bonito, G and Corradi, N and Grigoriev, I and Gryganskyi, A and James, TY and O'Donnell, K and Roberson, RW and Taylor, TN and Uehling, J and Vilgalys, R and White, MM and Stajich, JE},
title = {A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.},
journal = {Mycologia},
volume = {108},
number = {5},
pages = {1028-1046},
doi = {10.3852/16-042},
pmid = {27738200},
issn = {0027-5514},
support = {S10 OD016290/OD/NIH HHS/United States ; },
mesh = {Fungi/*classification/*genetics ; *Genome, Fungal ; *Phylogeny ; },
abstract = {Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.},
}
@article {pmid27733125,
year = {2016},
author = {Höhn, S and Hallmann, A},
title = {Distinct shape-shifting regimes of bowl-shaped cell sheets - embryonic inversion in the multicellular green alga Pleodorina.},
journal = {BMC developmental biology},
volume = {16},
number = {1},
pages = {35},
doi = {10.1186/s12861-016-0134-9},
pmid = {27733125},
issn = {1471-213X},
mesh = {Biological Evolution ; Cell Division ; Chlorophyta/*cytology/*embryology/ultrastructure ; Microscopy, Electron, Transmission ; *Models, Biological ; *Morphogenesis ; Photogrammetry ; Time Factors ; },
abstract = {BACKGROUND: The multicellular volvocine alga Pleodorina is intermediate in organismal complexity between its unicellular relative, Chlamydomonas, and its multicellular relative, Volvox, which shows complete division of labor between different cell types. The volvocine green microalgae form a group of genera closely related to the genus Volvox within the order Volvocales (Chlorophyta). Embryos of multicellular volvocine algae consist of a cellular monolayer that, depending on the species, is either bowl-shaped or comprises a sphere. During embryogenesis, multicellular volvocine embryos turn their cellular monolayer right-side out to expose their flagella. This process is called 'inversion' and serves as simple model for epithelial folding in metazoa. While the development of spherical Volvox embryos has been the subject of detailed studies, the inversion process of bowl-shaped embryos is less well understood. Therefore, it has been unclear how the inversion of a sphere might have evolved from less complicated processes.<br><br>RESULTS: In this study we characterized the inversion of initially bowl-shaped embryos of the 64- to 128-celled volvocine species Pleodorina californica. We focused on the movement patterns of the cell sheet, cell shape changes and changes in the localization of cytoplasmic bridges (CBs) connecting the cells. The development of living embryos was recorded using time-lapse light microscopy. Moreover, fixed and sectioned embryos throughout inversion and at successive stages of development were analyzed by light and transmission electron microscopy. We generated three-dimensional models of the identified cell shapes including the localization of CBs.<br><br>CONCLUSIONS: In contrast to descriptions concerning volvocine embryos with lower cell numbers, the embryonic cells of P. californica undergo non-simultaneous and non-uniform cell shape changes. In P. californica, cell wedging in combination with a relocation of the CBs to the basal cell tips explains the curling of the cell sheet during inversion. In volvocine genera with lower organismal complexity, the cell shape changes and relocation of CBs are less pronounced in comparison to P. californica, while they are more pronounced in all members of the genus Volvox. This finding supports an increasing significance of the temporal and spatial regulation of cell shape changes and CB relocations with both increasing cell number and organismal complexity during evolution of differentiated multicellularity.},
}
@article {pmid27697546,
year = {2017},
author = {Cai, W and Zhang, K and Li, P and Zhu, L and Xu, J and Yang, B and Hu, X and Lu, Z and Chen, J},
title = {Dysfunction of the neurovascular unit in ischemic stroke and neurodegenerative diseases: An aging effect.},
journal = {Ageing research reviews},
volume = {34},
number = {},
pages = {77-87},
doi = {10.1016/j.arr.2016.09.006},
pmid = {27697546},
issn = {1872-9649},
support = {R01 NS089534/NS/NINDS NIH HHS/United States ; R01 NS095671/NS/NINDS NIH HHS/United States ; I01 BX002495/BX/BLRD VA/United States ; I01 RX000420/RX/RRD VA/United States ; R01 NS036736/NS/NINDS NIH HHS/United States ; R01 NS045048/NS/NINDS NIH HHS/United States ; },
mesh = {Aging/*physiology ; Blood-Brain Barrier ; *Brain/blood supply/pathology/physiopathology ; Humans ; *Neurodegenerative Diseases/pathology/physiopathology ; Neurovascular Coupling/*physiology ; *Stroke/pathology/physiopathology ; },
abstract = {Current understanding on the mechanisms of brain injury and neurodegeneration highlights an appreciation of multicellular interactions within the neurovascular unit (NVU), which include the evolution of blood-brain barrier (BBB) damage, neuronal cell death or degeneration, glial reaction, and immune cell infiltration. Aging is an important factor that influences the integrity of the NVU. The age-related physiological or pathological changes in the cellular components of the NVU have been shown to increase the vulnerability of the NVU to ischemia/reperfusion injury or neurodegeneration, and to result in deteriorated brain damage. This review describes the impacts of aging on each NVU component and discusses the mechanisms by which aging increases NVU sensitivity to stroke and neurodegenerative diseases. Prophylactic or therapeutic perspectives that may delay or diminish aging and thus prevent the incidence of these neurological disorders will also be reviewed.},
}
@article {pmid27693864,
year = {2016},
author = {Kuburich, NA and Adhikari, N and Hadwiger, JA},
title = {Acanthamoeba and Dictyostelium Use Different Foraging Strategies.},
journal = {Protist},
volume = {167},
number = {6},
pages = {511-525},
doi = {10.1016/j.protis.2016.08.006},
pmid = {27693864},
issn = {1618-0941},
support = {R15 GM097717/GM/NIGMS NIH HHS/United States ; },
mesh = {Acanthamoeba/classification/genetics/*physiology ; *Chemotaxis ; Dictyostelium/classification/genetics/*physiology ; Phylogeny ; Protozoan Proteins/genetics ; Signal Transduction ; },
abstract = {Amoeba often use cell movement as a mechanism to find food, such as bacteria, in their environment. The chemotactic movement of the soil amoeba Dictyostelium to folate or other pterin compounds released by bacteria is a well-documented foraging mechanism. Acanthamoeba can also feed on bacteria but relatively little is known about the mechanism(s) by which this amoeba locates bacteria. Acanthamoeba movement in the presence of folate or bacteria was analyzed in above agar assays and compared to that observed for Dictyostelium. The overall mobility of Acanthamoeba was robust like that of Dictyostelium but Acanthamoeba did not display a chemotactic response to folate. In the presence of bacteria, Acanthamoeba only showed a marginal bias in directed movement whereas Dictyostelium displayed a strong chemotactic response. A comparison of genomes revealed that Acanthamoeba and Dictyostelium share some similarities in G protein signaling components but that specific G proteins used in Dictyostelium chemotactic responses were not present in current Acanthamoeba genome sequence data. The results of this study suggest that Acanthamoeba does not use chemotaxis as the primary mechanism to find bacterial food sources and that the chemotactic responses of Dictyostelium to bacteria may have co-evolved with chemotactic responses that facilitate multicellular development.},
}
@article {pmid27686422,
year = {2017},
author = {Mills, DB and Canfield, DE},
title = {A trophic framework for animal origins.},
journal = {Geobiology},
volume = {15},
number = {2},
pages = {197-210},
doi = {10.1111/gbi.12216},
pmid = {27686422},
issn = {1472-4669},
mesh = {Animals ; *Biological Evolution ; Feeding Behavior ; *Heterotrophic Processes ; Organic Chemicals/*metabolism ; *Phagocytosis ; },
abstract = {Metazoans emerged in a microbial world and play a unique role in the biosphere as the only complex multicellular eukaryotes capable of phagocytosis. While the bodyplan and feeding mode of the last common metazoan ancestor remain unresolved, the earliest multicellular stem-metazoans likely subsisted on picoplankton (planktonic microbes 0.2-2 μm in diameter) and dissolved organic matter (DOM), similarly to modern sponges. Once multicellular stem-metazoans emerged, they conceivably modulated both the local availability of picoplankton, which they preferentially removed from the water column for feeding, and detrital particles 2-100 μm in diameter, which they expelled and deposited into the benthos as waste products. By influencing the availability of these heterotrophic food sources, the earliest multicellular stem-metazoans would have acted as ecosystem engineers, helping create the ecological conditions under which other metazoans, namely detritivores and non-sponge suspension feeders incapable of subsisting on picoplankton and DOM, could emerge and diversify. This early style of metazoan feeding, specifically the phagocytosis of small eukaryotic prey, could have also encouraged the evolution of larger, even multicellular, eukaryotic forms less prone to metazoan consumption. Therefore, the first multicellular stem-metazoans, through their feeding, arguably helped bridge the strictly microbial food webs of the Proterozoic Eon (2.5-0.541 billion years ago) to the more macroscopic, metazoan-sustaining food webs of the Phanerozoic Eon (0.541-0 billion years ago).},
}
@article {pmid27686281,
year = {2016},
author = {Wu, CI and Wang, HY and Ling, S and Lu, X},
title = {The Ecology and Evolution of Cancer: The Ultra-Microevolutionary Process.},
journal = {Annual review of genetics},
volume = {50},
number = {},
pages = {347-369},
doi = {10.1146/annurev-genet-112414-054842},
pmid = {27686281},
issn = {1545-2948},
mesh = {Animals ; *Biological Evolution ; Ecology ; Genetic Variation ; Genetics, Population ; Genome, Human ; Genotype ; Humans ; Neoplasms/*etiology/genetics ; Phenotype ; Population Growth ; *Selection, Genetic ; },
abstract = {Although tumorigenesis has been accepted as an evolutionary process (20 , 102), many forces may operate differently in cancers than in organisms, as they evolve at vastly different time scales. Among such forces, natural selection, here defined as differential cellular proliferation among distinct somatic cell genotypes, is particularly interesting because its action might be thwarted in multicellular organisms (20 , 29). In this review, selection is analyzed in two stages of cancer evolution: Stage I is the evolution between tumors and normal tissues, and Stage II is the evolution within tumors. The Cancer Genome Atlas (TCGA) data show a low degree of convergent evolution in Stage I, where genetic changes are not extensively shared among cases. An equally important, albeit much less highlighted, discovery using TCGA data is that there is almost no net selection in cancer evolution. Both positive and negative selection are evident but they neatly cancel each other out, rendering total selection ineffective in the absence of recombination. The efficacy of selection is even lower in Stage II, where neutral (non-Darwinian) evolution is increasingly supported by high-density sampling studies (81 , 123). Because natural selection is not a strong deterministic force, cancers usually evolve divergently even in similar tissue environments.},
}
@article {pmid27663838,
year = {2017},
author = {Ageitos, JM and Sánchez-Pérez, A and Calo-Mata, P and Villa, TG},
title = {Antimicrobial peptides (AMPs): Ancient compounds that represent novel weapons in the fight against bacteria.},
journal = {Biochemical pharmacology},
volume = {133},
number = {},
pages = {117-138},
doi = {10.1016/j.bcp.2016.09.018},
pmid = {27663838},
issn = {1873-2968},
mesh = {Amino Acid Sequence ; Animals ; Antimicrobial Cationic Peptides/*chemistry/genetics/*pharmacology ; Biological Products/*chemistry/*pharmacology ; Cell Wall/drug effects/physiology ; Drug Resistance, Multiple, Bacterial/*drug effects/physiology ; Humans ; Methicillin-Resistant Staphylococcus aureus/drug effects/physiology ; Microbial Sensitivity Tests/methods ; Protein Structure, Secondary ; },
abstract = {Antimicrobial peptides (AMPs) are short peptidic molecules produced by most living creatures. They help unicellular organisms to successfully compete for nutrients with other organisms sharing their biological niche, while AMPs form part of the immune system of multicellular creatures. Thus, these molecules represent biological weapons that have evolved over millions of years as a result of an escalating arms race for survival among living organisms. All AMPs share common features, such as a small size, with cationic and hydrophobic sequences within a linear or cyclic structure. AMPs can inhibit or kill bacteria at micromolar concentrations, often by non-specific mechanisms; hence the appearance of resistance to these antimicrobials is rare. Moreover, AMPs can kill antibiotic-resistant bacteria, including insidious microbes such as Acinetobacter baumannii and the methicillin-resistant Staphylococcus aureus. This review gives a detailed insight into a selection of the most prominent and interesting AMPs with antibacterial activity. In the near future AMPs, due to their properties and despite their ancient origin, should represent a novel alternative to antibiotics in the struggle to control pathogenic microorganisms and maintain the current human life expectancy.},
}
@article {pmid27628442,
year = {2016},
author = {Li, S and Hauser, F and Skadborg, SK and Nielsen, SV and Kirketerp-Møller, N and Grimmelikhuijzen, CJ},
title = {Adipokinetic hormones and their G protein-coupled receptors emerged in Lophotrochozoa.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {32789},
doi = {10.1038/srep32789},
pmid = {27628442},
issn = {2045-2322},
mesh = {Adipokines/*metabolism ; Animals ; *Biological Evolution ; CHO Cells ; Cloning, Molecular ; Computational Biology ; Crassostrea/metabolism ; Cricetinae ; Cricetulus ; Drosophila melanogaster ; Gonadotropin-Releasing Hormone/metabolism ; Humans ; Insect Hormones/*metabolism ; Insect Proteins/metabolism ; Insecta ; Invertebrates/*metabolism ; Ligands ; Neuropeptides/metabolism ; Oligopeptides/*metabolism ; Peptides/metabolism ; Phylogeny ; Pyrrolidonecarboxylic Acid/*analogs &amp; derivatives/metabolism ; Receptors, G-Protein-Coupled/*metabolism ; Signal Transduction ; },
abstract = {Most multicellular animals belong to two evolutionary lineages, the Proto- and Deuterostomia, which diverged 640-760 million years (MYR) ago. Neuropeptide signaling is abundant in animals belonging to both lineages, but it is often unclear whether there exist evolutionary relationships between the neuropeptide systems used by proto- or deuterostomes. An exception, however, are members of the gonadotropin-releasing hormone (GnRH) receptor superfamily, which occur in both evolutionary lineages, where GnRHs are the ligands in Deuterostomia and GnRH-like peptides, adipokinetic hormone (AKH), corazonin, and AKH/corazonin-related peptide (ACP) are the ligands in Protostomia. AKH is a well-studied insect neuropeptide that mobilizes lipids and carbohydrates from the insect fat body during flight. In our present paper, we show that AKH is not only widespread in insects, but also in other Ecdysozoa and in Lophotrochozoa. Furthermore, we have cloned and deorphanized two G protein-coupled receptors (GPCRs) from the oyster Crassostrea gigas (Mollusca) that are activated by low nanomolar concentrations of oyster AKH (pQVSFSTNWGSamide). Our discovery of functional AKH receptors in molluscs is especially significant, because it traces the emergence of AKH signaling back to about 550 MYR ago and brings us closer to a more complete understanding of the evolutionary origins of the GnRH receptor superfamily.},
}
@article {pmid27619696,
year = {2016},
author = {Lehtonen, J and Kokko, H and Parker, GA},
title = {What do isogamous organisms teach us about sex and the two sexes?.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1706},
pages = {},
doi = {10.1098/rstb.2015.0532},
pmid = {27619696},
issn = {1471-2970},
mesh = {*Biological Evolution ; Eukaryota/*physiology ; Germ Cells/*physiology ; Reproduction ; *Sex ; },
abstract = {Isogamy is a reproductive system where all gametes are morphologically similar, especially in terms of size. Its importance goes beyond specific cases: to this day non-anisogamous systems are common outside of multicellular animals and plants, they can be found in all eukaryotic super-groups, and anisogamous organisms appear to have isogamous ancestors. Furthermore, because maleness is synonymous with the production of small gametes, an explanation for the initial origin of males and females is synonymous with understanding the transition from isogamy to anisogamy. As we show here, this transition may also be crucial for understanding why sex itself remains common even in taxa with high costs of male production (the twofold cost of sex). The transition to anisogamy implies the origin of male and female sexes, kickstarts the subsequent evolution of sex roles, and has a major impact on the costliness of sexual reproduction. Finally, we combine some of the consequences of isogamy and anisogamy in a thought experiment on the maintenance of sexual reproduction. We ask what happens if there is a less than twofold benefit to sex (not an unlikely scenario as large short-term benefits have proved difficult to find), and argue that this could lead to a situation where lineages that evolve anisogamy-and thus the highest costs of sex-end up being associated with constraints that make invasion by asexual reproduction unlikely (the 'anisogamy gateway' hypothesis).This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.},
}
@article {pmid27617970,
year = {2016},
author = {Bowman, JL and Sakakibara, K and Furumizu, C and Dierschke, T},
title = {Evolution in the Cycles of Life.},
journal = {Annual review of genetics},
volume = {50},
number = {},
pages = {133-154},
doi = {10.1146/annurev-genet-120215-035227},
pmid = {27617970},
issn = {1545-2948},
mesh = {*Biological Evolution ; Bryophyta/genetics ; Chlorophyta/genetics ; Diploidy ; Eukaryota ; Fungi/genetics ; Haploidy ; Homeodomain Proteins/genetics ; Magnoliopsida/genetics ; Phaeophyta/genetics ; Phylogeny ; Plants/*genetics ; Rhodophyta/genetics ; },
abstract = {The life cycles of eukaryotes alternate between haploid and diploid phases, which are initiated by meiosis and gamete fusion, respectively. In both ascomycete and basidiomycete fungi and chlorophyte algae, the haploid-to-diploid transition is regulated by a pair of paralogous homeodomain protein encoding genes. That a common genetic program controls the haploid-to-diploid transition in phylogenetically disparate eukaryotic lineages suggests this may be the ancestral function for homeodomain proteins. Multicellularity has evolved independently in many eukaryotic lineages in either one or both phases of the life cycle. Organisms, such as land plants, exhibiting a life cycle whereby multicellular bodies develop in both the haploid and diploid phases are often referred to as possessing an alternation of generations. We review recent progress on understanding the genetic basis for the land plant alternation of generations and highlight the roles that homeodomain-encoding genes may have played in the evolution of complex multicellularity in this lineage.},
}
@article {pmid27595342,
year = {2017},
author = {Ishizaki, K},
title = {Evolution of land plants: insights from molecular studies on basal lineages.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {81},
number = {1},
pages = {73-80},
doi = {10.1080/09168451.2016.1224641},
pmid = {27595342},
issn = {1347-6947},
mesh = {Embryophyta/*genetics/metabolism ; *Evolution, Molecular ; Introduced Species ; },
abstract = {The invasion of the land by plants, or terrestrialization, was one of the most critical events in the history of the Earth. The evolution of land plants included significant transformations in body plans: the emergence of a multicellular diploid sporophyte, transition from gametophyte-dominant to sporophyte-dominant life histories, and development of many specialized tissues and organs, such as stomata, vascular tissues, roots, leaves, seeds, and flowers. Recent advances in molecular genetics in two model basal plants, bryophytes Physcomitrella patens and Marchantia polymorpha, have begun to provide answers to several key questions regarding land plant evolution. This paper discusses the evolution of the genes and regulatory mechanisms that helped drive such significant morphological innovations among land-based plants.},
}
@article {pmid27589960,
year = {2016},
author = {Lee, J and Cho, CH and Park, SI and Choi, JW and Song, HS and West, JA and Bhattacharya, D and Yoon, HS},
title = {Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants.},
journal = {BMC biology},
volume = {14},
number = {},
pages = {75},
doi = {10.1186/s12915-016-0299-5},
pmid = {27589960},
issn = {1741-7007},
mesh = {Conserved Sequence/*genetics ; Cycadopsida/*genetics ; *Evolution, Molecular ; Genetic Variation ; *Genome, Plastid ; Magnoliopsida/*genetics ; Multigene Family ; Phylogeny ; Rhodophyta/*genetics ; Seeds/*genetics ; Synteny/genetics ; },
abstract = {BACKGROUND: The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles.<br><br>RESULTS: We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms.<br><br>CONCLUSIONS: Our results provide a comprehensive account of plastid gene loss and rearrangement events involving genome architecture within Archaeplastida and lead to one over-arching conclusion: from an ancestral pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display high conservation in plastid genome architecture. This phenomenon correlates with, and could be explained by, the independent and widely divergent (separated by >400 million years) origins of complex sexual cycles and reproductive structures that led to the rapid diversification of these lineages.},
}
@article {pmid27579832,
year = {2016},
author = {Xu, Y and Yu, XL and Hu, CM and Hao, G},
title = {Morphological and Molecular Phylogenetic Data Reveal a New Species of Primula (Primulaceae) from Hunan, China.},
journal = {PloS one},
volume = {11},
number = {8},
pages = {e0161172},
doi = {10.1371/journal.pone.0161172},
pmid = {27579832},
issn = {1932-6203},
mesh = {China ; Genetic Markers ; *Phylogeny ; Plant Proteins/*genetics ; *Primula/anatomy &amp; histology/classification/genetics ; },
abstract = {A new species of Primulaceae, Primula undulifolia, is described from the hilly area of Hunan province in south-central China. Its morphology and distributional range suggest that it is allied to P. kwangtungensis, both adapted to subtropical climate, having contiguous distribution and similar habitat, growing on shady and moist cliffs. Petioles, scapes and pedicels of them are densely covered with rusty multicellular hairs, but the new species can be easily distinguished by its smaller flowers and narrowly oblong leaves with undulate margins. Molecular phylogenetic analysis based on four DNA markers (ITS, matK, trnL-F and rps16) confirmed the new species as an independent lineage and constitutes a main clade together with P. kwangtungensis, P. kweichouensis, P. wangii and P. hunanensis of Primula sect. Carolinella.},
}
@article {pmid27571751,
year = {2016},
author = {Leducq, JB and Nielly-Thibault, L and Charron, G and Eberlein, C and Verta, JP and Samani, P and Sylvester, K and Hittinger, CT and Bell, G and Landry, CR},
title = {Speciation driven by hybridization and chromosomal plasticity in a wild yeast.},
journal = {Nature microbiology},
volume = {1},
number = {},
pages = {15003},
doi = {10.1038/nmicrobiol.2015.3},
pmid = {27571751},
issn = {2058-5276},
mesh = {*Chromosomes, Fungal ; Forests ; *Genetic Speciation ; *Genetic Variation ; *Hybridization, Genetic ; North America ; *Recombination, Genetic ; Saccharomyces/*classification/*genetics/isolation &amp; purification ; },
abstract = {Hybridization is recognized as a powerful mechanism of speciation and a driving force in generating biodiversity. However, only few multicellular species, limited to a handful of plants and animals, have been shown to fulfil all the criteria of homoploid hybrid speciation. This lack of evidence could lead to the interpretation that speciation by hybridization has a limited role in eukaryotes, particularly in single-celled organisms. Laboratory experiments have revealed that fungi such as budding yeasts can rapidly develop reproductive isolation and novel phenotypes through hybridization, showing that in principle homoploid speciation could occur in nature. Here, we report a case of homoploid hybrid speciation in natural populations of the budding yeast Saccharomyces paradoxus inhabiting the North American forests. We show that the rapid evolution of chromosome architecture and an ecological context that led to secondary contact between nascent species drove the formation of an incipient hybrid species with a potentially unique ecological niche.},
}
@article {pmid27559062,
year = {2016},
author = {Schoustra, S and Hwang, S and Krug, J and de Visser, JA},
title = {Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus.},
journal = {Proceedings. Biological sciences},
volume = {283},
number = {1837},
pages = {},
doi = {10.1098/rspb.2016.1376},
pmid = {27559062},
issn = {1471-2954},
mesh = {Aspergillus nidulans/*genetics ; *Epistasis, Genetic ; *Genetic Fitness ; Genotype ; Models, Genetic ; *Mutation ; },
abstract = {Adaptive evolution ultimately is fuelled by mutations generating novel genetic variation. Non-additivity of fitness effects of mutations (called epistasis) may affect the dynamics and repeatability of adaptation. However, understanding the importance and implications of epistasis is hampered by the observation of substantial variation in patterns of epistasis across empirical studies. Interestingly, some recent studies report increasingly smaller benefits of beneficial mutations once genotypes become better adapted (called diminishing-returns epistasis) in unicellular microbes and single genes. Here, we use Fisher's geometric model (FGM) to generate analytical predictions about the relationship between the effect size of mutations and the extent of epistasis. We then test these predictions using the multicellular fungus Aspergillus nidulans by generating a collection of 108 strains in either a poor or a rich nutrient environment that each carry a beneficial mutation and constructing pairwise combinations using sexual crosses. Our results support the predictions from FGM and indicate negative epistasis among beneficial mutations in both environments, which scale with mutational effect size. Hence, our findings show the importance of diminishing-returns epistasis among beneficial mutations also for a multicellular organism, and suggest that this pattern reflects a generic constraint operating at diverse levels of biological organization.},
}
@article {pmid27534782,
year = {2016},
author = {Šmardová, J and Koptíková, J},
title = {[Two Approaches to Cancer Development].},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {29},
number = {4},
pages = {259-266},
pmid = {27534782},
issn = {0862-495X},
mesh = {Carcinogenesis/*genetics ; Cell Proliferation/*genetics ; Epigenesis, Genetic/genetics ; Humans ; Mutation/*genetics ; Neoplasms/*genetics ; Tumor Microenvironment ; },
abstract = {BACKGROUND: The somatic mutation theory explaining the process of carcinogenesis is generally accepted. The theory postulates that carcinogenesis begins in a first renegade cell that undergoes gradual transformation from a healthy to a fully malignant state through the accumulation of genetic and epigenetic &quot;hits&quot;. This theory focuses specifically on mutations and genetic aberrations, and their impact on cells. It considers tumors as populations of sick cells that lose control of their own proliferation. The theory was put forward by Robert Weinberg and Douglas Hanahan, and is the predominant view in current cancer biology. By contrast, the tissue organization field theory proposed by Carlos Sonnenschein and Ana Soto considers loss of physiological structure and function by a tissue as key events in tumor development. According to this theory, tumors arise at a tissue rather than at a cellular level. It is based on a presumption that proliferation status, rather than quiescence, is the default position of cells in multicellular organisms.<br><br>AIM: The article aims to provide answers to following questions: Are the views of proponents of the somatic mutation theory (the reductionists) and proponents of the tissue organization field theory (the organicists) incompatible and incommensurable, even when the mainstream of tumor biology has shifted its attention from tumor cells toward the tumor microenvironment? Where to find a third interconnecting systemic approach? Is it useful to be aware of the controversy between reductionists and organicists? What this awareness contributes to? How do these alternative views influence practical oncology and tumor biology in general?<br><br>CONCLUSION: Whether the true position is held by reductionists or organicists is unimportant. What is important is to be aware of the existence of these two concepts because this knowledge makes the way we think about tumor origin and development, and how we set up and interpret our experiments, more precise.<br><br>KEY WORDS: carcinogenesis - mutation - cell - tissues - cell proliferation - cell quiescenceThis study was supported by grant of Internal Grant Agency of the Czech ministry of Health No. NT/13784-4/2012.The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.Submitted: 29. 7. 2015Accepted: 27. 4. 2016.},
}
@article {pmid27518838,
year = {2016},
author = {El Kafsi, H and Gorochov, G and Larsen, M},
title = {Host genetics affect microbial ecosystems via host immunity.},
journal = {Current opinion in allergy and clinical immunology},
volume = {16},
number = {5},
pages = {413-420},
doi = {10.1097/ACI.0000000000000302},
pmid = {27518838},
issn = {1473-6322},
mesh = {Animals ; Biological Evolution ; Ecosystem ; *Gene-Environment Interaction ; *Genetic Phenomena ; Homeostasis ; *Host-Pathogen Interactions ; Humans ; Immunity/*genetics ; Mice ; *Microbiota ; Symbiosis ; },
abstract = {PURPOSE OF REVIEW: Genetic evolution of multicellular organisms has occurred in response to environmental challenges, including competition for nutrients, climate change, physical and chemical stressors, and pathogens. However, fitness of an organism is dependent not only on defense efficacy, but also on the ability to take advantage of symbiotic organisms. Indeed, microbes not only encompass pathogenicity, but also enable efficient nutrient uptake from diets nondegradable by the host itself. Moreover, microbes play important roles in the development of host immunity. Here we review associations between specific host genes and variance in microbiota composition and compare with interactions between microbes and host immunity.<br><br>RECENT FINDINGS: Recent genome-wide association studies reveal that symbiosis between host and microbiota is the exquisite result of genetic coevolution. Moreover, a subset of microbes from human and mouse microbiota have been identified to interact with humoral and cellular immunity. Interestingly, microbes associated with both host genetics and host immunity are taxonomically related. Most involved are Bifidobacterium, Lactobacillus, and Akkermansia, which are dually associated with both host immunity and host genetics.<br><br>SUMMARY: We conclude that future therapeutics targeting microbiota in the context of chronic inflammatory diseases need to consider both immune and genetic host features associated with microbiota homeostasis.},
}
@article {pmid27512113,
year = {2016},
author = {Derelle, R and López-García, P and Timpano, H and Moreira, D},
title = {A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts).},
journal = {Molecular biology and evolution},
volume = {33},
number = {11},
pages = {2890-2898},
doi = {10.1093/molbev/msw168},
pmid = {27512113},
issn = {1537-1719},
support = {322669//European Research Council/International ; },
mesh = {*Biological Evolution ; DNA, Ribosomal/genetics ; Diatoms/genetics ; Evolution, Molecular ; Heterotrophic Processes ; Phylogeny ; Sequence Analysis, DNA/methods ; Stramenopiles/*genetics ; },
abstract = {Stramenopiles or heterokonts constitute one of the most speciose and diverse clades of protists. It includes ecologically important algae (such as diatoms or large multicellular brown seaweeds), as well as heterotrophic (e.g., bicosoecids, MAST groups) and parasitic (e.g., Blastocystis, oomycetes) species. Despite their evolutionary and ecological relevance, deep phylogenetic relationships among stramenopile groups, inferred mostly from small-subunit rDNA phylogenies, remain unresolved, especially for the heterotrophic taxa. Taking advantage of recently released stramenopile transcriptome and genome sequences, as well as data from the genomic assembly of the MAST-3 species Incisomonas marina generated in our laboratory, we have carried out the first extensive phylogenomic analysis of stramenopiles, including representatives of most major lineages. Our analyses, based on a large data set of 339 widely distributed proteins, strongly support a root of stramenopiles lying between two clades, Bigyra and Gyrista (Pseudofungi plus Ochrophyta). Additionally, our analyses challenge the Phaeista-Khakista dichotomy of photosynthetic stramenopiles (ochrophytes) as two groups previously considered to be part of the Phaeista (Pelagophyceae and Dictyochophyceae), branch with strong support with the Khakista (Bolidophyceae and Diatomeae). We propose a new classification of ochrophytes within the two groups Chrysista and Diatomista to reflect the new phylogenomic results. Our stramenopile phylogeny provides a robust phylogenetic framework to investigate the evolution and diversification of this group of ecologically relevant protists.},
}
@article {pmid27510329,
year = {2017},
author = {Pesce, M and Santoro, R},
title = {Feeling the right force: How to contextualize the cell mechanical behavior in physiologic turnover and pathologic evolution of the cardiovascular system.},
journal = {Pharmacology &amp; therapeutics},
volume = {171},
number = {},
pages = {75-82},
doi = {10.1016/j.pharmthera.2016.08.002},
pmid = {27510329},
issn = {1879-016X},
mesh = {Animals ; Cardiovascular Diseases/*physiopathology ; Cardiovascular System/*cytology/metabolism/physiopathology ; Cell Differentiation/*physiology ; Cell Engineering/methods ; Embryonic Development/physiology ; Gene Expression/physiology ; Humans ; },
abstract = {Although traditionally linked to the physiology of tissues in 'motion', the ability of the cells to transduce external forces into coordinated gene expression programs is emerging as an integral component of the fundamental structural organization of multicellular organisms with consequences for cell differentiation even from the beginning of embryonic development. The ability of the cells to 'feel' the surrounding mechanical environment, even in the absence of tissue motion, is then translated into 'positional' or 'social' sensing that instructs, before the organ renewal, the correct patterning of the embryos. In the present review, we will highlight how these basic concepts, emerging from the employment of novel cell engineering tools, can be linked to pathophysiology of the cardiovascular system, and may contribute to understanding the molecular bases of some of the major cardiovascular diseases like heart failure, heart valve stenosis and failure of the venous aorto-coronary bypass.},
}
@article {pmid27501943,
year = {2016},
author = {Sojo, V and Dessimoz, C and Pomiankowski, A and Lane, N},
title = {Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life.},
journal = {Molecular biology and evolution},
volume = {33},
number = {11},
pages = {2874-2884},
doi = {10.1093/molbev/msw164},
pmid = {27501943},
issn = {1537-1719},
support = {BB/L018241/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Adaptation, Biological ; Archaea/genetics ; Bacteria/genetics ; Biological Evolution ; Databases, Protein ; Eukaryota/genetics ; Evolution, Molecular ; Homeostasis ; Membrane Proteins/*genetics/metabolism ; Phylogeny ; Prokaryotic Cells ; Proteins/*genetics/metabolism ; Sequence Analysis, Protein/*methods ; Solubility ; Water/metabolism ; },
abstract = {Membrane proteins are crucial in transport, signaling, bioenergetics, catalysis, and as drug targets. Here, we show that membrane proteins have dramatically fewer detectable orthologs than water-soluble proteins, less than half in most species analyzed. This sparse distribution could reflect rapid divergence or gene loss. We find that both mechanisms operate. First, membrane proteins evolve faster than water-soluble proteins, particularly in their exterior-facing portions. Second, we demonstrate that predicted ancestral membrane proteins are preferentially lost compared with water-soluble proteins in closely related species of archaea and bacteria. These patterns are consistent across the whole tree of life, and in each of the three domains of archaea, bacteria, and eukaryotes. Our findings point to a fundamental evolutionary principle: membrane proteins evolve faster due to stronger adaptive selection in changing environments, whereas cytosolic proteins are under more stringent purifying selection in the homeostatic interior of the cell. This effect should be strongest in prokaryotes, weaker in unicellular eukaryotes (with intracellular membranes), and weakest in multicellular eukaryotes (with extracellular homeostasis). We demonstrate that this is indeed the case. Similarly, we show that extracellular water-soluble proteins exhibit an even stronger pattern of low homology than membrane proteins. These striking differences in conservation of membrane proteins versus water-soluble proteins have important implications for evolution and medicine.},
}
@article {pmid27490201,
year = {2016},
author = {Denver, DR and Brown, AM and Howe, DK and Peetz, AB and Zasada, IA},
title = {Genome Skimming: A Rapid Approach to Gaining Diverse Biological Insights into Multicellular Pathogens.},
journal = {PLoS pathogens},
volume = {12},
number = {8},
pages = {e1005713},
doi = {10.1371/journal.ppat.1005713},
pmid = {27490201},
issn = {1553-7374},
mesh = {Animals ; Genome ; Humans ; Nematoda/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
}
@article {pmid27476447,
year = {2017},
author = {Jubin, T and Kadam, A and Gani, AR and Singh, M and Dwivedi, M and Begum, R},
title = {Poly ADP-ribose polymerase-1: Beyond transcription and towards differentiation.},
journal = {Seminars in cell &amp; developmental biology},
volume = {63},
number = {},
pages = {167-179},
doi = {10.1016/j.semcdb.2016.07.027},
pmid = {27476447},
issn = {1096-3634},
mesh = {Animals ; Cell Differentiation/*genetics ; Embryonic Development/genetics ; Gene Expression Regulation ; Humans ; Models, Biological ; Poly(ADP-ribose) Polymerases/*metabolism ; *Transcription, Genetic ; },
abstract = {Gene regulation mediates the processes of cellular development and differentiation leading to the origin of different cell types each having their own signature gene expression profile. However, the compact chromatin structure and the timely recruitment of molecules involved in various signaling pathways are of prime importance for temporal and spatial gene regulation that eventually contribute towards cell type and specificity. Poly (ADP-ribose) polymerase-1 (PARP-1), a 116-kDa nuclear multitasking protein is involved in modulation of chromatin condensation leading to altered gene expression. In response to activation signals, it adds ADP-ribose units to various target proteins including itself, thus regulating various key cellular processes like DNA repair, cell death, transcription, mRNA splicing etc. This review provides insights into the role of PARP-1 in gene regulation, cell differentiation and multicellular morphogenesis. In addition, the review also explores involvement of PARP-1 in immune cells development and therapeutic possibilities to treat various human diseases.},
}
@article {pmid27458458,
year = {2016},
author = {Zhang, X and Soldati, T},
title = {Of Amoebae and Men: Extracellular DNA Traps as an Ancient Cell-Intrinsic Defense Mechanism.},
journal = {Frontiers in immunology},
volume = {7},
number = {},
pages = {269},
doi = {10.3389/fimmu.2016.00269},
pmid = {27458458},
issn = {1664-3224},
abstract = {Since the discovery of the formation of DNA-based extracellular traps (ETs) by neutrophils as an innate immune defense mechanism (1), hundreds of articles describe the involvement of ETs in physiological and pathological human and animal conditions [reviewed in Ref. (2), and the previous Frontiers Research Topic on NETosis: http://www.frontiersin.org/books/NETosis_At_the_Intersection_of_Cell_Biology_Microbiology_and_Immunology/195]. Interestingly, a few reports reveal that ETs can be formed by immune cells of more ancient organisms, as far back as the common ancestor of vertebrates and invertebrates (3). Recently, we reported that the Sentinel cells of the multicellular slug of the social amoeba Dictyostelium discoideum also produce ETs to trap and kill slug-invading bacteria [see Box 1; and Figure 1 Ref. (4)]. This is a strong evidence that DNA-based cell-intrinsic defense mechanisms emerged much earlier than thought, about 1.3 billion years ago. Amazingly, using extrusion of DNA as a weapon to capture and kill uningestable microbes has its rationale. During the emergence of multicellularity, a primitive innate immune system developed in the form of a dedicated set of specialized phagocytic cells. This professionalization of immunity allowed the evolution of sophisticated defense mechanisms including the sacrifice of a small set of cells by a mechanism related to NETosis. This altruistic behavior likely emerged in steps, starting from the release of &quot;dispensable&quot; mitochondrial DNA by D. discoideum Sentinel cells. Grounded in this realization, one can anticipate that in the near future, many more examples of the invention and fine-tuning of ETs by early metazoan ancestors will be identified. Consequently, it can be expected that this more complete picture of the evolution of ETs will impact our views of the involvement and pathologies linked to ETs in human and animals.},
}
@article {pmid27451296,
year = {2016},
author = {Matt, G and Umen, J},
title = {Volvox: A simple algal model for embryogenesis, morphogenesis and cellular differentiation.},
journal = {Developmental biology},
volume = {419},
number = {1},
pages = {99-113},
doi = {10.1016/j.ydbio.2016.07.014},
pmid = {27451296},
issn = {1095-564X},
support = {R01 GM078376/GM/NIGMS NIH HHS/United States ; },
mesh = {Cell Cycle ; Cell Lineage ; Cell Size ; Cellular Senescence ; *Models, Biological ; Morphogenesis ; Mutation ; Phylogeny ; Reproduction, Asexual ; Seeds ; Volvox/*cytology/genetics/physiology ; },
abstract = {Patterning of a multicellular body plan involves a coordinated set of developmental processes that includes cell division, morphogenesis, and cellular differentiation. These processes have been most intensively studied in animals and land plants; however, deep insight can also be gained by studying development in simpler multicellular organisms. The multicellular green alga Volvox carteri (Volvox) is an excellent model for the investigation of developmental mechanisms and their evolutionary origins. Volvox has a streamlined body plan that contains only a few thousand cells and two distinct cell types: reproductive germ cells and terminally differentiated somatic cells. Patterning of the Volvox body plan is achieved through a stereotyped developmental program that includes embryonic cleavage with asymmetric cell division, morphogenesis, and cell-type differentiation. In this review we provide an overview of how these three developmental processes give rise to the adult form in Volvox and how developmental mutants have provided insights into the mechanisms behind these events. We highlight the accessibility and tractability of Volvox and its relatives that provide a unique opportunity for studying development.},
}
@article {pmid27431524,
year = {2016},
author = {Moses, M and Bezerra, G and Edwards, B and Brown, J and Forrest, S},
title = {Energy and time determine scaling in biological and computer designs.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1701},
pages = {},
doi = {10.1098/rstb.2015.0446},
pmid = {27431524},
issn = {1471-2970},
support = {T32 EB009414/EB/NIBIB NIH HHS/United States ; },
mesh = {Animals ; *Basal Metabolism ; Biological Evolution ; *Electric Power Supplies ; Mammals/*physiology ; *Microcomputers ; Models, Biological ; Models, Theoretical ; Selection, Genetic ; },
abstract = {Metabolic rate in animals and power consumption in computers are analogous quantities that scale similarly with size. We analyse vascular systems of mammals and on-chip networks of microprocessors, where natural selection and human engineering, respectively, have produced systems that minimize both energy dissipation and delivery times. Using a simple network model that simultaneously minimizes energy and time, our analysis explains empirically observed trends in the scaling of metabolic rate in mammals and power consumption and performance in microprocessors across several orders of magnitude in size. Just as the evolutionary transitions from unicellular to multicellular animals in biology are associated with shifts in metabolic scaling, our model suggests that the scaling of power and performance will change as computer designs transition to decentralized multi-core and distributed cyber-physical systems. More generally, a single energy-time minimization principle may govern the design of many complex systems that process energy, materials and information.This article is part of the themed issue 'The major synthetic evolutionary transitions'.},
}
@article {pmid27431522,
year = {2016},
author = {Libby, E and Conlin, PL and Kerr, B and Ratcliff, WC},
title = {Stabilizing multicellularity through ratcheting.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1701},
pages = {},
doi = {10.1098/rstb.2015.0444},
pmid = {27431522},
issn = {1471-2970},
mesh = {*Adaptation, Biological ; *Biological Evolution ; Eukaryota/genetics/*physiology ; Models, Genetic ; *Selection, Genetic ; },
abstract = {The evolutionary transition to multicellularity probably began with the formation of simple undifferentiated cellular groups. Such groups evolve readily in diverse lineages of extant unicellular taxa, suggesting that there are few genetic barriers to this first key step. This may act as a double-edged sword: labile transitions between unicellular and multicellular states may facilitate the evolution of simple multicellularity, but reversion to a unicellular state may inhibit the evolution of increased complexity. In this paper, we examine how multicellular adaptations can act as evolutionary 'ratchets', limiting the potential for reversion to unicellularity. We consider a nascent multicellular lineage growing in an environment that varies between favouring multicellularity and favouring unicellularity. The first type of ratcheting mutations increase cell-level fitness in a multicellular context but are costly in a single-celled context, reducing the fitness of revertants. The second type of ratcheting mutations directly decrease the probability that a mutation will result in reversion (either as a pleiotropic consequence or via direct modification of switch rates). We show that both types of ratcheting mutations act to stabilize the multicellular state. We also identify synergistic effects between the two types of ratcheting mutations in which the presence of one creates the selective conditions favouring the other. Ratcheting mutations may play a key role in diverse evolutionary transitions in individuality, sustaining selection on the new higher-level organism by constraining evolutionary reversion.This article is part of the themed issue 'The major synthetic evolutionary transitions'.},
}
@article {pmid27431521,
year = {2016},
author = {Newman, SA},
title = {'Biogeneric' developmental processes: drivers of major transitions in animal evolution.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1701},
pages = {},
doi = {10.1098/rstb.2015.0443},
pmid = {27431521},
issn = {1471-2970},
mesh = {Animals ; *Biological Evolution ; Evolution, Molecular ; Extremities/anatomy &amp; histology ; Fishes/anatomy &amp; histology/*physiology ; Invertebrates/*physiology ; *Morphogenesis ; },
abstract = {Using three examples drawn from animal systems, I advance the hypothesis that major transitions in multicellular evolution often involved the constitution of new cell-based materials with unprecedented morphogenetic capabilities. I term the materials and formative processes that arise when highly evolved cells are incorporated into mesoscale matter 'biogeneric', to reflect their commonality with, and distinctiveness from, the organizational properties of non-living materials. The first transition arose by the innovation of classical cell-adhesive cadherins with transmembrane linkage to the cytoskeleton and the appearance of the morphogen Wnt, transforming some ancestral unicellular holozoans into 'liquid tissues', and thereby originating the metazoans. The second transition involved the new capabilities, within a basal metazoan population, of producing a mechanically stable basal lamina, and of planar cell polarization. This gave rise to the eumetazoans, initially diploblastic (two-layered) forms, and then with the addition of extracellular matrices promoting epithelial-mesenchymal transformation, three-layered triploblasts. The last example is the fin-to-limb transition. Here, the components of a molecular network that promoted the development of species-idiosyncratic endoskeletal elements in gnathostome ancestors are proposed to have evolved to a dynamical regime in which they constituted a Turing-type reaction-diffusion system capable of organizing the stereotypical arrays of elements of lobe-finned fish and tetrapods. The contrasting implications of the biogeneric materials-based and neo-Darwinian perspectives for understanding major evolutionary transitions are discussed.This article is part of the themed issue 'The major synthetic evolutionary transitions'.},
}
@article {pmid27412854,
year = {2016},
author = {Smeds, L and Qvarnström, A and Ellegren, H},
title = {Direct estimate of the rate of germline mutation in a bird.},
journal = {Genome research},
volume = {26},
number = {9},
pages = {1211-1218},
doi = {10.1101/gr.204669.116},
pmid = {27412854},
issn = {1549-5469},
mesh = {Animals ; *Evolution, Molecular ; Genome ; Germ-Line Mutation/*genetics ; High-Throughput Nucleotide Sequencing ; Mutation Rate ; Pedigree ; Songbirds/*genetics ; },
abstract = {The fidelity of DNA replication together with repair mechanisms ensure that the genetic material is properly copied from one generation to another. However, on extremely rare occasions when damages to DNA or replication errors are not repaired, germline mutations can be transmitted to the next generation. Because of the rarity of these events, studying the rate at which new mutations arise across organisms has been a great challenge, especially in multicellular nonmodel organisms with large genomes. We sequenced the genomes of 11 birds from a three-generation pedigree of the collared flycatcher (Ficedula albicollis) and used highly stringent bioinformatic criteria for mutation detection and used several procedures to validate mutations, including following the stable inheritance of new mutations to subsequent generations. We identified 55 de novo mutations with a 10-fold enrichment of mutations at CpG sites and with only a modest male mutation bias. The estimated rate of mutation per site per generation was 4.6 × 10(-9), which corresponds to 2.3 × 10(-9) mutations per site per year. Compared to mammals, this is similar to mouse but about half of that reported for humans, which may be due to the higher frequency of male mutations in humans. We confirm that mutation rate scales positively with genome size and that there is a strong negative relationship between mutation rate and effective population size, in line with the drift-barrier hypothesis. Our study illustrates that it should be feasible to obtain direct estimates of the rate of mutation in essentially any organism from which family material can be obtained.},
}
@article {pmid27411810,
year = {2016},
author = {Cook, LM and Araujo, A and Pow-Sang, JM and Budzevich, MM and Basanta, D and Lynch, CC},
title = {Predictive computational modeling to define effective treatment strategies for bone metastatic prostate cancer.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {29384},
