@article {pmid39366961,
year = {2024},
author = {Jin, M and Li, W and Ji, Z and Di, G and Yuan, M and Zhang, Y and Kang, Y and Zhao, C},
title = {Coordinated cellular behavior regulated by epinephrine neurotransmitters in the nerveless placozoa.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8626},
pmid = {39366961},
issn = {2041-1723},
support = {Nos. 32125015//National Natural Science Foundation of China (National Science Foundation of China)/ ; Nos. 31991194//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32200415//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Epinephrine/pharmacology/metabolism ; Animals ; *Placozoa/metabolism ; *Neurotransmitter Agents/metabolism ; *Receptors, G-Protein-Coupled/metabolism/genetics ; Signal Transduction/drug effects ; Cilia/metabolism/drug effects ; Calcium Signaling/drug effects ; Cell Communication/drug effects ; Humans ; },
abstract = {Understanding how cells communicated before the evolution of nervous systems in early metazoans is key to unraveling the origins of multicellular life. We focused on Trichoplax adhaerens, one of the earliest multicellular animals, to explore this question. Through screening a small compound library targeting G protein-coupled receptors (GPCRs), we found that Trichoplax exhibits distinctive rotational movements when exposed to epinephrine. Further studies suggested that, akin to those in humans, this basal organism also utilizes adrenergic signals to regulate its negative taxis behavior, with the downstream signaling pathway being more straightforward and efficient. Mechanistically, the binding of ligands activates downstream calcium signaling, subsequently modulating ciliary redox signals. This process ultimately regulates the beating direction of cilia, governing the coordinated movement of the organism. Our findings not only highlight the enduring presence of adrenergic signaling in stress responses during evolution but also underscore the importance of early metazoan expansion of GPCR families. This amplification empowers us with the ability to sense external cues and modulate cellular communication effectively.},
}

*Epinephrine/pharmacology/metabolism
Animals
*Placozoa/metabolism
*Neurotransmitter Agents/metabolism
*Receptors, G-Protein-Coupled/metabolism/genetics
Signal Transduction/drug effects
Cilia/metabolism/drug effects
Calcium Signaling/drug effects
Cell Communication/drug effects
Humans

@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 {pmid34571874,
year = {2021},
author = {Buravkova, L and Larina, I and Andreeva, E and Grigoriev, A},
title = {Microgravity Effects on the Matrisome.},
journal = {Cells},
volume = {10},
number = {9},
pages = {},
pmid = {34571874},
issn = {2073-4409},
support = {65.3//Program of Basic Research of IBMP RAS/ ; 19-29-04026//Russian Foundation for Fundamental Investigations/ ; },
mesh = {Animals ; Extracellular Matrix/*physiology ; Gravity, Altered ; Humans ; Space Flight/methods ; Weightlessness ; },
abstract = {Gravity is fundamental factor determining all processes of development and vital activity on Earth. During evolution, a complex mechanism of response to gravity alterations was formed in multicellular organisms. It includes the "gravisensors" in extracellular and intracellular spaces. Inside the cells, the cytoskeleton molecules are the principal gravity-sensitive structures, and outside the cells these are extracellular matrix (ECM) components. The cooperation between the intracellular and extracellular compartments is implemented through specialized protein structures, integrins. The gravity-sensitive complex is a kind of molecular hub that coordinates the functions of various tissues and organs in the gravitational environment. The functioning of this system is of particular importance under extremal conditions, such as spaceflight microgravity. This review covers the current understanding of ECM and associated molecules as the matrisome, the features of the above components in connective tissues, and the role of the latter in the cell and tissue responses to the gravity alterations. Special attention is paid to contemporary methodological approaches to the matrisome composition analysis under real space flights and ground-based simulation of its effects on Earth.},
}

Animals
Extracellular Matrix/*physiology
Gravity, Altered
Humans
Space Flight/methods
Weightlessness

@article {pmid39366767,
year = {2024},
author = {Mazur-Marzec, H and Andersson, AF and Błaszczyk, A and Dąbek, P and Górecka, E and Grabski, M and Jankowska, K and Jurczak-Kurek, A and Kaczorowska, AK and Kaczorowski, T and Karlson, B and Kataržytė, M and Kobos, J and Kotlarska, E and Krawczyk, B and Łuczkiewicz, A and Piwosz, K and Rybak, B and Rychert, K and Sjöqvist, C and Surosz, W and Szymczycha, B and Toruńska-Sitarz, A and Węgrzyn, G and Witkowski, A and Węgrzyn, A},
title = {Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuae024},
pmid = {39366767},
issn = {1574-6976},
abstract = {Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North-East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments.},
}

@article {pmid39345370,
year = {2024},
author = {Leon, F and Espinoza-Esparza, JM and Deng, V and Coyle, MC and Espinoza, S and Booth, DS},
title = {Cell differentiation controls iron assimilation in a choanoflagellate.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.25.595918},
pmid = {39345370},
issn = {2692-8205},
abstract = {Marine microeukaryotes have evolved diverse cellular features that link their life histories to surrounding environments. How those dynamic life histories intersect with the ecological functions of microeukaryotes remains a frontier to understand their roles in essential biogeochemical cycles [1,2] . Choanoflagellates, phagotrophs that cycle nutrients through filter feeding, provide models to explore this intersection, for many choanoflagellate species transition between life history stages by differentiating into distinct cell types [3-6] . Here we report that cell differentiation in the marine choanoflagellate Salpingoeca rosetta endows one of its cell types with the ability to utilize insoluble ferric colloids for improved growth through the expression of a cytochrome b561 iron reductase (cytb561a). This gene is an ortholog of the mammalian duodenal cytochrome b561 (DCYTB) that reduces ferric cations prior to their uptake in gut epithelia [7] and is part of an iron utilization toolkit that choanoflagellates and their closest living relatives, the animals, inherited from a last common eukaryotic ancestor. In a database of oceanic metagenomes [8,9] , the abundance of cytb561a transcripts from choanoflagellates positively correlates with upwellings, which are a major source of ferric colloids in marine environments [10] . As this predominant form of iron [11,12] is largely inaccessible to cell-walled microbes [13,14] , choanoflagellates and other phagotrophic eukaryotes may serve critical ecological roles by first acquiring ferric colloids through phagocytosis and then cycling this essential nutrient through iron utilization pathways [13-15] . These findings provide insight into the ecological roles choanoflagellates perform and inform reconstructions of early animal evolution where functionally distinct cell types became an integrated whole at the origin of animal multicellularity [16-22] .},
}

@article {pmid39343888,
year = {2024},
author = {Ahmad, F and Abdullah, M and Khan, Z and Stępień, P and Rehman, SU and Akram, U and Rahman, MHU and Ali, Z and Ahmad, D and Gulzar, RMA and Ali, MA and Salama, EAA},
title = {Genome-wide analysis and prediction of chloroplast and mitochondrial RNA editing sites of AGC gene family in cotton (Gossypium hirsutum L.) for abiotic stress tolerance.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {888},
pmid = {39343888},
issn = {1471-2229},
support = {32130075//National Natural Science Foundation of China/ ; 32130075//National Natural Science Foundation of China/ ; 32130075//National Natural Science Foundation of China/ ; 2021AB008, 2020CB003//Science Technology and Achievement Transformation Project of the Xinjiang Production and Construction Corps/ ; 2021AB008, 2020CB003//Science Technology and Achievement Transformation Project of the Xinjiang Production and Construction Corps/ ; 2021AB008, 2020CB003//Science Technology and Achievement Transformation Project of the Xinjiang Production and Construction Corps/ ; ADP-LO21002838 Punjab, Pak//ADP Funded Project entitled National Crop Genomics and Speed Breeding Center for Agri-cultural Sustainability/ ; ADP-LO21002838 Punjab, Pak//ADP Funded Project entitled National Crop Genomics and Speed Breeding Center for Agri-cultural Sustainability/ ; ADP-LO21002838 Punjab, Pak//ADP Funded Project entitled National Crop Genomics and Speed Breeding Center for Agri-cultural Sustainability/ ; ADP-LO21002838 Punjab, Pak//ADP Funded Project entitled National Crop Genomics and Speed Breeding Center for Agri-cultural Sustainability/ ; ADP-LO21002838 Punjab, Pak//ADP Funded Project entitled National Crop Genomics and Speed Breeding Center for Agri-cultural Sustainability/ ; RSP2024R306//King Saud University, Riyadh, Saudi Arabia/ ; },
mesh = {*Gossypium/genetics/physiology ; *RNA Editing/genetics ; *Stress, Physiological/genetics ; *Phylogeny ; *Chloroplasts/genetics ; Genome, Plant ; Mitochondria/genetics ; Plant Proteins/genetics/metabolism ; Multigene Family ; Genome-Wide Association Study ; Gene Expression Regulation, Plant ; RNA, Mitochondrial/genetics ; Genes, Plant ; },
abstract = {BACKGROUND: Cotton is one of the topmost fiber crops throughout the globe. During the last decade, abrupt changes in the climate resulted in drought, heat, and salinity. These stresses have seriously affected cotton production and significant losses all over the textile industry. The GhAGC kinase, a subfamily of AGC group and member of serine/threonine (Ser/Thr) protein kinases group and is highly conserved among eukaryotic organisms. The AGC kinases are compulsory elements of cell development, metabolic processes, and cell death in mammalian systems. The investigation of RNA editing sites within the organelle genomes of multicellular vascular plants, such as Gossypium hirsutum holds significant importance in understanding the regulation of gene expression at the post-transcriptional level.

METHODS: In present work, we characterized twenty-eight GhAGC genes in cotton and constructed phylogenetic tree using nine different species from the most primitive to the most recent.

RESULTS: In sequence logos analyses, highly conserved amino acid residues were found in G. hirsutum, G. arboretum, G. raimondii and A. thaliana. The occurrence of cis-acting growth and stress-related elements in the promoter regions of GhAGCs highlight the significance of these factors in plant development and abiotic stress tolerance. Ka/Ks levels demonstrated that purifying selection pressure resulting from segmental events was applied to GhAGC with little functional divergence. We focused on identifying RNA editing sites in G. hirsutum organelles, specifically in the chloroplast and mitochondria, across all 28 AGC genes.

CONCLUSION: The positive role of GhAGCs was explored by quantifying the expression in the plant tissues under abiotic stress. These findings help in understanding the role of GhAGC genes under abiotic stresses which may further be used in cotton breeding for the development of climate smart varieties in abruptly changing climate.},
}

*Gossypium/genetics/physiology
*RNA Editing/genetics
*Stress, Physiological/genetics
*Phylogeny
*Chloroplasts/genetics
Genome, Plant
Mitochondria/genetics
Plant Proteins/genetics/metabolism
Multigene Family
Genome-Wide Association Study
Gene Expression Regulation, Plant
RNA, Mitochondrial/genetics
Genes, Plant

@article {pmid39341686,
year = {2024},
author = {Kalita, AI and Keller Valsecchi, CI},
title = {Dosage compensation in non-model insects - progress and perspectives.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2024.08.010},
pmid = {39341686},
issn = {0168-9525},
abstract = {In many multicellular eukaryotes, heteromorphic sex chromosomes are responsible for determining the sexual characteristics and reproductive functions of individuals. Sex chromosomes can cause a dosage imbalance between sexes, which in some species is re-equilibrated by dosage compensation (DC). Recent genomic advances have extended our understanding of DC mechanisms in insects beyond model organisms such as Drosophila melanogaster. We review current knowledge of insect DC, focusing on its conservation and divergence across orders, the evolutionary dynamics of neo-sex chromosomes, and the diversity of molecular mechanisms. We propose a framework to uncover DC regulators in non-model insects that relies on integrating evolutionary, genomic, and functional approaches. This comprehensive approach will facilitate a deeper understanding of the evolution and essentiality of gene regulatory mechanisms.},
}

@article {pmid39302848,
year = {2024},
author = {Batista, RA and Wang, L and Bogaert, KA and Coelho, SM},
title = {Insights into the molecular bases of multicellular development from brown algae.},
journal = {Development (Cambridge, England)},
volume = {151},
number = {20},
pages = {},
doi = {10.1242/dev.203004},
pmid = {39302848},
issn = {1477-9129},
support = {//Max-Planck-Institut für Bildungsforschung/ ; 864038/ERC_/European Research Council/International ; //Gordon and Betty Moore Foundation/ ; //Fondation Bettencourt Schueller/ ; },
mesh = {*Phaeophyceae/genetics ; Biological Evolution ; },
abstract = {The transition from simple to complex multicellularity represents a major evolutionary step that occurred in only a few eukaryotic lineages. Comparative analyses of these lineages provide insights into the molecular and cellular mechanisms driving this transition, but limited understanding of the biology of some complex multicellular lineages, such as brown algae, has hampered progress. This Review explores how recent advances in genetic and genomic technologies now allow detailed investigations into the molecular bases of brown algae development. We highlight how forward genetic techniques have identified mutants that enhance our understanding of pattern formation and sexual differentiation in these organisms. Additionally, the existence and nature of morphogens in brown algae and the potential influence of the microbiome in key developmental processes are examined. Outstanding questions, such as the identity of master regulators, the definition and characterization of cell types, and the molecular bases of developmental plasticity are discussed, with insights into how recent technical advances could provide answers. Overall, this Review highlights how brown algae are emerging as alternative model organisms, contributing to our understanding of the evolution of multicellular life and the diversity of body plans.},
}

*Phaeophyceae/genetics
Biological Evolution

@article {pmid39288812,
year = {2024},
author = {Castelli, M and Nardi, T and Giovannini, M and Sassera, D},
title = {Addictive manipulation: a perspective on the role of reproductive parasitism in the evolution of bacteria-eukaryote symbioses.},
journal = {Biology letters},
volume = {20},
number = {9},
pages = {20240310},
doi = {10.1098/rsbl.2024.0310},
pmid = {39288812},
issn = {1744-957X},
mesh = {*Symbiosis ; Animals ; *Biological Evolution ; *Reproduction ; Eukaryota/physiology ; Arthropods/microbiology/physiology ; Wolbachia/physiology/genetics ; Toxin-Antitoxin Systems/genetics ; Bacteria/genetics ; },
abstract = {Wolbachia bacteria encompass noteworthy reproductive manipulators of their arthropod hosts. which influence host reproduction to favour their own transmission, also exploiting toxin-antitoxin systems. Recently, multiple other bacterial symbionts of arthropods have been shown to display comparable manipulative capabilities. Here, we wonder whether such phenomena are truly restricted to arthropod hosts. We focused on protists, primary models for evolutionary investigations on eukaryotes due to their diversity and antiquity, but still overall under-investigated. After a thorough re-examination of the literature on bacterial-protist interactions with this question in mind, we conclude that such bacterial 'addictive manipulators' of protists do exist, are probably widespread, and have been overlooked until now as a consequence of the fact that investigations are commonly host-centred, thus ineffective to detect such behaviour. Additionally, we posit that toxin-antitoxin systems are crucial in these phenomena of addictive manipulation of protists, as a result of recurrent evolutionary repurposing. This indicates intriguing functional analogy and molecular homology with plasmid-bacterial interplays. Finally, we remark that multiple addictive manipulators are affiliated with specific bacterial lineages with ancient associations with diverse eukaryotes. This suggests a possible role of addictive manipulation of protists in paving the way to the evolution of bacteria associated with multicellular organisms.},
}

*Symbiosis
Animals
*Biological Evolution
*Reproduction
Eukaryota/physiology
Arthropods/microbiology/physiology
Wolbachia/physiology/genetics
Toxin-Antitoxin Systems/genetics
Bacteria/genetics

@article {pmid39288797,
year = {2024},
author = {Ågren, JA and Arnqvist, G and Rowe, L},
title = {The resolution of evolutionary conflicts within species.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2031},
pages = {20241594},
pmid = {39288797},
issn = {1471-2954},
mesh = {*Biological Evolution ; Animals ; Population Dynamics ; Humans ; },
abstract = {Evolutionary conflicts of interest occur at all levels, scales and forms of biological organization. They are a fundamental component of the living world and range from conflicts between genetic elements and cells, to conflicts between the sexes and between competing individuals. Yet, the existence of admirably well functioning genomes, bodies, mating pairs and societies suggests that processes must exist to resolve or mitigate such conflicts. We organized this special feature 'The resolution of evolutionary conflicts within species' to encourage the flow of knowledge between fields that traditionally have often taken different approaches to study evolutionary conflicts. Contributed papers discuss data from bacteria, plants and animals (including humans) and present theory, molecular mechanisms and population dynamics of how conflicts are resolved in nature. Together, they contribute to a synthetic theory of conflict resolution.},
}

