@article {pmid37765506,
year = {2023},
author = {Wegner, L and Porth, ML and Ehlers, K},
title = {Multicellularity and the Need for Communication-A Systematic Overview on (Algal) Plasmodesmata and Other Types of Symplasmic Cell Connections.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {18},
pages = {},
doi = {10.3390/plants12183342},
pmid = {37765506},
issn = {2223-7747},
support = {EH 372/1-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {In the evolution of eukaryotes, the transition from unicellular to simple multicellular organisms has happened multiple times. For the development of complex multicellularity, characterized by sophisticated body plans and division of labor between specialized cells, symplasmic intercellular communication is supposed to be indispensable. We review the diversity of symplasmic connectivity among the eukaryotes and distinguish between distinct types of non-plasmodesmatal connections, plasmodesmata-like structures, and 'canonical' plasmodesmata on the basis of developmental, structural, and functional criteria. Focusing on the occurrence of plasmodesmata (-like) structures in extant taxa of fungi, brown algae (Phaeophyceae), green algae (Chlorophyta), and streptophyte algae, we present a detailed critical update on the available literature which is adapted to the present classification of these taxa and may serve as a tool for future work. From the data, we conclude that, actually, development of complex multicellularity correlates with symplasmic connectivity in many algal taxa, but there might be alternative routes. Furthermore, we deduce a four-step process towards the evolution of canonical plasmodesmata and demonstrate similarity of plasmodesmata in streptophyte algae and land plants with respect to the occurrence of an ER component. Finally, we discuss the urgent need for functional investigations and molecular work on cell connections in algal organisms.},
}

@article {pmid37409939,
year = {2023},
author = {Aanen, DK and van 't Padje, A and Auxier, B},
title = {Longevity of Fungal Mycelia and Nuclear Quality Checks: a New Hypothesis for the Role of Clamp Connections in Dikaryons.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {87},
number = {3},
pages = {e0002221},
pmid = {37409939},
issn = {1098-5557},
support = {865.14.007 (VICI)//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; ALWGR.2017.010 (Groen II)//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; },
mesh = {*Mycelium ; *Hyphae/genetics ; Fungi ; },
abstract = {This paper addresses the stability of mycelial growth in fungi and differences between ascomycetes and basidiomycetes. Starting with general evolutionary theories of multicellularity and the role of sex, we then discuss individuality in fungi. Recent research has demonstrated the deleterious consequences of nucleus-level selection in fungal mycelia, favoring cheaters with a nucleus-level benefit during spore formation but a negative effect on mycelium-level fitness. Cheaters appear to generally be loss-of-fusion (LOF) mutants, with a higher propensity to form aerial hyphae developing into asexual spores. Since LOF mutants rely on heterokaryosis with wild-type nuclei, we argue that regular single-spore bottlenecks can efficiently select against such cheater mutants. We then zoom in on ecological differences between ascomycetes being typically fast-growing but short-lived with frequent asexual-spore bottlenecks and basidiomycetes being generally slow-growing but long-lived and usually without asexual-spore bottlenecks. We argue that these life history differences have coevolved with stricter nuclear quality checks in basidiomycetes. Specifically, we propose a new function for clamp connections, structures formed during the sexual stage in ascomycetes and basidiomycetes but during somatic growth only in basidiomycete dikaryons. During dikaryon cell division, the two haploid nuclei temporarily enter a monokaryotic phase, by alternatingly entering a retrograde-growing clamp cell, which subsequently fuses with the subapical cell to recover the dikaryotic cell. We hypothesize that clamp connections act as screening devices for nuclear quality, with both nuclei continuously testing each other for fusion ability, a test that LOF mutants will fail. By linking differences in longevity of the mycelial phase to ecology and stringency of nuclear quality checks, we propose that mycelia have a constant and low lifetime cheating risk, irrespective of their size and longevity.},
}

*Mycelium
*Hyphae/genetics
Fungi

@article {pmid37727086,
year = {2023},
author = {Kalambokidis, M and Travisano, M},
title = {Multispecies interactions shape the transition to multicellularity.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2007},
pages = {20231055},
doi = {10.1098/rspb.2023.1055},
pmid = {37727086},
issn = {1471-2954},
mesh = {*Saccharomyces cerevisiae ; Coculture Techniques ; *Earth, Planet ; },
abstract = {The origin of multicellularity transformed the adaptive landscape on Earth, opening diverse avenues for further innovation. The transition to multicellular life is understood as the evolution of cooperative groups which form a new level of individuality. Despite the potential for community-level interactions, most studies have not addressed the competitive context of this transition, such as competition between species. Here, we explore how interspecific competition shapes the emergence of multicellularity in an experimental system with two yeast species, Saccharomyces cerevisiae and Kluyveromyces lactis, where multicellularity evolves in response to selection for faster settling ability. We find that the multispecies context slows the rate of the transition to multicellularity, and the transition to multicellularity significantly impacts community composition. Multicellular K. lactis emerges first and sweeps through populations in monocultures faster than in cocultures with S. cerevisiae. Following the transition, the between-species competitive dynamics shift, likely in part to intraspecific cooperation in K. lactis. Hence, we document an eco-evolutionary feedback across the transition to multicellularity, underscoring how ecological context is critical for understanding the causes and consequences of innovation. By including two species, we demonstrate that cooperation and competition across several biological scales shapes the origin and persistence of multicellularity.},
}

*Saccharomyces cerevisiae
Coculture Techniques
*Earth, Planet

@article {pmid36856076,
year = {2023},
author = {Takeuchi, K and Senda, M and Ikeda, Y and Okuwaki, K and Fukuzawa, K and Nakagawa, S and Sasaki, M and Sasaki, AT and Senda, T},
title = {Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ.},
journal = {The FEBS journal},
volume = {290},
number = {18},
pages = {4419-4428},
pmid = {36856076},
issn = {1742-4658},
support = {R01 CA255331/CA/NCI NIH HHS/United States ; R01 NS089815/NS/NINDS NIH HHS/United States ; R01 GM144426/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Guanosine Triphosphate/metabolism ; *Adenosine Triphosphate/metabolism ; *Evolution, Molecular ; Mammals/metabolism ; },
abstract = {Over 4 billion years of evolution, multiple mutations, including nucleotide substitutions, gene and genome duplications and recombination, have established de novo genes that translate into proteins with novel properties essential for high-order cellular functions. However, molecular processes through which a protein evolutionarily acquires a novel function are mostly speculative. Recently, we have provided evidence for a potential evolutionary mechanism underlying how, in mammalian cells, phosphatidylinositol 5-phosphate 4-kinase β (PI5P4Kβ) evolved into a GTP sensor from ATP-utilizing kinase. Mechanistically, PI5P4Kβ has acquired the guanine efficient association (GEA) motif by mutating its nucleotide base recognition sequence, enabling the evolutionary transition from an ATP-dependent kinase to a distinct GTP/ATP dual kinase with its KM for GTP falling into physiological GTP concentrations-the genesis of GTP sensing activity. Importantly, the GTP sensing activity of PI5P4Kβ is critical for the manifestation of cellular metabolism and tumourigenic activity in the multicellular organism. The combination of structural, biochemical and biophysical analyses used in our study provides a novel framework for analysing how a protein can evolutionarily acquire a novel activity, which potentially introduces a critical function to the cell.},
}

Animals
Guanosine Triphosphate/metabolism
*Adenosine Triphosphate/metabolism
*Evolution, Molecular
Mammals/metabolism

@article {pmid37727796,
year = {2023},
author = {Craig, JM and Kumar, S and Hedges, SB},
title = {The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen.},
journal = {Frontiers in bioinformatics},
volume = {3},
number = {},
pages = {1233281},
pmid = {37727796},
issn = {2673-7647},
abstract = {The origin of eukaryotes was among the most important events in the history of life, spawning a new evolutionary lineage that led to all complex multicellular organisms. However, the timing of this event, crucial for understanding its environmental context, has been difficult to establish. The fossil and biomarker records are sparse and molecular clocks have thus far not reached a consensus, with dates spanning 2.1-0.91 billion years ago (Ga) for critical nodes. Notably, molecular time estimates for the last common ancestor of eukaryotes are typically hundreds of millions of years younger than the Great Oxidation Event (GOE, 2.43-2.22 Ga), leading researchers to question the presumptive link between eukaryotes and oxygen. We obtained a new time estimate for the origin of eukaryotes using genetic data of both archaeal and bacterial origin, the latter rarely used in past studies. We also avoided potential calibration biases that may have affected earlier studies. We obtained a conservative interval of 2.2-1.5 Ga, with an even narrower core interval of 2.0-1.8 Ga, for the origin of eukaryotes, a period closely aligned with the rise in oxygen. We further reconstructed the history of biological complexity across the tree of life using three universal measures: cell types, genes, and genome size. We found that the rise in complexity was temporally consistent with and followed a pattern similar to the rise in oxygen. This suggests a causal relationship stemming from the increased energy needs of complex life fulfilled by oxygen.},
}

@article {pmid37438660,
year = {2023},
author = {Huang, L and Tu, Z and Wei, L and Sun, W and Wang, Y and Bi, S and He, F and Du, L and Chen, J and Kzhyshkowska, J and Wang, H and Chen, D and Zhang, S},
title = {Generating Functional Multicellular Organoids from Human Placenta Villi.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {10},
number = {26},
pages = {e2301565},
pmid = {37438660},
issn = {2198-3844},
support = {2022YFC2702501//National Key Research and Development Program of China/ ; 2022YFC2704500//National Key Research and Development Program of China/ ; 81830045//Key Program of National Natural Science Foundation of China/ ; 81071652//National Natural Science Foundation of China/ ; 82171666//National Natural Science Foundation of China/ ; 82201861//National Natural Science Foundation of China/ ; 82271695//National Natural Science Foundation of China/ ; M-0586//Mobility program of Sino German Center/ ; 202201020573//Science and Technology Program of Guangzhou/ ; 2023A03J0378//Science and Technology Program of Guangzhou/ ; 2021B1515120070//China Guangdong Basic and Applied Basic Research Fund/ ; },
mesh = {Pregnancy ; Female ; Humans ; *Placenta/metabolism ; *Chorionic Villi/metabolism/pathology ; Placentation ; Trophoblasts/metabolism ; Organoids/metabolism ; },
abstract = {The interaction between trophoblasts, stroma cells, and immune cells at the maternal-fetal interface constitutes the functional units of the placenta, which is crucial for successful pregnancy outcomes. However, the investigation of this intricate interplay is restricted due to the absence of efficient experimental models. To address this challenge, a robust, reliable methodology for generating placenta villi organoids (PVOs) from early, late, or diseased pregnancies using air-liquid surface culture is developed. PVOs contain cytotrophoblasts that can self-renew and differentiate directly, along with stromal elements that retain native immune cells. Analysis of scRNA sequencing and WES data reveals that PVOs faithfully recapitulate the cellular components and genetic alterations of the corresponding source tissue. Additionally, PVOs derived from patients with preeclampsia exhibit specific pathological features such as inflammation, antiangiogenic imbalance, and decreased syncytin expression. The PVO-based propagation of primary placenta villi should enable a deeper investigation of placenta development and exploration of the underlying pathogenesis and therapeutics of placenta-originated diseases.},
}

Pregnancy
Female
Humans
*Placenta/metabolism
*Chorionic Villi/metabolism/pathology
Placentation
Trophoblasts/metabolism
Organoids/metabolism

@article {pmid37406343,
year = {2023},
author = {Ruiz-Trillo, I and Kin, K and Casacuberta, E},
title = {The Origin of Metazoan Multicellularity: A Potential Microbial Black Swan Event.},
journal = {Annual review of microbiology},
volume = {77},
number = {},
pages = {499-516},
doi = {10.1146/annurev-micro-032421-120023},
pmid = {37406343},
issn = {1545-3251},
mesh = {Animals ; Retrospective Studies ; *Biological Evolution ; },
abstract = {The emergence of animals from their unicellular ancestors is a major evolutionary event. Thanks to the study of diverse close unicellular relatives of animals, we now have a better grasp of what the unicellular ancestor of animals was like. However, it is unclear how that unicellular ancestor of animals became the first animals. To explain this transition, two popular theories, the choanoblastaea and the synzoospore, have been proposed. We will revise and expose the flaws in these two theories while showing that, due to the limits of our current knowledge, the origin of animals is a biological black swan event. As such, the origin of animals defies retrospective explanations. Therefore, we should be extra careful not to fall for confirmation biases based on few data and, instead, embrace this uncertainty and be open to alternative scenarios. With the aim to broaden the potential explanations on how animals emerged, we here propose two novel and alternative scenarios. In any case, to find the answer to how animals evolved, additional data will be required, as will the hunt for microscopic creatures that are closely related to animals but have not yet been sampled and studied.},
}

Animals
Retrospective Studies
*Biological Evolution

@article {pmid37586948,
year = {2023},
author = {Shalev, O and Ye, X and Ratzke, C},
title = {Replaying the evolution of multicellularity.},
journal = {Trends in ecology & evolution},
volume = {38},
number = {10},
pages = {910-912},
doi = {10.1016/j.tree.2023.07.007},
pmid = {37586948},
issn = {1872-8383},
mesh = {Earth, Planet ; *Origin of Life ; *Biological Evolution ; Yeasts ; },
abstract = {The first organisms on Earth were presumably unicellular. At one point, evolution shaped these individual cells into multicellular organisms, which was a significant transition in the history of life on Earth. To investigate how this change happened, Bozdag et al. re-ran evolution in the lab and observed how single-celled yeast forms large multicellular aggregates.},
}

Earth, Planet
*Origin of Life
*Biological Evolution
Yeasts

@article {pmid37699344,
year = {2023},
author = {Azimzadeh, J and Durand, B},
title = {Evolution: The ancient history of cilia assembly regulation.},
journal = {Current biology : CB},
volume = {33},
number = {17},
pages = {R898-R900},
doi = {10.1016/j.cub.2023.07.053},
pmid = {37699344},
issn = {1879-0445},
mesh = {Animals ; *Cilia ; },
abstract = {A new study identifies a conserved regulatory mechanism for cilia assembly in the closest unicellular relatives of animals, suggesting that this mechanism was already present in a common unicellular ancestor and was repurposed during the transition to multicellularity.},
}

Animals
*Cilia

@article {pmid36587372,
year = {2023},
author = {Palmiero, M and Cantarosso, I and di Blasio, L and Monica, V and Peracino, B and Primo, L and Puliafito, A},
title = {Collective directional migration drives the formation of heteroclonal cancer cell clusters.},
journal = {Molecular oncology},
volume = {17},
number = {9},
pages = {1699-1725},
pmid = {36587372},
issn = {1878-0261},
support = {IG 23211//Associazione Italiana per la Ricerca sul Cancro/ ; MFAG 25040//Associazione Italiana per la Ricerca sul Cancro/ ; //Fondazione Piemontese per la Ricerca sul Cancro/ ; //Fondazione Umberto Veronesi/ ; //Italian Ministry of Health/ ; 2019 PULA_RILO_19_01//Università degli Studi di Torino/ ; },
mesh = {Humans ; Cell Movement ; *Phosphatidylinositol 3-Kinases ; Actins/metabolism ; *Neoplasms ; },
abstract = {Metastasisation occurs through the acquisition of invasive and survival capabilities that allow tumour cells to colonise distant sites. While the role of multicellular aggregates in cancer dissemination is acknowledged, the mechanisms that drive the formation of multiclonal cell aggregates are not fully elucidated. Here, we show that cancer cells of different tissue of origins can perform collective directional migration and can actively form heteroclonal aggregates in 3D, through a proliferation-independent mechanism. Coalescence of distant cell clusters is mediated by subcellular actin-rich protrusions and multicellular outgrowths that extend towards neighbouring aggregates. Coherently, perturbation of cytoskeletal dynamics impairs collective migration while myosin II activation is necessary for multicellular movements. We put forward the hypothesis that cluster attraction is mediated by secreted soluble factors. Such a hypothesis is consistent with the abrogation of aggregation by inhibition of PI3K/AKT/mTOR and MEK/ERK, the chemoattracting activity of conditioned culture media and with a wide screening of secreted proteins. Our results present a novel collective migration model and shed light on the mechanisms of formation of heteroclonal aggregates in cancer.},
}

Humans
Cell Movement
*Phosphatidylinositol 3-Kinases
Actins/metabolism
*Neoplasms

@article {pmid37668864,
year = {2023},
author = {Garte, S},
title = {Targeted Hypermutation as a Survival Strategy: A Theoretical Approach.},
journal = {Acta biotheoretica},
volume = {71},
number = {4},
pages = {20},
pmid = {37668864},
issn = {1572-8358},
mesh = {Animals ; Mutation ; *Mutation Rate ; Probability ; *Mammals ; },
abstract = {Targeted hypermutation has proven to be a useful survival strategy for bacteria under severe stress and is also used by multicellular organisms in specific instances such as the mammalian immune system. This might appear surprising, given the generally observed deleterious effects of poor replication fidelity/high mutation rate. A previous theoretical model designed to explore the role of replication fidelity in the origin of life was applied to a simulated hypermutation scenario. The results confirmed that the same model is useful for analyzing hypermutation and can predict the effects of the same parameters (survival probability, replication fidelity, mutation effect, and others) on the survival of cellular populations undergoing hypermutation as a result of severe stress.},
}

Animals
Mutation
*Mutation Rate
Probability
*Mammals

@article {pmid37481138,
year = {2023},
author = {Corallo, D and Dalla Vecchia, M and Lazic, D and Taschner-Mandl, S and Biffi, A and Aveic, S},
title = {The molecular basis of tumor metastasis and current approaches to decode targeted migration-promoting events in pediatric neuroblastoma.},
journal = {Biochemical pharmacology},
volume = {215},
number = {},
pages = {115696},
doi = {10.1016/j.bcp.2023.115696},
pmid = {37481138},
issn = {1873-2968},
mesh = {Humans ; *Neuroblastoma/drug therapy/genetics/pathology ; },
abstract = {Cell motility is a crucial biological process that plays a critical role in the development of multicellular organisms and is essential for tissue formation and regeneration. However, uncontrolled cell motility can lead to the development of various diseases, including neoplasms. In this review, we discuss recent advances in the discovery of regulatory mechanisms underlying the metastatic spread of neuroblastoma, a solid pediatric tumor that originates in the embryonic migratory cells of the neural crest. The highly motile phenotype of metastatic neuroblastoma cells requires targeting of intracellular and extracellular processes, that, if affected, would be helpful for the treatment of high-risk patients with neuroblastoma, for whom current therapies remain inadequate. Development of new potentially migration-inhibiting compounds and standardized preclinical approaches for the selection of anti-metastatic drugs in neuroblastoma will also be discussed.},
}

Humans
*Neuroblastoma/drug therapy/genetics/pathology

@article {pmid37475643,
year = {2023},
author = {Kato, D and Aoyama, Y and Nishida, K and Takahashi, Y and Sakamoto, T and Takeda, I and Tatematsu, T and Go, S and Saito, Y and Kunishima, S and Cheng, J and Hou, L and Tachibana, Y and Sugio, S and Kondo, R and Eto, F and Sato, S and Moorhouse, AJ and Yao, I and Kadomatsu, K and Setou, M and Wake, H},
title = {Regulation of lipid synthesis in myelin modulates neural activity and is required for motor learning.},
journal = {Glia},
volume = {71},
number = {11},
pages = {2591-2608},
doi = {10.1002/glia.24441},
pmid = {37475643},
issn = {1098-1136},
support = {JPMJCR1755//Core Research for Evolutional Science and Technology/ ; JPMJCR22P6//Core Research for Evolutional Science and Technology/ ; 20H05699//Grants-in-Aid for Transformative Research Areas (A)/ ; 21H05587//Grants-in-Aid for Transformative Research Areas (A)/ ; JP23gm1410011 h0002//Japan Agency for Medical Research and Development/ ; JP22ak0101150//Japan Agency for Medical Research and Development/ ; 26710004//Grants-in-Aid for Young Scientists (A)/ ; JPMJFR2145//FOREST program/ ; 20K16574//Grants-in-Aid for Young Scientists/ ; //Nagoya University CIBoG WISE program from MEXT/ ; 25110732//Grants-in-Aid for Scientific Research on Innovative Areas/ ; 19H05219//Grants-in-Aid for Scientific Research on Innovative Areas/ ; 19H04753//Grants-in-Aid for Scientific Research on Innovative Areas/ ; 20KK0170//Fostering Joint International Research (B)/ ; 21H02662//Grants-in-Aid for Scientific Research (B)/ ; 18H02598//Grants-in-Aid for Scientific Research (B)/ ; },
mesh = {Mice ; Animals ; *Myelin Sheath/metabolism ; *Galactosylceramides/metabolism ; Axons/metabolism ; Neurons/metabolism ; Oligodendroglia/physiology ; },
abstract = {Brain function relies on both rapid electrical communication in neural circuitry and appropriate patterns or synchrony of neural activity. Rapid communication between neurons is facilitated by wrapping nerve axons with insulation by a myelin sheath composed largely of different lipids. Recent evidence has indicated that the extent of myelination of nerve axons can adapt based on neural activity levels and this adaptive myelination is associated with improved learning of motor tasks, suggesting such plasticity may enhance effective learning. In this study, we examined whether another aspect of myelin plasticity-changes in myelin lipid synthesis and composition-may also be associated with motor learning. We combined a motor learning task in mice with in vivo two-photon imaging of neural activity in the primary motor cortex (M1) to distinguish early and late stages of learning and then probed levels of some key myelin lipids using mass spectrometry analysis. Sphingomyelin levels were elevated in the early stage of motor learning while galactosylceramide levels were elevated in the middle and late stages of motor learning, and these changes were correlated across individual mice with both learning performance and neural activity changes. Targeted inhibition of oligodendrocyte-specific galactosyltransferase expression, the enzyme that synthesizes myelin galactosylceramide, impaired motor learning. Our results suggest regulation of myelin lipid composition could be a novel facet of myelin adaptations associated with learning.},
}

Mice
Animals
*Myelin Sheath/metabolism
*Galactosylceramides/metabolism
Axons/metabolism
Neurons/metabolism
Oligodendroglia/physiology

@article {pmid37649301,
year = {2023},
author = {Borg, M and Krueger-Hadfield, SA and Destombe, C and Collén, J and Lipinska, A and Coelho, SM},
title = {Red macroalgae in the genomic era.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19211},
pmid = {37649301},
issn = {1469-8137},
support = {//Bettencourt Schuller Foundation/ ; //Gordon and Betty Moore Foundation/ ; 864038//H2020 European Research Council/ ; DEB-2141971//National Science Foundation/ ; //Max Planck Society/ ; },
abstract = {Rhodophyta (or red algae) are a diverse and species-rich group that forms one of three major lineages in the Archaeplastida, a eukaryotic supergroup whose plastids arose from a single primary endosymbiosis. Red algae are united by several features, such as relatively small intron-poor genomes and a lack of cytoskeletal structures associated with motility like flagella and centrioles, as well as a highly efficient photosynthetic capacity. Multicellular red algae (or macroalgae) are one of the earliest diverging eukaryotic lineages to have evolved complex multicellularity, yet despite their ecological, evolutionary, and commercial importance, they have remained a largely understudied group of organisms. Considering the increasing availability of red algal genome sequences, we present a broad overview of fundamental aspects of red macroalgal biology and posit on how this is expected to accelerate research in many domains of red algal biology in the coming years.},
}