doi = {10.1038/srep29384},
pmid = {27411810},
issn = {2045-2322},
support = {P30 CA076292/CA/NCI NIH HHS/United States ; R01 CA143094/CA/NCI NIH HHS/United States ; U01 CA151924/CA/NCI NIH HHS/United States ; U01 CA202958/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Bone Neoplasms/*secondary/*therapy ; Bone and Bones/pathology ; Cell Differentiation ; Cell Survival ; *Computer Simulation ; Humans ; Male ; Mice ; Mice, SCID ; Neoplasm Metastasis ; Osteoblasts/cytology ; Osteoclasts/cytology ; Osteolysis ; Prostate/pathology ; Prostatic Neoplasms/*pathology/*therapy ; Transforming Growth Factor beta1/antagonists &amp; inhibitors/*metabolism ; },
abstract = {The ability to rapidly assess the efficacy of therapeutic strategies for incurable bone metastatic prostate cancer is an urgent need. Pre-clinical in vivo models are limited in their ability to define the temporal effects of therapies on simultaneous multicellular interactions in the cancer-bone microenvironment. Integrating biological and computational modeling approaches can overcome this limitation. Here, we generated a biologically driven discrete hybrid cellular automaton (HCA) model of bone metastatic prostate cancer to identify the optimal therapeutic window for putative targeted therapies. As proof of principle, we focused on TGFβ because of its known pleiotropic cellular effects. HCA simulations predict an optimal effect for TGFβ inhibition in a pre-metastatic setting with quantitative outputs indicating a significant impact on prostate cancer cell viability, osteoclast formation and osteoblast differentiation. In silico predictions were validated in vivo with models of bone metastatic prostate cancer (PAIII and C4-2B). Analysis of human bone metastatic prostate cancer specimens reveals heterogeneous cancer cell use of TGFβ. Patient specific information was seeded into the HCA model to predict the effect of TGFβ inhibitor treatment on disease evolution. Collectively, we demonstrate how an integrated computational/biological approach can rapidly optimize the efficacy of potential targeted therapies on bone metastatic prostate cancer.},
}
@article {pmid27402737,
year = {2016},
author = {Wahl, ME and Murray, AW},
title = {Multicellularity makes somatic differentiation evolutionarily stable.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {113},
number = {30},
pages = {8362-8367},
doi = {10.1073/pnas.1608278113},
pmid = {27402737},
issn = {1091-6490},
support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; },
mesh = {Biological Evolution ; *Cell Differentiation ; Cell Division/genetics ; *Cell Lineage ; Cell Survival/genetics ; Genetic Engineering/methods ; Germ Cells/*cytology/metabolism ; *Models, Biological ; Mutation ; Saccharomyces cerevisiae/cytology/genetics ; },
abstract = {Many multicellular organisms produce two cell lineages: germ cells, whose descendants produce the next generation, and somatic cells, which support, protect, and disperse the germ cells. This germ-soma demarcation has evolved independently in dozens of multicellular taxa but is absent in unicellular species. A common explanation holds that in these organisms, inefficient intercellular nutrient exchange compels the fitness cost of producing nonreproductive somatic cells to outweigh any potential benefits. We propose instead that the absence of unicellular, soma-producing populations reflects their susceptibility to invasion by nondifferentiating mutants that ultimately eradicate the soma-producing lineage. We argue that multicellularity can prevent the victory of such mutants by giving germ cells preferential access to the benefits conferred by somatic cells. The absence of natural unicellular, soma-producing species previously prevented these hypotheses from being directly tested in vivo: to overcome this obstacle, we engineered strains of the budding yeast Saccharomyces cerevisiae that differ only in the presence or absence of multicellularity and somatic differentiation, permitting direct comparisons between organisms with different lifestyles. Our strains implement the essential features of irreversible conversion from germ line to soma, reproductive division of labor, and clonal multicellularity while maintaining sufficient generality to permit broad extension of our conclusions. Our somatic cells can provide fitness benefits that exceed the reproductive costs of their production, even in unicellular strains. We find that nondifferentiating mutants overtake unicellular populations but are outcompeted by multicellular, soma-producing strains, suggesting that multicellularity confers evolutionary stability to somatic differentiation.},
}
@article {pmid27401232,
year = {2016},
author = {Francois, CM and Duret, L and Simon, L and Mermillod-Blondin, F and Malard, F and Konecny-Dupré, L and Planel, R and Penel, S and Douady, CJ and Lefébure, T},
title = {No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes.},
journal = {Molecular biology and evolution},
volume = {33},
number = {10},
pages = {2605-2620},
doi = {10.1093/molbev/msw131},
pmid = {27401232},
issn = {1537-1719},
mesh = {Amino Acids/genetics/metabolism ; Animals ; Ecosystem ; Isopoda/*genetics/*metabolism ; Nitrogen/*deficiency/*metabolism ; Nucleotides/genetics/metabolism ; Phylogeny ; Proteome ; Selection, Genetic ; Transcriptome ; },
abstract = {The field of stoichiogenomics aims at understanding the influence of nutrient limitations on the elemental composition of the genome, transcriptome, and proteome. The 20 amino acids and the 4 nt differ in the number of nutrients they contain, such as nitrogen (N). Thus, N limitation shall theoretically select for changes in the composition of proteins or RNAs through preferential use of N-poor amino acids or nucleotides, which will decrease the N-budget of an organism. While these N-saving mechanisms have been evidenced in microorganisms, they remain controversial in multicellular eukaryotes. In this study, we used 13 surface and subterranean isopod species pairs that face strongly contrasted N limitations, either in terms of quantity or quality. We combined in situ nutrient quantification and transcriptome sequencing to test if N limitation selected for N-savings through changes in the expression and composition of the transcriptome and proteome. No evidence of N-savings was found in the total N-budget of transcriptomes or proteomes or in the average protein N-cost. Nevertheless, subterranean species evolving in N-depleted habitats displayed lower N-usage at their third codon positions. To test if this convergent compositional change was driven by natural selection, we developed a method to detect the strand-asymmetric signature that stoichiogenomic selection should leave in the substitution pattern. No such signature was evidenced, indicating that the observed stoichiogenomic-like patterns were attributable to nonadaptive processes. The absence of stoichiogenomic signal despite strong N limitation within a powerful phylogenetic framework casts doubt on the existence of stoichiogenomic mechanisms in metazoans.},
}
@article {pmid27391808,
year = {2016},
author = {Jeong, SY and Lee, JH and Shin, Y and Chung, S and Kuh, HJ},
title = {Co-Culture of Tumor Spheroids and Fibroblasts in a Collagen Matrix-Incorporated Microfluidic Chip Mimics Reciprocal Activation in Solid Tumor Microenvironment.},
journal = {PloS one},
volume = {11},
number = {7},
pages = {e0159013},
doi = {10.1371/journal.pone.0159013},
pmid = {27391808},
issn = {1932-6203},
mesh = {Coculture Techniques/instrumentation/methods ; Collagen/*chemistry ; Colorectal Neoplasms/*metabolism/pathology ; Extracellular Matrix/chemistry ; Fibroblasts/*metabolism/pathology ; Humans ; *Lab-On-A-Chip Devices ; Spheroids, Cellular/*metabolism/pathology ; *Tumor Microenvironment ; },
abstract = {Multicellular 3D culture and interaction with stromal components are considered essential elements in establishing a 'more clinically relevant' tumor model. Matrix-embedded 3D cultures using a microfluidic chip platform can recapitulate the microscale interaction within tumor microenvironments. As a major component of tumor microenvironment, cancer-associated fibroblasts (CAFs) play a role in cancer progression and drug resistance. Here, we present a microfluidic chip-based tumor tissue culture model that integrates 3D tumor spheroids (TSs) with CAF in proximity within a hydrogel scaffold. HT-29 human colorectal carcinoma cells grew into 3D TSs and the growth was stimulated when co-cultured with fibroblasts as shown by 1.5-folds increase of % changes in diameter over 5 days. TS cultured for 6 days showed a reduced expression of Ki-67 along with increased expression of fibronectin when co-cultured with fibroblasts compared to mono-cultured TSs. Fibroblasts were activated under co-culture conditions, as demonstrated by increases in α-SMA expression and migratory activity. When exposed to paclitaxel, a survival advantage was observed in TSs co-cultured with activated fibroblasts. Overall, we demonstrated the reciprocal interaction between TSs and fibroblasts in our 7-channel microfluidic chip. The co-culture of 3D TS-CAF in a collagen matrix-incorporated microfluidic chip may be useful to study the tumor microenvironment and for evaluation of drug screening and evaluation.},
}
@article {pmid27383475,
year = {2016},
author = {Baek, SY and Jang, KH and Choi, EH and Ryu, SH and Kim, SK and Lee, JH and Lim, YJ and Lee, J and Jun, J and Kwak, M and Lee, YS and Hwang, JS and Venmathi Maran, BA and Chang, CY and Kim, IH and Hwang, UW},
title = {DNA Barcoding of Metazoan Zooplankton Copepods from South Korea.},
journal = {PloS one},
volume = {11},
number = {7},
pages = {e0157307},
doi = {10.1371/journal.pone.0157307},
pmid = {27383475},
issn = {1932-6203},
mesh = {Animals ; Copepoda/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genes, Mitochondrial ; Genetic Variation ; Geography ; Phylogeny ; Republic of Korea ; Sequence Analysis, DNA ; Species Specificity ; Zooplankton/*genetics ; },
abstract = {Copepods, small aquatic crustaceans, are the most abundant metazoan zooplankton and outnumber every other group of multicellular animals on earth. In spite of ecological and biological importance in aquatic environment, their morphological plasticity, originated from their various lifestyles and their incomparable capacity to adapt to a variety of environments, has made the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of cryptic or sibling species based on DNA sequence data. We examined sequence variation of a partial mitochondrial cytochrome C oxidase I gene (COI) from 133 copepod individuals collected from the Korean Peninsula, in order to identify and discriminate 94 copepod species covering six copepod orders of Calanoida, Cyclopoida, Harpacticoida, Monstrilloida, Poecilostomatoida and Siphonostomatoida. The results showed that there exists a clear gap with ca. 20 fold difference between the averages of within-specific sequence divergence (2.42%) and that of between-specific sequence divergence (42.79%) in COI, suggesting the plausible utility of this gene in delimitating copepod species. The results showed, with the COI barcoding data among 94 copepod species, that a copepod species could be distinguished from the others very clearly, only with four exceptions as followings: Mesocyclops dissimilis-Mesocyclops pehpeiensis (0.26% K2P distance in percent) and Oithona davisae-Oithona similis (1.1%) in Cyclopoida, Ostrincola japonica-Pseudomyicola spinosus (1.5%) in Poecilostomatoida, and Hatschekia japonica-Caligus quadratus (5.2%) in Siphonostomatoida. Thus, it strongly indicated that COI may be a useful tool in identifying various copepod species and make an initial progress toward the construction of a comprehensive DNA barcode database for copepods inhabiting the Korean Peninsula.},
}
@article {pmid27379901,
year = {2016},
author = {Olson, BJ and Nedelcu, AM},
title = {Co-option during the evolution of multicellular and developmental complexity in the volvocine green algae.},
journal = {Current opinion in genetics &amp; development},
volume = {39},
number = {},
pages = {107-115},
doi = {10.1016/j.gde.2016.06.003},
pmid = {27379901},
issn = {1879-0380},
mesh = {Cell Differentiation/*genetics ; Chlamydomonas/classification/genetics/growth &amp; development ; Chlorophyta/classification/*genetics/growth &amp; development ; *Evolution, Molecular ; Germ Cells/growth &amp; development ; *Phylogeny ; Volvox/classification/genetics/growth &amp; development ; },
abstract = {Despite its major impact on the evolution of Life on Earth, the transition to multicellularity remains poorly understood, especially in terms of its genetic basis. The volvocine algae are a group of closely related species that range in morphology from unicellular individuals (Chlamydomonas) to undifferentiated multicellular forms (Gonium) and complex organisms with distinct developmental programs and one (Pleodorina) or two (Volvox) specialized cell types. Modern genetic approaches, complemented by the recent sequencing of genomes from several key species, revealed that co-option of existing genes and pathways is the primary driving force for the evolution of multicellularity in this lineage. The initial transition to undifferentiated multicellularity, as typified by the extant Gonium, was driven primarily by the co-option of cell cycle regulation. Further morphological and developmental innovations in the lineage leading to Volvox resulted from additional co-option events involving genes important for embryonic inversion, asymmetric cell division, somatic and germ cell differentiation and the structure and function of the extracellular matrix. Because of their relatively low but variable levels of morphological and developmental complexity, simple underlying genetics and recent evolutionary history, the volvocine algae are providing significant insight into our understanding of the genetics and evolution of major developmental and morphological traits.},
}
@article {pmid27374341,
year = {2016},
author = {Mikhailov, KV and Slyusarev, GS and Nikitin, MA and Logacheva, MD and Penin, AA and Aleoshin, VV and Panchin, YV},
title = {The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians.},
journal = {Current biology : CB},
volume = {26},
number = {13},
pages = {1768-1774},
doi = {10.1016/j.cub.2016.05.007},
pmid = {27374341},
issn = {1879-0445},
mesh = {Animals ; Female ; *Genome ; Host-Parasite Interactions ; Invertebrates/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Orthonectids are rare parasites of marine invertebrates [1] that are commonly treated in textbooks as a taxon of uncertain affinity [2]. Trophic forms of orthonectids reside in the tissues of their hosts as multinucleated plasmodia, generating short-lived, worm-like ciliated female and male organisms that exit into the environment for copulation [3]. These ephemeral males and females are composed of just several hundred somatic cells and are deprived of digestive, circulatory, or excretory systems. Since their discovery in the 19(th) century, the orthonectids were described as organisms with no differentiated cell types and considered as part of Mesozoa, a putative link between multicellular animals and their unicellular relatives. More recently, this view was challenged as the new data suggested that orthonectids are animals that became simplified due to their parasitic way of life [3, 4]. Here, we report the genomic sequence of Intoshia linei, one of about 20 known species of orthonectids. The genomic data confirm recent morphological analysis asserting that orthonectids are members of Spiralia and possess muscular and nervous systems [5]. The 43-Mbp genome of I. linei encodes about 9,000 genes and retains those essential for the development and activity of muscular and nervous systems. The simplification of orthonectid body plan is associated with considerable reduction of metazoan developmental genes, leaving what might be viewed as the minimal gene set necessary to retain critical bilaterian features.},
}
@article {pmid27357338,
year = {2016},
author = {Glöckner, G and Lawal, HM and Felder, M and Singh, R and Singer, G and Weijer, CJ and Schaap, P},
title = {The multicellularity genes of dictyostelid social amoebas.},
journal = {Nature communications},
volume = {7},
number = {},
pages = {12085},
doi = {10.1038/ncomms12085},
pmid = {27357338},
issn = {2041-1723},
support = {BB/G020426/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; },
mesh = {*Biological Evolution ; Cell Differentiation/genetics ; Dictyostelium/*genetics ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genes, Essential ; Whole Genome Sequencing ; },
abstract = {The evolution of multicellularity enabled specialization of cells, but required novel signalling mechanisms for regulating cell differentiation. Early multicellular organisms are mostly extinct and the origins of these mechanisms are unknown. Here using comparative genome and transcriptome analysis across eight uni- and multicellular amoebozoan genomes, we find that 80% of proteins essential for the development of multicellular Dictyostelia are already present in their unicellular relatives. This set is enriched in cytosolic and nuclear proteins, and protein kinases. The remaining 20%, unique to Dictyostelia, mostly consists of extracellularly exposed and secreted proteins, with roles in sensing and recognition, while several genes for synthesis of signals that induce cell-type specialization were acquired by lateral gene transfer. Across Dictyostelia, changes in gene expression correspond more strongly with phenotypic innovation than changes in protein functional domains. We conclude that the transition to multicellularity required novel signals and sensors rather than novel signal processing mechanisms.},
}
@article {pmid27356975,
year = {2016},
author = {Yerramsetty, P and Stata, M and Siford, R and Sage, TL and Sage, RF and Wong, GK and Albert, VA and Berry, JO},
title = {Evolution of RLSB, a nuclear-encoded S1 domain RNA binding protein associated with post-transcriptional regulation of plastid-encoded rbcL mRNA in vascular plants.},
journal = {BMC evolutionary biology},
volume = {16},
number = {1},
pages = {141},
doi = {10.1186/s12862-016-0713-1},
pmid = {27356975},
issn = {1471-2148},
mesh = {Chloroplasts/genetics ; *Evolution, Molecular ; *Gene Expression Regulation, Plant ; Magnoliopsida/*genetics ; Photosynthesis ; Phylogeny ; Plant Leaves/genetics ; Plant Proteins/*genetics/metabolism ; Plastids/*genetics/metabolism ; Poaceae/genetics ; RNA Processing, Post-Transcriptional ; RNA, Messenger/metabolism ; RNA-Binding Proteins/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Zea mays/genetics ; },
abstract = {BACKGROUND: RLSB, an S-1 domain RNA binding protein of Arabidopsis, selectively binds rbcL mRNA and co-localizes with Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) within chloroplasts of C3 and C4 plants. Previous studies using both Arabidopsis (C3) and maize (C4) suggest RLSB homologs are post-transcriptional regulators of plastid-encoded rbcL mRNA. While RLSB accumulates in all Arabidopsis leaf chlorenchyma cells, in C4 leaves RLSB-like proteins accumulate only within Rubisco-containing bundle sheath chloroplasts of Kranz-type species, and only within central compartment chloroplasts in the single cell C4 plant Bienertia. Our recent evidence implicates this mRNA binding protein as a primary determinant of rbcL expression, cellular localization/compartmentalization, and photosynthetic function in all multicellular green plants. This study addresses the hypothesis that RLSB is a highly conserved Rubisco regulatory factor that occurs in the chloroplasts all higher plants.<br><br>RESULTS: Phylogenetic analysis has identified RLSB orthologs and paralogs in all major plant groups, from ancient liverworts to recent angiosperms. RLSB homologs were also identified in algae of the division Charophyta, a lineage closely related to land plants. RLSB-like sequences were not identified in any other algae, suggesting that it may be specific to the evolutionary line leading to land plants. The RLSB family occurs in single copy across most angiosperms, although a few species with two copies were identified, seemingly randomly distributed throughout the various taxa, although perhaps correlating in some cases with known ancient whole genome duplications. Monocots of the order Poales (Poaceae and Cyperaceae) were found to contain two copies, designated here as RLSB-a and RLSB-b, with only RLSB-a implicated in the regulation of rbcL across the maize developmental gradient. Analysis of microsynteny in angiosperms revealed high levels of conservation across eudicot species and for both paralogs in grasses, highlighting the possible importance of maintaining this gene and its surrounding genomic regions.<br><br>CONCLUSIONS: Findings presented here indicate that the RLSB family originated as a unique gene in land plant evolution, perhaps in the common ancestor of charophytes and higher plants. Purifying selection has maintained this as a highly conserved single- or two-copy gene across most extant species, with several conserved gene duplications. Together with previous findings, this study suggests that RLSB has been sustained as an important regulatory protein throughout the course of land plant evolution. While only RLSB-a has been directly implicated in rbcL regulation in maize, RLSB-b could have an overlapping function in the co-regulation of rbcL, or may have diverged as a regulator of one or more other plastid-encoded mRNAs. This analysis confirms that RLSB is an important and unique photosynthetic regulatory protein that has been continuously expressed in land plants as they emerged and diversified from their ancient common ancestor.},
}
@article {pmid29368868,
year = {2016},
author = {Zakharov, IA},
title = {[Horizontal gene transfer into the genomes of insects].},
journal = {Genetika},
volume = {52},
number = {7},
pages = {804-809},
pmid = {29368868},
issn = {0016-6758},
mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Insecta/*genetics ; },
abstract = {Horizontal gene transfer (HGT) is widespread in the world of prokaryotes, but the examples of this phenomenon among multicellular animals, particularly insects, are few. This review examines the transfer of genetic material to the nuclear genomes of insects from the mitochondrial genome (intracellular HGT), as well as from the genomes of viruses, bacteria, fungi, and unrelated insects. In most cases, the mechanisms of this transfer are unknown. Many pro- and eukaryotic genes that moved through the HGT are expressed in the insect genome and in some cases can provide the evolutionary innovations that are considered as aromorphoses.},
}
@article {pmid27339473,
year = {2016},
author = {Chisholm, RH and Lorenzi, T and Clairambault, J},
title = {Cell population heterogeneity and evolution towards drug resistance in cancer: Biological and mathematical assessment, theoretical treatment optimisation.},
journal = {Biochimica et biophysica acta},
volume = {1860},
number = {11 Pt B},
pages = {2627-2645},
doi = {10.1016/j.bbagen.2016.06.009},
pmid = {27339473},
issn = {0006-3002},
mesh = {Drug Resistance, Neoplasm/*drug effects ; Humans ; Immunotherapy/methods ; Models, Biological ; Models, Theoretical ; Neoplasms/*drug therapy/*pathology ; Phenotype ; },
abstract = {BACKGROUND: Drug-induced drug resistance in cancer has been attributed to diverse biological mechanisms at the individual cell or cell population scale, relying on stochastically or epigenetically varying expression of phenotypes at the single cell level, and on the adaptability of tumours at the cell population level.<br><br>SCOPE OF REVIEW: We focus on intra-tumour heterogeneity, namely between-cell variability within cancer cell populations, to account for drug resistance. To shed light on such heterogeneity, we review evolutionary mechanisms that encompass the great evolution that has designed multicellular organisms, as well as smaller windows of evolution on the time scale of human disease. We also present mathematical models used to predict drug resistance in cancer and optimal control methods that can circumvent it in combined therapeutic strategies.<br><br>MAJOR CONCLUSIONS: Plasticity in cancer cells, i.e., partial reversal to a stem-like status in individual cells and resulting adaptability of cancer cell populations, may be viewed as backward evolution making cancer cell populations resistant to drug insult. This reversible plasticity is captured by mathematical models that incorporate between-cell heterogeneity through continuous phenotypic variables. Such models have the benefit of being compatible with optimal control methods for the design of optimised therapeutic protocols involving combinations of cytotoxic and cytostatic treatments with epigenetic drugs and immunotherapies.<br><br>GENERAL SIGNIFICANCE: Gathering knowledge from cancer and evolutionary biology with physiologically based mathematical models of cell population dynamics should provide oncologists with a rationale to design optimised therapeutic strategies to circumvent drug resistance, that still remains a major pitfall of cancer therapeutics. This article is part of a Special Issue entitled &quot;System Genetics&quot; Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.},
}
@article {pmid27320726,
year = {2016},
author = {Bao, W and Greenwold, MJ and Sawyer, RH},
title = {Expressed miRNAs target feather related mRNAs involved in cell signaling, cell adhesion and structure during chicken epidermal development.},
journal = {Gene},
volume = {591},
number = {2},
pages = {393-402},
doi = {10.1016/j.gene.2016.06.027},
pmid = {27320726},
issn = {1879-0038},
support = {P20 GM103499/GM/NIGMS NIH HHS/United States ; P20 RR016461/RR/NCRR NIH HHS/United States ; },
mesh = {Animals ; *Cell Adhesion ; Chickens ; Epidermis/cytology/growth &amp; development/*metabolism ; Evolution, Molecular ; Feathers/*metabolism ; MicroRNAs/*metabolism ; RNA, Messenger/*metabolism ; *Signal Transduction ; Tenascin/metabolism ; Tissue Array Analysis ; },
abstract = {MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level. Previous studies have shown that miRNA regulation contributes to a diverse set of processes including cellular differentiation and morphogenesis which leads to the creation of different cell types in multicellular organisms and is thus key to animal development. Feathers are one of the most distinctive features of extant birds and are important for multiple functions including flight, thermal regulation, and sexual selection. However, the role of miRNAs in feather development has been woefully understudied despite the identification of cell signaling pathways, cell adhesion molecules and structural genes involved in feather development. In this study, we performed a microarray experiment comparing the expression of miRNAs and mRNAs among three embryonic stages of development and two tissues (scutate scale and feather) of the chicken. We combined this expression data with miRNA target prediction tools and a curated list of feather related genes to produce a set of 19 miRNA-mRNA duplexes. These targeted mRNAs have been previously identified as important cell signaling and cell adhesion genes as well as structural genes involved in feather and scale morphogenesis. Interestingly, the miRNA target site of the cell signaling pathway gene, Aldehyde Dehydrogenase 1 Family, Member A3 (ALDH1A3), is unique to birds indicating a novel role in Aves. The identified miRNA target site of the cell adhesion gene, Tenascin C (TNC), is only found in specific chicken TNC splice variants that are differentially expressed in developing scutate scale and feather tissue indicating an important role of miRNA regulation in epidermal differentiation. Additionally, we found that β-keratins, a major structural component of avian and reptilian epidermal appendages, are targeted by multiple miRNA genes. In conclusion, our work provides quantitative expression data on miRNAs and mRNAs during feather and scale development and has produced a highly diverse, but manageable list of miRNA-mRNA duplexes for future validation experiments.},
}
@article {pmid27319135,
year = {2016},
author = {Salasa, A and Mercadoc, MI and Zampini, IC and Ponessa, GI and Isla, MI},
title = {Determination of Botanical Origin of Propolis from Monte Region of Argentina by Histological and Chemical Methods.},
journal = {Natural product communications},
volume = {11},
number = {5},
pages = {627-630},
pmid = {27319135},
issn = {1934-578X},
mesh = {Argentina ; Fabaceae/*cytology ; Larrea/cytology ; Propolis/*analysis/chemistry ; },
abstract = {Propolis production by honey bees is the result of a selective harvest of exudates from plants in the neighborhood of the hive. This product is used in Argentina as a food supplement and alternative medicine. The aim of this study was to determine the botanical origin of propolis from the arid regions of Monte of Argentina using rapid histochemical techniques and by comparison of TLC and HPLC-DAD chromatographic profiles with extract profiles obtained from Zuccagnia punctata, Larrea divaricata and Larrea cuneifolia, plant species that grow in the study area as a natural community named &quot;jarillal&quot;. Microscopical analysis revealed the presence of several Z. punctata structures, such as multicellular trichomes, leaflets, stems and young leaves. Remarkable was the richness of the propolis in two bioactive chalcones, also present in Z. punctata resin; these compounds can be regarded as possible markers for propolis identification and justify its use as a dietary supplement, functional food and medicinal product. This study indicates that the source of resin used by honey bees to produce propolis in the Monte region of Argentina is only Z. punctata, a native shrub widespread in this phytogeographical region, while other more abundant species (L. divaricata and L. cuneifolia) in the region were not found, indicating that this propolis could be defined as a mono-resin, type-Zuccagnia.},
}
@article {pmid27318691,
year = {2016},
author = {Adamska, M},
title = {Sponges as models to study emergence of complex animals.},
journal = {Current opinion in genetics &amp; development},
volume = {39},
number = {},
pages = {21-28},
doi = {10.1016/j.gde.2016.05.026},
pmid = {27318691},
issn = {1879-0380},
mesh = {Animals ; *Evolution, Molecular ; Gene Regulatory Networks/*genetics ; Genome ; Germ Cells/*growth &amp; development ; Porifera/anatomy &amp; histology/*genetics/growth &amp; development ; Stem Cells/metabolism ; },
abstract = {The emergence of complex animal life forms remains poorly understood despite substantial interest and research in this area. To be informative, the ideal models to study transitions from single-cell organisms to the first animals and then to mammalian-level complexity should be phylogenetically strategically placed and retain ancestral characters. Sponges (Porifera) are likely to be the earliest branching animal phylum. When analysed from morphological, genomic and developmental perspectives, sponges appear to combine features of single-cell eukaryotic organisms and the complex multicellular animals (Eumetazoa). Intriguingly, homologues of components of the eumetazoan regulatory networks specifying the endoderm, the germ-cells and stem cells and (neuro) sensory cells are expressed in sponge choanocytes, archaeocytes and larval sensory cells. Studies using sponges as model systems are already bringing insights into animal evolution, and have opened avenues to further research benefitting from the recent spectacular expansion of genomic technologies.},
}
@article {pmid27318097,
year = {2016},
author = {Schaap, P},
title = {Evolution of developmental signalling in Dictyostelid social amoebas.},
journal = {Current opinion in genetics &amp; development},
volume = {39},
number = {},
pages = {29-34},
doi = {10.1016/j.gde.2016.05.014},
pmid = {27318097},
issn = {1879-0380},
support = {100293/Z/12/Z//Wellcome Trust/United Kingdom ; BB/K000799/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Cyclic AMP/genetics ; Developmental Biology ; Dictyostelium/*genetics/growth &amp; development ; *Evolution, Molecular ; *Phylogeny ; Signal Transduction/genetics ; Stress, Physiological/*genetics ; },
abstract = {Dictyostelia represent a tractable system to resolve the evolution of cell-type specialization, with some taxa differentiating into spores only, and other taxa with additionally one or up to four somatic cell types. One of the latter forms, Dictyostelium discoideum, is a popular model system for cell biology and developmental biology with key signalling pathways controlling cell-specialization being resolved recently. For the most dominant pathways, evolutionary origins were retraced to a stress response in the unicellular ancestor, while modifications in the ancestral pathway were associated with acquisition of multicellular complexity. This review summarizes our current understanding of developmental signalling in D. discoideum and its evolution.},
}
@article {pmid27300174,
year = {2016},
author = {De Felici, M},
title = {The Formation and Migration of Primordial Germ Cells in Mouse and Man.},
journal = {Results and problems in cell differentiation},
volume = {58},
number = {},
pages = {23-46},
doi = {10.1007/978-3-319-31973-5_2},
pmid = {27300174},
issn = {0080-1844},
mesh = {Animals ; Epigenesis, Genetic ; Female ; Germ Cells/*cytology ; Gonads/cytology/*growth &amp; development ; Humans ; Male ; Meiosis ; Mice ; Ovary/cytology ; Testis/cytology ; },
abstract = {In most multicellular organisms, including mammals, germ cells are at the origin of new organisms and ensure the continuation of the genetic and epigenetic information across the generations.In the mammalian germ line, the primordial germ cells (PGCs) are the precursors of the primary oocytes and prospermatogonia of fetal ovaries and testes, respectively. In mammals such as the primates, in which the formation of the primary oocytes is largely asynchronous and occurs during a relatively long period, PGCs after the arrival into the XX gonadal ridges are termed oogonia which then become primary oocytes when entering into meiotic prophase I. In the fetal testes, germ cells derived from the PGCs after gonad colonization are termed prospermatogonia or gonocytes.One of the most fascinating aspect of the mammalian germline development is that it is probably the first cell lineage to be established in the embryo by epigenetic mechanisms and that these inductive events happen in extraembryonic tissues much earlier that gonad develop inside the embryo proper. Moreover, such events prepare the germ cells for totipotency through genetic and epigenetic regulations of their genome function. How this occurs remained a mystery until short time ago.In this chapter, I will report and discuss the most recent advances in the cellular and molecular mechanisms underlying the formation in extraembryonic tissues and migration of PGCs toward the gonadal ridges made primarily by studies carried out in the mouse with some perspective in the human. Established concepts about these processes will be only summarized when necessary since they are widely described and discussed in many excellent reviews; most of them are cited in the text below.},
}
@article {pmid27298474,
year = {2016},
author = {Foley, RA},
title = {Mosaic evolution and the pattern of transitions in the hominin lineage.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1698},
pages = {},
doi = {10.1098/rstb.2015.0244},
pmid = {27298474},
issn = {1471-2970},
mesh = {*Adaptation, Biological ; Animals ; *Biological Evolution ; Fossils/*anatomy &amp; histology ; Hominidae/*anatomy &amp; histology ; Humans ; },
abstract = {Humans are uniquely unique, in terms of the extreme differences between them and other living organisms, and the impact they are having on the biosphere. The evolution of humans can be seen, as has been proposed, as one of the major transitions in evolution, on a par with the origins of multicellular organisms or the eukaryotic cell (Maynard Smith &amp; Szathmáry 1997 Major transitions in evolution). Major transitions require the evolution of greater complexity and the emergence of new evolutionary levels or processes. Does human evolution meet these conditions? I explore the diversity of evidence on the nature of transitions in human evolution. Four levels of transition are proposed-baseline, novel taxa, novel adaptive zones and major transitions-and the pattern of human evolution considered in the light of these. The primary conclusions are that changes in human evolution occur continuously and cumulatively; that novel taxa and the appearance of new adaptations are not clustered very tightly in particular periods, although there are three broad transitional phases (Pliocene, Plio-Pleistocene and later Quaternary). Each phase is distinctive, with the first based on ranging and energetics, the second on technology and niche expansion, and the third on cognition and cultural processes. I discuss whether this constitutes a 'major transition' in the context of the evolutionary processes more broadly; the role of behaviour in evolution; and the opportunity provided by the rich genetic, phenotypic (fossil morphology) and behavioural (archaeological) record to examine in detail major transitions and the microevolutionary patterns underlying macroevolutionary change. It is suggested that the evolution of the hominin lineage is consistent with a mosaic pattern of change.This article is part of the themed issue 'Major transitions in human evolution'.},
}
@article {pmid27282029,
year = {2016},
author = {Félix, MA},
title = {Phenotypic Evolution With and Beyond Genome Evolution.},
journal = {Current topics in developmental biology},
volume = {119},
number = {},
pages = {291-347},
doi = {10.1016/bs.ctdb.2016.04.002},
pmid = {27282029},
issn = {1557-8933},
mesh = {Animals ; *Biological Evolution ; Cell Cycle ; DNA ; Environment ; Genes ; Genetic Association Studies ; *Genetic Variation ; *Genome ; Genotype ; Phenotype ; Selection, Genetic ; },
abstract = {DNA does not make phenotypes on its own. In this volume entitled &quot;Genes and Phenotypic Evolution,&quot; the present review draws the attention on the process of phenotype construction-including development of multicellular organisms-and the multiple interactions and feedbacks between DNA, organism, and environment at various levels and timescales in the evolutionary process. First, during the construction of an individual's phenotype, DNA is recruited as a template for building blocks within the cellular context and may in addition be involved in dynamical feedback loops that depend on the environmental and organismal context. Second, in the production of phenotypic variation among individuals, stochastic, environmental, genetic, and parental sources of variation act jointly. While in controlled laboratory settings, various genetic and environmental factors can be tested one at a time or in various combinations, they cannot be separated in natural populations because the environment is not controlled and the genotype can rarely be replicated. Third, along generations, genotype and environment each have specific properties concerning the origin of their variation, the hereditary transmission of this variation, and the evolutionary feedbacks. Natural selection acts as a feedback from phenotype and environment to genotype. This review integrates recent results and concrete examples that illustrate these three points. Although some themes are shared with recent calls and claims to a new conceptual framework in evolutionary biology, the viewpoint presented here only means to add flesh to the standard evolutionary synthesis.},
}
@article {pmid27273532,
year = {2016},
author = {West, JA and Zuccarello, GC and de Goër, SL and Stavrias, LA and Verbruggen, H},
title = {Rhodenigma contortum, an obscure new genus and species of Rhodogorgonales (Rhodophyta) from Western Australia.},
journal = {Journal of phycology},
volume = {52},
number = {3},
pages = {397-403},
doi = {10.1111/jpy.12402},
pmid = {27273532},
issn = {1529-8817},
mesh = {Algal Proteins/genetics/metabolism ; Phylogeny ; RNA, Algal/genetics/metabolism ; Rhodophyta/*anatomy &amp; histology/*classification/genetics ; Sequence Analysis, DNA ; Western Australia ; },
abstract = {An unknown microscopic, branched filamentous red alga was isolated into culture from coral fragments collected in Coral Bay, Western Australia. It grew well unattached or attached to glass with no reproduction other than fragmentation of filaments. Cells of some branch tips became slightly contorted and digitated, possibly as a substrate-contact-response seen at filament tips of various algae. Attached multicellular compact disks on glass had a very different cellular configuration and size than the free filaments. In culture the filaments did not grow on or in coral fragments. Molecular phylogenies based on four markers (rbcL, cox1, 18S, 28S) clearly showed it belongs to the order Rhodogorgonales, as a sister clade of Renouxia. Based on these results, the alga is described as the new genus and species Rhodenigma contortum in the Rhodogorgonaceae. It had no morphological similarity to either of the other genera in Rhodogorgonaceae and illustrates the unknown diversity in cryptic habitats such as tropical coral rubble.},
}
@article {pmid27271841,
year = {2016},
author = {Greischar, MA and Mideo, N and Read, AF and Bjørnstad, ON},
title = {Predicting optimal transmission investment in malaria parasites.},
journal = {Evolution; international journal of organic evolution},
volume = {70},
number = {7},
pages = {1542-1558},
doi = {10.1111/evo.12969},
pmid = {27271841},
issn = {1558-5646},
support = {R01 GM089932/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Culicidae/*parasitology ; Genetic Fitness ; *Host-Parasite Interactions ; Malaria/*transmission ; Models, Biological ; Plasmodium/genetics/*physiology ; Population Dynamics ; Reproduction ; },
abstract = {In vertebrate hosts, malaria parasites face a tradeoff between replicating and the production of transmission stages that can be passed onto mosquitoes. This tradeoff is analogous to growth-reproduction tradeoffs in multicellular organisms. We use a mathematical model tailored to the life cycle and dynamics of malaria parasites to identify allocation strategies that maximize cumulative transmission potential to mosquitoes. We show that plastic strategies can substantially outperform fixed allocation because parasites can achieve greater fitness by investing in proliferation early and delaying the production of transmission stages. Parasites should further benefit from restraining transmission investment later in infection, because such a strategy can help maintain parasite numbers in the face of resource depletion. Early allocation decisions are predicted to have the greatest impact on parasite fitness. If the immune response saturates as parasite numbers increase, parasites should benefit from even longer delays prior to transmission investment. The presence of a competing strain selects for consistently lower levels of transmission investment and dramatically increased exploitation of the red blood cell resource. While we provide a detailed analysis of tradeoffs pertaining to malaria life history, our approach for identifying optimal plastic allocation strategies may be broadly applicable.},
}
@article {pmid27265398,
year = {2016},
author = {Breuninger, H and Thamm, A and Streubel, S and Sakayama, H and Nishiyama, T and Dolan, L},
title = {Diversification of a Transcription Factor Family Led to the Evolution of Antagonistically Acting Genetic Regulators of Root Hair Growth.},
journal = {Current biology : CB},
volume = {26},
number = {12},
pages = {1622-1628},
doi = {10.1016/j.cub.2016.04.060},
pmid = {27265398},
issn = {1879-0445},
mesh = {Basic Helix-Loop-Helix Transcription Factors/*genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Expression ; *Gene Regulatory Networks ; Multigene Family ; Plant Development/*genetics ; Plant Roots/growth &amp; development ; Plants/*genetics ; },
abstract = {Streptophytes colonized the land some time before 470 million years ago [1-3]. The colonization coincided with an increase in morphological and cellular diversity [4-7]. This increase in diversity is correlated with a proliferation in transcription factors encoded in genomes [8-10]. This suggests that gene duplication and subsequent diversification of function was instrumental in the generation of land plant diversity. Here, we investigate the diversification of the streptophyte-specific Lotus japonicus ROOTHAIRLESS LIKE (LRL) transcription factor (TF) [11, 12] subfamily of basic loop helix (bHLH) proteins by comparing gene function in early divergent and derived land plant species. We report that the single Marchantia polymorpha LRL gene acts as a general growth regulator required for rhizoid development, a function that has been partially conserved throughout multicellular streptophytes. In contrast, the five relatively derived Arabidopsis thaliana LRL genes comprise two antagonistically acting groups of differentially expressed genes. The diversification of LRL genes accompanied the evolution of an antagonistic regulatory element controlling root hair development.},
}
@article {pmid27263360,
year = {2016},
author = {Weissenbach, J},
title = {The rise of genomics.},
journal = {Comptes rendus biologies},
volume = {339},
number = {7-8},
pages = {231-239},
doi = {10.1016/j.crvi.2016.05.002},
pmid = {27263360},
issn = {1768-3238},
mesh = {Animals ; Computational Biology ; DNA/genetics ; Evolution, Molecular ; Genome ; Genomics/*history ; History, 20th Century ; History, 21st Century ; Humans ; },
abstract = {A brief history of the development of genomics is provided. Complete sequencing of genomes of uni- and multicellular organisms is based on important progress in sequencing and bioinformatics. Evolution of these methods is ongoing and has triggered an explosion in data production and analysis. Initial analyses focused on the inventory of genes encoding proteins. Completeness and quality of gene prediction remains crucial. Genome analyses profoundly modified our views on evolution, biodiversity and contributed to the detection of new functions, yet to be fully elucidated, such as those fulfilled by non-coding RNAs. Genomics has become the basis for the study of biology and provides the molecular support for a bunch of large-scale studies, the omics.},
}
@article {pmid27252218,
year = {2016},
author = {Colley, NJ and Nilsson, DE},
title = {Photoreception in Phytoplankton.},
journal = {Integrative and comparative biology},
volume = {56},
number = {5},
pages = {764-775},
doi = {10.1093/icb/icw037},
pmid = {27252218},
issn = {1557-7023},
support = {P30 EY016665/EY/NEI NIH HHS/United States ; R01 EY008768/EY/NEI NIH HHS/United States ; },
mesh = {Animals ; *Light ; Locomotion ; Phytoplankton/*physiology ; Ultraviolet Rays ; },
abstract = {In many species of phytoplankton, simple photoreceptors monitor ambient lighting. Photoreceptors provide a number of selective advantages including the ability to assess the time of day for circadian rhythms, seasonal changes, and the detection of excessive light intensities and harmful UV light. Photoreceptors also serve as depth gauges in the water column for behaviors such as diurnal vertical migration. Photoreceptors can be organized together with screening pigment into visible eyespots. In a wide variety of motile phytoplankton, including Chlamydomonas, Volvox, Euglena, and Kryptoperidinium, eyespots are light-sensitive organelles residing within the cell. Eyespots are composed of photoreceptor proteins and typically red to orange carotenoid screening pigments. This association of photosensory pigment with screening pigment allows for detection of light directionality, needed for light-guided behaviors such as positive and negative phototaxis. In Chlamydomonas, the eyespot is located in the chloroplast and Chlamydomonas expresses a number of photosensory pigments including the microbial channelrhodopsins (ChR1 and ChR2). Dinoflagellates are unicellular protists that are ecologically important constituents of the phytoplankton. They display a great deal of diversity in morphology, nutritional modes and symbioses, and can be photosynthetic or heterotrophic, feeding on smaller phytoplankton. Dinoflagellates, such as Kryptoperidinium foliaceum, have eyespots that are used for light-mediated tasks including phototaxis. Dinoflagellates belonging to the family Warnowiaceae have a more elaborate eye. Their eye-organelle, called an ocelloid, is a large, elaborate structure consisting of a focusing lens, highly ordered retinal membranes, and a shield of dark pigment. This complex eye-organelle is similar to multicellular camera eyes, such as our own. Unraveling the molecular makeup, structure and function of dinoflagellate eyes, as well as light-guided behaviors in phytoplankton can inform us about the selective forces that drove evolution in the important steps from light detection to vision. We show here that the evolution from simple photoreception to vision seems to have independently followed identical paths and principles in phytoplankton and animals, significantly strengthening our understanding of this important biological process.},
}
@article {pmid27250874,
year = {2016},
author = {Horst, NA and Katz, A and Pereman, I and Decker, EL and Ohad, N and Reski, R},
title = {A single homeobox gene triggers phase transition, embryogenesis and asexual reproduction.},
journal = {Nature plants},
volume = {2},
number = {},
pages = {15209},
doi = {10.1038/nplants.2015.209},
pmid = {27250874},
issn = {2055-0278},
mesh = {Bryopsida/embryology/*genetics/physiology ; Diploidy ; Genes, Homeobox/*genetics ; Germ Cells, Plant/physiology ; Haploidy ; Reproduction, Asexual ; },
abstract = {Plants characteristically alternate between haploid gametophytic and diploid sporophytic stages. Meiosis and fertilization respectively initiate these two different ontogenies(1). Genes triggering ectopic embryo development on vegetative sporophytic tissues are well described(2,3); however, a genetic control of embryo development from gametophytic tissues remains elusive. Here, in the moss Physcomitrella patens we show that ectopic overexpression of the homeobox gene BELL1 induces embryo formation and subsequently reproductive diploid sporophytes from specific gametophytic cells without fertilization. In line with this, BELL1 loss-of-function mutants have a wild-type phenotype, except that their egg cells are bigger and unable to form embryos. Our results identify BELL1 as a master regulator for the gametophyte-to-sporophyte transition in P. patens and provide mechanistic insights into the evolution of embryos that can generate multicellular diploid sporophytes. This developmental innovation facilitated the colonization of land by plants about 500 million years ago(4) and thus shaped our current ecosystems.},
}
@article {pmid27248802,
year = {2016},
author = {Howe, K and Schiffer, PH and Zielinski, J and Wiehe, T and Laird, GK and Marioni, JC and Soylemez, O and Kondrashov, F and Leptin, M},
title = {Structure and evolutionary history of a large family of NLR proteins in the zebrafish.},
journal = {Open biology},
volume = {6},
number = {4},
pages = {160009},
doi = {10.1098/rsob.160009},
pmid = {27248802},
issn = {2046-2441},
support = {335980//European Research Council/International ; 55007424//Howard Hughes Medical Institute/United States ; HG002659/HG/NHGRI NIH HHS/United States ; //Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; *Evolution, Molecular ; Genome ; Multigene Family ; NLR Proteins/*chemistry/*genetics ; Protein Domains ; Time Factors ; Zebrafish/genetics/*metabolism ; Zebrafish Proteins/*chemistry/*genetics ; },
abstract = {Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing (NLR) proteins. Mammals have small numbers of NLR proteins, whereas in some species, mostly those without adaptive immune systems, NLRs have expanded into very large families. We describe a family of nearly 400 NLR proteins encoded in the zebrafish genome. The proteins share a defining overall structure, which arose in fishes after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided into four groups based on their NACHT domains. Gene conversion acting differentially on the NACHT and B30.2 domains has shaped the family and created the groups. Evidence of positive selection in the B30.2 domain indicates that this domain rather than the leucine-rich repeats acts as the pathogen recognition module. In an unusual chromosomal organization, the majority of the genes are located on one chromosome arm, interspersed with other large multigene families, including a new family encoding zinc-finger proteins. The NLR-B30.2 proteins represent a new family with diversity in the specific recognition module that is present in fishes in spite of the parallel existence of an adaptive immune system.},