*Biological Evolution
Animals
Population Dynamics
Humans

@article {pmid39262521,
year = {2024},
author = {Mary Martin, T and K, MS},
title = {Seaweeds and Their Secondary Metabolites: A Promising Drug Candidate With Novel Mechanisms Against Cancers and Tumor Angiogenesis.},
journal = {Cureus},
volume = {16},
number = {8},
pages = {e66662},
pmid = {39262521},
issn = {2168-8184},
abstract = {Cancer continually remains a severe threat to public health and requires constant demand for novel therapeutic drug candidates. Due to their multi-target orientation, lesser toxicity, and easy availability, natural compounds attract more attention from current scientific research interest than synthetic drug molecules. The plants and microorganisms produce a huge variety of secondary metabolites because of their physiological diversification, and the seaweeds occupy a prominent position as effective drug resources. Seaweeds comprise microscopic or macroscopic photosynthetic, multicellular, eukaryotic marine algae that commonly inhabit the coastal regions. Several molecules (such as polysaccharides, lipids, proteinaceous fractions, phenolic compounds, and alkaloids) are derived from seaweeds, and those small molecules are well attractive and more effective in cancer research programs. Their structural variation, derivative diversity, and quantity vary with seaweed species and geographical origin. Their smaller molecular weight, unique derivatives, hydrophobicity, and degree of sulfation are reported to be causes of their crucial role against different cancer cells in vitro. Several reports showed that those compounds selectively discriminate between normal and cancer cells based on receptor variations, enzyme deficiency, and structural properties. The present review aimed to give a concise explanation regarding their structural diversity, extractability, and mechanism of action related to their anti-cancer activities based on recently published data.},
}

@article {pmid39236709,
year = {2024},
author = {Gallo, E and De Renzis, S and Sharpe, J and Mayor, R and Hartmann, J},
title = {Versatile system cores as a conceptual basis for generality in cell and developmental biology.},
journal = {Cell systems},
volume = {15},
number = {9},
pages = {790-807},
doi = {10.1016/j.cels.2024.08.001},
pmid = {39236709},
issn = {2405-4720},
mesh = {*Developmental Biology/methods ; Animals ; Humans ; Morphogenesis ; Cell Biology ; Gastrulation/physiology ; Models, Biological ; Biological Evolution ; },
abstract = {The discovery of general principles underlying the complexity and diversity of cellular and developmental systems is a central and long-standing aim of biology. While new technologies collect data at an ever-accelerating rate, there is growing concern that conceptual progress is not keeping pace. We contend that this is due to a paucity of conceptual frameworks that support meaningful generalizations. This led us to develop the core and periphery (C&P) hypothesis, which posits that many biological systems can be decomposed into a highly versatile core with a large behavioral repertoire and a specific periphery that configures said core to perform one particular function. Versatile cores tend to be widely reused across biology, which confers generality to theories describing them. Here, we introduce this concept and describe examples at multiple scales, including Turing patterning, actomyosin dynamics, multi-cellular morphogenesis, and vertebrate gastrulation. We also sketch its evolutionary basis and discuss key implications and open questions. We propose that the C&P hypothesis could unlock new avenues of conceptual progress in mesoscale biology.},
}

*Developmental Biology/methods
Animals
Humans
Morphogenesis
Cell Biology
Gastrulation/physiology
Models, Biological
Biological Evolution

@article {pmid39201358,
year = {2024},
author = {Kaminskaya, AN and Evpak, AS and Belogurov, AA and Kudriaeva, AA},
title = {Tracking of Ubiquitin Signaling through 3.5 Billion Years of Combinatorial Conjugation.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
pmid = {39201358},
issn = {1422-0067},
mesh = {Humans ; *Ubiquitin/metabolism ; *Ubiquitination ; *Evolution, Molecular ; Animals ; *Signal Transduction ; *Ubiquitin-Conjugating Enzymes/metabolism/genetics/chemistry ; Ubiquitin-Protein Ligases/metabolism/genetics/chemistry ; Protein Processing, Post-Translational ; Phylogeny ; },
abstract = {Ubiquitination is an evolutionary, ancient system of post-translational modification of proteins that occurs through a cascade involving ubiquitin activation, transfer, and conjugation. The maturation of this system has followed two main pathways. The first is the conservation of a universal structural fold of ubiquitin and ubiquitin-like proteins, which are present in both Archaea and Bacteria, as well as in multicellular Eukaryotes. The second is the rise of the complexity of the superfamily of ligases, which conjugate ubiquitin-like proteins to substrates, in terms of an increase in the number of enzyme variants, greater variation in structural organization, and the diversification of their catalytic domains. Here, we examine the diversity of the ubiquitination system among different organisms, assessing the variety and conservation of the key domains of the ubiquitination enzymes and ubiquitin itself. Our data show that E2 ubiquitin-conjugating enzymes of metazoan phyla are highly conservative, whereas the homology of E3 ubiquitin ligases with human orthologues gradually decreases depending on "molecular clock" timing and evolutionary distance. Surprisingly, Chordata and Echinodermata, which diverged over 0.5 billion years ago during the Cambrian explosion, share almost the same homology with humans in the amino acid sequences of E3 ligases but not in their adaptor proteins. These observations may suggest that, firstly, the E2 superfamily already existed in its current form in the last common metazoan ancestor and was generally not affected by purifying selection in metazoans. Secondly, it may indicate convergent evolution of the ubiquitination system and highlight E3 adaptor proteins as the "upper deck" of the ubiquitination system, which plays a crucial role in chordate evolution.},
}

Humans
*Ubiquitin/metabolism
*Ubiquitination
*Evolution, Molecular
Animals
*Signal Transduction
*Ubiquitin-Conjugating Enzymes/metabolism/genetics/chemistry
Ubiquitin-Protein Ligases/metabolism/genetics/chemistry
Protein Processing, Post-Translational
Phylogeny

@article {pmid39198502,
year = {2024},
author = {Takeuchi, Y and Hata, H and Sasaki, M and Mvula, A and Mizuhara, S and Rusuwa, B and Maruyama, A},
title = {Preying on cyprinid snout warts (pearl organs) as a novel and peculiar habit in the Lake Malawi cichlid Docimodus evelynae.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19300},
pmid = {39198502},
issn = {2045-2322},
support = {202210033//Mitsubishi Foundation/ ; 20K06851//Japan Society for the Promotion of Science/ ; 23KK0131//Japan Society for the Promotion of Science/ ; 18KK0208//Japan Society for the Promotion of Science/ ; 23-6406//Toray Science Foundation/ ; },
mesh = {Animals ; *Cichlids ; *Lakes ; Malawi ; Predatory Behavior ; Phylogeny ; Feeding Behavior ; Gastrointestinal Contents ; },
abstract = {Cichlid fishes in the African Great Lakes have undergone explosive speciation, acquiring markedly varying ecologies and diets. There are multiple lineages of scale-eating cichlids, and their natural history and evolutionary ecology is only partially understood. We examined the feeding habit of Docimodus evelynae, a known scale eater, in Lake Malawi. The stomach contents of young individuals mainly consisted of unknown 1 mm hard, white warts (> 30%). To clarify the origin of these warts, we conducted an X-ray fluorometer analysis, and found they were rich in sulphur but low in silicon and calcium, suggesting they were epidermal tissues. Histological and morphological analyses revealed they were multicellular and cup-shaped. These characteristics matched only those of the pearl organs of the coexisting cyprinid Labeo cylindricus. DNA was extracted from the warts found in the stomach of five D. evelynae individuals, followed by PCR using primers targeting the partial COI gene of L. cylindricus. The resulting sequences exhibited 98% similarity to those of L. cylindricus. Pearl organs, never reported as a primary food for fish, could offer a substantial nutritional source based on calorific calculations. Understanding how this peculiar diet is foraged is essential for full comprehension of the food-web structure in this lake.},
}

Animals
*Cichlids
*Lakes
Malawi
Predatory Behavior
Phylogeny
Feeding Behavior
Gastrointestinal Contents

@article {pmid39187082,
year = {2024},
author = {Dujon, AM and Boutry, J and Tissot, S and Meliani, J and Miltiadous, A and Tokolyi, J and Ujvari, B and Thomas, F},
title = {The widespread vulnerability of Hydra oligactis to tumourigenesis confirms its value as a model for studying the effects of tumoural processes on the ecology and evolution of species.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175785},
doi = {10.1016/j.scitotenv.2024.175785},
pmid = {39187082},
issn = {1879-1026},
mesh = {*Hydra ; Animals ; *Carcinogenesis ; *Biological Evolution ; Neoplasms ; Australia ; Ecology ; Ecosystem ; },
abstract = {Tumoural processes, ubiquitous phenomena in multicellular organisms, influence evolutionary trajectories of all species. To gain a holistic understanding of their impact on species' biology, suitable laboratory models are required. Such models are characterised by a widespread availability, ease of cultivation, and reproducible tumour induction. It is especially important to explore, through experimental approaches, how tumoural processes alter ecosystem functioning. The cnidarian Hydra oligactis is currently emerging as a promising model due to its development of both transmissible and non-transmissible tumours and the wide breadth of experiments that can be conducted with this species (at the individual, population, mechanistic, and evolutionary levels). However, tumoural hydras are, so far, only documented in Europe, and it is not clear if the phenomenon is local or widespread. In this study we demonstrate that Australian hydras from two independent river networks develop tumours in the laboratory consisting of interstitial stem cells and display phenotypic alterations (supernumerary tentacles) akin to European counterparts. This finding confirms the value of this model for ecological and evolutionary research on host-tumour interactions.},
}

*Hydra
Animals
*Carcinogenesis
*Biological Evolution
Neoplasms
Australia
Ecology
Ecosystem

@article {pmid39151881,
year = {2024},
author = {Shirokawa, Y},
title = {Evolutionary stability of developmental commitment.},
journal = {Bio Systems},
volume = {244},
number = {},
pages = {105309},
doi = {10.1016/j.biosystems.2024.105309},
pmid = {39151881},
issn = {1872-8324},
mesh = {*Dictyostelium/physiology/growth & development ; *Biological Evolution ; Models, Biological ; Mutation ; },
abstract = {Evolution of unicellular to multicellular organisms must resolve conflicts in reproductive interests between individual cells and the group. The social amoeba Dictyostelium discoideum is a soil-living eukaryote with facultative sociality. While cells grow in the presence of nutrients, cells aggregate under starvation to form fruiting bodies containing spores and altruistic stalk cells. Once cells socially committed, they complete formation of fruiting bodies, even if a new source of nutrients becomes available. The persistence of this social commitment raises questions as it inhibits individual cells from swiftly returning to solitary growth. I hypothesize that traits enabling premature de-commitment are hindered from being selected. Recent work has revealed outcomes of the premature de-commitment through forced refeeding; The de-committed cells take an altruistic prestalk-like position due to their reduced cohesiveness through interactions with socially committed cells. I constructed an evolutionary model assuming their division of labor. The results revealed a valley in the fitness landscape that prevented invasion of de-committing mutants, indicating evolutionary stability of the social commitment. The findings provide a general scheme that maintains multicellularity by evolving a specific division of labor, in which less cohesive individuals become altruists.},
}

*Dictyostelium/physiology/growth & development
*Biological Evolution
Models, Biological
Mutation

@article {pmid39140743,
year = {2024},
author = {Hake, KH and West, PT and McDonald, K and Laundon, D and Reyes-Rivera, J and Garcia De Las Bayonas, A and Feng, C and Burkhardt, P and Richter, DJ and Banfield, JF and King, N},
title = {A large colonial choanoflagellate from Mono Lake harbors live bacteria.},
journal = {mBio},
volume = {15},
number = {9},
pages = {e0162324},
pmid = {39140743},
issn = {2150-7511},
support = {n/a//Howard Hughes Medical Institute (HHMI)/ ; DGE 1106400//National Science Foundation (NSF)/ ; DGE 1752814//National Science Foundation (NSF)/ ; 100010434//'la Caixa' Foundation ('la Caixa')/ ; },
mesh = {*Choanoflagellata/classification/physiology ; *Lakes/microbiology ; California ; *Phylogeny ; Gammaproteobacteria/isolation & purification/classification/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/isolation & purification/genetics ; Alphaproteobacteria/classification/isolation & purification/genetics ; Sequence Analysis, DNA ; },
abstract = {UNLABELLED: As the closest living relatives of animals, choanoflagellates offer insights into the ancestry of animal cell physiology. Here, we report the isolation and characterization of a colonial choanoflagellate from Mono Lake, California. The choanoflagellate forms large spherical colonies that are an order of magnitude larger than those formed by the closely related choanoflagellate Salpingoeca rosetta. In cultures maintained in the laboratory, the lumen of the spherical colony is filled with a branched network of extracellular matrix and colonized by bacteria, including diverse Gammaproteobacteria and Alphaproteobacteria. We propose to erect Barroeca monosierra gen. nov., sp. nov. Hake, Burkhardt, Richter, and King to accommodate this extremophile choanoflagellate. The physical association between bacteria and B. monosierra in culture presents a new experimental model for investigating interactions among bacteria and eukaryotes. Future work will investigate the nature of these interactions in wild populations and the mechanisms underpinning the colonization of B. monosierra spheres by bacteria.

IMPORTANCE: The diversity of organisms that live in the extreme environment of Mono Lake (California, USA) is limited. We sought to investigate whether the closest living relatives of animals, the choanoflagellates, exist in Mono Lake, a hypersaline, alkaline, arsenic-rich environment. We repeatedly isolated members of a new species of choanoflagellate, which we have named Barroeca monosierra. Characterization of B. monosierra revealed that it forms large spherical colonies containing diverse co-isolated bacteria, providing an opportunity to investigate mechanisms underlying physical associations between eukaryotes and bacteria.},
}

*Choanoflagellata/classification/physiology
*Lakes/microbiology
California
*Phylogeny
Gammaproteobacteria/isolation & purification/classification/genetics/physiology
RNA, Ribosomal, 16S/genetics
Bacteria/classification/isolation & purification/genetics
Alphaproteobacteria/classification/isolation & purification/genetics
Sequence Analysis, DNA

@article {pmid39127170,
year = {2024},
author = {Cravero, BH and Prez, G and Lombardo, VA and Guastaferri, FV and Delprato, CB and Altabe, S and de Mendoza, D and Binolfi, A},
title = {A high-resolution [13]C NMR approach for profiling fatty acid unsaturation in lipid extracts and in live Caenorhabditiselegans.},
journal = {Journal of lipid research},
volume = {65},
number = {9},
pages = {100618},
pmid = {39127170},
issn = {1539-7262},
mesh = {Animals ; *Caenorhabditis elegans/metabolism ; *Fatty Acids, Unsaturated/metabolism/analysis ; Carbon-13 Magnetic Resonance Spectroscopy ; Fatty Acids/metabolism/analysis ; Lipids/analysis/chemistry ; },
abstract = {Unsaturated fatty acids (UFA) play a crucial role in central cellular processes in animals, including membrane function, development, and disease. Disruptions in UFA homeostasis can contribute to the onset of metabolic, cardiovascular, and neurodegenerative disorders. Consequently, there is a high demand for analytical techniques to study lipid compositions in live cells and multicellular organisms. Conventional analysis of UFA compositions in cells, tissues, and organisms involves solvent extraction procedures coupled with analytical techniques such as gas chromatography, MS and/or NMR spectroscopy. As a nondestructive and nontargeted technique, NMR spectroscopy is uniquely capable of characterizing the chemical profiling of living cells and multicellular organisms. Here, we use NMR spectroscopy to analyze Caenorhabditis elegans, enabling the determination of their lipid compositions and fatty acid unsaturation levels both in cell-free lipid extracts and in vivo. The NMR spectra of lipid extracts from WT and fat-3 mutant C. elegans strains revealed notable differences due to the absence of Δ-6 fatty acid desaturase activity, including the lack of arachidonic and eicosapentaenoic acyl chains. Uniform [13]C-isotope labeling and high-resolution 2D solution-state NMR of live worms confirmed these findings, indicating that the signals originated from fast-tumbling lipid molecules within lipid droplets. Overall, this strategy permits the analysis of lipid storage in intact worms and has enough resolution and sensitivity to identify differences between WT and mutant animals with impaired fatty acid desaturation. Our results establish methodological benchmarks for future investigations of fatty acid regulation in live C. elegans using NMR.},
}