@article {pmid37645274,
year = {2022},
author = {Hall, G and Kelly, S and Schaap, P and Schilde, C},
title = {Phylogeny-wide analysis of G-protein coupled receptors in social amoebas and implications for the evolution of multicellularity.},
journal = {Open research Europe},
volume = {2},
number = {},
pages = {134},
pmid = {37645274},
issn = {2732-5121},
abstract = {G-protein coupled receptors (GPCRs) are seven-transmembrane proteins and constitute the largest group of receptors within eukaryotes. The presence of a large set of GPCRs in the unicellular Amoebozoa was surprising and is indicative of the largely undiscovered environmental sensing capabilities in this group. Evolutionary transitions from unicellular to multicellular lifestyles, like we see in social amoebas, have occurred several times independently in the Amoebozoa, and GPCRs may have been co-opted for new functions in cell-cell communication. Methods We have analysed a set of GPCRs from fully sequenced Amoebozoan genomes by Bayesian inference, compared their phylogenetic distribution and domain composition, and analysed their temporal and spatial expression patterns in five species of dictyostelids. Results We found evidence that most GPCRs are conserved deeply in the Amoebozoa and are probably performing roles in general cell functions and complex environmental sensing. All families of GPCRs (apart from the family 4 fungal pheromone receptors) are present in dictyostelids with family 5 being the largest and family 2 the one with the fewest members. For the first time, we identify the presence of family 1 rhodopsin-like GPCRs in dictyostelids. Some GPCRs have been amplified in the dictyostelids and in specific lineages thereof and through changes in expression patterns may have been repurposed for signalling in multicellular development. Discussion Our phylogenetic analysis suggests that GPCR families 1, 2 and 6 already diverged early in the Amoebozoa, whereas families 3 and 5 expanded later within the dictyostelids. The family 6 cAMP receptors that have experimentally supported roles in multicellular development in dictyostelids (carA-carD; tasA/B) originated at the root of all dictyostelids and only have weakly associated homologs in Physarum polycephalum. Our analysis identified candidate GPCRs which have evolved in the dictyostelids and could have been co-opted for multicellular development.},
}

@article {pmid37565532,
year = {2023},
author = {Cervantes, S and Kesälahti, R and Kumpula, TA and Mattila, TM and Helanterä, H and Pyhäjärvi, T},
title = {Strong Purifying Selection in Haploid Tissue-Specific Genes of Scots Pine Supports the Masking Theory.},
journal = {Molecular biology and evolution},
volume = {40},
number = {8},
pages = {},
pmid = {37565532},
issn = {1537-1719},
mesh = {Haploidy ; *Selection, Genetic ; Mutation ; *Biological Evolution ; Diploidy ; Plants ; },
abstract = {The masking theory states that genes expressed in a haploid stage will be under more efficient selection. In contrast, selection will be less efficient in genes expressed in a diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can be hidden from selection in heterozygous form. This difference can influence several evolutionary processes such as the maintenance of genetic variation, adaptation rate, and genetic load. Masking theory expectations have been confirmed in single-cell haploid and diploid organisms. However, in multicellular organisms, such as plants, the effects of haploid selection are not clear-cut. In plants, the great majority of studies indicating haploid selection have been carried out using male haploid tissues in angiosperms. Hence, evidence in these systems is confounded with the effects of sexual selection and intraspecific competition. Evidence from other plant groups is scarce, and results show no support for the masking theory. Here, we have used a gymnosperm Scots pine megagametophyte, a maternally derived seed haploid tissue, and four diploid tissues to test the strength of purifying selection on a set of genes with tissue-specific expression. By using targeted resequencing data of those genes, we obtained estimates of genetic diversity, the site frequency spectrum of 0-fold and 4-fold sites, and inferred the distribution of fitness effects of new mutations in haploid and diploid tissue-specific genes. Our results show that purifying selection is stronger for tissue-specific genes expressed in the haploid megagametophyte tissue and that this signal of strong selection is not an artifact driven by high expression levels.},
}

Haploidy
*Selection, Genetic
Mutation
*Biological Evolution
Diploidy
Plants

@article {pmid37337232,
year = {2023},
author = {Sarkar, MMH and Rahman, MS and Islam, MR and Rahman, A and Islam, MS and Banu, TA and Akter, S and Goswami, B and Jahan, I and Habib, MA and Uddin, MM and Mia, MZ and Miah, MI and Shaikh, AA and Khan, MS},
title = {Comparative phylogenetic analysis and transcriptomic profiling of Dengue (DENV-3 genotype I) outbreak in 2021 in Bangladesh.},
journal = {Virology journal},
volume = {20},
number = {1},
pages = {127},
pmid = {37337232},
issn = {1743-422X},
mesh = {Humans ; Phylogeny ; Bangladesh/epidemiology ; *Transcriptome ; *Dengue/epidemiology ; Disease Outbreaks ; Genotype ; Serogroup ; },
abstract = {BACKGROUND: The next-generation sequencing (NGS) technology facilitates in-depth study of host-pathogen metatranscriptome. We, therefore, implicated phylodynamic and transcriptomic approaches through NGS technology to know/understand the dengue virus (DENV) origin and host response with dengue fever.

METHODS: In this study, blood serum RNA was extracted from 21 dengue patients and 3 healthy individuals. Total transcriptomic data were analyzed for phylogenetic, phylodynamic, differential express gene (DEG), and gene ontology (GO) using respective bioinformatics tools.

RESULTS: The viral genome sequence revealed dengue viral genome size ranges 10647 to 10707 nucleotide. Phylogenetic and phylodynamic analysis showed that the 2021 epidemic isolates were DENV-3 genotype-I and maintained as a new clade in compared to 2019 epidemic. Transcriptome analysis showed a total of 2686 genes were DEG in dengue patients compared to control with a q-value < 0.05. DESeq2 plot counts function of the top 24 genes with the smallest q-values of differential gene expression of RNA-seq data showed that 11 genes were upregulated, whereas 13 genes were downregulated. GO analysis showed a significant upregulation (p = < 0.001) in a process of multicellular organismal, nervous system, sensory perception of chemical stimulus, and G protein-coupled receptor signaling pathways in the dengue patients. However, there were a significant downregulation (p = < 0.001) of intracellular component, cellular anatomical entity, and protein-containing complex in dengue patients. Most importantly, there was a significant increase of a class of immunoregulatory proteins in dengue patients in compared to the controls, with increased GO of immune system process. In addition, upregulation of toll receptor (TLR) signaling pathways were found in dengue patients. These TLR pathways were particularly involved for the activation of innate system coupled with adaptive immune system that probably involved the rapid elimination of dengue virus infected cells. These differentially expressed genes could be further investigated for target based prophylactic interventions for dengue.

CONCLUSION: This is a first report describing DENV complete genomic features and differentially expressed genes in patients in Bangladesh. These genes may have diagnostic and therapeutic values for dengue infection. Continual genomic surveillance is required to further investigate the shift in dominant genotypes in relation to viral pathogenesis.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12985-023-02030-1.},
}

Humans
Phylogeny
Bangladesh/epidemiology
*Transcriptome
*Dengue/epidemiology
Disease Outbreaks
Genotype
Serogroup

@article {pmid37498572,
year = {2023},
author = {Ma, X and Shi, X and Wang, Q and Zhao, M and Zhang, Z and Zhong, B},
title = {A Reinvestigation of Multiple Independent Evolution and Triassic-Jurassic Origins of Multicellular Volvocine Algae.},
journal = {Genome biology and evolution},
volume = {15},
number = {8},
pages = {},
pmid = {37498572},
issn = {1759-6653},
mesh = {Phylogeny ; *Plants ; *Biological Evolution ; },
abstract = {The evolution of multicellular organisms is considered to be a major evolutionary transition, profoundly affecting the ecology and evolution of nearly all life on earth. The volvocine algae, a unique clade of chlorophytes with diverse cell morphology, provide an appealing model for investigating the evolution of multicellularity and development. However, the phylogenetic relationship and timescale of the volvocine algae are not fully resolved. Here, we use extensive taxon and gene sampling to reconstruct the phylogeny of the volvocine algae. Our results support that the colonial volvocine algae are not monophyletic group and multicellularity independently evolve at least twice in the volvocine algae, once in Tetrabaenaceae and another in the Goniaceae + Volvocaceae. The simulation analyses suggest that incomplete lineage sorting is a major factor for the tree topology discrepancy, which imply that the multispecies coalescent model better fits the data used in this study. The coalescent-based species tree supports that the Goniaceae is monophyletic and Crucicarteria is the earliest diverging lineage, followed by Hafniomonas and Radicarteria within the Volvocales. By considering the multiple uncertainties in divergence time estimation, the dating analyses indicate that the volvocine algae occurred during the Cryogenian to Ediacaran (696.6-551.1 Ma) and multicellularity in the volvocine algae originated from the Triassic to Jurassic. Our phylogeny and timeline provide an evolutionary framework for studying the evolution of key traits and the origin of multicellularity in the volvocine algae.},
}

Phylogeny
*Plants
*Biological Evolution

@article {pmid37349567,
year = {2023},
author = {Merényi, Z and Krizsán, K and Sahu, N and Liu, XB and Bálint, B and Stajich, JE and Spatafora, JW and Nagy, LG},
title = {Genomes of fungi and relatives reveal delayed loss of ancestral gene families and evolution of key fungal traits.},
journal = {Nature ecology & evolution},
volume = {7},
number = {8},
pages = {1221-1231},
pmid = {37349567},
issn = {2397-334X},
support = {758161//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; },
mesh = {*Genome, Fungal ; Phylogeny ; *Evolution, Molecular ; Fungi/genetics ; Eukaryota/genetics ; },
abstract = {Fungi are ecologically important heterotrophs that have radiated into most niches on Earth and fulfil key ecological services. Despite intense interest in their origins, major genomic trends of their evolutionary route from a unicellular opisthokont ancestor to derived multicellular fungi remain poorly known. Here we provide a highly resolved genome-wide catalogue of gene family changes across fungal evolution inferred from the genomes of 123 fungi and relatives. We show that a dominant trend in early fungal evolution has been the gradual shedding of protist genes and the punctuated emergence of innovation by two main gene duplication events. We find that the gene content of non-Dikarya fungi resembles that of unicellular opisthokonts in many respects, owing to the conservation of protist genes in their genomes. The most rapidly duplicating gene groups included extracellular proteins and transcription factors, as well as ones linked to the coordination of nutrient uptake with growth, highlighting the transition to a sessile osmotrophic feeding strategy and subsequent lifestyle evolution as important elements of early fungal history. These results suggest that the genomes of pre-fungal ancestors evolved into the typical filamentous fungal genome by a combination of gradual gene loss, turnover and several large duplication events rather than by abrupt changes. Consequently, the taxonomically defined Fungi represents a genomically non-uniform assemblage of species.},
}

*Genome, Fungal
Phylogeny
*Evolution, Molecular
Fungi/genetics
Eukaryota/genetics

@article {pmid37540742,
year = {2023},
author = {Sartor, F and Xu, X and Popp, T and Dodd, AN and Kovács, ÁT and Merrow, M},
title = {The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systems.},
journal = {Science advances},
volume = {9},
number = {31},
pages = {eadh1308},
pmid = {37540742},
issn = {2375-2548},
mesh = {*Circadian Clocks ; Bacillus subtilis ; Circadian Rhythm ; Light ; Eukaryota ; },
abstract = {Circadian clocks are pervasive throughout nature, yet only recently has this adaptive regulatory program been described in nonphotosynthetic bacteria. Here, we describe an inherent complexity in the Bacillus subtilis circadian clock. We find that B. subtilis entrains to blue and red light and that circadian entrainment is separable from masking through fluence titration and frequency demultiplication protocols. We identify circadian rhythmicity in constant light, consistent with the Aschoff's rule, and entrainment aftereffects, both of which are properties described for eukaryotic circadian clocks. We report that circadian rhythms occur in wild isolates of this prokaryote, thus establishing them as a general property of this species, and that its circadian system responds to the environment in a complex fashion that is consistent with multicellular eukaryotic circadian systems.},
}

*Circadian Clocks
Bacillus subtilis
Circadian Rhythm
Light
Eukaryota

@article {pmid37511419,
year = {2023},
author = {Erenpreisa, J and Vainshelbaum, NM and Lazovska, M and Karklins, R and Salmina, K and Zayakin, P and Rumnieks, F and Inashkina, I and Pjanova, D and Erenpreiss, J},
title = {The Price of Human Evolution: Cancer-Testis Antigens, the Decline in Male Fertility and the Increase in Cancer.},
journal = {International journal of molecular sciences},
volume = {24},
number = {14},
pages = {},
pmid = {37511419},
issn = {1422-0067},
mesh = {Pregnancy ; Animals ; Humans ; Male ; Female ; *Testis/metabolism ; Placenta ; Spermatogenesis/genetics ; Reproduction ; *Neoplasms/genetics/metabolism ; Mammals ; Polyploidy ; Fertility/genetics ; },
abstract = {The increasing frequency of general and particularly male cancer coupled with the reduction in male fertility seen worldwide motivated us to seek a potential evolutionary link between these two phenomena, concerning the reproductive transcriptional modules observed in cancer and the expression of cancer-testis antigens (CTA). The phylostratigraphy analysis of the human genome allowed us to link the early evolutionary origin of cancer via the reproductive life cycles of the unicellulars and early multicellulars, potentially driving soma-germ transition, female meiosis, and the parthenogenesis of polyploid giant cancer cells (PGCCs), with the expansion of the CTA multi-families, very late during their evolution. CTA adaptation was aided by retrovirus domestication in the unstable genomes of mammals, for protecting male fertility in stress conditions, particularly that of humans, as compensation for the energy consumption of a large complex brain which also exploited retrotransposition. We found that the early and late evolutionary branches of human cancer are united by the immunity-proto-placental network, which evolved in the Cambrian and shares stress regulators with the finely-tuned sex determination system. We further propose that social stress and endocrine disruption caused by environmental pollution with organic materials, which alter sex determination in male foetuses and further spermatogenesis in adults, bias the development of PGCC-parthenogenetic cancer by default.},
}

Pregnancy
Animals
Humans
Male
Female
*Testis/metabolism
Placenta
Spermatogenesis/genetics
Reproduction
*Neoplasms/genetics/metabolism
Mammals
Polyploidy
Fertility/genetics

@article {pmid37494396,
year = {2023},
author = {Fichman, Y and Rowland, L and Oliver, MJ and Mittler, R},
title = {ROS are evolutionary conserved cell-to-cell stress signals.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {31},
pages = {e2305496120},
pmid = {37494396},
issn = {1091-6490},
support = {R01 GM111364/GM/NIGMS NIH HHS/United States ; GM111364/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Reactive Oxygen Species ; *Hydrogen Peroxide ; *Signal Transduction ; Cell Communication ; Plants ; Mammals ; },
abstract = {Cell-to-cell communication is fundamental to multicellular organisms and unicellular organisms living in a microbiome. It is thought to have evolved as a stress- or quorum-sensing mechanism in unicellular organisms. A unique cell-to-cell communication mechanism that uses reactive oxygen species (ROS) as a signal (termed the "ROS wave") was identified in flowering plants. This process is essential for systemic signaling and plant acclimation to stress and can spread from a small group of cells to the entire plant within minutes. Whether a similar signaling process is found in other organisms is however unknown. Here, we report that the ROS wave can be found in unicellular algae, amoeba, ferns, mosses, mammalian cells, and isolated hearts. We further show that this process can be triggered in unicellular and multicellular organisms by a local stress or H2O2 treatment and blocked by the application of catalase or NADPH oxidase inhibitors and that in unicellular algae it communicates important stress-response signals between cells. Taken together, our findings suggest that an active process of cell-to-cell ROS signaling, like the ROS wave, evolved before unicellular and multicellular organisms diverged. This mechanism could have communicated an environmental stress signal between cells and coordinated the acclimation response of many different cells living in a community. The finding of a signaling process, like the ROS wave, in mammalian cells further contributes to our understanding of different diseases and could impact the development of drugs that target for example cancer or heart disease.},
}

Animals
Reactive Oxygen Species
*Hydrogen Peroxide
*Signal Transduction
Cell Communication
Plants
Mammals

@article {pmid37468829,
year = {2023},
author = {Vroomans, RMA and Colizzi, ES},
title = {Evolution of selfish multicellularity: collective organisation of individual spatio-temporal regulatory strategies.},
journal = {BMC ecology and evolution},
volume = {23},
number = {1},
pages = {35},
pmid = {37468829},
issn = {2730-7182},
mesh = {Animals ; *Biological Evolution ; *Reproduction ; Cell Differentiation ; },
abstract = {BACKGROUND: The unicellular ancestors of modern-day multicellular organisms were remarkably complex. They had an extensive set of regulatory and signalling genes, an intricate life cycle and could change their behaviour in response to environmental changes. At the transition to multicellularity, some of these behaviours were co-opted to organise the development of the nascent multicellular organism. Here, we focus on the transition to multicellularity before the evolution of stable cell differentiation, to reveal how the emergence of clusters affects the evolution of cell behaviour.

RESULTS: We construct a computational model of a population of cells that can evolve the regulation of their behavioural state - either division or migration - and study both a unicellular and a multicellular context. Cells compete for reproduction and for resources to survive in a seasonally changing environment. We find that the evolution of multicellularity strongly determines the co-evolution of cell behaviour, by altering the competition dynamics between cells. When adhesion cannot evolve, cells compete for survival by rapidly migrating towards resources before dividing. When adhesion evolves, emergent collective migration alleviates the pressure on individual cells to reach resources. This allows individual cells to maximise their own replication. Migrating adhesive clusters display striking patterns of spatio-temporal cell state changes that visually resemble animal development.

CONCLUSIONS: Our model demonstrates how emergent selection pressures at the onset of multicellularity can drive the evolution of cellular behaviour to give rise to developmental patterns.},
}

Animals
*Biological Evolution
*Reproduction
Cell Differentiation

@article {pmid37445995,
year = {2023},
author = {Endres, K and Friedland, K},
title = {Talk to Me-Interplay between Mitochondria and Microbiota in Aging.},
journal = {International journal of molecular sciences},
volume = {24},
number = {13},
pages = {},
pmid = {37445995},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome/physiology ; *Microbiota ; Mitochondria ; Bacteria/metabolism ; },
abstract = {The existence of mitochondria in eukaryotic host cells as a remnant of former microbial organisms has been widely accepted, as has their fundamental role in several diseases and physiological aging. In recent years, it has become clear that the health, aging, and life span of multicellular hosts are also highly dependent on the still-residing microbiota, e.g., those within the intestinal system. Due to the common evolutionary origin of mitochondria and these microbial commensals, it is intriguing to investigate if there might be a crosstalk based on preserved common properties. In the light of rising knowledge on the gut-brain axis, such crosstalk might severely affect brain homeostasis in aging, as neuronal tissue has a high energy demand and low tolerance for according functional decline. In this review, we summarize what is known about the impact of both mitochondria and the microbiome on the host's aging process and what is known about the aging of both entities. For a long time, bacteria were assumed to be immortal; however, recent evidence indicates their aging and similar observations have been made for mitochondria. Finally, we present pathways by which mitochondria are affected by microbiota and give information about therapeutic anti-aging approaches that are based on current knowledge.},
}

*Gastrointestinal Microbiome/physiology
*Microbiota
Mitochondria
Bacteria/metabolism

@article {pmid37436957,
year = {2023},
author = {Geng, S and Hamaji, T and Ferris, PJ and Gao, M and Nishimura, Y and Umen, J},
title = {A conserved RWP-RK transcription factor VSR1 controls gametic differentiation in volvocine algae.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {29},
pages = {e2305099120},
doi = {10.1073/pnas.2305099120},
pmid = {37436957},
issn = {1091-6490},
support = {R01GM078376/NH/NIH HHS/United States ; },
mesh = {*Seeds ; Sex ; Reproduction ; Germ Cells ; Spermatozoa ; Biotin ; *Chlamydomonas ; },
abstract = {Volvocine green algae are a model for understanding the evolution of mating types and sexes. They are facultatively sexual, with gametic differentiation occurring in response to nitrogen starvation (-N) in most genera and to sex inducer hormone in Volvox. The conserved RWP-RK family transcription factor (TF) MID is encoded by the minus mating-type locus or male sex-determining region of heterothallic volvocine species and dominantly determines minus or male gametic differentiation. However, the factor(s) responsible for establishing the default plus or female differentiation programs have remained elusive. We performed a phylo-transcriptomic screen for autosomal RWP-RK TFs induced during gametogenesis in unicellular isogamous Chlamydomonas reinhardtii (Chlamydomonas) and in multicellular oogamous Volvox carteri (Volvox) and identified a single conserved ortho-group we named Volvocine Sex Regulator 1 (VSR1). Chlamydomonas vsr1 mutants of either mating type failed to mate and could not induce expression of key mating-type-specific genes. Similarly, Volvox vsr1 mutants in either sex could initiate sexual embryogenesis, but the presumptive eggs or androgonidia (sperm packet precursors) were infertile and unable to express key sex-specific genes. Yeast two-hybrid assays identified a conserved domain in VSR1 capable of self-interaction or interaction with the conserved N terminal domain of MID. In vivo coimmunoprecipitation experiments demonstrated association of VSR1 and MID in both Chlamydomonas and Volvox. These data support a new model for volvocine sexual differentiation where VSR1 homodimers activate expression of plus/female gamete-specific-genes, but when MID is present, MID-VSR1 heterodimers are preferentially formed and activate minus/male gamete-specific-genes.},
}

*Seeds
Sex
Reproduction
Germ Cells
Spermatozoa
Biotin
*Chlamydomonas

@article {pmid37436868,
year = {2023},
author = {Mondal, A and Bansal, MS},
title = {Generalizing the Domain-Gene-Species Reconciliation Framework to Microbial Genes and Domains.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBB.2023.3294480},
pmid = {37436868},
issn = {1557-9964},
abstract = {Protein domains play an important role in the function and evolution of many gene families. Previous studies have shown that domains are frequently lost or gained during gene family evolution. Yet, most computational approaches for studying gene family evolution do not account for domain-level evolution within genes. To address this limitation, a new three-level reconciliation framework, called the Domain-Gene-Species (DGS) reconciliation model, has been recently developed to simultaneously model the evolution of a domain family inside one or more gene families and the evolution of those gene families inside a species tree. However, the existing model applies only to multi-cellular eukaryotes where horizontal gene transfer is negligible. In this work, we generalize the existing DGS reconciliation model by allowing for the spread of genes and domains across species boundaries through horizontal transfer. We show that the problem of computing optimal generalized DGS reconciliations, though NP-hard, is approximable to within a constant factor, where the specific approximation ratio depends on the "event costs" used. We provide two different approximation algorithms for the problem and demonstrate the impact of the generalized framework using both simulated and real biological data. Our results show that our new algorithms result in highly accurate reconstructions of domain family evolution for microbes.},
}