}
@article {pmid27226324,
year = {2016},
author = {Hunter, GL and Hadjivasiliou, Z and Bonin, H and He, L and Perrimon, N and Charras, G and Baum, B},
title = {Coordinated control of Notch/Delta signalling and cell cycle progression drives lateral inhibition-mediated tissue patterning.},
journal = {Development (Cambridge, England)},
volume = {143},
number = {13},
pages = {2305-2310},
doi = {10.1242/dev.134213},
pmid = {27226324},
issn = {1477-9129},
support = {P40 OD018537/OD/NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; //Cancer Research UK/United Kingdom ; },
mesh = {Animals ; *Body Patterning ; *Cell Cycle ; Drosophila Proteins/*metabolism ; Drosophila melanogaster/cytology/*embryology/*metabolism ; Epithelial Cells/cytology/metabolism ; Intracellular Signaling Peptides and Proteins/*metabolism ; Membrane Proteins/*metabolism ; Receptors, Notch/*metabolism ; Sense Organs/cytology ; *Signal Transduction ; Stem Cells/cytology/metabolism ; Time Factors ; Vibrissae/cytology/embryology ; },
abstract = {Coordinating cell differentiation with cell growth and division is crucial for the successful development, homeostasis and regeneration of multicellular tissues. Here, we use bristle patterning in the fly notum as a model system to explore the regulatory and functional coupling of cell cycle progression and cell fate decision-making. The pattern of bristles and intervening epithelial cells (ECs) becomes established through Notch-mediated lateral inhibition during G2 phase of the cell cycle, as neighbouring cells physically interact with each other via lateral contacts and/or basal protrusions. Since Notch signalling controls cell division timing downstream of Cdc25, ECs in lateral contact with a Delta-expressing cell experience higher levels of Notch signalling and divide first, followed by more distant neighbours, and lastly Delta-expressing cells. Conversely, mitotic entry and cell division makes ECs refractory to lateral inhibition signalling, fixing their fate. Using a combination of experiments and computational modelling, we show that this reciprocal relationship between Notch signalling and cell cycle progression acts like a developmental clock, providing a delimited window of time during which cells decide their fate, ensuring efficient and orderly bristle patterning.},
}
@article {pmid27208723,
year = {2017},
author = {Kim, HY and Jackson, TR and Davidson, LA},
title = {On the role of mechanics in driving mesenchymal-to-epithelial transitions.},
journal = {Seminars in cell &amp; developmental biology},
volume = {67},
number = {},
pages = {113-122},
doi = {10.1016/j.semcdb.2016.05.011},
pmid = {27208723},
issn = {1096-3634},
support = {R01 HD044750/HD/NICHD NIH HHS/United States ; T32 HL076124/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Biomechanical Phenomena ; Cadherins/genetics/metabolism ; Cell Division ; Cell Polarity ; Cellular Reprogramming/genetics ; Drosophila melanogaster/*genetics/growth &amp; development/metabolism ; Embryo, Mammalian ; Embryo, Nonmammalian ; Epithelial Cells/cytology/*metabolism ; Epithelial-Mesenchymal Transition/*genetics ; Extracellular Matrix/chemistry/metabolism ; Humans ; *Mechanotransduction, Cellular ; Mesenchymal Stromal Cells/cytology/*metabolism ; Morphogenesis/*genetics ; Vimentin/genetics/metabolism ; },
abstract = {The mesenchymal-to-epithelial transition (MET) is an intrinsically mechanical process describing a multi-step progression where autonomous mesenchymal cells gradually become tightly linked, polarized epithelial cells. METs are fundamental to a wide range of biological processes, including the evolution of multicellular organisms, generation of primary and secondary epithelia during development and organogenesis, and the progression of diseases including cancer. In these cases, there is an interplay between the establishment of cell polarity and the mechanics of neighboring cells and microenvironment. In this review, we highlight a spectrum of METs found in normal development as well as in pathological lesions, and provide insight into the critical role mechanics play at each step. We define MET as an independent process, distinct from a reverse-EMT, and propose questions to further explore the cellular and physical mechanisms of MET.},
}
@article {pmid27197218,
year = {2016},
author = {Basler, G and Nikoloski, Z and Larhlimi, A and Barabási, AL and Liu, YY},
title = {Control of fluxes in metabolic networks.},
journal = {Genome research},
volume = {26},
number = {7},
pages = {956-968},
doi = {10.1101/gr.202648.115},
pmid = {27197218},
issn = {1549-5469},
support = {P50 HG004233/HG/NHGRI NIH HHS/United States ; R01 HL118455/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Bacteria/genetics/metabolism ; Computational Biology ; Evolution, Molecular ; Fungi/genetics/metabolism ; Gene Expression Regulation ; Gene Regulatory Networks ; Humans ; *Metabolic Networks and Pathways ; Models, Biological ; Signal Transduction ; },
abstract = {Understanding the control of large-scale metabolic networks is central to biology and medicine. However, existing approaches either require specifying a cellular objective or can only be used for small networks. We introduce new coupling types describing the relations between reaction activities, and develop an efficient computational framework, which does not require any cellular objective for systematic studies of large-scale metabolism. We identify the driver reactions facilitating control of 23 metabolic networks from all kingdoms of life. We find that unicellular organisms require a smaller degree of control than multicellular organisms. Driver reactions are under complex cellular regulation in Escherichia coli, indicating their preeminent role in facilitating cellular control. In human cancer cells, driver reactions play pivotal roles in malignancy and represent potential therapeutic targets. The developed framework helps us gain insights into regulatory principles of diseases and facilitates design of engineering strategies at the interface of gene regulation, signaling, and metabolism.},
}
@article {pmid27196967,
year = {2016},
author = {Lou, Y and Chen, Y},
title = {Simulating the multicellular homeostasis with a cell-based discrete receptor dynamics model: The non-mutational origin of cancer and aging.},
journal = {Journal of theoretical biology},
volume = {404},
number = {},
pages = {15-29},
doi = {10.1016/j.jtbi.2016.04.035},
pmid = {27196967},
issn = {1095-8541},
mesh = {Aging/*genetics ; Animals ; Cell Proliferation ; *Computer Simulation ; *Homeostasis ; Humans ; *Models, Biological ; Mutation/*genetics ; Neoplasms/*genetics ; Phenotype ; Receptors, Cell Surface/*metabolism ; Reproducibility of Results ; Time Factors ; },
abstract = {The purpose of the study is to investigate the multicellular homeostasis in epithelial tissues over very large timescales. Inspired by the receptor dynamics of IBCell model proposed by Rejniak et al. an on-grid agent-based model for multicellular system is constructed. Instead of observing the multicellular architectural morphologies, the diversity of homeostatic states is quantitatively analyzed through a substantial number of simulations by measuring three new order parameters, the phenotypic population structure, the average proliferation age and the relaxation time to stable homeostasis. Nearby the interfaces of distinct homeostatic phases in 3D phase diagrams of the three order parameters, intermediate quasi-stable phases of slow dynamics that features quasi-stability with a large spectrum of relaxation timescales are found. A further exploration on the static and dynamic correlations among the three order parameters reveals that the quasi-stable phases evolve towards two terminations, tumorigenesis and degeneration, which are respectively accompanied by rejuvenation and aging. With the exclusion of the environmental impact and the mutational strategies, the results imply that cancer and aging may share the non-mutational origin in the intrinsic slow dynamics of the multicellular systems.},
}
@article {pmid27194700,
year = {2016},
author = {Okie, JG and Smith, VH and Martin-Cereceda, M},
title = {Major evolutionary transitions of life, metabolic scaling and the number and size of mitochondria and chloroplasts.},
journal = {Proceedings. Biological sciences},
volume = {283},
number = {1831},
pages = {},
doi = {10.1098/rspb.2016.0611},
pmid = {27194700},
issn = {1471-2954},
mesh = {*Biological Evolution ; Chloroplasts/*metabolism ; Eukaryota/*physiology ; Mitochondria/*metabolism ; Models, Biological ; *Symbiosis ; },
abstract = {We investigate the effects of trophic lifestyle and two types of major evolutionary transitions in individuality-the endosymbiotic acquisition of organelles and development of multicellularity-on organellar and cellular metabolism and allometry. We develop a quantitative framework linking the size and metabolic scaling of eukaryotic cells to the abundance, size and metabolic scaling of mitochondria and chloroplasts and analyse a newly compiled, unprecedented database representing unicellular and multicellular cells covering diverse phyla and tissues. Irrespective of cellularity, numbers and total volumes of mitochondria scale linearly with cell volume, whereas chloroplasts scale sublinearly and sizes of both organelles remain largely invariant with cell size. Our framework allows us to estimate the metabolic scaling exponents of organelles and cells. Photoautotrophic cells and organelles exhibit photosynthetic scaling exponents always less than one, whereas chemoheterotrophic cells and organelles have steeper respiratory scaling exponents close to one. Multicellularity has no discernible effect on the metabolic scaling of organelles and cells. In contrast, trophic lifestyle has a profound and uniform effect, and our results suggest that endosymbiosis fundamentally altered the metabolic scaling of free-living bacterial ancestors of mitochondria and chloroplasts, from steep ancestral scaling to a shallower scaling in their endosymbiotic descendants.},
}
@article {pmid27187178,
year = {2016},
author = {Pârvu, O and Gilbert, D},
title = {A Novel Method to Verify Multilevel Computational Models of Biological Systems Using Multiscale Spatio-Temporal Meta Model Checking.},
journal = {PloS one},
volume = {11},
number = {5},
pages = {e0154847},
doi = {10.1371/journal.pone.0154847},
pmid = {27187178},
issn = {1932-6203},
mesh = {Algorithms ; Animals ; Cell Cycle/physiology ; *Computer Simulation ; Hemodynamics ; Inflammation ; *Models, Biological ; Models, Cardiovascular ; Rats ; *Spatio-Temporal Analysis ; Workflow ; },
abstract = {Insights gained from multilevel computational models of biological systems can be translated into real-life applications only if the model correctness has been verified first. One of the most frequently employed in silico techniques for computational model verification is model checking. Traditional model checking approaches only consider the evolution of numeric values, such as concentrations, over time and are appropriate for computational models of small scale systems (e.g. intracellular networks). However for gaining a systems level understanding of how biological organisms function it is essential to consider more complex large scale biological systems (e.g. organs). Verifying computational models of such systems requires capturing both how numeric values and properties of (emergent) spatial structures (e.g. area of multicellular population) change over time and across multiple levels of organization, which are not considered by existing model checking approaches. To address this limitation we have developed a novel approximate probabilistic multiscale spatio-temporal meta model checking methodology for verifying multilevel computational models relative to specifications describing the desired/expected system behaviour. The methodology is generic and supports computational models encoded using various high-level modelling formalisms because it is defined relative to time series data and not the models used to generate it. In addition, the methodology can be automatically adapted to case study specific types of spatial structures and properties using the spatio-temporal meta model checking concept. To automate the computational model verification process we have implemented the model checking approach in the software tool Mule (http://mule.modelchecking.org). Its applicability is illustrated against four systems biology computational models previously published in the literature encoding the rat cardiovascular system dynamics, the uterine contractions of labour, the Xenopus laevis cell cycle and the acute inflammation of the gut and lung. Our methodology and software will enable computational biologists to efficiently develop reliable multilevel computational models of biological systems.},
}
@article {pmid27172191,
year = {2016},
author = {Paranjape, NP and Calvi, BR},
title = {The Histone Variant H3.3 Is Enriched at Drosophila Amplicon Origins but Does Not Mark Them for Activation.},
journal = {G3 (Bethesda, Md.)},
volume = {6},
number = {6},
pages = {1661-1671},
doi = {10.1534/g3.116.028068},
pmid = {27172191},
issn = {2160-1836},
support = {R01 GM061290/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *DNA Replication ; Drosophila/*genetics/*metabolism ; Drosophila Proteins/genetics/metabolism ; Gene Amplification ; Histones/genetics/*metabolism ; Mitosis/genetics ; Mutation ; Oogenesis/genetics ; *Replication Origin ; Transcription, Genetic ; },
abstract = {Eukaryotic DNA replication begins from multiple origins. The origin recognition complex (ORC) binds origin DNA and scaffolds assembly of a prereplicative complex (pre-RC), which is subsequently activated to initiate DNA replication. In multicellular eukaryotes, origins do not share a strict DNA consensus sequence, and their activity changes in concert with chromatin status during development, but mechanisms are ill-defined. Previous genome-wide analyses in Drosophila and other organisms have revealed a correlation between ORC binding sites and the histone variant H3.3. This correlation suggests that H3.3 may designate origin sites, but this idea has remained untested. To address this question, we examined the enrichment and function of H3.3 at the origins responsible for developmental gene amplification in the somatic follicle cells of the Drosophila ovary. We found that H3.3 is abundant at these amplicon origins. H3.3 levels remained high when replication initiation was blocked, indicating that H3.3 is abundant at the origins before activation of the pre-RC. H3.3 was also enriched at the origins during early oogenesis, raising the possibility that H3.3 bookmarks sites for later amplification. However, flies null mutant for both of the H3.3 genes in Drosophila did not have overt defects in developmental gene amplification or genomic replication, suggesting that H3.3 is not essential for the assembly or activation of the pre-RC at origins. Instead, our results imply that the correlation between H3.3 and ORC sites reflects other chromatin attributes that are important for origin function.},
}
@article {pmid27172135,
year = {2016},
author = {Kaczanowski, S},
title = {Apoptosis: its origin, history, maintenance and the medical implications for cancer and aging.},
journal = {Physical biology},
volume = {13},
number = {3},
pages = {031001},
doi = {10.1088/1478-3975/13/3/031001},
pmid = {27172135},
issn = {1478-3975},
mesh = {Animals ; Antineoplastic Agents/pharmacology ; Apoptosis/drug effects/*physiology ; Biological Evolution ; Cell Respiration ; Cellular Senescence/*physiology ; Humans ; Mitochondria/*metabolism/pathology ; Neoplasms/drug therapy/*pathology ; Neurodegenerative Diseases/pathology ; Phylogeny ; },
abstract = {Programmed cell death is a basic cellular mechanism. Apoptotic-like programmed cell death (called apoptosis in animals) occurs in both unicellular and multicellular eukaryotes, and some apoptotic mechanisms are observed in bacteria. Endosymbiosis between mitochondria and eukaryotic cells took place early in the eukaryotic evolution, and some of the apoptotic-like mechanisms of mitochondria that were retained after this event now serve as parts of the eukaryotic apoptotic machinery. Apoptotic mechanisms have several functions in unicellular organisms: they include kin-selected altruistic suicide that controls population size, sharing common goods, and responding to viral infection. Apoptotic factors also have non-apoptotic functions. Apoptosis is involved in the cellular aging of eukaryotes, including humans. In addition, apoptosis is a key part of the innate tumor-suppression mechanism. Several anticancer drugs induce apoptosis, because apoptotic mechanisms are inactivated during oncogenesis. Because of the ancient history of apoptosis, I hypothesize that there is a deep relationship between mitochondrial metabolism, its role in aerobic versus anaerobic respiration, and the connection between apoptosis and cancer. Whereas normal cells rely primarily on oxidative mitochondrial respiration, most cancer cells use anaerobic metabolism. According to the Warburg hypothesis, the remodeling of the metabolism is one of the processes that leads to cancer. Recent studies indicate that anaerobic, non-mitochondrial respiration is particularly active in embryonic cells, stem cells, and aggressive stem-like cancer cells. Mitochondrial respiration is particularly active during the pathological aging of human cells in neurodegenerative diseases. According to the reversed Warburg hypothesis formulated by Demetrius, pathological aging is induced by mitochondrial respiration. Here, I advance the hypothesis that the stimulation of mitochondrial metabolism leads to pathological aging.},
}
@article {pmid27160599,
year = {2016},
author = {Rolff, J and Schmid-Hempel, P},
title = {Perspectives on the evolutionary ecology of arthropod antimicrobial peptides.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {371},
number = {1695},
pages = {},
doi = {10.1098/rstb.2015.0297},
pmid = {27160599},
issn = {1471-2970},
mesh = {Animals ; Anti-Infective Agents/metabolism ; Antimicrobial Cationic Peptides/*genetics ; Arthropods/*genetics/immunology/microbiology ; *Evolution, Molecular ; *Gene Expression ; Host-Pathogen Interactions ; Immunity, Innate ; Insect Proteins/*genetics ; Insecta/genetics/immunology/microbiology ; Selection, Genetic ; },
abstract = {Antimicrobial peptides (AMPs) are important elements of the innate immune defence in multicellular organisms that target and kill microbes. Here, we reflect on the various points that are raised by the authors of the 11 contributions to a special issue of Philosophical Transactions on the 'evolutionary ecology of arthropod antimicrobial peptides'. We see five interesting topics emerging. (i) AMP genes in insects, and perhaps in arthropods more generally, evolve much slower than most other immune genes. One explanation refers to the constraints set by AMPs being part of a finely tuned defence system. A new view argues that AMPs are under strong stabilizing selection. Regardless, this striking observation still invites many more questions than have been answered so far. (ii) AMPs almost always are expressed in combinations and sometimes show expression patterns that are dependent on the infectious agent. While it is often assumed that this can be explained by synergistic interactions, such interactions have rarely been demonstrated and need to be studied further. Moreover, how to define synergy in the first place remains difficult and needs to be addressed. (iii) AMPs play a very important role in mediating the interaction between a host and its mutualistic or commensal microbes. This has only been studied in a very small number of (insect) species. It has become clear that the very same AMPs play different roles in different situations and hence are under concurrent selection. (iv) Different environments shape the physiology of organisms; especially the host-associated microbial communities should impact on the evolution host AMPs. Studies in social insects and some organisms from extreme environments seem to support this notion, but, overall, the evidence for adaptation of AMPs to a given environment is scant. (v) AMPs are considered or already developed as new drugs in medicine. However, bacteria can evolve resistance to AMPs. Therefore, in the light of our limited understanding of AMP evolution in the natural context, and also the very limited understanding of the evolution of resistance against AMPs in bacteria in particular, caution is recommended. What is clear though is that study of the ecology and evolution of AMPs in natural systems could inform many of these outstanding questions, including those related to medical applications and pathogen control.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'.},
}
@article {pmid27146690,
year = {2016},
author = {Pentz, JT and Taylor, BP and Ratcliff, WC},
title = {Apoptosis in snowflake yeast: novel trait, or side effect of toxic waste?.},
journal = {Journal of the Royal Society, Interface},
volume = {13},
number = {118},
pages = {},
doi = {10.1098/rsif.2016.0121},
pmid = {27146690},
issn = {1742-5662},
mesh = {Apoptosis/*genetics ; *Fungal Proteins/genetics/metabolism ; *Quantitative Trait Loci ; *Transcription Factors/genetics/metabolism ; *Yeasts/genetics/metabolism ; },
abstract = {Recent experiments evolving de novo multicellularity in yeast have found that large cluster-forming genotypes also exhibit higher rates of programmed cell death (apoptosis). This was previously interpreted as the evolution of a simple form of cellular division of labour: apoptosis results in the scission of cell-cell connections, allowing snowflake yeast to produce proportionally smaller, faster-growing propagules. Through spatial simulations, Duran-Nebreda and Solé (J. R. Soc. Interface 12, 20140982 (doi:10.1073/pnas.1115323109)) develop the novel null hypothesis that apoptosis is not an adaptation, per se, but is instead caused by the accumulation of toxic metabolites in large clusters. Here we test this hypothesis by synthetically creating unicellular derivatives of snowflake yeast through functional complementation with the ancestral ACE2 allele. We find that multicellular snowflake yeast with elevated apoptosis exhibit a similar rate of apoptosis when cultured as single cells. We also show that larger snowflake yeast clusters tend to contain a greater fraction of older, senescent cells, which may explain why larger clusters of a given genotype are more apoptotic. Our results show that apoptosis is not caused by side effects of spatial structure, such as starvation or waste product accumulation, and are consistent with the hypothesis that elevated apoptosis is a trait that co-evolves with large cluster size.},
}
@article {pmid27145840,
year = {2016},
author = {Joerger, AC and Fersht, AR},
title = {The p53 Pathway: Origins, Inactivation in Cancer, and Emerging Therapeutic Approaches.},
journal = {Annual review of biochemistry},
volume = {85},
number = {},
pages = {375-404},
doi = {10.1146/annurev-biochem-060815-014710},
pmid = {27145840},
issn = {1545-4509},
support = {MC_EX_G0901534//Medical Research Council/United Kingdom ; MC_UP_A024_1010//Medical Research Council/United Kingdom ; },
mesh = {Animals ; Antineoplastic Agents, Alkylating/chemical synthesis/*therapeutic use ; Clinical Trials as Topic ; Drug Design ; *Gene Expression Regulation, Neoplastic ; Humans ; Molecular Docking Simulation ; *Molecular Targeted Therapy ; Mutation ; Neoplasms/*drug therapy/genetics/metabolism/pathology ; Nuclear Proteins/antagonists &amp; inhibitors/chemistry/genetics/metabolism ; Protein Multimerization ; Protein Structure, Secondary ; Proto-Oncogene Proteins/antagonists &amp; inhibitors/chemistry/genetics/metabolism ; Proto-Oncogene Proteins c-mdm2/antagonists &amp; inhibitors/chemistry/genetics/metabolism ; Signal Transduction ; Tumor Suppressor Protein p53/*agonists/chemistry/genetics/metabolism ; },
abstract = {Inactivation of the transcription factor p53, through either direct mutation or aberrations in one of its many regulatory pathways, is a hallmark of virtually every tumor. In recent years, screening for p53 activators and a better understanding of the molecular mechanisms of oncogenic perturbations of p53 function have opened up a host of novel avenues for therapeutic intervention in cancer: from the structure-guided design of chemical chaperones to restore the function of conformationally unstable p53 cancer mutants, to the development of potent antagonists of the negative regulators MDM2 and MDMX and other modulators of the p53 pathway for the treatment of cancers with wild-type p53. Some of these compounds have now moved from proof-of-concept studies into clinical trials, with prospects for further, personalized anticancer medicines. We trace the structural evolution of the p53 pathway, from germ-line surveillance in simple multicellular organisms to its pluripotential role in humans.},
}
@article {pmid27139940,
year = {2016},
author = {Joachimczak, M and Suzuki, R and Arita, T},
title = {Artificial Metamorphosis: Evolutionary Design of Transforming, Soft-Bodied Robots.},
journal = {Artificial life},
volume = {22},
number = {3},
pages = {271-298},
doi = {10.1162/ARTL_a_00207},
pmid = {27139940},
issn = {1064-5462},
mesh = {Animals ; Biological Evolution ; Larva ; Locomotion ; *Metamorphosis, Biological ; *Models, Biological ; *Robotics ; },
abstract = {We show how the concept of metamorphosis, together with a biologically inspired model of multicellular development, can be used to evolve soft-bodied robots that are adapted to two very different tasks, such as being able to move in an aquatic and in a terrestrial environment. Each evolved solution defines two pairs of morphologies and controllers, together with a process of transforming one pair into the other. Animats develop from a single cell and grow through cellular divisions and deaths until they reach an initial larval form adapted to a first environment. To obtain the adult form adapted to a second environment, the larva undergoes metamorphosis, during which new cells are added or removed and its controller is modified. Importantly, our approach assumes nothing about what morphologies or methods of locomotion are preferred. Instead, it successfully searches the vast space of possible designs and comes up with complex, surprising, lifelike solutions that are reminiscent of amphibian metamorphosis. We analyze obtained solutions and investigate whether the morphological changes during metamorphosis are indeed adaptive. We then compare the effectiveness of three different types of selective pressures used to evolve metamorphic individuals. Finally, we investigate potential advantages of using metamorphosis to automatically produce soft-bodied designs by comparing the performance of metamorphic individuals with their specialized counterparts and designs that are robust to both environments.},
}
@article {pmid27139112,
year = {2016},
author = {Bastiaans, E and Debets, AJ and Aanen, DK},
title = {Experimental evolution reveals that high relatedness protects multicellular cooperation from cheaters.},
journal = {Nature communications},
volume = {7},
number = {},
pages = {11435},
doi = {10.1038/ncomms11435},
pmid = {27139112},
issn = {2041-1723},
mesh = {Cell Proliferation ; *Clonal Evolution ; *Microbial Interactions ; Mutation ; Neurospora crassa/*genetics/growth &amp; development ; Spores, Fungal/genetics/growth &amp; development ; },
abstract = {In multicellular organisms, there is a potential risk that cheating mutants gain access to the germline. Development from a single-celled zygote resets relatedness among cells to its maximum value each generation, which should accomplish segregation of cheating mutants from non-cheaters and thereby protect multicellular cooperation. Here we provide the crucial direct comparison between high- and low-relatedness conditions to test this hypothesis. We allow two variants of the fungus Neurospora crassa to evolve, one with and one without the ability to form chimeras with other individuals, thus generating two relatedness levels. While multicellular cooperation remains high in the high-relatedness lines, it significantly decreases in all replicate low-relatedness lines, resulting in an average threefold decrease in spore yield. This reduction is caused by cheating mutants with reduced investment in somatic functions, but increased competitive success when fusing with non-cheaters. Our experiments demonstrate that high genetic relatedness is crucial to sustain multicellular cooperation.},
}
@article {pmid27122563,
year = {2016},
author = {Boisseau, RP and Vogel, D and Dussutour, A},
title = {Habituation in non-neural organisms: evidence from slime moulds.},
journal = {Proceedings. Biological sciences},
volume = {283},
number = {1829},
pages = {},
doi = {10.1098/rspb.2016.0446},
pmid = {27122563},
issn = {1471-2954},
mesh = {Animals ; Biological Evolution ; Caffeine ; Chemotaxis/physiology ; Habituation, Psychophysiologic/*physiology ; Learning/physiology ; Models, Biological ; Phylogeny ; Physarum polycephalum/*physiology ; Quinine ; },
abstract = {Learning, defined as a change in behaviour evoked by experience, has hitherto been investigated almost exclusively in multicellular neural organisms. Evidence for learning in non-neural multicellular organisms is scant, and only a few unequivocal reports of learning have been described in single-celled organisms. Here we demonstrate habituation, an unmistakable form of learning, in the non-neural organism Physarum polycephalum In our experiment, using chemotaxis as the behavioural output and quinine or caffeine as the stimulus, we showed that P. polycephalum learnt to ignore quinine or caffeine when the stimuli were repeated, but responded again when the stimulus was withheld for a certain time. Our results meet the principle criteria that have been used to demonstrate habituation: responsiveness decline and spontaneous recovery. To distinguish habituation from sensory adaptation or motor fatigue, we also show stimulus specificity. Our results point to the diversity of organisms lacking neurons, which likely display a hitherto unrecognized capacity for learning, and suggest that slime moulds may be an ideal model system in which to investigate fundamental mechanisms underlying learning processes. Besides, documenting learning in non-neural organisms such as slime moulds is centrally important to a comprehensive, phylogenetic understanding of when and where in the tree of life the earliest manifestations of learning evolved.},
}
@article {pmid27114036,
year = {2016},
author = {Sebé-Pedrós, A and Ballaré, C and Parra-Acero, H and Chiva, C and Tena, JJ and Sabidó, E and Gómez-Skarmeta, JL and Di Croce, L and Ruiz-Trillo, I},
title = {The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity.},
journal = {Cell},
volume = {165},
number = {5},
pages = {1224-1237},
doi = {10.1016/j.cell.2016.03.034},
pmid = {27114036},
issn = {1097-4172},
support = {616960//European Research Council/International ; },
mesh = {Animals ; *Biological Evolution ; Eukaryota/classification/cytology/*genetics ; Gene Regulatory Networks ; Genome ; Histones/metabolism ; Humans ; Protein Processing, Post-Translational ; RNA, Untranslated ; *Regulatory Elements, Transcriptional ; },
abstract = {The unicellular ancestor of animals had a complex repertoire of genes linked to multicellular processes. This suggests that changes in the regulatory genome, rather than in gene innovation, were key to the origin of animals. Here, we carry out multiple functional genomic assays in Capsaspora owczarzaki, the unicellular relative of animals with the largest known gene repertoire for transcriptional regulation. We show that changing chromatin states, differential lincRNA expression, and dynamic cis-regulatory sites are associated with life cycle transitions in Capsaspora. Moreover, we demonstrate conservation of animal developmental transcription-factor networks and extensive network interconnection in this premetazoan organism. In contrast, however, Capsaspora lacks animal promoter types, and its regulatory sites are small, proximal, and lack signatures of animal enhancers. Overall, our results indicate that the emergence of animal multicellularity was linked to a major shift in genome cis-regulatory complexity, most notably the appearance of distal enhancer regulation.},
}
@article {pmid27112670,
year = {2016},
author = {Obermeier, B and Verma, A and Ransohoff, RM},
title = {The blood-brain barrier.},
journal = {Handbook of clinical neurology},
volume = {133},
number = {},
pages = {39-59},
doi = {10.1016/B978-0-444-63432-0.00003-7},
pmid = {27112670},
issn = {0072-9752},
mesh = {Animals ; Biological Transport/physiology ; Blood-Brain Barrier/anatomy &amp; histology/*physiology ; Cerebrospinal Fluid/physiology ; Endothelial Cells/physiology ; Humans ; Neovascularization, Physiologic/*physiology ; Neuroglia/physiology ; Neurons/physiology ; },
abstract = {In autoimmune neurologic disorders, the blood-brain barrier (BBB) plays a central role in immunopathogenesis, since this vascular interface is an entry path for cells and effector molecules of the peripheral immune system to reach the target organ, the central nervous system (CNS). The BBB's unique anatomic structure and the tightly regulated interplay of its cellular and acellular components allow for maintenance of brain homeostasis, regulation of influx and efflux, and protection from harm; these ensure an optimal environment for the neuronal network to function properly. In both health and disease, the BBB acts as mediator between the periphery and the CNS. For example, immune cell trafficking through the cerebral vasculature is essential to clear microbes or cell debris from neural tissues, while poorly regulated cellular transmigration can underlie or worsen CNS pathology. In this chapter, we focus on the specialized multicellular structure and function of the BBB/neurovascular unit and discuss how BBB breakdown can precede or be a consequence of neuroinflammation. We introduce the blood-cerebrospinal fluid barrier and include a brief aside about evolutionary aspects of barrier formation and refinements. Lastly, since restoration of barrier function is considered key to ameliorate neurologic disease, we speculate about new therapeutic avenues to repair a damaged BBB.},
}
@article {pmid27102219,
year = {2016},
author = {Hanschen, ER and Marriage, TN and Ferris, PJ and Hamaji, T and Toyoda, A and Fujiyama, A and Neme, R and Noguchi, H and Minakuchi, Y and Suzuki, M and Kawai-Toyooka, H and Smith, DR and Sparks, H and Anderson, J and Bakarić, R and Luria, V and Karger, A and Kirschner, MW and Durand, PM and Michod, RE and Nozaki, H and Olson, BJ},
title = {The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity.},
journal = {Nature communications},
volume = {7},
number = {},
pages = {11370},
doi = {10.1038/ncomms11370},
pmid = {27102219},
issn = {2041-1723},
support = {P20 GM103418/GM/NIGMS NIH HHS/United States ; GM103785-02/GM/NIGMS NIH HHS/United States ; P20 GM103638/GM/NIGMS NIH HHS/United States ; R01 GM103785/GM/NIGMS NIH HHS/United States ; GM084905/GM/NIGMS NIH HHS/United States ; P20GM103638/GM/NIGMS NIH HHS/United States ; P20GM103418/GM/NIGMS NIH HHS/United States ; T32 GM084905/GM/NIGMS NIH HHS/United States ; },
mesh = {Biological Evolution ; Cell Cycle Checkpoints/*genetics ; Chlamydomonas/cytology/*genetics ; Chlorophyta/classification/cytology/*genetics ; *Gene Expression Regulation, Plant ; Genome Size ; *Genome, Plant ; Phylogeny ; Plant Cells/metabolism ; Plasmids/chemistry/metabolism ; Retinoblastoma Protein/genetics/metabolism ; Transformation, Genetic ; },
abstract = {The transition to multicellularity has occurred numerous times in all domains of life, yet its initial steps are poorly understood. The volvocine green algae are a tractable system for understanding the genetic basis of multicellularity including the initial formation of cooperative cell groups. Here we report the genome sequence of the undifferentiated colonial alga, Gonium pectorale, where group formation evolved by co-option of the retinoblastoma cell cycle regulatory pathway. Significantly, expression of the Gonium retinoblastoma cell cycle regulator in unicellular Chlamydomonas causes it to become colonial. The presence of these changes in undifferentiated Gonium indicates extensive group-level adaptation during the initial step in the evolution of multicellularity. These results emphasize an early and formative step in the evolution of multicellularity, the evolution of cell cycle regulation, one that may shed light on the evolutionary history of other multicellular innovations and evolutionary transitions.},
}
@article {pmid27094475,
year = {2016},
author = {Horst, NA and Reski, R},
title = {Alternation of generations - unravelling the underlying molecular mechanism of a 165-year-old botanical observation.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {18},
number = {4},
pages = {549-551},
doi = {10.1111/plb.12468},
pmid = {27094475},
issn = {1438-8677},
mesh = {Animals ; Bryopsida/*genetics/growth &amp; development/physiology ; Diploidy ; *Evolution, Molecular ; Germ Cells, Plant ; Haploidy ; *Life Cycle Stages ; Meiosis ; Models, Molecular ; Phylogeny ; Plant Proteins/*genetics ; Reproduction ; Reproduction, Asexual ; },
abstract = {Characteristically, land plants exhibit a life cycle with an 'alternation of generations' and thus alternate between a haploid gametophyte and a diploid sporophyte. At meiosis and fertilisation the transitions between these two ontogenies take place in distinct single stem cells. The evolutionary invention of an embryo, and thus an upright multicellular sporophyte, in the ancestor of land plants formed the basis for the evolution of increasingly complex plant morphologies shaping Earth's ecosystems. Recent research employing the moss Physcomitrella patens revealed the homeotic gene BELL1 as a master regulator of the gametophyte-to-sporophyte transition. Here, we discuss these findings in the context of classical botanical observations.},
}
@article {pmid27086973,
year = {2016},
author = {Woolsey, TA},
title = {Re: Woolsey TA, van der Loos H. 1970. The structural organization of layer IV in the somatosensory region (S I) of mouse cerebral cortex. Brain Res. 17: 205-242.},
journal = {Brain research},
volume = {1645},
number = {},
pages = {22-24},
doi = {10.1016/j.brainres.2016.04.029},
pmid = {27086973},
issn = {1872-6240},
mesh = {Animals ; Autoradiography/history ; History, 20th Century ; Mice ; Neuroanatomical Tract-Tracing Techniques/history/methods ; Neuroanatomy/*history/methods ; Somatosensory Cortex/*anatomy &amp; histology ; Vibrissae ; },
abstract = {UNLABELLED: Axoplasmically transported proteins synthesized in neuronal somata labeled by radioactively labeled amino acids (tritium), following local targeted injections for tracing of pathways in the central nervous system using autoradiography. Results from a number of neuronal systems, including: the rat olfactory bulb; cortico-thalamic projections in the mouse; commissural connections of the rat hippocampus; and retinal projections in the monkey and chick are documented. Pathway origins are clear, as the number and distribution of the labeled cells and the normal structure of the injection site is preserved. Light and electron microscopic autoradiography shows that proteins are transported, at two rates: rapid transport (>100mm/day) of fewer proteins accumulating in axon terminals; and, slow transport (1-5mm/day) of the bulk of labeled proteins distributed along the length of axons. Different survival times can be selected to evaluate terminal projection field(s) or pathways from origin to termination. The clarity of autoradiographic labeling of pathways and their terminations is comparable to other techniques (such as the Nauta-Gygax and the Fink-Heimer methods and the electron microscopy of terminal degeneration). Labeled amino acids do not label molecules in fibers of passage and there is no retrograde transport of labeled material from the axon terminals. The functional polarity of fiber pathways can be easily established. We summarize the merits of this technique is based upon an established physiological properties of neurons that are summarized in contrast to currently used techniques dependent upon pathological changes in neurons, axons, or axonal terminals.<br><br>ABSTRACT: The cytoarchitecture of layer IV in mouse SmI cerebral cortex was examined in.formalin-fixed, Nissl-stained and Cox-fixed, Golgi-Nissl-stained sections cut coronally and tangentially to the pia, A multicellular cytoarchitectonic unit is described in layer IV, roughly cylindrical, 100-400um in diameter, and perpendicular to the pia. Because of their characteristic shape we call these structures barrels. Each barrel is a ring of neurons, the side, which surrounds a less cellular hollow. The nearly acellular reigion surrounding each barrel and separating adjacent barrels is the septum. Barrels are discussed in relation to observations reported in several earlier papers on the mouse cortex. The barrel field (all barrels) has remarkable constancy by all measures: from one hemisphere to the next and from one specimen to the next. A consistent part of the barrel field is the postero-medial barrel subield (PMBSF). Barrels in the PMBSF are larger, elliptical in shape, organized into five distinct rows and their numbers are constant. It is postulated that each barrel in the PMBSF is the cortical correlate of a contralateral mystacial vibrissa (whisker). On the basis of counts of barrels and of all facial sinus hairs a 'one barrel-one vibrissa' hypothesis is proposed. The general hypothesis is that barrels are the morphological manifestation in layer IV of the functional cortical columns discovered by physiologists. The barrels offer excellent opportunities for integrated studies of sensory cerebral cortex at a degree of resolution previously not possible. This article is part of a Special Issue entitled SI:50th Anniversary Issue.},
}
@article {pmid27077531,
year = {2016},
author = {Møller, HD and Bojsen, RK and Tachibana, C and Parsons, L and Botstein, D and Regenberg, B},
title = {Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {110},
pages = {e54239 |},
doi = {10.3791/54239},
pmid = {27077531},
issn = {1940-087X},
mesh = {DNA, Circular/genetics/*isolation &amp; purification ; DNA, Fungal/genetics/*isolation &amp; purification ; Eukaryotic Cells ; Extrachromosomal Inheritance/*genetics ; Genome ; Genome, Fungal ; Saccharomyces cerevisiae/*genetics ; },
abstract = {Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and how environmental and biological factors induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, deep sequencing, and mapping. Extensive exonuclease treatment was required for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by φ29 polymerase enriched for circular DNA over linear DNA. Validation of the Circle-Seq method on three S. cerevisiae CEN.PK populations of 10(10) cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30, HXT6, HXT7 genes on circular DNA in both S288c and CEN.PK suggests that DNA circularization is conserved between strains at these loci. In sum, the Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.},
}
@article {pmid27044515,
year = {2016},
author = {Barth, E and Hübler, R and Baniahmad, A and Marz, M},
title = {The Evolution of COP9 Signalosome in Unicellular and Multicellular Organisms.},
journal = {Genome biology and evolution},
volume = {8},
number = {4},
pages = {1279-1289},
doi = {10.1093/gbe/evw073},
pmid = {27044515},
issn = {1759-6653},
mesh = {Alternative Splicing ; Animals ; COP9 Signalosome Complex ; *Evolution, Molecular ; Exons ; Humans ; Introns ; Multiprotein Complexes/*genetics ; Peptide Hydrolases/*genetics ; Phylogeny ; Protein Subunits/genetics ; },
abstract = {The COP9 signalosome (CSN) is a highly conserved protein complex, recently being crystallized for human. In mammals and plants the COP9 complex consists of nine subunits, CSN 1-8 and CSNAP. The CSN regulates the activity of culling ring E3 ubiquitin and plays central roles in pleiotropy, cell cycle, and defense of pathogens. Despite the interesting and essential functions, a thorough analysis of the CSN subunits in evolutionary comparative perspective is missing. Here we compared 61 eukaryotic genomes including plants, animals, and yeasts genomes and show that the most conserved subunits of eukaryotes among the nine subunits are CSN2 and CSN5. This may indicate a strong evolutionary selection for these two subunits. Despite the strong conservation of the protein sequence, the genomic structures of the intron/exon boundaries indicate no conservation at genomic level. This suggests that the gene structure is exposed to a much less selection compared with the protein sequence. We also show the conservation of important active domains, such as PCI (proteasome lid-CSN-initiation factor) and MPN (MPR1/PAD1 amino-terminal). We identified novel exons and alternative splicing variants for all CSN subunits. This indicates another level of complexity of the CSN. Notably, most COP9-subunits were identified in all multicellular and unicellular eukaryotic organisms analyzed, but not in prokaryotes or archaeas. Thus, genes encoding CSN subunits present in all analyzed eukaryotes indicate the invention of the signalosome at the root of eukaryotes. The identification of alternative splice variants indicates possible &quot;mini-complexes&quot; or COP9 complexes with independent subunits containing potentially novel and not yet identified functions.},
}
@article {pmid27040616,
year = {2016},
author = {Moody, LA and Saidi, Y and Gibbs, DJ and Choudhary, A and Holloway, D and Vesty, EF and Bansal, KK and Bradshaw, SJ and Coates, JC},
title = {An ancient and conserved function for Armadillo-related proteins in the control of spore and seed germination by abscisic acid.},
journal = {The New phytologist},
volume = {211},
number = {3},
pages = {940-951},
doi = {10.1111/nph.13938},
pmid = {27040616},
issn = {1469-8137},
support = {BB/D007550/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Abscisic Acid/*pharmacology ; Arabidopsis/drug effects/*metabolism ; Armadillo Domain Proteins/*metabolism ; Bryopsida/drug effects/*metabolism ; *Conserved Sequence ; *Germination/drug effects ; Mutation/genetics ; Plant Proteins/*metabolism ; Seeds/drug effects/*metabolism ; Selaginellaceae/drug effects/*metabolism ; Sequence Homology, Amino Acid ; Spores/metabolism ; },
abstract = {Armadillo-related proteins regulate development throughout eukaryotic kingdoms. In the flowering plant Arabidopsis thaliana, Armadillo-related ARABIDILLO proteins promote multicellular root branching. ARABIDILLO homologues exist throughout land plants, including early-diverging species lacking true roots, suggesting that early-evolving ARABIDILLOs had additional biological roles. Here we investigated, using molecular genetics, the conservation and diversification of ARABIDILLO protein function in plants separated by c. 450 million years of evolution. We demonstrate that ARABIDILLO homologues in the moss Physcomitrella patens regulate a previously undiscovered inhibitory effect of abscisic acid (ABA) on spore germination. Furthermore, we show that A. thaliana ARABIDILLOs function similarly during seed germination. Early-diverging ARABIDILLO homologues from both P. patens and the lycophyte Selaginella moellendorffii can substitute for ARABIDILLO function during A. thaliana root development and seed germination. We conclude that (1) ABA was co-opted early in plant evolution to regulate functionally analogous processes in spore- and seed-producing plants and (2) plant ARABIDILLO germination functions were co-opted early into both gametophyte and sporophyte, with a specific rooting function evolving later in the land plant lineage.},
}
@article {pmid27034283,
year = {2016},
author = {Rosenberg, E and Zilber-Rosenberg, I},
title = {Microbes Drive Evolution of Animals and Plants: the Hologenome Concept.},
journal = {mBio},
volume = {7},
number = {2},
pages = {e01395},
doi = {10.1128/mBio.01395-15},
pmid = {27034283},
issn = {2150-7511},
mesh = {Adaptation, Biological ; Animals ; *Biological Evolution ; *Biota ; Humans ; *Microbiota ; Plants ; Recombination, Genetic ; Selection, Genetic ; *Symbiosis ; },
abstract = {The hologenome concept of evolution postulates that the holobiont (host plus symbionts) with its hologenome (host genome plus microbiome) is a level of selection in evolution. Multicellular organisms can no longer be considered individuals by the classical definitions of the term. Every natural animal and plant is a holobiont consisting of the host and diverse symbiotic microbes and viruses. Microbial symbionts can be transmitted from parent to offspring by a variety of methods, including via cytoplasmic inheritance, coprophagy, direct contact during and after birth, and the environment. A large number of studies have demonstrated that these symbionts contribute to the anatomy, physiology, development, innate and adaptive immunity, and behavior and finally also to genetic variation and to the origin and evolution of species. Acquisition of microbes and microbial genes is a powerful mechanism for driving the evolution of complexity. Evolution proceeds both via cooperation and competition, working in parallel.},
}
@article {pmid27032420,
year = {2017},
author = {Huang, Y and Chen, DH and Liu, BY and Shen, WH and Ruan, Y},
title = {Conservation and diversification of polycomb repressive complex 2 (PRC2) proteins in the green lineage.},
journal = {Briefings in functional genomics},
volume = {16},
number = {2},
pages = {106-119},
doi = {10.1093/bfgp/elw007},
pmid = {27032420},
issn = {2041-2657},
mesh = {*Gene Expression Regulation, Plant ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plants/*classification/*metabolism ; Polycomb Repressive Complex 2/genetics/*metabolism ; Protein Interaction Domains and Motifs ; },
abstract = {The polycomb group (PcG) proteins are key epigenetic regulators of gene expression in animals and plants. They act in multiprotein complexes, of which the best characterized is the polycomb repressive complex 2 (PRC2), which catalyses the trimethylation of histone H3 at lysine 27 (H3K27me3) at chromatin targets. In Arabidopsis thaliana, PRC2 proteins are involved in the regulation of diverse developmental processes, including cell fate determination, vegetative growth and development, flowering time control and embryogenesis. Here, we systematically analysed the evolutionary conservation and diversification of PRC2 components in lower and higher plants. We searched for and identified PRC2 homologues from the sequenced genomes of several green lineage species, from the unicellular green alga Ostreococcus lucimarinus to more complicated angiosperms. We found that some PRC2 core components, e.g. E(z), ESC/FIE and MSI/p55, are ancient and have multiplied coincidently with multicellular evolution. For one component, some members are newly formed, especially in the Cruciferae. During evolution, higher plants underwent copy number multiplication of various PRC2 components, which occurred independently for each component, without any obvious co-amplification of PRC2 members. Among the amplified members, usually one was well-conserved and the others were more diversified. Gene amplification occurred at different times for different PcG members during green lineage evolution. Certain PRC2 core components or members of them were highly conserved. Our study provides an insight into the evolutionary conservation and diversification of PcG proteins and may guide future functional characterization of these important epigenetic regulators in plants other than Arabidopsis.},
}
@article {pmid27030801,
year = {2016},
author = {Panday, A and Grove, A},
title = {The high mobility group protein HMO1 functions as a linker histone in yeast.},
journal = {Epigenetics &amp; chromatin},
volume = {9},
number = {},
pages = {13},
doi = {10.1186/s13072-016-0062-8},
pmid = {27030801},
issn = {1756-8935},