Animals
*Caenorhabditis elegans/metabolism
*Fatty Acids, Unsaturated/metabolism/analysis
Carbon-13 Magnetic Resonance Spectroscopy
Fatty Acids/metabolism/analysis
Lipids/analysis/chemistry

@article {pmid39098975,
year = {2024},
author = {Oishi, R and Takeda, I and Ode, Y and Okada, Y and Kato, D and Nakashima, H and Imagama, S and Wake, H},
title = {Neuromodulation with transcranial direct current stimulation contributes to motor function recovery via microglia in spinal cord injury.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18031},
pmid = {39098975},
issn = {2045-2322},
support = {20H05899//Japan Society for the Promotion of Science/ ; PMJCR22P6//Japan Science and Technology Agency/ ; 19H04753, 19H05219, and 25110732//Grants-in-Aid for Scientific Research on Innovative Areas/ ; JPMJCR1755, JPMJCR22P6//JST CREST/ ; },
mesh = {*Spinal Cord Injuries/therapy/physiopathology ; Animals ; *Microglia/metabolism ; *Transcranial Direct Current Stimulation/methods ; Mice ; *Motor Cortex/physiopathology ; *Recovery of Function ; *Mice, Inbred C57BL ; Disease Models, Animal ; Male ; Spinal Cord/physiopathology/pathology ; Female ; },
abstract = {Spinal cord injury (SCI) is damage or trauma to the spinal cord, which often results in loss of function, sensation, or mobility below the injury site. Transcranial direct current stimulation (tDCS) is a non-invasive and affordable brain stimulation technique used to modulate neuronal circuits, which changes the morphology and activity of microglia in the cerebral cortex. However, whether similar morphological changes can be observed in the spinal cord remains unclear. Therefore, we evaluated neuronal population activity in layer 5 (L5) of M1 following SCI and investigated whether changes in the activities of L5 neurons affect microglia-axon interactions using C57BL/6J mice. We discovered that L5 of the primary motor cortex (corticospinal neurons) exhibited reduced synchronized activity after SCI that correlates with microglial morphology, which was recovered using tDCS. This indicates that tDCS promotes changes in the morphological properties and recovery of microglia after SCI. Combining immunotherapy with tDCS may be effective in treating SCI.},
}

*Spinal Cord Injuries/therapy/physiopathology
Animals
*Microglia/metabolism
*Transcranial Direct Current Stimulation/methods
Mice
*Motor Cortex/physiopathology
*Recovery of Function
*Mice, Inbred C57BL
Disease Models, Animal
Male
Spinal Cord/physiopathology/pathology
Female

@article {pmid39067992,
year = {2024},
author = {Hariom, SK and Nelson, EJR},
title = {Cardiovascular adaptations in microgravity conditions.},
journal = {Life sciences in space research},
volume = {42},
number = {},
pages = {64-71},
doi = {10.1016/j.lssr.2024.05.001},
pmid = {39067992},
issn = {2214-5532},
mesh = {Humans ; *Weightlessness ; *Adaptation, Physiological ; Animals ; Cardiovascular System/physiopathology ; Weightlessness Simulation ; Cardiovascular Deconditioning/physiology ; Orthostatic Intolerance/physiopathology ; Space Flight ; },
abstract = {Gravity has had a significant impact on the evolution of life on Earth with organisms developing necessary biological adaptations over billions of years to counter this ever-existing force. There has been an exponential increase in experiments using real and simulated gravity environments in the recent years. Although an understanding followed by discovery of counter measures to negate diminished gravity in space had been the driving force of research initially, there has since been a phenomenal leap wherein a force unearthly as microgravity is beginning to show promising potential. The current review summarizes pathophysiological changes that occur in multiple aspects of the cardiovascular system when exposed to an altered gravity environment leading to cardiovascular deconditioning and orthostatic intolerance. Gravity influences not just the complex multicellular systems but even the survival of organisms at the molecular level by intervening fundamental cellular processes, directly affecting those linked to actin and microtubule organization via mechano-transduction pathways. The reach of gravity ranges from cytoskeletal rearrangement that regulates cell adhesion and migration to intracellular dynamics that dictate cell fate commitment and differentiation. An understanding that microgravity itself is not present on Earth propels the scope of simulated gravity conditions to be a unique and useful environment that could be explored for enhancing the potential of stem cells for a wide range of applications as has been highlighted here.},
}

Humans
*Weightlessness
*Adaptation, Physiological
Animals
Cardiovascular System/physiopathology
Weightlessness Simulation
Cardiovascular Deconditioning/physiology
Orthostatic Intolerance/physiopathology
Space Flight

@article {pmid39060315,
year = {2024},
author = {Jia, Z and Wang, J and Meng, X and Yang, X and Tian, Y and Wang, B and Chen, M and Yang, J and Das, D and Cao, Y},
title = {Evolution and stress response potential of the plant splicing factor U1C.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17212},
pmid = {39060315},
issn = {2045-2322},
support = {32172104//National Natural Science Foundation of China/ ; 3217150246//National Natural Science Foundation of China/ ; 32172104//National Natural Science Foundation of China/ ; 32172104//National Natural Science Foundation of China/ ; 32172104//National Natural Science Foundation of China/ ; 3217150246//National Natural Science Foundation of China/ ; 32172104//National Natural Science Foundation of China/ ; 32172104//National Natural Science Foundation of China/ ; 3217150246//National Natural Science Foundation of China/ ; KFJN2325//Large Instruments Open Foundation of Nantong University/ ; KFJN2325//Large Instruments Open Foundation of Nantong University/ ; SBK2020042924//Natural Science Foundation of Jiangsu Province/ ; SBK2020042924//Natural Science Foundation of Jiangsu Province/ ; SBK2020042924//Natural Science Foundation of Jiangsu Province/ ; },
mesh = {*Stress, Physiological/genetics ; *Gene Expression Regulation, Plant ; *Phylogeny ; *Plant Proteins/genetics/metabolism ; Evolution, Molecular ; Oryza/genetics/metabolism ; Alternative Splicing ; Droughts ; Promoter Regions, Genetic ; },
abstract = {Alternative splicing is a crucial process in multicellular eukaryote, facilitated by the assembly of spliceosomal complexes comprising numerous small ribonucleoproteins. At an early stage, U1C is thought to be required for 5' splice site recognition and base pairing. However, a systematic analysis of the U1C gene family in response to developmental cues and stress conditions has not yet been conducted in plants. This study identified 114 U1C genes in 72 plant species using basic bioinformatics analyses. Phylogenetic analysis was used to compare gene and protein structures, promoter motifs, and tissue- and stress-specific expression levels, revealing their functional commonalities or diversity in response to developmental cues, such as embryonic expression, or stress treatments, including drought and heat. Fluorescence quantitative expression analysis showed that U1C gene expression changed under salt, low temperature, drought, and Cd stress in rice seedlings. However, gene expression in shoots and roots was not consistent under different stress conditions, suggesting a complex regulatory mechanism. This research provides foundational insights into the U1C gene family's role in plant development and stress responses, highlighting potential targets for future studies.},
}

*Stress, Physiological/genetics
*Gene Expression Regulation, Plant
*Phylogeny
*Plant Proteins/genetics/metabolism
Evolution, Molecular
Oryza/genetics/metabolism
Alternative Splicing
Droughts
Promoter Regions, Genetic

@article {pmid39032813,
year = {2024},
author = {Yamauchi, A},
title = {Evolution of labor division in reproduction and multiple group tasks.},
journal = {Journal of theoretical biology},
volume = {593},
number = {},
pages = {111910},
doi = {10.1016/j.jtbi.2024.111910},
pmid = {39032813},
issn = {1095-8541},
mesh = {*Reproduction/physiology ; *Biological Evolution ; Animals ; Fertility/physiology ; Models, Biological ; },
abstract = {Labor division is a phenomenon observed across various biological contexts, including examples such as the differentiation between germ/somatic cells in multicellular organisms and the division between reproductive/worker individuals within social animal groups. In such cases, certain members contribute to tasks that enhance the viability of the entire group, even if this requires a reduction in their individual reproductive efforts. Given that group members have the potential to adopt varying contribution levels, a comprehensive analysis of the evolution becomes intricate due to the problem's high dimensionality. In this paper, I introduce a novel method for analyzing the evolution of the distribution of contribution levels to group viability, with a particular formulation centered on the success of clonal strains. The analysis demonstrates that the curvature of the fecundity function in relation to contributions to the group plays a pivotal role in determining the occurrence of labor division between reproductive and non-reproductive tasks, aligning in part with results from prior research. Furthermore, I extend this analysis to encompass contributions to multiple categories of tasks for group viability. My findings indicate that investments in non-reproductive tasks are selected based on the average contributions for each task, with individual variation playing a less significant role as long as average values remain consistent. Additionally, I explore the impact of group size and relatedness within the group on labor division. The results highlight that increases in group size and relatedness have a positive influence on the evolution of cooperation, although their effects are not directly tied to labor division itself.},
}

*Reproduction/physiology
*Biological Evolution
Animals
Fertility/physiology
Models, Biological

@article {pmid38990205,
year = {2024},
author = {Sims, NA},
title = {Osteoclast-derived coupling factors: origins and state-of-play Louis V Avioli lecture, ASBMR 2023.},
journal = {Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research},
volume = {39},
number = {10},
pages = {1377-1385},
pmid = {38990205},
issn = {1523-4681},
support = {//National Health and Medical Research Council/ ; //St. Vincent's Institute Foundation/ ; //Victorian State Government's Operational Infrastructure Support Program/ ; },
mesh = {*Osteoclasts/metabolism ; Humans ; Animals ; Bone Remodeling ; },
abstract = {Coupling, the mechanism that controls the sequence of events in bone remodeling, is a fundamental theory for understanding the way the skeleton changes throughout life. This review is an adapted version of the Louis V Avioli lecture, delivered at the Annual Scientific Meeting of the American Society of Bone and Mineral Research in 2023. It outlines the history of the coupling concept, details how coupling is thought to occur within trabecular and cortical bone, and describes its multiple contexts and the many mechanisms suggested to couple bone-forming osteoblasts to the prior action of osteoclasts on the same bone surface. These mechanisms include signals produced at each stage of the remodeling sequence (resorption, reversal, and formation), such as factors released by osteoclasts through their resorptive action and through protein synthesis, molecules deposited in the cement line during the reversal phase, and potential signals from osteocytes within the local bone environment. The review highlights two examples of coupling factors (Cardiotrophin 1 and EphrinB2:EphB4) to illustrate the limited data available, the need to integrate the many functions of these factors within the basic multicellular unit (BMU), and the multiple origins of these factors, including the other cell types present during the remodeling sequence (such as osteocytes, macrophages, endothelial cells, and T-cells).},
}

*Osteoclasts/metabolism
Humans
Animals
Bone Remodeling

@article {pmid38985841,
year = {2024},
author = {Valencia-Montoya, WA and Pierce, NE and Bellono, NW},
title = {Evolution of Sensory Receptors.},
journal = {Annual review of cell and developmental biology},
volume = {40},
number = {1},
pages = {353-379},
doi = {10.1146/annurev-cellbio-120123-112853},
pmid = {38985841},
issn = {1530-8995},
mesh = {Animals ; *Sensory Receptor Cells/metabolism ; *Biological Evolution ; Humans ; Chemoreceptor Cells/metabolism ; },
abstract = {Sensory receptors are at the interface between an organism and its environment and thus represent key sites for biological innovation. Here, we survey major sensory receptor families to uncover emerging evolutionary patterns. Receptors for touch, temperature, and light constitute part of the ancestral sensory toolkit of animals, often predating the evolution of multicellularity and the nervous system. In contrast, chemoreceptors exhibit a dynamic history of lineage-specific expansions and contractions correlated with the disparate complexity of chemical environments. A recurring theme includes independent transitions from neurotransmitter receptors to sensory receptors of diverse stimuli from the outside world. We then provide an overview of the evolutionary mechanisms underlying sensory receptor diversification and highlight examples where signatures of natural selection are used to identify novel sensory adaptations. Finally, we discuss sensory receptors as evolutionary hotspots driving reproductive isolation and speciation, thereby contributing to the stunning diversity of animals.},
}

Animals
*Sensory Receptor Cells/metabolism
*Biological Evolution
Humans
Chemoreceptor Cells/metabolism

@article {pmid38977899,
year = {2024},
author = {Kollmar, M and Welz, T and Ravi, A and Kaufmann, T and Alzahofi, N and Hatje, K and Alghamdi, A and Kim, J and Briggs, DA and Samol-Wolf, A and Pylypenko, O and Hume, AN and Burkhardt, P and Faix, J and Kerkhoff, E},
title = {Actomyosin organelle functions of SPIRE actin nucleators precede animal evolution.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {832},
pmid = {38977899},
issn = {2399-3642},
support = {KE 447/18-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FA 330/12-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KE 447/10-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KE 447/21-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KO 2251/13-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Organelles/metabolism ; *Actomyosin/metabolism ; Microfilament Proteins/metabolism/genetics ; Myosin Type V/metabolism/genetics ; Actins/metabolism ; Humans ; Choanoflagellata/metabolism ; Actin Cytoskeleton/metabolism ; Biological Evolution ; Evolution, Molecular ; Formins/metabolism ; rab GTP-Binding Proteins/metabolism ; Phylogeny ; Nuclear Proteins ; },
abstract = {An important question in cell biology is how cytoskeletal proteins evolved and drove the development of novel structures and functions. Here we address the origin of SPIRE actin nucleators. Mammalian SPIREs work with RAB GTPases, formin (FMN)-subgroup actin assembly proteins and class-5 myosin (MYO5) motors to transport organelles along actin filaments towards the cell membrane. However, the origin and extent of functional conservation of SPIRE among species is unknown. Our sequence searches show that SPIRE exist throughout holozoans (animals and their closest single-celled relatives), but not other eukaryotes. SPIRE from unicellular holozoans (choanoflagellate), interacts with RAB, FMN and MYO5 proteins, nucleates actin filaments and complements mammalian SPIRE function in organelle transport. Meanwhile SPIRE and MYO5 proteins colocalise to organelles in Salpingoeca rosetta choanoflagellates. Based on these observations we propose that SPIRE originated in unicellular ancestors of animals providing an actin-myosin driven exocytic transport mechanism that may have contributed to the evolution of complex multicellular animals.},
}

Animals
*Organelles/metabolism
*Actomyosin/metabolism
Microfilament Proteins/metabolism/genetics
Myosin Type V/metabolism/genetics
Actins/metabolism
Humans
Choanoflagellata/metabolism
Actin Cytoskeleton/metabolism
Biological Evolution
Evolution, Molecular
Formins/metabolism
rab GTP-Binding Proteins/metabolism
Phylogeny
Nuclear Proteins

@article {pmid38975338,
year = {2024},
author = {Amanya, SB and Oyewole-Said, D and Ernste, KJ and Bisht, N and Murthy, A and Vazquez-Perez, J and Konduri, V and Decker, WK},
title = {The mARS complex: a critical mediator of immune regulation and homeostasis.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1423510},
pmid = {38975338},
issn = {1664-3224},
support = {R01 AI127387/AI/NIAID NIH HHS/United States ; R01 AI153326/AI/NIAID NIH HHS/United States ; },
mesh = {*Homeostasis/immunology ; Animals ; Humans ; *Amino Acyl-tRNA Synthetases/immunology/metabolism ; Immunomodulation ; },
abstract = {Over the course of evolution, many proteins have undergone adaptive structural changes to meet the increasing homeostatic regulatory demands of multicellularity. Aminoacyl tRNA synthetases (aaRS), enzymes that catalyze the attachment of each amino acid to its cognate tRNA, are such proteins that have acquired new domains and motifs that enable non-canonical functions. Through these new domains and motifs, aaRS can assemble into large, multi-subunit complexes that enhance the efficiency of many biological functions. Moreover, because the complexity of multi-aminoacyl tRNA synthetase (mARS) complexes increases with the corresponding complexity of higher eukaryotes, a contribution to regulation of homeostatic functions in multicellular organisms is hypothesized. While mARS complexes in lower eukaryotes may enhance efficiency of aminoacylation, little evidence exists to support a similar role in chordates or other higher eukaryotes. Rather, mARS complexes are reported to regulate multiple and variegated cellular processes that include angiogenesis, apoptosis, inflammation, anaphylaxis, and metabolism. Because all such processes are critical components of immune homeostasis, it is important to understand the role of mARS complexes in immune regulation. Here we provide a conceptual analysis of the current understanding of mARS complex dynamics and emerging mARS complex roles in immune regulation, the increased understanding of which should reveal therapeutic targets in immunity and immune-mediated disease.},
}