@article {pmid37401921,
year = {2023},
author = {Stevenson, ZC and Moerdyk-Schauwecker, MJ and Banse, SA and Patel, DS and Lu, H and Phillips, PC},
title = {High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS).},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {37401921},
issn = {2050-084X},
support = {R01 AG056436/AG/NIA NIH HHS/United States ; R35 GM131838/GM/NIGMS NIH HHS/United States ; R01AG056436/NH/NIH HHS/United States ; R35GM131838/NH/NIH HHS/United States ; },
mesh = {Humans ; Animals ; *Caenorhabditis elegans/genetics ; Transgenes ; Animals, Genetically Modified ; *Gene Transfer Techniques ; Gene Library ; },
abstract = {High-throughput transgenesis using synthetic DNA libraries is a powerful method for systematically exploring genetic function. Diverse synthesized libraries have been used for protein engineering, identification of protein-protein interactions, characterization of promoter libraries, developmental and evolutionary lineage tracking, and various other exploratory assays. However, the need for library transgenesis has effectively restricted these approaches to single-cell models. Here, we present Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS), a simple yet powerful approach to large-scale transgenesis that overcomes typical limitations encountered in multicellular systems. TARDIS splits the transgenesis process into a two-step process: creation of individuals carrying experimentally introduced sequence libraries, followed by inducible extraction and integration of individual sequences/library components from the larger library cassette into engineered genomic sites. Thus, transformation of a single individual, followed by lineage expansion and functional transgenesis, gives rise to thousands of genetically unique transgenic individuals. We demonstrate the power of this system using engineered, split selectable TARDIS sites in Caenorhabditis elegans to generate (1) a large set of individually barcoded lineages and (2) transcriptional reporter lines from predefined promoter libraries. We find that this approach increases transformation yields up to approximately 1000-fold over current single-step methods. While we demonstrate the utility of TARDIS using C. elegans, in principle the process is adaptable to any system where experimentally generated genomic loci landing pads and diverse, heritable DNA elements can be generated.},
}

Humans
Animals
*Caenorhabditis elegans/genetics
Transgenes
Animals, Genetically Modified
*Gene Transfer Techniques
Gene Library

@article {pmid37384647,
year = {2023},
author = {Kapsetaki, SE and Fortunato, A and Compton, Z and Rupp, SM and Nour, Z and Riggs-Davis, S and Stephenson, D and Duke, EG and Boddy, AM and Harrison, TM and Maley, CC and Aktipis, A},
title = {Is chimerism associated with cancer across the tree of life?.},
journal = {PloS one},
volume = {18},
number = {6},
pages = {e0287901},
pmid = {37384647},
issn = {1932-6203},
mesh = {Animals ; *Chimerism ; *Neoplasms/genetics ; Problem Solving ; Mammals ; },
abstract = {Chimerism is a widespread phenomenon across the tree of life. It is defined as a multicellular organism composed of cells from other genetically distinct entities. This ability to 'tolerate' non-self cells may be linked to susceptibility to diseases like cancer. Here we test whether chimerism is associated with cancers across obligately multicellular organisms in the tree of life. We classified 12 obligately multicellular taxa from lowest to highest chimerism levels based on the existing literature on the presence of chimerism in these species. We then tested for associations of chimerism with tumour invasiveness, neoplasia (benign or malignant) prevalence and malignancy prevalence in 11 terrestrial mammalian species. We found that taxa with higher levels of chimerism have higher tumour invasiveness, though there was no association between malignancy or neoplasia and chimerism among mammals. This suggests that there may be an important biological relationship between chimerism and susceptibility to tissue invasion by cancerous cells. Studying chimerism might help us identify mechanisms underlying invasive cancers and also could provide insights into the detection and management of emerging transmissible cancers.},
}

Animals
*Chimerism
*Neoplasms/genetics
Problem Solving
Mammals

@article {pmid37384391,
year = {2023},
author = {Römling, U and Cao, LY and Bai, FW},
title = {Evolution of cyclic di-GMP signalling on a short and long term time scale.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {6},
pages = {},
pmid = {37384391},
issn = {1465-2080},
mesh = {Humans ; *Signal Transduction ; *Second Messenger Systems ; Amino Acid Substitution ; Biofilms ; Gene Transfer, Horizontal ; },
abstract = {Diversifying radiation of domain families within specific lineages of life indicates the importance of their functionality for the organisms. The foundation for the diversifying radiation of the cyclic di-GMP signalling network that occurred within the bacterial kingdom is most likely based in the outmost adaptability, flexibility and plasticity of the system. Integrative sensing of multiple diverse extra- and intracellular signals is made possible by the N-terminal sensory domains of the modular cyclic di-GMP turnover proteins, mutations in the protein scaffolds and subsequent signal reception by diverse receptors, which eventually rewires opposite host-associated as well as environmental life styles including parallel regulated target outputs. Natural, laboratory and microcosm derived microbial variants often with an altered multicellular biofilm behaviour as reading output demonstrated single amino acid substitutions to substantially alter catalytic activity including substrate specificity. Truncations and domain swapping of cyclic di-GMP signalling genes and horizontal gene transfer suggest rewiring of the network. Presence of cyclic di-GMP signalling genes on horizontally transferable elements in particular observed in extreme acidophilic bacteria indicates that cyclic di-GMP signalling and biofilm components are under selective pressure in these types of environments. On a short and long term evolutionary scale, within a species and in families within bacterial orders, respectively, the cyclic di-GMP signalling network can also rapidly disappear. To investigate variability of the cyclic di-GMP signalling system on various levels will give clues about evolutionary forces and discover novel physiological and metabolic pathways affected by this intriguing second messenger signalling system.},
}

Humans
*Signal Transduction
*Second Messenger Systems
Amino Acid Substitution
Biofilms
Gene Transfer, Horizontal

@article {pmid37382119,
year = {2023},
author = {Saritas, T},
title = {The use of tissue clearing to study renal transport mechanisms and kidney remodelling.},
journal = {Current opinion in nephrology and hypertension},
volume = {32},
number = {5},
pages = {458-466},
doi = {10.1097/MNH.0000000000000904},
pmid = {37382119},
issn = {1473-6543},
mesh = {Animals ; Humans ; *Imaging, Three-Dimensional/methods ; *Kidney ; },
abstract = {PURPOSE OF REVIEW: Tissue clearing enables examination of biological structures at subcellular resolution in three dimensions. It uncovered the spatial and temporal plasticity of multicellular kidney structures that occur during homeostatic stress. This article will review the recent development in tissue clearing protocols and how it facilitated the study of renal transport mechanisms and remodelling of the kidney.

RECENT FINDINGS: Tissue clearing methods have evolved from primarily labelling proteins in thin tissue or individual organs to visualizing both RNA and protein simultaneously in whole animals or human organs. The use of small antibody fragments and innovative imaging techniques improved immunolabelling and resolution. These advances opened up new avenues for studying organ crosstalk and diseases that affect multiple parts of the organism. Accumulating evidence suggests that tubule remodelling can occur rapidly in response to homeostatic stress or injury, allowing for adjustments in the quantitative expression of renal transporters. Tissue clearing helped to better understand the development of tubule cystogenesis, renal hypertension and salt wasting syndromes, and revealed potential progenitor cells in the kidney.

SUMMARY: The continued evolution and improvement of tissue clearing methods can help to gain deep biological insights into the structure and function of the kidney, which will have clinical implications.},
}

Animals
Humans
*Imaging, Three-Dimensional/methods
*Kidney

@article {pmid37379342,
year = {2023},
author = {Zare, M and Mirhoseini, SZ and Ghovvati, S and Yakhkeshi, S and Hesaraki, M and Barati, M and Sayyahpour, FA and Baharvand, H and Hassani, SN},
title = {The constitutively active pSMAD2/3 relatively improves the proliferation of chicken primordial germ cells.},
journal = {Molecular reproduction and development},
volume = {90},
number = {6},
pages = {339-357},
doi = {10.1002/mrd.23689},
pmid = {37379342},
issn = {1098-2795},
mesh = {Animals ; *Chickens/metabolism ; *Transforming Growth Factor beta/metabolism ; Transcription Factors/metabolism ; Germ Cells ; Cell Proliferation ; Cells, Cultured ; },
abstract = {In many multicellular organisms, mature gametes originate from primordial germ cells (PGCs). Improvements in the culture of PGCs are important not only for developmental biology research, but also for preserving endangered species, and for genome editing and transgenic animal technologies. SMAD2/3 appear to be powerful regulators of gene expression; however, their potential positive impact on the regulation of PGC proliferation has not been taken into consideration. Here, the effect of TGF-β signaling as the upstream activator of SMAD2/3 transcription factors was evaluated on chicken PGCs' proliferation. For this, chicken PGCs at stages 26-28 Hamburger-Hamilton were obtained from the embryonic gonadal regions and cultured on different feeders or feeder-free substrates. The results showed that TGF-β signaling agonists (IDE1 and Activin-A) improved PGC proliferation to some extent while treatment with SB431542, the antagonist of TGF-β, disrupted PGCs' proliferation. However, the transfection of PGCs with constitutively active SMAD2/3 (SMAD2/3CA) resulted in improved PGC proliferation for more than 5 weeks. The results confirmed the interactions between overexpressed SMAD2/3CA and pluripotency-associated genes NANOG, OCT4, and SOX2. According to the results, the application of SMAD2/3CA could represent a step toward achieving an efficient expansion of avian PGCs.},
}

Animals
*Chickens/metabolism
*Transforming Growth Factor beta/metabolism
Transcription Factors/metabolism
Germ Cells
Cell Proliferation
Cells, Cultured

@article {pmid37353784,
year = {2023},
author = {Fang, H and Sun, Q and Zhou, J and Zhang, H and Song, Q and Zhang, H and Yu, G and Guo, Y and Huang, C and Mou, Y and Jia, C and Song, Y and Liu, A and Song, K and Lu, C and Tian, R and Wei, S and Yang, D and Chen, Y and Li, T and Wang, K and Yu, Y and Lv, Y and Mo, K and Sun, P and Yu, X and Song, X},
title = {m[6]A methylation reader IGF2BP2 activates endothelial cells to promote angiogenesis and metastasis of lung adenocarcinoma.},
journal = {Molecular cancer},
volume = {22},
number = {1},
pages = {99},
pmid = {37353784},
issn = {1476-4598},
support = {ts20190991//Taishan Scholars Project/ ; ZR2021MH323//The Natural Science Fund of Shandong Province grant/ ; 2022YD037//The Science and Technology Innovation Development Plan of Yantai/ ; 201909370036//China Scholarship Council/ ; 82103646//The National Natural Science Fund of China grant/ ; },
mesh = {Humans ; Methylation ; Ecosystem ; Endothelial Cells ; Phosphatidylinositol 3-Kinases ; Neoplasm Recurrence, Local ; *Adenocarcinoma of Lung/genetics ; *Lung Neoplasms/genetics ; Tumor Microenvironment ; RNA-Binding Proteins/genetics ; },
abstract = {BACKGROUND: Lung adenocarcinoma (LUAD) is a common type of lung cancer with a high risk of metastasis, but the exact molecular mechanisms of metastasis are not yet understood.

METHODS: This study acquired single-cell transcriptomics profiling of 11 distal normal lung tissues, 11 primary LUAD tissues, and 4 metastatic LUAD tissues from the GSE131907 dataset. The lung multicellular ecosystems were characterized at a single-cell resolution, and the potential mechanisms underlying angiogenesis and metastasis of LUAD were explored.

RESULTS: We constructed a global single-cell landscape of 93,610 cells from primary and metastatic LUAD and found that IGF2BP2 was specifically expressed both in a LUAD cell subpopulation (termed as LUAD_IGF2BP2), and an endothelial cell subpopulation (termed as En_IGF2BP2). The LUAD_IGF2BP2 subpopulation progressively formed and dominated the ecology of metastatic LUAD during metastatic evolution. IGF2BP2 was preferentially secreted by exosomes in the LUAD_IGF2BP2 subpopulation, which was absorbed by the En_IGF2BP2 subpopulation in the tumor microenvironment. Subsequently, IGF2BP2 improved the RNA stability of FLT4 through m[6]A modification, thereby activating the PI3K-Akt signaling pathway, and eventually promoting angiogenesis and metastasis. Analysis of clinical data showed that IGF2BP2 was linked with poor overall survival and relapse-free survival for LUAD patients.

CONCLUSIONS: Overall, these findings provide a novel insight into the multicellular ecosystems of primary and metastatic LUAD, and demonstrate that a specific LUAD_IGF2BP2 subpopulation is a key orchestrator promoting angiogenesis and metastasis, with implications for the gene regulatory mechanisms of LUAD metastatic evolution, representing themselves as potential antiangiogenic targets.},
}

Humans
Methylation
Ecosystem
Endothelial Cells
Phosphatidylinositol 3-Kinases
Neoplasm Recurrence, Local
*Adenocarcinoma of Lung/genetics
*Lung Neoplasms/genetics
Tumor Microenvironment
RNA-Binding Proteins/genetics

@article {pmid37338964,
year = {2023},
author = {Caspi, Y and Pantazopoulou, CK and Prompers, JJ and Pieterse, CMJ and Hulshoff Pol, H and Kajala, K},
title = {Why did glutamate, GABA, and melatonin become intercellular signalling molecules in plants?.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {37338964},
issn = {2050-084X},
mesh = {Animals ; *Melatonin/metabolism ; Glutamic Acid/metabolism ; Plants/metabolism ; gamma-Aminobutyric Acid/metabolism ; Signal Transduction ; },
abstract = {Intercellular signalling is an indispensable part of multicellular life. Understanding the commonalities and differences in how signalling molecules function in two remote branches of the tree of life may shed light on the reasons these molecules were originally recruited for intercellular signalling. Here we review the plant function of three highly studied animal intercellular signalling molecules, namely glutamate, γ-aminobutyric acid (GABA), and melatonin. By considering both their signalling function in plants and their broader physiological function, we suggest that molecules with an original function as key metabolites or active participants in reactive ion species scavenging have a high chance of becoming intercellular signalling molecules. Naturally, the evolution of machinery to transduce a message across the plasma membrane is necessary. This fact is demonstrated by three other well-studied animal intercellular signalling molecules, namely serotonin, dopamine, and acetylcholine, for which there is currently no evidence that they act as intercellular signalling molecules in plants.},
}

Animals
*Melatonin/metabolism
Glutamic Acid/metabolism
Plants/metabolism
gamma-Aminobutyric Acid/metabolism
Signal Transduction

@article {pmid37322016,
year = {2023},
author = {Chavhan, Y and Dey, S and Lind, PA},
title = {Bacteria evolve macroscopic multicellularity by the genetic assimilation of phenotypically plastic cell clustering.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3555},
pmid = {37322016},
issn = {2041-1723},
mesh = {*Biological Evolution ; *Eukaryota ; Adaptation, Physiological ; Phenotype ; Bacteria ; },
abstract = {The evolutionary transition from unicellularity to multicellularity was a key innovation in the history of life. Experimental evolution is an important tool to study the formation of undifferentiated cellular clusters, the likely first step of this transition. Although multicellularity first evolved in bacteria, previous experimental evolution research has primarily used eukaryotes. Moreover, it focuses on mutationally driven (and not environmentally induced) phenotypes. Here we show that both Gram-negative and Gram-positive bacteria exhibit phenotypically plastic (i.e., environmentally induced) cell clustering. Under high salinity, they form elongated clusters of ~ 2 cm. However, under habitual salinity, the clusters disintegrate and grow planktonically. We used experimental evolution with Escherichia coli to show that such clustering can be assimilated genetically: the evolved bacteria inherently grow as macroscopic multicellular clusters, even without environmental induction. Highly parallel mutations in genes linked to cell wall assembly formed the genomic basis of assimilated multicellularity. While the wildtype also showed cell shape plasticity across high versus low salinity, it was either assimilated or reversed after evolution. Interestingly, a single mutation could genetically assimilate multicellularity by modulating plasticity at multiple levels of organization. Taken together, we show that phenotypic plasticity can prime bacteria for evolving undifferentiated macroscopic multicellularity.},
}

*Biological Evolution
*Eukaryota
Adaptation, Physiological
Phenotype
Bacteria

@article {pmid37295595,
year = {2023},
author = {Jacob, MS},
title = {Toward a Bio-Organon: A model of interdependence between energy, information and knowledge in living systems.},
journal = {Bio Systems},
volume = {230},
number = {},
pages = {104939},
doi = {10.1016/j.biosystems.2023.104939},
pmid = {37295595},
issn = {1872-8324},
mesh = {Humans ; *Biological Evolution ; *Models, Theoretical ; },
abstract = {What is an organism? In the absence of a fundamental biological definition, what constitutes a living organism, whether it is a unicellular microbe, a multicellular being or a multi-organismal society, remains an open question. New models of living systems are needed to address the scale of this question, with implications for the relationship between humanity and planetary ecology. Here we develop a generic model of an organism that can be applied across multiple scales and through major evolutionary transitions to form a toolkit, or bio-organon, for theoretical studies of planetary-wide physiology. The tool identifies the following core organismic principles that cut across spatial scale: (1) evolvability through self-knowledge, (2) entanglement between energy and information, and (3) extrasomatic "technology" to scaffold increases in spatial scale. Living systems are generally defined by their ability to self-sustain against entropic forces of degradation. Life "knows" how to survive from the inside, not from its genetic code alone, but by utilizing this code through dynamically embodied and functionally specialized flows of information and energy. That is, entangled metabolic and communication networks bring encoded knowledge to life in order to sustain life. However, knowledge is itself evolved and is evolving. The functional coupling between knowledge, energy and information has ancient origins, enabling the original, cellular "biotechnology," and cumulative evolutionary creativity in biochemical products and forms. Cellular biotechnology also enabled the nesting of specialized cells into multicellular organisms. This nested organismal hierarchy can be extended further, suggesting that an organism of organisms, or a human "superorganism," is not only possible, but in keeping with evolutionary trends.},
}

Humans
*Biological Evolution
*Models, Theoretical

@article {pmid37285440,
year = {2023},
author = {Zhang, F and Ji, Q and Chaturvedi, J and Morales, M and Mao, Y and Meng, X and Dong, L and Deng, J and Qian, SB and Xiang, Y},
title = {Human SAMD9 is a poxvirus-activatable anticodon nuclease inhibiting codon-specific protein synthesis.},
journal = {Science advances},
volume = {9},
number = {23},
pages = {eadh8502},
pmid = {37285440},
issn = {2375-2548},
support = {R01 AI151638/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Anticodon/genetics ; *RNA, Transfer, Phe/genetics/metabolism ; Codon ; RNA, Transfer/metabolism ; Intracellular Signaling Peptides and Proteins/genetics ; },
abstract = {As a defense strategy against viruses or competitors, some microbes use anticodon nucleases (ACNases) to deplete essential tRNAs, effectively halting global protein synthesis. However, this mechanism has not been observed in multicellular eukaryotes. Here, we report that human SAMD9 is an ACNase that specifically cleaves phenylalanine tRNA (tRNA[Phe]), resulting in codon-specific ribosomal pausing and stress signaling. While SAMD9 ACNase activity is normally latent in cells, it can be activated by poxvirus infection or rendered constitutively active by SAMD9 mutations associated with various human disorders, revealing tRNA[Phe] depletion as an antiviral mechanism and a pathogenic condition in SAMD9 disorders. We identified the N-terminal effector domain of SAMD9 as the ACNase, with substrate specificity primarily determined by a eukaryotic tRNA[Phe]-specific 2'-O-methylation at the wobble position, making virtually all eukaryotic tRNA[Phe] susceptible to SAMD9 cleavage. Notably, the structure and substrate specificity of SAMD9 ACNase differ from known microbial ACNases, suggesting convergent evolution of a common immune defense strategy targeting tRNAs.},
}

Humans
*Anticodon/genetics
*RNA, Transfer, Phe/genetics/metabolism
Codon
RNA, Transfer/metabolism
Intracellular Signaling Peptides and Proteins/genetics

@article {pmid37264211,
year = {2023},
author = {Lamolle, G and Simón, D and Iriarte, A and Musto, H},
title = {Main Factors Shaping Amino Acid Usage Across Evolution.},
journal = {Journal of molecular evolution},
volume = {91},
number = {4},
pages = {382-390},
pmid = {37264211},
issn = {1432-1432},
mesh = {Animals ; *Amino Acids/genetics ; Codon/genetics ; *Genetic Code ; Base Composition ; Proteome/genetics ; Evolution, Molecular ; Mammals/genetics ; },
abstract = {The standard genetic code determines that in most species, including viruses, there are 20 amino acids that are coded by 61 codons, while the other three codons are stop triplets. Considering the whole proteome each species features its own amino acid frequencies, given the slow rate of change, closely related species display similar GC content and amino acids usage. In contrast, distantly related species display different amino acid frequencies. Furthermore, within certain multicellular species, as mammals, intragenomic differences in the usage of amino acids are evident. In this communication, we shall summarize some of the most prominent and well-established factors that determine the differences found in the amino acid usage, both across evolution and intragenomically.},
}

Animals
*Amino Acids/genetics
Codon/genetics
*Genetic Code
Base Composition
Proteome/genetics
Evolution, Molecular
Mammals/genetics

@article {pmid37264002,
year = {2023},
author = {Galand, PE and Ruscheweyh, HJ and Salazar, G and Hochart, C and Henry, N and Hume, BCC and Oliveira, PH and Perdereau, A and Labadie, K and Belser, C and Boissin, E and Romac, S and Poulain, J and Bourdin, G and Iwankow, G and Moulin, C and Armstrong, EJ and Paz-García, DA and Ziegler, M and Agostini, S and Banaigs, B and Boss, E and Bowler, C and de Vargas, C and Douville, E and Flores, M and Forcioli, D and Furla, P and Gilson, E and Lombard, F and Pesant, S and Reynaud, S and Thomas, OP and Troublé, R and Zoccola, D and Voolstra, CR and Thurber, RV and Sunagawa, S and Wincker, P and Allemand, D and Planes, S},
title = {Diversity of the Pacific Ocean coral reef microbiome.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3039},
pmid = {37264002},
issn = {2041-1723},
mesh = {Animals ; Coral Reefs ; Pacific Ocean ; *Anthozoa ; Biodiversity ; *Microbiota ; Fishes ; Plankton ; },
abstract = {Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.},
}

Animals
Coral Reefs
Pacific Ocean
*Anthozoa
Biodiversity
*Microbiota
Fishes
Plankton