abstract = {BACKGROUND: Eukaryotic chromatin consists of nucleosome core particles connected by linker DNA of variable length. Histone H1 associates with the linker DNA to stabilize the higher-order chromatin structure and to modulate the ability of regulatory factors to access their nucleosomal targets. In Saccharomyces cerevisiae, the protein with greatest sequence similarity to H1 is Hho1p. However, during vegetative growth, hho1∆ cells do not show any discernible cell growth defects or the changes in bulk chromatin structure that are characteristic of chromatin from multicellular eukaryotes in which H1 is depleted. In contrast, the yeast high mobility group (HMGB) protein HMO1 has been reported to compact chromatin, as evidenced by increased nuclease sensitivity in hmo1∆ cells. HMO1 has an unusual domain architecture compared to vertebrate HMGB proteins in that the HMG domains are followed by a lysine-rich extension instead of an acidic domain. We address here the hypothesis that HMO1 serves the role of H1 in terms of chromatin compaction and that this function requires the lysine-rich extension.<br><br>RESULTS: We show here that HMO1 fulfills this function of a linker histone. For histone H1, chromatin compaction requires its basic C-terminal domain, and we find that the same pertains to HMO1, as deletion of its C-terminal lysine-rich extension renders chromatin nuclease sensitive. On rDNA, deletion of both HMO1 and Hho1p is required for significantly increased nuclease sensitivity. Expression of human histone H1 completely reverses the nuclease sensitivity characteristic of chromatin isolated from hmo1∆ cells. While chromatin remodeling events associated with repair of DNA double-strand breaks occur faster in the more dynamic chromatin environment created by the hmo1 deletion, expression of human histone H1 results in chromatin remodeling and double-strand break repair similar to that observed in wild-type cells.<br><br>CONCLUSION: Our data suggest that S. cerevisiae HMO1 protects linker DNA from nuclease digestion, a property also characteristic of mammalian linker histone H1. Notably, association with HMO1 creates a less dynamic chromatin environment that depends on its lysine-rich domain. That HMO1 has linker histone function has implications for investigations of chromatin structure and function as well as for evolution of proteins with roles in chromatin compaction.},
}
@article {pmid27023049,
year = {2016},
author = {Roesch, A and Paschen, A and Landsberg, J and Helfrich, I and Becker, JC and Schadendorf, D},
title = {Phenotypic tumour cell plasticity as a resistance mechanism and therapeutic target in melanoma.},
journal = {European journal of cancer (Oxford, England : 1990)},
volume = {59},
number = {},
pages = {109-112},
doi = {10.1016/j.ejca.2016.02.023},
pmid = {27023049},
issn = {1879-0852},
mesh = {Drug Resistance, Neoplasm/immunology/*physiology ; Epithelial-Mesenchymal Transition/immunology/physiology ; Humans ; Melanoma/*drug therapy/pathology ; Molecular Targeted Therapy/*methods ; Neoplastic Stem Cells/immunology/physiology ; Phenotype ; Tumor Escape/immunology/physiology ; Tumor Microenvironment/immunology/physiology ; },
abstract = {Despite the recent success of MAPK and immune checkpoint inhibitors in advanced melanoma, intrinsic and acquired resistance mechanisms determine the efficacy of these therapeutic approaches. Therapy resistance in melanoma is not solely driven by genetic evolution, but also by epigenetically driven adaptive plasticity. Melanoma cells are shifting between different transcriptional programs, cell cycle states and differentiation phenotypes reflecting a highly dynamic potential to adapt to various exogenous stressors including immune attack or cancer therapies. This review will focus on the dynamic interconversion and overlap between different melanoma cell phenotypes in the context of therapy resistance and a dynamically changing multicellular microenvironment.},
}
@article {pmid26999858,
year = {2015},
author = {Titov, VN},
title = {[THE INCONSISTENCIES OF REGULATION OF METABOLISM IN PHYLOGENESIS AT THREE LEVELS OF &quot;RELATIVE BIOLOGICAL PERFECTION&quot;: ETIOLOGY OF METABOLIC PANDEMICS].},
journal = {Klinicheskaia laboratornaia diagnostika},
volume = {60},
number = {11},
pages = {4-12},
pmid = {26999858},
issn = {0869-2084},
mesh = {Adipocytes/classification/metabolism/pathology ; Albumins/metabolism ; Diabetes Mellitus/*epidemiology/genetics/metabolism/pathology ; Essential Hypertension ; Fatty Acids, Nonesterified/metabolism ; Humans ; Hypertension/*epidemiology/genetics/metabolism/pathology ; Insulin/metabolism ; Insulin Resistance ; Macrophages/metabolism/pathology ; Metabolic Networks and Pathways/genetics ; Metabolic Syndrome/*epidemiology/genetics/metabolism/pathology ; Microcirculation/genetics ; Obesity/*epidemiology/genetics/metabolism/pathology ; Organogenesis/genetics ; *Pandemics ; Paracrine Communication/genetics ; *Phylogeny ; },
abstract = {The regulation of metabolism in vivo can be comprehended by considering stages of becoming inphylogenesis of humoral, hormonal, vegetative regulators separately: at the level of cells; in paracrin-regulated cenosises of cells; organs and systems under open blood circulation and closed system of blood flow. The levels of regulations formed at different stages of phylogenesis. Their completion occurred at achievement of &quot;relative biological perfection&quot;. Only this way need of cells in functional, structural interaction and forming of multicellular developed. The development of organs and systems of organs also completed at the level of &quot;relative biological perfection&quot;. From the same level the third stage of becoming of regulation of metabolism at the level of organism started. When three conditions of &quot;relative biological perfection&quot; achieved consequently at level in vivo are considered in species Homo sapiens using system approach it is detected that &quot;relative biological perfection&quot; in vivo is accompanied by different inconsistencies of regulation of metabolism. They are etiologic factors of &quot;metabolic pandemics &quot;. The inconsistencies (etiological factors) are consider as exemplified by local (at the level of paracrin-regulated cenosises of cells) and system (at the level of organism) regulation of biological reaction metabolism-microcirculation that results in dysfunction of target organs and development of pathogenesis of essential metabolic arterial hypertension. The article describes phylogenetic difference between visceral fatty cells and adpocytes, regulation of metabolism by phylogenetically late insulin, reaction of albumin at increasing of content of unesterified fatty acids in blood plasma, difference of function of resident macrophage and monocytes-macrophages in pathogenesis of atherosclerosis, metabolic syndrome, insulin resistance, obesity, under diabetes mellitus and essential metabolic arterial hypertension.},
}
@article {pmid26993504,
year = {2016},
author = {D'Asti, E and Chennakrishnaiah, S and Lee, TH and Rak, J},
title = {Extracellular Vesicles in Brain Tumor Progression.},
journal = {Cellular and molecular neurobiology},
volume = {36},
number = {3},
pages = {383-407},
doi = {10.1007/s10571-015-0296-1},
pmid = {26993504},
issn = {1573-6830},
mesh = {Animals ; Brain Neoplasms/diagnosis/genetics/*metabolism/*pathology/therapy ; Cell Communication ; Cell Transformation, Neoplastic/pathology ; *Disease Progression ; Extracellular Vesicles/*metabolism ; Humans ; Mutation/genetics ; },
abstract = {Brain tumors can be viewed as multicellular 'ecosystems' with increasingly recognized cellular complexity and systemic impact. While the emerging diversity of malignant disease entities affecting brain tissues is often described in reference to their signature alterations within the cellular genome and epigenome, arguably these cell-intrinsic changes can be regarded as hardwired adaptations to a variety of cell-extrinsic microenvironmental circumstances. Conversely, oncogenic events influence the microenvironment through their impact on the cellular secretome, including emission of membranous structures known as extracellular vesicles (EVs). EVs serve as unique carriers of bioactive lipids, secretable and non-secretable proteins, mRNA, non-coding RNA, and DNA and constitute pathway(s) of extracellular exit of molecules into the intercellular space, biofluids, and blood. EVs are also highly heterogeneous as reflected in their nomenclature (exosomes, microvesicles, microparticles) attempting to capture their diverse origin, as well as structural, molecular, and functional properties. While EVs may act as a mechanism of molecular expulsion, their non-random uptake by heterologous cellular recipients defines their unique roles in the intercellular communication, horizontal molecular transfer, and biological activity. In the central nervous system, EVs have been implicated as mediators of homeostasis and repair, while in cancer they may act as regulators of cell growth, clonogenicity, angiogenesis, thrombosis, and reciprocal tumor-stromal interactions. EVs produced by specific brain tumor cell types may contain the corresponding oncogenic drivers, such as epidermal growth factor receptor variant III (EGFRvIII) in glioblastoma (and hence are often referred to as 'oncosomes'). Through this mechanism, mutant oncoproteins and nucleic acids may be transferred horizontally between cellular populations altering their individual and collective phenotypes. Oncogenic pathways also impact the emission rates, types, cargo, and biogenesis of EVs, as reflected by preliminary analyses pointing to differences in profiles of EV-regulating genes (vesiculome) between molecular subtypes of glioblastoma, and in other brain tumors. Molecular regulators of vesiculation can also act as oncogenes. These intimate connections suggest the context-specific roles of different EV subsets in the progression of specific brain tumors. Advanced efforts are underway to capture these events through the use of EVs circulating in biofluids as biomarker reservoirs and to guide diagnostic and therapeutic decisions.},
}
@article {pmid26988968,
year = {2016},
author = {Hugenholtz, P and Skarshewski, A and Parks, DH},
title = {Genome-Based Microbial Taxonomy Coming of Age.},
journal = {Cold Spring Harbor perspectives in biology},
volume = {8},
number = {6},
pages = {},
doi = {10.1101/cshperspect.a018085},
pmid = {26988968},
issn = {1943-0264},
mesh = {Animals ; Archaea/genetics ; *Biodiversity ; Biological Evolution ; *Classification ; Genome ; *Genomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Reconstructing the complete evolutionary history of extant life on our planet will be one of the most fundamental accomplishments of scientific endeavor, akin to the completion of the periodic table, which revolutionized chemistry. The road to this goal is via comparative genomics because genomes are our most comprehensive and objective evolutionary documents. The genomes of plant and animal species have been systematically targeted over the past decade to provide coverage of the tree of life. However, multicellular organisms only emerged in the last 550 million years of more than three billion years of biological evolution and thus comprise a small fraction of total biological diversity. The bulk of biodiversity, both past and present, is microbial. We have only scratched the surface in our understanding of the microbial world, as most microorganisms cannot be readily grown in the laboratory and remain unknown to science. Ground-breaking, culture-independent molecular techniques developed over the past 30 years have opened the door to this so-called microbial dark matter with an accelerating momentum driven by exponential increases in sequencing capacity. We are on the verge of obtaining representative genomes across all life for the first time. However, historical use of morphology, biochemical properties, behavioral traits, and single-marker genes to infer organismal relationships mean that the existing highly incomplete tree is riddled with taxonomic errors. Concerted efforts are now needed to synthesize and integrate the burgeoning genomic data resources into a coherent universal tree of life and genome-based taxonomy.},
}
@article {pmid26988136,
year = {2016},
author = {Dornbos, SQ and Oji, T and Kanayama, A and Gonchigdorj, S},
title = {A new Burgess Shale-type deposit from the Ediacaran of western Mongolia.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {23438},
doi = {10.1038/srep23438},
pmid = {26988136},
issn = {2045-2322},
mesh = {Animals ; Biological Evolution ; Biota ; Fossils ; Geologic Sediments/*analysis ; Mongolia ; },
abstract = {Preservation of soft-bodied organisms is exceedingly rare in the fossil record. One way that such fossils are preserved is as carbonaceous compressions in fined-grained marine sedimentary rocks. These deposits of exceptional preservation are known as Burgess Shale-type (BST) deposits. During the Cambrian Period, BST deposits are more common and provide a crucial view of early animal evolution. The earliest definitive fossil evidence for macroscopic animal-grade organisms is found in the preceding Ediacaran Period. BST deposits from the Ediacaran are rarer and lack conclusive evidence for animals. Here we report the discovery of a new Ediacaran BST deposit with exceptional preservation of non-mineralizing macro-organisms in thinly bedded black shale from Zavkhan Province, western Mongolia. This fossil assemblage, here named the Zuun-Arts biota, currently consists of two new species of probable macroscopic multicellular benthic algae. One species, Chinggiskhaania bifurcata n. gen., n. sp., dominates the biota. The other species, Zuunartsphyton delicatum n. gen., n. sp., is known from three specimens. SEM-EDS analysis shows that the fossils are composed of aluminosilicate clay minerals and some carbon, a composition comparable to fossils from the Cambrian Burgess Shale biota. This discovery opens a new window through which to view late Precambrian life.},
}
@article {pmid26987708,
year = {2016},
author = {Rensing, SA},
title = {(Why) Does Evolution Favour Embryogenesis?.},
journal = {Trends in plant science},
volume = {21},
number = {7},
pages = {562-573},
doi = {10.1016/j.tplants.2016.02.004},
pmid = {26987708},
issn = {1878-4372},
mesh = {*Biological Evolution ; Embryonic Development/*physiology ; Phaeophyta/physiology ; Plants/metabolism ; },
abstract = {Complex multicellular organisms typically possess life cycles in which zygotes (formed by gamete fusion) and meiosis occur. Canonical animal embryogenesis describes development from zygote to birth. It involves polarisation of the egg/zygote, asymmetric cell divisions, establishment of axes, symmetry breaking, formation of organs, and parental nutrition (at least in early stages). Similar developmental patterns have independently evolved in other eukaryotic lineages, including land plants and brown algae. The question arises whether embryo-like structures and associated developmental processes recurrently emerge because they are local optima of the evolutionary landscape. To understand which evolutionary principles govern complex multicellularity, we need to analyse why and how similar processes evolve convergently - von Baer's and Haeckel's phylotypic stage revisited in other phyla.},
}
@article {pmid26986966,
year = {2016},
author = {Jaiteh, M and Taly, A and Hénin, J},
title = {Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors.},
journal = {PloS one},
volume = {11},
number = {3},
pages = {e0151934},
doi = {10.1371/journal.pone.0151934},
pmid = {26986966},
issn = {1932-6203},
mesh = {Animals ; Archaea/classification/genetics/physiology ; Conserved Sequence/genetics/physiology ; Cysteine Loop Ligand-Gated Ion Channel Receptors/genetics/physiology ; Eukaryota/genetics/physiology ; Evolution, Molecular ; Fungi/genetics/physiology ; Invertebrates/genetics/physiology ; Ligand-Gated Ion Channels/*genetics/physiology ; Phylogeny ; Plants/genetics ; Receptors, Neurotransmitter/*genetics/physiology ; Sequence Alignment ; },
abstract = {Pentameric ligand-gated ion channels (pLGICs) are ubiquitous neurotransmitter receptors in Bilateria, with a small number of known prokaryotic homologues. Here we describe a new inventory and phylogenetic analysis of pLGIC genes across all kingdoms of life. Our main finding is a set of pLGIC genes in unicellular eukaryotes, some of which are metazoan-like Cys-loop receptors, and others devoid of Cys-loop cysteines, like their prokaryotic relatives. A number of such &quot;Cys-less&quot; receptors also appears in invertebrate metazoans. Together, those findings draw a new distribution of pLGICs in eukaryotes. A broader distribution of prokaryotic channels also emerges, including a major new archaeal taxon, Thaumarchaeota. More generally, pLGICs now appear nearly ubiquitous in major taxonomic groups except multicellular plants and fungi. However, pLGICs are sparsely present in unicellular taxa, suggesting a high rate of gene loss and a non-essential character, contrasting with their essential role as synaptic receptors of the bilaterian nervous system. Multiple alignments of these highly divergent sequences reveal a small number of conserved residues clustered at the interface between the extracellular and transmembrane domains. Only the &quot;Cys-loop&quot; proline is absolutely conserved, suggesting the more fitting name &quot;Pro loop&quot; for that motif, and &quot;Pro-loop receptors&quot; for the superfamily. The infered molecular phylogeny shows a Cys-loop and a Cys-less clade in eukaryotes, both containing metazoans and unicellular members. This suggests new hypotheses on the evolutionary history of the superfamily, such as a possible origin of the Cys-loop cysteines in an ancient unicellular eukaryote. Deeper phylogenetic relationships remain uncertain, particularly around the split between bacteria, archaea, and eukaryotes.},
}
@article {pmid26986787,
year = {2015},
author = {Qiu, H and Price, DC and Yang, EC and Yoon, HS and Bhattacharya, D},
title = {Evidence of ancient genome reduction in red algae (Rhodophyta).},
journal = {Journal of phycology},
volume = {51},
number = {4},
pages = {624-636},
doi = {10.1111/jpy.12294},
pmid = {26986787},
issn = {1529-8817},
abstract = {Red algae (Rhodophyta) comprise a monophyletic eukaryotic lineage of ~6,500 species with a fossil record that extends back 1.2 billion years. A surprising aspect of red algal evolution is that sequenced genomes encode a relatively limited gene inventory (~5-10 thousand genes) when compared with other free-living algae or to other eukaryotes. This suggests that the common ancestor of red algae may have undergone extensive genome reduction, which can result from lineage specialization to a symbiotic or parasitic lifestyle or adaptation to an extreme or oligotrophic environment. We gathered genome and transcriptome data from a total of 14 red algal genera that represent the major branches of this phylum to study genome evolution in Rhodophyta. Analysis of orthologous gene gains and losses identifies two putative major phases of genome reduction: (i) in the stem lineage leading to all red algae resulting in the loss of major functions such as flagellae and basal bodies, the glycosyl-phosphatidylinositol anchor biosynthesis pathway, and the autophagy regulation pathway; and (ii) in the common ancestor of the extremophilic Cyanidiophytina. Red algal genomes are also characterized by the recruitment of hundreds of bacterial genes through horizontal gene transfer that have taken on multiple functions in shared pathways and have replaced eukaryotic gene homologs. Our results suggest that Rhodophyta may trace their origin to a gene depauperate ancestor. Unlike plants, it appears that a limited gene inventory is sufficient to support the diversification of a major eukaryote lineage that possesses sophisticated multicellular reproductive structures and an elaborate triphasic sexual cycle.},
}
@article {pmid26973658,
year = {2016},
author = {Rahman, H and Yang, J and Xu, YP and Munyampundu, JP and Cai, XZ},
title = {Phylogeny of Plant CAMTAs and Role of AtCAMTAs in Nonhost Resistance to Xanthomonas oryzae pv. oryzae.},
journal = {Frontiers in plant science},
volume = {7},
number = {},
pages = {177},
doi = {10.3389/fpls.2016.00177},
pmid = {26973658},
issn = {1664-462X},
abstract = {Calmodulin-binding transcription activator (CAMTA) constitutes one of the most important Ca(2+)/CaM-regulated transcription factor families in plants. Nevertheless, the phylogeny, protein interaction network, and role in nonhost resistance of plant CAMTAs are not well understood. In this study, 200 CAMTA genes were identified from 35 species representing four major plant lineages. The CAMTA genes were conserved in multicellular land plants but absent in unicellular eukaryotes, and were likely to emerge from the fusion of two separate genes encoding a CAMTA-like protein and an IQ/CaM binding motif containing protein, respectively, in the embryophyta lineage ancestor. Approximately one fourth of plant CAMTAs did not contain a TIG domain. This non-TIG class of CAMTAs seems to have newly evolved through mutation of some key amino acids in the TIG domain of flowering land plants after divergence from the non-flowering plants. Phylogenetic analysis classified CAMTA proteins into three major groups and nine distinct subgroups, a result supported by protein domain and motif conservation analyses. Most (59.0 and 21.5%) of the identified CAMTA genes contained 12 or 11 introns, respectively. Gene duplication, intron invasion, enlargement and turnover, as well as exon rearrangements and skipping have apparently occurred during evolution of the CAMTA family. Moreover, 38 potential interactors of six Arabidopsis CAMTAs were predicted and 10 predicted target genes of AtCAMTA3 exhibited changes in expression between Atcamta3 mutants and wild-type plants. The majority of predicted interactors are transcription factors and/or Ca(2+)/CaM-regulated proteins, suggesting that transcriptional regulation of the target genes might be the dominant functional mechanism of AtCAMTAs, and AtCAMTAs might act together with other Ca(2+) signaling components to regulate Ca(2+)-related biological processes. Furthermore, functional analyses employing Atcamta mutants revealed that AtCAMTA3 negatively regulated the immunity triggered by flg22 and nonhost resistance to Xanthomonas oryzae pv. oryzae via repressing accumulation of reactive oxygen species probably by targeting CBP60G, EDS1, and NDR1 and involving SA pathway.},
}
@article {pmid26970004,
year = {2016},
author = {Woodland, HR},
title = {The Birth of Animal Development: Multicellularity and the Germline.},
journal = {Current topics in developmental biology},
volume = {117},
number = {},
pages = {609-630},
doi = {10.1016/bs.ctdb.2015.10.020},
pmid = {26970004},
issn = {1557-8933},
mesh = {Animals ; *Biological Evolution ; Germ Cells/*cytology ; Reproduction/*physiology ; },
abstract = {The evolution of multicellular animals has been attributed to many kinds of selective advantage; here I suggest that the evolution of somatic cells to feed and protect the germline was central to the appearance of animals. This would have been driven by selection for extreme anisogamy--the evolution of sperm and egg. Evidence is adduced from the germline stem cells of simple animals (defining germline as any cell that normally produces the next generation via the sexual process) and from the control circuitry ubiquitous in animal germlines. With the soma and its elaboration came animal development, as we understand it.},
}
@article {pmid26961431,
year = {2016},
author = {Morrill, GA and Kostellow, AB and Liu, L and Gupta, RK and Askari, A},
title = {Evolution of the α-Subunit of Na/K-ATPase from Paramecium to Homo sapiens: Invariance of Transmembrane Helix Topology.},
journal = {Journal of molecular evolution},
volume = {82},
number = {4-5},
pages = {183-198},
doi = {10.1007/s00239-016-9732-1},
pmid = {26961431},
issn = {1432-1432},
support = {P01 HL036573/HL/NHLBI NIH HHS/United States ; R01 GM071324/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Biological Evolution ; Cell Membrane/metabolism ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; Protein Conformation, alpha-Helical/physiology ; Sodium/metabolism ; Sodium-Potassium-Exchanging ATPase/*genetics/metabolism ; },
abstract = {Na/K-ATPase is a key plasma membrane enzyme involved in cell signaling, volume regulation, and maintenance of electrochemical gradients. The α-subunit, central to these functions, belongs to a large family of P-type ATPases. Differences in transmembrane (TM) helix topology, sequence homology, helix-helix contacts, cell signaling, and protein domains of Na/K-ATPase α-subunit were compared in fungi (Beauveria), unicellular organisms (Paramecia), primitive multicellular organisms (Hydra), and vertebrates (Xenopus, Homo sapiens), and correlated with evolution of physiological functions in the α-subunit. All α-subunits are of similar length, with groupings of four and six helices in the N- and C-terminal regions, respectively. Minimal homology was seen for protein domain patterns in Paramecium and Hydra, with high correlation between Hydra and vertebrates. Paramecium α-subunits display extensive disorder, with minimal helix contacts. Increases in helix contacts in Hydra approached vertebrates. Protein motifs known to be associated with membrane lipid rafts and cell signaling reveal significant positional shifts between Paramecium and Hydra vulgaris, indicating that regional membrane fluidity changes occur during evolution. Putative steroid binding sites overlapping TM-3 occurred in all species. Sites associated with G-protein-receptor stimulation occur both in vertebrates and amphibia but not in Hydra or Paramecia. The C-terminus moiety &quot;KETYY,&quot; necessary for the Na(+) activation of pump phosphorylation, is not present in unicellular species indicating the absence of classical Na(+)/K(+)-pumps. The basic protein topology evolved earliest, followed by increases in protein domains and ordered helical arrays, correlated with appearance of α-subunit regions known to involve cell signaling, membrane recycling, and ion channel formation.},
}
@article {pmid26958911,
year = {2015},
author = {Zwart, MP and Elena, SF},
title = {Matters of Size: Genetic Bottlenecks in Virus Infection and Their Potential Impact on Evolution.},
journal = {Annual review of virology},
volume = {2},
number = {1},
pages = {161-179},
doi = {10.1146/annurev-virology-100114-055135},
pmid = {26958911},
issn = {2327-0578},
mesh = {Animals ; *Biological Evolution ; *Genome Size ; Humans ; Virus Diseases/*virology ; Virus Physiological Phenomena ; Viruses/classification/*genetics/isolation &amp; purification ; },
abstract = {For virus infections of multicellular hosts, narrow genetic bottlenecks during transmission and within-host spread appear to be widespread. These bottlenecks will affect the maintenance of genetic variation in a virus population and the prevalence of mixed-strain infections, thereby ultimately determining the strength with which different random forces act during evolution. Here we consider different approaches for estimating bottleneck sizes and weigh their merits. We then review quantitative estimates of bottleneck size during cellular infection, within-host spread, horizontal transmission, and finally vertical transmission. In most cases we find that bottlenecks do regularly occur, although in many cases they appear to be virion-concentration dependent. Finally, we consider the evolutionary implications of genetic bottlenecks during virus infection. Although on average strong bottlenecks will lead to declines in fitness, we consider a number of scenarios in which bottlenecks could also be advantageous for viruses.},
}
@article {pmid26941230,
year = {2016},
author = {Reyes-Bermudez, A and Villar-Briones, A and Ramirez-Portilla, C and Hidaka, M and Mikheyev, AS},
title = {Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks.},
journal = {Genome biology and evolution},
volume = {8},
number = {3},
pages = {851-870},
doi = {10.1093/gbe/evw042},
pmid = {26941230},
issn = {1759-6653},
mesh = {Animals ; Anthozoa/*genetics/growth &amp; development ; Cell Differentiation/genetics ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks/*genetics ; Larva/*genetics/growth &amp; development ; Transcriptome/*genetics ; },
abstract = {Corals belong to the most basal class of the Phylum Cnidaria, which is considered the sister group of bilaterian animals, and thus have become an emerging model to study the evolution of developmental mechanisms. Although cell renewal, differentiation, and maintenance of pluripotency are cellular events shared by multicellular animals, the cellular basis of these fundamental biological processes are still poorly understood. To understand how changes in gene expression regulate morphogenetic transitions at the base of the eumetazoa, we performed quantitative RNA-seq analysis duringAcropora digitifera's development. We collected embryonic, larval, and adult samples to characterize stage-specific transcription profiles, as well as broad expression patterns. Transcription profiles reconstructed development revealing two main expression clusters. The first cluster grouped blastula and gastrula and the second grouped subsequent developmental time points. Consistently, we observed clear differences in gene expression between early and late developmental transitions, with higher numbers of differentially expressed genes and fold changes around gastrulation. Furthermore, we identified three coexpression clusters that represented discrete gene expression patterns. During early transitions, transcriptional networks seemed to regulate cellular fate and morphogenesis of the larval body. In late transitions, these networks seemed to play important roles preparing planulae for switch in lifestyle and regulation of adult processes. Although developmental progression inA. digitiferais regulated to some extent by differential coexpression of well-defined gene networks, stage-specific transcription profiles appear to be independent entities. While negative regulation of transcription is predominant in early development, cell differentiation was upregulated in larval and adult stages.},
}
@article {pmid26933058,
year = {2016},
author = {Singletary, LA and Karlinsey, JE and Libby, SJ and Mooney, JP and Lokken, KL and Tsolis, RM and Byndloss, MX and Hirao, LA and Gaulke, CA and Crawford, RW and Dandekar, S and Kingsley, RA and Msefula, CL and Heyderman, RS and Fang, FC},
title = {Loss of Multicellular Behavior in Epidemic African Nontyphoidal Salmonella enterica Serovar Typhimurium ST313 Strain D23580.},
journal = {mBio},
volume = {7},
number = {2},
pages = {e02265},
doi = {10.1128/mBio.02265-15},
pmid = {26933058},
issn = {2150-7511},
support = {R01 AI112640/AI/NIAID NIH HHS/United States ; AI91966/AI/NIAID NIH HHS/United States ; AI44486/AI/NIAID NIH HHS/United States ; T32AI60555/AI/NIAID NIH HHS/United States ; AI90882/AI/NIAID NIH HHS/United States ; R01 AI044486/AI/NIAID NIH HHS/United States ; AI98078/AI/NIAID NIH HHS/United States ; AI1112640/AI/NIAID NIH HHS/United States ; AI43274/AI/NIAID NIH HHS/United States ; },
mesh = {*Adaptation, Biological ; Africa South of the Sahara/epidemiology ; Animals ; Catalase/genetics/metabolism ; Disease Models, Animal ; Epidemics ; Glucosyltransferases/genetics/metabolism ; Humans ; Macaca mulatta ; Mice ; Mutant Proteins/genetics/metabolism ; Salmonella Infections/epidemiology/*microbiology ; Salmonella typhimurium/*enzymology/genetics/isolation &amp; purification/*physiology ; *Stress, Physiological ; },
abstract = {UNLABELLED: Nontyphoidal Salmonella enterica serovar Typhimurium is a frequent cause of bloodstream infections in children and HIV-infected adults in sub-Saharan Africa. Most isolates from African patients with bacteremia belong to a single sequence type, ST313, which is genetically distinct from gastroenteritis-associated ST19 strains, such as 14028s and SL1344. Some studies suggest that the rapid spread of ST313 across sub-Saharan Africa has been facilitated by anthroponotic (person-to-person) transmission, eliminating the need for Salmonella survival outside the host. While these studies have not ruled out zoonotic or other means of transmission, the anthroponotic hypothesis is supported by evidence of extensive genomic decay, a hallmark of host adaptation, in the sequenced ST313 strain D23580. We have identified and demonstrated 2 loss-of-function mutations in D23580, not present in the ST19 strain 14028s, that impair multicellular stress resistance associated with survival outside the host. These mutations result in inactivation of the KatE stationary-phase catalase that protects high-density bacterial communities from oxidative stress and the BcsG cellulose biosynthetic enzyme required for the RDAR (red, dry, and rough) colonial phenotype. However, we found that like 14028s, D23580 is able to elicit an acute inflammatory response and cause enteritis in mice and rhesus macaque monkeys. Collectively, these observations suggest that African S. Typhimurium ST313 strain D23580 is becoming adapted to an anthroponotic mode of transmission while retaining the ability to infect and cause enteritis in multiple host species.<br><br>IMPORTANCE: The last 3 decades have witnessed an epidemic of invasive nontyphoidal Salmonella infections in sub-Saharan Africa. Genomic analysis and clinical observations suggest that the Salmonella strains responsible for these infections are evolving to become more typhoid-like with regard to patterns of transmission and virulence. This study shows that a prototypical African nontyphoidal Salmonella strain has lost traits required for environmental stress resistance, consistent with an adaptation to a human-to-human mode of transmission. However, in contrast to predictions, the strain remains capable of causing acute inflammation in the mammalian intestine. This suggests that the systemic clinical presentation of invasive nontyphoidal Salmonella infections in Africa reflects the immune status of infected hosts rather than intrinsic differences in the virulence of African Salmonella strains. Our study provides important new insights into the evolution of host adaptation in bacterial pathogens.},
}
@article {pmid26932355,
year = {2016},
author = {Luo, T and He, X and Xing, K},
title = {Lineage analysis by microsatellite loci deep sequencing in mice.},
journal = {Molecular reproduction and development},
volume = {83},
number = {5},
pages = {387-391},
doi = {10.1002/mrd.22632},
pmid = {26932355},
issn = {1098-2795},
mesh = {Animals ; Female ; *Genetic Loci ; Genome-Wide Association Study ; *High-Throughput Nucleotide Sequencing ; Male ; Mice ; *Microsatellite Repeats ; },
abstract = {Lineage analysis is the identification of all the progeny of a single progenitor cell, and has become particularly useful for studying developmental processes and cancer biology. Here, we propose a novel and effective method for lineage analysis that combines sequence capture and next-generation sequencing technology. Genome-wide mononucleotide and dinucleotide microsatellite loci in eight samples from two mice were identified and used to construct phylogenetic trees based on somatic indel mutations at these loci, which were unique enough to distinguish and parse samples from different mice into different groups along the lineage tree. For example, biopsies from the liver and stomach, which originate from the endoderm, were located in the same clade, while samples in kidney, which originate from the mesoderm, were located in another clade. Yet, tissue with a common developmental origin may still contain cells of a mixed ancestry. This genome-wide approach thus provides a non-invasive lineage analysis method based on mutations that accumulate in the genomes of opaque multicellular organism somatic cells. Mol. Reprod. Dev. 83: 387-391, 2016. © 2016 Wiley Periodicals, Inc.},
}
@article {pmid26931797,
year = {2016},
author = {Smith, J and Strassmann, JE and Queller, DC},
title = {Fine-scale spatial ecology drives kin selection relatedness among cooperating amoebae.},
journal = {Evolution; international journal of organic evolution},
volume = {70},
number = {4},
pages = {848-859},
doi = {10.1111/evo.12895},
pmid = {26931797},
issn = {1558-5646},
mesh = {Dictyostelium/*genetics/physiology ; Ecology ; Genotype ; *Microbial Interactions ; Population Density ; *Selection, Genetic ; Soil Microbiology ; },
abstract = {Cooperation among microbes is important for traits as diverse as antibiotic resistance, pathogen virulence, and sporulation. The evolutionary stability of cooperation against &quot;cheater&quot; mutants depends critically on the extent to which microbes interact with genetically similar individuals. The causes of this genetic social structure in natural microbial systems, however, are unknown. Here, we show that social structure among cooperative Dictyostelium amoebae is driven by the population ecology of colonization, growth, and dispersal acting at spatial scales as small as fruiting bodies themselves. Despite the fact that amoebae disperse while grazing, all it takes to create substantial genetic clonality within multicellular fruiting bodies is a few millimeters distance between the cells colonizing a feeding site. Even adjacent fruiting bodies can consist of different genotypes. Soil populations of amoebae are sparse and patchily distributed at millimeter scales. The fine-scale spatial structure of cells and genotypes can thus account for the otherwise unexplained high genetic uniformity of spores in fruiting bodies from natural substrates. These results show how a full understanding of microbial cooperation requires understanding ecology and social structure at the small spatial scales microbes themselves experience.},
}
@article {pmid26931578,
year = {2016},
author = {Zaccard, CR and Rinaldo, CR and Mailliard, RB},
title = {Linked in: immunologic membrane nanotube networks.},
journal = {Journal of leukocyte biology},
volume = {100},
number = {1},
pages = {81-94},
doi = {10.1189/jlb.4VMR0915-395R},
pmid = {26931578},
issn = {1938-3673},
support = {S10 OD010625/OD/NIH HHS/United States ; R37 AI041870/AI/NIAID NIH HHS/United States ; U01 AI035041/AI/NIAID NIH HHS/United States ; UM1 AI035043/AI/NIAID NIH HHS/United States ; T32 AI065380/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Antigen Presentation/*immunology ; Cell Membrane/*immunology ; Dendritic Cells/*immunology ; Humans ; Immunity, Cellular/*immunology ; *Nanotubes ; },
abstract = {Membrane nanotubes, also termed tunneling nanotubes, are F-actin-based structures that can form direct cytoplasmic connections and support rapid communication between distant cells. These nanoscale conduits have been observed in diverse cell types, including immune, neuronal, stromal, cancer, and stem cells. Until recently, little was known about the mechanisms involved in membrane nanotube development in myeloid origin APCs or how membrane nanotube networks support their ability to bridge innate and adaptive immunity. New research has provided insight into the modes of induction and regulation of the immune process of &quot;reticulation&quot; or the development of multicellular membrane nanotube networks in dendritic cells. Preprogramming by acute type 1 inflammatory mediators at their immature stage licenses mature type 1-polarized dendritic cells to reticulate upon subsequent interaction with CD40 ligand-expressing CD4(+) Th cells. Dendritic cell reticulation can support direct antigen transfer for amplification of specific T cell responses and can be positively or negatively regulated by signals from distinct Th cell subsets. Membrane nanotubes not only enhance the ability of immature dendritic cells to sense pathogens and rapidly mobilize nearby antigen-presenting cells in the peripheral tissues but also likely support communication of pathogen-related information from mature migratory dendritic cells to resident dendritic cells in lymph nodes. Therefore, the reticulation process facilitates a coordinated multicellular response for the efficient initiation of cell-mediated adaptive immune responses. Herein, we discuss studies focused on the molecular mechanisms of membrane nanotube formation, structure, and function in the context of immunity and how pathogens, such as HIV-1, may use dendritic cell reticulation to circumvent host defenses.},
}
@article {pmid26927887,
year = {2016},
author = {Zhang, X and Zhuchenko, O and Kuspa, A and Soldati, T},
title = {Social amoebae trap and kill bacteria by casting DNA nets.},
journal = {Nature communications},
volume = {7},
number = {},
pages = {10938},
doi = {10.1038/ncomms10938},
pmid = {26927887},
issn = {2041-1723},
support = {P01 HD039691/HD/NICHD NIH HHS/United States ; HD39691/HD/NICHD NIH HHS/United States ; },
mesh = {Bacteria ; DNA/*physiology ; Dictyostelium/*physiology ; Extracellular Traps/*physiology ; Klebsiella pneumoniae/*physiology ; *Microbial Viability ; Pseudomonas aeruginosa/*physiology ; Reactive Oxygen Species ; },
abstract = {Extracellular traps (ETs) from neutrophils are reticulated nets of DNA decorated with anti-microbial granules, and are capable of trapping and killing extracellular pathogens. Various phagocytes of mammals and invertebrates produce ETs, however, the evolutionary history of this DNA-based host defence strategy is unclear. Here we report that Sentinel (S) cells of the multicellular slug stage of the social amoeba Dictyostelium discoideum produce ETs upon stimulation with bacteria or lipopolysaccharide in a reactive oxygen species-dependent manner. The production of ETs by S cells requires a Toll/Interleukin-1 receptor domain-containing protein TirA and reactive oxygen species-generating NADPH oxidases. Disruption of these genes results in decreased clearance of bacterial infections. Our results demonstrate that D. discoideum is a powerful model organism to study the evolution and conservation of mechanisms of cell-intrinsic immunity, and suggest that the origin of DNA-based ETs as an innate immune defence predates the emergence of metazoans.},
}
@article {pmid26921294,
year = {2016},
author = {Hamaji, T and Mogi, Y and Ferris, PJ and Mori, T and Miyagishima, S and Kabeya, Y and Nishimura, Y and Toyoda, A and Noguchi, H and Fujiyama, A and Olson, BJ and Marriage, TN and Nishii, I and Umen, JG and Nozaki, H},
title = {Sequence of the Gonium pectorale Mating Locus Reveals a Complex and Dynamic History of Changes in Volvocine Algal Mating Haplotypes.},
journal = {G3 (Bethesda, Md.)},
volume = {6},
number = {5},
pages = {1179-1189},
doi = {10.1534/g3.115.026229},
pmid = {26921294},
issn = {2160-1836},
support = {R01 GM078376/GM/NIGMS NIH HHS/United States ; },
mesh = {Chromosome Walking ; Computational Biology ; Evolution, Molecular ; Gene Expression ; Genetic Linkage ; Genome, Plant ; Genomics/methods ; *Haplotypes ; High-Throughput Nucleotide Sequencing ; Phylogeny ; *Quantitative Trait Loci ; Reproduction/*genetics ; Sex Determination Processes/genetics ; Volvox/classification/*genetics ; },
abstract = {Sex-determining regions (SDRs) or mating-type (MT) loci in two sequenced volvocine algal species, Chlamydomonas reinhardtii and Volvox carteri, exhibit major differences in size, structure, gene content, and gametolog differentiation. Understanding the origin of these differences requires investigation of MT loci from related species. Here, we determined the sequences of the minus and plus MT haplotypes of the isogamous 16-celled volvocine alga, Gonium pectorale, which is more closely related to the multicellular V. carteri than to C. reinhardtii Compared to C. reinhardtii MT, G. pectorale MT is moderately larger in size, and has a less complex structure, with only two major syntenic blocs of collinear gametologs. However, the gametolog content of G. pectorale MT has more overlap with that of V. carteri MT than with C. reinhardtii MT, while the allelic divergence between gametologs in G. pectorale is even lower than that in C. reinhardtii Three key sex-related genes are conserved in G. pectorale MT: GpMID and GpMTD1 in MT-, and GpFUS1 in MT+. GpFUS1 protein exhibited specific localization at the plus-gametic mating structure, indicating a conserved function in fertilization. Our results suggest that the G. pectorale-V. carteri common ancestral MT experienced at least one major reformation after the split from C. reinhardtii, and that the V. carteri ancestral MT underwent a subsequent expansion and loss of recombination after the divergence from G. pectorale These data begin to polarize important changes that occurred in volvocine MT loci, and highlight the potential for discontinuous and dynamic evolution in SDRs.},
}
@article {pmid26917726,
year = {2016},
author = {Vilanova, E and Santos, GR and Aquino, RS and Valle-Delgado, JJ and Anselmetti, D and Fernàndez-Busquets, X and Mourão, PA},
title = {Carbohydrate-Carbohydrate Interactions Mediated by Sulfate Esters and Calcium Provide the Cell Adhesion Required for the Emergence of Early Metazoans.},
journal = {The Journal of biological chemistry},
volume = {291},
number = {18},
pages = {9425-9437},
doi = {10.1074/jbc.M115.708958},
pmid = {26917726},
issn = {1083-351X},
mesh = {Animals ; *Biological Evolution ; Calcium/*chemistry/metabolism ; Microscopy, Atomic Force ; Polysaccharides/*chemistry/metabolism/ultrastructure ; Porifera/*chemistry/metabolism/ultrastructure ; Sulfates/*chemistry/metabolism ; },
abstract = {Early metazoans had to evolve the first cell adhesion mechanism addressed to maintain a distinctive multicellular morphology. As the oldest extant animals, sponges are good candidates for possessing remnants of the molecules responsible for this crucial evolutionary innovation. Cell adhesion in sponges is mediated by the calcium-dependent multivalent self-interactions of sulfated polysaccharides components of extracellular membrane-bound proteoglycans, namely aggregation factors. Here, we used atomic force microscopy to demonstrate that the aggregation factor of the sponge Desmapsamma anchorata has a circular supramolecular structure and that it thus belongs to the spongican family. Its sulfated polysaccharide units, which were characterized via nuclear magnetic resonance analysis, consist preponderantly of a central backbone composed of 3-α-Glc1 units partially sulfated at 2- and 4-positions and branches of Pyr(4,6)α-Gal1→3-α-Fuc2(SO3)1→3-α-Glc4(SO3)1→3-α-Glc→4-linked to the central α-Glc units. Single-molecule force measurements of self-binding forces of this sulfated polysaccharide and their chemically desulfated and carboxyl-reduced derivatives revealed that the sulfate epitopes and extracellular calcium are essential for providing the strength and stability necessary to sustain cell adhesion in sponges. We further discuss these findings within the framework of the role of molecular structures in the early evolution of metazoans.},
}
@article {pmid26916163,
year = {2016},
author = {Cai, M and Hruby, VJ},
title = {The Melanocortin Receptor System: A Target for Multiple Degenerative Diseases.},
journal = {Current protein &amp; peptide science},
volume = {17},
number = {5},
pages = {488-496},
pmid = {26916163},
issn = {1875-5550},
support = {R01 GM108040/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Drug Design ; Humans ; *Ligands ; Melanocortins/chemistry/genetics/metabolism ; Melanocyte-Stimulating Hormones/chemistry/metabolism ; Models, Molecular ; Molecular Mimicry ; Molecular Structure ; Peptides/chemistry/metabolism ; Protein Conformation ; Receptors, Melanocortin/*chemistry/genetics/*metabolism ; Structure-Activity Relationship ; },
abstract = {The melanocortin receptor system consists of five closely related G-protein coupled receptors (MC1R, MC2R, MC3R, MC4R and MC5R). These receptors are involved in many of the key biological functions for multicellular animals, including human beings. The natural agonist ligands for these receptors are derived by processing of a primordial animal gene product, proopiomelanocortin (POMC). The ligand for the MC2R is ACTH (Adrenal Corticotropic Hormone), a larger processed peptide from POMC. The natural ligands for the other 4 melanocortin receptors are smaller peptides including α-melanocyte stimulating hormone (α-MSH) and related peptides from POMC (β-MSH and γ-MSH). They all contain the sequence His-Phe-Arg-Trp that is conserved throughout evolution. Thus, there has been considerable difficulty in developing highly selective ligands for the MC1R, MC3R, MC4R and MC5R. In this brief review, we discuss the various approaches that have been taken to design agonist and antagonist analogues and derivatives of the POMC peptides that are selective for the MC1R, MC3R, MC4R and MC5R receptors, via peptide, nonpeptide and peptidomimetic derivatives and analogues and their differential interactions with receptors that may help account for these selectivities.},
}
@article {pmid26909677,
year = {2016},
author = {Strassmann, JE},
title = {Kin Discrimination in Dictyostelium Social Amoebae.},
journal = {The Journal of eukaryotic microbiology},
volume = {63},
number = {3},
pages = {378-383},
doi = {10.1111/jeu.12307},
pmid = {26909677},
issn = {1550-7408},
mesh = {Amoeba/genetics/*physiology ; Animals ; Biological Evolution ; Cell Adhesion/genetics ; Cell Movement ; Dictyostelium/*genetics/*physiology ; Fruiting Bodies, Fungal/genetics ; Protozoan Proteins/genetics ; },
abstract = {Evolved cooperation is stable only when the benefactor is compensated, either directly or through its relatives. Social amoebae cooperate by forming a mobile multicellular body in which, about 20% of participants ultimately die to form a stalk. This benefits the remaining individuals that become hardy spores at the top of the stalk, together making up the fruiting body. In studied species with stalked migration, P. violaceum, D. purpureum, and D. giganteum, sorting based on clone identity occurs in laboratory mixes, maintaining high relatedness within the fruiting bodies. D. discoideum has unstalked migration, where cell fate is not fixed until the slug forms a fruiting body. Laboratory mixes show some degree of both spatial and genotype-based sorting, yet most laboratory fruiting bodies remain chimeric. However, wild fruiting bodies are made up mostly of clonemates. A genetic mechanism for sorting is likely to be cell adhesion genes tgrB1 and tgrC1, which bind to each other. They are highly variable, as expected for a kin discrimination gene. It is a puzzle that these genes do not cause stronger discrimination between mixed wild clones, but laboratory conditions or strong sorting early in the social stage diminished by later slug fusion could be explanations.},
}
@article {pmid26904394,
year = {2016},
author = {Grahame Hardie, D},
title = {Regulation of AMP-activated protein kinase by natural and synthetic activators.},
journal = {Acta pharmaceutica Sinica. B},
volume = {6},
number = {1},
pages = {1-19},
doi = {10.1016/j.apsb.2015.06.002},
pmid = {26904394},
issn = {2211-3835},
abstract = {The AMP-activated protein kinase (AMPK) is a sensor of cellular energy status that is almost universally expressed in eukaryotic cells. While it appears to have evolved in single-celled eukaryotes to regulate energy balance in a cell-autonomous manner, during the evolution of multicellular animals its role has become adapted so that it also regulates energy balance at the whole body level, by responding to hormones that act primarily on the hypothalamus. AMPK monitors energy balance at the cellular level by sensing the ratios of AMP/ATP and ADP/ATP, and recent structural analyses of the AMPK heterotrimer that have provided insight into the complex mechanisms for these effects will be discussed. Given the central importance of energy balance in diseases that are major causes of morbidity or death in humans, such as type 2 diabetes, cancer and inflammatory disorders, there has been a major drive to develop pharmacological activators of AMPK. Many such activators have been described, and the various mechanisms by which these activate AMPK will be discussed. A particularly large class of AMPK activators are natural products of plants derived from traditional herbal medicines. While the mechanism by which most of these activate AMPK has not yet been addressed, I will argue that many of them may be defensive compounds produced by plants to deter infection by pathogens or grazing by insects or herbivores, and that many of them will turn out to be inhibitors of mitochondrial function.},
}
@article {pmid26898901,
year = {2016},
author = {Yeo, JH and McAllan, BM and Fraser, ST},
title = {Scanning Electron Microscopy Reveals Two Distinct Classes of Erythroblastic Island Isolated from Adult Mammalian Bone Marrow.},
journal = {Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada},
volume = {22},
number = {2},
pages = {368-378},
doi = {10.1017/S1431927616000155},
pmid = {26898901},
issn = {1435-8115},
mesh = {Animals ; Antigens, CD/analysis ; Blood Group Antigens/analysis ; Bone Marrow/*anatomy &amp; histology ; Bone Marrow Cells/*ultrastructure ; Erythroblasts/*ultrastructure ; Guinea Pigs ; Marsupialia ; Membrane Proteins/analysis ; *Microscopy, Electron, Scanning ; Microscopy, Immunoelectron ; Receptors, Transferrin/analysis ; },