*Homeostasis/immunology
Animals
Humans
*Amino Acyl-tRNA Synthetases/immunology/metabolism
Immunomodulation

@article {pmid38971326,
year = {2024},
author = {Prosdocimi, F and de Farias, ST},
title = {Major evolutionary transitions before cells: A journey from molecules to organisms.},
journal = {Progress in biophysics and molecular biology},
volume = {191},
number = {},
pages = {11-24},
doi = {10.1016/j.pbiomolbio.2024.07.002},
pmid = {38971326},
issn = {1873-1732},
mesh = {*Biological Evolution ; Evolution, Molecular ; },
abstract = {Basing on logical assumptions and necessary steps of complexification along biological evolution, we propose here an evolutionary path from molecules to cells presenting four ages and three major transitions. At the first age, the basic biomolecules were formed and become abundant. The first transition happened with the event of a chemical symbiosis between nucleic acids and peptides worlds, which marked the emergence of both life and the process of organic encoding. FUCA, the first living process, was composed of self-replicating RNAs linked to amino acids and capable to catalyze their binding. The second transition, from the age of FUCA to the age of progenotes, involved the duplication and recombination of proto-genomes, leading to specialization in protein production and the exploration of protein to metabolite interactions in the prebiotic soup. Enzymes and metabolic pathways were incorporated into biology from protobiotic reactions that occurred without chemical catalysts, step by step. Then, the fourth age brought origin of organisms and lineages, occurring when specific proteins capable to stackle together facilitated the formation of peptidic capsids. LUCA was constituted as a progenote capable to operate the basic metabolic functions of a cell, but still unable to interact with lipid molecules. We present evidence that the evolution of lipid interaction pathways occurred at least twice, with the development of bacterial-like and archaeal-like membranes. Also, data in literature suggest at least two paths for the emergence of DNA biosynthesis, allowing the stabilization of early life strategies in viruses, archaeas and bacterias. Two billion years later, the eukaryotes arouse, and after 1,5 billion years of evolution, they finally learn how to evolve multicellularity via tissue specialization.},
}

*Biological Evolution
Evolution, Molecular

@article {pmid38970827,
year = {2024},
author = {Ernesto Alvarez, F and Clairambault, J},
title = {Phenotype divergence and cooperation in isogenic multicellularity and in cancer.},
journal = {Mathematical medicine and biology : a journal of the IMA},
volume = {41},
number = {2},
pages = {135-155},
doi = {10.1093/imammb/dqae005},
pmid = {38970827},
issn = {1477-8602},
mesh = {*Neoplasms/pathology/physiopathology ; Humans ; *Phenotype ; Animals ; *Models, Biological ; Cell Differentiation/physiology ; Mathematical Concepts ; Cell Communication/physiology ; Biological Evolution ; },
abstract = {We discuss the mathematical modelling of two of the main mechanisms that pushed forward the emergence of multicellularity: phenotype divergence in cell differentiation and between-cell cooperation. In line with the atavistic theory of cancer, this disease being specific of multicellular animals, we set special emphasis on how both mechanisms appear to be reversed, however not totally impaired, rather hijacked, in tumour cell populations. Two settings are considered: the completely innovating, tinkering, situation of the emergence of multicellularity in the evolution of species, which we assume to be constrained by external pressure on the cell populations, and the completely planned-in the body plan-situation of the physiological construction of a developing multicellular animal from the zygote, or of bet hedging in tumours, assumed to be of clonal formation, although the body plan is largely-but not completely-lost in its constituting cells. We show how cancer impacts these two settings and we sketch mathematical models for them. We present here our contribution to the question at stake with a background from biology, from mathematics and from philosophy of science.},
}

*Neoplasms/pathology/physiopathology
Humans
*Phenotype
Animals
*Models, Biological
Cell Differentiation/physiology
Mathematical Concepts
Cell Communication/physiology
Biological Evolution

@article {pmid38960448,
year = {2024},
author = {Parker, J},
title = {Organ Evolution: Emergence of Multicellular Function.},
journal = {Annual review of cell and developmental biology},
volume = {40},
number = {1},
pages = {51-74},
doi = {10.1146/annurev-cellbio-111822-121620},
pmid = {38960448},
issn = {1530-8995},
mesh = {Animals ; *Biological Evolution ; Humans ; },
abstract = {Instances of multicellularity across the tree of life have fostered the evolution of complex organs composed of distinct cell types that cooperate, producing emergent biological functions. How organs originate is a fundamental evolutionary problem that has eluded deep mechanistic and conceptual understanding. Here I propose a cell- to organ-level transitions framework, whereby cooperative division of labor originates and becomes entrenched between cell types through a process of functional niche creation, cell-type subfunctionalization, and irreversible ratcheting of cell interdependencies. Comprehending this transition hinges on explaining how these processes unfold molecularly in evolving populations. Recent single-cell transcriptomic studies and analyses of terminal fate specification indicate that cellular functions are conferred by modular gene expression programs. These discrete components of functional variation may be deployed or combined within cells to introduce new properties into multicellular niches, or partitioned across cells to establish division of labor. Tracing gene expression program evolution at the level of single cells in populations may reveal transitions toward organ complexity.},
}

Animals
*Biological Evolution
Humans

@article {pmid38924758,
year = {2024},
author = {Crockett, WW and Shaw, JO and Simpson, C and Kempes, CP},
title = {Physical constraints during Snowball Earth drive the evolution of multicellularity.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2025},
pages = {20232767},
pmid = {38924758},
issn = {1471-2954},
mesh = {*Biological Evolution ; Ice Cover ; Eukaryota/physiology ; Earth, Planet ; Fossils ; Temperature ; },
abstract = {Molecular and fossil evidence suggests that complex eukaryotic multicellularity evolved during the late Neoproterozoic era, coincident with Snowball Earth glaciations, where ice sheets covered most of the globe. During this period, environmental conditions-such as seawater temperature and the availability of photosynthetically active light in the oceans-likely changed dramatically. Such changes would have had significant effects on both resource availability and optimal phenotypes. Here, we construct and apply mechanistic models to explore (i) how environmental changes during Snowball Earth and biophysical constraints generated selective pressures, and (ii) how these pressures may have had differential effects on organisms with different forms of biological organization. By testing a series of alternative-and commonly debated-hypotheses, we demonstrate how multicellularity was likely acquired differently in eukaryotes and prokaryotes owing to selective differences on their size due to the biophysical and metabolic regimes they inhabit: decreasing temperatures and resource availability instigated by the onset of glaciations generated selective pressures towards smaller sizes in organisms in the diffusive regime and towards larger sizes in motile heterotrophs. These results suggest that changing environmental conditions during Snowball Earth glaciations gave multicellular eukaryotes an evolutionary advantage, paving the way for the complex multicellular lineages that followed.},
}

*Biological Evolution
Ice Cover
Eukaryota/physiology
Earth, Planet
Fossils
Temperature

@article {pmid38907301,
year = {2024},
author = {Martinez, P and Bailly, X and Sprecher, SG and Hartenstein, V},
title = {The Acoel nervous system: morphology and development.},
journal = {Neural development},
volume = {19},
number = {1},
pages = {9},
pmid = {38907301},
issn = {1749-8104},
support = {PID2021-124415NB-I00//Spanish "Ministerio de Ciencia, Innovación y Universidades"/ ; 310030_219348/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Animals ; *Nervous System/growth & development/embryology ; *Neurogenesis/physiology ; Platyhelminths/growth & development/physiology ; Biological Evolution ; Neurons/cytology/physiology ; },
abstract = {Acoel flatworms have played a relevant role in classical (and current) discussions on the evolutionary origin of bilaterian animals. This is mostly derived from the apparent simplicity of their body architectures. This tenet has been challenged over the last couple of decades, mostly because detailed studies of their morphology and the introduction of multiple genomic technologies have unveiled a complexity of cell types, tissular arrangements and patterning mechanisms that were hidden below this 'superficial' simplicity. One tissue that has received a particular attention has been the nervous system (NS). The combination of ultrastructural and single cell methodologies has revealed unique cellular diversity and developmental trajectories for most of their neurons and associated sensory systems. Moreover, the great diversity in NS architectures shown by different acoels offers us with a unique group of animals where to study key aspects of neurogenesis and diversification od neural systems over evolutionary time.In this review we revisit some recent developments in the characterization of the acoel nervous system structure and the regulatory mechanisms that contribute to their embryological development. We end up by suggesting some promising avenues to better understand how this tissue is organized in its finest cellular details and how to achieve a deeper knowledge of the functional roles that genes and gene networks play in its construction.},
}

Animals
*Nervous System/growth & development/embryology
*Neurogenesis/physiology
Platyhelminths/growth & development/physiology
Biological Evolution
Neurons/cytology/physiology

@article {pmid38894655,
year = {2024},
author = {Murayama, F and Asai, H and Patra, AK and Wake, H and Miyata, T and Hattori, Y},
title = {A novel preparation for histological analyses of intraventricular macrophages in the embryonic brain.},
journal = {Development, growth & differentiation},
volume = {66},
number = {5},
pages = {329-337},
doi = {10.1111/dgd.12935},
pmid = {38894655},
issn = {1440-169X},
support = {JPMJCR22P6//Core Research for Evolutional Science and Technology/ ; JPMJFR214C//Fusion Oriented REsearch for disruptive Science and Technology/ ; JP20H05899//Japan Society for the Promotion of Science/ ; JP21H02656//Japan Society for the Promotion of Science/ ; JP23H02658//Japan Society for the Promotion of Science/ ; JP23H04161//Japan Society for the Promotion of Science/ ; //The Uehara Memorial Foundation/ ; //Takeda Science Foundation/ ; //The Sumitomo Foundation/ ; //The Nakajima Foundation/ ; //Tokai Pathways to Global Excellence (T-GEx)/ ; },
mesh = {Animals ; *Macrophages/cytology ; Mice ; *Brain/embryology/cytology ; Microglia/cytology/metabolism ; Cerebral Ventricles/embryology/cytology ; },
abstract = {Microglia colonize the brain starting on embryonic day (E) 9.5 in mice, and their population increases with development. We have previously demonstrated that some microglia are derived from intraventricular macrophages, which frequently infiltrate the pallium at E12.5. To address how the infiltration of intraventricular macrophages is spatiotemporally regulated, histological analyses detecting how these cells associate with the surrounding cells at the site of infiltration into the pallial surface are essential. Using two-photon microscopy-based in vivo imaging, we demonstrated that most intraventricular macrophages adhere to the ventricular surface. This is a useful tool for imaging intraventricular macrophages maintaining their original position, but this method cannot be used for observing deeper brain regions. Meanwhile, we found that conventional cryosection-based and naked pallial slice-based observation resulted in unexpected detachment from the ventricular surface of intraventricular macrophages and their mislocation, suggesting that previous histological analyses might have failed to determine their physiological number and location in the ventricular space. To address this, we sought to establish a methodological preparation that enables us to delineate the structure and cellular interactions when intraventricular macrophages infiltrate the pallium. Here, we report that brain slices pretreated with agarose-embedding maintained adequate density and proper positioning of intraventricular macrophages on the ventricular surface. This method also enabled us to perform the immunostaining. We believe that this is helpful for conducting histological analyses to elucidate the mechanisms underlying intraventricular macrophage infiltration into the pallium and their cellular properties, leading to further understanding of the process of microglial colonization into the developing brain.},
}

Animals
*Macrophages/cytology
Mice
*Brain/embryology/cytology
Microglia/cytology/metabolism
Cerebral Ventricles/embryology/cytology

@article {pmid38883608,
year = {2024},
author = {Puginier, E and Leal-Fischer, K and Gaitan, J and Lallouet, M and Scotti, PA and Raoux, M and Lang, J},
title = {Extracellular electrophysiology on clonal human β-cell spheroids.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1402880},
pmid = {38883608},
issn = {1664-2392},
mesh = {Humans ; *Insulin-Secreting Cells/physiology/metabolism/cytology ; *Spheroids, Cellular ; Electrophysiological Phenomena ; Insulin Secretion/physiology ; Glucose/metabolism/pharmacology ; Insulin/metabolism ; Action Potentials/physiology ; Animals ; },
abstract = {BACKGROUND: Pancreatic islets are important in nutrient homeostasis and improved cellular models of clonal origin may very useful especially in view of relatively scarce primary material. Close 3D contact and coupling between β-cells are a hallmark of physiological function improving signal/noise ratios. Extracellular electrophysiology using micro-electrode arrays (MEA) is technically far more accessible than single cell patch clamp, enables dynamic monitoring of electrical activity in 3D organoids and recorded multicellular slow potentials (SP) provide unbiased insight in cell-cell coupling.

OBJECTIVE: We have therefore asked whether 3D spheroids enhance clonal β-cell function such as electrical activity and hormone secretion using human EndoC-βH1, EndoC-βH5 and rodent INS-1 832/13 cells.

METHODS: Spheroids were formed either by hanging drop or proprietary devices. Extracellular electrophysiology was conducted using multi-electrode arrays with appropriate signal extraction and hormone secretion measured by ELISA.

RESULTS: EndoC-βH1 spheroids exhibited increased signals in terms of SP frequency and especially amplitude as compared to monolayers and even single cell action potentials (AP) were quantifiable. Enhanced electrical signature in spheroids was accompanied by an increase in the glucose stimulated insulin secretion index. EndoC-βH5 monolayers and spheroids gave electrophysiological profiles similar to EndoC-βH1, except for a higher electrical activity at 3 mM glucose, and exhibited moreover a biphasic profile. Again, physiological concentrations of GLP-1 increased AP frequency. Spheroids also exhibited a higher secretion index. INS-1 cells did not form stable spheroids, but overexpression of connexin 36, required for cell-cell coupling, increased glucose responsiveness, dampened basal activity and consequently augmented the stimulation index.

CONCLUSION: In conclusion, spheroid formation enhances physiological function of the human clonal β-cell lines and these models may provide surrogates for primary islets in extracellular electrophysiology.},
}

Humans
*Insulin-Secreting Cells/physiology/metabolism/cytology
*Spheroids, Cellular
Electrophysiological Phenomena
Insulin Secretion/physiology
Glucose/metabolism/pharmacology
Insulin/metabolism
Action Potentials/physiology
Animals

@article {pmid38813885,
year = {2024},
author = {Bennett, GM and Kwak, Y and Maynard, R},
title = {Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again.},
journal = {Genome biology and evolution},
volume = {16},
number = {6},
pages = {},
pmid = {38813885},
issn = {1759-6653},
support = {NSF-1347116//National Science Foundation/ ; GT15982/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Symbiosis ; *Biological Evolution ; Animals ; Bacteria/genetics ; Biodiversity ; Evolution, Molecular ; },
abstract = {Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution, and insights from the field at large. The accumulated work illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land-plant endosymbioses with fungi and bacteria to nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g. mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet.},
}

*Symbiosis
*Biological Evolution
Animals
Bacteria/genetics
Biodiversity
Evolution, Molecular

@article {pmid38798503,
year = {2024},
author = {Perotti, O and Esparza, GV and Booth, DS},
title = {A red algal polysaccharide influences the multicellular development of the choanoflagellate Salpingoeca rosetta.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38798503},
issn = {2692-8205},
support = {R24 GM137782/GM/NIGMS NIH HHS/United States ; T32 GM139786/GM/NIGMS NIH HHS/United States ; },
abstract = {We uncovered an interaction between a choanoflagellate and alga, in which porphyran, a polysaccharide produced by the red alga Porphyra umbilicalis, induces multicellular development in the choanoflagellate Salpingoeca rosetta. We first noticed this possible interaction when we tested the growth of S. rosetta in media that was steeped with P. umbilicalis as a nutritional source. Under those conditions, S. rosetta formed multicellular rosette colonies even in the absence of any bacterial species that can induce rosette development. In biochemical purifications, we identified porphyran, a extracellular polysaccharide produced by red algae, as the rosette inducing factor The response of S. rosetta to porphyran provides a biochemical insight for associations between choanoflagellates and algae that have been observed since the earliest descriptions of choanoflagellates. Moreover, this work provides complementary evidence to ecological and geochemical studies that show the profound impact algae have exerted on eukaryotes and their evolution, including a rise in algal productivity that coincided with the origin of animals, the closest living relatives of choanoflagellates.},
}

@article {pmid38791309,
year = {2024},
author = {Bibo-Verdugo, B and Salvesen, G},
title = {Evolution of Caspases and the Invention of Pyroptosis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {10},
pages = {},
pmid = {38791309},
issn = {1422-0067},
mesh = {*Pyroptosis ; Humans ; *Caspases/metabolism ; Animals ; *Immunity, Innate ; Evolution, Molecular ; Apoptosis ; },
abstract = {The protein scaffold that includes the caspases is ancient and found in all domains of life. However, the stringent specificity that defines the caspase biologic function is relatively recent and found only in multicellular animals. During the radiation of the Chordata, members of the caspase family adopted roles in immunity, events coinciding with the development of substrates that define the modern innate immune response. This review focuses on the switch from the non-inflammatory cellular demise of apoptosis to the highly inflammatory innate response driven by distinct members of the caspase family, and the interplay between these two regulated cell death pathways.},
}

*Pyroptosis
Humans
*Caspases/metabolism
Animals
*Immunity, Innate
Evolution, Molecular
Apoptosis

@article {pmid38790063,
year = {2024},
author = {Zhang, B and Xiao, L and Lyu, L and Zhao, F and Miao, M},
title = {Exploring the landscape of symbiotic diversity and distribution in unicellular ciliated protists.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {96},
pmid = {38790063},
issn = {2049-2618},
mesh = {*Symbiosis ; *Ciliophora/genetics/classification/physiology ; *Bacteria/genetics/classification ; Archaea/genetics/classification ; Phylogeny ; Metagenome ; Biodiversity ; },
abstract = {BACKGROUND: The eukaryotic-bacterial symbiotic system plays an important role in various physiological, developmental, and evolutionary processes. However, our current understanding is largely limited to multicellular eukaryotes without adequate consideration of diverse unicellular protists, including ciliates.