@article {pmid37256696,
year = {2023},
author = {Blomme, J and Wichard, T and Jacobs, TB and De Clerck, O},
title = {Ulva: An emerging green seaweed model for systems biology.},
journal = {Journal of phycology},
volume = {59},
number = {3},
pages = {433-440},
doi = {10.1111/jpy.13341},
pmid = {37256696},
issn = {1529-8817},
mesh = {*Ulva ; *Seaweed ; Ecosystem ; Systems Biology ; *Chlorophyta ; },
abstract = {Green seaweeds exhibit a wide range of morphologies and occupy various ecological niches, spanning from freshwater to marine and terrestrial habitats. These organisms, which predominantly belong to the class Ulvophyceae, showcase a remarkable instance of parallel evolution toward complex multicellularity and macroscopic thalli in the Viridiplantae lineage. Within the green seaweeds, several Ulva species ("sea lettuce") are model organisms for studying carbon assimilation, interactions with bacteria, life cycle progression, and morphogenesis. Ulva species are also notorious for their fast growth and capacity to dominate nutrient-rich, anthropogenically disturbed coastal ecosystems during "green tide" blooms. From an economic perspective, Ulva has garnered increasing attention as a promising feedstock for the production of food, feed, and biobased products, also as a means of removing excess nutrients from the environment. We propose that Ulva is poised to further develop as a model in green seaweed research. In this perspective, we focus explicitly on Ulva mutabilis/compressa as a model species and highlight the molecular data and tools that are currently available or in development. We discuss several areas that will benefit from future research or where exciting new developments have been reported in other Ulva species.},
}

*Ulva
*Seaweed
Ecosystem
Systems Biology
*Chlorophyta

@article {pmid37256290,
year = {2023},
author = {Jiang, P and Kreitman, M and Reinitz, J},
title = {The effect of mutational robustness on the evolvability of multicellular organisms and eukaryotic cells.},
journal = {Journal of evolutionary biology},
volume = {36},
number = {6},
pages = {906-924},
pmid = {37256290},
issn = {1420-9101},
support = {R01 OD010936/OD/NIH HHS/United States ; },
mesh = {*Evolution, Molecular ; *Eukaryotic Cells ; Models, Genetic ; Mutation ; Phenotype ; },
abstract = {Canalization involves mutational robustness, the lack of phenotypic change as a result of genetic mutations. Given the large divergence in phenotype across species, understanding the relationship between high robustness and evolvability has been of interest to both theorists and experimentalists. Although canalization was originally proposed in the context of multicellular organisms, the effect of multicellularity and other classes of hierarchical organization on evolvability has not been considered by theoreticians. We address this issue using a Boolean population model with explicit representation of an environment in which individuals with explicit genotype and a hierarchical phenotype representing multicellularity evolve. Robustness is described by a single real number between zero and one which emerges from the genotype-phenotype map. We find that high robustness is favoured in constant environments, and lower robustness is favoured after environmental change. Multicellularity and hierarchical organization severely constrain robustness: peak evolvability occurs at an absolute level of robustness of about 0.99 compared with values of about 0.5 in a classical neutral network model. These constraints result in a sharp peak of evolvability in which the maximum is set by the fact that the fixation of adaptive mutations becomes more improbable as robustness decreases. When robustness is put under genetic control, robustness levels leading to maximum evolvability are selected for, but maximal relative fitness appears to require recombination.},
}

*Evolution, Molecular
*Eukaryotic Cells
Models, Genetic
Mutation
Phenotype

@article {pmid37253212,
year = {2023},
author = {Hoch, NC},
title = {Tissue Specificity of DNA Damage and Repair.},
journal = {Physiology (Bethesda, Md.)},
volume = {38},
number = {5},
pages = {0},
doi = {10.1152/physiol.00006.2023},
pmid = {37253212},
issn = {1548-9221},
mesh = {Humans ; Organ Specificity ; *DNA Damage ; *DNA Repair ; Aging/genetics ; DNA/genetics/metabolism ; },
abstract = {DNA is a remarkable biochemical macromolecule tasked with storing the genetic information that instructs life on planet Earth. However, its inherent chemical instability within the cellular milieu is incompatible with the accurate transmission of genetic information to subsequent generations. Therefore, biochemical pathways that continuously survey and repair DNA are essential to sustain life, and the fundamental mechanisms by which different DNA lesions are repaired have remained well conserved throughout evolution. Nonetheless, the emergence of multicellular organisms led to profound differences in cellular context and physiology, leading to large variations in the predominant sources of DNA damage between different cell types and in the relative contribution of different DNA repair pathways toward genome maintenance in different tissues. While we continue to make large strides into understanding how individual DNA repair mechanisms operate on a molecular level, much less attention is given to these cell type-specific differences. This short review aims to provide a broad overview of DNA damage and repair mechanisms to nonspecialists and to highlight some fundamental open questions in tissue and cell-type-specificity of these processes, which may have profound implications for our understanding of important pathophysiological processes such as cancer, neurodegeneration, and aging.},
}

Humans
Organ Specificity
*DNA Damage
*DNA Repair
Aging/genetics
DNA/genetics/metabolism

@article {pmid37247371,
year = {2023},
author = {McCourt, RM and Lewis, LA and Strother, PK and Delwiche, CF and Wickett, NJ and de Vries, J and Bowman, JL},
title = {Green land: Multiple perspectives on green algal evolution and the earliest land plants.},
journal = {American journal of botany},
volume = {110},
number = {5},
pages = {e16175},
doi = {10.1002/ajb2.16175},
pmid = {37247371},
issn = {1537-2197},
mesh = {Biological Evolution ; Ecosystem ; *Embryophyta/genetics ; Phylogeny ; Plants/genetics ; *Chlorophyta/genetics ; Evolution, Molecular ; },
abstract = {Green plants, broadly defined as green algae and the land plants (together, Viridiplantae), constitute the primary eukaryotic lineage that successfully colonized Earth's emergent landscape. Members of various clades of green plants have independently made the transition from fully aquatic to subaerial habitats many times throughout Earth's history. The transition, from unicells or simple filaments to complex multicellular plant bodies with functionally differentiated tissues and organs, was accompanied by innovations built upon a genetic and phenotypic toolkit that have served aquatic green phototrophs successfully for at least a billion years. These innovations opened an enormous array of new, drier places to live on the planet and resulted in a huge diversity of land plants that have dominated terrestrial ecosystems over the past 500 million years. This review examines the greening of the land from several perspectives, from paleontology to phylogenomics, to water stress responses and the genetic toolkit shared by green algae and plants, to the genomic evolution of the sporophyte generation. We summarize advances on disparate fronts in elucidating this important event in the evolution of the biosphere and the lacunae in our understanding of it. We present the process not as a step-by-step advancement from primitive green cells to an inevitable success of embryophytes, but rather as a process of adaptations and exaptations that allowed multiple clades of green plants, with various combinations of morphological and physiological terrestrialized traits, to become diverse and successful inhabitants of the land habitats of Earth.},
}

Biological Evolution
Ecosystem
*Embryophyta/genetics
Phylogeny
Plants/genetics
*Chlorophyta/genetics
Evolution, Molecular

@article {pmid37233789,
year = {2023},
author = {Wu, N and Wei, L and Zhu, Z and Liu, Q and Li, K and Mao, F and Qiao, J and Zhao, X},
title = {Innovative insights into extrachromosomal circular DNAs in gynecologic tumors and reproduction.},
journal = {Protein & cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/procel/pwad032},
pmid = {37233789},
issn = {1674-8018},
abstract = {Originating but free from chromosomal DNA, extrachromosomal circular DNAs (eccDNAs) are organized in circular form and have long been found in unicellular and multicellular eukaryotes. Their biogenesis and function are poorly understood as they are characterized by sequence homology with linear DNA, for which few detection methods are available. Recent advances in high-throughput sequencing technologies have revealed that eccDNAs play crucial roles in tumor formation, evolution, and drug resistance as well as aging, genomic diversity, and other biological processes, bringing it back to the research hotspot. Several mechanisms of eccDNA formation have been proposed, including the breakage-fusion-bridge (BFB) and translocation-deletion-amplification models. Gynecologic tumors and disorders of embryonic and fetal development are major threats to human reproductive health. The roles of eccDNAs in these pathological processes have been partially elucidated since the first discovery of eccDNA in pig sperm and the double minutes in ovarian cancer ascites. The present review summarized the research history, biogenesis, and currently available detection and analytical methods for eccDNAs and clarified their functions in gynecologic tumors and reproduction. We also proposed the application of eccDNAs as drug targets and liquid biopsy markers for prenatal diagnosis and the early detection, prognosis, and treatment of gynecologic tumors. This review lays theoretical foundations for future investigations into the complex regulatory networks of eccDNAs in vital physiological and pathological processes.},
}

@article {pmid37223732,
year = {2023},
author = {Hengge, R and Pruteanu, M and Stülke, J and Tschowri, N and Turgay, K},
title = {Recent advances and perspectives in nucleotide second messenger signaling in bacteria.},
journal = {microLife},
volume = {4},
number = {},
pages = {uqad015},
pmid = {37223732},
issn = {2633-6693},
abstract = {Nucleotide second messengers act as intracellular 'secondary' signals that represent environmental or cellular cues, i.e. the 'primary' signals. As such, they are linking sensory input with regulatory output in all living cells. The amazing physiological versatility, the mechanistic diversity of second messenger synthesis, degradation, and action as well as the high level of integration of second messenger pathways and networks in prokaryotes has only recently become apparent. In these networks, specific second messengers play conserved general roles. Thus, (p)ppGpp coordinates growth and survival in response to nutrient availability and various stresses, while c-di-GMP is the nucleotide signaling molecule to orchestrate bacterial adhesion and multicellularity. c-di-AMP links osmotic balance and metabolism and that it does so even in Archaea may suggest a very early evolutionary origin of second messenger signaling. Many of the enzymes that make or break second messengers show complex sensory domain architectures, which allow multisignal integration. The multiplicity of c-di-GMP-related enzymes in many species has led to the discovery that bacterial cells are even able to use the same freely diffusible second messenger in local signaling pathways that can act in parallel without cross-talking. On the other hand, signaling pathways operating with different nucleotides can intersect in elaborate signaling networks. Apart from the small number of common signaling nucleotides that bacteria use for controlling their cellular "business," diverse nucleotides were recently found to play very specific roles in phage defense. Furthermore, these systems represent the phylogenetic ancestors of cyclic nucleotide-activated immune signaling in eukaryotes.},
}

@article {pmid37220133,
year = {2023},
author = {Lipińska-Zubrycka, L and Grochowski, M and Bähler, J and Małecki, M},
title = {Pervasive mRNA uridylation in fission yeast is catalysed by both Cid1 and Cid16 terminal uridyltransferases.},
journal = {PloS one},
volume = {18},
number = {5},
pages = {e0285576},
pmid = {37220133},
issn = {1932-6203},
support = {095598/Z/11/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {RNA, Messenger ; *Schizosaccharomyces ; Saccharomyces cerevisiae ; RNA ; Catalysis ; UDPglucose-Hexose-1-Phosphate Uridylyltransferase ; Nucleotidyltransferases ; *Schizosaccharomyces pombe Proteins ; },
abstract = {Messenger RNA uridylation is pervasive and conserved among eukaryotes, but the consequences of this modification for mRNA fate are still under debate. Utilising a simple model organism to study uridylation may facilitate efforts to understand the cellular function of this process. Here we demonstrate that uridylation can be detected using simple bioinformatics approach. We utilise it to unravel widespread transcript uridylation in fission yeast and demonstrate the contribution of both Cid1 and Cid16, the only two annotated terminal uridyltransferases (TUT-ases) in this yeast. To detect uridylation in transcriptome data, we used a RNA-sequencing (RNA-seq) library preparation protocol involving initial linker ligation to fragmented RNA-an approach borrowed from small RNA sequencing that was commonly used in older RNA-seq protocols. We next explored the data to detect uridylation marks. Our analysis show that uridylation in yeast is pervasive, similarly to the one in multicellular organisms. Importantly, our results confirm the role of the cytoplasmic uridyltransferase Cid1 as the primary uridylation catalyst. However, we also observed an auxiliary role of the second uridyltransferase, Cid16. Thus both fission yeast uridyltransferases are involved in mRNA uridylation. Intriguingly, we found no physiological phenotype of the single and double deletion mutants of cid1 and cid16 and only minimal impact of uridylation on steady-state mRNA levels. Our work establishes fission yeast as a potent model to study uridylation in a simple eukaryote, and we demonstrate that it is possible to detect uridylation marks in RNA-seq data without the need for specific methodologies.},
}

RNA, Messenger
*Schizosaccharomyces
Saccharomyces cerevisiae
RNA
Catalysis
UDPglucose-Hexose-1-Phosphate Uridylyltransferase
Nucleotidyltransferases
*Schizosaccharomyces pombe Proteins

@article {pmid37219671,
year = {2023},
author = {Gmiter, D and Pacak, I and Nawrot, S and Czerwonka, G and Kaca, W},
title = {Genomes comparison of two Proteus mirabilis clones showing varied swarming ability.},
journal = {Molecular biology reports},
volume = {50},
number = {7},
pages = {5817-5826},
pmid = {37219671},
issn = {1573-4978},
support = {2019/33/N/NZ6/02406//Narodowym Centrum Nauki/ ; 2017/01/X/NZ6/01141//Narodowe Centrum Nauki/ ; },
mesh = {Humans ; Proteus mirabilis/genetics ; *Urinary Tract Infections/genetics/microbiology ; Clone Cells ; *Proteus Infections/microbiology ; },
abstract = {BACKGROUND: Proteus mirabilis is a Gram-negative bacteria most noted for its involvement with catheter-associated urinary tract infections. It is also known for its multicellular migration over solid surfaces, referred to as 'swarming motility'. Here we analyzed the genomic sequences of two P. mirabilis isolates, designated K38 and K39, which exhibit varied swarming ability.

METHODS AND RESULTS: The isolates genomes were sequenced using Illumina NextSeq sequencer, resulting in about 3.94 Mbp, with a GC content of 38.6%, genomes. Genomes were subjected for in silico comparative investigation. We revealed that, despite a difference in swarming motility, the isolates showed high genomic relatedness (up to 100% ANI similarity), suggesting that one of the isolates probably originated from the other.

CONCLUSIONS: The genomic sequences will allow us to investigate the mechanism driving this intriguing phenotypic heterogeneity between closely related P. mirabilis isolates. Phenotypic heterogeneity is an adaptive strategy of bacterial cells to several environmental pressures. It is also an important factor related to their pathogenesis. Therefore, the availability of these genomic sequences will facilitate studies that focus on the host-pathogen interactions during catheter-associated urinary tract infections.},
}

Humans
Proteus mirabilis/genetics
*Urinary Tract Infections/genetics/microbiology
Clone Cells
*Proteus Infections/microbiology

@article {pmid37211257,
year = {2023},
author = {Fields, C and Levin, M},
title = {Regulative development as a model for origin of life and artificial life studies.},
journal = {Bio Systems},
volume = {229},
number = {},
pages = {104927},
doi = {10.1016/j.biosystems.2023.104927},
pmid = {37211257},
issn = {1872-8324},
mesh = {Humans ; *Artificial Life ; Thermodynamics ; },
abstract = {Using the formal framework of the Free Energy Principle, we show how generic thermodynamic requirements on bidirectional information exchange between a system and its environment can generate complexity. This leads to the emergence of hierarchical computational architectures in systems that operate sufficiently far from thermal equilibrium. In this setting, the environment of any system increases its ability to predict system behavior by "engineering" the system towards increased morphological complexity and hence larger-scale, more macroscopic behaviors. When seen in this light, regulative development becomes an environmentally-driven process in which "parts" are assembled to produce a system with predictable behavior. We suggest on this basis that life is thermodynamically favorable and that, when designing artificial living systems, human engineers are acting like a generic "environment".},
}

Humans
*Artificial Life
Thermodynamics

@article {pmid37202179,
year = {2023},
author = {Sobala, ŁF},
title = {Evolution and phylogenetic distribution of endo-α-mannosidase.},
journal = {Glycobiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/glycob/cwad041},
pmid = {37202179},
issn = {1460-2423},
abstract = {While glycans underlie many biological processes, such as protein folding, cell adhesion and cell-cell recognition, deep evolution of glycosylation machinery remains an understudied topic. N-linked glycosylation is a conserved process in which mannosidases are key trimming enzymes. One of them is the glycoprotein endo-α-1,2-mannosidase which participates in the initial trimming of mannose moieties from an N-linked glycan inside the cis-Golgi. It is unique as the only endo-acting mannosidase found in this organelle. Relatively little is known about its origins and evolutionary history; so far it was reported to occur only in vertebrates. In this work, a taxon-rich bioinformatic survey to unravel the evolutionary history of this enzyme, including all major eukaryotic clades and a wide representation of animals, is presented. The endomannosidase was found to be more widely distributed in animals and other eukaryotes. The protein motif changes in context of the canonical animal enzyme were tracked. Additionally, the data show the two canonical vertebrate endomannosidase genes, MANEA and MANEAL, arose at the second round of the two vertebrate genome duplications and one more vertebrate paralog, CMANEAL, is uncovered. Finally, a framework where N-glycosylation co-evolved with complex multicellularity is described. A better understanding of the evolution of core glycosylation pathways is pivotal to understanding biology of eukaryotes in general, and the Golgi apparatus in particular. This systematic analysis of the endomannosidase evolution is one step towards this goal.},
}

@article {pmid37195672,
year = {2023},
author = {Fernandes, J},
title = {Virus-Induced Lysis of Tumor and Other Pathogenic Unicellular Entities and Its Potential to Treat Leishmaniasis.},
journal = {DNA and cell biology},
volume = {42},
number = {6},
pages = {305-314},
doi = {10.1089/dna.2023.0048},
pmid = {37195672},
issn = {1557-7430},
mesh = {Humans ; *Leishmaniasis/drug therapy/parasitology ; *Leishmania/metabolism ; Cell Death ; *Neoplasms ; Saccharomyces cerevisiae ; *Viruses ; },
abstract = {This article is focused on the main pathways used by viruses to achieve infection and lysis of unicellular eukaryotes described as pathogenic for multicellular organisms. In light of the recent discussions on how tumor cells exhibit unicellular behavior, highly malignant cells can be considered as another unicellular pathogenic entity, but with endogenous origin. Thus, a comparative panel of viral lysis of exogenous pathogenic unicellular eukaryotes such as Acanthamoeba sp., yeast, and tumors is presented. The important intracellular parasite Leishmania sp is also presented, which, in contrast, has its virulence improved by viral infections. The possible exploitation of viral-mediated eukaryotic cell lysis to overcome infections of Leishmania sp is discussed.},
}

Humans
*Leishmaniasis/drug therapy/parasitology
*Leishmania/metabolism
Cell Death
*Neoplasms
Saccharomyces cerevisiae
*Viruses

@article {pmid37183897,
year = {2023},
author = {Kaucka, M},
title = {Cis-regulatory landscapes in the evolution and development of the mammalian skull.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {378},
number = {1880},
pages = {20220079},
pmid = {37183897},
issn = {1471-2970},
mesh = {Animals ; *Evolution, Molecular ; *Mammals/genetics ; Gene Regulatory Networks ; Skull ; Head ; },
abstract = {Extensive morphological variation found in mammals reflects the wide spectrum of their ecological adaptations. The highest morphological diversity is present in the craniofacial region, where geometry is mainly dictated by the bony skull. Mammalian craniofacial development represents complex multistep processes governed by numerous conserved genes that require precise spatio-temporal control. A central question in contemporary evolutionary biology is how a defined set of conserved genes can orchestrate formation of fundamentally different structures, and therefore how morphological variability arises. In principle, differential gene expression patterns during development are the source of morphological variation. With the emergence of multicellular organisms, precise regulation of gene expression in time and space is attributed to cis-regulatory elements. These elements contribute to higher-order chromatin structure and together with trans-acting factors control transcriptional landscapes that underlie intricate morphogenetic processes. Consequently, divergence in cis-regulation is believed to rewire existing gene regulatory networks and form the core of morphological evolution. This review outlines the fundamental principles of the genetic code and genomic regulation interplay during development. Recent work that deepened our comprehension of cis-regulatory element origin, divergence and function is presented here to illustrate the state-of-the-art research that uncovered the principles of morphological novelty. This article is part of the theme issue 'The mammalian skull: development, structure and function'.},
}

Animals
*Evolution, Molecular
*Mammals/genetics
Gene Regulatory Networks
Skull
Head

@article {pmid37176080,
year = {2023},
author = {Suwannachuen, N and Leetanasaksakul, K and Roytrakul, S and Phaonakrop, N and Thaisakun, S and Roongsattham, P and Jantasuriyarat, C and Sanevas, N and Sirikhachornkit, A},
title = {Palmelloid Formation and Cell Aggregation Are Essential Mechanisms for High Light Tolerance in a Natural Strain of Chlamydomonas reinhardtii.},
journal = {International journal of molecular sciences},
volume = {24},
number = {9},
pages = {},
pmid = {37176080},
issn = {1422-0067},
support = {This project is funded by National Research Council of Thailand (NRCT) and Kasetsart Univer-sity : N42A650287. This research and innovation activity is funded by National Research Council of Thailand (NRCT). This research is supported in part by the Grad//This project is funded by National Research Council of Thailand (NRCT) and Kasetsart Univer-sity : N42A650287. This research and innovation activity is funded by National Research Council of Thailand (NRCT). This research is supported in part by the Grad/ ; },
mesh = {*Chlamydomonas reinhardtii/metabolism ; Reactive Oxygen Species/metabolism ; Proteomics ; *Chlamydomonas/metabolism ; Photosynthesis/physiology ; },
abstract = {Photosynthetic organisms, such as higher plants and algae, require light to survive. However, an excessive amount of light can be harmful due to the production of reactive oxygen species (ROS), which cause cell damage and, if it is not effectively regulated, cell death. The study of plants' responses to light can aid in the development of methods to improve plants' growth and productivity. Due to the multicellular nature of plants, there may be variations in the results based on plant age and tissue type. Chlamydomonas reinhardtii, a unicellular green alga, has also been used as a model organism to study photosynthesis and photoprotection. Nonetheless, the majority of the research has been conducted with strains that have been consistently utilized in laboratories and originated from the same source. Despite the availability of many field isolates of this species, very few studies have compared the light responses of field isolates. This study examined the responses of two field isolates of Chlamydomonas to high light stress. The light-tolerant strain, CC-4414, managed reactive oxygen species (ROS) slightly better than the sensitive strain, CC-2344, did. The proteomic data of cells subjected to high light revealed cellular modifications of the light-tolerant strain toward membrane proteins. The morphology of cells under light stress revealed that this strain utilized the formation of palmelloid structures and cell aggregation to shield cells from excessive light. As indicated by proteome data, morphological modifications occur simultaneously with the increase in protein degradation and autophagy. By protecting cells from stress, cells are able to continue to upregulate ROS management mechanisms and prevent cell death. This is the first report of palmelloid formation in Chlamydomonas under high light stress.},
}