abstract = {Erythroblastic islands are multicellular clusters in which a central macrophage supports the development and maturation of red blood cell (erythroid) progenitors. These clusters play crucial roles in the pathogenesis observed in animal models of hematological disorders. The precise structure and function of erythroblastic islands is poorly understood. Here, we have combined scanning electron microscopy and immuno-gold labeling of surface proteins to develop a better understanding of the ultrastructure of these multicellular clusters. The erythroid-specific surface antigen Ter-119 and the transferrin receptor CD71 exhibited distinct patterns of protein sorting during erythroid cell maturation as detected by immuno-gold labeling. During electron microscopy analysis we observed two distinct classes of erythroblastic islands. The islands varied in size and morphology, and the number and type of erythroid cells interacting with the central macrophage. Assessment of femoral marrow isolated from a cavid rodent species (guinea pig, Cavis porcellus) and a marsupial carnivore species (fat-tailed dunnarts, Sminthopsis crassicaudata) showed that while the morphology of the central macrophage varied, two different types of erythroblastic islands were consistently identifiable. Our findings suggest that these two classes of erythroblastic islands are conserved in mammalian evolution and may play distinct roles in red blood cell production.},
}
@article {pmid26897340,
year = {2016},
author = {Liongue, C and Taznin, T and Ward, AC},
title = {Signaling via the CytoR/JAK/STAT/SOCS pathway: Emergence during evolution.},
journal = {Molecular immunology},
volume = {71},
number = {},
pages = {166-175},
doi = {10.1016/j.molimm.2016.02.002},
pmid = {26897340},
issn = {1872-9142},
mesh = {Animals ; *Biological Evolution ; Cell Communication/*genetics ; Computational Biology ; Humans ; Janus Kinases/genetics ; Phylogeny ; Receptors, Cytokine/*genetics ; STAT Transcription Factors/genetics ; Signal Transduction/*genetics ; Suppressor of Cytokine Signaling Proteins ; },
abstract = {Cell-cell signaling represents an essential hallmark of multicellular organisms, which necessarily require a means of communicating between different cell populations, particularly immune cells. Cytokine receptor signaling through the Janus kinase/Signal Transducer and Activator of Transcription/Suppressor of Cytokine Signaling (CytoR/JAK/STAT/SOCS) pathway embodies one important paradigm by which this is achieved. This pathway has been extensively studied in vertebrates and protostomes and shown to play fundamental roles in development and function of immune and other cells. However, our understanding of the origins of the individual pathway components and their assembly into a functional pathway has remained limited. This study examined the origins of each component of this pathway through bioinformatics analysis of key extant species. This has revealed step-wise accretion of individual components over a large evolutionary time-frame, but only in bilateria did a series of innovations allow their final coalescence to form a complete pathway. Assembly of the CytoR/JAK/STAT pathway has followed the retrograde model of pathway evolution, whereas addition of the SOCS component has adhered to the patchwork model.},
}
@article {pmid26892537,
year = {2016},
author = {Yang, EC and Boo, SM and Bhattacharya, D and Saunders, GW and Knoll, AH and Fredericq, S and Graf, L and Yoon, HS},
title = {Divergence time estimates and the evolution of major lineages in the florideophyte red algae.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {21361},
doi = {10.1038/srep21361},
pmid = {26892537},
issn = {2045-2322},
mesh = {Biological Evolution ; *Evolution, Molecular ; Fossils ; *Phylogeny ; Rhodophyta/*classification/*genetics ; },
abstract = {The Florideophyceae is the most abundant and taxonomically diverse class of red algae (Rhodophyta). However, many aspects of the systematics and divergence times of the group remain unresolved. Using a seven-gene concatenated dataset (nuclear EF2, LSU and SSU rRNAs, mitochondrial cox1, and plastid rbcL, psaA and psbA genes), we generated a robust phylogeny of red algae to provide an evolutionary timeline for florideophyte diversification. Our relaxed molecular clock analysis suggests that the Florideophyceae diverged approximately 943 (817-1,049) million years ago (Ma). The major divergences in this class involved the emergence of Hildenbrandiophycidae [ca. 781 (681-879) Ma], Nemaliophycidae [ca. 661 (597-736) Ma], Corallinophycidae [ca. 579 (543-617) Ma], and the split of Ahnfeltiophycidae and Rhodymeniophycidae [ca. 508 (442-580) Ma]. Within these clades, extant diversity reflects largely Phanerozoic diversification. Divergences within Florideophyceae were accompanied by evolutionary changes in the carposporophyte stage, leading to a successful strategy for maximizing spore production from each fertilization event. Our research provides robust estimates for the divergence times of major lineages within the Florideophyceae. This timeline was used to interpret the emergence of key morphological innovations that characterize these multicellular red algae.},
}
@article {pmid26886723,
year = {2016},
author = {Papaevgeniou, N and Sakellari, M and Jha, S and Tavernarakis, N and Holmberg, CI and Gonos, ES and Chondrogianni, N},
title = {18α-Glycyrrhetinic Acid Proteasome Activator Decelerates Aging and Alzheimer's Disease Progression in Caenorhabditis elegans and Neuronal Cultures.},
journal = {Antioxidants &amp; redox signaling},
volume = {25},
number = {16},
pages = {855-869},
doi = {10.1089/ars.2015.6494},
pmid = {26886723},
issn = {1557-7716},
mesh = {Aging/*metabolism ; Alzheimer Disease/*metabolism/*pathology ; Amyloid beta-Peptides/metabolism ; Animals ; Caenorhabditis elegans ; Caenorhabditis elegans Proteins/metabolism ; Cell Death ; Cells, Cultured ; Disease Progression ; Glycyrrhetinic Acid/*analogs &amp; derivatives/metabolism/pharmacology ; Longevity ; Neurons/drug effects/*metabolism ; Oxidation-Reduction ; Phenotype ; Proteasome Endopeptidase Complex/*metabolism ; Protein Aggregation, Pathological/metabolism ; },
abstract = {AIMS: Proteasomes are constituents of the cellular proteolytic networks that maintain protein homeostasis through regulated proteolysis of normal and abnormal (in any way) proteins. Genetically mediated proteasome activation in multicellular organisms has been shown to promote longevity and to exert protein antiaggregation activity. In this study, we investigate whether compound-mediated proteasome activation is feasible in a multicellular organism and we dissect the effects of such approach in aging and Alzheimer's disease (AD) progression.<br><br>RESULTS: Feeding of wild-type Caenorhabditis elegans with 18α-glycyrrhetinic acid (18α-GA; a previously shown proteasome activator in cell culture) results in enhanced levels of proteasome activities that lead to a skinhead-1- and proteasome activation-dependent life span extension. The elevated proteasome function confers lower paralysis rates in various AD nematode models accompanied by decreased Aβ deposits, thus ultimately decelerating the progression of AD phenotype. More importantly, similar positive results are also delivered when human and murine cells of nervous origin are subjected to 18α-GA treatment.<br><br>INNOVATION: This is the first report of the use of 18α-GA, a diet-derived compound as prolongevity and antiaggregation factor in the context of a multicellular organism.<br><br>CONCLUSION: Our results suggest that proteasome activation with downstream positive outcomes on aging and AD, an aggregation-related disease, is feasible in a nongenetic manipulation manner in a multicellular organism. Moreover, they unveil the need for identification of antiaging and antiamyloidogenic compounds among the nutrients found in our normal diet. Antioxid. Redox Signal. 25, 855-869.},
}
@article {pmid26873616,
year = {2016},
author = {Paz-Y-Miño-C, G and Espinosa, A},
title = {Kin Discrimination in Protists: From Many Cells to Single Cells and Backwards.},
journal = {The Journal of eukaryotic microbiology},
volume = {63},
number = {3},
pages = {367-377},
doi = {10.1111/jeu.12306},
pmid = {26873616},
issn = {1550-7408},
support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; },
mesh = {Alleles ; Animals ; Biological Evolution ; Eukaryota/*classification/*genetics/physiology ; Genetic Fitness ; Phenotype ; },
abstract = {During four decades (1960-1990s), the conceptualization and experimental design of studies in kin recognition relied on work with multicellular eukaryotes, particularly Unikonta (including invertebrates and vertebrates) and some Bikonta (including plants). This pioneering research had an animal behavior approach. During the 2000s, work on taxa-, clone- and kin-discrimination and recognition in protists produced genetic and molecular evidence that unicellular organisms (e.g. Saccharomyces, Dictyostelium, Polysphondylium, Tetrahymena, Entamoeba and Plasmodium) could distinguish between same (self or clone) and different (diverse clones), as well as among conspecifics of close or distant genetic relatedness. Here, we discuss some of the research on the genetics of kin discrimination/recognition and highlight the scientific progress made by switching emphasis from investigating multicellular to unicellular systems (and backwards). We document how studies with protists are helping us to understand the microscopic, cellular origins and evolution of the mechanisms of kin discrimination/recognition and their significance for the advent of multicellularity. We emphasize that because protists are among the most ancient organisms on Earth, belong to multiple taxonomic groups and occupy all environments, they can be central to reexamining traditional hypotheses in the field of kin recognition, reformulating concepts, and generating new knowledge.},
}
@article {pmid26872675,
year = {2016},
author = {Moe, GW and Marín-García, J},
title = {Role of cell death in the progression of heart failure.},
journal = {Heart failure reviews},
volume = {21},
number = {2},
pages = {157-167},
doi = {10.1007/s10741-016-9532-0},
pmid = {26872675},
issn = {1573-7322},
mesh = {*Cell Death ; *Disease Progression ; Heart Failure/*physiopathology ; Humans ; Mitochondria, Heart/*metabolism ; Myocytes, Cardiac/*pathology ; Signal Transduction/physiology ; },
abstract = {All multicellular organisms develop during evolution the highly regulated and interconnected pathways of cell death. This complex network contributes to the pathogenesis of various cardiovascular disorders including ischemia/reperfusion injury, myocardial infarction, heart failure, dysrhythmias and atherosclerosis. Chronic cardiac remodeling response and transition to overt HF have been associated with modestly increased apoptosis, although the actual burden of chronic cell loss attributable to apoptosis is not clear. Central mediators of cardiomyocyte survival and death are the mitochondrial organelles. Based on its morphological characteristics, cell death can be classified into three major types: apoptosis, necrosis and autophagy. Recently, a new pathway of regulated necrosis, necroptosis, has also been reported in the failing heart. The mitochondrial (intrinsic) and the death-receptor-mediated (extrinsic) converge at mitochondria inducing release of mitochondrial apoptogens to initiate the caspase cascade and eventually degradation of the doomed cardiomyocyte. Activation of death receptors can initiate not only extrinsic apoptotic pathway, but also necrosis. On the other hand, autophagy, which is characterized by the massive formation of lysosomal-derived vesicles, containing degenerating cytoplasmic contents, is primarily a survival response to nutrient deprivation, and a selective form of autophagy, mitophagy, is also a protective mechanism that allows to eliminate damaged mitochondria and thereby to attenuate mitochondria-mediated apoptosis and necrosis in the myocardium. Further insight into the molecular mechanisms underlying cell death will increase the efficiency and repertoire of therapeutic interventions available in cardiovascular disease.},
}
@article {pmid26871911,
year = {2016},
author = {Boucher, B and Lee, AY and Hallett, M and Jenna, S},
title = {Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways.},
journal = {PLoS computational biology},
volume = {12},
number = {2},
pages = {e1004738},
doi = {10.1371/journal.pcbi.1004738},
pmid = {26871911},
issn = {1553-7358},
mesh = {Animals ; Caenorhabditis elegans/*genetics ; Caenorhabditis elegans Proteins/*genetics/metabolism ; Computational Biology ; Gene Regulatory Networks/*genetics ; Models, Biological ; Protein Interaction Maps/*genetics ; },
abstract = {A genetic interaction (GI) is defined when the mutation of one gene modifies the phenotypic expression associated with the mutation of a second gene. Genome-wide efforts to map GIs in yeast revealed structural and functional properties of a GI network. This provided insights into the mechanisms underlying the robustness of yeast to genetic and environmental insults, and also into the link existing between genotype and phenotype. While a significant conservation of GIs and GI network structure has been reported between distant yeast species, such a conservation is not clear between unicellular and multicellular organisms. Structural and functional characterization of a GI network in these latter organisms is consequently of high interest. In this study, we present an in-depth characterization of ~1.5K GIs in the nematode Caenorhabditis elegans. We identify and characterize six distinct classes of GIs by examining a wide-range of structural and functional properties of genes and network, including co-expression, phenotypical manifestations, relationship with protein-protein interaction dense subnetworks (PDS) and pathways, molecular and biological functions, gene essentiality and pleiotropy. Our study shows that GI classes link genes within pathways and display distinctive properties, specifically towards PDS. It suggests a model in which pathways are composed of PDS-centric and PDS-independent GIs coordinating molecular machines through two specific classes of GIs involving pleiotropic and non-pleiotropic connectors. Our study provides the first in-depth characterization of a GI network within pathways of a multicellular organism. It also suggests a model to understand better how GIs control system robustness and evolution.},
}
@article {pmid26866800,
year = {2016},
author = {Koga, H and Fujitani, H and Morino, Y and Miyamoto, N and Tsuchimoto, J and Shibata, TF and Nozawa, M and Shigenobu, S and Ogura, A and Tachibana, K and Kiyomoto, M and Amemiya, S and Wada, H},
title = {Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton.},
journal = {PloS one},
volume = {11},
number = {2},
pages = {e0149067},
doi = {10.1371/journal.pone.0149067},
pmid = {26866800},
issn = {1932-6203},
mesh = {Animals ; Biological Evolution ; Echinodermata/genetics/*physiology ; Gene Expression Profiling ; *Gene Expression Regulation ; Homeodomain Proteins/*genetics/*physiology ; Immunohistochemistry ; In Situ Hybridization ; Larva/genetics/physiology ; Phenotype ; Phylogeny ; Sea Cucumbers/genetics/physiology ; Sequence Analysis, RNA ; Starfish/*genetics/*physiology ; Strongylocentrotus purpuratus/genetics/physiology ; Vascular Endothelial Growth Factor A/metabolism ; },
abstract = {Over the course of evolution, the acquisition of novel structures has ultimately led to wide variation in morphology among extant multicellular organisms. Thus, the origins of genetic systems for new morphological structures are a subject of great interest in evolutionary biology. The larval skeleton is a novel structure acquired in some echinoderm lineages via the activation of the adult skeletogenic machinery. Previously, VEGF signaling was suggested to have played an important role in the acquisition of the larval skeleton. In the present study, we compared expression patterns of Alx genes among echinoderm classes to further explore the factors involved in the acquisition of a larval skeleton. We found that the alx1 gene, originally described as crucial for sea urchin skeletogenesis, may have also played an essential role in the evolution of the larval skeleton. Unlike those echinoderms that have a larval skeleton, we found that alx1 of starfish was barely expressed in early larvae that have no skeleton. When alx1 overexpression was induced via injection of alx1 mRNA into starfish eggs, the expression patterns of certain genes, including those possibly involved in skeletogenesis, were altered. This suggested that a portion of the skeletogenic program was induced solely by alx1. However, we observed no obvious external phenotype or skeleton. We concluded that alx1 was necessary but not sufficient for the acquisition of the larval skeleton, which, in fact, requires several genetic events. Based on these results, we discuss how the larval expression of alx1 contributed to the acquisition of the larval skeleton in the putative ancestral lineage of echinoderms.},
}
@article {pmid26864038,
year = {2016},
author = {Singer, MA},
title = {The Origins of Aging: Evidence that Aging is an Adaptive Phenotype.},
journal = {Current aging science},
volume = {9},
number = {2},
pages = {95-115},
pmid = {26864038},
issn = {1874-6128},
mesh = {*Adaptation, Physiological ; *Aging ; Animals ; Biological Evolution ; Cellular Senescence ; Ecosystem ; Humans ; Models, Biological ; },
abstract = {BACKGROUND: Aging can be defined as the time-related decline in biological functions which ultimately results in organismal death. Beyond the stage of reproductive maturity as fertility declines, cell and tissue functions come under reduced selection pressure since organismal survival is considered no longer an evolutionary priority. Repair mechanisms become less robust and the resulting stochastic accumulation of tissue and genomic damage is believed to underlie the aging process. The objective of this review is to challenge this construct and to present evidence that aging represents a species-specific adaptive developmental program.<br><br>METHODS: Through a review of published data, the cellular aging programs of both single cell and multicellular organisms are described. Since all organisms live in communities (ecosystems) of diverse species, the role of multi-level selection is discussed within this context and a proposal is advanced that aging represents an adaptive phenotype.<br><br>RESULTS: Single cell organisms evolved an aging phenotype in which the primary feature was replicative arrest prior to cell death. The evolution of multicellularity represented the emergence of a new level of biological organization. Multicellularity required cell-cell cooperation as well as a division of labor. In simple multicellular organisms aging was rooted in an age-related decline in stem cell function (renewal and differentiation). In complex multicellular organisms cellular aging/ death programs (senescence, autophagy, apoptosis) were used as a form of cell &quot;altruistic&quot; suicide carried out for the benefit of the whole organism (morphogenesis, tissue repair and maintenance). Organisms do not live in isolation. Species occupy ecological niches and communities of diverse species comprise an ecosystem. Ecosystems are highly regulated and structured biological organizations. The effective functioning and productivity of an ecosystem is determined by its biological diversity and relative species densities. Multilevel selection acts to balance optimal functioning of both the whole ecosystem and its compositional species/organisms.<br><br>CONCLUSIONS: Organismal aging and death programs are adaptive; these programs provide a mechanism for regulating species population densities within the constraints imposed by the ecosystem organization. A unique feature of humans has been the development of a second inheritance system, culture. Through cultural practices, humans have expanded our ecological niche to be global in size. Our technology enriched urban ecosystem is very different from natural ecosystems. Our future evolution, including aging and lifespan, will be determined by our unique urban ecosystem through geneculture co-evolution.},
}
@article {pmid26863993,
year = {2016},
author = {Lavrov, AI and Kosevich, IA},
title = {Sponge cell reaggregation: Cellular structure and morphogenetic potencies of multicellular aggregates.},
journal = {Journal of experimental zoology. Part A, Ecological genetics and physiology},
volume = {325},
number = {2},
pages = {158-177},
doi = {10.1002/jez.2006},
pmid = {26863993},
issn = {1932-5231},
mesh = {Animals ; Cell Aggregation ; Cell Movement ; Cellular Structures/cytology ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; *Morphogenesis ; Porifera/*cytology/*growth &amp; development/ultrastructure ; Species Specificity ; },
abstract = {Sponges (phylum Porifera) are one of the most ancient extant multicellular animals and can provide valuable insights into origin and early evolution of Metazoa. High plasticity of cell differentiations and anatomical structure is characteristic feature of sponges. Present study deals with sponge cell reaggregation after dissociation as the most outstanding case of sponge plasticity. Dynamic of cell reaggregation and structure of multicellular aggregates of three demosponge species (Halichondria panicea (Pallas, 1766), Haliclona aquaeductus (Sсhmidt, 1862), and Halisarca dujardinii Johnston, 1842) were studied. Sponge tissue dissociation was performed mechanically. Resulting cell suspensions were cultured at 8-10°C for at least 5 days. Structure of multicellular aggregates was studied by light, transmission and scanning electron microscopy. Studied species share common stages of cell reaggregation-primary multicellular aggregates, early-stage primmorphs and primmorphs, but the rate of reaggregation varies considerably among species. Only cells of H. dujardinii are able to reconstruct functional and viable sponge after primmorphs formation. Sponge reconstruction in this species occurs due to active cell locomotion. Development of H. aquaeductus and H. panicea cells ceases at the stages of early primmorphs and primmorphs, respectively. Development of aggregates of these species is most likely arrested due to immobility of the majority of cells inside them. However, the inability of certain sponge species to reconstruct functional and viable individuals during cell reaggregation may be not a permanent species-specific characteristic, but depends on various factors, including the stage of the life cycle and experimental conditions.},
}
@article {pmid26836977,
year = {2016},
author = {Trapani, MR and Parisi, MG and Parrinello, D and Sanfratello, MA and Benenati, G and Palla, F and Cammarata, M},
title = {Specific inflammatory response of Anemonia sulcata (Cnidaria) after bacterial injection causes tissue reaction and enzymatic activity alteration.},
journal = {Journal of invertebrate pathology},
volume = {135},
number = {},
pages = {15-21},
doi = {10.1016/j.jip.2016.01.010},
pmid = {26836977},
issn = {1096-0805},
mesh = {Alkaline Phosphatase/metabolism ; Animals ; Densitometry ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/*physiology ; Esterases/metabolism ; Fibrinogen/metabolism ; Fibrinolysis ; Gelatin/metabolism ; Host-Pathogen Interactions ; Inflammation ; Peptide Hydrolases/metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Sea Anemones/enzymology/*microbiology/physiology ; Vibrio alginolyticus/*physiology ; },
abstract = {The evolution of multicellular organisms was marked by adaptations to protect against pathogens. The mechanisms for discriminating the ''self'' from ''non-self&quot; have evolved into a long history of cellular and molecular strategies, from damage repair to the co-evolution of host-pathogen interactions. We investigated the inflammatory response in Anemonia sulcata (Cnidaria: Anthozoa) following injection of substances that varied in type and dimension, and observed clear, strong and specific reactions, especially after injection of Escherichia coli and Vibrio alginolyticus. Moreover, we analyzed enzymatic activity of protease, phosphatase and esterase, showing how the injection of different bacterial strains alters the expression of these enzymes and suggesting a correlation between the appearance of the inflammatory reaction and the modification of enzymatic activities. Our study shows for the first time, a specific reaction and enzymatic responses following injection of bacteria in a cnidarian.},
}
@article {pmid26833268,
year = {2016},
author = {Ripamonti, U},
title = {Redefining the induction of periodontal tissue regeneration in primates by the osteogenic proteins of the transforming growth factor-β supergene family.},
journal = {Journal of periodontal research},
volume = {51},
number = {6},
pages = {699-715},
doi = {10.1111/jre.12356},
pmid = {26833268},
issn = {1600-0765},
mesh = {Animals ; Cementogenesis/drug effects ; Collagen/pharmacology ; Drug Combinations ; Laminin/pharmacology ; Papio ursinus ; Periodontium/drug effects/*physiology ; Primates ; Proteoglycans/pharmacology ; Regeneration/*drug effects/physiology ; Transforming Growth Factor beta/genetics/*pharmacology ; },
abstract = {The molecular bases of periodontal tissue induction and regeneration are the osteogenic proteins of the transforming growth factor-β (TGF-β) supergene family. These morphogens act as soluble mediators for the induction of tissues morphogenesis sculpting the multicellular mineralized structures of the periodontal tissues with functionally oriented ligament fibers into newly formed cementum. Human TGF-β3 (hTGF-β3) in growth factor-reduced Matrigel® matrix induces cementogenesis when implanted in class II mandibular furcation defects surgically prepared in the non-human primate Chacma baboon, Papio ursinus. The newly formed periodontal ligament space is characterized by running fibers tightly attached to the cementoid surface penetrating as mineralized constructs within the newly formed cementum assembling and initiating within the mineralized dentine. Angiogenesis heralds the newly formed periodontal ligament space, and newly sprouting capillaries are lined by cellular elements with condensed chromatin interpreted as angioblasts responsible for the rapid and sustained induction of angiogenesis. The inductive activity of hTGF-β3 in Matrigel® matrix is enhanced by the addition of autogenous morcellated fragments of the rectus abdominis muscle potentially providing myoblastic, pericytic/perivascular stem cells for continuous tissue induction and morphogenesis. The striated rectus abdominis muscle is endowed with stem cell niches in para/perivascular location, which can be dominant, thus imposing stem cell features or stemness to the surrounding cells. This capacity to impose stemness is morphologically shown by greater alveolar bone induction and cementogenesis when hTGF-β3 in Matrigel® matrix is combined with morcellated fragments of autogenous rectus abdominis muscle. The induction of periodontal tissue morphogenesis develops as a mosaic structure in which the osteogenic proteins of the TGF-β supergene family singly, synergistically and synchronously initiate and maintain tissue induction and morphogenesis. In primates, the presence of several homologous yet molecularly different isoforms with osteogenic activity highlights the biological significance of this apparent redundancy and indicates multiple interactions during embryonic development and bone regeneration in postnatal life. Molecular redundancy with associated different biological functionalities in primate tissues may simply represent the fine-tuning of speciation-related molecular evolution in anthropoid apes at the early Pliocene boundary, which resulted in finer tuning of the bone induction cascade.},
}
@article {pmid26831906,
year = {2016},
author = {Jindrich, K and Degnan, BM},
title = {The diversification of the basic leucine zipper family in eukaryotes correlates with the evolution of multicellularity.},
journal = {BMC evolutionary biology},
volume = {16},
number = {},
pages = {28},
doi = {10.1186/s12862-016-0598-z},
pmid = {26831906},
issn = {1471-2148},
mesh = {Animals ; Chromosome Mapping ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; Fungi/genetics ; Leucine Zippers ; Phylogeny ; Plants/genetics ; Protein Structure, Tertiary ; Transcription Factors/chemistry/*genetics ; },
abstract = {BACKGROUND: Multicellularity evolved multiple times in eukaryotes. In all cases, this required an elaboration of the regulatory mechanisms controlling gene expression. Amongst the conserved eukaryotic transcription factor families, the basic leucine zipper (bZIP) superfamily is one of the most ancient and best characterised. This gene family plays a diversity of roles in the specification, differentiation and maintenance of cell types in plants and animals. bZIPs are also involved in stress responses and the regulation of cell proliferation in fungi, amoebozoans and heterokonts.<br><br>RESULTS: Using 49 sequenced genomes from across the Eukaryota, we demonstrate that the bZIP superfamily has evolved from a single ancestral eukaryotic gene and undergone multiple independent expansions. bZIP family diversification is largely restricted to multicellular lineages, consistent with bZIPs contributing to the complex regulatory networks underlying differential and cell type-specific gene expression in these lineages. Analyses focused on the Metazoa suggest an elaborate bZIP network was in place in the most recent shared ancestor of all extant animals that was comprised of 11 of the 12 previously recognized families present in modern taxa. In addition this analysis identifies three bZIP families that appear to have been lost in mammals. Thus the ancestral metazoan and eumetazoan bZIP repertoire consists of 12 and 16 bZIPs, respectively. These diversified from 7 founder genes present in the holozoan ancestor.<br><br>CONCLUSIONS: Our results reveal the ancestral opisthokont, holozoan and metazoan bZIP repertoire and provide insights into the progressive expansion and divergence of bZIPs in the five main eukaryotic kingdoms, suggesting that the early diversification of bZIPs in multiple eukaryotic lineages was a prerequisite for the evolution of complex multicellular organisms.},
}
@article {pmid26822195,
year = {2016},
author = {Herron, MD},
title = {Origins of multicellular complexity: Volvox and the volvocine algae.},
journal = {Molecular ecology},
volume = {25},
number = {6},
pages = {1213-1223},
doi = {10.1111/mec.13551},
pmid = {26822195},
issn = {1365-294X},
support = {NNA17BB05A//Intramural NASA/United States ; },
mesh = {*Biological Evolution ; Cell Differentiation ; Cell Movement ; Chlamydomonas/genetics/physiology ; Congresses as Topic ; Phylogeny ; Volvox/*genetics/*physiology ; },
abstract = {The collection of evolutionary transformations known as the 'major transitions' or 'transitions in individuality' resulted in changes in the units of evolution and in the hierarchical structure of cellular life. Volvox and related algae have become an important model system for the major transition from unicellular to multicellular life, which touches on several fundamental questions in evolutionary biology. The Third International Volvox Conference was held at the University of Cambridge in August 2015 to discuss recent advances in the biology and evolution of this group of algae. Here, I highlight the benefits of integrating phylogenetic comparative methods and experimental evolution with detailed studies of developmental genetics in a model system with substantial genetic and genomic resources. I summarize recent research on Volvox and its relatives and comment on its implications for the genomic changes underlying major evolutionary transitions, evolution and development of complex traits, evolution of sex and sexes, evolution of cellular differentiation and the biophysics of motility. Finally, I outline challenges and suggest future directions for research into the biology and evolution of the volvocine algae.},
}
@article {pmid26777340,
year = {2016},
author = {Neill, D},
title = {Individual Cell Longevity, 'Life's Timekeeper', and Metazoan Evolution.},
journal = {Current aging science},
volume = {9},
number = {2},
pages = {87-98},
pmid = {26777340},
issn = {1874-6128},
mesh = {Animals ; *Biological Evolution ; Cell Survival ; *Cellular Senescence ; Humans ; Signal Transduction ; },
abstract = {It is proposed that a primary and fundamental aspect of metazoan evolution is an ability to control and extend the longevity of individual cells. This was achieved through an intracellular oscillator, dubbed 'Life's Timekeeper', which evolved in the hypothetical ancestor of all metazoans. Slower oscillatory frequencies directed metazoan evolution towards extended longevity of individual cells, enabling generation of many specialised types of terminally differentiated cells. As the longevity of these cells was still relatively short in more primitive metazoans, stem cells, capable of differentiating into all specialised cell types, were retained in order to replace senescent cells. With increasing cell longevity, continual replacement of all senescent cells was no longer necessary. Cells such as neurons could be sustained throughout life, enabling the evolution of brains, hence, complex behaviour and intelligence. In multicellular metazoans the oscillator remains synchronised across all cells. It coordinates the timing of all cell-cell signalling systems, hence controls the timing of development and aging/senescence. In advanced metazoans, where senescent cells are not continually replaced, it controls lifespan. With regards to morphological evolution the oscillator, through alterations to developmental timing, controls change in size and shape. With regards to life history theory it functions as the key variable mediating the correlation between life history traits. This theory is compatible with a prominent role for environmental selection but, as it implicates some degree of internal mediation and direction, it is not entirely compatible with the 'modern synthesis' view of natural selection.},
}
@article {pmid26775799,
year = {2016},
author = {Mukherjee, S and Karmakar, S and Babu, SP},
title = {TLR2 and TLR4 mediated host immune responses in major infectious diseases: a review.},
journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases},
volume = {20},
number = {2},
pages = {193-204},
doi = {10.1016/j.bjid.2015.10.011},
pmid = {26775799},
issn = {1678-4391},
mesh = {Communicable Diseases/*immunology ; Host-Parasite Interactions/*immunology ; Host-Pathogen Interactions/*immunology ; Humans ; Immunity, Humoral/*immunology ; Toll-Like Receptor 2/*immunology ; Toll-Like Receptor 4/*immunology ; },
abstract = {During the course of evolution, multicellular organisms have been orchestrated with an efficient and versatile immune system to counteract diverse group of pathogenic organisms. Pathogen recognition is considered as the most critical step behind eliciting adequate immune response during an infection. Hitherto Toll-like receptors (TLRs), especially the surface ones viz. TLR2 and TLR4 have gained immense importance due to their extreme ability of identifying distinct molecular patterns from invading pathogens. These pattern recognition receptors (PRRs) not only act as innate sensor but also shape and bridge innate and adaptive immune responses. In addition, they also play a pivotal role in regulating the balance between Th1 and Th2 type of response essential for the survivability of the host. In this work, major achievements rather findings made on the typical signalling and immunopathological attributes of TLR2 and TLR4 mediated host response against the major infectious diseases have been reviewed. Infectious diseases like tuberculosis, trypanosomiasis, malaria, and filariasis are still posing myriad threat to mankind. Furthermore, increasing resistance of the causative organisms against available therapeutics is also an emerging problem. Thus, stimulation of host immune response with TLR2 and TLR4 agonist can be the option of choice to treat such diseases in future.},
}
@article {pmid26774793,
year = {2016},
author = {Soares, MP and Yilmaz, B},
title = {Microbiota Control of Malaria Transmission.},
journal = {Trends in parasitology},
volume = {32},
number = {2},
pages = {120-130},
doi = {10.1016/j.pt.2015.11.004},
pmid = {26774793},
issn = {1471-5007},
mesh = {Antibodies/immunology ; Biological Evolution ; Host-Pathogen Interactions/*immunology ; Humans ; Intestines/microbiology ; Malaria, Falciparum/immunology/*microbiology/prevention &amp; control/*transmission ; Microbiota/immunology/*physiology ; Plasmodium falciparum/physiology ; Polysaccharides/immunology ; Protozoan Vaccines/immunology ; },
abstract = {Stable mutualistic interactions between multicellular organisms and microbes are an evolutionarily conserved process with a major impact on host physiology and fitness. Humans establish such interactions with a consortium of microorganisms known as the microbiota. Despite the mutualistic nature of these interactions, some bacterial components of the human microbiota express immunogenic glycans that elicit glycan-specific antibody (Ab) responses. The ensuing circulating Abs are protective against infections by pathogens that express those glycans, as demonstrated for Plasmodium, the causative agent of malaria. Presumably, a similar protective Ab response acts against other vector-borne diseases.},
}
@article {pmid26761184,
year = {2016},
author = {Chhetri, J and Gueven, N},
title = {Targeting mitochondrial function to protect against vision loss.},
journal = {Expert opinion on therapeutic targets},
volume = {20},
number = {6},
pages = {721-736},
doi = {10.1517/14728222.2015.1134489},
pmid = {26761184},
issn = {1744-7631},
mesh = {Animals ; Eye Diseases/etiology/*prevention &amp; control ; Humans ; Mitochondria/metabolism/*pathology ; Mitochondrial Diseases/*complications/physiopathology ; Neurodegenerative Diseases/complications/physiopathology ; Vision Disorders/etiology/prevention &amp; control ; },
abstract = {INTRODUCTION: Mitochondria, essential to multicellular life, convert food into ATP to satisfy cellular energy demands. Since different tissues have different energy requirements, mitochondrial density is high in tissues with high metabolic needs, such as the visual system, which is therefore highly susceptible to limited energy supply as a result of mitochondrial dysfunction.<br><br>AREAS COVERED: Vision impairment is a common feature of most mitochondrial diseases. At the same time, there is mounting evidence that mitochondrial impairment contributes to the pathogenesis of major eye diseases such as glaucoma and might also be involved in the reported vision impairment in neurodegenerative disorders such as Alzheimer's disease.<br><br>EXPERT OPINION: Rather than relying on symptomatic treatment, acknowledging the mitochondrial origin of visual disorders in mitochondrial, neurodegenerative and ocular diseases could lead to novel therapeutics that aim to modulate mitochondrial function in order to protect against vision loss. This approach has already shown some promising clinical results in inherited retinal disorders, which supports the idea that targeting mitochondria could also be a treatment option for other optic neuropathies.},
}
@article {pmid26756664,
year = {2016},
author = {Ambrose, BA and Vasco, A},
title = {Bringing the multicellular fern meristem into focus.},
journal = {The New phytologist},
volume = {210},
number = {3},
pages = {790-793},
doi = {10.1111/nph.13825},
pmid = {26756664},
issn = {1469-8137},
mesh = {Ferns/*cytology/genetics/metabolism ; Genes, Plant ; Meristem/*cytology/genetics/metabolism ; Phylogeny ; Plant Proteins/metabolism ; },
}
@article {pmid26740169,
year = {2016},
author = {Anderson, DP and Whitney, DS and Hanson-Smith, V and Woznica, A and Campodonico-Burnett, W and Volkman, BF and King, N and Thornton, JW and Prehoda, KE},
title = {Evolution of an ancient protein function involved in organized multicellularity in animals.},
journal = {eLife},
volume = {5},
number = {},
pages = {e10147},
doi = {10.7554/eLife.10147},
pmid = {26740169},
issn = {2050-084X},
support = {UL1 TR000430/TR/NCATS NIH HHS/United States ; R01GM089977/GM/NIGMS NIH HHS/United States ; //Canadian Institutes of Health Research/Canada ; R01 GM087457/GM/NIGMS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; R01 GM089977/GM/NIGMS NIH HHS/United States ; R01 GM104397/GM/NIGMS NIH HHS/United States ; R01GM087457/GM/NIGMS NIH HHS/United States ; R01GM104397/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Cell Cycle ; Cell Cycle Proteins/chemistry/*genetics/*metabolism ; *Evolution, Molecular ; Guanylate Kinases/chemistry/*genetics/*metabolism ; Models, Molecular ; Protein Binding ; Protein Multimerization ; Spindle Apparatus/*metabolism ; },
abstract = {To form and maintain organized tissues, multicellular organisms orient their mitotic spindles relative to neighboring cells. A molecular complex scaffolded by the GK protein-interaction domain (GKPID) mediates spindle orientation in diverse animal taxa by linking microtubule motor proteins to a marker protein on the cell cortex localized by external cues. Here we illuminate how this complex evolved and commandeered control of spindle orientation from a more ancient mechanism. The complex was assembled through a series of molecular exploitation events, one of which - the evolution of GKPID's capacity to bind the cortical marker protein - can be recapitulated by reintroducing a single historical substitution into the reconstructed ancestral GKPID. This change revealed and repurposed an ancient molecular surface that previously had a radically different function. We show how the physical simplicity of this binding interface enabled the evolution of a new protein function now essential to the biological complexity of many animals.},
}
@article {pmid26725198,
year = {2016},
author = {Proust, H and Honkanen, S and Jones, VA and Morieri, G and Prescott, H and Kelly, S and Ishizaki, K and Kohchi, T and Dolan, L},
title = {RSL Class I Genes Controlled the Development of Epidermal Structures in the Common Ancestor of Land Plants.},
journal = {Current biology : CB},
volume = {26},
number = {1},
pages = {93-99},
doi = {10.1016/j.cub.2015.11.042},
pmid = {26725198},
issn = {1879-0445},
mesh = {Amino Acid Sequence ; Basic Helix-Loop-Helix Transcription Factors/*genetics/metabolism ; *Biological Evolution ; Bryophyta/genetics/growth &amp; development ; Bryopsida/genetics ; Gene Expression Regulation, Plant ; *Genes, Plant ; Germ Cells, Plant/growth &amp; development ; Indoleacetic Acids/metabolism ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Epidermis/cytology/*genetics/*growth &amp; development ; Plant Proteins/genetics/metabolism ; Plants, Genetically Modified ; Transcription Factors/metabolism ; },
abstract = {The colonization of the land by plants, sometime before 470 million years ago, was accompanied by the evolution tissue systems [1-3]. Specialized structures with diverse functions-from nutrient acquisition to reproduction-derived from single cells in the outermost layer (epidermis) were important sources of morphological innovation at this time [2, 4, 5]. In extant plants, these structures may be unicellular extensions, such as root hairs or rhizoids [6-9], or multicellular structures, such as asexual propagules or secretory hairs (papillae) [10-12]. Here, we show that a ROOTHAIR DEFECTIVE SIX-LIKE (RSL) class I basic helix-loop-helix transcription factor positively regulates the development of the unicellular and multicellular structures that develop from individual cells that expand out of the epidermal plane of the liverwort Marchantia polymorpha; mutants that lack MpRSL1 function do not develop rhizoids, slime papillae, mucilage papillae, or gemmae. Furthermore, we discovered that RSL class I genes are also required for the development of multicellular axillary hairs on the gametophyte of the moss Physcomitrella patens. Because class I RSL proteins also control the development of rhizoids in mosses and root hairs in angiosperms [13, 14], these data demonstrate that the function of RSL class I genes was to control the development of structures derived from single epidermal cells in the common ancestor of the land plants. Class I RSL genes therefore controlled the generation of adaptive morphological diversity as plants colonized the land from the water.},
}
@article {pmid29513353,
year = {2016},
author = {Cummings, FW},
title = {Early metazoan development: the origin of the Cambrian exuberance.},
journal = {Theoretical biology forum},
volume = {109},
number = {1-2},
pages = {71-92},
doi = {10.19272/201611402005},
pmid = {29513353},
issn = {0035-6050},
mesh = {*Algorithms ; Animals ; *Biological Evolution ; Blastula/growth &amp; development ; *Body Patterning ; Cell Movement ; Mesoderm/cytology/growth &amp; development ; *Models, Biological ; Wnt Signaling Pathway ; },
abstract = {DESCRIPTION: A number of common features can be observed in the earliest developing embryos of all animal phyla. A simple extant model of morphogenesis is outlined here, with the aim of giving a model of the relatively rapid appearance of Cambrian animals, 541-515 mya. Developmental patterning, elucidated by a simple linear model with only short-range diffusion of ligands, is given as the origin of the most primitive animals. The key aspect of the model involves the interaction between the emergence of the Wnt and Hedgehog (Hh) signaling pathways. The non-canonical Wnt pathway is crucial in first establishing a sphere of cells, by way of cell-cell connection fi bers. A mutation in the Wnt pathway at the dawn of multicellular organisms is argued to have given rise to the early Hh pathway, and their interaction gives two spatially separate gene determination regions, the key goal of biological patterning.},
}
@article {pmid26714105,
year = {2015},
author = {Shou, W},
title = {Acknowledging selection at sub-organismal levels resolves controversy on pro-cooperation mechanisms.},
journal = {eLife},
volume = {4},
number = {},
pages = {},
doi = {10.7554/eLife.10106},
pmid = {26714105},
issn = {2050-084X},
mesh = {*Biological Evolution ; Eukaryota ; *Symbiosis ; },
abstract = {Cooperators who pay a cost to produce publically-available benefits can be exploited by cheaters who do not contribute fairly. How might cooperation persist against cheaters? Two classes of mechanisms are known to promote cooperation: 'partner choice', where a cooperator preferentially interacts with cooperative over cheating partners; and 'partner fidelity feedback', where repeated interactions between individuals ensure that cheaters suffer as their cooperative partners languish (see, for example, Momeni et al., 2013). However when both mechanisms can act, differentiating them has generated controversy. Here, I resolve this controversy by noting that selection can operate on organismal and sub-organismal 'entities' such that partner fidelity feedback at sub-organismal level can appear as partner choice at organismal level. I also show that cooperation between multicellular eukaryotes and mitochondria is promoted by partner fidelity feedback and partner choice between sub-organismal entities, in addition to being promoted by partner fidelity feedback between hosts and symbionts, as was previously known.},
}
@article {pmid26709836,
year = {2016},
author = {Mallet, J and Besansky, N and Hahn, MW},
title = {How reticulated are species?.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {38},
number = {2},
pages = {140-149},
doi = {10.1002/bies.201500149},
pmid = {26709836},
issn = {1521-1878},
support = {BB/G006903/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI076584/AI/NIAID NIH HHS/United States ; R01 AI76584/AI/NIAID NIH HHS/United States ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genetic Speciation ; Genomics/methods ; Organisms, Genetically Modified/genetics ; *Phylogeny ; Plants/genetics ; },
abstract = {Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree-like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.},
}
@article {pmid26704468,
year = {2016},
author = {McCoy-Simandle, K and Hanna, SJ and Cox, D},
title = {Exosomes and nanotubes: Control of immune cell communication.},
journal = {The international journal of biochemistry &amp; cell biology},
volume = {71},
number = {},
pages = {44-54},
doi = {10.1016/j.biocel.2015.12.006},
pmid = {26704468},
issn = {1878-5875},
support = {P01 CA100324/CA/NCI NIH HHS/United States ; K12GM102779/GM/NIGMS NIH HHS/United States ; K12 GM102779/GM/NIGMS NIH HHS/United States ; R01 GM071828/GM/NIGMS NIH HHS/United States ; P30 CA013330/CA/NCI NIH HHS/United States ; },
mesh = {Cell Communication/*immunology ; Exosomes/*metabolism ; Humans ; },
abstract = {Cell-cell communication is critical to coordinate the activity and behavior of a multicellular organism. The cells of the immune system not only must communicate with similar cells, but also with many other cell types in the body. Therefore, the cells of the immune system have evolved multiple ways to communicate. Exosomes and tunneling nanotubes (TNTs) are two means of communication used by immune cells that contribute to immune functions. Exosomes are small membrane vesicles secreted by most cell types that can mediate intercellular communication and in the immune system they are proposed to play a role in antigen presentation and modulation of gene expression. TNTs are membranous structures that mediate direct cell-cell contact over several cell diameters in length (and possibly longer) and facilitate the interaction and/or the transfer of signals, material and other cellular organelles between connected cells. Recent studies have revealed additional, but sometimes conflicting, structural and functional features of both exosomes and TNTs. Despite the new and exciting information in exosome and TNT composition, origin and in vitro function, biologically significant functions are still being investigated and determined. In this review, we discuss the current field regarding exosomes and TNTs in immune cells providing evaluation and perspectives of the current literature.},
}
@article {pmid26695632,
year = {2015},
author = {Dewachter, L and Verstraeten, N and Monteyne, D and Kint, CI and Versées, W and Pérez-Morga, D and Michiels, J and Fauvart, M},
title = {A Single-Amino-Acid Substitution in Obg Activates a New Programmed Cell Death Pathway in Escherichia coli.},
journal = {mBio},
volume = {6},
number = {6},
pages = {e01935-15},
doi = {10.1128/mBio.01935-15},
pmid = {26695632},
issn = {2150-7511},
mesh = {*Amino Acid Substitution ; *Apoptosis ; DNA Fragmentation ; Escherichia coli/genetics/*physiology ; Escherichia coli Proteins/*genetics/*metabolism ; Membrane Potentials ; Microbial Viability ; Monomeric GTP-Binding Proteins/*genetics/*metabolism ; Mutant Proteins/genetics/metabolism ; Phosphatidylserines/analysis ; },
abstract = {UNLABELLED: Programmed cell death (PCD) is an important hallmark of multicellular organisms. Cells self-destruct through a regulated series of events for the benefit of the organism as a whole. The existence of PCD in bacteria has long been controversial due to the widely held belief that only multicellular organisms would profit from this kind of altruistic behavior at the cellular level. However, over the past decade, compelling experimental evidence has established the existence of such pathways in bacteria. Here, we report that expression of a mutant isoform of the essential GTPase ObgE causes rapid loss of viability in Escherichia coli. The physiological changes that occur upon expression of this mutant protein--including loss of membrane potential, chromosome condensation and fragmentation, exposure of phosphatidylserine on the cell surface, and membrane blebbing--point to a PCD mechanism. Importantly, key regulators and executioners of known bacterial PCD pathways were shown not to influence this cell death program. Collectively, our results suggest that the cell death pathway described in this work constitutes a new mode of bacterial PCD.<br><br>IMPORTANCE: Programmed cell death (PCD) is a well-known phenomenon in higher eukaryotes. In these organisms, PCD is essential for embryonic development--for example, the disappearance of the interdigital web--and also functions in tissue homeostasis and elimination of pathogen-invaded cells. The existence of PCD mechanisms in unicellular organisms like bacteria, on the other hand, has only recently begun to be recognized. We here demonstrate the existence of a bacterial PCD pathway that induces characteristics that are strikingly reminiscent of eukaryotic apoptosis, such as fragmentation of DNA, exposure of phosphatidylserine on the cell surface, and membrane blebbing. Our results can provide more insight into the mechanism and evolution of PCD pathways in higher eukaryotes. More importantly, especially in the light of the looming antibiotic crisis, they may point to a bacterial Achilles' heel and can inspire innovative ways of combating bacterial infections, directed at the targeted activation of PCD pathways.},
}
@article {pmid26667994,
year = {2016},
author = {Hervé, C and Siméon, A and Jam, M and Cassin, A and Johnson, KL and Salmeán, AA and Willats, WG and Doblin, MS and Bacic, A and Kloareg, B},