RESULTS: To investigate the bacterial profiles associated with unicellular organisms, we collected 246 ciliate samples spanning the entire Ciliophora phylum and conducted single-cell based metagenome sequencing. This effort has yielded the most extensive collection of bacteria linked to unicellular protists to date. From this dataset, we identified 883 bacterial species capable of cohabiting with ciliates, unveiling the genomes of 116 novel bacterial cohabitants along with 7 novel archaeal cohabitants. Highlighting the intimate relationship between ciliates and their cohabitants, our study unveiled that over 90% of ciliates coexist with bacteria, with individual hosts fostering symbiotic relationships with multiple bacteria concurrently, resulting in the observation of seven distinct symbiotic patterns among bacteria. Our exploration of symbiotic mechanisms revealed the impact of host digestion on the intracellular diversity of cohabitants. Additionally, we identified the presence of eukaryotic-like proteins in bacteria as a potential contributing factor to their resistance against host digestion, thereby expanding their potential host range.

CONCLUSIONS: As the first large-scale analysis of prokaryotic associations with ciliate protists, this study provides a valuable resource for future research on eukaryotic-bacterial symbioses. Video Abstract.},
}

*Symbiosis
*Ciliophora/genetics/classification/physiology
*Bacteria/genetics/classification
Archaea/genetics/classification
Phylogeny
Metagenome
Biodiversity

@article {pmid38778808,
year = {2023},
author = {Ondracka, A and Dudin, O and Bråte, J},
title = {Time-resolved small RNA transcriptomics of the ichthyosporean Sphaeroforma arctica.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {542},
pmid = {38778808},
issn = {2046-1402},
mesh = {*Transcriptome ; Mesomycetozoea/genetics ; MicroRNAs/genetics ; Gene Expression Profiling ; },
abstract = {Ichthyosporea, a clade of holozoans, represent a clade closely related to animals, and thus hold a key phylogenetic position for understanding the origin of animals. We have previously discovered that an ichthyosporean, Sphaeroforma arctica, contains microRNAs (miRNAs) as well as the miRNA processing machinery. This was the first discovery of miRNAs among the closest single-celled relatives of animals and raised intriguing questions about the roles of regulatory small RNAs in cell development and differentiation in unicellular eukaryotes. Like many ichthyosporeans, S. arctica also undergoes a transient multicellular developmental life cycle. As miRNAs are, among other roles, key regulators of gene expression during development in animals, we wanted to investigate the dynamics of miRNAs during the developmental cycle in S. arctica. Here we have therefore collected a comprehensive time-resolved small RNA transcriptome linked to specific life stages with a substantially higher sequencing depth than before, which can enable further discovery of functionally relevant small RNAs. The data consists of Illumina-sequenced small RNA libraries from two independent biological replicates of the entire life cycle of S. arctica with high temporal resolution. The dataset is directly linked and comes from the same samples as a previously published mRNA-seq dataset, thus enabling direct cross-functional analyses.},
}

*Transcriptome
Mesomycetozoea/genetics
MicroRNAs/genetics
Gene Expression Profiling

@article {pmid38735988,
year = {2024},
author = {Aprile, D and Patrone, D and Peluso, G and Galderisi, U},
title = {Multipotent/pluripotent stem cell populations in stromal tissues and peripheral blood: exploring diversity, potential, and therapeutic applications.},
journal = {Stem cell research & therapy},
volume = {15},
number = {1},
pages = {139},
pmid = {38735988},
issn = {1757-6512},
support = {PE0000006 MNESYS//European Commission/ ; },
mesh = {Humans ; *Pluripotent Stem Cells/cytology/metabolism ; *Multipotent Stem Cells/cytology/metabolism ; Cell Differentiation ; Stromal Cells/cytology/metabolism ; Animals ; },
abstract = {The concept of "stemness" incorporates the molecular mechanisms that regulate the unlimited self-regenerative potential typical of undifferentiated primitive cells. These cells possess the unique ability to navigate the cell cycle, transitioning in and out of the quiescent G0 phase, and hold the capacity to generate diverse cell phenotypes. Stem cells, as undifferentiated precursors endow with extraordinary regenerative capabilities, exhibit a heterogeneous and tissue-specific distribution throughout the human body. The identification and characterization of distinct stem cell populations across various tissues have revolutionized our understanding of tissue homeostasis and regeneration. From the hematopoietic to the nervous and musculoskeletal systems, the presence of tissue-specific stem cells underlines the complex adaptability of multicellular organisms. Recent investigations have revealed a diverse cohort of non-hematopoietic stem cells (non-HSC), primarily within bone marrow and other stromal tissue, alongside established hematopoietic stem cells (HSC). Among these non-HSC, a rare subset exhibits pluripotent characteristics. In vitro and in vivo studies have demonstrated the remarkable differentiation potential of these putative stem cells, known by various names including multipotent adult progenitor cells (MAPC), marrow-isolated adult multilineage inducible cells (MIAMI), small blood stem cells (SBSC), very small embryonic-like stem cells (VSELs), and multilineage differentiating stress enduring cells (MUSE). The diverse nomenclatures assigned to these primitive stem cell populations may arise from different origins or varied experimental methodologies. This review aims to present a comprehensive comparison of various subpopulations of multipotent/pluripotent stem cells derived from stromal tissues. By analysing isolation techniques and surface marker expression associated with these populations, we aim to delineate the similarities and distinctions among stromal tissue-derived stem cells. Understanding the nuances of these tissue-specific stem cells is critical for unlocking their therapeutic potential and advancing regenerative medicine. The future of stem cells research should prioritize the standardization of methodologies and collaborative investigations in shared laboratory environments. This approach could mitigate variability in research outcomes and foster scientific partnerships to fully exploit the therapeutic potential of pluripotent stem cells.},
}

Humans
*Pluripotent Stem Cells/cytology/metabolism
*Multipotent Stem Cells/cytology/metabolism
Cell Differentiation
Stromal Cells/cytology/metabolism
Animals

@article {pmid38720073,
year = {2024},
author = {Yaron-Barir, TM and Joughin, BA and Huntsman, EM and Kerelsky, A and Cizin, DM and Cohen, BM and Regev, A and Song, J and Vasan, N and Lin, TY and Orozco, JM and Schoenherr, C and Sagum, C and Bedford, MT and Wynn, RM and Tso, SC and Chuang, DT and Li, L and Li, SS and Creixell, P and Krismer, K and Takegami, M and Lee, H and Zhang, B and Lu, J and Cossentino, I and Landry, SD and Uduman, M and Blenis, J and Elemento, O and Frame, MC and Hornbeck, PV and Cantley, LC and Turk, BE and Yaffe, MB and Johnson, JL},
title = {The intrinsic substrate specificity of the human tyrosine kinome.},
journal = {Nature},
volume = {629},
number = {8014},
pages = {1174-1181},
pmid = {38720073},
issn = {1476-4687},
support = {P01 CA117969/CA/NCI NIH HHS/United States ; P01 CA120964/CA/NCI NIH HHS/United States ; R35 ES028374/ES/NIEHS NIH HHS/United States ; R01 GM104047/GM/NIGMS NIH HHS/United States ; R01 GM135331/GM/NIGMS NIH HHS/United States ; R35 CA197588/CA/NCI NIH HHS/United States ; R01 CA226898/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Humans ; Amino Acid Motifs ; Evolution, Molecular ; Mass Spectrometry ; Phosphoproteins/chemistry/metabolism ; Phosphorylation ; *Phosphotyrosine/metabolism ; *Protein-Tyrosine Kinases/drug effects/metabolism ; Proteome/chemistry/metabolism ; Proteomics ; Signal Transduction ; src Homology Domains ; *Substrate Specificity ; *Tyrosine/metabolism/chemistry ; },
abstract = {Phosphorylation of proteins on tyrosine (Tyr) residues evolved in metazoan organisms as a mechanism of coordinating tissue growth[1]. Multicellular eukaryotes typically have more than 50 distinct protein Tyr kinases that catalyse the phosphorylation of thousands of Tyr residues throughout the proteome[1-3]. How a given Tyr kinase can phosphorylate a specific subset of proteins at unique Tyr sites is only partially understood[4-7]. Here we used combinatorial peptide arrays to profile the substrate sequence specificity of all human Tyr kinases. Globally, the Tyr kinases demonstrate considerable diversity in optimal patterns of residues surrounding the site of phosphorylation, revealing the functional organization of the human Tyr kinome by substrate motif preference. Using this information, Tyr kinases that are most compatible with phosphorylating any Tyr site can be identified. Analysis of mass spectrometry phosphoproteomic datasets using this compendium of kinase specificities accurately identifies specific Tyr kinases that are dysregulated in cells after stimulation with growth factors, treatment with anti-cancer drugs or expression of oncogenic variants. Furthermore, the topology of known Tyr signalling networks naturally emerged from a comparison of the sequence specificities of the Tyr kinases and the SH2 phosphotyrosine (pTyr)-binding domains. Finally we show that the intrinsic substrate specificity of Tyr kinases has remained fundamentally unchanged from worms to humans, suggesting that the fidelity between Tyr kinases and their protein substrate sequences has been maintained across hundreds of millions of years of evolution.},
}

Animals
Humans
Amino Acid Motifs
Evolution, Molecular
Mass Spectrometry
Phosphoproteins/chemistry/metabolism
Phosphorylation
*Phosphotyrosine/metabolism
*Protein-Tyrosine Kinases/drug effects/metabolism
Proteome/chemistry/metabolism
Proteomics
Signal Transduction
src Homology Domains
*Substrate Specificity
*Tyrosine/metabolism/chemistry

@article {pmid38705386,
year = {2024},
author = {Enström, A and Carlsson, R and Buizza, C and Lewi, M and Paul, G},
title = {Pericyte-Specific Secretome Profiling in Hypoxia Using TurboID in a Multicellular in Vitro Spheroid Model.},
journal = {Molecular & cellular proteomics : MCP},
volume = {23},
number = {6},
pages = {100782},
pmid = {38705386},
issn = {1535-9484},
mesh = {*Pericytes/metabolism ; Humans ; *Spheroids, Cellular/metabolism ; *Coculture Techniques ; *Cell Hypoxia ; Secretome/metabolism ; Endothelial Cells/metabolism ; Astrocytes/metabolism ; Proteomics/methods ; Cell Communication ; Blood-Brain Barrier/metabolism ; Cells, Cultured ; Brain/metabolism ; Mass Spectrometry ; Signal Transduction ; },
abstract = {Cellular communication within the brain is imperative for maintaining homeostasis and mounting effective responses to pathological triggers like hypoxia. However, a comprehensive understanding of the precise composition and dynamic release of secreted molecules has remained elusive, confined primarily to investigations using isolated monocultures. To overcome these limitations, we utilized the potential of TurboID, a non-toxic biotin ligation enzyme, to capture and enrich secreted proteins specifically originating from human brain pericytes in spheroid cocultures with human endothelial cells and astrocytes. This approach allowed us to characterize the pericyte secretome within a more physiologically relevant multicellular setting encompassing the constituents of the blood-brain barrier. Through a combination of mass spectrometry and multiplex immunoassays, we identified a wide spectrum of different secreted proteins by pericytes. Our findings demonstrate that the pericytes secretome is profoundly shaped by their intercellular communication with other blood-brain barrier-residing cells. Moreover, we identified substantial differences in the secretory profiles between hypoxic and normoxic pericytes. Mass spectrometry analysis showed that hypoxic pericytes in coculture increase their release of signals related to protein secretion, mTOR signaling, and the complement system, while hypoxic pericytes in monocultures showed an upregulation in proliferative pathways including G2M checkpoints, E2F-, and Myc-targets. In addition, hypoxic pericytes show an upregulation of proangiogenic proteins such as VEGFA but display downregulation of canonical proinflammatory cytokines such as CXCL1, MCP-1, and CXCL6. Understanding the specific composition of secreted proteins in the multicellular brain microvasculature is crucial for advancing our knowledge of brain homeostasis and the mechanisms underlying pathology. This study has implications for the identification of targeted therapeutic strategies aimed at modulating microvascular signaling in brain pathologies associated with hypoxia.},
}

*Pericytes/metabolism
Humans
*Spheroids, Cellular/metabolism
*Coculture Techniques
*Cell Hypoxia
Secretome/metabolism
Endothelial Cells/metabolism
Astrocytes/metabolism
Proteomics/methods
Cell Communication
Blood-Brain Barrier/metabolism
Cells, Cultured
Brain/metabolism
Mass Spectrometry
Signal Transduction

@article {pmid38700417,
year = {2024},
author = {Maloney, KM and Halverson, GP and Lechte, M and Gibson, TM and Bui, TH and Schiffbauer, JD and Laflamme, M},
title = {The paleoredox context of early eukaryotic evolution: insights from the Tonian Mackenzie Mountains Supergroup, Canada.},
journal = {Geobiology},
volume = {22},
number = {3},
pages = {e12598},
doi = {10.1111/gbi.12598},
pmid = {38700417},
issn = {1472-4669},
support = {//National Science Foundation/ ; //Polar Continental Shelf Program/ ; //Queen Elizabeth II Graduate Scholarship in Science & Technology (QEII-GSST)/ ; //Agouron Institute/ ; //Geological Society of America Graduate Research Grant/ ; GH RGPIN2017-04025//National Science and Engineering Research Council of Canada (NSERC)/ ; ML RGPIN435402//National Science and Engineering Research Council of Canada (NSERC)/ ; NSF IF 1636643//Northern Scientific Training Program/ ; },
mesh = {*Oxidation-Reduction ; *Fossils ; *Biological Evolution ; Geologic Sediments/chemistry/analysis ; Eukaryota ; Canada ; Ecosystem ; Chlorophyta ; },
abstract = {Tonian (ca. 1000-720 Ma) marine environments are hypothesised to have experienced major redox changes coinciding with the evolution and diversification of multicellular eukaryotes. In particular, the earliest Tonian stratigraphic record features the colonisation of benthic habitats by multicellular macroscopic algae, which would have been powerful ecosystem engineers that contributed to the oxygenation of the oceans and the reorganisation of biogeochemical cycles. However, the paleoredox context of this expansion of macroalgal habitats in Tonian nearshore marine environments remains uncertain due to limited well-preserved fossils and stratigraphy. As such, the interdependent relationship between early complex life and ocean redox state is unclear. An assemblage of macrofossils including the chlorophyte macroalga Archaeochaeta guncho was recently discovered in the lower Mackenzie Mountains Supergroup in Yukon (Canada), which archives marine sedimentation from ca. 950-775 Ma, permitting investigation into environmental evolution coincident with eukaryotic ecosystem evolution and expansion. Here we present multi-proxy geochemical data from the lower Mackenzie Mountains Supergroup to constrain the paleoredox environment within which these large benthic macroalgae thrived. Two transects show evidence for basin-wide anoxic (ferruginous) oceanic conditions (i.e., high FeHR/FeT, low Fepy/FeHR), with muted redox-sensitive trace metal enrichments and possible seasonal variability. However, the weathering of sulfide minerals in the studied samples may obscure geochemical signatures of euxinic conditions. These results suggest that macroalgae colonized shallow environments in an ocean that remained dominantly anoxic with limited evidence for oxygenation until ca. 850 Ma. Collectively, these geochemical results provide novel insights into the environmental conditions surrounding the evolution and expansion of benthic macroalgae and the eventual dominance of oxygenated oceanic conditions required for the later emergence of animals.},
}