*Chlamydomonas reinhardtii/metabolism
Reactive Oxygen Species/metabolism
Proteomics
*Chlamydomonas/metabolism
Photosynthesis/physiology

@article {pmid37173684,
year = {2023},
author = {Foo, YZ and Lagisz, M and O'Dea, RE and Nakagawa, S},
title = {The influence of immune challenges on the mean and variance in reproductive investment: a meta-analysis of the terminal investment hypothesis.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {107},
pmid = {37173684},
issn = {1741-7007},
mesh = {Animals ; *Reproduction/physiology ; },
abstract = {Finding the optimal balance between survival and reproduction is a central puzzle in life-history theory. The terminal investment hypothesis predicts that when individuals encounter a survival threat that compromises future reproductive potential, they will increase immediate reproductive investment to maximise fitness. Despite decades of research on the terminal investment hypothesis, findings remain mixed. We examined the terminal investment hypothesis with a meta-analysis of studies that measured reproductive investment of multicellular iteroparous animals after a non-lethal immune challenge. We had two main aims. The first was to investigate whether individuals, on average, increase reproductive investment in response to an immune threat, as predicted by the terminal investment hypothesis. We also examined whether such responses vary adaptively on factors associated with the amount of reproductive opportunities left (residual reproductive value) in the individuals, as predicted by the terminal investment hypothesis. The second was to provide a quantitative test of a novel prediction based on the dynamic threshold model: that an immune threat increases between-individual variance in reproductive investment. Our results provided some support for our hypotheses. Older individuals, who are expected to have lower residual reproductive values, showed stronger mean terminal investment response than younger individuals. In terms of variance, individuals showed a divergence in responses, leading to an increase in variance. This increase in variance was especially amplified in longer-living species, which was consistent with our prediction that individuals in longer-living species should respond with greater individual variation due to increased phenotypic plasticity. We find little statistical evidence of publication bias. Together, our results highlight the need for a more nuanced view on the terminal investment hypothesis and a greater focus on the factors that drive individual responses.},
}

Animals
*Reproduction/physiology

@article {pmid37165189,
year = {2023},
author = {Bozdag, GO and Zamani-Dahaj, SA and Day, TC and Kahn, PC and Burnetti, AJ and Lac, DT and Tong, K and Conlin, PL and Balwani, AH and Dyer, EL and Yunker, PJ and Ratcliff, WC},
title = {De novo evolution of macroscopic multicellularity.},
journal = {Nature},
volume = {617},
number = {7962},
pages = {747-754},
pmid = {37165189},
issn = {1476-4687},
support = {R35 GM138354/GM/NIGMS NIH HHS/United States ; },
mesh = {*Acclimatization ; *Biological Evolution ; Models, Biological ; *Saccharomyces cerevisiae/cytology/metabolism ; Anaerobiosis ; Aerobiosis ; Oxygen/analysis/metabolism ; Cell Shape ; *Cell Aggregation/physiology ; },
abstract = {While early multicellular lineages necessarily started out as relatively simple groups of cells, little is known about how they became Darwinian entities capable of sustained multicellular evolution[1-3]. Here we investigate this with a multicellularity long-term evolution experiment, selecting for larger group size in the snowflake yeast (Saccharomyces cerevisiae) model system. Given the historical importance of oxygen limitation[4], our ongoing experiment consists of three metabolic treatments[5]-anaerobic, obligately aerobic and mixotrophic yeast. After 600 rounds of selection, snowflake yeast in the anaerobic treatment group evolved to be macroscopic, becoming around 2 × 10[4] times larger (approximately mm scale) and about 10[4]-fold more biophysically tough, while retaining a clonal multicellular life cycle. This occurred through biophysical adaptation-evolution of increasingly elongate cells that initially reduced the strain of cellular packing and then facilitated branch entanglements that enabled groups of cells to stay together even after many cellular bonds fracture. By contrast, snowflake yeast competing for low oxygen[5] remained microscopic, evolving to be only around sixfold larger, underscoring the critical role of oxygen levels in the evolution of multicellular size. Together, this research provides unique insights into an ongoing evolutionary transition in individuality, showing how simple groups of cells overcome fundamental biophysical limitations through gradual, yet sustained, multicellular evolution.},
}

*Acclimatization
*Biological Evolution
Models, Biological
*Saccharomyces cerevisiae/cytology/metabolism
Anaerobiosis
Aerobiosis
Oxygen/analysis/metabolism
Cell Shape
*Cell Aggregation/physiology

@article {pmid37160092,
year = {2023},
author = {Conlin, PL and Ratcliff, WC},
title = {Evolution: Understanding the origins of facultative multicellular life cycles.},
journal = {Current biology : CB},
volume = {33},
number = {9},
pages = {R356-R358},
doi = {10.1016/j.cub.2023.03.065},
pmid = {37160092},
issn = {1879-0445},
mesh = {Animals ; *Life Cycle Stages ; *Saccharomyces cerevisiae ; },
abstract = {Multicellular organisms exhibit a fascinating diversity of life cycles, but little is known about the factors governing life-cycle evolution. New studies of wild yeast and cyanobacteria provide insight into how and why facultative multicellular life cycles arise.},
}

Animals
*Life Cycle Stages
*Saccharomyces cerevisiae

@article {pmid37155901,
year = {2023},
author = {Cooney, DB and Levin, SA and Mori, Y and Plotkin, JB},
title = {Evolutionary dynamics within and among competing groups.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {20},
pages = {e2216186120},
pmid = {37155901},
issn = {1091-6490},
mesh = {Humans ; *Cooperative Behavior ; *Biological Evolution ; Selection, Genetic ; Game Theory ; },
abstract = {Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible for profound transitions in evolutionary history, including the origin of cellular life, multicellular life, and even societies. Here, we synthesize a growing literature that extends evolutionary game theory to describe multilevel evolutionary dynamics, using nested birth-death processes and partial differential equations to model natural selection acting on competition within and among groups of individuals. We analyze how mechanisms known to promote cooperation within a single group-including assortment, reciprocity, and population structure-alter evolutionary outcomes in the presence of competition among groups. We find that population structures most conducive to cooperation in multiscale systems can differ from those most conducive within a single group. Likewise, for competitive interactions with a continuous range of strategies we find that among-group selection may fail to produce socially optimal outcomes, but it can nonetheless produce second-best solutions that balance individual incentives to defect with the collective incentives for cooperation. We conclude by describing the broad applicability of multiscale evolutionary models to problems ranging from the production of diffusible metabolites in microbes to the management of common-pool resources in human societies.},
}

Humans
*Cooperative Behavior
*Biological Evolution
Selection, Genetic
Game Theory

@article {pmid37140022,
year = {2023},
author = {Krasovec, M and Hoshino, M and Zheng, M and Lipinska, AP and Coelho, SM},
title = {Low Spontaneous Mutation Rate in Complex Multicellular Eukaryotes with a Haploid-Diploid Life Cycle.},
journal = {Molecular biology and evolution},
volume = {40},
number = {6},
pages = {},
pmid = {37140022},
issn = {1537-1719},
mesh = {Animals ; Haploidy ; *Diploidy ; Mutation Rate ; Eukaryota ; Life Cycle Stages/genetics ; Plants ; *Phaeophyta/genetics ; },
abstract = {The spontaneous mutation rate µ is a crucial parameter to understand evolution and biodiversity. Mutation rates are highly variable across species, suggesting that µ is susceptible to selection and drift and that species life cycle and life history may impact its evolution. In particular, asexual reproduction and haploid selection are expected to affect the mutation rate, but very little empirical data are available to test this expectation. Here, we sequence 30 genomes of a parent-offspring pedigree in the model brown alga Ectocarpus sp.7, and 137 genomes of an interspecific cross of the closely related brown alga Scytosiphon to have access to the spontaneous mutation rate of representative organisms of a complex multicellular eukaryotic lineage outside animals and plants, and to evaluate the potential impact of life cycle on the mutation rate. Brown algae alternate between a haploid and a diploid stage, both multicellular and free living, and utilize both sexual and asexual reproduction. They are, therefore, excellent models to empirically test expectations of the effect of asexual reproduction and haploid selection on mutation rate evolution. We estimate that Ectocarpus has a base substitution rate of µbs = 4.07 × 10-10 per site per generation, whereas the Scytosiphon interspecific cross had µbs = 1.22 × 10-9. Overall, our estimations suggest that these brown algae, despite being multicellular complex eukaryotes, have unusually low mutation rates. In Ectocarpus, effective population size (Ne) could not entirely explain the low µbs. We propose that the haploid-diploid life cycle, combined with extensive asexual reproduction, may be additional key drivers of the mutation rate in these organisms.},
}

Animals
Haploidy
*Diploidy
Mutation Rate
Eukaryota
Life Cycle Stages/genetics
Plants
*Phaeophyta/genetics

@article {pmid37107699,
year = {2023},
author = {Grochau-Wright, ZI and Nedelcu, AM and Michod, RE},
title = {The Genetics of Fitness Reorganization during the Transition to Multicellularity: The Volvocine regA-like Family as a Model.},
journal = {Genes},
volume = {14},
number = {4},
pages = {},
pmid = {37107699},
issn = {2073-4425},
mesh = {Phylogeny ; *Chlorophyta ; *Volvox/genetics ; Models, Biological ; Cell Differentiation/genetics ; },
abstract = {The evolutionary transition from single-celled to multicellular individuality requires organismal fitness to shift from the cell level to a cell group. This reorganization of fitness occurs by re-allocating the two components of fitness, survival and reproduction, between two specialized cell types in the multicellular group: soma and germ, respectively. How does the genetic basis for such fitness reorganization evolve? One possible mechanism is the co-option of life history genes present in the unicellular ancestors of a multicellular lineage. For instance, single-celled organisms must regulate their investment in survival and reproduction in response to environmental changes, particularly decreasing reproduction to ensure survival under stress. Such stress response life history genes can provide the genetic basis for the evolution of cellular differentiation in multicellular lineages. The regA-like gene family in the volvocine green algal lineage provides an excellent model system to study how this co-option can occur. We discuss the origin and evolution of the volvocine regA-like gene family, including regA-the gene that controls somatic cell development in the model organism Volvox carteri. We hypothesize that the co-option of life history trade-off genes is a general mechanism involved in the transition to multicellular individuality, making volvocine algae and the regA-like family a useful template for similar investigations in other lineages.},
}

Phylogeny
*Chlorophyta
*Volvox/genetics
Models, Biological
Cell Differentiation/genetics

@article {pmid37107559,
year = {2023},
author = {Casotti, MC and Meira, DD and Zetum, ASS and Araújo, BC and Silva, DRCD and Santos, EVWD and Garcia, FM and Paula, F and Santana, GM and Louro, LS and Alves, LNR and Braga, RFR and Trabach, RSDR and Bernardes, SS and Louro, TES and Chiela, ECF and Lenz, G and Carvalho, EF and Louro, ID},
title = {Computational Biology Helps Understand How Polyploid Giant Cancer Cells Drive Tumor Success.},
journal = {Genes},
volume = {14},
number = {4},
pages = {},
pmid = {37107559},
issn = {2073-4425},
mesh = {Humans ; Cell Line, Tumor ; *Neoplasm Recurrence, Local/pathology ; *Giant Cells/metabolism/pathology ; Polyploidy ; Computational Biology ; },
abstract = {Precision and organization govern the cell cycle, ensuring normal proliferation. However, some cells may undergo abnormal cell divisions (neosis) or variations of mitotic cycles (endopolyploidy). Consequently, the formation of polyploid giant cancer cells (PGCCs), critical for tumor survival, resistance, and immortalization, can occur. Newly formed cells end up accessing numerous multicellular and unicellular programs that enable metastasis, drug resistance, tumor recurrence, and self-renewal or diverse clone formation. An integrative literature review was carried out, searching articles in several sites, including: PUBMED, NCBI-PMC, and Google Academic, published in English, indexed in referenced databases and without a publication time filter, but prioritizing articles from the last 3 years, to answer the following questions: (i) "What is the current knowledge about polyploidy in tumors?"; (ii) "What are the applications of computational studies for the understanding of cancer polyploidy?"; and (iii) "How do PGCCs contribute to tumorigenesis?"},
}

Humans
Cell Line, Tumor
*Neoplasm Recurrence, Local/pathology
*Giant Cells/metabolism/pathology
Polyploidy
Computational Biology

@article {pmid37098330,
year = {2023},
author = {Colgren, J and Burkhardt, P},
title = {Evolution: Was the nuclear-to-cytoplasmic ratio a key factor in the origin of animal multicellularity?.},
journal = {Current biology : CB},
volume = {33},
number = {8},
pages = {R298-R300},
doi = {10.1016/j.cub.2023.03.010},
pmid = {37098330},
issn = {1879-0445},
mesh = {Animals ; *Eukaryota ; *Mesomycetozoea ; Cytoplasm ; Cytosol ; Biological Evolution ; },
abstract = {The ichthyosporean Sphaeroforma arctica, a protist closely related to animals, displays coenocytic development followed by cellularization and cell release. A new study reveals that the nuclear-to-cytoplasmic ratio drives cellularization in these fascinating organisms.},
}

Animals
*Eukaryota
*Mesomycetozoea
Cytoplasm
Cytosol
Biological Evolution

@article {pmid37096591,
year = {2023},
author = {Stéger, A and Palmgren, M},
title = {Hypothesis paper: the development of a regulatory layer in P2B autoinhibited Ca[2+]-ATPases may have facilitated plant terrestrialization and animal multicellularization.},
journal = {Plant signaling & behavior},
volume = {18},
number = {1},
pages = {2204284},
pmid = {37096591},
issn = {1559-2324},
mesh = {Animals ; *Adenosine Triphosphatases ; *Calmodulin/metabolism ; Protein Binding ; Calcium Signaling ; Calcium/metabolism ; },
abstract = {With the appearance of plants and animals, new challenges emerged. These multicellular eukaryotes had to solve for example the difficulties of multifaceted communication between cells and adaptation to new habitats. In this paper, we are looking for one piece of the puzzle that made the development of complex multicellular eukaryotes possible with a focus on regulation of P2B autoinhibited Ca[2+]-ATPases. P2B ATPases pump Ca[2+] out of the cytosol at the expense of ATP hydrolysis, and thereby maintain a steep gradient between the extra- and intracytosolic compartments which is utilized for Ca[2+]-mediated rapid cell signaling. The activity of these enzymes is regulated by a calmodulin (CaM)-responsive autoinhibitory region, which can be located in either termini of the protein, at the C-terminus in animals and at the N-terminus in plants. When the cytoplasmic Ca[2+] level reaches a threshold, the CaM/Ca[2+] complex binds to a calmodulin-binding domain (CaMBD) in the autoinhibitor, which leads to the upregulation of pump activity. In animals, protein activity is also controlled by acidic phospholipids that bind to a cytosolic portion of the pump. Here, we analyze the appearance of CaMBDs and the phospholipid-activating sequence and show that their evolution in animals and plants was independent. Furthermore, we hypothesize that different causes may have initiated the appearance of these regulatory layers: in animals, it is linked to the appearance of multicellularity, while in plants it co-occurs with their water-to-land transition.},
}

Animals
*Adenosine Triphosphatases
*Calmodulin/metabolism
Protein Binding
Calcium Signaling
Calcium/metabolism

@article {pmid37094139,
year = {2023},
author = {Ros-Rocher, N and Kidner, RQ and Gerdt, C and Davidson, WS and Ruiz-Trillo, I and Gerdt, JP},
title = {Chemical factors induce aggregative multicellularity in a close unicellular relative of animals.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {18},
pages = {e2216668120},
pmid = {37094139},
issn = {1091-6490},
support = {R35 GM138376/GM/NIGMS NIH HHS/United States ; T32 GM131994/GM/NIGMS NIH HHS/United States ; S10 OD024988/OD/NIH HHS/United States ; },
mesh = {Animals ; *Eukaryota/genetics ; *Biological Evolution ; Phylogeny ; },
abstract = {Regulated cellular aggregation is an essential process for development and healing in many animal tissues. In some animals and a few distantly related unicellular species, cellular aggregation is regulated by diffusible chemical cues. However, it is unclear whether regulated cellular aggregation was part of the life cycles of the first multicellular animals and/or their unicellular ancestors. To fill this gap, we investigated the triggers of cellular aggregation in one of animals' closest unicellular living relatives-the filasterean Capsaspora owczarzaki. We discovered that Capsaspora aggregation is induced by chemical cues, as observed in some of the earliest branching animals and other unicellular species. Specifically, we found that calcium ions and lipids present in lipoproteins function together to induce aggregation of viable Capsaspora cells. We also found that this multicellular stage is reversible as depletion of the cues triggers disaggregation, which can be overcome upon reinduction. Our finding demonstrates that chemically regulated aggregation is important across diverse members of the holozoan clade. Therefore, this phenotype was plausibly integral to the life cycles of the unicellular ancestors of animals.},
}

Animals
*Eukaryota/genetics
*Biological Evolution
Phylogeny

@article {pmid37093889,
year = {2023},
author = {Kumar, T and Sethuraman, R and Mitra, S and Ravindran, B and Narayanan, M},
title = {MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication.},
journal = {PLoS computational biology},
volume = {19},
number = {4},
pages = {e1011022},
pmid = {37093889},
issn = {1553-7358},
mesh = {Humans ; *Brain ; Gene Regulatory Networks/genetics ; *Alzheimer Disease/genetics ; },
abstract = {With the evolution of multicellularity, communication among cells in different tissues and organs became pivotal to life. Molecular basis of such communication has long been studied, but genome-wide screens for genes and other biomolecules mediating tissue-tissue signaling are lacking. To systematically identify inter-tissue mediators, we present a novel computational approach MultiCens (Multilayer/Multi-tissue network Centrality measures). Unlike single-layer network methods, MultiCens can distinguish within- vs. across-layer connectivity to quantify the "influence" of any gene in a tissue on a query set of genes of interest in another tissue. MultiCens enjoys theoretical guarantees on convergence and decomposability, and performs well on synthetic benchmarks. On human multi-tissue datasets, MultiCens predicts known and novel genes linked to hormones. MultiCens further reveals shifts in gene network architecture among four brain regions in Alzheimer's disease. MultiCens-prioritized hypotheses from these two diverse applications, and potential future ones like "Multi-tissue-expanded Gene Ontology" analysis, can enable whole-body yet molecular-level systems investigations in humans.},
}

Humans
*Brain
Gene Regulatory Networks/genetics
*Alzheimer Disease/genetics

@article {pmid37086724,
year = {2023},
author = {Hashimoto, A and Kawamura, N and Tarusawa, E and Takeda, I and Aoyama, Y and Ohno, N and Inoue, M and Kagamiuchi, M and Kato, D and Matsumoto, M and Hasegawa, Y and Nabekura, J and Schaefer, A and Moorhouse, AJ and Yagi, T and Wake, H},
title = {Microglia enable cross-modal plasticity by removing inhibitory synapses.},
journal = {Cell reports},
volume = {42},
number = {5},
pages = {112383},
doi = {10.1016/j.celrep.2023.112383},
pmid = {37086724},
issn = {2211-1247},
mesh = {Animals ; *Microglia ; Neurons/physiology ; Synapses/physiology ; Pyramidal Cells ; *Visual Cortex/physiology ; Neuronal Plasticity/physiology ; Vibrissae/physiology ; Somatosensory Cortex/physiology ; },
abstract = {Cross-modal plasticity is the repurposing of brain regions associated with deprived sensory inputs to improve the capacity of other sensory modalities. The functional mechanisms of cross-modal plasticity can indicate how the brain recovers from various forms of injury and how different sensory modalities are integrated. Here, we demonstrate that rewiring of the microglia-mediated local circuit synapse is crucial for cross-modal plasticity induced by visual deprivation (monocular deprivation [MD]). MD relieves the usual inhibition of functional connectivity between the somatosensory cortex and secondary lateral visual cortex (V2L). This results in enhanced excitatory responses in V2L neurons during whisker stimulation and a greater capacity for vibrissae sensory discrimination. The enhanced cross-modal response is mediated by selective removal of inhibitory synapse terminals on pyramidal neurons by the microglia in the V2L via matrix metalloproteinase 9 signaling. Our results provide insights into how cortical circuits integrate different inputs to functionally compensate for neuronal damage.},
}

Animals
*Microglia
Neurons/physiology
Synapses/physiology
Pyramidal Cells
*Visual Cortex/physiology
Neuronal Plasticity/physiology
Vibrissae/physiology
Somatosensory Cortex/physiology

@article {pmid37083675,
year = {2023},
author = {Isaksson, H and Brännström, Å and Libby, E},
title = {Minor variations in multicellular life cycles have major effects on adaptation.},
journal = {PLoS computational biology},
volume = {19},
number = {4},
pages = {e1010698},
pmid = {37083675},
issn = {1553-7358},
mesh = {Animals ; *Life Cycle Stages ; *Models, Theoretical ; Biological Evolution ; Acclimatization ; Phenotype ; },
abstract = {Multicellularity has evolved several independent times over the past hundreds of millions of years and given rise to a wide diversity of complex life. Recent studies have found that large differences in the fundamental structure of early multicellular life cycles can affect fitness and influence multicellular adaptation. Yet, there is an underlying assumption that at some scale or categorization multicellular life cycles are similar in terms of their adaptive potential. Here, we consider this possibility by exploring adaptation in a class of simple multicellular life cycles of filamentous organisms that only differ in one respect, how many daughter filaments are produced. We use mathematical models and evolutionary simulations to show that despite the similarities, qualitatively different mutations fix. In particular, we find that mutations with a tradeoff between cell growth and group survival, i.e. "selfish" or "altruistic" traits, spread differently. Specifically, altruistic mutations more readily spread in life cycles that produce few daughters while in life cycles producing many daughters either type of mutation can spread depending on the environment. Our results show that subtle changes in multicellular life cycles can fundamentally alter adaptation.},
}

Animals
*Life Cycle Stages
*Models, Theoretical
Biological Evolution
Acclimatization
Phenotype