title = {Arabinogalactan proteins have deep roots in eukaryotes: identification of genes and epitopes in brown algae and their role in Fucus serratus embryo development.},
journal = {The New phytologist},
volume = {209},
number = {4},
pages = {1428-1441},
doi = {10.1111/nph.13786},
pmid = {26667994},
issn = {1469-8137},
mesh = {Amino Acid Sequence ; Cell Division/radiation effects ; Cell Wall/metabolism/radiation effects ; Epitopes/*metabolism ; Fucus/*genetics/*growth &amp; development/radiation effects ; Genes, Plant ; Genome ; Indicators and Reagents ; Light ; Models, Biological ; Mucoproteins/chemistry/*metabolism ; Phylogeny ; Plant Proteins/chemistry/metabolism ; Protein Domains ; Sequence Homology, Nucleic Acid ; Zygote/metabolism ; },
abstract = {Arabinogalactan proteins (AGPs) are highly glycosylated, hydroxyproline-rich proteins found at the cell surface of plants, where they play key roles in developmental processes. Brown algae are marine, multicellular, photosynthetic eukaryotes. They belong to the phylum Stramenopiles, which is unrelated to land plants and green algae (Chloroplastida). Brown algae share common evolutionary features with other multicellular organisms, including a carbohydrate-rich cell wall. They differ markedly from plants in their cell wall composition, and AGPs have not been reported in brown algae. Here we investigated the presence of chimeric AGP-like core proteins in this lineage. We report that the genome sequence of the brown algal model Ectocarpus siliculosus encodes AGP protein backbone motifs, in a gene context that differs considerably from what is known in land plants. We showed the occurrence of AGP glycan epitopes in a range of brown algal cell wall extracts. We demonstrated that these chimeric AGP-like core proteins are developmentally regulated in embryos of the order Fucales and showed that AGP loss of function seriously impairs the course of early embryogenesis. Our findings shine a new light on the role of AGPs in cell wall sensing and raise questions about the origin and evolution of AGPs in eukaryotes.},
}
@article {pmid26663204,
year = {2016},
author = {Fisher, RM and Bell, T and West, SA},
title = {Multicellular group formation in response to predators in the alga Chlorella vulgaris.},
journal = {Journal of evolutionary biology},
volume = {29},
number = {3},
pages = {551-559},
doi = {10.1111/jeb.12804},
pmid = {26663204},
issn = {1420-9101},
mesh = {Animals ; Biological Evolution ; Chlorella vulgaris/*physiology ; Predatory Behavior ; Tetrahymena thermophila/*physiology ; },
abstract = {A key step in the evolution of multicellular organisms is the formation of cooperative multicellular groups. It has been suggested that predation pressure may promote multicellular group formation in some algae and bacteria, with cells forming groups to lower their chance of being eaten. We use the green alga Chlorella vulgaris and the protist Tetrahymena thermophila to test whether predation pressure can initiate the formation of colonies. We found that: (1) either predators or just predator exoproducts promote colony formation; (2) higher predator densities cause more colonies to form; and (3) colony formation in this system is facultative, with populations returning to being unicellular when the predation pressure is removed. These results provide empirical support for the hypothesis that predation pressure promotes multicellular group formation. The speed of the reversion of populations to unicellularity suggests that this response is due to phenotypic plasticity and not evolutionary change.},
}
@article {pmid26648040,
year = {2015},
author = {Longo, G and Montevil, M and Sonnenschein, C and Soto, AM},
title = {In search of principles for a Theory of Organisms.},
journal = {Journal of biosciences},
volume = {40},
number = {5},
pages = {955-968},
pmid = {26648040},
issn = {0973-7138},
support = {R01 ES008314/ES/NIEHS NIH HHS/United States ; U01 ES020888/ES/NIEHS NIH HHS/United States ; ES08314/ES/NIEHS NIH HHS/United States ; U01-ES020888/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; *Biological Evolution ; Biophysics/methods ; Cell Division ; Mice, Inbred C57BL ; *Models, Biological ; *Morphogenesis ; Physics/methods ; Thermodynamics ; },
abstract = {Lacking an operational theory to explain the organization and behaviour of matter in unicellular and multicellular organisms hinders progress in biology. Such a theory should address life cycles from ontogenesis to death. This theory would complement the theory of evolution that addresses phylogenesis, and would posit theoretical extensions to accepted physical principles and default states in order to grasp the living state of matter and define proper biological observables. Thus, we favour adopting the default state implicit in Darwin's theory, namely, cell proliferation with variation plus motility, and a framing principle, namely, life phenomena manifest themselves as non-identical iterations of morphogenetic processes. From this perspective, organisms become a consequence of the inherent variability generated by proliferation, motility and self-organization. Morphogenesis would then be the result of the default state plus physical constraints, like gravity, and those present in living organisms, like muscular tension.},
}
@article {pmid26644562,
year = {2015},
author = {Alié, A and Hayashi, T and Sugimura, I and Manuel, M and Sugano, W and Mano, A and Satoh, N and Agata, K and Funayama, N},
title = {The ancestral gene repertoire of animal stem cells.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {51},
pages = {E7093-100},
doi = {10.1073/pnas.1514789112},
pmid = {26644562},
issn = {1091-6490},
mesh = {Animals ; Evolution, Molecular ; Genomic Instability ; Hydra/cytology/genetics ; Mammals ; Phylogeny ; Porifera/cytology/genetics ; RNA, Small Interfering/genetics ; RNA-Binding Proteins/genetics ; Stem Cells/*metabolism ; Transcription Factors/genetics ; Transcriptome ; },
abstract = {Stem cells are pivotal for development and tissue homeostasis of multicellular animals, and the quest for a gene toolkit associated with the emergence of stem cells in a common ancestor of all metazoans remains a major challenge for evolutionary biology. We reconstructed the conserved gene repertoire of animal stem cells by transcriptomic profiling of totipotent archeocytes in the demosponge Ephydatia fluviatilis and by tracing shared molecular signatures with flatworm and Hydra stem cells. Phylostratigraphy analyses indicated that most of these stem-cell genes predate animal origin, with only few metazoan innovations, notably including several partners of the Piwi machinery known to promote genome stability. The ancestral stem-cell transcriptome is strikingly poor in transcription factors. Instead, it is rich in RNA regulatory actors, including components of the &quot;germ-line multipotency program&quot; and many RNA-binding proteins known as critical regulators of mammalian embryonic stem cells.},
}
@article {pmid26644561,
year = {2015},
author = {Schaible, R and Scheuerlein, A and Dańko, MJ and Gampe, J and Martínez, DE and Vaupel, JW},
title = {Constant mortality and fertility over age in Hydra.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {51},
pages = {15701-15706},
doi = {10.1073/pnas.1521002112},
pmid = {26644561},
issn = {1091-6490},
support = {R01 AG037965/AG/NIA NIH HHS/United States ; AG037965/AG/NIA NIH HHS/United States ; },
mesh = {Animals ; Biological Evolution ; Fertility ; Hydra/*physiology ; Life Expectancy ; },
abstract = {Senescence, the increase in mortality and decline in fertility with age after maturity, was thought to be inevitable for all multicellular species capable of repeated breeding. Recent theoretical advances and compilations of data suggest that mortality and fertility trajectories can go up or down, or remain constant with age, but the data are scanty and problematic. Here, we present compelling evidence for constant age-specific death and reproduction rates in Hydra, a basal metazoan, in a set of experiments comprising more than 3.9 million days of observations of individual Hydra. Our data show that 2,256 Hydra from two closely related species in two laboratories in 12 cohorts, with cohort age ranging from 0 to more than 41 y, have extremely low, constant rates of mortality. Fertility rates for Hydra did not systematically decline with advancing age. This falsifies the universality of the theories of the evolution of aging that posit that all species deteriorate with age after maturity. The nonsenescent life history of Hydra implies levels of maintenance and repair that are sufficient to prevent the accumulation of damage for at least decades after maturity, far longer than the short life expectancy of Hydra in the wild. A high proportion of stem cells, constant and rapid cell turnover, few cell types, a simple body plan, and the fact that the germ line is not segregated from the soma are characteristics of Hydra that may make nonsenescence feasible. Nonsenescence may be optimal because lifetime reproduction may be enhanced more by extending adult life spans than by increasing daily fertility.},
}
@article {pmid26638678,
year = {2015},
author = {Libertini, G},
title = {Phylogeny of Aging and Related Phenoptotic Phenomena.},
journal = {Biochemistry. Biokhimiia},
volume = {80},
number = {12},
pages = {1529-1546},
doi = {10.1134/S0006297915120019},
pmid = {26638678},
issn = {1608-3040},
mesh = {Aging/*genetics ; Animals ; Apoptosis/physiology ; Biological Evolution ; DNA/genetics ; Humans ; Phylogeny ; Telomere/genetics ; },
abstract = {The interpretation of aging as adaptive, i.e. as a phenomenon genetically determined and modulated, and with an evolutionary advantage, implies that aging, as any physiologic mechanism, must have phylogenetic connections with similar phenomena. This review tries to find the phylogenetic connections between vertebrate aging and some related phenomena in other species, especially within those phenomena defined as phenoptotic, i.e. involving the death of one or more individuals for the benefit of other individuals. In particular, the aim of the work is to highlight and analyze similarities and connections, in the mechanisms and in the evolutionary causes, between: (i) proapoptosis in prokaryotes and apoptosis in unicellular eukaryotes; (ii) apoptosis in unicellular and multicellular eukaryotes; (iii) aging in yeast and in vertebrates; and (iv) the critical importance of the DNA subtelomeric segment in unicellular and multicellular eukaryotes. In short, there is strong evidence that vertebrate aging has clear similarities and connections with phenomena present in organisms with simpler organization. These phylogenetic connections are a necessary element for the sustainability of the thesis of aging explained as an adaptive phenomenon, and, on the contrary, are incompatible with the opposite view of aging as being due to the accumulation of random damages of various kinds.},
}
@article {pmid26637532,
year = {2015},
author = {Igaki, T},
title = {Communicating the molecular basis of cancer cell-by-cell: an interview with Tatsushi Igaki.},
journal = {Disease models &amp; mechanisms},
volume = {8},
number = {12},
pages = {1491-1494},
doi = {10.1242/dmm.024059},
pmid = {26637532},
issn = {1754-8411},
mesh = {Animals ; Apoptosis ; Cell Communication ; Drosophila/cytology ; History, 20th Century ; History, 21st Century ; Humans ; Japan ; Neoplasms/*history ; },
abstract = {Tatsushi Igaki is currently based at the Kyoto University Graduate School of Biostudies, where he leads a research group dedicated to using Drosophila genetics to build a picture of the cell-cell communications underlying the establishment and maintenance of multicellular systems. His work has provided insight into the molecular bases of cell competition in the context of development and tumorigenesis, including the landmark discovery that oncogenic cells communicate with normal cells in the tumor microenvironment to induce tumor progression in a non-autonomous fashion. In this interview, he describes his career path, highlighting the shift in his research focus from the basic principles of apoptosis to clonal evolution in cancer, and also explains why Drosophila provides a powerful model system for studying cancer biology.},
}
@article {pmid26636317,
year = {2016},
author = {Li, XQ},
title = {Natural Attributes and Agricultural Implications of Somatic Genome Variation.},
journal = {Current issues in molecular biology},
volume = {20},
number = {},
pages = {29-46},
pmid = {26636317},
issn = {1467-3045},
mesh = {Agriculture ; Animals ; Evolution, Molecular ; *Genetic Variation ; Genome ; Humans ; Livestock/*genetics ; Models, Genetic ; Mutation ; Ploidies ; },
abstract = {This article proposes the concept of genome network, describes different variations of the somatic genome network, and reviews the agricultural implications of such variations. All genetic materials in a cell constitute the genome network of the cell and can jointly influence the cell's function and fate. The somatic genome of a plant is the genome network of cells in somatic tissues and of nonreproductive cells in pollen and ovules. Somatic genome variation (SGV, approximately equivalent to somagenetic variation) occurs at multiple levels, including stoichiometric, ploidy, and sequence variations. For a multicellular organism, the term &quot;somatic genome variation&quot; covers both the variation in part of the organism and the generation of new genotype individuals through somatic means from a sexually produced original genotype. For unicellular organisms, genome variation in somatic nuclei occurs at the whole organism level because there is only a single cell per individual. Growth, development and evolution of living organisms require both stability and instability of their genomes. Somatic genome variation displays many more attributes than genetic mutation and has strong implications for agriculture.},
}
@article {pmid26634291,
year = {2016},
author = {Boehm, CR and Ueda, M and Nishimura, Y and Shikanai, T and Haseloff, J},
title = {A Cyan Fluorescent Reporter Expressed from the Chloroplast Genome of Marchantia polymorpha.},
journal = {Plant &amp; cell physiology},
volume = {57},
number = {2},
pages = {291-299},
doi = {10.1093/pcp/pcv160},
pmid = {26634291},
issn = {1471-9053},
support = {BB/F011458/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Base Sequence ; Fluorescence ; *Genome, Chloroplast ; Green Fluorescent Proteins/chemistry/genetics/*metabolism ; Marchantia/*genetics ; Molecular Sequence Data ; Plants, Genetically Modified ; Transformation, Genetic ; },
abstract = {Recently, the liverwort Marchantia polymorpha has received increasing attention as a basal plant model for multicellular studies. Its ease of handling, well-characterized plastome and proven protocols for biolistic plastid transformation qualify M. polymorpha as an attractive platform to study the evolution of chloroplasts during the transition from water to land. In addition, chloroplasts of M. polymorpha provide a convenient test-bed for the characterization of genetic elements involved in plastid gene expression due to the absence of mechanisms for RNA editing. While reporter genes have proven valuable to the qualitative and quantitative study of gene expression in chloroplasts, expression of green fluorescent protein (GFP) in chloroplasts of M. polymorpha has proven problematic. We report the design of a codon-optimized gfp varian, mturq2cp, which allowed successful expression of a cyan fluorescent protein under control of the tobacco psbA promoter from the chloroplast genome of M. polymorpha. We demonstrate the utility of mturq2cp in (i) early screening for transplastomic events following biolistic transformation of M. polymorpha spores; (ii) visualization of stromules as elements of plastid structure in Marchantia; and (iii) quantitative microscopy for the analysis of promoter activity.},
}
@article {pmid26627241,
year = {2015},
author = {Chang, ES and Neuhof, M and Rubinstein, ND and Diamant, A and Philippe, H and Huchon, D and Cartwright, P},
title = {Genomic insights into the evolutionary origin of Myxozoa within Cnidaria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {48},
pages = {14912-14917},
doi = {10.1073/pnas.1511468112},
pmid = {26627241},
issn = {1091-6490},
mesh = {Animals ; *Evolution, Molecular ; *Genome ; Genomics ; Myxobolus/*genetics ; *Phylogeny ; Polypodium/parasitology ; },
abstract = {The Myxozoa comprise over 2,000 species of microscopic obligate parasites that use both invertebrate and vertebrate hosts as part of their life cycle. Although the evolutionary origin of myxozoans has been elusive, a close relationship with cnidarians, a group that includes corals, sea anemones, jellyfish, and hydroids, is supported by some phylogenetic studies and the observation that the distinctive myxozoan structure, the polar capsule, is remarkably similar to the stinging structures (nematocysts) in cnidarians. To gain insight into the extreme evolutionary transition from a free-living cnidarian to a microscopic endoparasite, we analyzed genomic and transcriptomic assemblies from two distantly related myxozoan species, Kudoa iwatai and Myxobolus cerebralis, and compared these to the transcriptome and genome of the less reduced cnidarian parasite, Polypodium hydriforme. A phylogenomic analysis, using for the first time to our knowledge, a taxonomic sampling that represents the breadth of myxozoan diversity, including four newly generated myxozoan assemblies, confirms that myxozoans are cnidarians and are a sister taxon to P. hydriforme. Estimations of genome size reveal that myxozoans have one of the smallest reported animal genomes. Gene enrichment analyses show depletion of expressed genes in categories related to development, cell differentiation, and cell-cell communication. In addition, a search for candidate genes indicates that myxozoans lack key elements of signaling pathways and transcriptional factors important for multicellular development. Our results suggest that the degeneration of the myxozoan body plan from a free-living cnidarian to a microscopic parasitic cnidarian was accompanied by extreme reduction in genome size and gene content.},
}
@article {pmid26610912,
year = {2015},
author = {Mao, M and Alavi, MV and Labelle-Dumais, C and Gould, DB},
title = {Type IV Collagens and Basement Membrane Diseases: Cell Biology and Pathogenic Mechanisms.},
journal = {Current topics in membranes},
volume = {76},
number = {},
pages = {61-116},
doi = {10.1016/bs.ctm.2015.09.002},
pmid = {26610912},
issn = {1063-5823},
mesh = {Animals ; Basement Membrane/metabolism/*pathology ; *Cell Biology ; *Collagen Type IV/chemistry/genetics/metabolism ; *Disease ; Genomics ; Humans ; },
abstract = {Basement membranes are highly specialized extracellular matrices. Once considered inert scaffolds, basement membranes are now viewed as dynamic and versatile environments that modulate cellular behaviors to regulate tissue development, function, and repair. Increasing evidence suggests that, in addition to providing structural support to neighboring cells, basement membranes serve as reservoirs of growth factors that direct and fine-tune cellular functions. Type IV collagens are a major component of all basement membranes. They evolved along with the earliest multicellular organisms and have been integrated into diverse fundamental biological processes as time and evolution shaped the animal kingdom. The roles of basement membranes in humans are as complex and diverse as their distributions and molecular composition. As a result, basement membrane defects result in multisystem disorders with ambiguous and overlapping boundaries that likely reflect the simultaneous interplay and integration of multiple cellular pathways and processes. Consequently, there will be no single treatment for basement membrane disorders, and therapies are likely to be as varied as the phenotypes. Understanding tissue-specific pathology and the underlying molecular mechanism is the present challenge; personalized medicine will rely upon understanding how a given mutation impacts diverse cellular functions.},
}
@article {pmid26596625,
year = {2015},
author = {Borowiec, ML and Lee, EK and Chiu, JC and Plachetzki, DC},
title = {Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa.},
journal = {BMC genomics},
volume = {16},
number = {},
pages = {987},
doi = {10.1186/s12864-015-2146-4},
pmid = {26596625},
issn = {1471-2164},
mesh = {Animals ; Bias ; Ctenophora/*genetics ; *Data Mining ; Evolution, Molecular ; Genetic Loci/genetics ; *Genomics ; Humans ; *Phylogeny ; },
abstract = {BACKGROUND: Understanding the phylogenetic relationships among major lineages of multicellular animals (the Metazoa) is a prerequisite for studying the evolution of complex traits such as nervous systems, muscle tissue, or sensory organs. Transcriptome-based phylogenies have dramatically improved our understanding of metazoan relationships in recent years, although several important questions remain. The branching order near the base of the tree, in particular the placement of the poriferan (sponges, phylum Porifera) and ctenophore (comb jellies, phylum Ctenophora) lineages is one outstanding issue. Recent analyses have suggested that the comb jellies are sister to all remaining metazoan phyla including sponges. This finding is surprising because it suggests that neurons and other complex traits, present in ctenophores and eumetazoans but absent in sponges or placozoans, either evolved twice in Metazoa or were independently, secondarily lost in the lineages leading to sponges and placozoans.<br><br>RESULTS: To address the question of basal metazoan relationships we assembled a novel dataset comprised of 1080 orthologous loci derived from 36 publicly available genomes representing major lineages of animals. From this large dataset we procured an optimized set of partitions with high phylogenetic signal for resolving metazoan relationships. This optimized data set is amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. Our analyses strongly support the Ctenophora as the sister lineage to other Metazoa. We find no support for the traditional view uniting the ctenophores and Cnidaria. Our findings are supported by Bayesian comparisons of topological hypotheses and we find no evidence that they are biased by long-branch attraction.<br><br>CONCLUSIONS: Our study further clarifies relationships among early branching metazoan lineages. Our phylogeny supports the still-controversial position of ctenophores as sister group to all other metazoans. This study also provides a workflow and computational tools for minimizing systematic bias in genome-based phylogenetic analyses. Future studies of metazoan phylogeny will benefit from ongoing efforts to sequence the genomes of additional invertebrate taxa that will continue to inform our view of the relationships among the major lineages of animals.},
}
@article {pmid26575626,
year = {2015},
author = {Lynch, M and Marinov, GK},
title = {The bioenergetic costs of a gene.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {51},
pages = {15690-15695},
doi = {10.1073/pnas.1514974112},
pmid = {26575626},
issn = {1091-6490},
support = {R01 GM036827/GM/NIGMS NIH HHS/United States ; R01-GM036827/GM/NIGMS NIH HHS/United States ; },
mesh = {*Energy Metabolism ; *Evolution, Molecular ; Genetic Drift ; Selection, Genetic ; },
abstract = {An enduring mystery of evolutionary genomics concerns the mechanisms responsible for lineage-specific expansions of genome size in eukaryotes, especially in multicellular species. One idea is that all excess DNA is mutationally hazardous, but weakly enough so that genome-size expansion passively emerges in species experiencing relatively low efficiency of selection owing to small effective population sizes. Another idea is that substantial gene additions were impossible without the energetic boost provided by the colonizing mitochondrion in the eukaryotic lineage. Contrary to this latter view, analysis of cellular energetics and genomics data from a wide variety of species indicates that, relative to the lifetime ATP requirements of a cell, the costs of a gene at the DNA, RNA, and protein levels decline with cell volume in both bacteria and eukaryotes. Moreover, these costs are usually sufficiently large to be perceived by natural selection in bacterial populations, but not in eukaryotes experiencing high levels of random genetic drift. Thus, for scaling reasons that are not yet understood, by virtue of their large size alone, eukaryotic cells are subject to a broader set of opportunities for the colonization of novel genes manifesting weakly advantageous or even transiently disadvantageous phenotypic effects. These results indicate that the origin of the mitochondrion was not a prerequisite for genome-size expansion.},
}
@article {pmid26573836,
year = {2015},
author = {Yuan, S and Zheng, T and Li, P and Yang, R and Ruan, J and Huang, S and Wu, Z and Xu, A},
title = {Characterization of Amphioxus IFN Regulatory Factor Family Reveals an Archaic Signaling Framework for Innate Immune Response.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {195},
number = {12},
pages = {5657-5666},
doi = {10.4049/jimmunol.1501927},
pmid = {26573836},
issn = {1550-6606},
mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Humans ; Immunity, Innate ; Interferon Regulatory Factor-1/genetics/*metabolism ; Interferon Regulatory Factors/genetics/*metabolism ; *Lancelets ; Molecular Sequence Data ; Protein Structure, Tertiary/genetics ; Sequence Homology, Amino Acid ; Species Specificity ; },
abstract = {The IFN regulatory factor (IRF) family encodes transcription factors that play important roles in immune defense, stress response, reproduction, development, and carcinogenesis. Although the origin of the IRF family has been dated back to multicellular organisms, invertebrate IRFs differ from vertebrate IRFs in genomic structure and gene synteny, and little is known about their functions. Through comparison of multiple amphioxus genomes, in this study we suggested that amphioxus contains nine IRF members, whose orthologs are supposed to be shared among three amphioxus species. As the orthologs to the vertebrate IRF1 and IRF4 subgroups, Branchiostoma belcheri tsingtauense (bbt)IRF1 and bbtIRF8 bind the IFN-stimulated response element (ISRE) and were upregulated when amphioxus intestinal cells were stimulated with poly(I:C). As amphioxus-specific IRFs, both bbtIRF3 and bbtIRF7 bind ISRE. When activated, they can be phosphorylated by bbtTBK1 and then translocate into nucleus for target gene transcription. As transcriptional repressors, bbtIRF2 and bbtIRF4 can inhibit the transcriptional activities of bbtIRF1, 3, 7, and 8 by competing for the binding of ISRE. Interestingly, amphioxus IRF2, IRF8, and Rel were identified as target genes of bbtIRF1, bbtIRF7, and bbtIRF3, respectively, suggesting a dynamic feedback regulation among amphioxus IRF and NF-κB. Collectively, to our knowledge we present for the first time an archaic IRF signaling framework in a basal chordate, shedding new insights into the origin and evolution of vertebrate IFN-based antiviral networks.},
}
@article {pmid26569502,
year = {2015},
author = {Amano, R and Nakayama, H and Morohoshi, Y and Kawakatsu, Y and Ferjani, A and Kimura, S},
title = {A Decrease in Ambient Temperature Induces Post-Mitotic Enlargement of Palisade Cells in North American Lake Cress.},
journal = {PloS one},
volume = {10},
number = {11},
pages = {e0141247},
doi = {10.1371/journal.pone.0141247},
pmid = {26569502},
issn = {1932-6203},
mesh = {Arabidopsis/cytology/genetics/*growth &amp; development ; Cell Communication ; Cell Cycle ; Cell Proliferation ; *Cell Size ; Environment ; Gene Expression Regulation, Plant ; *Mitosis ; Phenotype ; Phylogeny ; Plant Leaves/cytology ; Plant Physiological Phenomena ; Rorippa/cytology/genetics/*growth &amp; development ; Species Specificity ; *Temperature ; },
abstract = {In order to maintain organs and structures at their appropriate sizes, multicellular organisms orchestrate cell proliferation and post-mitotic cell expansion during morphogenesis. Recent studies using Arabidopsis leaves have shown that compensation, which is defined as post-mitotic cell expansion induced by a decrease in the number of cells during lateral organ development, is one example of such orchestration. Some of the basic molecular mechanisms underlying compensation have been revealed by genetic and chimeric analyses. However, to date, compensation had been observed only in mutants, transgenics, and γ-ray-treated plants, and it was unclear whether it occurs in plants under natural conditions. Here, we illustrate that a shift in ambient temperature could induce compensation in Rorippa aquatica (Brassicaceae), a semi-aquatic plant found in North America. The results suggest that compensation is a universal phenomenon among angiosperms and that the mechanism underlying compensation is shared, in part, between Arabidopsis and R. aquatica.},
}
@article {pmid26560631,
year = {2015},
author = {Cayrou, C and Ballester, B and Peiffer, I and Fenouil, R and Coulombe, P and Andrau, JC and van Helden, J and Méchali, M},
title = {The chromatin environment shapes DNA replication origin organization and defines origin classes.},
journal = {Genome research},
volume = {25},
number = {12},
pages = {1873-1885},
doi = {10.1101/gr.192799.115},
pmid = {26560631},
issn = {1549-5469},
mesh = {Animals ; Base Composition ; Chromatin/*genetics/*metabolism ; Chromatin Assembly and Disassembly ; Chromosome Mapping ; Cluster Analysis ; Computational Biology/methods ; *DNA Replication ; Embryonic Stem Cells ; Genome ; Genomics ; Heterochromatin/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Histones ; Humans ; Mice ; Nucleosomes/genetics/metabolism ; Nucleotide Motifs ; Origin Recognition Complex ; *Replication Origin ; Transcriptional Activation ; },
abstract = {To unveil the still-elusive nature of metazoan replication origins, we identified them genome-wide and at unprecedented high-resolution in mouse ES cells. This allowed initiation sites (IS) and initiation zones (IZ) to be differentiated. We then characterized their genetic signatures and organization and integrated these data with 43 chromatin marks and factors. Our results reveal that replication origins can be grouped into three main classes with distinct organization, chromatin environment, and sequence motifs. Class 1 contains relatively isolated, low-efficiency origins that are poor in epigenetic marks and are enriched in an asymmetric AC repeat at the initiation site. Late origins are mainly found in this class. Class 2 origins are particularly rich in enhancer elements. Class 3 origins are the most efficient and are associated with open chromatin and polycomb protein-enriched regions. The presence of Origin G-rich Repeated elements (OGRE) potentially forming G-quadruplexes (G4) was confirmed at most origins. These coincide with nucleosome-depleted regions located upstream of the initiation sites, which are associated with a labile nucleosome containing H3K64ac. These data demonstrate that specific chromatin landscapes and combinations of specific signatures regulate origin localization. They explain the frequently observed links between DNA replication and transcription. They also emphasize the plasticity of metazoan replication origins and suggest that in multicellular eukaryotes, the combination of distinct genetic features and chromatin configurations act in synergy to define and adapt the origin profile.},
}
@article {pmid26554049,
year = {2015},
author = {Jékely, G and Keijzer, F and Godfrey-Smith, P},
title = {An option space for early neural evolution.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {370},
number = {1684},
pages = {},
doi = {10.1098/rstb.2015.0181},
pmid = {26554049},
issn = {1471-2970},
mesh = {Animals ; *Biological Evolution ; Motor Activity ; Nervous System/*anatomy &amp; histology ; *Nervous System Physiological Phenomena ; },
abstract = {The origin of nervous systems has traditionally been discussed within two conceptual frameworks. Input-output models stress the sensory-motor aspects of nervous systems, while internal coordination models emphasize the role of nervous systems in coordinating multicellular activity, especially muscle-based motility. Here we consider both frameworks and apply them to describe aspects of each of three main groups of phenomena that nervous systems control: behaviour, physiology and development. We argue that both frameworks and all three aspects of nervous system function need to be considered for a comprehensive discussion of nervous system origins. This broad mapping of the option space enables an overview of the many influences and constraints that may have played a role in the evolution of the first nervous systems.},
}
@article {pmid26537913,
year = {2015},
author = {Eyres, I and Boschetti, C and Crisp, A and Smith, TP and Fontaneto, D and Tunnacliffe, A and Barraclough, TG},
title = {Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats.},
journal = {BMC biology},
volume = {13},
number = {},
pages = {90},
doi = {10.1186/s12915-015-0202-9},
pmid = {26537913},
issn = {1741-7007},
support = {233232//European Research Council/International ; BB/F020562/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F020856/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Desiccation ; *Ecosystem ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phylogeny ; Rotifera/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Although prevalent in prokaryotes, horizontal gene transfer (HGT) is rarer in multicellular eukaryotes. Bdelloid rotifers are microscopic animals that contain a higher proportion of horizontally transferred, non-metazoan genes in their genomes than typical of animals. It has been hypothesized that bdelloids incorporate foreign DNA when they repair their chromosomes following double-strand breaks caused by desiccation. HGT might thereby contribute to species divergence and adaptation, as in prokaryotes. If so, we expect that species should differ in their complement of foreign genes, rather than sharing the same set of foreign genes inherited from a common ancestor. Furthermore, there should be more foreign genes in species that desiccate more frequently. We tested these hypotheses by surveying HGT in four congeneric species of bdelloids from different habitats: two from permanent aquatic habitats and two from temporary aquatic habitats that desiccate regularly.<br><br>RESULTS: Transcriptomes of all four species contain many genes with a closer match to non-metazoan genes than to metazoan genes. Whole genome sequencing of one species confirmed the presence of these foreign genes in the genome. Nearly half of foreign genes are shared between all four species and an outgroup from another family, but many hundreds are unique to particular species, which indicates that HGT is ongoing. Using a dated phylogeny, we estimate an average of 12.8 gains versus 2.0 losses of foreign genes per million years. Consistent with the desiccation hypothesis, the level of HGT is higher in the species that experience regular desiccation events than those that do not. However, HGT still contributed hundreds of foreign genes to the species from permanently aquatic habitats. Foreign genes were mainly enzymes with various annotated functions that include catabolism of complex polysaccharides and stress responses. We found evidence of differential loss of ancestral foreign genes previously associated with desiccation protection in the two non-desiccating species.<br><br>CONCLUSIONS: Nearly half of foreign genes were acquired before the divergence of bdelloid families over 60 Mya. Nonetheless, HGT is ongoing in bdelloids and has contributed to putative functional differences among species. Variation among our study species is consistent with the hypothesis that desiccating habitats promote HGT.},
}
@article {pmid26518483,
year = {2016},
author = {Ninova, M and Ronshaugen, M and Griffiths-Jones, S},
title = {MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum.},
journal = {Genome research},
volume = {26},
number = {1},
pages = {85-96},
doi = {10.1101/gr.193367.115},
pmid = {26518483},
issn = {1549-5469},
support = {MR/M008908/1//Medical Research Council/United Kingdom ; 093161/Z/10/Z//Wellcome Trust/United Kingdom ; BB/M011275/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Down-Regulation ; Drosophila/genetics ; Embryonic Development/genetics ; *Evolution, Molecular ; *Gene Expression Regulation, Developmental ; Gene Library ; MicroRNAs/*genetics/metabolism ; Molecular Sequence Annotation ; Sequence Analysis, RNA ; Tribolium/*embryology/*genetics ; },
abstract = {MicroRNAs are well-established players in the development of multicellular animals. Most of our understanding of microRNA function in arthropod development comes from studies in Drosophila. Despite their advantages as model systems, the long germband embryogenesis of fruit flies is an evolutionary derived state restricted to several holometabolous insect lineages. MicroRNA evolution and expression across development in animals exhibiting the ancestral and more widespread short germband mode of embryogenesis has not been characterized. We sequenced small RNA libraries of oocytes and successive intervals covering the embryonic development of the short germband model organism, Tribolium castaneum. We analyzed the evolution and temporal expression of the microRNA complement and sequenced libraries of total RNA to investigate the relationships with microRNA target expression. We show microRNA maternal loading and sequence-specific 3' end nontemplate oligoadenylation of maternally deposited microRNAs that is conserved between Tribolium and Drosophila. We further uncover large clusters encoding multiple paralogs from several Tribolium-specific microRNA families expressed during a narrow interval of time immediately after the activation of zygotic transcription. These novel microRNAs, together with several early expressed conserved microRNAs, target a significant number of maternally deposited transcripts. Comparison with Drosophila shows that microRNA-mediated maternal transcript targeting is a conserved process in insects, but the number and sequences of microRNAs involved have diverged. The expression of fast-evolving and species-specific microRNAs in the early blastoderm of T. castaneum is consistent with previous findings in Drosophila and shows that the unique permissiveness for microRNA innovation at this stage is a conserved phenomenon.},
}
@article {pmid26518480,
year = {2016},
author = {Keith, N and Tucker, AE and Jackson, CE and Sung, W and Lucas Lledó, JI and Schrider, DR and Schaack, S and Dudycha, JL and Ackerman, M and Younge, AJ and Shaw, JR and Lynch, M},
title = {High mutational rates of large-scale duplication and deletion in Daphnia pulex.},
journal = {Genome research},
volume = {26},
number = {1},
pages = {60-69},
doi = {10.1101/gr.191338.115},
pmid = {26518480},
issn = {1549-5469},
support = {R01GM036827/GM/NIGMS NIH HHS/United States ; R01 GM101672/GM/NIGMS NIH HHS/United States ; R01ES019324/ES/NIEHS NIH HHS/United States ; R01 GM036827/GM/NIGMS NIH HHS/United States ; R01GM101672-01A1/GM/NIGMS NIH HHS/United States ; R01 ES019324/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; DNA Copy Number Variations ; Daphnia/*genetics ; Evolution, Molecular ; Female ; *Gene Deletion ; *Gene Duplication ; Genetic Association Studies ; Genetic Variation ; Heterozygote ; Male ; *Mutation Rate ; Sequence Analysis, DNA ; },
abstract = {Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. pulex can be propagated ameiotically while maintaining a naturally heterozygous, diploid genome, allowing the capture of the full spectrum of genomic changes that arise in a heterozygous state. While base-substitution mutation rates are similar to those in other multicellular eukaryotes (about 4 × 10(-9) per site per generation), we find that the rates of large-scale (>100 kb) de novo copy-number variants (CNVs) are significantly elevated relative to those seen in previous MA studies. The heterozygosity maintained in this experiment allowed for estimates of gene-conversion processes. While most of the conversion tract lengths we report are similar to those generated by meiotic processes, we also find larger tract lengths that are indicative of mitotic processes. Comparison of MA lines to natural isolates reveals that a majority of large-scale CNVs in natural populations are removed by purifying selection. The mutations observed here share similarities with disease-causing, complex, large-scale CNVs, thereby demonstrating that MA studies in D. pulex serve as a system for studying the processes leading to such alterations.},
}
@article {pmid26501252,
year = {2015},
author = {Tan, DX and Manchester, LC and Esteban-Zubero, E and Zhou, Z and Reiter, RJ},
title = {Melatonin as a Potent and Inducible Endogenous Antioxidant: Synthesis and Metabolism.},
journal = {Molecules (Basel, Switzerland)},
volume = {20},
number = {10},
pages = {18886-18906},
doi = {10.3390/molecules201018886},
pmid = {26501252},
issn = {1420-3049},
mesh = {Animals ; Antioxidants/*metabolism ; Biosynthetic Pathways ; Humans ; Melatonin/*biosynthesis ; Oxidative Stress ; Reactive Nitrogen Species/metabolism ; Reactive Oxygen Species/metabolism ; },
abstract = {Melatonin is a tryptophan-derived molecule with pleiotropic activities. It is present in almost all or all organisms. Its synthetic pathway depends on the species in which it is measured. For example, the tryptophan to melatonin pathway differs in plants and animals. It is speculated that the melatonin synthetic machinery in eukaryotes was inherited from bacteria as a result of endosymbiosis. However, melatonin's synthetic mechanisms in microorganisms are currently unknown. Melatonin metabolism is highly complex with these enzymatic processes having evolved from cytochrome C. In addition to its enzymatic degradation, melatonin is metabolized via pseudoenzymatic and free radical interactive processes. The metabolic products of these processes overlap and it is often difficult to determine which process is dominant. However, under oxidative stress, the free radical interactive pathway may be featured over the others. Because of the complexity of the melatonin degradative processes, it is expected that additional novel melatonin metabolites will be identified in future investigations. The original and primary function of melatonin in early life forms such as in unicellular organisms was as a free radical scavenger and antioxidant. During evolution, melatonin was selected as a signaling molecule to transduce the environmental photoperiodic information into an endocrine message in multicellular organisms and for other purposes as well. As an antioxidant, melatonin exhibits several unique features which differ from the classic antioxidants. These include its cascade reaction with free radicals and its capacity to be induced under moderate oxidative stress. These features make melatonin a potent endogenously-occurring antioxidant that protects organisms from catastrophic oxidative stress.},
}
@article {pmid26497146,
year = {2015},
author = {Gutzwiller, F and Carmo, CR and Miller, DE and Rice, DW and Newton, IL and Hawley, RS and Teixeira, L and Bergman, CM},
title = {Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle.},
journal = {G3 (Bethesda, Md.)},
volume = {5},
number = {12},
pages = {2843-2856},
doi = {10.1534/g3.115.021931},
pmid = {26497146},
issn = {2160-1836},
support = {BB/L002817/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Cluster Analysis ; Computational Biology ; Drosophila melanogaster/*growth &amp; development/microbiology ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/genetics ; Life Cycle Stages ; Phylogeny ; Stress, Physiological/genetics ; Symbiosis ; Transcriptome ; Wolbachia/*genetics ; },
abstract = {Symbiotic interactions between microbes and their multicellular hosts have manifold biological consequences. To better understand how bacteria maintain symbiotic associations with animal hosts, we analyzed genome-wide gene expression for the endosymbiotic α-proteobacteria Wolbachia pipientis across the entire life cycle of Drosophila melanogaster. We found that the majority of Wolbachia genes are expressed stably across the D. melanogaster life cycle, but that 7.8% of Wolbachia genes exhibit robust stage- or sex-specific expression differences when studied in the whole-organism context. Differentially-expressed Wolbachia genes are typically up-regulated after Drosophila embryogenesis and include many bacterial membrane, secretion system, and ankyrin repeat-containing proteins. Sex-biased genes are often organized as small operons of uncharacterized genes and are mainly up-regulated in adult Drosophila males in an age-dependent manner. We also systematically investigated expression levels of previously-reported candidate genes thought to be involved in host-microbe interaction, including those in the WO-A and WO-B prophages and in the Octomom region, which has been implicated in regulating bacterial titer and pathogenicity. Our work provides comprehensive insight into the developmental dynamics of gene expression for a widespread endosymbiont in its natural host context, and shows that public gene expression data harbor rich resources to probe the functional basis of the Wolbachia-Drosophila symbiosis and annotate the transcriptional outputs of the Wolbachia genome.},
}
@article {pmid26486321,
year = {2016},
author = {Wagner, GP},
title = {What is &quot;homology thinking&quot; and what is it for?.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {326},
number = {1},
pages = {3-8},
doi = {10.1002/jez.b.22656},
pmid = {26486321},
issn = {1552-5015},
mesh = {Animals ; *Biological Evolution ; Developmental Biology ; Genetics, Population ; Models, Biological ; Phenotype ; Phylogeny ; },
abstract = {In this paper I examine the thesis by Marc Ereshefsky that, in evolutionary biology, there is a third style of thinking, besides the well-known &quot;population thinking&quot; and &quot;tree thinking.&quot; Ereshefsky proposes &quot;homology thinking&quot; as a third approach, focused on the transformation of organismal phenotypes. In this short commentary, I aim at identifying the underlying biological assumptions for homology thinking and how they can be put to work in a research program within evolutionary biology. I propose that homology thinking is based on three insights: 1) multicellular organisms consist of developmentally individualized parts (sub-systems); 2) that developmental individuation entails evolutionary individuation, that is, variational quasi-independence; and 3) these individuated body parts are inherited, though indirectly, and form lineages that are recognized as homologies. These facts support a research program focused on the modification and origination of individuated body parts that supplements and puts into perspective the population genetic and phylogenetic approaches to the study of evolution.},
}
@article {pmid26465111,
year = {2015},
author = {de Mendoza, A and Suga, H and Permanyer, J and Irimia, M and Ruiz-Trillo, I},
title = {Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals.},
journal = {eLife},
volume = {4},
number = {},
pages = {e08904},
doi = {10.7554/eLife.08904},
pmid = {26465111},
issn = {2050-084X},
support = {206883//European Research Council/International ; 616960//European Research Council/International ; },
mesh = {Animals ; *Cell Differentiation ; *Gene Expression Regulation ; Mesomycetozoea/*genetics/growth &amp; development/*physiology ; Proteome/analysis ; },
abstract = {Cell-type specification through differential genome regulation is a hallmark of complex multicellularity. However, it remains unclear how this process evolved during the transition from unicellular to multicellular organisms. To address this question, we investigated transcriptional dynamics in the ichthyosporean Creolimax fragrantissima, a relative of animals that undergoes coenocytic development. We find that Creolimax utilizes dynamic regulation of alternative splicing, long inter-genic non-coding RNAs and co-regulated gene modules associated with animal multicellularity in a cell-type specific manner. Moreover, our study suggests that the different cell types of the three closest animal relatives (ichthyosporeans, filastereans and choanoflagellates) are the product of lineage-specific innovations. Additionally, a proteomic survey of the secretome reveals adaptations to a fungal-like lifestyle. In summary, the diversity of cell types among protistan relatives of animals and their complex genome regulation demonstrates that the last unicellular ancestor of animals was already capable of elaborate specification of cell types.},
}
@article {pmid26462996,
year = {2015},
author = {Kin, K},
title = {Inferring cell type innovations by phylogenetic methods-concepts, methods, and limitations.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {324},
number = {8},
pages = {653-661},
doi = {10.1002/jez.b.22657},
pmid = {26462996},
issn = {1552-5015},
mesh = {Animals ; *Biological Evolution ; Cell Differentiation/genetics ; Cell Lineage/genetics ; *Cells/classification/cytology ; Embryonic Development ; Gene Regulatory Networks ; *Phylogeny ; },
abstract = {Multicellular organisms are composed of distinct cell types that have specific roles in the body. Each cell type is a product of two kinds of historical processes-development and evolution. Although the concept of a cell type is difficult to define, the cell type concept based on the idea of the core regulatory network (CRN), a gene regulatory network that determines the identity of a cell type, illustrates the essential aspects of the cell type concept. The first step toward elucidating cell type evolution is to reconstruct the evolutionary relationships of cell types, or the cell type tree. The sister cell type model assumes that a new cell type evolves through divergence from a multifunctional ancestral cell type, creating tree-like evolutionary relationships between cell types. The process of generating a cell type tree can also be understood as the sequential addition of a new branching point on an ancestral cell differentiation hierarchy in evolution. A cell type tree thus represents an intertwined history of cell type evolution and development. Cell type trees can be reconstructed from high-throughput sequencing data, and the reconstruction of a cell type tree leads to the discovery of genes that are functionally important for a cell type. Although many issues including the lack of cross-species comparisons and the lack of a proper model for cell type evolution remain, the study of the origin of a new cell type using phylogenetic methods offers a promising new research avenue in developmental evolution. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 653-661, 2015. © 2015 Wiley Periodicals, Inc.},
}
@article {pmid26439347,
year = {2015},
author = {Butterfield, NJ},
title = {The Neoproterozoic.},
journal = {Current biology : CB},
volume = {25},
number = {19},
pages = {R859-63},
doi = {10.1016/j.cub.2015.07.021},
pmid = {26439347},
issn = {1879-0445},
mesh = {Archaea/physiology ; Bacterial Physiological Phenomena ; *Biological Evolution ; Earth (Planet) ; Eukaryota/physiology ; *Evolution, Planetary ; Fossils/anatomy &amp; histology ; },
abstract = {The Neoproterozoic era was arguably the most revolutionary in Earth history. Extending from 1000 to 541 million years ago, it stands at the intersection of the two great tracts of evolutionary time: on the one side, some three billion years of pervasively microbial 'Precambrian' life, and on the other the modern 'Phanerozoic' biosphere with its extraordinary diversity of large multicellular organisms. The disturbance doesn't stop here, however: over this same stretch of time the planet itself was in the throes of change. Tectonically, it saw major super-continental reconfigurations, climatically its deepest ever glacial freeze, and geochemically some of the most anomalous perturbations on record. What lies behind this dramatic convergence of biological and geological phenomena, and how exactly did it give rise to the curiously complex world that we now inhabit?},
}
@article {pmid26431572,
year = {2015},
author = {Shklover, J and Levy-Adam, F and Kurant, E},
title = {Apoptotic Cell Clearance in Development.},
journal = {Current topics in developmental biology},
volume = {114},
number = {},
pages = {297-334},
doi = {10.1016/bs.ctdb.2015.07.024},
pmid = {26431572},
issn = {1557-8933},
mesh = {Animals ; Apoptosis/*physiology ; Caenorhabditis elegans/cytology/growth &amp; development ; Caspases/metabolism ; Central Nervous System/cytology/*growth &amp; development ; Drosophila melanogaster/cytology/growth &amp; development ; Mice ; Neuroglia/cytology ; Phagocytes/*cytology/physiology ; Phagocytosis ; Signal Transduction ; Zebrafish/growth &amp; development ; },