*Oxidation-Reduction
*Fossils
*Biological Evolution
Geologic Sediments/chemistry/analysis
Eukaryota
Canada
Ecosystem
Chlorophyta

@article {pmid38691595,
year = {2024},
author = {Yu, P and Li, Y and Fang, W and Feng, XQ and Li, B},
title = {Mechanochemical dynamics of collective cells and hierarchical topological defects in multicellular lumens.},
journal = {Science advances},
volume = {10},
number = {18},
pages = {eadn0172},
pmid = {38691595},
issn = {2375-2548},
mesh = {*Mechanotransduction, Cellular ; *Models, Biological ; *Morphogenesis ; Biomechanical Phenomena ; Animals ; },
abstract = {Collective cell dynamics is essential for tissue morphogenesis and various biological functions. However, it remains incompletely understood how mechanical forces and chemical signaling are integrated to direct collective cell behaviors underlying tissue morphogenesis. Here, we propose a three-dimensional (3D) mechanochemical theory accounting for biochemical reaction-diffusion and cellular mechanotransduction to investigate the dynamics of multicellular lumens. We show that the interplay between biochemical signaling and mechanics can trigger either pitchfork or Hopf bifurcation to induce diverse static mechanochemical patterns or generate oscillations with multiple modes both involving marked mechanical deformations in lumens. We uncover the crucial role of mechanochemical feedback in emerging morphodynamics and identify the evolution and morphogenetic functions of hierarchical topological defects including cell-level hexatic defects and tissue-level orientational defects. Our theory captures the common mechanochemical traits of collective dynamics observed in experiments and could provide a mechanistic context for understanding morphological symmetry breaking in 3D lumen-like tissues.},
}

*Mechanotransduction, Cellular
*Models, Biological
*Morphogenesis
Biomechanical Phenomena
Animals

@article {pmid38690760,
year = {2024},
author = {},
title = {Transitions in development - an interview with Thibaut Brunet.},
journal = {Development (Cambridge, England)},
volume = {151},
number = {9},
pages = {},
doi = {10.1242/dev.202942},
pmid = {38690760},
issn = {1477-9129},
mesh = {Animals ; *Biological Evolution ; *Developmental Biology/history ; *Choanoflagellata ; History, 21st Century ; Morphogenesis ; History, 20th Century ; },
abstract = {Thibaut Brunet is a group leader at the Institut Pasteur in Paris, France, where he works on choanoflagellates (known as 'choanos' for short). These unicellular organisms are close relatives of animals that have the potential to form multicellular assemblies under certain conditions, and Thibaut's lab are leveraging them to gain insights into how animal morphogenesis evolved. We met with Thibaut over Zoom to discuss his career path so far, and learnt how an early interest in dinosaurs contributed to his life-long fascination with evolutionary biology.},
}

Animals
*Biological Evolution
*Developmental Biology/history
*Choanoflagellata
History, 21st Century
Morphogenesis
History, 20th Century

@article {pmid38662765,
year = {2024},
author = {Singleton, MD and Eisen, MB},
title = {Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation.},
journal = {PLoS computational biology},
volume = {20},
number = {4},
pages = {e1012028},
pmid = {38662765},
issn = {1553-7358},
mesh = {Drosophila melanogaster/genetics ; *Intrinsically Disordered Proteins/chemistry/genetics/metabolism ; *Drosophila Proteins/chemistry/genetics/metabolism ; Evolution, Molecular ; Sequence Homology ; Amino Acid Sequence ; },
abstract = {Intrinsically disordered regions (IDRs) are segments of proteins without stable three-dimensional structures. As this flexibility allows them to interact with diverse binding partners, IDRs play key roles in cell signaling and gene expression. Despite the prevalence and importance of IDRs in eukaryotic proteomes and various biological processes, associating them with specific molecular functions remains a significant challenge due to their high rates of sequence evolution. However, by comparing the observed values of various IDR-associated properties against those generated under a simulated model of evolution, a recent study found most IDRs across the entire yeast proteome contain conserved features. Furthermore, it showed clusters of IDRs with common "evolutionary signatures," i.e. patterns of conserved features, were associated with specific biological functions. To determine if similar patterns of conservation are found in the IDRs of other systems, in this work we applied a series of phylogenetic models to over 7,500 orthologous IDRs identified in the Drosophila genome to dissect the forces driving their evolution. By comparing models of constrained and unconstrained continuous trait evolution using the Brownian motion and Ornstein-Uhlenbeck models, respectively, we identified signals of widespread constraint, indicating conservation of distributed features is mechanism of IDR evolution common to multiple biological systems. In contrast to the previous study in yeast, however, we observed limited evidence of IDR clusters with specific biological functions, which suggests a more complex relationship between evolutionary constraints and function in the IDRs of multicellular organisms.},
}

Drosophila melanogaster/genetics
*Intrinsically Disordered Proteins/chemistry/genetics/metabolism
*Drosophila Proteins/chemistry/genetics/metabolism
Evolution, Molecular
Sequence Homology
Amino Acid Sequence

@article {pmid38659912,
year = {2024},
author = {Tong, K and Datta, S and Cheng, V and Haas, DJ and Gourisetti, S and Yopp, HL and Day, TC and Lac, DT and Conlin, PL and Bozdag, GO and Ratcliff, WC},
title = {Whole-genome duplication in the Multicellularity Long Term Evolution Experiment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38659912},
issn = {2692-8205},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; },
abstract = {Whole-genome duplication (WGD) is widespread across eukaryotes and can promote adaptive evolution[1-4]. However, given the instability of newly-formed polyploid genomes[5-7], understanding how WGDs arise in a population, persist, and underpin adaptations remains a challenge. Using our ongoing Multicellularity Long Term Evolution Experiment (MuLTEE)[8], we show that diploid snowflake yeast (Saccharomyces cerevisiae) under selection for larger multicellular size rapidly undergo spontaneous WGD. From its origin within the first 50 days of the experiment, tetraploids persist for the next 950 days (nearly 5,000 generations, the current leading edge of our experiment) in ten replicate populations, despite being genomically unstable. Using synthetic reconstruction, biophysical modeling, and counter-selection experiments, we found that tetraploidy evolved because it confers immediate fitness benefits in this environment, by producing larger, longer cells that yield larger clusters. The same selective benefit also maintained tetraploidy over long evolutionary timescales, inhibiting the reversion to diploidy that is typically seen in laboratory evolution experiments. Once established, tetraploidy facilitated novel genetic routes for adaptation, playing a key role in the evolution of macroscopic multicellular size via the origin of evolutionarily conserved aneuploidy. These results provide unique empirical insights into the evolutionary dynamics and impacts of WGD, showing how it can initially arise due to its immediate adaptive benefits, be maintained by selection, and fuel long-term innovations by creating additional dimensions of heritable genetic variation.},
}

@article {pmid38654432,
year = {2024},
author = {Chen, C and Chen, H and Wang, P and Wang, X and Wang, X and Chen, C},
title = {Ca[2+] Overload Decreased Cellular Viability in Magnetic Hyperthermia without a Macroscopic Temperature Rise.},
journal = {ACS biomaterials science & engineering},
volume = {10},
number = {5},
pages = {2995-3005},
doi = {10.1021/acsbiomaterials.3c01875},
pmid = {38654432},
issn = {2373-9878},
mesh = {*Calcium/metabolism ; *Cell Survival ; *Reactive Oxygen Species/metabolism ; *TRPV Cation Channels/metabolism ; Humans ; *Hyperthermia, Induced/methods ; *Magnetic Fields ; Temperature ; Ferritins/metabolism ; Hyperthermia/metabolism ; },
abstract = {Magnetic hyperthermia is a crucial medical engineering technique for treating diseases, which usually uses alternating magnetic fields (AMF) to interplay with magnetic substances to generate heat. Recently, it has been found that in some cases, there is no detectable temperature increment after applying an AMF, which caused corresponding effects surprisingly. The mechanisms involved in this phenomenon are not yet fully understood. In this study, we aimed to explore the role of Ca[2+] overload in the magnetic hyperthermia effect without a perceptible temperature rise. A cellular system expressing the fusion proteins TRPV1 and ferritin was prepared. The application of an AMF (518 kHz, 16 kA/m) could induce the fusion protein to release a large amount of iron ions, which then participates in the production of massive reactive oxygen radicals (ROS). Both ROS and its induced lipid oxidation enticed the opening of ion channels, causing intracellular Ca[2+] overload, which further led to decreased cellular viability. Taken together, Ca[2+] overload triggered by elevated ROS and the induced oxidation of lipids contributes to the magnetic hyperthermia effect without a perceptible temperature rise. These findings would be beneficial for expanding the application of temperature-free magnetic hyperthermia, such as in cellular and neural regulation, design of new cancer treatment methods.},
}

*Calcium/metabolism
*Cell Survival
*Reactive Oxygen Species/metabolism
*TRPV Cation Channels/metabolism
Humans
*Hyperthermia, Induced/methods
*Magnetic Fields
Temperature
Ferritins/metabolism
Hyperthermia/metabolism

@article {pmid38652695,
year = {2024},
author = {Xin, H and Wang, Y and Zhang, W and Bao, Y and Neumann, P and Ning, Y and Zhang, T and Wu, Y and Jiang, N and Jiang, J and Xi, M},
title = {Celine, a long interspersed nuclear element retrotransposon, colonizes in the centromeres of poplar chromosomes.},
journal = {Plant physiology},
volume = {195},
number = {4},
pages = {2787-2798},
pmid = {38652695},
issn = {1532-2548},
support = {IOS-1740874//National Science Foundation/ ; MICL2707//United States Department of Agriculture National Institute of Food and Agriculture and AgBioResearch at Michigan State University/ ; ISO-2029959//NSF/ ; //National Natural Science Foundation of China/ ; },
mesh = {*Populus/genetics ; *Centromere/genetics/metabolism ; *Chromosomes, Plant/genetics ; *Retroelements/genetics ; Long Interspersed Nucleotide Elements/genetics ; Phylogeny ; Histones/metabolism/genetics ; },
abstract = {Centromeres in most multicellular eukaryotes are composed of long arrays of repetitive DNA sequences. Interestingly, several transposable elements, including the well-known long terminal repeat centromeric retrotransposon of maize (CRM), were found to be enriched in functional centromeres marked by the centromeric histone H3 (CENH3). Here, we report a centromeric long interspersed nuclear element (LINE), Celine, in Populus species. Celine has colonized preferentially in the CENH3-associated chromatin of every poplar chromosome, with 84% of the Celine elements localized in the CENH3-binding domains. In contrast, only 51% of the CRM elements were bound to CENH3 domains in Populus trichocarpa. These results suggest different centromere targeting mechanisms employed by Celine and CRM elements. Nevertheless, the high target specificity seems to be detrimental to further amplification of the Celine elements, leading to a shorter life span and patchy distribution among plant species compared with the CRM elements. Using a phylogenetically guided approach, we were able to identify Celine-like LINE elements in tea plant (Camellia sinensis) and green ash tree (Fraxinus pennsylvanica). The centromeric localization of these Celine-like LINEs was confirmed in both species. We demonstrate that the centromere targeting property of Celine-like LINEs is of primitive origin and has been conserved among distantly related plant species.},
}

*Populus/genetics
*Centromere/genetics/metabolism
*Chromosomes, Plant/genetics
*Retroelements/genetics
Long Interspersed Nucleotide Elements/genetics
Phylogeny
Histones/metabolism/genetics

@article {pmid38648729,
year = {2024},
author = {Chen, C and Chen, H and Wang, P and Wang, X and Wang, X and Chen, C and Pan, W},
title = {Reactive Oxygen Species Activate a Ferritin-Linked TRPV4 Channel under a Static Magnetic Field.},
journal = {ACS chemical biology},
volume = {19},
number = {5},
pages = {1151-1160},
doi = {10.1021/acschembio.4c00090},
pmid = {38648729},
issn = {1554-8937},
mesh = {*TRPV Cation Channels/metabolism ; Humans ; *Reactive Oxygen Species/metabolism ; HEK293 Cells ; *Ferritins/metabolism/chemistry ; *Magnetic Fields ; Iron/metabolism ; Calcium/metabolism ; },
abstract = {Magnetogenetics has shown great potential for cell function and neuromodulation using heat or force effects under different magnetic fields; however, there is still a contradiction between experimental effects and underlying mechanisms by theoretical computation. In this study, we aimed to investigate the role of reactive oxygen species (ROS) in mechanical force-dependent regulation from a physicochemical perspective. The transient receptor potential vanilloid 4 (TRPV4) cation channels fused to ferritin (T4F) were overexpressed in HEK293T cells and exposed to static magnetic fields (sMF, 1.4-5.0 mT; gradient: 1.62 mT/cm). An elevation of ROS levels was found under sMF in T4F-overexpressing cells, which could lead to lipid oxidation. Compared with the overexpression of TRPV4, ferritin in T4F promoted the generation of ROS under the stimulation of sMF, probably related to the release of iron ions from ferritin. Then, the resulting ROS regulated the opening of the TRPV4 channel, which was attenuated by the direct addition of ROS inhibitors or an iron ion chelator, highlighting a close relationship among iron release, ROS production, and TRPV4 channel activation. Taken together, these findings indicate that the produced ROS under sMF act on the TRPV4 channel, regulating the influx of calcium ions. The study would provide a scientific basis for the application of magnetic regulation in cellular or neural regulation and disease treatment and contribute to the development of the more sensitive regulatory technology.},
}

*TRPV Cation Channels/metabolism
Humans
*Reactive Oxygen Species/metabolism
HEK293 Cells
*Ferritins/metabolism/chemistry
*Magnetic Fields
Iron/metabolism
Calcium/metabolism

@article {pmid38621413,
year = {2024},
author = {Egorova, KS and Kibardin, AV and Posvyatenko, AV and Ananikov, VP},
title = {Mechanisms of Biological Effects of Ionic Liquids: From Single Cells to Multicellular Organisms.},
journal = {Chemical reviews},
volume = {124},
number = {8},
pages = {4679-4733},
doi = {10.1021/acs.chemrev.3c00420},
pmid = {38621413},
issn = {1520-6890},
mesh = {Animals ; Humans ; Apoptosis/drug effects ; *Ionic Liquids/chemistry/pharmacology ; Oxidative Stress/drug effects ; },
abstract = {The review presents a detailed discussion of the evolving field studying interactions between ionic liquids (ILs) and biological systems. Originating from molten salt electrolytes to present multiapplication substances, ILs have found usage across various fields due to their exceptional physicochemical properties, including excellent tunability. However, their interactions with biological systems and potential influence on living organisms remain largely unexplored. This review examines the cytotoxic effects of ILs on cell cultures, biomolecules, and vertebrate and invertebrate organisms. Our understanding of IL toxicity, while growing in recent years, is yet nascent. The established findings include correlations between harmful effects of ILs and their ability to disturb cellular membranes, their potential to trigger oxidative stress in cells, and their ability to cause cell death via apoptosis. Future research directions proposed in the review include studying the distribution of various ILs within cellular compartments and organelles, investigating metabolic transformations of ILs in cells and organisms, detailed analysis of IL effects on proteins involved in oxidative stress and apoptosis, correlation studies between IL doses, exposure times and resulting adverse effects, and examination of effects of subtoxic concentrations of ILs on various biological objects. This review aims to serve as a critical analysis of the current body of knowledge on IL-related toxicity mechanisms. Furthermore, it can guide researchers toward the design of less toxic ILs and the informed use of ILs in drug development and medicine.},
}

Animals
Humans
Apoptosis/drug effects
*Ionic Liquids/chemistry/pharmacology
Oxidative Stress/drug effects