@article {pmid37081145,
year = {2023},
author = {Cornwallis, CK and Svensson-Coelho, M and Lindh, M and Li, Q and Stábile, F and Hansson, LA and Rengefors, K},
title = {Single-cell adaptations shape evolutionary transitions to multicellularity in green algae.},
journal = {Nature ecology & evolution},
volume = {7},
number = {6},
pages = {889-902},
pmid = {37081145},
issn = {2397-334X},
support = {2018.0138//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 60501//John Templeton Foundation (JTF)/ ; 20210788//Crafoordska Stiftelsen (Crafoord Foundation)/ ; 2022-03503//Vetenskapsrådet (Swedish Research Council)/ ; 2016-03552//Vetenskapsrådet (Swedish Research Council)/ ; },
mesh = {Animals ; *Biological Evolution ; *Chlorophyta ; Acclimatization ; Predatory Behavior ; },
abstract = {The evolution of multicellular life has played a pivotal role in shaping biological diversity. However, we know surprisingly little about the natural environmental conditions that favour the formation of multicellular groups. Here we experimentally examine how key environmental factors (predation, nitrogen and water turbulence) combine to influence multicellular group formation in 35 wild unicellular green algae strains (19 Chlorophyta species). All environmental factors induced the formation of multicellular groups (more than four cells), but there was no evidence this was adaptive, as multicellularity (% cells in groups) was not related to population growth rate under any condition. Instead, population growth was related to extracellular matrix (ECM) around single cells and palmelloid formation, a unicellular life-cycle stage where two to four cells are retained within a mother-cell wall after mitosis. ECM production increased with nitrogen levels resulting in more cells being in palmelloids and higher rates of multicellular group formation. Examining the distribution of 332 algae species across 478 lakes monitored over 55 years, showed that ECM and nitrogen availability also predicted patterns of obligate multicellularity in nature. Our results highlight that adaptations of unicellular organisms to cope with environmental challenges may be key to understanding evolutionary routes to multicellular life.},
}

Animals
*Biological Evolution
*Chlorophyta
Acclimatization
Predatory Behavior

@article {pmid37080197,
year = {2023},
author = {Cadart, C and Bartz, J and Oaks, G and Liu, MZ and Heald, R},
title = {Polyploidy in Xenopus lowers metabolic rate by decreasing total cell surface area.},
journal = {Current biology : CB},
volume = {33},
number = {9},
pages = {1744-1752.e7},
pmid = {37080197},
issn = {1879-0445},
support = {R35 GM118183/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Triploidy ; Xenopus laevis/genetics ; *Polyploidy ; Ploidies ; Diploidy ; Cell Membrane ; },
abstract = {Although polyploidization is frequent in development, cancer, and evolution, impacts on animal metabolism are poorly understood. In Xenopus frogs, the number of genome copies (ploidy) varies across species and can be manipulated within a species. Here, we show that triploid tadpoles contain fewer, larger cells than diploids and consume oxygen at a lower rate. Drug treatments revealed that the major processes accounting for tadpole energy expenditure include cell proliferation, biosynthesis, and maintenance of plasma membrane potential. While inhibiting cell proliferation did not abolish the oxygen consumption difference between diploids and triploids, treatments that altered cellular biosynthesis or electrical potential did. Combining these results with a simple mathematical framework, we propose that the decrease in total cell surface area lowered production and activity of plasma membrane components including the Na[+]/K[+] ATPase, reducing energy consumption in triploids. Comparison of Xenopus species that evolved through polyploidization revealed that metabolic differences emerged during development when cell size scaled with genome size. Thus, ploidy affects metabolism by altering the cell surface area to volume ratio in a multicellular organism.},
}

Animals
*Triploidy
Xenopus laevis/genetics
*Polyploidy
Ploidies
Diploidy
Cell Membrane

@article {pmid37048099,
year = {2023},
author = {Leitner, N and Ertl, R and Gabner, S and Fuchs-Baumgartinger, A and Walter, I and Hlavaty, J},
title = {Isolation and Characterization of Novel Canine Osteosarcoma Cell Lines from Chemotherapy-Naïve Patients.},
journal = {Cells},
volume = {12},
number = {7},
pages = {},
pmid = {37048099},
issn = {2073-4409},
mesh = {Animals ; Dogs ; Cell Line, Tumor ; *Osteosarcoma/pathology ; *MicroRNAs/genetics ; Gene Expression Profiling ; *Bone Neoplasms/metabolism ; },
abstract = {The present study aimed to establish novel canine osteosarcoma cell lines (COS3600, COS3600B, COS4074) and characterize the recently described COS4288 cells. The established D-17 cell line served as a reference. Analyzed cell lines differed notably in their biological characteristics. Calculated doubling times were between 22 h for COS3600B and 426 h for COS4074 cells. COS3600B and COS4288 cells produced visible colonies after anchorage-independent growth in soft agar. COS4288 cells were identified as cells with the highest migratory capacity. All cells displayed the ability to invade through an artificial basement membrane matrix. Immunohistochemical analyses revealed the mesenchymal origin of all COS cell lines as well as positive staining for the osteosarcoma-relevant proteins alkaline phosphatase and karyopherin α2. Expression of p53 was confirmed in all tested cell lines. Gene expression analyses of selected genes linked to cellular immune checkpoints (CD270, CD274, CD276), kinase activity (MET, ERBB2), and metastatic potential (MMP-2, MMP-9) as well as selected long non-coding RNA (MALAT1) and microRNAs (miR-9, miR-34a, miR-93) are provided. All tested cell lines were able to grow as multicellular spheroids. In all spheroids except COS4288, calcium deposition was detected by von Kossa staining. We believe that these new cell lines serve as useful biological models for future studies.},
}

Animals
Dogs
Cell Line, Tumor
*Osteosarcoma/pathology
*MicroRNAs/genetics
Gene Expression Profiling
*Bone Neoplasms/metabolism

@article {pmid37047167,
year = {2023},
author = {Vinogradov, AE and Anatskaya, OV},
title = {Systemic Alterations of Cancer Cells and Their Boost by Polyploidization: Unicellular Attractor (UCA) Model.},
journal = {International journal of molecular sciences},
volume = {24},
number = {7},
pages = {},
pmid = {37047167},
issn = {1422-0067},
support = {No. 075-15-2021-1075//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Animals ; Humans ; Biological Evolution ; *Brachyura ; Carcinogenesis/genetics ; Cell Transformation, Neoplastic ; *Neoplasms/genetics ; },
abstract = {Using meta-analyses, we introduce a unicellular attractor (UCA) model integrating essential features of the 'atavistic reversal', 'cancer attractor', 'somatic mutation', 'genome chaos', and 'tissue organization field' theories. The 'atavistic reversal' theory is taken as a keystone. We propose a possible mechanism of this reversal, its refinement called 'gradual atavism', and evidence for the 'serial atavism' model. We showed the gradual core-to-periphery evolutionary growth of the human interactome resulting in the higher protein interaction density and global interactome centrality in the UC center. In addition, we revealed that UC genes are more actively expressed even in normal cells. The modeling of random walk along protein interaction trajectories demonstrated that random alterations in cellular networks, caused by genetic and epigenetic changes, can result in a further gradual activation of the UC center. These changes can be induced and accelerated by cellular stress that additionally activates UC genes (especially during cell proliferation), because the genes involved in cellular stress response and cell cycle are mostly of UC origin. The functional enrichment analysis showed that cancer cells demonstrate the hyperactivation of energetics and the suppression of multicellular genes involved in communication with the extracellular environment (especially immune surveillance). Collectively, these events can unleash selfish cell behavior aimed at survival at all means. All these changes are boosted by polyploidization. The UCA model may facilitate an understanding of oncogenesis and promote the development of therapeutic strategies.},
}

Animals
Humans
Biological Evolution
*Brachyura
Carcinogenesis/genetics
Cell Transformation, Neoplastic
*Neoplasms/genetics

@article {pmid37046079,
year = {2023},
author = {Li, G and Chen, L and Pang, K and Tang, Q and Wu, C and Yuan, X and Zhou, C and Xiao, S},
title = {Tonian carbonaceous compressions indicate that Horodyskia is one of the oldest multicellular and coenocytic macro-organisms.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {399},
pmid = {37046079},
issn = {2399-3642},
mesh = {*Eukaryota ; *Fossils ; China ; },
abstract = {Macrofossils with unambiguous biogenic origin and predating the one-billion-year-old multicellular fossils Bangiomorpha and Proterocladus interpreted as crown-group eukaryotes are quite rare. Horodyskia is one of these few macrofossils, and it extends from the early Mesoproterozoic Era to the terminal Ediacaran Period. The biological interpretation of this enigmatic fossil, however, has been a matter of controversy since its discovery in 1982, largely because there was no evidence for the preservation of organic walls. Here we report new carbonaceous compressions of Horodyskia from the Tonian successions (~950-720 Ma) in North China. The macrofossils herein with bona fide organic walls reinforce the biogenicity of Horodyskia. Aided by the new material, we reconstruct Horodyskia as a colonial organism composed of a chain of organic-walled vesicles that likely represent multinucleated (coenocytic) cells of early eukaryotes. Two species of Horodyskia are differentiated on the basis of vesicle sizes, and their co-existence in the Tonian assemblage provides a link between the Mesoproterozoic (H. moniliformis) and the Ediacaran (H. minor) species. Our study thus provides evidence that eukaryotes have acquired macroscopic size through the combination of coenocytism and colonial multicellularity at least ~1.48 Ga, and highlights an exceptionally long range and morphological stasis of this Proterozoic macrofossils.},
}

*Eukaryota
*Fossils
China

@article {pmid37029839,
year = {2023},
author = {Varilla González, JD and Macedo Alves, F and Bagnatori Sartori, ÂL and de Oliveira Arruda, RDC},
title = {Diversity and evolution of leaflet anatomical characters in the Pterocarpus clade (Fabaceae: Papilionoideae).},
journal = {Journal of plant research},
volume = {136},
number = {4},
pages = {453-481},
pmid = {37029839},
issn = {1618-0860},
support = {88882.461305/2019-01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Phylogeny ; *Pterocarpus ; *Fabaceae ; Trichomes ; Microscopy, Electron, Scanning ; },
abstract = {The Pterocarpus clade includes 23 genera previously attributed to different Fabaceae tribes. The recent rearrangements of many genera in the clade do not recognize morphological synapomorphies. This study aimed to identify new synapomorphies for the Pterocarpus clade, to identify characters supporting inter-generic relationships currently resolved only by molecular data and to identify diagnostic characters at the genus and species levels. Subterminal leaflets of the studied genera were selected and analyzed using light and scanning electron microscopy. Ancestral reconstruction was performed using morphological and anatomical characters of 16 genera of the Pterocarpus clade. The convex epidermal relief in the region of the main vein indicated the relationship among all genera of the group. Anchor-like multicellular trichomes are features shared by Brya and Cranocarpus, which are the sister group to the other genera of the clade. Subepidermal layers are features shared by the Centrolobium, Etaballia, Paramachaerium, Pterocarpus and Tipuana genera, and the sclerenchyma sheath in the leaflet margin is reported in the Discolobium, Riedeliella and Platymiscium genera. Bulbous based glandular trichomes and vesicular glandular trichomes are diagnostic at the species level in Centrolobium and Pterocarpus, respectively. The leaflet characters investigated can be useful for the taxonomic delimitation at both the genus and species levels of the Pterocarpus clade. Our dataset provides new synapomorphies, elucidates the inter-generic relationships and reinforces the phylogenetic classification of the Pterocarpus clade resolved by molecular data.},
}

Phylogeny
*Pterocarpus
*Fabaceae
Trichomes
Microscopy, Electron, Scanning

@article {pmid37023182,
year = {2023},
author = {Darras, H and Berney, C and Hasin, S and Drescher, J and Feldhaar, H and Keller, L},
title = {Obligate chimerism in male yellow crazy ants.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6640},
pages = {55-58},
doi = {10.1126/science.adf0419},
pmid = {37023182},
issn = {1095-9203},
mesh = {Animals ; Male ; *Ants/cytology/genetics/growth & development ; *Chimerism ; Diploidy ; *Reproduction ; Semen/cytology ; Germ Cells/cytology ; },
abstract = {Multicellular organisms typically develop from a single fertilized egg and therefore consist of clonal cells. We report an extraordinary reproductive system in the yellow crazy ant. Males are chimeras of haploid cells from two divergent lineages: R and W. R cells are overrepresented in the males' somatic tissues, whereas W cells are overrepresented in their sperm. Chimerism occurs when parental nuclei bypass syngamy and divide separately within the same egg. When syngamy takes place, the diploid offspring either develops into a queen when the oocyte is fertilized by an R sperm or into a worker when fertilized by a W sperm. This study reveals a mode of reproduction that may be associated with a conflict between lineages to preferentially enter the germ line.},
}

Animals
Male
*Ants/cytology/genetics/growth & development
*Chimerism
Diploidy
*Reproduction
Semen/cytology
Germ Cells/cytology

@article {pmid37019107,
year = {2023},
author = {Barrere, J and Nanda, P and Murray, AW},
title = {Alternating selection for dispersal and multicellularity favors regulated life cycles.},
journal = {Current biology : CB},
volume = {33},
number = {9},
pages = {1809-1817.e3},
pmid = {37019107},
issn = {1879-0445},
support = {R01 GM043987/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Saccharomyces cerevisiae/physiology ; *Biological Evolution ; Phenotype ; Life Cycle Stages ; Reproduction ; },
abstract = {The evolution of complex multicellularity opened paths to increased morphological diversity and organizational novelty. This transition involved three processes: cells remained attached to one another to form groups, cells within these groups differentiated to perform different tasks, and the groups evolved new reproductive strategies.[1][,][2][,][3][,][4][,][5] Recent experiments identified selective pressures and mutations that can drive the emergence of simple multicellularity and cell differentiation,[6][,][7][,][8][,][9][,][10][,][11] but the evolution of life cycles, particularly how simple multicellular forms reproduce, has been understudied. The selective pressure and mechanisms that produced a regular alternation between single cells and multicellular collectives are still unclear.[12] To probe the factors regulating simple multicellular life cycles, we examined a collection of wild isolates of the budding yeast S. cerevisiae.[12][,][13] We found that all these strains can exist as multicellular clusters, a phenotype that is controlled by the mating-type locus and strongly influenced by the nutritional environment. Inspired by this variation, we engineered inducible dispersal in a multicellular laboratory strain and demonstrated that a regulated life cycle has an advantage over constitutively single-celled or constitutively multicellular life cycles when the environment alternates between favoring intercellular cooperation (a low sucrose concentration) and dispersal (a patchy environment generated by emulsion). Our results suggest that the separation of mother and daughter cells is under selection in wild isolates and is regulated by their genetic composition and the environments they encounter and that alternating patterns of resource availability may have played a role in the evolution of life cycles.},
}

Animals
*Saccharomyces cerevisiae/physiology
*Biological Evolution
Phenotype
Life Cycle Stages
Reproduction

@article {pmid37011504,
year = {2023},
author = {Morehouse, BR},
title = {Phage defense origin of animal immunity.},
journal = {Current opinion in microbiology},
volume = {73},
number = {},
pages = {102295},
doi = {10.1016/j.mib.2023.102295},
pmid = {37011504},
issn = {1879-0364},
mesh = {Animals ; *Bacteria/genetics ; Prokaryotic Cells ; Archaea/genetics ; Immunity, Innate ; *Bacteriophages/genetics ; },
abstract = {The innate immune system is the first line of defense against microbial pathogens. Many of the features of eukaryotic innate immunity have long been viewed as lineage-specific innovations, evolved to deal with the challenges and peculiarities of multicellular life. However, it has become increasingly apparent that in addition to evolving their own unique antiviral immune strategies, all lifeforms have some shared defense strategies in common. Indeed, critical fixtures of animal innate immunity bear striking resemblance in both structure and function to the multitude of diverse bacteriophage (phage) defense pathways discovered hidden in plain sight within the genomes of bacteria and archaea. This review will highlight many surprising examples of the recently revealed connections between prokaryotic and eukaryotic antiviral immune systems.},
}

Animals
*Bacteria/genetics
Prokaryotic Cells
Archaea/genetics
Immunity, Innate
*Bacteriophages/genetics

@article {pmid37005641,
year = {2023},
author = {Guan, X and Zhang, L and Lai, S and Zhang, J and Wei, J and Wang, K and Zhang, W and Li, C and Tong, J and Lei, Z},
title = {Green synthesis of glyco-CuInS2 QDs with visible/NIR dual emission for 3D multicellular tumor spheroid and in vivo imaging.},
journal = {Journal of nanobiotechnology},
volume = {21},
number = {1},
pages = {118},
pmid = {37005641},
issn = {1477-3155},
support = {21965032; 22267012; 21761032; 52162034//National Natural Science Foundation of China/ ; 20JR5RA525; 20JR10RA143//Natural Science Foundation of Gansu Province/ ; 2020BSZX08//Doctoral Program Fund of Lanzhou University of Arts and Sciences/ ; },
mesh = {Humans ; Diagnostic Imaging ; *Nanoparticles ; *Quantum Dots ; HeLa Cells ; Water ; },
abstract = {Glyco-quantum dots (glyco-QDs) have attracted significant interest in bioimaging applications, notably in cancer imaging, because they effectively combine the glycocluster effect with the exceptional optical properties of QDs. The key challenge now lies in how to eliminate the high heavy metal toxicity originating from traditional toxic Cd-based QDs for in vivo bioimaging. Herein, we report an eco-friendly pathway to prepare nontoxic Cd-free glyco-QDs in water by the "direct" reaction of thiol-ending monosaccharides with metal salts precursors. The formation of glyco-CuInS2 QDs could be explained by a nucleation-growth mechanism following the LaMer model. As-prepared four glyco-CuInS2 QDs were water-soluble, monodispersed, spherical in shape and exhibited size range of 3.0-4.0 nm. They exhibited well-separated dual emission in the visible region (500-590 nm) and near-infrared range (~ 827 nm), which may be attributable to visible excitonic emission and near-infrared surface defect emission. Meanwhile, the cell imaging displayed the reversibly distinct dual-color (green and red) fluorescence in tumor cells (HeLa, A549, MKN-45) and excellent membrane-targeting properties of glyco-CuInS2 QDs based on their good biorecognition ability. Importantly, these QDs succeed in penetrating uniformly into the interior (the necrotic zone) of 3D multicellular tumor spheroids (MCTS) due to their high negative charge (zeta potential values ranging from - 23.9 to - 30.1 mV), which overcame the problem of poor penetration depth of existing QDs in in vitro spheroid models. So, confocal analysis confirmed their excellent ability to penetrate and label tumors. Thus, the successful application in in vivo bioimaging of these glyco-QDs verified that this design strategy is an effective, low cost and simple procedure for developing green nanoparticles as cheap and promising fluorescent bioprobes.},
}

Humans
Diagnostic Imaging
*Nanoparticles
*Quantum Dots
HeLa Cells
Water

@article {pmid37002899,
year = {2023},
author = {LeBleu, VS and Dai, J and Tsutakawa, S and MacDonald, BA and Alge, JL and Sund, M and Xie, L and Sugimoto, H and Tainer, J and Zon, LI and Kalluri, R},
title = {Identification of unique α4 chain structure and conserved antiangiogenic activity of α3NC1 type IV collagen in zebrafish.},
journal = {Developmental dynamics : an official publication of the American Association of Anatomists},
volume = {252},
number = {7},
pages = {1046-1060},
doi = {10.1002/dvdy.590},
pmid = {37002899},
issn = {1097-0177},
mesh = {Animals ; Humans ; *Collagen Type IV/genetics ; *Zebrafish ; Endothelial Cells ; Protein Subunits/analysis/metabolism ; Basement Membrane/metabolism ; },
abstract = {BACKGROUND: Type IV collagen is an abundant component of basement membranes in all multicellular species and is essential for the extracellular scaffold supporting tissue architecture and function. Lower organisms typically have two type IV collagen genes, encoding α1 and α2 chains, in contrast with the six genes in humans, encoding α1-α6 chains. The α chains assemble into trimeric protomers, the building blocks of the type IV collagen network. The detailed evolutionary conservation of type IV collagen network remains to be studied.

RESULTS: We report on the molecular evolution of type IV collagen genes. The zebrafish α4 non-collagenous (NC1) domain, in contrast with its human ortholog, contains an additional cysteine residue and lacks the M93 and K211 residues involved in sulfilimine bond formation between adjacent protomers. This may alter α4 chain interactions with other α chains, as supported by temporal and anatomic expression patterns of collagen IV chains during the zebrafish development. Despite the divergence between zebrafish and human α3 NC1 domain (endogenous angiogenesis inhibitor, Tumstatin), the zebrafish α3 NC1 domain exhibits conserved antiangiogenic activity in human endothelial cells.