abstract = {Programmed cell death and its specific form apoptosis play an important role during development of multicellular organisms. They are crucial for morphogenesis and organ sculpting as well as for adjusting cell number in different systems. Removal of apoptotic cells is the last critical step of apoptosis. Apoptotic cells are properly and efficiently recognized and eliminated through phagocytosis, which is performed by professional and nonprofessional phagocytes. Phagocytosis of apoptotic cells or apoptotic cell clearance is a dynamic multistep process, involving interactions between phagocytic receptors and ligands on apoptotic cells, which are highly conserved in evolution. However, this process is extremely redundant in mammals, containing multiple factors playing similar roles in the process. Using model organisms such as Caenorhabditis elegans, Drosophila melanogaster, zebrafish, and mouse permits addressing fundamental questions in developmental cell clearance by a comprehensive approach including powerful genetics and cell biological tools enriched by live imaging. Recent studies in model organisms have enhanced significantly our understanding of the molecular and cellular basis of apoptotic cell clearance during development. Here, we review the current knowledge and illuminate the great potential of the research performed in genetic models, which opens new directions in developmental biology.},
}
@article {pmid26423844,
year = {2015},
author = {Drobnitch, ST and Jensen, KH and Prentice, P and Pittermann, J},
title = {Convergent evolution of vascular optimization in kelp (Laminariales).},
journal = {Proceedings. Biological sciences},
volume = {282},
number = {1816},
pages = {20151667},
doi = {10.1098/rspb.2015.1667},
pmid = {26423844},
issn = {1471-2954},
mesh = {*Biological Evolution ; Macrocystis/growth &amp; development/*physiology ; Models, Biological ; },
abstract = {Terrestrial plants and mammals, although separated by a great evolutionary distance, have each arrived at a highly conserved body plan in which universal allometric scaling relationships govern the anatomy of vascular networks and key functional metabolic traits. The universality of allometric scaling suggests that these phyla have each evolved an 'optimal' transport strategy that has been overwhelmingly adopted by extant species. To truly evaluate the dominance and universality of vascular optimization, however, it is critical to examine other, lesser-known, vascularized phyla. The brown algae (Phaeophyceae) are one such group--as distantly related to plants as mammals, they have convergently evolved a plant-like body plan and a specialized phloem-like transport network. To evaluate possible scaling and optimization in the kelp vascular system, we developed a model of optimized transport anatomy and tested it with measurements of the giant kelp, Macrocystis pyrifera, which is among the largest and most successful of macroalgae. We also evaluated three classical allometric relationships pertaining to plant vascular tissues with a diverse sampling of kelp species. Macrocystis pyrifera displays strong scaling relationships between all tested vascular parameters and agrees with our model; other species within the Laminariales display weak or inconsistent vascular allometries. The lack of universal scaling in the kelps and the presence of optimized transport anatomy in M. pyrifera raises important questions about the evolution of optimization and the possible competitive advantage conferred by optimized vascular systems to multicellular phyla.},
}
@article {pmid26416251,
year = {2015},
author = {Haug, JT and Labandeira, CC and Santiago-Blay, JA and Haug, C and Brown, S},
title = {Life habits, hox genes, and affinities of a 311 million-year-old holometabolan larva.},
journal = {BMC evolutionary biology},
volume = {15},
number = {},
pages = {208},
doi = {10.1186/s12862-015-0428-8},
pmid = {26416251},
issn = {1471-2148},
mesh = {Animals ; Biological Evolution ; Eye/anatomy &amp; histology ; *Fossils ; Genes, Homeobox ; Head/anatomy &amp; histology ; Insecta/*anatomy &amp; histology/*genetics/growth &amp; development/physiology ; Larva/anatomy &amp; histology/genetics/physiology ; Phylogeny ; },
abstract = {BACKGROUND: Holometabolous insects are the most diverse, speciose and ubiquitous group of multicellular organisms in terrestrial and freshwater ecosystems. The enormous evolutionary and ecological success of Holometabola has been attributed to their unique postembryonic life phases in which nonreproductive and wingless larvae differ significantly in morphology and life habits from their reproductive and mostly winged adults, separated by a resting stage, the pupa. Little is known of the evolutionary developmental mechanisms that produced the holometabolous larval condition and their Paleozoic origin based on fossils and phylogeny.<br><br>RESULTS: We provide a detailed anatomic description of a 311 million-year-old specimen, the oldest known holometabolous larva, from the Mazon Creek deposits of Illinois, U.S.A. The head is ovoidal, downwardly oriented, broadly attached to the anterior thorax, and bears possible simple eyes and antennae with insertions encircled by molting sutures; other sutures are present but often indistinct. Mouthparts are generalized, consisting of five recognizable segments: a clypeo-labral complex, mandibles, possible hypopharynx, a maxilla bearing indistinct palp-like appendages, and labium. Distinctive mandibles are robust, triangular, and dicondylic. The thorax is delineated into three, nonoverlapping regions of distinctive surface texture, each with legs of seven elements, the terminal-most bearing paired claws. The abdomen has ten segments deployed in register with overlapping tergites; the penultimate segment bears a paired, cercus-like structure. The anterior eight segments bear clawless leglets more diminutive than the thoracic legs in length and cross-sectional diameter, and inserted more ventrolaterally than ventrally on the abdominal sidewall.<br><br>CONCLUSIONS: Srokalarva berthei occurred in an evolutionary developmental context likely responsible for the early macroevolutionary success of holometabolous insects. Srokalarva berthei bore head and prothoracic structures, leglet series on successive abdominal segments - in addition to comparable features on a second taxon eight million-years-younger - that indicates Hox-gene regulation of segmental and appendage patterning among earliest Holometabola. Srokalarva berthei body features suggest a caterpillar-like body plan and head structures indicating herbivory consistent with known, contemporaneous insect feeding damage on seed plants. Taxonomic resolution places Srokalarva berthei as an extinct lineage, apparently possessing features closer to neuropteroid than other holometabolous lineages.},
}
@article {pmid26385555,
year = {2016},
author = {Górz, A and Boroń, P},
title = {The Yeast Fungus Trichosporon lactis Found as an Epizoic Colonizer of Dung Beetle Exoskeletons.},
journal = {Microbial ecology},
volume = {71},
number = {2},
pages = {422-427},
doi = {10.1007/s00248-015-0674-8},
pmid = {26385555},
issn = {1432-184X},
mesh = {Animal Shells/*microbiology ; Animals ; Coleoptera/*microbiology ; Phylogeny ; Trichosporon/classification/genetics/growth &amp; development/*isolation &amp; purification ; },
abstract = {The study on the biology and biodiversity of coprophagous Scarabaeoidea carried out in the Polish Carpathians revealed the occurrence of unusual epizoic excrescences on various dung beetles species of the genus Onthophagus. The excrescences occur on the elytra, prothorax, and head of the studied beetles. Detailed research on this phenomenon determined that the fungus grew in the form of multicellular thalli. The ITS-based identification of fungal material collected from beetles' exoskeletons resulted in a 100 % match with Trichosporon lactis. Until now, only a yeast lifestyle/stage was known for this basidiomycete species. Therefore, in this paper, we describe a new substrate for growth of T. lactis and its unknown and intriguing relationship with dung beetles. The results obtained in this study open up numerous research possibilities on the new role of dung beetles in terrestrial ecosystems, as well as on using the physiological properties of T. lactis to restore soils.},
}
@article {pmid26381745,
year = {2015},
author = {Salali, GD and Whitehouse, H and Hochberg, ME},
title = {A Life-Cycle Model of Human Social Groups Produces a U-Shaped Distribution in Group Size.},
journal = {PloS one},
volume = {10},
number = {9},
pages = {e0138496},
doi = {10.1371/journal.pone.0138496},
pmid = {26381745},
issn = {1932-6203},
mesh = {*Cultural Evolution ; *Group Processes ; Humans ; *Models, Theoretical ; *Social Behavior ; *Social Environment ; },
abstract = {One of the central puzzles in the study of sociocultural evolution is how and why transitions from small-scale human groups to large-scale, hierarchically more complex ones occurred. Here we develop a spatially explicit agent-based model as a first step towards understanding the ecological dynamics of small and large-scale human groups. By analogy with the interactions between single-celled and multicellular organisms, we build a theory of group lifecycles as an emergent property of single cell demographic and expansion behaviours. We find that once the transition from small-scale to large-scale groups occurs, a few large-scale groups continue expanding while small-scale groups gradually become scarcer, and large-scale groups become larger in size and fewer in number over time. Demographic and expansion behaviours of groups are largely influenced by the distribution and availability of resources. Our results conform to a pattern of human political change in which religions and nation states come to be represented by a few large units and many smaller ones. Future enhancements of the model should include decision-making rules and probabilities of fragmentation for large-scale societies. We suggest that the synthesis of population ecology and social evolution will generate increasingly plausible models of human group dynamics.},
}
@article {pmid26373338,
year = {2015},
author = {Pascoe, B and Méric, G and Murray, S and Yahara, K and Mageiros, L and Bowen, R and Jones, NH and Jeeves, RE and Lappin-Scott, HM and Asakura, H and Sheppard, SK},
title = {Enhanced biofilm formation and multi-host transmission evolve from divergent genetic backgrounds in Campylobacter jejuni.},
journal = {Environmental microbiology},
volume = {17},
number = {11},
pages = {4779-4789},
doi = {10.1111/1462-2920.13051},
pmid = {26373338},
issn = {1462-2920},
support = {//Wellcome Trust/United Kingdom ; 088786/C09/Z//Wellcome Trust/United Kingdom ; BB/I02464X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1//Medical Research Council/United Kingdom ; },
mesh = {Biofilms/*growth &amp; development ; Biological Evolution ; Campylobacter jejuni/classification/*genetics/isolation &amp; purification ; *Genetic Background ; Genetic Variation/*genetics ; Genome-Wide Association Study ; Humans ; Oxygen/metabolism ; },
abstract = {Multicellular biofilms are an ancient bacterial adaptation that offers a protective environment for survival in hostile habitats. In microaerophilic organisms such as Campylobacter, biofilms play a key role in transmission to humans as the bacteria are exposed to atmospheric oxygen concentrations when leaving the reservoir host gut. Genetic determinants of biofilm formation differ between species, but little is known about how strains of the same species achieve the biofilm phenotype with different genetic backgrounds. Our approach combines genome-wide association studies with traditional microbiology techniques to investigate the genetic basis of biofilm formation in 102 Campylobacter jejuni isolates. We quantified biofilm formation among the isolates and identified hotspots of genetic variation in homologous sequences that correspond to variation in biofilm phenotypes. Thirteen genes demonstrated a statistically robust association including those involved in adhesion, motility, glycosylation, capsule production and oxidative stress. The genes associated with biofilm formation were different in the host generalist ST-21 and ST-45 clonal complexes, which are frequently isolated from multiple host species and clinical samples. This suggests the evolution of enhanced biofilm from different genetic backgrounds and a possible role in colonization of multiple hosts and transmission to humans.},
}
@article {pmid26370559,
year = {2015},
author = {Baskaran, P and Rödelsperger, C and Prabh, N and Serobyan, V and Markov, GV and Hirsekorn, A and Dieterich, C},
title = {Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus.},
journal = {BMC evolutionary biology},
volume = {15},
number = {},
pages = {185},
doi = {10.1186/s12862-015-0466-2},
pmid = {26370559},
issn = {1471-2148},
mesh = {Animals ; Biological Evolution ; Caenorhabditis elegans/genetics ; *Gene Duplication ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Library ; Larva/growth &amp; development ; Multigene Family ; Nematoda/*genetics/growth &amp; development ; Phylogeny ; },
abstract = {BACKGROUND: The development of multicellular organisms is accompanied by gene expression changes in differentiating cells. Profiling stage-specific expression during development may reveal important insights into gene sets that contributed to the morphological diversity across the animal kingdom.<br><br>RESULTS: We sequenced RNA-seq libraries throughout a developmental timecourse of the nematode Pristionchus pacificus. The transcriptomes reflect early larval stages, adult worms including late larvae, and growth-arrested dauer larvae and allowed the identification of developmentally regulated gene clusters. Our data reveals similar trends as previous transcriptome profiling of dauer worms and represents the first expression data for early larvae in P. pacificus. Gene expression clusters characterizing early larval stages show most significant enrichments of chaperones, while collagens are most significantly enriched in transcriptomes of late larvae and adult worms. By combining expression data with phylogenetic analysis, we found that developmentally regulated genes are found in paralogous clusters that have arisen through lineage-specific duplications after the split from the Caenorhabditis elegans branch.<br><br>CONCLUSIONS: We propose that gene duplications of developmentally regulated genes represent a plausible evolutionary mechanism to increase the dosage of stage-specific expression. Consequently, this may contribute to the substantial divergence in expression profiles that has been observed across larger evolutionary time scales.},
}
@article {pmid26347030,
year = {2015},
author = {Long, A and Liti, G and Luptak, A and Tenaillon, O},
title = {Elucidating the molecular architecture of adaptation via evolve and resequence experiments.},
journal = {Nature reviews. Genetics},
volume = {16},
number = {10},
pages = {567-582},
doi = {10.1038/nrg3937},
pmid = {26347030},
issn = {1471-0064},
support = {310944//European Research Council/International ; R01 GM094929/GM/NIGMS NIH HHS/United States ; },
mesh = {Adaptation, Physiological/*genetics ; Animals ; Bacteria/genetics ; Biological Evolution ; Drosophila melanogaster/genetics ; Epistasis, Genetic ; Evolution, Molecular ; Genetics, Microbial/methods ; Genetics, Population/*methods ; High-Throughput Nucleotide Sequencing ; Mutation ; RNA Folding ; *Selection, Genetic ; },
abstract = {Evolve and resequence (E&amp;R) experiments use experimental evolution to adapt populations to a novel environment, then next-generation sequencing to analyse genetic changes. They enable molecular evolution to be monitored in real time on a genome-wide scale. Here, we review the field of E&amp;R experiments across diverse systems, ranging from simple non-living RNA to bacteria, yeast and the complex multicellular organism Drosophila melanogaster. We explore how different evolutionary outcomes in these systems are largely consistent with common population genetics principles. Differences in outcomes across systems are largely explained by different starting population sizes, levels of pre-existing genetic variation, recombination rates and adaptive landscapes. We highlight emerging themes and inconsistencies that future experiments must address.},
}
@article {pmid26333839,
year = {2015},
author = {Lorin, T and Salzburger, W and Böhne, A},
title = {Evolutionary Fate of the Androgen Receptor-Signaling Pathway in Ray-Finned Fishes with a Special Focus on Cichlids.},
journal = {G3 (Bethesda, Md.)},
volume = {5},
number = {11},
pages = {2275-2283},
doi = {10.1534/g3.115.020685},
pmid = {26333839},
issn = {2160-1836},
mesh = {Animals ; Cichlids/*genetics ; *Evolution, Molecular ; Fish Proteins/*genetics/metabolism ; Gene Duplication ; Receptors, Androgen/*genetics/metabolism ; Selection, Genetic ; Signal Transduction ; },
abstract = {The emergence of the steroid system is coupled to the evolution of multicellular animals. In vertebrates in particular, the steroid receptor repertoire has been shaped by genome duplications characteristic to this lineage. Here, we investigate for the first time the composition of the androgen receptor-signaling pathway in ray-finned fish genomes by focusing in particular on duplicates that emerged from the teleost-specific whole-genome duplication. We trace lineage- and species-specific duplications and gene losses for the genomic and nongenomic pathway of androgen signaling and subsequently investigate the sequence evolution of these genes. In one particular fish lineage, the cichlids, we find evidence for differing selection pressures acting on teleost-specific whole-genome duplication paralogs at a derived evolutionary stage. We then look into the expression of these duplicated genes in four cichlid species from Lake Tanganyika indicating, once more, rapid changes in expression patterns in closely related fish species. We focus on a particular case, the cichlid specific duplication of the rac1 GTPase, which shows possible signs of a neofunctionalization event.},
}
@article {pmid26315993,
year = {2015},
author = {Zhang, J and Debets, AJ and Verweij, PE and Melchers, WJ and Zwaan, BJ and Schoustra, SE},
title = {Asexual sporulation facilitates adaptation: The emergence of azole resistance in Aspergillus fumigatus.},
journal = {Evolution; international journal of organic evolution},
volume = {69},
number = {10},
pages = {2573-2586},
doi = {10.1111/evo.12763},
pmid = {26315993},
issn = {1558-5646},
mesh = {Adaptation, Biological/genetics ; Aspergillus fumigatus/*drug effects/*genetics ; Biological Evolution ; Drug Resistance, Multiple, Fungal/*genetics ; Fungicides, Industrial/*pharmacology ; Genes, Fungal ; *Mutation ; Reproduction, Asexual/*drug effects/*genetics ; *Selection, Genetic ; Triazoles/*pharmacology ; },
abstract = {Understanding the occurrence and spread of azole resistance in Aspergillus fumigatus is crucial for public health. It has been hypothesized that asexual sporulation, which is abundant in nature, is essential for phenotypic expression of azole resistance mutations in A. fumigatus facilitating subsequent spread through natural selection. Furthermore, the disease aspergilloma is associated with asexual sporulation within the lungs of patients and the emergence of azole resistance. This study assessed the evolutionary advantage of asexual sporulation by growing the fungus under pressure of one of five different azole fungicides over seven weeks and by comparing the rate of adaptation between scenarios of culturing with and without asexual sporulation. Results unequivocally show that asexual sporulation facilitates adaptation. This can be explained by the combination of more effective selection because of the transition from a multicellular to a unicellular stage, and by increased mutation supply due to the production of spores, which involves numerous mitotic divisions. Insights from this study are essential to unravel the resistance mechanisms of sporulating pathogens to chemical compounds and disease agents in general, and for designing strategies that prevent or overcome the emerging threat of azole resistance in particular.},
}
@article {pmid26311623,
year = {2015},
author = {Wegener Parfrey, L},
title = {Mock communities highlight the diversity of host-associated eukaryotes.},
journal = {Molecular ecology},
volume = {24},
number = {17},
pages = {4337-4339},
doi = {10.1111/mec.13311},
pmid = {26311623},
issn = {1365-294X},
mesh = {Animals ; Apicomplexa ; *Biodiversity ; Eukaryota ; *High-Throughput Nucleotide Sequencing ; Oligochaeta/microbiology ; *Soil Microbiology ; Symbiosis ; },
abstract = {Host-associated microbes are ubiquitous. Every multicellular eukaryote, and even many unicellular eukaryotes (protists), hosts a diverse community of microbes. High-throughput sequencing (HTS) tools have illuminated the vast diversity of host-associated microbes and shown that they have widespread influence on host biology, ecology and evolution (McFall-Ngai et al.). Bacteria receive most of the attention, but protists are also important components of microbial communities associated with humans (Parfrey et al.) and other hosts. As HTS tools are increasingly used to study eukaryotes, the presence of numerous and diverse host-associated eukaryotes is emerging as a common theme across ecosystems. Indeed, HTS studies demonstrate that host-associated lineages account for between 2 and 12% of overall eukaryotic sequences detected in soil, marine and freshwater data sets, with much higher relative abundances observed in some samples (Ramirez et al. ; Simon et al. ; de Vargas et al.). Previous studies in soil detected large numbers of predominantly parasitic lineages such as Apicomplexa, but did not delve into their origin [e.g. (Ramirez et al.)]. In this issue of Molecular Ecology, Geisen et al. () use mock communities to show that many of the eukaryotic organisms detected by environmental sequencing in soils are potentially associated with animal hosts rather than free-living. By isolating the host-associated fraction of soil microbial communities, Geisen and colleagues help explain the surprisingly high diversity of parasitic eukaryotic lineages often detected in soil/terrestrial studies using high-throughput sequencing (HTS) and reinforce the ubiquity of these host-associated microbes. It is clear that we can no longer assume that organisms detected in bulk environmental sequencing are free-living, but instead need to design studies that specifically enumerate the diversity and function of host-associated eukaryotes. Doing so will allow the field to determine the role host-associated eukaryotes play in soils and other environments and to evaluate hypotheses on assembly of host-associated communities, disease ecology and more.},
}
@article {pmid26307549,
year = {2015},
author = {McCormack, R and Podack, ER},
title = {Perforin-2/Mpeg1 and other pore-forming proteins throughout evolution.},
journal = {Journal of leukocyte biology},
volume = {98},
number = {5},
pages = {761-768},
doi = {10.1189/jlb.4MR1114-523RR},
pmid = {26307549},
issn = {1938-3673},
support = {F31AI106290/AI/NIAID NIH HHS/United States ; R56AI107062/AI/NIAID NIH HHS/United States ; R01 NR015649/NR/NINR NIH HHS/United States ; R01AI110810/AI/NIAID NIH HHS/United States ; R56 AI107062/AI/NIAID NIH HHS/United States ; F31 AI106290/AI/NIAID NIH HHS/United States ; R01 AI110810/AI/NIAID NIH HHS/United States ; R01NR015649/NR/NINR NIH HHS/United States ; },
mesh = {Animals ; Complement Membrane Attack Complex/*immunology ; *Evolution, Molecular ; Humans ; Membrane Proteins/*immunology ; Pore Forming Cytotoxic Proteins/*immunology ; Protein Structure, Tertiary ; },
abstract = {Development of the ancient innate immune system required not only a mechanism to recognize foreign organisms from self but also to destroy them. Pore-forming proteins containing the membrane attack complex Perforin domain were one of the first triumphs of an innate immune system needing to eliminate microbes and virally infected cells. Membrane attack complex of complement and Perforin domain proteins is unique from other immune effector molecules in that the mechanism of attack is strictly physical and unspecific. The large water-filled holes created by membrane attack complex of complement and Perforin domain pore formation allow access for additional effectors to complete the destruction of the foreign organism via chemical or enzymatic attack. Perforin-2/macrophage-expressed protein 1 is one of the oldest membrane attack complexes of complement and Perforin domain protein involved in immune defense, and it is still functional today in vertebrates. Here, we trace the impact of Perforin-2/macrophage-expressed protein 1 from the earliest multicellular organisms to modern vertebrates, as well as review the development of other membrane attack complexes of complement and Perforin domain member proteins.},
}
@article {pmid26293347,
year = {2015},
author = {Vázquez, E and Antequera, F},
title = {Replication dynamics in fission and budding yeasts through DNA polymerase tracking.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {37},
number = {10},
pages = {1067-1073},
doi = {10.1002/bies.201500072},
pmid = {26293347},
issn = {1521-1878},
mesh = {DNA ; *DNA Replication ; DNA, Fungal/metabolism ; DNA-Directed DNA Polymerase/analysis/*metabolism ; Genome, Fungal ; Genomic Instability ; Replication Origin ; Saccharomyces cerevisiae/genetics ; Saccharomycetales/*genetics ; Schizosaccharomyces/*genetics ; },
abstract = {The dynamics of eukaryotic DNA polymerases has been difficult to establish because of the difficulty of tracking them along the chromosomes during DNA replication. Recent work has addressed this problem in the yeasts Schizosaccharomyces pombe and Saccharomyces cerevisiae through the engineering of replicative polymerases to render them prone to incorporating ribonucleotides at high rates. Their use as tracers of the passage of each polymerase has provided a picture of unprecedented resolution of the organization of replicons and replication origins in the two yeasts and has uncovered important differences between them. Additional studies have found an overlapping distribution of DNA polymorphisms and the junctions of Okazaki fragments along mononucleosomal DNA. This sequence instability is caused by the premature release of polymerase δ and the retention of non proof-read DNA tracts replicated by polymerase α. The possible implementation of these new experimental approaches in multicellular organisms opens the door to the analysis of replication dynamics under a broad range of genetic backgrounds and physiological or pathological conditions.},
}
@article {pmid26284972,
year = {2015},
author = {Du, Q and Kawabe, Y and Schilde, C and Chen, ZH and Schaap, P},
title = {The Evolution of Aggregative Multicellularity and Cell-Cell Communication in the Dictyostelia.},
journal = {Journal of molecular biology},
volume = {427},
number = {23},
pages = {3722-3733},
doi = {10.1016/j.jmb.2015.08.008},
pmid = {26284972},
issn = {1089-8638},
support = {100293//Wellcome Trust/United Kingdom ; 100293/Z/12/Z//Wellcome Trust/United Kingdom ; BB/K000799/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Biological Evolution ; Cyclic AMP/genetics/*metabolism ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Cyclic GMP/analogs &amp; derivatives/metabolism ; Dictyostelium/metabolism/*physiology ; Genome, Protozoan ; Genomics/methods ; Hexanones/metabolism ; Histidine Kinase ; Protein Kinases/metabolism ; Protozoan Proteins/genetics/*metabolism ; Quorum Sensing ; Signal Transduction ; },
abstract = {Aggregative multicellularity, resulting in formation of a spore-bearing fruiting body, evolved at least six times independently amongst both eukaryotes and prokaryotes. Amongst eukaryotes, this form of multicellularity is mainly studied in the social amoeba Dictyostelium discoideum. In this review, we summarise trends in the evolution of cell-type specialisation and behavioural complexity in the four major groups of Dictyostelia. We describe the cell-cell communication systems that control the developmental programme of D. discoideum, highlighting the central role of cAMP in the regulation of cell movement and cell differentiation. Comparative genomic studies showed that the proteins involved in cAMP signalling are deeply conserved across Dictyostelia and their unicellular amoebozoan ancestors. Comparative functional analysis revealed that cAMP signalling in D. discoideum originated from a second messenger role in amoebozoan encystation. We highlight some molecular changes in cAMP signalling genes that were responsible for the novel roles of cAMP in multicellular development.},
}
@article {pmid26268215,
year = {2015},
author = {Burgess, AL and David, R and Searle, IR},
title = {Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae.},
journal = {BMC plant biology},
volume = {15},
number = {},
pages = {199},
doi = {10.1186/s12870-015-0580-8},
pmid = {26268215},
issn = {1471-2229},
mesh = {5-Methylcytosine/*metabolism ; Cell Nucleus/genetics ; Chloroplasts/genetics ; *Evolution, Molecular ; Methylation ; Methyltransferases/genetics ; Mitochondria/genetics ; Phylogeny ; Plants/*genetics/metabolism ; RNA, Transfer/*genetics/metabolism ; RNA, Untranslated/genetics ; Transcriptome ; },
abstract = {BACKGROUND: Post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m(5)C) is an important modification that regulates RNA metabolism and occurs in both eukaryotes and prokaryotes. Yet, to date, no transcriptome-wide identification of m(5)C sites has been undertaken in plants. Plants provide a unique comparative system for investigating the origin and evolution of m(5)C as they contain three different genomes, the nucleus, mitochondria and chloroplast. Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m(5)C sites in non-coding ribosomal RNAs and transfer RNAs of all three sub-cellular transcriptomes across six diverse species that included, the single-celled algae Nannochloropsis oculata, the macro algae Caulerpa taxifolia and multi-cellular higher plants Arabidopsis thaliana, Brassica rapa, Triticum durum and Ginkgo biloba.<br><br>RESULTS: Using the plant model Arabidopsis thaliana, we identified a total of 39 highly methylated m(5)C sites in predicted structural positions of nuclear tRNAs and 7 m(5)C sites in rRNAs from nuclear, chloroplast and mitochondrial transcriptomes. Both the nucleotide position and percent methylation of tRNAs and rRNAs m(5)C sites were conserved across all species analysed, from single celled algae N. oculata to multicellular plants. Interestingly the mitochondrial and chloroplast encoded tRNAs were devoid of m(5)C in A. thaliana and this is generally conserved across Plantae. This suggests independent evolution of organelle methylation in animals and plants, as animal mitochondrial tRNAs have m(5)C sites. Here we characterize 5 members of the RNA 5-methylcytosine family in Arabidopsis and extend the functional characterization of TRDMT1 and NOP2A/OLI2. We demonstrate that nuclear tRNA methylation requires two evolutionarily conserved methyltransferases, TRDMT1 and TRM4B. trdmt1 trm4b double mutants are hypersensitive to the antibiotic hygromycin B, demonstrating the function of tRNA methylation in regulating translation. Additionally we demonstrate that nuclear large subunit 25S rRNA methylation requires the conserved RNA methyltransferase NSUN5. Our results also suggest functional redundancy of at least two of the NOP2 paralogs in Arabidopsis.<br><br>CONCLUSIONS: Our data demonstrates widespread occurrence and conservation of non-coding RNA methylation in the kingdom Plantae, suggesting important and highly conserved roles of this post-transcriptional modification.},
}
@article {pmid26248158,
year = {2015},
author = {Palfree, RG and Bennett, HP and Bateman, A},
title = {The Evolution of the Secreted Regulatory Protein Progranulin.},
journal = {PloS one},
volume = {10},
number = {8},
pages = {e0133749},
doi = {10.1371/journal.pone.0133749},
pmid = {26248158},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Animals ; Databases, Genetic ; *Evolution, Molecular ; Fungi/metabolism ; Humans ; Intercellular Signaling Peptides and Proteins/chemistry/genetics/*metabolism ; Likelihood Functions ; Molecular Sequence Data ; Plants/metabolism ; Protein Structure, Tertiary ; Sequence Alignment ; },
abstract = {Progranulin is a secreted growth factor that is active in tumorigenesis, wound repair, and inflammation. Haploinsufficiency of the human progranulin gene, GRN, causes frontotemporal dementia. Progranulins are composed of chains of cysteine-rich granulin modules. Modules may be released from progranulin by proteolysis as 6kDa granulin polypeptides. Both intact progranulin and some of the granulin polypeptides are biologically active. The granulin module occurs in certain plant proteases and progranulins are present in early diverging metazoan clades such as the sponges, indicating their ancient evolutionary origin. There is only one Grn gene in mammalian genomes. More gene-rich Grn families occur in teleost fish with between 3 and 6 members per species including short-form Grns that have no tetrapod counterparts. Our goals are to elucidate progranulin and granulin module evolution by investigating (i): the origins of metazoan progranulins (ii): the evolutionary relationships between the single Grn of tetrapods and the multiple Grn genes of fish (iii): the evolution of granulin module architectures of vertebrate progranulins (iv): the conservation of mammalian granulin polypeptide sequences and how the conserved granulin amino acid sequences map to the known three dimensional structures of granulin modules. We report that progranulin-like proteins are present in unicellular eukaryotes that are closely related to metazoa suggesting that progranulin is among the earliest extracellular regulatory proteins still employed by multicellular animals. From the genomes of the elephant shark and coelacanth we identified contemporary representatives of a precursor for short-from Grn genes of ray-finned fish that is lost in tetrapods. In vertebrate Grns pathways of exon duplication resulted in a conserved module architecture at the amino-terminus that is frequently accompanied by an unusual pattern of tandem nearly identical module repeats near the carboxyl-terminus. Polypeptide sequence conservation of mammalian granulin modules identified potential structure-activity relationships that may be informative in designing progranulin based therapeutics.},
}
@article {pmid26247819,
year = {2015},
author = {Ferrante, E and Turgut, AE and Duéñez-Guzmán, E and Dorigo, M and Wenseleers, T},
title = {Evolution of Self-Organized Task Specialization in Robot Swarms.},
journal = {PLoS computational biology},
volume = {11},
number = {8},
pages = {e1004273},
doi = {10.1371/journal.pcbi.1004273},
pmid = {26247819},
issn = {1553-7358},
mesh = {Animals ; Ants/physiology ; *Artificial Intelligence ; *Biological Evolution ; Computational Biology ; *Models, Biological ; *Robotics/instrumentation/methods ; *Social Behavior ; Task Performance and Analysis ; Work ; },
abstract = {Division of labor is ubiquitous in biological systems, as evidenced by various forms of complex task specialization observed in both animal societies and multicellular organisms. Although clearly adaptive, the way in which division of labor first evolved remains enigmatic, as it requires the simultaneous co-occurrence of several complex traits to achieve the required degree of coordination. Recently, evolutionary swarm robotics has emerged as an excellent test bed to study the evolution of coordinated group-level behavior. Here we use this framework for the first time to study the evolutionary origin of behavioral task specialization among groups of identical robots. The scenario we study involves an advanced form of division of labor, common in insect societies and known as &quot;task partitioning&quot;, whereby two sets of tasks have to be carried out in sequence by different individuals. Our results show that task partitioning is favored whenever the environment has features that, when exploited, reduce switching costs and increase the net efficiency of the group, and that an optimal mix of task specialists is achieved most readily when the behavioral repertoires aimed at carrying out the different subtasks are available as pre-adapted building blocks. Nevertheless, we also show for the first time that self-organized task specialization could be evolved entirely from scratch, starting only from basic, low-level behavioral primitives, using a nature-inspired evolutionary method known as Grammatical Evolution. Remarkably, division of labor was achieved merely by selecting on overall group performance, and without providing any prior information on how the global object retrieval task was best divided into smaller subtasks. We discuss the potential of our method for engineering adaptively behaving robot swarms and interpret our results in relation to the likely path that nature took to evolve complex sociality and task specialization.},
}
@article {pmid26245677,
year = {2015},
author = {Yang, EC and Kim, KM and Kim, SY and Lee, J and Boo, GH and Lee, JH and Nelson, WA and Yi, G and Schmidt, WE and Fredericq, S and Boo, SM and Bhattacharya, D and Yoon, HS},
title = {Highly Conserved Mitochondrial Genomes among Multicellular Red Algae of the Florideophyceae.},
journal = {Genome biology and evolution},
volume = {7},
number = {8},
pages = {2394-2406},
doi = {10.1093/gbe/evv147},
pmid = {26245677},
issn = {1759-6653},
mesh = {Conserved Sequence ; *Evolution, Molecular ; *Genome, Mitochondrial ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Rhodophyta/classification/*genetics ; Synteny ; },
abstract = {Two red algal classes, the Florideophyceae (approximately 7,100 spp.) and Bangiophyceae (approximately 193 spp.), comprise 98% of red algal diversity in marine and freshwater habitats. These two classes form well-supported monophyletic groups in most phylogenetic analyses. Nonetheless, the interordinal relationships remain largely unresolved, in particular in the largest subclass Rhodymeniophycidae that includes 70% of all species. To elucidate red algal phylogenetic relationships and study organelle evolution, we determined the sequence of 11 mitochondrial genomes (mtDNA) from 5 florideophycean subclasses. These mtDNAs were combined with existing data, resulting in a database of 25 florideophytes and 12 bangiophytes (including cyanidiophycean species). A concatenated alignment of mt proteins was used to resolve ordinal relationships in the Rhodymeniophycidae. Red algal mtDNA genome comparisons showed 47 instances of gene rearrangement including 12 that distinguish Bangiophyceae from Hildenbrandiophycidae, and 5 that distinguish Hildenbrandiophycidae from Nemaliophycidae. These organelle data support a rapid radiation and surprisingly high conservation of mtDNA gene syntheny among the morphologically divergent multicellular lineages of Rhodymeniophycidae. In contrast, we find extensive mitochondrial gene rearrangements when comparing Bangiophyceae and Florideophyceae and multiple examples of gene loss among the different red algal lineages.},
}
@article {pmid26239915,
year = {2015},
author = {Sinkovics, JG},
title = {The cnidarian origin of the proto-oncogenes NF-κB/STAT and WNT-like oncogenic pathway drives the ctenophores (Review).},
journal = {International journal of oncology},
volume = {47},
number = {4},
pages = {1211-1229},
doi = {10.3892/ijo.2015.3102},
pmid = {26239915},
issn = {1791-2423},
mesh = {Animals ; Cnidaria/*physiology ; Ctenophora/*physiology ; Humans ; Lymphoma/*metabolism ; NF-kappa B/*metabolism ; Proto-Oncogenes/physiology ; Wnt Proteins/*metabolism ; Wnt Signaling Pathway/*physiology ; },
abstract = {The cell survival pathways of the diploblastic early multicellular eukaryotic hosts contain and operate the molecular machinery resembling those of malignantly transformed individual cells of highly advanced multicellular hosts (including Homo). In the present review, the STAT/NF-κB pathway of the cnidarian Nematostella vectensis is compared with that of human tumors (malignant lymphomas, including Reed-Sternberg cells) pointing out similarities, including possible viral initiation in both cases. In the ctenophore genome and proteome, β-catenin gains intranuclear advantages due to a physiologically weak destructive complex in the cytoplasm, and lack of natural inhibitors (the dickkopfs). Thus, a scenario similar to what tumor cells initiate and achieve is presented through several constitutive loss-of-function type mutations in the destructive complex and in the elimination of inhibitors. Vice versa, malignantly transformed individual cells of advanced multicellular hosts assume pheno-genotypic resemblance to cells of unicellular or early multicellular hosts, and presumably to their ancient predecessors, by returning to the semblance of immortality and to the resumption of the state of high degree of resistance to physicochemical insults. Human leukemogenic and oncogenic pathways are presented for comparisons. The supreme bioengineers RNA/DNA complex encoded both the malignantly transformed immortal cell and the human cerebral cortex. The former generates molecules for the immortality of cellular life in the Universe. The latter invents the inhibitors of the process in order to gain control over it.},
}
@article {pmid26216949,
year = {2015},
author = {Chen, L and Rashid, F and Shah, A and Awan, HM and Wu, M and Liu, A and Wang, J and Zhu, T and Luo, Z and Shan, G},
title = {The isolation of an RNA aptamer targeting to p53 protein with single amino acid mutation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {32},
pages = {10002-10007},
doi = {10.1073/pnas.1502159112},
pmid = {26216949},
issn = {1091-6490},
mesh = {Administration, Intravenous ; Amino Acid Substitution ; Amino Acids/*genetics ; Animals ; Aptamers, Nucleotide/*isolation &amp; purification ; Base Sequence ; Cell Proliferation ; Enzyme-Linked Immunosorbent Assay ; HEK293 Cells ; HeLa Cells ; Humans ; Mice ; Molecular Sequence Data ; Mutant Proteins/metabolism ; Mutation/*genetics ; Nanoparticles/chemistry ; Neoplasms/pathology ; SELEX Aptamer Technique ; Tumor Suppressor Protein p53/*genetics/*metabolism ; Xenograft Model Antitumor Assays ; },
abstract = {p53, known as a tumor suppressor, is a DNA binding protein that regulates cell cycle, activates DNA repair proteins, and triggers apoptosis in multicellular animals. More than 50% of human cancers contain a mutation or deletion of the p53 gene, and p53R175 is one of the hot spots of p53 mutation. Nucleic acid aptamers are short single-stranded oligonucleotides that are able to bind various targets, and they are typically isolated from an experimental procedure called systematic evolution of ligand exponential enrichment (SELEX). Using a previously unidentified strategy of contrast screening with SELEX, we have isolated an RNA aptamer targeting p53R175H. This RNA aptamer (p53R175H-APT) has a significantly stronger affinity to p53R175H than to the wild-type p53 in both in vitro and in vivo assays. p53R175H-APT decreased the growth rate, weakened the migration capability, and triggered apoptosis in human lung cancer cells harboring p53R175H. Further analysis actually indicated that p53R175H-APT might partially rescue or correct the p53R175H to function more like the wild-type p53. In situ injections of p53R175H-APT to the tumor xenografts confirmed the effects of this RNA aptamer on p53R175H mutation in mice.},
}
@article {pmid26206087,
year = {2016},
author = {Causeret, F and Sumia, I and Pierani, A},
title = {Kremen1 and Dickkopf1 control cell survival in a Wnt-independent manner.},
journal = {Cell death and differentiation},
volume = {23},
number = {2},
pages = {323-332},
doi = {10.1038/cdd.2015.100},
pmid = {26206087},
issn = {1476-5403},
mesh = {Animals ; Apoptosis ; Cell Survival ; Embryo Culture Techniques ; Evolution, Molecular ; HEK293 Cells ; Humans ; Intercellular Signaling Peptides and Proteins/*physiology ; Membrane Proteins/*physiology ; Mice ; Mutation ; Neoplasms/genetics ; Wnt Proteins/metabolism ; *Wnt Signaling Pathway ; },
abstract = {In multicellular organisms, a tight control of cell death is required to ensure normal development and tissue homeostasis. Improper function of apoptotic or survival pathways can not only affect developmental programs but also favor cancer progression. Here we describe a novel apoptotic signaling pathway involving the transmembrane receptor Kremen1 and its ligand, the Wnt-antagonist Dickkopf1. Using a whole embryo culture system, we first show that Dickkopf1 treatment promotes cell survival in a mouse model exhibiting increased apoptosis in the developing neural plate. Remarkably, this effect was not recapitulated by chemical Wnt inhibition. We then show that Dickkopf1 receptor Kremen1 is a bona fide dependence receptor, triggering cell death unless bound to its ligand. We performed Wnt-activity assays to demonstrate that the pro-apoptotic and anti-Wnt functions mediated by Kremen1 are strictly independent. Furthermore, we combined phylogenetic and mutagenesis approaches to identify a specific motif in the cytoplasmic tail of Kremen1, which is (i) specifically conserved in the lineage of placental mammals and (ii) strictly required for apoptosis induction. Finally, we show that somatic mutations of kremen1 found in human cancers can affect its pro-apoptotic activity, supporting a tumor suppressor function. Our findings thus reveal a new Wnt-independent function for Kremen1 and Dickkopf1 in the regulation of cell survival with potential implications in cancer therapies.},
}
@article {pmid26199361,
year = {2015},
author = {Nores, MJ and López, HA and Anton, AM and Rudall, PJ},
title = {Contrasting models of the female reproductive tract in four o'clocks (Nyctaginaceae).},
journal = {American journal of botany},
volume = {102},
number = {7},
pages = {1026-1039},
doi = {10.3732/ajb.1400521},
pmid = {26199361},
issn = {1537-2197},
mesh = {Biological Evolution ; Cluster Analysis ; Fertilization ; Flowers/genetics/*ultrastructure ; *Models, Structural ; Nyctaginaceae/genetics/*ultrastructure ; Pollen Tube/genetics/ultrastructure ; Pollination ; Reproduction ; Species Specificity ; },
abstract = {UNLABELLED: •<br><br>PREMISE OF THE STUDY: In angiosperms, several carpel tissues are specialized to facilitate pollen-tube elongation to achieve fertilization. We evaluated the possible evolutionary pathways of the diverse female reproductive tracts in Nyctaginaceae.•<br><br>METHODS: We studied the anatomy of a range of species representing different tribes, using light, fluorescence, scanning electron, and transmission electron microscopy.•<br><br>KEY RESULTS: Stigmas have multicellular, multiseriate papillae, except for Boerhavia diffusa with unicellular papillae. The styles are solid, with a strand of transmitting tissue linking the stigma with the ventral ovary wall. In Allionia, Boerhavia, and Mirabilis, the transmitting tissue branches into two independent tracts at the base of the ovary and continues across the lateral margins of the funicle to the micropyle; it is composed of cells with thick walls surrounded by abundant extracellular matrix. Bougainvillea, Pisonia, and Pisoniella have a diffuse transmitting tissue and an obturator, a proliferation of cells covered by a layer of secretory papillae that encloses the funicle, placenta, and ventral wall of the gynoecium and contacts with the micropyle.•<br><br>CONCLUSIONS: We propose two models of female reproductive tract, (A) one in which an obturator is absent and the transmitting tissue is compact and branched and (B) one in which an obturator is present and the transmitting tissue is diffuse. On the basis of character optimization, we hypothesize that model B represents the ancestral (plesiomorphic) condition in the family and model A originated once during evolution, within the tribe Nyctagineae.},
}
@article {pmid26198319,
year = {2015},
author = {Ramilowski, JA and Goldberg, T and Harshbarger, J and Kloppmann, E and Lizio, M and Satagopam, VP and Itoh, M and Kawaji, H and Carninci, P and Rost, B and Forrest, AR},
title = {A draft network of ligand-receptor-mediated multicellular signalling in human.},
journal = {Nature communications},
volume = {6},
number = {},
pages = {7866},
doi = {10.1038/ncomms8866},
pmid = {26198319},
issn = {2041-1723},
support = {U54 GM095315/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Cell Communication ; Evolution, Molecular ; Humans ; Ligands ; Receptors, Cell Surface/*metabolism ; Software ; },
abstract = {Cell-to-cell communication across multiple cell types and tissues strictly governs proper functioning of metazoans and extensively relies on interactions between secreted ligands and cell-surface receptors. Herein, we present the first large-scale map of cell-to-cell communication between 144 human primary cell types. We reveal that most cells express tens to hundreds of ligands and receptors to create a highly connected signalling network through multiple ligand-receptor paths. We also observe extensive autocrine signalling with approximately two-thirds of partners possibly interacting on the same cell type. We find that plasma membrane and secreted proteins have the highest cell-type specificity, they are evolutionarily younger than intracellular proteins, and that most receptors had evolved before their ligands. We provide an online tool to interactively query and visualize our networks and demonstrate how this tool can reveal novel cell-to-cell interactions with the prediction that mast cells signal to monoblastic lineages via the CSF1-CSF1R interacting pair.},
}
@article {pmid26195746,
year = {2015},
author = {Speijer, D and Lukeš, J and Eliáš, M},
title = {Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {29},
pages = {8827-8834},
doi = {10.1073/pnas.1501725112},
pmid = {26195746},
issn = {1091-6490},
mesh = {Cell Fusion ; Eukaryotic Cells/*physiology ; Genome ; Meiosis ; Mitochondria/metabolism ; Molecular Sequence Data ; Reactive Oxygen Species/metabolism ; *Reproduction ; Sequence Analysis, DNA ; },
abstract = {Sexual reproduction and clonality in eukaryotes are mostly seen as exclusive, the latter being rather exceptional. This view might be biased by focusing almost exclusively on metazoans. We analyze and discuss reproduction in the context of extant eukaryotic diversity, paying special attention to protists. We present results of phylogenetically extended searches for homologs of two proteins functioning in cell and nuclear fusion, respectively (HAP2 and GEX1), providing indirect evidence for these processes in several eukaryotic lineages where sex has not been observed yet. We argue that (i) the debate on the relative significance of sex and clonality in eukaryotes is confounded by not appropriately distinguishing multicellular and unicellular organisms; (ii) eukaryotic sex is extremely widespread and already present in the last eukaryotic common ancestor; and (iii) the general mode of existence of eukaryotes is best described by clonally propagating cell lines with episodic sex triggered by external or internal clues. However, important questions concern the relative longevity of true clonal species (i.e., species not able to return to sexual procreation anymore). Long-lived clonal species seem strikingly rare. We analyze their properties in the light of meiotic sex development from existing prokaryotic repair mechanisms. Based on these considerations, we speculate that eukaryotic sex likely developed as a cellular survival strategy, possibly in the context of internal reactive oxygen species stress generated by a (proto) mitochondrion. Thus, in the context of the symbiogenic model of eukaryotic origin, sex might directly result from the very evolutionary mode by which eukaryotic cells arose.},
}
@article {pmid26194954,
year = {2015},
author = {Wynns, AA},
title = {Convergent evolution of highly reduced fruiting bodies in Pezizomycotina suggests key adaptations to the bee habitat.},
journal = {BMC evolutionary biology},
volume = {15},
number = {},
pages = {145},
doi = {10.1186/s12862-015-0401-6},
pmid = {26194954},
issn = {1471-2148},
mesh = {Animals ; Ascomycota/*classification/genetics/*isolation &amp; purification/physiology ; Bees/microbiology/*physiology ; *Biological Evolution ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Phylogeny ; },