@article {pmid38604731,
year = {2024},
author = {Reis-Cunha, JL and Pimenta-Carvalho, SA and Almeida, LV and Coqueiro-Dos-Santos, A and Marques, CA and Black, JA and Damasceno, J and McCulloch, R and Bartholomeu, DC and Jeffares, DC},
title = {Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites.},
journal = {Genome research},
volume = {34},
number = {3},
pages = {441-453},
pmid = {38604731},
issn = {1549-5469},
support = {/WT_/Wellcome Trust/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/T016019/1/MRC_/Medical Research Council/United Kingdom ; 224501/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Aneuploidy ; *Chromosome Duplication ; *Gene Expression Regulation ; *Genome, Protozoan ; Evolution, Molecular ; Trypanosomatina/genetics ; Phylogeny ; },
abstract = {Aneuploidy is widely observed in both unicellular and multicellular eukaryotes, usually associated with adaptation to stress conditions. Chromosomal duplication stability is a tradeoff between the fitness cost of having unbalanced gene copies and the potential fitness gained from increased dosage of specific advantageous genes. Trypanosomatids, a family of protozoans that include species that cause neglected tropical diseases, are a relevant group to study aneuploidies. Their life cycle has several stressors that could select for different patterns of chromosomal duplications and/or losses, and their nearly universal use of polycistronic transcription increases their reliance on gene expansion/contraction, as well as post-transcriptional control as mechanisms for gene expression regulation. By evaluating the data from 866 isolates covering seven trypanosomatid genera, we have revealed that aneuploidy tolerance is an ancestral characteristic of trypanosomatids but has a reduced occurrence in a specific monophyletic clade that has undergone large genomic reorganization and chromosomal fusions. We have also identified an ancient chromosomal duplication that was maintained across these parasite's speciation, named collectively as the trypanosomatid ancestral supernumerary chromosome (TASC). TASC has most genes in the same coding strand, is expressed as a disomic chromosome (even having four copies), and has increased potential for functional variation, but it purges highly deleterious mutations more efficiently than other chromosomes. The evidence of stringent control over gene expression in this chromosome suggests that these parasites have adapted to mitigate the fitness cost associated with this ancient chromosomal duplication.},
}

*Aneuploidy
*Chromosome Duplication
*Gene Expression Regulation
*Genome, Protozoan
Evolution, Molecular
Trypanosomatina/genetics
Phylogeny

@article {pmid38553457,
year = {2024},
author = {Kapsetaki, SE and Cisneros, LH and Maley, CC},
title = {Cell-in-cell phenomena across the tree of life.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {7535},
pmid = {38553457},
issn = {2045-2322},
support = {U54 CA217376/CA/NCI NIH HHS/United States ; U2C CA233254/CA/NCI NIH HHS/United States ; U54 CA217376/GF/NIH HHS/United States ; R01 CA140657/CA/NCI NIH HHS/United States ; R21 CA257980/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Child, Preschool ; *Biological Evolution ; *Neoplasms ; },
abstract = {Cells in obligately multicellular organisms by definition have aligned fitness interests, minimum conflict, and cannot reproduce independently. However, some cells eat other cells within the same body, sometimes called cell cannibalism. Such cell-in-cell events have not been thoroughly discussed in the framework of major transitions to multicellularity. We performed a systematic screening of 508 articles, from which we chose 115 relevant articles in a search for cell-in-cell events across the tree of life, the age of cell-in-cell-related genes, and whether cell-in-cell events are associated with normal multicellular development or cancer. Cell-in-cell events are found across the tree of life, from some unicellular to many multicellular organisms, including non-neoplastic and neoplastic tissue. Additionally, out of the 38 cell-in-cell-related genes found in the literature, 14 genes were over 2.2 billion years old, i.e., older than the common ancestor of some facultatively multicellular taxa. All of this suggests that cell-in-cell events may have originated before the origins of obligate multicellularity. Thus, our results show that cell-in-cell events exist in obligate multicellular organisms, but are not a defining feature of them. The idea of eradicating cell-in-cell events from obligate multicellular organisms as a way of treating cancer, without considering that cell-in-cell events are also part of normal development, should be abandoned.},
}

Humans
Child, Preschool
*Biological Evolution
*Neoplasms

@article {pmid38547507,
year = {2024},
author = {Odelgard, A and Hägglund, E and Guy, L and Andersson, SGE},
title = {Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota.},
journal = {Genome biology and evolution},
volume = {16},
number = {4},
pages = {},
pmid = {38547507},
issn = {1759-6653},
support = {//Swedish Research Council/ ; 2017.0322//Knut and Alice Wallenberg Foundation/ ; },
mesh = {*Protein Serine-Threonine Kinases/genetics/metabolism ; Phylogeny ; *Planctomycetes ; Proteome/genetics ; Bacteria/genetics/metabolism ; Threonine/genetics ; Serine/genetics ; },
abstract = {The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that "Ca. Uabimicrobium amorphum" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in "Ca. Uabimicrobium amorphum", of which 66 families contained eukaryotic-like Serine/Threonine kinases with Pkinase domains. In total, we predicted 525 functional Serine/Threonine kinases in "Ca. Uabimicrobium amorphum", which represent 8% of the proteome and is the highest fraction of Serine/Threonine kinases in a bacterial proteome. The majority of Serine/Threonine kinases in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the Serine/Threonine kinases of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the Serine/Threonine kinases in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the Serine/Threonine kinases in "Ca. Uabimicrobium amorphum". The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.},
}

*Protein Serine-Threonine Kinases/genetics/metabolism
Phylogeny
*Planctomycetes
Proteome/genetics
Bacteria/genetics/metabolism
Threonine/genetics
Serine/genetics

@article {pmid38531970,
year = {2024},
author = {Domazet-Lošo, M and Široki, T and Šimičević, K and Domazet-Lošo, T},
title = {Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2663},
pmid = {38531970},
issn = {2041-1723},
support = {IP-2016-06-5924//Hrvatska Zaklada za Znanost (Croatian Science Foundation)/ ; KK.01.1.1.01.0009 DATACROSS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; },
mesh = {*Biological Evolution ; *Genome ; Phylogeny ; Evolution, Molecular ; },
abstract = {The gain and loss of genes fluctuate over evolutionary time in major eukaryotic clades. However, the full profile of these macroevolutionary trajectories is still missing. To give a more inclusive view on the changes in genome complexity across the tree of life, here we recovered the evolutionary dynamics of gene family gain and loss ranging from the ancestor of cellular organisms to 352 eukaryotic species. We show that in all considered lineages the gene family content follows a common evolutionary pattern, where the number of gene families reaches the highest value at a major evolutionary and ecological transition, and then gradually decreases towards extant organisms. This supports theoretical predictions and suggests that the genome complexity is often decoupled from commonly perceived organismal complexity. We conclude that simplification by gene family loss is a dominant force in Phanerozoic genomes of various lineages, probably underpinned by intense ecological specializations and functional outsourcing.},
}

*Biological Evolution
*Genome
Phylogeny
Evolution, Molecular

@article {pmid38519635,
year = {2024},
author = {},
title = {Multicellularity drives ecological diversity in a long-term evolution experiment.},
journal = {Nature ecology & evolution},
volume = {8},
number = {5},
pages = {856-857},
pmid = {38519635},
issn = {2397-334X},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; },
mesh = {*Biological Evolution ; *Biodiversity ; Animals ; },
}

*Biological Evolution
*Biodiversity
Animals

@article {pmid38514634,
year = {2024},
author = {Carreira de Paula, J and García Olmedo, P and Gómez-Moracho, T and Buendía-Abad, M and Higes, M and Martín-Hernández, R and Osuna, A and de Pablos, LM},
title = {Promastigote EPS secretion and haptomonad biofilm formation as evolutionary adaptations of trypanosomatid parasites for colonizing honeybee hosts.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {27},
pmid = {38514634},
issn = {2055-5008},
mesh = {Humans ; Bees ; Animals ; *Parasites ; Ecosystem ; *Trypanosomatina/parasitology ; Biological Evolution ; },
abstract = {Bees are major pollinators involved in the maintenance of all terrestrial ecosystems. Biotic and abiotic factors placing these insects at risk is a research priority for ecological and agricultural sustainability. Parasites are one of the key players of this global decline and the study of their mechanisms of action is essential to control honeybee colony losses. Trypanosomatid parasites and particularly the Lotmaria passim are widely spread in honeybees, however their lifestyle is poorly understood. In this work, we show how these parasites are able to differentiate into a new parasitic lifestyle: the trypanosomatid biofilms. Using different microscopic techniques, we demonstrated that the secretion of Extracellular Polymeric Substances by free-swimming unicellular promastigote forms is a prerequisite for the generation and adherence of multicellular biofilms to solid surfaces in vitro and in vivo. Moreover, compared to human-infective trypanosomatid parasites our study shows how trypanosomatid parasites of honeybees increases their resistance and thus resilience to drastic changes in environmental conditions such as ultralow temperatures and hypoosmotic shock, which would explain their success thriving within or outside their hosts. These results set up the basis for the understanding of the success of this group of parasites in nature and to unveil the impact of such pathogens in honeybees, a keystones species in most terrestrial ecosystems.},
}

Humans
Bees
Animals
*Parasites
Ecosystem
*Trypanosomatina/parasitology
Biological Evolution

@article {pmid38513029,
year = {2024},
author = {Luthringer, R and Raphalen, M and Guerra, C and Colin, S and Martinho, C and Zheng, M and Hoshino, M and Badis, Y and Lipinska, AP and Haas, FB and Barrera-Redondo, J and Alva, V and Coelho, SM},
title = {Repeated co-option of HMG-box genes for sex determination in brown algae and animals.},
journal = {Science (New York, N.Y.)},
volume = {383},
number = {6689},
pages = {eadk5466},
doi = {10.1126/science.adk5466},
pmid = {38513029},
issn = {1095-9203},
mesh = {Animals ; Biological Evolution ; *Phaeophyceae/genetics ; *Sex Chromosomes/genetics ; *Sex Determination Processes/genetics ; Y Chromosome ; *HMGB Proteins/genetics ; Chromosomes, Plant/genetics ; HMG-Box Domains ; *Edible Seaweeds/genetics ; *Laminaria/genetics ; Pollen/genetics ; },
abstract = {In many eukaryotes, genetic sex determination is not governed by XX/XY or ZW/ZZ systems but by a specialized region on the poorly studied U (female) or V (male) sex chromosomes. Previous studies have hinted at the existence of a dominant male-sex factor on the V chromosome in brown algae, a group of multicellular eukaryotes distantly related to animals and plants. The nature of this factor has remained elusive. Here, we demonstrate that an HMG-box gene acts as the male-determining factor in brown algae, mirroring the role HMG-box genes play in sex determination in animals. Over a billion-year evolutionary timeline, these lineages have independently co-opted the HMG box for male determination, representing a paradigm for evolution's ability to recurrently use the same genetic "toolkit" to accomplish similar tasks.},
}

Animals
Biological Evolution
*Phaeophyceae/genetics
*Sex Chromosomes/genetics
*Sex Determination Processes/genetics
Y Chromosome
*HMGB Proteins/genetics
Chromosomes, Plant/genetics
HMG-Box Domains
*Edible Seaweeds/genetics
*Laminaria/genetics
Pollen/genetics

@article {pmid38498818,
year = {2024},
author = {Bozdag, GO and Szeinbaum, N and Conlin, PL and Chen, K and Fos, SM and Garcia, A and Penev, PI and Schaible, GA and Trubl, G},
title = {Chapter 5: Major Biological Innovations in the History of Life on Earth.},
journal = {Astrobiology},
volume = {24},
number = {S1},
pages = {S107-S123},
pmid = {38498818},
issn = {1557-8070},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; },
mesh = {Phylogeny ; *Biological Evolution ; *Earth, Planet ; Oxygen ; Photosynthesis ; },
abstract = {All organisms living on Earth descended from a single, common ancestral population of cells, known as LUCA-the last universal common ancestor. Since its emergence, the diversity and complexity of life have increased dramatically. This chapter focuses on four key biological innovations throughout Earth's history that had a significant impact on the expansion of phylogenetic diversity, organismal complexity, and ecospace habitation. First is the emergence of the last universal common ancestor, LUCA, which laid the foundation for all life-forms on Earth. Second is the evolution of oxygenic photosynthesis, which resulted in global geochemical and biological transformations. Third is the appearance of a new type of cell-the eukaryotic cell-which led to the origin of a new domain of life and the basis for complex multicellularity. Fourth is the multiple independent origins of multicellularity, resulting in the emergence of a new level of complex individuality. A discussion of these four key events will improve our understanding of the intertwined history of our planet and its inhabitants and better inform the extent to which we can expect life at different degrees of diversity and complexity elsewhere.},
}

Phylogeny
*Biological Evolution
*Earth, Planet
Oxygen
Photosynthesis

@article {pmid38497809,
year = {2024},
author = {Hörandl, E},
title = {Apomixis and the paradox of sex in plants.},
journal = {Annals of botany},
volume = {134},
number = {1},
pages = {1-18},
pmid = {38497809},
issn = {1095-8290},
support = {HO 4395/10-2//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Apomixis/genetics/physiology ; *Magnoliopsida/genetics/physiology ; Reproduction, Asexual ; Biological Evolution ; Ferns/genetics/physiology ; Reproduction/physiology ; Phylogeny ; Meiosis ; Plants/genetics ; },
abstract = {BACKGROUND: The predominance of sex in eukaryotes, despite the high costs of meiosis and mating, remains an evolutionary enigma. Many theories have been proposed, none of them being conclusive on its own, and they are, in part, not well applicable to land plants. Sexual reproduction is obligate in embryophytes for the great majority of species.

SCOPE: This review compares the main forms of sexual and asexual reproduction in ferns and angiosperms, based on the generation cycling of sporophyte and gametophyte (leaving vegetative propagation aside). The benefits of sexual reproduction for maintenance of genomic integrity in comparison to asexuality are discussed in the light of developmental, evolutionary, genetic and phylogenetic studies.

CONCLUSIONS: Asexual reproduction represents modifications of the sexual pathway, with various forms of facultative sexuality. For sexual land plants, meiosis provides direct DNA repair mechanisms for oxidative damage in reproductive tissues. The ploidy alternations of meiosis-syngamy cycles and prolonged multicellular stages in the haploid phase in the gametophytes provide a high efficiency of purifying selection against recessive deleterious mutations. Asexual lineages might buffer effects of such mutations via polyploidy and can purge the mutational load via facultative sexuality. The role of organelle-nuclear genome compatibility for maintenance of genome integrity is not well understood. In plants in general, the costs of mating are low because of predominant hermaphroditism. Phylogenetic patterns in the archaeplastid clade suggest that high frequencies of sexuality in land plants are concomitant with a stepwise increase of intrinsic and extrinsic stress factors. Furthermore, expansion of genome size in land plants would increase the potential mutational load. Sexual reproduction appears to be essential for keeping long-term genomic integrity, and only rare combinations of extrinsic and intrinsic factors allow for shifts to asexuality.},
}

*Apomixis/genetics/physiology
*Magnoliopsida/genetics/physiology
Reproduction, Asexual
Biological Evolution
Ferns/genetics/physiology
Reproduction/physiology
Phylogeny
Meiosis
Plants/genetics

@article {pmid38471558,
year = {2024},
author = {Jung, J and Loschko, T and Reich, S and Rassoul-Agha, M and Werner, MS},
title = {Newly identified nematodes from the Great Salt Lake are associated with microbialites and specially adapted to hypersaline conditions.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2018},
pages = {20232653},
pmid = {38471558},
issn = {1471-2954},
mesh = {Animals ; *Ecosystem ; Lakes/chemistry ; Phylogeny ; *Nematoda ; Bacteria ; },
abstract = {Extreme environments enable the study of simplified food-webs and serve as models for evolutionary bottlenecks and early Earth ecology. We investigated the biodiversity of invertebrate meiofauna in the benthic zone of the Great Salt Lake (GSL), Utah, USA, one of the most hypersaline lake systems in the world. The hypersaline bays within the GSL are currently thought to support only two multicellular animals: brine fly larvae and brine shrimp. Here, we report the presence, habitat, and microbial interactions of novel free-living nematodes. Nematode diversity drops dramatically along a salinity gradient from a freshwater river into the south arm of the lake. In Gilbert Bay, nematodes primarily inhabit reef-like organosedimentary structures built by bacteria called microbialites. These structures likely provide a protective barrier to UV and aridity, and bacterial associations within them may support life in hypersaline environments. Notably, sampling from Owens Lake, another terminal lake in the Great Basin that lacks microbialites, did not recover nematodes from similar salinities. Phylogenetic divergence suggests that GSL nematodes represent previously undescribed members of the family Monhysteridae-one of the dominant fauna of the abyssal zone and deep-sea hydrothermal vents. These findings update our understanding of halophile ecosystems and the habitable limit of animals.},
}