CONCLUSIONS: Our work supports type IV collagen is largely conserved between zebrafish and humans, with a possible difference involving the α4 chain.},
}

Animals
Humans
*Collagen Type IV/genetics
*Zebrafish
Endothelial Cells
Protein Subunits/analysis/metabolism
Basement Membrane/metabolism

@article {pmid37000909,
year = {2023},
author = {Little, JC and Kaaronen, RO and Hukkinen, JI and Xiao, S and Sharpee, T and Farid, AM and Nilchiani, R and Barton, CM},
title = {Earth Systems to Anthropocene Systems: An Evolutionary, System-of-Systems, Convergence Paradigm for Interdependent Societal Challenges.},
journal = {Environmental science & technology},
volume = {57},
number = {14},
pages = {5504-5520},
doi = {10.1021/acs.est.2c06203},
pmid = {37000909},
issn = {1520-5851},
mesh = {Animals ; Humans ; *Agriculture ; *Biodiversity ; Urbanization ; Mammals ; },
abstract = {Humans have made profound changes to the Earth. The resulting societal challenges of the Anthropocene (e.g., climate change and impacts, renewable energy, adaptive infrastructure, disasters, pandemics, food insecurity, and biodiversity loss) are complex and systemic, with causes, interactions, and consequences that cascade across a globally connected system of systems. In this Critical Review, we turn to our "origin story" for insight, briefly tracing the formation of the Universe and the Earth, the emergence of life, the evolution of multicellular organisms, mammals, primates, and humans, as well as the more recent societal transitions involving agriculture, urbanization, industrialization, and computerization. Focusing on the evolution of the Earth, genetic evolution, the evolution of the brain, and cultural evolution, which includes technological evolution, we identify a nested evolutionary sequence of geophysical, biophysical, sociocultural, and sociotechnical systems, emphasizing the causal mechanisms that first formed, and then transformed, Earth systems into Anthropocene systems. Describing how the Anthropocene systems coevolved, and briefly illustrating how the ensuing societal challenges became tightly integrated across multiple spatial, temporal, and organizational scales, we conclude by proposing an evolutionary, system-of-systems, convergence paradigm for the entire family of interdependent societal challenges of the Anthropocene.},
}

Animals
Humans
*Agriculture
*Biodiversity
Urbanization
Mammals

@article {pmid36996815,
year = {2023},
author = {Olivetta, M and Dudin, O},
title = {The nuclear-to-cytoplasmic ratio drives cellularization in the close animal relative Sphaeroforma arctica.},
journal = {Current biology : CB},
volume = {33},
number = {8},
pages = {1597-1605.e3},
doi = {10.1016/j.cub.2023.03.019},
pmid = {36996815},
issn = {1879-0445},
mesh = {Animals ; *Eukaryota/genetics ; *Mesomycetozoea/genetics ; Cell Nucleus ; Cytosol ; Genome ; },
abstract = {The ratio of nuclear content to cytoplasmic volume (N/C ratio) is a key regulator driving the maternal-to-zygotic transition in most animal embryos. Altering this ratio often impacts zygotic genome activation and deregulates the timing and outcome of embryogenesis.[1][,][2][,][3] Despite being ubiquitous across animals, little is known about when the N/C ratio evolved to control multicellular development. Such capacity either originated with the emergence of animal multicellularity or was co-opted from the mechanisms present in unicellular organisms.[4] An effective strategy to tackle this question is to investigate the close relatives of animals exhibiting life cycles with transient multicellular stages.[5] Among these are ichthyosporeans, a lineage of protists undergoing coenocytic development followed by cellularization and cell release.[6][,][7][,][8] During cellularization, a transient multicellular stage resembling animal epithelia is generated, offering a unique opportunity to examine whether the N/C ratio regulates multicellular development. Here, we use time-lapse microscopy to characterize how the N/C ratio affects the life cycle of the best-studied ichthyosporean model, Sphaeroforma arctica. We uncover that the last stages of cellularization coincide with a significant increase in the N/C ratio. Increasing the N/C ratio by reducing the coenocytic volume accelerates cellularization, whereas decreasing the N/C ratio by lowering the nuclear content halts it. Moreover, centrifugation and pharmacological inhibitor experiments suggest that the N/C ratio is locally sensed at the cortex and relies on phosphatase activity. Altogether, our results show that the N/C ratio drives cellularization in S. arctica, suggesting that its capacity to control multicellular development predates animal emergence.},
}

Animals
*Eukaryota/genetics
*Mesomycetozoea/genetics
Cell Nucleus
Cytosol
Genome

@article {pmid36996248,
year = {2023},
author = {Herold, J and Behle, E and Rosenbauer, J and Ferruzzi, J and Schug, A},
title = {Development of a scoring function for comparing simulated and experimental tumor spheroids.},
journal = {PLoS computational biology},
volume = {19},
number = {3},
pages = {e1010471},
pmid = {36996248},
issn = {1553-7358},
support = {U01 CA202123/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Spheroids, Cellular ; Collagen/chemistry ; Extracellular Matrix ; *Neoplasms ; *Neoplasms, Experimental ; },
abstract = {Progress continues in the field of cancer biology, yet much remains to be unveiled regarding the mechanisms of cancer invasion. In particular, complex biophysical mechanisms enable a tumor to remodel the surrounding extracellular matrix (ECM), allowing cells to invade alone or collectively. Tumor spheroids cultured in collagen represent a simplified, reproducible 3D model system, which is sufficiently complex to recapitulate the evolving organization of cells and interaction with the ECM that occur during invasion. Recent experimental approaches enable high resolution imaging and quantification of the internal structure of invading tumor spheroids. Concurrently, computational modeling enables simulations of complex multicellular aggregates based on first principles. The comparison between real and simulated spheroids represents a way to fully exploit both data sources, but remains a challenge. We hypothesize that comparing any two spheroids requires first the extraction of basic features from the raw data, and second the definition of key metrics to match such features. Here, we present a novel method to compare spatial features of spheroids in 3D. To do so, we define and extract features from spheroid point cloud data, which we simulated using Cells in Silico (CiS), a high-performance framework for large-scale tissue modeling previously developed by us. We then define metrics to compare features between individual spheroids, and combine all metrics into an overall deviation score. Finally, we use our features to compare experimental data on invading spheroids in increasing collagen densities. We propose that our approach represents the basis for defining improved metrics to compare large 3D data sets. Moving forward, this approach will enable the detailed analysis of spheroids of any origin, one application of which is informing in silico spheroids based on their in vitro counterparts. This will enable both basic and applied researchers to close the loop between modeling and experiments in cancer research.},
}

Animals
Spheroids, Cellular
Collagen/chemistry
Extracellular Matrix
*Neoplasms
*Neoplasms, Experimental

@article {pmid36980921,
year = {2023},
author = {Han, M and Ren, J and Guo, H and Tong, X and Hu, H and Lu, K and Dai, Z and Dai, F},
title = {Mutation Rate and Spectrum of the Silkworm in Normal and Temperature Stress Conditions.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
pmid = {36980921},
issn = {2073-4425},
mesh = {Animals ; *Bombyx/genetics ; Temperature ; Mutation Rate ; Insecta/genetics ; Genome ; },
abstract = {Mutation rate is a crucial parameter in evolutionary genetics. However, the mutation rate of most species as well as the extent to which the environment can alter the genome of multicellular organisms remain poorly understood. Here, we used parents-progeny sequencing to investigate the mutation rate and spectrum of the domestic silkworm (Bombyx mori) among normal and two temperature stress conditions (32 °C and 0 °C). The rate of single-nucleotide mutations in the normal temperature rearing condition was 0.41 × 10[-8] (95% confidence interval, 0.33 × 10[-8]-0.49 × 10[-8]) per site per generation, which was up to 1.5-fold higher than in four previously studied insects. Moreover, the mutation rates of the silkworm under the stresses are significantly higher than in normal conditions. Furthermore, the mutation rate varies less in gene regions under normal and temperature stresses. Together, these findings expand the known diversity of the mutation rate among eukaryotes but also have implications for evolutionary analysis that assumes a constant mutation rate among species and environments.},
}

Animals
*Bombyx/genetics
Temperature
Mutation Rate
Insecta/genetics
Genome

@article {pmid36980213,
year = {2023},
author = {Merino, MM and Garcia-Sanz, JA},
title = {Stemming Tumoral Growth: A Matter of Grotesque Organogenesis.},
journal = {Cells},
volume = {12},
number = {6},
pages = {},
pmid = {36980213},
issn = {2073-4409},
mesh = {Humans ; *Neoplasm Recurrence, Local ; *Organogenesis ; Neoplastic Stem Cells ; Cell Transformation, Neoplastic ; },
abstract = {The earliest metazoans probably evolved from single-celled organisms which found the colonial system to be a beneficial organization. Over the course of their evolution, these primary colonial organisms increased in size, and division of labour among the cells became a remarkable feature, leading to a higher level of organization: the biological organs. Primitive metazoans were the first organisms in evolution to show organ-type structures, which set the grounds for complex organs to evolve. Throughout evolution, and concomitant with organogenesis, is the appearance of tissue-specific stem cells. Tissue-specific stem cells gave rise to multicellular living systems with distinct organs which perform specific physiological functions. This setting is a constructive role of evolution; however, rebel cells can take over the molecular mechanisms for other purposes: nowadays we know that cancer stem cells, which generate aberrant organ-like structures, are at the top of a hierarchy. Furthermore, cancer stem cells are the root of metastasis, therapy resistance, and relapse. At present, most therapeutic drugs are unable to target cancer stem cells and therefore, treatment becomes a challenging issue. We expect that future research will uncover the mechanistic "forces" driving organ growth, paving the way to the implementation of new strategies to impair human tumorigenesis.},
}

Humans
*Neoplasm Recurrence, Local
*Organogenesis
Neoplastic Stem Cells
Cell Transformation, Neoplastic

@article {pmid36964572,
year = {2023},
author = {Barrera-Redondo, J and Lotharukpong, JS and Drost, HG and Coelho, SM},
title = {Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {54},
pmid = {36964572},
issn = {1474-760X},
mesh = {Animals ; Phylogeny ; *Biological Evolution ; *Genomics/methods ; Fungi/genetics ; Plants/genetics ; Evolution, Molecular ; },
abstract = {We present GenEra (https://github.com/josuebarrera/GenEra), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage-dependent, suggesting that plants are more prone to evolve novelty through the emergence of new genes compared to animals and fungi.},
}

Animals
Phylogeny
*Biological Evolution
*Genomics/methods
Fungi/genetics
Plants/genetics
Evolution, Molecular

@article {pmid36959212,
year = {2023},
author = {Nofech-Mozes, I and Soave, D and Awadalla, P and Abelson, S},
title = {Pan-cancer classification of single cells in the tumour microenvironment.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1615},
pmid = {36959212},
issn = {2041-1723},
mesh = {Humans ; Female ; *Tumor Microenvironment ; *Breast Neoplasms/pathology ; Gene Expression Profiling/methods ; Transcriptome ; Stromal Cells/pathology ; },
abstract = {Single-cell RNA sequencing can reveal valuable insights into cellular heterogeneity within tumour microenvironments (TMEs), paving the way for a deep understanding of cellular mechanisms contributing to cancer. However, high heterogeneity among the same cancer types and low transcriptomic variation in immune cell subsets present challenges for accurate, high-resolution confirmation of cells' identities. Here we present scATOMIC; a modular annotation tool for malignant and non-malignant cells. We trained scATOMIC on >300,000 cancer, immune, and stromal cells defining a pan-cancer reference across 19 common cancers and employ a hierarchical approach, outperforming current classification methods. We extensively confirm scATOMIC's accuracy on 225 tumour biopsies encompassing >350,000 cancer and a variety of TME cells. Lastly, we demonstrate scATOMIC's practical significance to accurately subset breast cancers into clinically relevant subtypes and predict tumours' primary origin across metastatic cancers. Our approach represents a broadly applicable strategy to analyse multicellular cancer TMEs.},
}

Humans
Female
*Tumor Microenvironment
*Breast Neoplasms/pathology
Gene Expression Profiling/methods
Transcriptome
Stromal Cells/pathology

@article {pmid36945744,
year = {2023},
author = {Li, Y and Kim, EJ and Voshall, A and Moriyama, EN and Cerutti, H},
title = {Small RNAs >26 nt in length associate with AGO1 and are upregulated by nutrient deprivation in the alga Chlamydomonas.},
journal = {The Plant cell},
volume = {35},
number = {6},
pages = {1868-1887},
pmid = {36945744},
issn = {1532-298X},
mesh = {Animals ; *Chlamydomonas/genetics/metabolism ; RNA Interference ; Gene Expression Regulation ; Argonaute Proteins/genetics/metabolism ; *Chlamydomonas reinhardtii/genetics/metabolism ; },
abstract = {Small RNAs (sRNAs) associate with ARGONAUTE (AGO) proteins forming effector complexes with key roles in gene regulation and defense responses against molecular parasites. In multicellular eukaryotes, extensive duplication and diversification of RNA interference (RNAi) components have resulted in intricate pathways for epigenetic control of gene expression. The unicellular alga Chlamydomonas reinhardtii also has a complex RNAi machinery, including 3 AGOs and 3 DICER-like proteins. However, little is known about the biogenesis and function of most endogenous sRNAs. We demonstrate here that Chlamydomonas contains uncommonly long (>26 nt) sRNAs that associate preferentially with AGO1. Somewhat reminiscent of animal PIWI-interacting RNAs, these >26 nt sRNAs are derived from moderately repetitive genomic clusters and their biogenesis is DICER-independent. Interestingly, the sequences generating these >26-nt sRNAs have been conserved and amplified in several Chlamydomonas species. Moreover, expression of these longer sRNAs increases substantially under nitrogen or sulfur deprivation, concurrently with the downregulation of predicted target transcripts. We hypothesize that the transposon-like sequences from which >26-nt sRNAs are produced might have been ancestrally targeted for silencing by the RNAi machinery but, during evolution, certain sRNAs might have fortuitously acquired endogenous target genes and become integrated into gene regulatory networks.},
}

Animals
*Chlamydomonas/genetics/metabolism
RNA Interference
Gene Expression Regulation
Argonaute Proteins/genetics/metabolism
*Chlamydomonas reinhardtii/genetics/metabolism

@article {pmid36912901,
year = {2023},
author = {Ebinghaus, M and Dos Santos, MDM and Tonelli, GSSS and Macagnan, D and Carvalho, EA and Dianese, JC},
title = {Raveneliopsis, a new genus of ravenelioid rust fungi on Cenostigma (Caesalpinioideae) from the Brazilian Cerrado and Caatinga.},
journal = {Mycologia},
volume = {115},
number = {2},
pages = {263-276},
doi = {10.1080/00275514.2023.2177048},
pmid = {36912901},
issn = {1557-2536},
mesh = {Brazil ; Phylogeny ; *Basidiomycota/genetics ; *Fabaceae ; },
abstract = {The multicellular discoid convex teliospore heads represent a prominent generic feature of the genus Ravenelia. However, recent molecular phylogenetic work has shown that this is a convergent trait, and that this genus does not represent a natural group. In 2000, a rust fungus infecting the Caesalpinioid species Cenostigma macrophyllum (= C. gardnerianum) was described as Ravenelia cenostigmatis. This species shows some rare features, such as an extra layer of sterile cells between the cysts and the fertile teliospores, spirally ornamented urediniospores, as well as strongly incurved paraphyses giving the telia and uredinia a basket-like appearance. Using freshly collected specimens of Rav. cenostigmatis and Rav. spiralis on C. macrophyllum, our phylogenetic analyses based on the nuc 28S, nuc 18S, and mt CO3 (cytochrome c oxidase subunit 3) gene sequences demonstrated that these two rust fungi belong in a lineage within the Raveneliineae that is distinct from Ravenelia s. str. Besides proposing their recombination into the new genus Raveneliopsis (type species R. cenostigmatis) and briefly discussing their potentially close phylogenetic affiliations, we suggest that five other Ravenelia species that are morphologically and ecologically close to the type species of Raveneliopsis, i.e., Rav. corbula, Rav. corbuloides, Rav. parahybana, Rav. pileolarioides, and Rav. Striatiformis, may be recombined pending new collections and confirmation through molecular phylogenetic analyses.},
}

Brazil
Phylogeny
*Basidiomycota/genetics
*Fabaceae

@article {pmid36907967,
year = {2023},
author = {Lu, B and Hu, X and Warren, A and Song, W and Yan, Y},
title = {From oral structure to molecular evidence: new insights into the evolutionary phylogeny of the ciliate order Sessilida (Protista, Ciliophora), with the establishment of two new families and new contributions to the poorly studied family Vaginicolidae.},
journal = {Science China. Life sciences},
volume = {66},
number = {7},
pages = {1535-1553},
pmid = {36907967},
issn = {1869-1889},
mesh = {Humans ; Phylogeny ; *Ciliophora/genetics ; *Oligohymenophorea/genetics ; DNA, Ribosomal/genetics ; Cognition ; Sequence Analysis, DNA ; },
abstract = {Ciliated protists represent one of the most primitive and diverse lineages of eukaryotes, with nuclear dimorphism, a distinctive sexual process (conjugation), and extensive genome rearrangements. Among divergent ciliate lineages, the peritrich order Sessilida includes members with a colonial lifestyle, which may hint to an independent evolutionary attempt for multicellularity, although they are still single-celled organisms. To date, the evolution and phylogeny of this group are still far from clear, in part due to the paucity of molecular and/or morphological data for many taxa. In this study, we extend taxon sampling of a loricate group of sessilids by obtaining 69 new rDNA (SSU rDNA, ITS1-5.8S rDNA-ITS2, and LSU rDNA) sequences from 20 well-characterized representative species and analyze the phylogenetic relationships within Sessilida. The main findings are: (i) the genera Rhabdostyla and Campanella each represents a unique taxon at family level, supporting the establishment of two new families, i.e., Rhabdostylidae n. fam. and Campanellidae n. fam., respectively, the former being sister to a morphologically heterogeneous clade comprising Astylozoidae and several incertae sedis species and the latter occupying the basal position within the Sessilida clade; (ii) the structure of infundibular polykinety 3 is likely to be a phylogenetically informative character for resolving evolutionary relationships among sessilids; (iii) differences between sparsely and the densely arranged silverline systems could be a suprageneric taxonomic character; (iv) the monophyly of Vaginicolidae is confirmed, which is consistent with its specialized morphology, i.e., the possession of a typical peritrich lorica which might be an apomorphy for this group; (v) within Vaginicolidae, the monotypic Cothurniopsis sensu Stokes, 1893 is a synonym of Cothurnia Ehrenberg, 1831, and a new combination is created, i.e., Cothurnia valvata nov. comb.; (vi) Vaginicola sensu lato comprises at least two distinctly divergent clades, one affiliated with Thuricola and the other with a systematically puzzling clade represented by Vaginicola tincta.},
}

Humans
Phylogeny
*Ciliophora/genetics
*Oligohymenophorea/genetics
DNA, Ribosomal/genetics
Cognition
Sequence Analysis, DNA

@article {pmid36899423,
year = {2023},
author = {Ouyang, X and Wu, B and Yu, H and Dong, B},
title = {DYRK1-mediated phosphorylation of endocytic components is required for extracellular lumen expansion in ascidian notochord.},
journal = {Biological research},
volume = {56},
number = {1},
pages = {10},
pmid = {36899423},
issn = {0717-6287},
support = {2019YFE0190900//National Key Research and Development Program of China/ ; },
mesh = {Animals ; Humans ; *Ciona intestinalis/metabolism ; Notochord/metabolism ; Phosphorylation ; Embryonic Development ; Morphogenesis ; },
abstract = {BACKGROUND: The biological tube is a basal biology structure distributed in all multicellular animals, from worms to humans, and has diverse biological functions. Formation of tubular system is crucial for embryogenesis and adult metabolism. Ascidian Ciona notochord lumen is an excellent in vivo model for tubulogenesis. Exocytosis has been known to be essential for tubular lumen formation and expansion. The roles of endocytosis in tubular lumen expansion remain largely unclear.

RESULTS: In this study, we first identified a dual specificity tyrosine-phosphorylation-regulated kinase 1 (DYRK1), the protein kinase, which was upregulated and required for ascidian notochord extracellular lumen expansion. We demonstrated that DYRK1 interacted with and phosphorylated one of the endocytic components endophilin at Ser263 that was essential for notochord lumen expansion. Moreover, through phosphoproteomic sequencing, we revealed that in addition to endophilin, the phosphorylation of other endocytic components was also regulated by DYRK1. The loss of function of DYRK1 disturbed endocytosis. Then, we demonstrated that clathrin-mediated endocytosis existed and was required for notochord lumen expansion. In the meantime, the results showed that the secretion of notochord cells is vigorous in the apical membrane.

CONCLUSIONS: We found the co-existence of endocytosis and exocytosis activities in apical membrane during lumen formation and expansion in Ciona notochord. A novel signaling pathway is revealed that DYRK1 regulates the endocytosis by phosphorylation that is required for lumen expansion. Our finding thus indicates a dynamic balance between endocytosis and exocytosis is crucial to maintain apical membrane homeostasis that is essential for lumen growth and expansion in tubular organogenesis.},
}

Animals
Humans
*Ciona intestinalis/metabolism
Notochord/metabolism
Phosphorylation
Embryonic Development
Morphogenesis

@article {pmid36897970,
year = {2023},
author = {Davidescu, MR and Romanczuk, P and Gregor, T and Couzin, ID},
title = {Growth produces coordination trade-offs in Trichoplax adhaerens, an animal lacking a central nervous system.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {11},
pages = {e2206163120},
pmid = {36897970},
issn = {1091-6490},
support = {R01 GM097275/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Placozoa/physiology ; Body Size ; Central Nervous System ; Biological Evolution ; },
abstract = {How collectives remain coordinated as they grow in size is a fundamental challenge affecting systems ranging from biofilms to governments. This challenge is particularly apparent in multicellular organisms, where coordination among a vast number of cells is vital for coherent animal behavior. However, the earliest multicellular organisms were decentralized, with indeterminate sizes and morphologies, as exemplified by Trichoplax adhaerens, arguably the earliest-diverged and simplest motile animal. We investigated coordination among cells in T. adhaerens by observing the degree of collective order in locomotion across animals of differing sizes and found that larger individuals exhibit increasingly disordered locomotion. We reproduced this effect of size on order through a simulation model of active elastic cellular sheets and demonstrate that this relationship is best recapitulated across all body sizes when the simulation parameters are tuned to a critical point in the parameter space. We quantify the trade-off between increasing size and coordination in a multicellular animal with a decentralized anatomy that shows evidence of criticality and hypothesize as to the implications of this on the evolution hierarchical structures such as nervous systems in larger organisms.},
}

Animals
*Placozoa/physiology
Body Size
Central Nervous System
Biological Evolution

@article {pmid36877741,
year = {2023},
author = {Luque, LM and Carlevaro, CM and Llamoza Torres, CJ and Lomba, E},
title = {Physics-based tissue simulator to model multicellular systems: A study of liver regeneration and hepatocellular carcinoma recurrence.},
journal = {PLoS computational biology},
volume = {19},
number = {3},
pages = {e1010920},
pmid = {36877741},
issn = {1553-7358},
mesh = {Humans ; *Carcinoma, Hepatocellular ; Liver Regeneration ; *Liver Neoplasms ; Hepatectomy ; Models, Biological ; Neoplasm Recurrence, Local ; Tumor Microenvironment ; },
abstract = {We present a multiagent-based model that captures the interactions between different types of cells with their microenvironment, and enables the analysis of the emergent global behavior during tissue regeneration and tumor development. Using this model, we are able to reproduce the temporal dynamics of regular healthy cells and cancer cells, as well as the evolution of their three-dimensional spatial distributions. By tuning the system with the characteristics of the individual patients, our model reproduces a variety of spatial patterns of tissue regeneration and tumor growth, resembling those found in clinical imaging or biopsies. In order to calibrate and validate our model we study the process of liver regeneration after surgical hepatectomy in different degrees. In the clinical context, our model is able to predict the recurrence of a hepatocellular carcinoma after a 70% partial hepatectomy. The outcomes of our simulations are in agreement with experimental and clinical observations. By fitting the model parameters to specific patient factors, it might well become a useful platform for hypotheses testing in treatments protocols.},
}

Humans
*Carcinoma, Hepatocellular
Liver Regeneration
*Liver Neoplasms
Hepatectomy
Models, Biological
Neoplasm Recurrence, Local
Tumor Microenvironment

@article {pmid36876435,
year = {2023},
author = {Bernardo, N and Crespo, I and Cuppari, A and Meijer, WJJ and Boer, DR},
title = {A tetramerization domain in prokaryotic and eukaryotic transcription regulators homologous to p53.},
journal = {Acta crystallographica. Section D, Structural biology},
volume = {79},
number = {Pt 3},
pages = {259-267},
pmid = {36876435},
issn = {2059-7983},
support = {BIO2016-77883-C2-2-P//Ministerio de Economía y Competitividad, Agencia Estatal de Investigación/ ; PID2020-117028GB-I00//Ministerio de Economía y Competitividad, Agencia Estatal de Investigación/ ; FIS2015-72574-EXP//Ministerio de Economía y Competitividad, Agencia Estatal de Investigación/ ; PID2019-108778GB-C21//Ministerio de Economía y Competitividad, Agencia Estatal de Investigación/ ; BIO2016-77883-C2-1-P//Ministerio de Economía y Competitividad, Agencia Estatal de Investigación/ ; },
mesh = {Humans ; *Eukaryota ; Tumor Suppressor Protein p53 ; *Bacillus ; Bacillus subtilis ; Transcription Factors ; DNA ; },
abstract = {Transcriptional regulation usually requires the action of several proteins that either repress or activate a promotor of an open reading frame. These proteins can counteract each other, thus allowing tight regulation of the transcription of the corresponding genes, where tight repression is often linked to DNA looping or cross-linking. Here, the tetramerization domain of the bacterial gene repressor Rco from Bacillus subtilis plasmid pLS20 (RcopLS20) has been identified and its structure is shown to share high similarity to the tetramerization domain of the well known p53 family of human tumor suppressors, despite lacking clear sequence homology. In RcopLS20, this tetramerization domain is responsible for inducing DNA looping, a process that involves multiple tetramers. In accordance, it is shown that RcopLS20 can form octamers. This domain was named TetDloop and its occurrence was identified in other Bacillus species. The TetDloop fold was also found in the structure of a transcriptional repressor from Salmonella phage SPC32H. It is proposed that the TetDloop fold has evolved through divergent evolution and that the TetDloop originates from a common ancestor predating the occurrence of multicellular life.},
}