abstract = {BACKGROUND: Among the understudied fungi found in nature are those living in close association with social and solitary bees. The bee-specialist genera Bettsia, Ascosphaera and Eremascus are remarkable not only for their specialized niche but also for their simple fruiting bodies or ascocarps, which are morphologically anomalous in Pezizomycotina. Bettsia and Ascosphaera are characterized by a unicellular cyst-like cleistothecium known as a spore cyst, while Eremascus is characterized by completely naked asci, or asci not formed within a protective ascocarp. Before molecular phylogenetics the placement of these genera within Pezizomycotina remained tentative; morphological characters were misleading because they do not produce multicellular ascocarps, a defining character of Pezizomycotina. Because of their unique fruiting bodies, the close relationship of these bee-specialist fungi and their monophyly appeared certain. However, recent molecular studies have shown that Bettsia is not closely related to Ascosphaera. In this study, I isolated the very rare fungus Eremascus fertilis (Ascomycota, Pezizomycotina) from the bee bread of honey bees. These isolates represent the second report of E. fertilis both in nature and in the honey bee hive. To establish the systematic position of E. fertilis and Bettsia alvei, I performed phylogenetic analyses of nuclear ribosomal LSU + SSU DNA sequences from these species and 63 additional ascomycetes.<br><br>RESULTS: The phylogenetic analyses revealed that Eremascus is not monophyletic. Eremascus albus is closely related to Ascosphaera in Eurotiomycetes while E. fertilis belongs in Myxotrichaceae, a putative member of Leotiomycetes. Bettsia is not closely related to Ascosphaera and like E. fertilis apparently belongs in Leotiomycetes. These results indicate that both the naked ascus and spore cyst evolved twice in the Pezizomycotina and in distantly related lineages. The new genus Skoua is described to accommodate E. fertilis.<br><br>CONCLUSIONS: The naked ascus and spore cyst are both shown to have evolved convergently within the bee habitat. The convergent evolution of these unusual ascocarps is hypothesized to be adaptive for bee-mediated dispersal. Elucidating the dispersal strategies of these fungal symbionts contributes to our understanding of their interaction with bees and provides insight into the factors which potentially drive the evolution of reduced ascocarps in Pezizomycotina.},
}
@article {pmid26184597,
year = {2015},
author = {Soucy, SM and Huang, J and Gogarten, JP},
title = {Horizontal gene transfer: building the web of life.},
journal = {Nature reviews. Genetics},
volume = {16},
number = {8},
pages = {472-482},
doi = {10.1038/nrg3962},
pmid = {26184597},
issn = {1471-0064},
mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics/*physiology ; *Models, Genetic ; *Phylogeny ; *Selection, Genetic ; Symbiosis/*genetics ; },
abstract = {Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent-offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome.},
}
@article {pmid26178988,
year = {2015},
author = {Gutiérrez, S and Pirolles, E and Yvon, M and Baecker, V and Michalakis, Y and Blanc, S},
title = {The Multiplicity of Cellular Infection Changes Depending on the Route of Cell Infection in a Plant Virus.},
journal = {Journal of virology},
volume = {89},
number = {18},
pages = {9665-9675},
doi = {10.1128/JVI.00537-15},
pmid = {26178988},
issn = {1098-5514},
mesh = {Animals ; Aphids/virology ; Brassica rapa/metabolism/*virology ; Genome, Viral/*physiology ; Plant Leaves/metabolism/*virology ; Tymovirus/*physiology ; *Viral Tropism ; },
abstract = {UNLABELLED: The multiplicity of cellular infection (MOI) is the number of virus genomes of a given virus species that infect individual cells. This parameter chiefly impacts the severity of within-host population bottlenecks as well as the intensity of genetic exchange, competition, and complementation among viral genotypes. Only a few formal estimations of the MOI currently are available, and most theoretical reports have considered this parameter as constant within the infected host. Nevertheless, the colonization of a multicellular host is a complex process during which the MOI may dramatically change in different organs and at different stages of the infection. We have used both qualitative and quantitative approaches to analyze the MOI during the colonization of turnip plants by Turnip mosaic virus. Remarkably, different MOIs were observed at two phases of the systemic infection of a leaf. The MOI was very low in primary infections from virus circulating within the vasculature, generally leading to primary foci founded by a single genome. Each lineage then moved from cell to cell at a very high MOI. Despite this elevated MOI during cell-to-cell progression, coinfection of cells by lineages originating in different primary foci is severely limited by the rapid onset of a mechanism inhibiting secondary infection. Thus, our results unveil an intriguing colonization pattern where individual viral genomes initiate distinct lineages within a leaf. Kin genomes then massively coinfect cells, but coinfection by two distinct lineages is strictly limited.<br><br>IMPORTANCE: The MOI is the size of the viral population colonizing cells and defines major phenomena in virus evolution, like the intensity of genetic exchange and the size of within-host population bottlenecks. However, few studies have quantified the MOI, and most consider this parameter as constant during infection. Our results reveal that the MOI can depend largely on the route of cell infection in a systemically infected leaf. The MOI is usually one genome per cell when cells are infected from virus particles moving long distances in the vasculature, whereas it is much higher during subsequent cell-to-cell movement in mesophyll. However, a fast-acting superinfection exclusion prevents cell coinfection by merging populations originating from different primary foci within a leaf. This complex colonization pattern results in a situation where within-cell interactions are occurring almost exclusively among kin and explains the common but uncharacterized phenomenon of genotype spatial segregation in infected plants.},
}
@article {pmid26173445,
year = {2015},
author = {Arenas-Mena, C and Coffman, JA},
title = {Developmental control of transcriptional and proliferative potency during the evolutionary emergence of animals.},
journal = {Developmental dynamics : an official publication of the American Association of Anatomists},
volume = {244},
number = {10},
pages = {1193-1201},
doi = {10.1002/dvdy.24305},
pmid = {26173445},
issn = {1097-0177},
support = {P20 GM103423/GM/NIGMS NIH HHS/United States ; P20 GM104318/GM/NIGMS NIH HHS/United States ; P20-GM103423/GM/NIGMS NIH HHS/United States ; P20-GM104318/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Biological Evolution ; *Cell Proliferation ; Chromatin/metabolism ; *Gene Expression Regulation, Developmental ; *Gene Regulatory Networks ; *Regulatory Elements, Transcriptional ; },
abstract = {It is proposed that the evolution of complex animals required repressive genetic mechanisms for controlling the transcriptional and proliferative potency of cells. Unicellular organisms are transcriptionally potent, able to express their full genetic complement as the need arises through their life cycle, whereas differentiated cells of multicellular organisms can only express a fraction of their genomic potential. Likewise, whereas cell proliferation in unicellular organisms is primarily limited by nutrient availability, cell proliferation in multicellular organisms is developmentally regulated. Repressive genetic controls limiting the potency of cells at the end of ontogeny would have stabilized the gene expression states of differentiated cells and prevented disruptive proliferation, allowing the emergence of diverse cell types and functional shapes. We propose that distal cis-regulatory elements represent the primary innovations that set the stage for the evolution of developmental gene regulatory networks and the repressive control of key multipotency and cell-cycle control genes. The testable prediction of this model is that the genomes of extant animals, unlike those of our unicellular relatives, encode gene regulatory circuits dedicated to the developmental control of transcriptional and proliferative potency.},
}
@article {pmid26159581,
year = {2016},
author = {Rosa, TM and Giovanna, PM and Maria, M and Angela, M and Matteo, C},
title = {Old Weapons for New Wars: Bioactive Molecules From Cnidarian Internal Defense Systems.},
journal = {Central nervous system agents in medicinal chemistry},
volume = {16},
number = {3},
pages = {183-196},
pmid = {26159581},
issn = {1875-6166},
mesh = {Animals ; Anti-Infective Agents/immunology/isolation &amp; purification/toxicity ; *Cnidaria ; Cnidarian Venoms/immunology/isolation &amp; purification/*toxicity ; Humans ; Neurotoxins/immunology/isolation &amp; purification/*toxicity ; Peptides/immunology/isolation &amp; purification/*toxicity ; Sodium Channel Blockers/immunology/isolation &amp; purification/toxicity ; },
abstract = {The renewed interest in the study of genes of immunity in Cnidaria has led to additional information to the scenario of the first stages of immunity evolution revealing the cellular processes involved in symbiosis, in the regulation of homeostasis and in the fight against infections. The recent study with new molecular and functional approach on these organisms have therefore contributed with unexpected information on the knowledge of the stages of capturing activities and defense mechanisms strongly associated with toxin production. Cnidarians are diblastic aquatic animals with radial symmetry; they represent the ancestral state of Metazoa, they are the simplest multicellular organisms that have reached the level of tissue organization.The Cnidaria phylum has evolved using biotoxins as defense or predation mechanisms for ensure survival in hostile and competitive environments such as the seas and oceans. From benthic and pelagic species a large number of toxic compounds that have been determined can have an active role in the development of various antiviral, anticancer and antibacterial functions. Although the immune defense response of these animals is scarcely known, the tissues and the mucus produced by cnidarians are involved in immune defense and contain a large variety of peptides such as sodium and potassium channel neurotoxins, cytolysins, phospholipase A2 (PLA2), acid-sensing ion channel peptide toxins (ASICs) and other toxins, classified following biochemical and pharmacological studies on the basis of functional, molecular and structural parameters. These basal metazoan in fact, are far from &amp;quot;simple&amp;quot; in the range of methods at their disposal to deal with potential prey but also invading microbes and pathogens. They could also take advantage of the multi-functionality of some of their toxins, for example, some bioactive molecules have characteristics of toxicity associated with a potential antimicrobial activity. The interest in cnidarians was not only directed to the study of toxins and venom, but also to the fact these animals have been suggested as source of new molecules potentially relevant for biotechnology and pharmaceutical applications. Here, we review the cnidarian type of toxins regarding their multifunctional role and the future possibility of drawing important applications in fields ranging from biology to pharmacology.},
}
@article {pmid26150498,
year = {2015},
author = {Rendueles, O and Zee, PC and Dinkelacker, I and Amherd, M and Wielgoss, S and Velicer, GJ},
title = {Rapid and widespread de novo evolution of kin discrimination.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {29},
pages = {9076-9081},
doi = {10.1073/pnas.1502251112},
pmid = {26150498},
issn = {1091-6490},
support = {R01 GM079690/GM/NIGMS NIH HHS/United States ; GM079690/GM/NIGMS NIH HHS/United States ; },
mesh = {Adaptation, Physiological ; *Biological Evolution ; Chimera ; Myxococcus xanthus/genetics/isolation &amp; purification/*physiology ; Phenotype ; Time Factors ; },
abstract = {Diverse forms of kin discrimination, broadly defined as alteration of social behavior as a function of genetic relatedness among interactants, are common among social organisms from microbes to humans. However, the evolutionary origins and causes of kin-discriminatory behavior remain largely obscure. One form of kin discrimination observed in microbes is the failure of genetically distinct colonies to merge freely upon encounter. Here, we first use natural isolates of the highly social bacterium Myxococcus xanthus to show that colony-merger incompatibilities can be strong barriers to social interaction, particularly by reducing chimerism in multicellular fruiting bodies that develop near colony-territory borders. We then use experimental laboratory populations to test hypotheses regarding the evolutionary origins of kin discrimination. We show that the generic process of adaptation, irrespective of selective environment, is sufficient to repeatedly generate kin-discriminatory behaviors between evolved populations and their common ancestor. Further, we find that kin discrimination pervasively evolves indirectly between allopatric replicate populations that adapt to the same ecological habitat and that this occurs generically in many distinct habitats. Patterns of interpopulation discrimination imply that kin discrimination phenotypes evolved via many diverse genetic mechanisms and mutation-accumulation patterns support this inference. Strong incompatibility phenotypes emerged abruptly in some populations but strengthened gradually in others. The indirect evolution of kin discrimination in an asexual microbe is analogous to the indirect evolution of reproductive incompatibility in sexual eukaryotes and linguistic incompatibility among human cultures, the commonality being indirect, noncoordinated divergence of complex systems evolving in isolation.},
}
@article {pmid26131935,
year = {2015},
author = {Gavelis, GS and Hayakawa, S and White, RA and Gojobori, T and Suttle, CA and Keeling, PJ and Leander, BS},
title = {Eye-like ocelloids are built from different endosymbiotically acquired components.},
journal = {Nature},
volume = {523},
number = {7559},
pages = {204-207},
doi = {10.1038/nature14593},
pmid = {26131935},
issn = {1476-4687},
mesh = {Dinoflagellida/*genetics/physiology/*ultrastructure ; Genome, Protozoan/genetics ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Mitochondria/metabolism/ultrastructure ; Molecular Sequence Data ; Plastids/metabolism/ultrastructure ; Protozoan Proteins/genetics ; Rhodophyta/genetics ; *Symbiosis ; },
abstract = {Multicellularity is often considered a prerequisite for morphological complexity, as seen in the camera-type eyes found in several groups of animals. A notable exception exists in single-celled eukaryotes called dinoflagellates, some of which have an eye-like 'ocelloid' consisting of subcellular analogues to a cornea, lens, iris, and retina. These planktonic cells are uncultivated and rarely encountered in environmental samples, obscuring the function and evolutionary origin of the ocelloid. Here we show, using a combination of electron microscopy, tomography, isolated-organelle genomics, and single-cell genomics, that ocelloids are built from pre-existing organelles, including a cornea-like layer made of mitochondria and a retinal body made of anastomosing plastids. We find that the retinal body forms the central core of a network of peridinin-type plastids, which in dinoflagellates and their relatives originated through an ancient endosymbiosis with a red alga. As such, the ocelloid is a chimaeric structure, incorporating organelles with different endosymbiotic histories. The anatomical complexity of single-celled organisms may be limited by the components available for differentiation, but the ocelloid shows that pre-existing organelles can be assembled into a structure so complex that it was initially mistaken for a multicellular eye. Although mitochondria and plastids are acknowledged chiefly for their metabolic roles, they can also be building blocks for greater structural complexity.},
}
@article {pmid26124052,
year = {2015},
author = {Tomic, B and Kusic-Tisma, J},
title = {HsOrc4-Dependent Dna Remodeling of the ori-β Dhfr Replicator.},
journal = {Cellular &amp; molecular biology letters},
volume = {20},
number = {4},
pages = {549-561},
doi = {10.1515/cmble-2015-0032},
pmid = {26124052},
issn = {1689-1392},
mesh = {AT Rich Sequence ; Animals ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism ; Binding Sites ; Cell Cycle Proteins/chemistry/genetics/*metabolism ; Cricetulus ; DNA Replication ; *Nucleic Acid Conformation ; Origin Recognition Complex/chemistry/genetics/*metabolism ; Plant Proteins/chemistry/metabolism ; Plasmids/chemistry/genetics ; *Replication Origin ; Single-Strand Specific DNA and RNA Endonucleases/chemistry/metabolism ; Tetrahydrofolate Dehydrogenase/*genetics ; },
abstract = {Replication of DNA in multicellular organisms initiates from origin of replication (ori) sequences, which significantly differ in length and complexity. One of the best characterized is hamster dihydrofolate reductase (DHFR), which contains the ori-β sequence with several functionally relevant domains, such as an AT-rich region, dinucleotide repeat element (DNR), sequence-induced bend DNA (BEND) and a RIP60 protein-binding site (RIP60). Prior to initiation, ori sequences are recognized by origin recognition complex (ORC), which is a hetero hexamer complex that serves as the landing pad for proteins of the pre-replication complex. The function of each ORC subunit is still unclear. In this study, we analyze the function of subunit 4 of the human ORC complex (HsOrc4) in interaction with a plasmid bearing the ori-β DHFR sequence. We show that the topologically closed DHFR ori-β replicator contains a bubble-like structure within its AT-rich region and that it is reversibly modified in the interaction with HsOrc4. The non-canonical structure of the AT-rich region in the topologically closed ori sequence is recognized and changed by HsOrc4 using the energy of supercoiled DNA. These findings could help to further elucidate DNA replication and its possible association with human genetic diseases.},
}
@article {pmid26124000,
year = {2015},
author = {Schwessinger, B and Rathjen, JP},
title = {Changing SERKs and priorities during plant life.},
journal = {Trends in plant science},
volume = {20},
number = {9},
pages = {531-533},
doi = {10.1016/j.tplants.2015.06.006},
pmid = {26124000},
issn = {1878-4372},
mesh = {Biological Evolution ; *Gene Expression Regulation, Plant ; Magnoliopsida/*genetics/metabolism ; Plant Proteins/*genetics/metabolism ; Protein Kinases/*genetics/metabolism ; *Signal Transduction ; },
abstract = {SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES (SERKs) are coreceptors for diverse extracellular signals. SERKs are involved in a wide array of developmental and immune related processes first discovered in Arabidopsis. Recent work demonstrates the evolutionary conservation of SERKs in all multicellular plants, and highlights their functional conservation in monocots and dicots.},
}
@article {pmid26116421,
year = {2016},
author = {Ishizaki, K and Nishihama, R and Yamato, KT and Kohchi, T},
title = {Molecular Genetic Tools and Techniques for Marchantia polymorpha Research.},
journal = {Plant &amp; cell physiology},
volume = {57},
number = {2},
pages = {262-270},
doi = {10.1093/pcp/pcv097},
pmid = {26116421},
issn = {1471-9053},
mesh = {Crosses, Genetic ; Marchantia/*genetics ; Molecular Biology/*methods ; Plastids/genetics ; *Research ; Transformation, Genetic ; },
abstract = {Liverworts occupy a basal position in the evolution of land plants, and are a key group to address a wide variety of questions in plant biology. Marchantia polymorpha is a common, easily cultivated, dioecious liverwort species, and is emerging as an experimental model organism. The haploid gametophytic generation dominates the diploid sporophytic generation in its life cycle. Genetically homogeneous lines in the gametophyte generation can be established easily and propagated through asexual reproduction, which aids genetic and biochemical experiments. Owing to its dioecy, male and female sexual organs are formed in separate individuals, which enables crossing in a fully controlled manner. Reproductive growth can be induced at the desired times under laboratory conditions, which helps genetic analysis. The developmental process from a single-celled spore to a multicellular body can be observed directly in detail. As a model organism, molecular techniques for M. polymorpha are well developed; for example, simple and efficient protocols of Agrobacterium-mediated transformation have been established. Based on them, various strategies for molecular genetics, such as introduction of reporter constructs, overexpression, gene silencing and targeted gene modification, are available. Herein, we describe the technologies and resources for reverse and forward genetics in M. polymorpha, which offer an excellent experimental platform to study the evolution and diversity of regulatory systems in land plants.},
}
@article {pmid26105654,
year = {2015},
author = {Koeduka, T and Ishizaki, K and Mwenda, CM and Hori, K and Sasaki-Sekimoto, Y and Ohta, H and Kohchi, T and Matsui, K},
title = {Biochemical characterization of allene oxide synthases from the liverwort Marchantia polymorpha and green microalgae Klebsormidium flaccidum provides insight into the evolutionary divergence of the plant CYP74 family.},
journal = {Planta},
volume = {242},
number = {5},
pages = {1175-1186},
doi = {10.1007/s00425-015-2355-8},
pmid = {26105654},
issn = {1432-2048},
mesh = {Cytochrome P-450 Enzyme System/genetics/*metabolism ; *Evolution, Molecular ; Intramolecular Oxidoreductases/genetics/*metabolism ; Marchantia/*enzymology ; Microalgae/*enzymology ; Plant Proteins/genetics/*metabolism ; },
abstract = {MAIN CONCLUSION: Allene oxide synthases (AOSs) were isolated from liverworts and charophytes. These AOSs exhibited enzymatic properties similar to those of angiosperms but formed a distinct phylogenetic clade. Allene oxide synthase (AOS) and hydroperoxide lyase (HPL) mediate the formation of precursors of jasmonates and carbon-six volatiles, respectively. AOS and HPL utilize fatty acid hydroperoxides and belong to the plant cytochrome P450 74 (CYP74) family that mediates plant defense against herbivores, pathogens, or abiotic stresses. Although members of the CYP74 family have been reported in mosses and other species, the evolution and function of multiple CYP74 genes in plants remain elusive. Here, we show that the liverwort Marchantia polymorpha belongs to a basal group in the evolution of land plants; has two closely related proteins (59% identity), MpAOS1 and MpAOS2, that are similar to moss PpAOS1 (49 and 47% identity, respectively); and exhibits AOS activity but not HPL activity. We also found that the green microalgae Klebsormidium flaccidum, consist of multicellular and non-branching filaments, contains an enzyme, KfAOS, that is similar to PpAOS1 (37% identity), and converts 13-hydroperoxide of linolenic acid to 12-oxo-phytodienoic acid in a coupled reaction with allene oxide cyclase. Phylogenetic analysis showed two evolutionarily distinct clusters. One cluster comprised AOS and HPL from charophytic algae, liverworts, and mosses, including MpAOSs and KfAOS. The other cluster was formed by angiosperm CYP74. Our results suggest that plant CYP74 enzymes with AOS, HPL, and divinyl ether synthase activities have arisen multiple times and in the two different clades, which occurred prior to the divergence of the flowering plant lineage.},
}
@article {pmid26100885,
year = {2015},
author = {Skippington, E and Barkman, TJ and Rice, DW and Palmer, JD},
title = {Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {27},
pages = {E3515-24},
doi = {10.1073/pnas.1504491112},
pmid = {26100885},
issn = {1091-6490},
mesh = {Base Sequence ; DNA, Mitochondrial/classification/*genetics ; Electron Transport Complex I/*genetics ; Genes, Mitochondrial/genetics ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics ; RNA, Plant/genetics ; RNA, Ribosomal/genetics ; Sequence Homology, Nucleic Acid ; Viscum/*genetics ; },
abstract = {Despite the enormous diversity among parasitic angiosperms in form and structure, life-history strategies, and plastid genomes, little is known about the diversity of their mitogenomes. We report the sequence of the wonderfully bizarre mitogenome of the hemiparasitic aerial mistletoe Viscum scurruloideum. This genome is only 66 kb in size, making it the smallest known angiosperm mitogenome by a factor of more than three and the smallest land plant mitogenome. Accompanying this size reduction is exceptional reduction of gene content. Much of this reduction arises from the unexpected loss of respiratory complex I (NADH dehydrogenase), universally present in all 300+ other angiosperms examined, where it is encoded by nine mitochondrial and many nuclear nad genes. Loss of complex I in a multicellular organism is unprecedented. We explore the potential relationship between this loss in Viscum and its parasitic lifestyle. Despite its small size, the Viscum mitogenome is unusually rich in recombinationally active repeats, possessing unparalleled levels of predicted sublimons resulting from recombination across short repeats. Many mitochondrial gene products exhibit extraordinary levels of divergence in Viscum, indicative of highly relaxed if not positive selection. In addition, all Viscum mitochondrial protein genes have experienced a dramatic acceleration in synonymous substitution rates, consistent with the hypothesis of genomic streamlining in response to a high mutation rate but completely opposite to the pattern seen for the high-rate but enormous mitogenomes of Silene. In sum, the Viscum mitogenome possesses a unique constellation of extremely unusual features, a subset of which may be related to its parasitic lifestyle.},
}
@article {pmid26079199,
year = {2015},
author = {Scianna, M and Bassino, E and Munaron, L},
title = {A cellular Potts model analyzing differentiated cell behavior during in vivo vascularization of a hypoxic tissue.},
journal = {Computers in biology and medicine},
volume = {63},
number = {},
pages = {143-156},
doi = {10.1016/j.compbiomed.2015.05.020},
pmid = {26079199},
issn = {1879-0534},
mesh = {Animals ; *Cell Differentiation ; Endothelial Cells/*metabolism ; Humans ; *Hypoxia/metabolism/physiopathology ; *Models, Cardiovascular ; *Neovascularization, Physiologic ; Protein Isoforms/metabolism ; Vascular Endothelial Growth Factor A/metabolism ; },
abstract = {Angiogenesis, the formation of new blood vessel networks from existing capillary or post-capillary venules, is an intrinsically multiscale process occurring in several physio-pathological conditions. In particular, hypoxic tissue cells activate downstream cascades culminating in the secretion of a wide range of angiogenic factors, including VEGF isoforms. Such diffusive chemicals activate the endothelial cells (ECs) forming the external walls of the nearby vessels that chemotactically migrate toward the hypoxic areas of the tissue as multicellular sprouts. A functional network eventually emerges by further branching and anastomosis processes. We here propose a CPM-based approach reproducing selected features of the angiogenic progression necessary for the reoxygenation of a hypoxic tissue. Our model is able to span the different scale involved in the angiogenic progression as it incorporates reaction-diffusion equations for the description of the evolution of microenvironmental variables in a discrete mesoscopic cellular Potts model (CPM) that reproduces the dynamics of the vascular cells. A key feature of this work is the explicit phenotypic differentiation of the ECs themselves, distinguished in quiescent, stalk and tip. The simulation results allow identifying a set of key mechanisms underlying tissue vascularization. Further, we provide evidence that the nascent pattern is characterized by precise topological properties. Finally, we link abnormal sprouting angiogenesis with alteration in selected cell behavior.},
}
@article {pmid26066639,
year = {2015},
author = {Peng, M and Aye, TT and Snel, B and van Breukelen, B and Scholten, A and Heck, AJ},
title = {Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution.},
journal = {Journal of proteome research},
volume = {14},
number = {7},
pages = {2976-2987},
doi = {10.1021/acs.jproteome.5b00370},
pmid = {26066639},
issn = {1535-3907},
mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; Catalytic Domain ; Conserved Sequence ; Cyclic AMP-Dependent Protein Kinases/*metabolism ; Molecular Sequence Data ; Phylogeny ; Proteomics ; Sequence Homology, Amino Acid ; *Signal Transduction ; Subcellular Fractions/enzymology ; },
abstract = {In phosphorylation-directed signaling, spatial and temporal control is organized by complex interaction networks that diligently direct kinases toward distinct substrates to fine-tune specificity. How these protein networks originate and evolve into complex regulatory machineries are among the most fascinating research questions in biology. Here, spatiotemporal signaling is investigated by tracing the evolutionary dynamics of each functional domain of cAMP-dependent protein kinase (PKA) and its diverse set of A-kinase anchoring proteins (AKAPs). Homologues of the catalytic (PKA-C) and regulatory (PKA-R) domains of the (PKA-R)2-(PKA-C)2 holoenzyme were found throughout evolution. Most variation was observed in the RIIa of PKA-R, crucial for dimerization and docking to AKAPs. The RIIa domain was not observed in all PKA-R homologues. In the fungi and distinct protist lineages, the RIIa domain emerges within PKA-R, but it displays large sequence variation. These organisms do not harbor homologues of AKAPs, suggesting that efficient docking to direct spatiotemporal PKA activity evolved in multicellular eukaryotes. To test this in silico hypothesis, we experimentally screened organisms with increasing complexity by cAMP-based chemical proteomics to reveal that the occurrence of PKA-AKAP interactions indeed coincided and expanded within vertebrates, suggesting a crucial role for AKAPs in the advent of metazoan multicellularity.},
}
@article {pmid26063749,
year = {2015},
author = {Maliet, O and Shelton, DE and Michod, RE},
title = {A model for the origin of group reproduction during the evolutionary transition to multicellularity.},
journal = {Biology letters},
volume = {11},
number = {6},
pages = {20150157},
doi = {10.1098/rsbl.2015.0157},
pmid = {26063749},
issn = {1744-957X},
mesh = {*Biological Evolution ; *Models, Biological ; Reproduction ; *Selection, Genetic ; Volvocida/*physiology ; },
abstract = {During the evolution of multicellular organisms, the unit of selection and adaptation, the individual, changes from the single cell to the multicellular group. To become individuals, groups must evolve a group life cycle in which groups reproduce other groups. Investigations into the origin of group reproduction have faced a chicken-and-egg problem: traits related to reproduction at the group level often appear both to be a result of and a prerequisite for natural selection at the group level. With a focus on volvocine algae, we model the basic elements of the cell cycle and show how group reproduction can emerge through the coevolution of a life-history trait with a trait underpinning cell cycle change. Our model explains how events in the cell cycle become reordered to create a group life cycle through continuous change in the cell cycle trait, but only if the cell cycle trait can coevolve with the life-history trait. Explaining the origin of group reproduction helps us understand one of life's most familiar, yet fundamental, aspects-its hierarchical structure.},
}
@article {pmid26056368,
year = {2015},
author = {Ewald, PW and Swain Ewald, HA},
title = {Infection and cancer in multicellular organisms.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {370},
number = {1673},
pages = {},
doi = {10.1098/rstb.2014.0224},
pmid = {26056368},
issn = {1471-2970},
mesh = {Animals ; Biological Evolution ; Environmental Pollutants/toxicity ; Humans ; Infection/*complications ; Models, Biological ; Neoplasms/*etiology ; Oncogenic Viruses/pathogenicity ; Tumor Virus Infections/etiology ; },
abstract = {Evolutionary considerations suggest that oncogenic infections should be pervasive among animal species. Infection-associated cancers are well documented in humans and domestic animals, less commonly reported in undomesticated captive animals, and rarely documented in nature. In this paper, we review the literature associating infectious agents with cancer to evaluate the reasons for this pattern. Non-malignant infectious neoplasms occur pervasively in multicellular life, but oncogenic progression to malignancy is often uncertain. Evidence from humans and domestic animals shows that non-malignant infectious neoplasms can develop into cancer, although generally with low frequency. Malignant neoplasms could be difficult to find in nature because of a low frequency of oncogenic transformation, short survival after malignancy and reduced survival prior to malignancy. Moreover, the evaluation of malignancy can be ambiguous in nature, because criteria for malignancy may be difficult to apply consistently across species. The information available in the literature therefore does not allow for a definitive assessment of the pervasiveness of infectious cancers in nature, but the presence of infectious neoplasias and knowledge about the progression of benign neoplasias to cancer is consistent with a widespread but largely undetected occurrence.},
}
@article {pmid26056363,
year = {2015},
author = {Aktipis, CA and Boddy, AM and Jansen, G and Hibner, U and Hochberg, ME and Maley, CC and Wilkinson, GS},
title = {Cancer across the tree of life: cooperation and cheating in multicellularity.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {370},
number = {1673},
pages = {},
doi = {10.1098/rstb.2014.0219},
pmid = {26056363},
issn = {1471-2970},
support = {R01 CA185138/CA/NCI NIH HHS/United States ; P01 CA091955/CA/NCI NIH HHS/United States ; R01 CA149566/CA/NCI NIH HHS/United States ; R01 CA170595/CA/NCI NIH HHS/United States ; P01 CA91955/CA/NCI NIH HHS/United States ; R01 CA140657/CA/NCI NIH HHS/United States ; BC132057/BC/NCI NIH HHS/United States ; },
mesh = {Animals ; Apoptosis ; Cell Communication ; Cell Differentiation ; Cell Proliferation ; Humans ; Models, Biological ; Neoplasms/etiology/*pathology/physiopathology ; Phylogeny ; Tumor Microenvironment ; },
abstract = {Multicellularity is characterized by cooperation among cells for the development, maintenance and reproduction of the multicellular organism. Cancer can be viewed as cheating within this cooperative multicellular system. Complex multicellularity, and the cooperation underlying it, has evolved independently multiple times. We review the existing literature on cancer and cancer-like phenomena across life, not only focusing on complex multicellularity but also reviewing cancer-like phenomena across the tree of life more broadly. We find that cancer is characterized by a breakdown of the central features of cooperation that characterize multicellularity, including cheating in proliferation inhibition, cell death, division of labour, resource allocation and extracellular environment maintenance (which we term the five foundations of multicellularity). Cheating on division of labour, exhibited by a lack of differentiation and disorganized cell masses, has been observed in all forms of multicellularity. This suggests that deregulation of differentiation is a fundamental and universal aspect of carcinogenesis that may be underappreciated in cancer biology. Understanding cancer as a breakdown of multicellular cooperation provides novel insights into cancer hallmarks and suggests a set of assays and biomarkers that can be applied across species and characterize the fundamental requirements for generating a cancer.},
}
@article {pmid26054350,
year = {2015},
author = {Olovnikov, AM},
title = {Chronographic theory of development, aging, and origin of cancer: role of chronomeres and printomeres.},
journal = {Current aging science},
volume = {8},
number = {1},
pages = {76-88},
pmid = {26054350},
issn = {1874-6128},
mesh = {*Aging ; Animals ; Humans ; *Neoplasms/genetics ; Polymers/*pharmacology ; Sex Characteristics ; Telomere ; Telomere Shortening ; },
abstract = {It is supposed that the development and aging of multicellular animals and humans are controlled by a special form of the clock mechanism - a chronograph. The development of animals and their aging are interconnected by the program of the species lifespan that has been selected in the evolution of each species to fit the resources of its ecological niche. The theory is based on the idea about a controlled loss by the neurons in the brain of hypothetical organelles - chronomeres that represent themselves small DNA molecules, which are amplificates of the segments of chromosomal DNA. A regular mode of the process of chronomere losses by neurons is provided by a pacemaker localized in the pineal gland and activated at least once per lunar month. Neurons, consecutively losing their chronomeres, are organized in the brain in the temporal relay race. Analogues of chronomeres, namely printomeres, are supposed to exist in dividing non-neuronal cells. Printomeres are not involved in a performance of temporal function, instead they are responsible for the maintenance in dividing cells of their memory about the state of differentiation. A critical shortening or loss of a printomere in a dividing cell leads to a cellular senescence, whereas telomere shortening is a bystander of this process. Thus, aging of a multicellular organism is associated with the loss of chronomeres, whereas senescence of dividing cells is associated with the loss of regulatory RNAs encoded by printomeres. If the cells that have lost their printomeres are environmentally forced to divide, they can transform into cancer cells.},
}
@article {pmid26048704,
year = {2015},
author = {Sheikh, S and Gloeckner, G and Kuwayama, H and Schaap, P and Urushihara, H and Baldauf, SL},
title = {Root of Dictyostelia based on 213 universal proteins.},
journal = {Molecular phylogenetics and evolution},
volume = {92},
number = {},
pages = {53-62},
doi = {10.1016/j.ympev.2015.05.017},
pmid = {26048704},
issn = {1095-9513},
support = {BB/E016308//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Amoeba/chemistry/metabolism ; Bayes Theorem ; Dictyostelium/*classification/genetics/*metabolism ; Genome/genetics ; *Phylogeny ; Proteins/*analysis/chemistry ; RNA, Ribosomal/genetics ; },
abstract = {Dictyostelia are common soil microbes that can aggregate when starved to form multicellular fruiting bodies, a characteristic that has also led to their long history of study and widespread use as model systems. Ribosomal RNA phylogeny of Dictyostelia identified four major divisions (Groups 1-4), none of which correspond to traditional genera. Group 1 was also tentatively identified as sister lineage to the other three Groups, although not consistently or with strong support. We tested the dictyostelid root using universal protein-coding genes identified by exhaustive comparison of six completely sequenced dictyostelid genomes, which include representatives of all four major molecular Groups. A set of 213 genes are low-copy number in all genomes, present in at least one amoebozoan outgroup taxon (Acanthamoeba castellanii or Physarum polycephalum), and phylogenetically congruent. Phylogenetic analysis of a concatenation of the deduced protein sequences produces a single topology dividing Dictyostelia into two major divisions: Groups 1+2 and Groups 3+4. All clades in the tree are fully supported by maximum likelihood and Bayesian inference, and all alternative roots are unambiguously rejected by the approximately unbiased (AU) test. The 1+2, 3+4 root is also fully supported even after deleting clusters with strong individual support for this root, or concatenating all clusters with low support for alternative roots. The 213 putatively ancestral amoebozoan proteins encode a wide variety of functions including 21 KOG categories out of a total of 25. These comprehensive analyses and consistent results indicate that it is time for full taxonomic revision of Dictyostelia, which will also enable more effective exploitation of its unique potential as an evolutionary model system.},
}
@article {pmid26047467,
year = {2015},
author = {Wideman, JG and Moore, BP},
title = {The Evolutionary History of MAPL (Mitochondria-Associated Protein Ligase) and Other Eukaryotic BAM/GIDE Domain Proteins.},
journal = {PloS one},
volume = {10},
number = {6},
pages = {e0128795},
doi = {10.1371/journal.pone.0128795},
pmid = {26047467},
issn = {1932-6203},
mesh = {Animals ; Biological Evolution ; Fungal Proteins/chemistry/genetics ; Fungi/chemistry/genetics ; Humans ; *Phylogeny ; Plant Proteins/chemistry/genetics ; Plants/chemistry/genetics ; Protein Structure, Tertiary ; Ubiquitin-Protein Ligases/chemistry/*genetics ; },
abstract = {MAPL (mitochondria-associated protein ligase, also called MULAN/GIDE/MUL1) is a multifunctional mitochondrial outer membrane protein found in human cells that contains a unique BAM (beside a membrane) domain and a C-terminal RING-finger domain. MAPL has been implicated in several processes that occur in animal cells such as NF-kB activation, innate immunity and antiviral signaling, suppression of PINK1/parkin defects, mitophagy in skeletal muscle, and caspase-dependent apoptosis. Previous studies demonstrated that the BAM domain is present in diverse organisms in which most of these processes do not occur, including plants, archaea, and bacteria. Thus the conserved function of MAPL and its BAM domain remains an open question. In order to gain insight into its conserved function, we investigated the evolutionary origins of MAPL by searching for homologues in predicted proteomes of diverse eukaryotes. We show that MAPL proteins with a conserved BAM-RING architecture are present in most animals, protists closely related to animals, a single species of fungus, and several multicellular plants and related green algae. Phylogenetic analysis demonstrated that eukaryotic MAPL proteins originate from a common ancestor and not from independent horizontal gene transfers from bacteria. We also determined that two independent duplications of MAPL occurred, one at the base of multicellular plants and another at the base of vertebrates. Although no other eukaryote genome examined contained a verifiable MAPL orthologue, BAM domain-containing proteins were identified in the protists Bigelowiella natans and Ectocarpus siliculosis. Phylogenetic analyses demonstrated that these proteins are more closely related to prokaryotic BAM proteins and therefore likely arose from independent horizontal gene transfers from bacteria. We conclude that MAPL proteins with BAM-RING architectures have been present in the holozoan and viridiplantae lineages since their very beginnings. Our work paves the way for future studies into MAPL function in alternative model organisms like Capsaspora owczarzaki and Chlamydomonas reinhardtii that will help to answer the question of MAPL's ancestral function in ways that cannot be answered by studying animal cells alone.},
}
@article {pmid26041885,
year = {2015},
author = {Kurakin, A and Bredesen, DE},
title = {Dynamic self-guiding analysis of Alzheimer's disease.},
journal = {Oncotarget},
volume = {6},
number = {16},
pages = {14092-14122},
doi = {10.18632/oncotarget.4221},
pmid = {26041885},
issn = {1949-2553},
support = {R21 AG036975/AG/NIA NIH HHS/United States ; AG16570/AG/NIA NIH HHS/United States ; AG034427/AG/NIA NIH HHS/United States ; AG036975/AG/NIA NIH HHS/United States ; P50 AG016570/AG/NIA NIH HHS/United States ; R01 AG034427/AG/NIA NIH HHS/United States ; },
mesh = {Algorithms ; Alzheimer Disease/*metabolism/*pathology ; Amyloid beta-Protein Precursor/metabolism ; Cell Adhesion/physiology ; Humans ; },
abstract = {We applied a self-guiding evolutionary algorithm to initiate the synthesis of the Alzheimer's disease-related data and literature. A protein interaction network associated with amyloid-beta precursor protein (APP) and a seed model that treats Alzheimer's disease as progressive dysregulation of APP-associated signaling were used as dynamic &quot;guides&quot; and structural &quot;filters&quot; in the recursive search, analysis, and assimilation of data to drive the evolution of the seed model in size, detail, and complexity. Analysis of data and literature across sub-disciplines and system-scale discovery platforms suggests a key role of dynamic cytoskeletal connectivity in the stability, plasticity, and performance of multicellular networks and architectures. Chronic impairment and/or dysregulation of cell adhesions/synapses, cytoskeletal networks, and/or reversible epithelial-to-mesenchymal-like transitions, which enable and mediate the stable and coherent yet dynamic and reconfigurable multicellular architectures, may lead to the emergence and persistence of the disordered, wound-like pockets/microenvironments of chronically disconnected cells. Such wound-like microenvironments support and are supported by pro-inflammatory, pro-secretion, de-differentiated cellular phenotypes with altered metabolism and signaling. The co-evolution of wound-like microenvironments and their inhabitants may lead to the selection and stabilization of degenerated cellular phenotypes, via acquisition of epigenetic modifications and mutations, which eventually result in degenerative disorders such as cancer and Alzheimer's disease.},
}
@article {pmid26040592,
year = {2015},
author = {Brumley, DR and Polin, M and Pedley, TJ and Goldstein, RE},
title = {Metachronal waves in the flagellar beating of Volvox and their hydrodynamic origin.},
journal = {Journal of the Royal Society, Interface},
volume = {12},
number = {108},
pages = {20141358},
doi = {10.1098/rsif.2014.1358},
pmid = {26040592},
issn = {1742-5662},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Flagella/*physiology ; Hydrodynamics ; *Models, Biological ; Volvox/*physiology ; },
abstract = {Groups of eukaryotic cilia and flagella are capable of coordinating their beating over large scales, routinely exhibiting collective dynamics in the form of metachronal waves. The origin of this behavior--possibly influenced by both mechanical interactions and direct biological regulation--is poorly understood, in large part due to a lack of quantitative experimental studies. Here we characterize in detail flagellar coordination on the surface of the multicellular alga Volvox carteri, an emerging model organism for flagellar dynamics. Our studies reveal for the first time that the average metachronal coordination observed is punctuated by periodic phase defects during which synchrony is partial and limited to specific groups of cells. A minimal model of hydrodynamically coupled oscillators can reproduce semi-quantitatively the characteristics of the average metachronal dynamics, and the emergence of defects. We systematically study the model's behaviour by assessing the effect of changing intrinsic rotor characteristics, including oscillator stiffness and the nature of their internal driving force, as well as their geometric properties and spatial arrangement. Our results suggest that metachronal coordination follows from deformations in the oscillators' limit cycles induced by hydrodynamic stresses, and that defects result from sufficiently steep local biases in the oscillators' intrinsic frequencies. Additionally, we find that random variations in the intrinsic rotor frequencies increase the robustness of the average properties of the emergent metachronal waves.},
}
@article {pmid26021328,
year = {2015},
author = {Santos, J and Monteagudo, Á},
title = {Analysis of behaviour transitions in tumour growth using a cellular automaton simulation.},
journal = {IET systems biology},
volume = {9},
number = {3},
pages = {75-87},
doi = {10.1049/iet-syb.2014.0015},
pmid = {26021328},
issn = {1751-8849},
mesh = {Animals ; Carcinogenesis/*pathology ; Cell Proliferation ; Computer Simulation ; Humans ; *Models, Biological ; Neoplasms/*pathology/*physiopathology ; Spheroids, Cellular/*pathology/*physiology ; },
abstract = {The authors used computational biology as an approach for analysing the emergent dynamics of tumour growth at cellular level. They applied cellular automata for modelling the behaviour of cells when the main cancer cell hallmarks are present. Their model is oriented to mimic the development of multicellular spheroids of tumour cells. In their modelling, cells have a genome associated with the different cancer hallmarks, indicating if those are acquired as a consequence of mutations. The presence of the cancer hallmarks defines cell states and cell mitotic behaviours. These hallmarks are associated with a series of parameters, and depending on their values and the activation of the hallmarks in each of the cells, the system can evolve to different dynamics. With the simulation tool the authors performed an analysis of the first phases of cancer growth, using different and alternative strategies: firstly, studying the evolution of cancer cells and hallmarks in different representative situations regarding initial conditions and parameters, analysing the relative importance of the hallmarks for tumour progression; secondly, being the focus of this work, inspecting the behaviour transitions when the cancer cells are killed with a given probability during the cellular system progression.},
}
@article {pmid26018043,
year = {2015},
author = {Ho, HI and Shaulsky, G},
title = {Temporal regulation of kin recognition maintains recognition-cue diversity and suppresses cheating.},
journal = {Nature communications},
volume = {6},
number = {},
pages = {7144},
doi = {10.1038/ncomms8144},
pmid = {26018043},
issn = {2041-1723},
support = {CA125123/CA/NCI NIH HHS/United States ; HD007495/HD/NICHD NIH HHS/United States ; T32 HD007495/HD/NICHD NIH HHS/United States ; U54 HD007495/HD/NICHD NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; DK56338/DK/NIDDK NIH HHS/United States ; P30 AI036211/AI/NIAID NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 GM098276/GM/NIGMS NIH HHS/United States ; P30 HD007495/HD/NICHD NIH HHS/United States ; },
mesh = {Biological Evolution ; Cues ; Dictyostelium/*genetics/metabolism ; Fruiting Bodies, Fungal/*genetics/metabolism ; *Genetic Variation ; Membrane Proteins/*genetics/metabolism ; *Microbial Interactions ; Polymorphism, Genetic ; Protozoan Proteins/*genetics/metabolism ; Spores, Protozoan ; },
abstract = {Kin recognition, the ability to distinguish kin from non-kin, can facilitate cooperation between relatives. Evolutionary theory predicts that polymorphism in recognition cues, which is essential for effective recognition, would be unstable. Individuals carrying rare recognition cues would benefit less from social interactions than individuals with common cues, leading to loss of the genetic-cue diversity. We test this evolutionary hypothesis in Dictyostelium discoideum, which forms multicellular fruiting bodies by aggregation and utilizes two polymorphic membrane proteins to facilitate preferential cooperation. Surprisingly, we find that rare recognition variants are tolerated and maintain their frequencies among incompatible majority during development. Although the rare variants are initially excluded from the aggregates, they subsequently rejoin the aggregate and produce spores. Social cheating is also refrained in late development, thus limiting the cost of chimerism. Our results suggest a potential mechanism to sustain the evolutionary stability of kin-recognition genes and to suppress cheating.},
}
@article {pmid26014922,
year = {2015},
author = {Torday, JS},
title = {The cell as the mechanistic basis for evolution.},
journal = {Wiley interdisciplinary reviews. Systems biology and medicine},
volume = {7},
number = {5},
pages = {275-284},
doi = {10.1002/wsbm.1305},
pmid = {26014922},
issn = {1939-005X},
mesh = {Animals ; *Biological Evolution ; Genotype ; Humans ; Lung/cytology/metabolism ; Phenotype ; *Phylogeny ; },
abstract = {The First Principles for Physiology originated in and emanate from the unicellular state of life. Viewing physiology as a continuum from unicellular to multicellular organisms provides fundamental insight to ontogeny and phylogeny as a functionally integral whole. Such mechanisms are most evident under conditions of physiologic stress; all of the molecular pathways that evolved in service to the vertebrate water-land transition aided and abetted the evolution of the vertebrate lung, for example. Reduction of evolution to cell biology has an important scientific feature—it is predictive. One implication of this perspective on evolution is the likelihood that it is the unicellular state that is actually the object of selection. By looking at the process of evolution from its unicellular origins, the causal relationships between genotype and phenotype are revealed, as are many other aspects of physiology and medicine that have