Humans
*Eukaryota
Tumor Suppressor Protein p53
*Bacillus
Bacillus subtilis
Transcription Factors
DNA

@article {pmid36854263,
year = {2023},
author = {Tang, S and Pichugin, Y and Hammerschmidt, K},
title = {An environmentally induced multicellular life cycle of a unicellular cyanobacterium.},
journal = {Current biology : CB},
volume = {33},
number = {4},
pages = {764-769.e5},
doi = {10.1016/j.cub.2023.01.069},
pmid = {36854263},
issn = {1879-0445},
mesh = {Animals ; *Cyanobacteria ; *Automobile Driving ; Biological Evolution ; Cell Death ; Life Cycle Stages ; },
abstract = {Understanding the evolutionary transition to multicellularity is a key problem in biology.[1][,][2][,][3][,][4] Nevertheless, the ecological conditions driving such transitions are not well understood. The first known transition to multicellularity occurred 2.5 billion years ago in cyanobacteria,[5][,][6][,][7] and today's cyanobacteria are characterized by enormous morphological diversity. They range from unicellular species; unicellular cyanobacteria with packet-like phenotypes, e.g., tetrads; and simple filamentous species to highly differentiated filamentous species.[8][,][9][,][10] The cyanobacterium Cyanothece sp. ATCC 51142, an isolate from the intertidal zone of the U.S. Gulf Coast,[11] was classified as a unicellular species.[12] We report a facultative life cycle of Cyanothece sp. in which multicellular filaments alternate with unicellular stages. In a series of experiments, we identified salinity and population density as environmental factors triggering the phenotypic switch between the two morphologies. Then, we used numerical models to test hypotheses regarding the nature of the environmental cues and the mechanisms underlying filament dissolution. While the results predict that the observed response is likely caused by an excreted compound in the medium, we cannot fully exclude changes in nutrient availability (as in Tuomi et al.[13] and Matz and Jürgens[14]). The best-fit modeling results show a nonlinear effect of the compound, which is characteristic of density-dependent sensing systems.[15][,][16] Furthermore, filament fragmentation is predicted to occur by connection cleavage rather than cell death of each alternating cell, which is supported by fluorescent and scanning electron microscopy results. The switch between unicellular and multicellular morphology constitutes an environmentally dependent life cycle that is likely an important step en route to permanent multicellularity.},
}

Animals
*Cyanobacteria
*Automobile Driving
Biological Evolution
Cell Death
Life Cycle Stages

@article {pmid36849252,
year = {2023},
author = {Göbel, T and Goebel, B and Hyprath, M and Lamminger, I and Weisser, H and Angioni, C and Mathes, M and Thomas, D and Kahnt, AS},
title = {Three-dimensional growth reveals fine-tuning of 5-lipoxygenase by proliferative pathways in cancer.},
journal = {Life science alliance},
volume = {6},
number = {5},
pages = {},
pmid = {36849252},
issn = {2575-1077},
mesh = {Humans ; *Arachidonate 5-Lipoxygenase/genetics ; Lipid Metabolism ; *Colonic Neoplasms ; Mechanistic Target of Rapamycin Complex 2 ; Phosphatidylinositol 3-Kinases ; },
abstract = {The leukotriene (LT) pathway is positively correlated with the progression of solid malignancies, but the factors that control the expression of 5-lipoxygenase (5-LO), the central enzyme in LT biosynthesis, in tumors are poorly understood. Here, we report that 5-LO along with other members of the LT pathway is up-regulated in multicellular colon tumor spheroids. This up-regulation was inversely correlated with cell proliferation and activation of PI3K/mTORC-2- and MEK-1/ERK-dependent pathways. Furthermore, we found that E2F1 and its target gene MYBL2 were involved in the repression of 5-LO during cell proliferation. Importantly, we found that this PI3K/mTORC-2- and MEK-1/ERK-dependent suppression of 5-LO is also existent in tumor cells from other origins, suggesting that this mechanism is widely applicable to other tumor entities. Our data show that tumor cells fine-tune 5-LO and LT biosynthesis in response to environmental changes repressing the enzyme during proliferation while making use of the enzyme under cell stress conditions, implying that tumor-derived 5-LO plays a role in the manipulation of the tumor stroma to quickly restore cell proliferation.},
}

Humans
*Arachidonate 5-Lipoxygenase/genetics
Lipid Metabolism
*Colonic Neoplasms
Mechanistic Target of Rapamycin Complex 2
Phosphatidylinositol 3-Kinases

@article {pmid36830620,
year = {2023},
author = {van Oosten-Hawle, P},
title = {Organismal Roles of Hsp90.},
journal = {Biomolecules},
volume = {13},
number = {2},
pages = {},
pmid = {36830620},
issn = {2218-273X},
mesh = {Humans ; Animals ; *HSP90 Heat-Shock Proteins/metabolism ; *Molecular Chaperones/metabolism ; Signal Transduction ; Proteostasis ; Stress, Physiological ; Mammals/metabolism ; },
abstract = {Heat shock protein 90 (Hsp90) is a highly conserved molecular chaperone that assists in the maturation of many client proteins involved in cellular signal transduction. As a regulator of cellular signaling processes, it is vital for the maintenance of cellular proteostasis and adaptation to environmental stresses. Emerging research shows that Hsp90 function in an organism goes well beyond intracellular proteostasis. In metazoans, Hsp90, as an environmentally responsive chaperone, is involved in inter-tissue stress signaling responses that coordinate and safeguard cell nonautonomous proteostasis and organismal health. In this way, Hsp90 has the capacity to influence evolution and aging, and effect behavioral responses to facilitate tissue-defense systems that ensure organismal survival. In this review, I summarize the literature on the organismal roles of Hsp90 uncovered in multicellular organisms, from plants to invertebrates and mammals.},
}

Humans
Animals
*HSP90 Heat-Shock Proteins/metabolism
*Molecular Chaperones/metabolism
Signal Transduction
Proteostasis
Stress, Physiological
Mammals/metabolism

@article {pmid36816026,
year = {2023},
author = {Horjales, S and Li Calzi, M and Francia, ME and Cayota, A and Garcia-Silva, MR},
title = {piRNA pathway evolution beyond gonad context: Perspectives from apicomplexa and trypanosomatids.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1129194},
pmid = {36816026},
issn = {1664-8021},
abstract = {piRNAs function as genome defense mechanisms against transposable elements insertions within germ line cells. Recent studies have unraveled that piRNA pathways are not limited to germ cells as initially reckoned, but are instead also found in non-gonadal somatic contexts. Moreover, these pathways have also been reported in bacteria, mollusks and arthropods, associated with safeguard of genomes against transposable elements, regulation of gene expression and with direct consequences in axon regeneration and memory formation. In this Perspective we draw attention to early branching parasitic protozoa, whose genome preservation is an essential function as in late eukaryotes. However, little is known about the defense mechanisms of these genomes. We and others have described the presence of putative PIWI-related machinery members in protozoan parasites. We have described the presence of a PIWI-like protein in Trypanosoma cruzi, bound to small non-coding RNAs (sRNAs) as cargo of secreted extracellular vesicles relevant in intercellular communication and host infection. Herein, we put forward the presence of members related to Argonaute pathways in both Trypanosoma cruzi and Toxoplasma gondii. The presence of PIWI-like machinery in Trypansomatids and Apicomplexa, respectively, could be evidence of an ancestral piRNA machinery that evolved to become more sophisticated and complex in multicellular eukaryotes. We propose a model in which ancient PIWI proteins were expressed broadly and had functions independent of germline maintenance. A better understanding of current and ancestral PIWI/piRNAs will be relevant to better understand key mechanisms of genome integrity conservation during cell cycle progression and modulation of host defense mechanisms by protozoan parasites.},
}

@article {pmid36813362,
year = {2023},
author = {Samuel, V and Rajeev, T and Ramesh, L and Sundararaman, A},
title = {Integrin receptor trafficking in health and disease.},
journal = {Progress in molecular biology and translational science},
volume = {196},
number = {},
pages = {271-302},
doi = {10.1016/bs.pmbts.2022.09.008},
pmid = {36813362},
issn = {1878-0814},
mesh = {Humans ; Protein Transport/physiology ; *Integrins/metabolism ; Cell Membrane/metabolism ; Signal Transduction ; *Neoplasms/metabolism ; Cell Adhesion/physiology ; Cell Movement/physiology ; },
abstract = {Integrins are a family of 24 different heterodimers that are indispensable for multicellular life. Cell polarity, adhesion and migration are controlled by integrins delivered to the cell surface which in turn is regulated by the exo- and endocytic trafficking of integrins. The deep integration between trafficking and cell signaling determines the spatial and temporal output from any biochemical cue. Integrin trafficking plays a key role in development and many pathological conditions, especially cancer. Several novel regulators of integrin traffic have been discovered in recent times, including a novel class of integrin carrying vesicles, the intracellular nanovesicles (INVs). The tight regulation of trafficking pathways by cell signaling, where kinases phosphorylate key small GTPases in the trafficking pathway enable coordination of cell response to the extracellular milieu. Integrin heterodimer expression and trafficking differ in different tissues and contexts. In this Chapter, we discuss recent studies on integrin trafficking and its contribution to normal physiological and pathophysiological states.},
}

Humans
Protein Transport/physiology
*Integrins/metabolism
Cell Membrane/metabolism
Signal Transduction
*Neoplasms/metabolism
Cell Adhesion/physiology
Cell Movement/physiology

@article {pmid36811171,
year = {2023},
author = {Furumizu, C and Aalen, RB},
title = {Peptide signaling through leucine-rich repeat receptor kinases: insight into land plant evolution.},
journal = {The New phytologist},
volume = {238},
number = {3},
pages = {977-982},
doi = {10.1111/nph.18827},
pmid = {36811171},
issn = {1469-8137},
mesh = {*Protein Serine-Threonine Kinases/metabolism ; Plant Proteins/metabolism ; Leucine ; Phylogeny ; Signal Transduction/physiology ; Peptides/genetics ; *Embryophyta/genetics/metabolism ; },
abstract = {Multicellular organisms need mechanisms for communication between cells so that they can fulfill their purpose in the organism as a whole. Over the last two decades, several small post-translationally modified peptides (PTMPs) have been identified as components of cell-to-cell signaling modules in flowering plants. Such peptides most often influence growth and development of organs not universally conserved among land plants. PTMPs have been matched to subfamily XI leucine-rich repeat receptor-like kinases with > 20 repeats. Phylogenetic analyses, facilitated by recently published genomic sequences of non-flowering plants, have identified seven clades of such receptors with a history back to the common ancestor of bryophytes and vascular plants. This raises a number of questions: When did peptide signaling arise during land plant evolution? Have orthologous peptide-receptor pairs preserved their biological functions? Has peptide signaling contributed to major innovations, such as stomata, vasculature, roots, seeds, and flowers? Using genomic, genetic, biochemical, and structural data and non-angiosperm model species, it is now possible to address these questions. The vast number of peptides that have not yet found their partners suggests furthermore that we have far more to learn about peptide signaling in the coming decades.},
}

*Protein Serine-Threonine Kinases/metabolism
Plant Proteins/metabolism
Leucine
Phylogeny
Signal Transduction/physiology
Peptides/genetics
*Embryophyta/genetics/metabolism

@article {pmid36809239,
year = {2023},
author = {Lambros, M and Sella, Y and Bergman, A},
title = {Phenotypic pliancy and the breakdown of epigenetic polycomb mechanisms.},
journal = {PLoS computational biology},
volume = {19},
number = {2},
pages = {e1010889},
pmid = {36809239},
issn = {1553-7358},
support = {R01 CA164468/CA/NCI NIH HHS/United States ; R01 DA033788/DA/NIDA NIH HHS/United States ; },
mesh = {Humans ; Polycomb-Group Proteins/genetics ; *Drosophila Proteins/metabolism ; Epigenesis, Genetic ; Cell Differentiation ; *Neoplasms/genetics ; Phenotype ; },
abstract = {Epigenetic regulatory mechanisms allow multicellular organisms to develop distinct specialized cell identities despite having the same total genome. Cell-fate choices are based on gene expression programs and environmental cues that cells experience during embryonic development, and are usually maintained throughout the life of the organism despite new environmental cues. The evolutionarily conserved Polycomb group (PcG) proteins form Polycomb Repressive Complexes that help orchestrate these developmental choices. Post-development, these complexes actively maintain the resulting cell fate, even in the face of environmental perturbations. Given the crucial role of these polycomb mechanisms in providing phenotypic fidelity (i.e. maintenance of cell fate), we hypothesize that their dysregulation after development will lead to decreased phenotypic fidelity allowing dysregulated cells to sustainably switch their phenotype in response to environmental changes. We call this abnormal phenotypic switching phenotypic pliancy. We introduce a general computational evolutionary model that allows us to test our systems-level phenotypic pliancy hypothesis in-silico and in a context-independent manner. We find that 1) phenotypic fidelity is an emergent systems-level property of PcG-like mechanism evolution, and 2) phenotypic pliancy is an emergent systems-level property resulting from this mechanism's dysregulation. Since there is evidence that metastatic cells behave in a phenotypically pliant manner, we hypothesize that progression to metastasis is driven by the emergence of phenotypic pliancy in cancer cells as a result of PcG mechanism dysregulation. We corroborate our hypothesis using single-cell RNA-sequencing data from metastatic cancers. We find that metastatic cancer cells are phenotypically pliant in the same manner as predicted by our model.},
}

Humans
Polycomb-Group Proteins/genetics
*Drosophila Proteins/metabolism
Epigenesis, Genetic
Cell Differentiation
*Neoplasms/genetics
Phenotype

@article {pmid36797913,
year = {2023},
author = {Leptos, KC and Chioccioli, M and Furlan, S and Pesci, AI and Goldstein, RE},
title = {Phototaxis of Chlamydomonas arises from a tuned adaptive photoresponse shared with multicellular Volvocine green algae.},
journal = {Physical review. E},
volume = {107},
number = {1-1},
pages = {014404},
doi = {10.1103/PhysRevE.107.014404},
pmid = {36797913},
issn = {2470-0053},
support = {207510/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Chlamydomonas ; Phylogeny ; Phototaxis ; *Chlorophyta ; Biological Evolution ; *Volvox ; },
abstract = {A fundamental issue in biology is the nature of evolutionary transitions from unicellular to multicellular organisms. Volvocine algae are models for this transition, as they span from the unicellular biflagellate Chlamydomonas to multicellular species of Volvox with up to 50,000 Chlamydomonas-like cells on the surface of a spherical extracellular matrix. The mechanism of phototaxis in these species is of particular interest since they lack a nervous system and intercellular connections; steering is a consequence of the response of individual cells to light. Studies of Volvox and Gonium, a 16-cell organism with a plate-like structure, have shown that the flagellar response to changing illumination of the cellular photosensor is adaptive, with a recovery time tuned to the rotation period of the colony around its primary axis. Here, combining high-resolution studies of the flagellar photoresponse of micropipette-held Chlamydomonas with 3D tracking of freely swimming cells, we show that such tuning also underlies its phototaxis. A mathematical model is developed based on the rotations around an axis perpendicular to the flagellar beat plane that occur through the adaptive response to oscillating light levels as the organism spins. Exploiting a separation of timescales between the flagellar photoresponse and phototurning, we develop an equation of motion that accurately describes the observed photoalignment. In showing that the adaptive timescales in Volvocine algae are tuned to the organisms' rotational periods across three orders of magnitude in cell number, our results suggest a unified picture of phototaxis in green algae in which the asymmetry in torques that produce phototurns arise from the individual flagella of Chlamydomonas, the flagellated edges of Gonium, and the flagellated hemispheres of Volvox.},
}

*Chlamydomonas
Phylogeny
Phototaxis
*Chlorophyta
Biological Evolution
*Volvox

@article {pmid36789784,
year = {2023},
author = {Rusin, LY},
title = {Evolution of homology: From archetype towards a holistic concept of cell type.},
journal = {Journal of morphology},
volume = {284},
number = {4},
pages = {e21569},
doi = {10.1002/jmor.21569},
pmid = {36789784},
issn = {1097-4687},
mesh = {Animals ; *Biological Evolution ; Phylogeny ; *Growth and Development ; Cell Lineage ; Phenotype ; },
abstract = {The concept of homology lies in the heart of comparative biological science. The distinction between homology as structure and analogy as function has shaped the evolutionary paradigm for a century and formed the axis of comparative anatomy and embryology, which accept the identity of structure as a ground measure of relatedness. The advent of single-cell genomics overturned the classical view of cell homology by establishing a backbone regulatory identity of cell types, the basic biological units bridging the molecular and phenotypic dimensions, to reveal that the cell is the most flexible unit of living matter and that many approaches of classical biology need to be revised to understand evolution and diversity at the cellular level. The emerging theory of cell types explicitly decouples cell identity from phenotype, essentially allowing for the divergence of evolutionarily related morphotypes beyond recognition, as well as it decouples ontogenetic cell lineage from cell-type phylogeny, whereby explicating that cell types can share common descent regardless of their structure, function or developmental origin. The article succinctly summarizes current progress and opinion in this field and formulates a more generalistic view of biological cell types as avatars, transient or terminal cell states deployed in a continuum of states by the developmental programme of one and the same omnipotent cell, capable of changing or combining identities with distinct evolutionary histories or inventing ad hoc identities that never existed in evolution or development. It highlights how the new logic grounded in the regulatory nature of cell identity transforms the concepts of cell homology and phenotypic stability, suggesting that cellular evolution is inherently and massively network-like, with one-to-one homologies being rather uncommon and restricted to shallower levels of the animal tree of life.},
}

Animals
*Biological Evolution
Phylogeny
*Growth and Development
Cell Lineage
Phenotype

@article {pmid36786569,
year = {2023},
author = {Cont, A and Vermeil, J and Persat, A},
title = {Material Substrate Physical Properties Control Pseudomonas aeruginosa Biofilm Architecture.},
journal = {mBio},
volume = {14},
number = {2},
pages = {e0351822},
pmid = {36786569},
issn = {2150-7511},
mesh = {Humans ; *Pseudomonas aeruginosa/genetics ; Biofilms ; Anti-Bacterial Agents/pharmacology ; *Pseudomonas Infections/microbiology ; },
abstract = {In the wild, bacteria are most frequently found in the form of multicellular structures called biofilms. Biofilms grow at the surface of abiotic and living materials with wide-ranging mechanical properties. The opportunistic pathogen Pseudomonas aeruginosa forms biofilms on indwelling medical devices and on soft tissues, including burn wounds and the airway mucosa. Despite the critical role of substrates in the foundation of biofilms, we still lack a clear understanding of how material mechanics regulate their architecture and the physiology of resident bacteria. Here, we demonstrate that physical properties of hydrogel material substrates define P. aeruginosa biofilm architecture. We show that hydrogel mesh size regulates twitching motility, a surface exploration mechanism priming biofilms, ultimately controlling the organization of single cells in the multicellular community. The resulting architectural transitions increase P. aeruginosa's tolerance to colistin, a last-resort antibiotic. In addition, mechanical regulation of twitching motility affects P. aeruginosa clonal lineages, so that biofilms are more mixed on relatively denser materials. Our results thereby establish material properties as a factor that dramatically affects biofilm architecture, antibiotic efficacy, and evolution of the resident population. IMPORTANCE The biofilm lifestyle is the most widespread survival strategy in the bacterial world. Pseudomonas aeruginosa biofilms cause chronic infections and are highly recalcitrant to antimicrobials. The genetic requirements allowing P. aeruginosa to grow into biofilms are known, but not the physical stimuli that regulate their formation. Despite colonizing biological tissues, investigations of biofilms on soft materials are limited. In this work, we show that biofilms take unexpected forms when growing on soft substrates. The physical properties of the material shape P. aeruginosa biofilms by regulating surface-specific twitching motility. Physical control of biofilm morphogenesis ultimately influences the resilience of biofilms to antimicrobials, linking physical environment with tolerance to treatment. Altogether, our work established that the physical properties of a surface are a critical environmental regulator of biofilm biogenesis and evolution.},
}

Humans
*Pseudomonas aeruginosa/genetics
Biofilms
Anti-Bacterial Agents/pharmacology
*Pseudomonas Infections/microbiology

@article {pmid36786333,
year = {2023},
author = {Godfroy, O and Zheng, M and Yao, H and Henschen, A and Peters, AF and Scornet, D and Colin, S and Ronchi, P and Hipp, K and Nagasato, C and Motomura, T and Cock, JM and Coelho, SM},
title = {The baseless mutant links protein phosphatase 2A with basal cell identity in the brown alga Ectocarpus.},
journal = {Development (Cambridge, England)},
volume = {150},
number = {4},
pages = {},
pmid = {36786333},
issn = {1477-9129},
support = {//Centre National de la Recherche Scientifique/ ; //Sorbonne Université/ ; //Max Planck Society/ ; 864038/ERC_/European Research Council/International ; 201608310119//China Scholarship Council/ ; },
mesh = {*Protein Phosphatase 2/genetics/metabolism ; Mutation/genetics ; Gene Expression Profiling ; Protein Processing, Post-Translational ; *Phaeophyta/genetics/metabolism ; },
abstract = {The first mitotic division of the initial cell is a key event in all multicellular organisms and is associated with the establishment of major developmental axes and cell fates. The brown alga Ectocarpus has a haploid-diploid life cycle that involves the development of two multicellular generations: the sporophyte and the gametophyte. Each generation deploys a distinct developmental programme autonomously from an initial cell, the first cell division of which sets up the future body pattern. Here, we show that mutations in the BASELESS (BAS) gene result in multiple cellular defects during the first cell division and subsequent failure to produce basal structures during both generations. BAS encodes a type B″ regulatory subunit of protein phosphatase 2A (PP2A), and transcriptomic analysis identified potential effector genes that may be involved in determining basal cell fate. The bas mutant phenotype is very similar to that observed in distag (dis) mutants, which lack a functional Tubulin-binding co-factor Cd1 (TBCCd1) protein, indicating that TBCCd1 and PP2A are two essential components of the cellular machinery that regulates the first cell division and mediates basal cell fate determination.},
}

*Protein Phosphatase 2/genetics/metabolism
Mutation/genetics
Gene Expression Profiling
Protein Processing, Post-Translational
*Phaeophyta/genetics/metabolism