Animals
*Ecosystem
Lakes/chemistry
Phylogeny
*Nematoda
Bacteria

@article {pmid38462458,
year = {2023},
author = {Libertini, G},
title = {Phenoptosis and the Various Types of Natural Selection.},
journal = {Biochemistry. Biokhimiia},
volume = {88},
number = {12},
pages = {2007-2022},
doi = {10.1134/S0006297923120052},
pmid = {38462458},
issn = {1608-3040},
mesh = {Animals ; Bees ; *Aging/genetics ; Ecosystem ; Selection, Genetic ; *Ants ; Reproduction ; Biological Evolution ; },
abstract = {In the first description of evolution, the fundamental mechanism is the natural selection favoring the individuals best suited for survival and reproduction (selection at the individual level or classical Darwinian selection). However, this is a very reductive description of natural selection that does not consider or explain a long series of known phenomena, including those in which an individual sacrifices or jeopardizes his life on the basis of genetically determined mechanisms (i.e., phenoptosis). In fact, in addition to (i) selection at the individual level, it is essential to consider other types of natural selection such as those concerning: (ii) kin selection and some related forms of group selection; (iii) the interactions between the innumerable species that constitute a holobiont; (iv) the origin of the eukaryotic cell from prokaryotic organisms; (v) the origin of multicellular eukaryotic organisms from unicellular organisms; (vi) eusociality (e.g., in many species of ants, bees, termites); (vii) selection at the level of single genes, or groups of genes; (viii) the interactions between individuals (or more precisely their holobionts) of the innumerable species that make up an ecosystem. These forms of natural selection, which are all effects and not violations of the classical Darwinian selection, also show how concepts as life, species, individual, and phenoptosis are somewhat not entirely defined and somehow arbitrary. Furthermore, the idea of organisms selected on the basis of their survival and reproduction capabilities is intertwined with that of organisms also selected on the basis of their ability to cooperate and interact, even by losing their lives or their distinct identities.},
}

Animals
Bees
*Aging/genetics
Ecosystem
Selection, Genetic
*Ants
Reproduction
Biological Evolution

@article {pmid38459017,
year = {2024},
author = {Stanojković, A and Skoupý, S and Johannesson, H and Dvořák, P},
title = {The global speciation continuum of the cyanobacterium Microcoleus.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2122},
pmid = {38459017},
issn = {2041-1723},
support = {19-12994Y//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 23-06507S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; },
mesh = {*Genetic Speciation ; *Genetic Drift ; Gene Flow ; Genome ; Phylogeny ; },
abstract = {Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium Microcoleus. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that Microcoleus represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.},
}

*Genetic Speciation
*Genetic Drift
Gene Flow
Genome
Phylogeny

@article {pmid38447933,
year = {2024},
author = {Park, S and Cho, SW},
title = {Bioengineering toolkits for potentiating organoid therapeutics.},
journal = {Advanced drug delivery reviews},
volume = {208},
number = {},
pages = {115238},
doi = {10.1016/j.addr.2024.115238},
pmid = {38447933},
issn = {1872-8294},
mesh = {Animals ; Mice ; *Organoids ; Tissue Engineering/methods ; Regenerative Medicine ; Bioengineering ; *Neoplasms ; },
abstract = {Organoids are three-dimensional, multicellular constructs that recapitulate the structural and functional features of specific organs. Because of these characteristics, organoids have been widely applied in biomedical research in recent decades. Remarkable advancements in organoid technology have positioned them as promising candidates for regenerative medicine. However, current organoids still have limitations, such as the absence of internal vasculature, limited functionality, and a small size that is not commensurate with that of actual organs. These limitations hinder their survival and regenerative effects after transplantation. Another significant concern is the reliance on mouse tumor-derived matrix in organoid culture, which is unsuitable for clinical translation due to its tumor origin and safety issues. Therefore, our aim is to describe engineering strategies and alternative biocompatible materials that can facilitate the practical applications of organoids in regenerative medicine. Furthermore, we highlight meaningful progress in organoid transplantation, with a particular emphasis on the functional restoration of various organs.},
}

Animals
Mice
*Organoids
Tissue Engineering/methods
Regenerative Medicine
Bioengineering
*Neoplasms

@article {pmid38424063,
year = {2024},
author = {Bayer, EM and Benitez-Alfonso, Y},
title = {Plasmodesmata: Channels Under Pressure.},
journal = {Annual review of plant biology},
volume = {75},
number = {1},
pages = {291-317},
doi = {10.1146/annurev-arplant-070623-093110},
pmid = {38424063},
issn = {1545-2123},
support = {MR/T04263X/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Plasmodesmata/metabolism/physiology ; *Cell Communication ; Plant Development/physiology ; Plants/metabolism ; Plant Physiological Phenomena ; },
abstract = {Multicellularity has emerged multiple times in evolution, enabling groups of cells to share a living space and reducing the burden of solitary tasks. While unicellular organisms exhibit individuality and independence, cooperation among cells in multicellular organisms brings specialization and flexibility. However, multicellularity also necessitates intercellular dependence and relies on intercellular communication. In plants, this communication is facilitated by plasmodesmata: intercellular bridges that allow the direct (cytoplasm-to-cytoplasm) transfer of information between cells. Plasmodesmata transport essential molecules that regulate plant growth, development, and stress responses. They are embedded in the extracellular matrix but exhibit flexibility, adapting intercellular flux to meet the plant's needs.In this review, we delve into the formation and functionality of plasmodesmata and examine the capacity of the plant communication network to respond to developmental and environmental cues. We illustrate how environmental pressure shapes cellular interactions and aids the plant in adapting its growth.},
}

*Plasmodesmata/metabolism/physiology
*Cell Communication
Plant Development/physiology
Plants/metabolism
Plant Physiological Phenomena

@article {pmid38400751,
year = {2024},
author = {Woudenberg, S and Hadid, F and Weijers, D and Borassi, C},
title = {The maternal embrace: the protection of plant embryos.},
journal = {Journal of experimental botany},
volume = {75},
number = {14},
pages = {4210-4218},
pmid = {38400751},
issn = {1460-2431},
support = {//Graduate School Experimental Plant Sciences/ ; /ERC_/European Research Council/International ; ENW-KLEIN2//Netherlands Organization for Scientific Research/ ; },
mesh = {*Seeds/growth & development ; Embryophyta/growth & development ; Biological Evolution ; },
abstract = {All land plants-the embryophytes-produce multicellular embryos, as do other multicellular organisms, such as brown algae and animals. A unique characteristic of plant embryos is their immobile and confined nature. Their embedding in maternal tissues may offer protection from the environment, but also physically constrains development. Across the different land plants, a huge discrepancy is present between their reproductive structures whilst leading to similarly complex embryos. Therefore, we review the roles that maternal tissues play in the control of embryogenesis across land plants. These nurturing, constraining, and protective roles include both direct and indirect effects. In this review, we explore how the maternal surroundings affect embryogenesis and which chemical and mechanical barriers are in place. We regard these questions through the lens of evolution, and identify key questions for future research.},
}

*Seeds/growth & development
Embryophyta/growth & development
Biological Evolution

@article {pmid38388648,
year = {2024},
author = {Ratajczak, MZ and Ratajczak, J},
title = {Leukemogenesis occurs in a microenvironment enriched by extracellular microvesicles/exosomes: recent discoveries and questions to be answered.},
journal = {Leukemia},
volume = {38},
number = {4},
pages = {692-698},
pmid = {38388648},
issn = {1476-5551},
support = {R01 DK074720/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Exosomes/metabolism ; *Cell-Derived Microparticles ; Cell Communication ; Signal Transduction ; Proteins/metabolism ; *Extracellular Vesicles/metabolism ; },
abstract = {In single-cell organisms, extracellular microvesicles (ExMVs) were one of the first cell-cell communication platforms that emerged very early during evolution. Multicellular organisms subsequently adapted this mechanism. Evidence indicates that all types of cells secrete these small circular structures surrounded by a lipid membrane that may be encrusted by ligands and receptors interacting with target cells and harboring inside a cargo comprising RNA species, proteins, bioactive lipids, signaling nucleotides, and even entire organelles "hijacked" from the cells of origin. ExMVs are secreted by normal cells and at higher levels by malignant cells, and there are some differences in their cargo. On the one hand, ExMVs secreted from malignant cells interact with cells in the microenvironment, and in return, they are exposed by a "two-way mechanism" to ExMVs secreted by non-leukemic cells. Therefore, leukemogenesis occurs and progresses in ExMVs enriched microenvironments, and this biological fact has pathologic, diagnostic, and therapeutic implications. We are still trying to decipher this intriguing cell-cell communication language better. We will present a current point of view on this topic and review some selected most recent discoveries and papers.},
}

Humans
*Exosomes/metabolism
*Cell-Derived Microparticles
Cell Communication
Signal Transduction
Proteins/metabolism
*Extracellular Vesicles/metabolism

@article {pmid38386708,
year = {2024},
author = {Ilker, E and Hinczewski, M},
title = {Bioenergetic costs and the evolution of noise regulation by microRNAs.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {9},
pages = {e2308796121},
pmid = {38386708},
issn = {1091-6490},
mesh = {*Eukaryota ; *MicroRNAs/genetics ; Mutant Proteins ; RNA, Messenger ; Energy Metabolism/genetics ; },
abstract = {Noise control, together with other regulatory functions facilitated by microRNAs (miRNAs), is believed to have played important roles in the evolution of multicellular eukaryotic organisms. miRNAs can dampen protein fluctuations via enhanced degradation of messenger RNA (mRNA), but this requires compensation by increased mRNA transcription to maintain the same expression levels. The overall mechanism is metabolically expensive, leading to questions about how it might have evolved in the first place. We develop a stochastic model of miRNA noise regulation, coupled with a detailed analysis of the associated metabolic costs. Additionally, we calculate binding free energies for a range of miRNA seeds, the short sequences which govern target recognition. We argue that natural selection may have fine-tuned the Michaelis-Menten constant [Formula: see text] describing miRNA-mRNA affinity and show supporting evidence from analysis of experimental data. [Formula: see text] is constrained by seed length, and optimal noise control (minimum protein variance at a given energy cost) is achievable for seeds of 6 to 7 nucleotides in length, the most commonly observed types. Moreover, at optimality, the degree of noise reduction approaches the theoretical bound set by the Wiener-Kolmogorov linear filter. The results illustrate how selective pressure toward energy efficiency has potentially shaped a crucial regulatory pathway in eukaryotes.},
}

*Eukaryota
*MicroRNAs/genetics
Mutant Proteins
RNA, Messenger
Energy Metabolism/genetics

@article {pmid38385784,
year = {2024},
author = {Hesse, E and O'Brien, S},
title = {Ecological dependencies and the illusion of cooperation in microbial communities.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {2},
pages = {},
pmid = {38385784},
issn = {1465-2080},
mesh = {Humans ; *Illusions ; *Microbiota ; Amino Acids ; Biological Evolution ; Nitrogen ; },
abstract = {Ecological dependencies - where organisms rely on other organisms for survival - are a ubiquitous feature of life on earth. Multicellular hosts rely on symbionts to provide essential vitamins and amino acids. Legume plants similarly rely on nitrogen-fixing rhizobia to convert atmospheric nitrogen to ammonia. In some cases, dependencies can arise via loss-of-function mutations that allow one partner to benefit from the actions of another. It is common in microbiology to label ecological dependencies between species as cooperation - making it necessary to invoke cooperation-specific frameworks to explain the phenomenon. However, in many cases, such traits are not (at least initially) cooperative, because they are not selected for because of the benefits they confer on a partner species. In contrast, dependencies in microbial communities may originate from fitness benefits gained from genomic-streamlining (i.e. Black Queen Dynamics). Here, we outline how the Black Queen Hypothesis predicts the formation of metabolic dependencies via loss-of-function mutations in microbial communities, without needing to invoke any cooperation-specific explanations. Furthermore we outline how the Black Queen Hypothesis can act as a blueprint for true cooperation as well as discuss key outstanding questions in the field. The nature of interactions in microbial communities can predict the ability of natural communities to withstand and recover from disturbances. Hence, it is vital to gain a deeper understanding of the factors driving these dynamic interactions over evolutionary time.},
}

Humans
*Illusions
*Microbiota
Amino Acids
Biological Evolution
Nitrogen

@article {pmid38382824,
year = {2024},
author = {Mikhailovsky, GE},
title = {Life, its definition, origin, evolution, and four-dimensional hierarchical structure.},
journal = {Bio Systems},
volume = {237},
number = {},
pages = {105158},
doi = {10.1016/j.biosystems.2024.105158},
pmid = {38382824},
issn = {1872-8324},
mesh = {*Biological Evolution ; Thermodynamics ; *Eukaryota ; Prokaryotic Cells ; },
abstract = {The main unique features of biological systems are reviewed, and four necessary and sufficient attributes of life are formulated, based on the ideas of Ervin Bauer. The possibility of the occurrence of each of these attributes during the origin of life is analyzed. As a result, different scenarios for the origin of life are presented, with their pros and cons. Next, the mainstream of biological evolution is discussed, considering it as a special case of general complexification, and structuredness is defined as a quantitative measure of structural complexity. By introducing the concepts of post-dissipative structure and ratcheting process based on "frozen" patterns, their role in the generation of biological structures underlying biological evolution is demonstrated. Furthermore, it is proposed that all living things can be divided into micro- (unicellular) and macro- (multicellular) creatures, which differ from each other even more radically than the difference between prokaryotes and unicellular eukaryotes. Then the fifth, sufficient, but not necessary attribute of life, hierarchicality, is formulated, which is fully applicable only to macrolife. It is also shown that living organisms are primarily chemodynamic rather than thermodynamic systems, and three basic laws of biochemodynamics are formulated. Finally, fifteen basic features of living beings, grouped into four basic blocks, are summarized.},
}

*Biological Evolution
Thermodynamics
*Eukaryota
Prokaryotic Cells

@article {pmid38377113,
year = {2024},
author = {Nino Barreat, JG and Katzourakis, A},
title = {Ecological and evolutionary dynamics of cell-virus-virophage systems.},
journal = {PLoS computational biology},
volume = {20},
number = {2},
pages = {e1010925},
pmid = {38377113},
issn = {1553-7358},
mesh = {Humans ; *Virophages ; Apoptosis ; Biological Evolution ; *Coinfection ; Antiviral Agents ; },
abstract = {Microbial eukaryotes, giant viruses and virophages form a unique hyperparasitic system. Virophages are parasites of the virus transcription machinery and can interfere with virus replication, resulting in a benefit to the eukaryotic host population. Surprisingly, virophages can integrate into the genomes of their cell or virus hosts, and have been shown to reactivate during coinfection. This raises questions about the role of integration in the dynamics of cell-virus-virophage systems. We use mathematical models and computational simulations to understand the effect of virophage integration on populations of cells and viruses. We also investigate multicellularity and programmed cell-death (PCD) as potential antiviral defence strategies used by cells. We found that virophages which enter the cell independently of the host virus, such as Mavirus, are expected to integrate commonly into the genomes of their cell hosts. Our models suggest that integrations from virophages without an independent mode of entry like Sputnik, are less likely to become fixed in the cell host population. Alternatively, we found that Sputnik virophages can stably persist integrated in the virus population, as long as they do not completely inhibit virus replication. We also show that increasing virophage inhibition can stabilise oscillatory dynamics, which may explain the long-term persistence of viruses and virophages in the environment. Our results demonstrate that inhibition by virophages and multicellularity are effective antiviral strategies that may act in synergy against viral infection in microbial species.},
}

Humans
*Virophages
Apoptosis
Biological Evolution
*Coinfection
Antiviral Agents

@article {pmid38375870,
year = {2024},
author = {Edelbroek, B and Kjellin, J and Biryukova, I and Liao, Z and Lundberg, T and Noegel, AA and Eichinger, L and Friedländer, MR and Söderbom, F},
title = {Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity.},
journal = {Nucleic acids research},
volume = {52},
number = {6},
pages = {3121-3136},
pmid = {38375870},
issn = {1362-4962},
support = {2021-05793//Swedish Research Council/ ; //Uppsala University/ ; },
mesh = {*Amoebozoa/classification/genetics ; Dictyostelium/genetics ; *MicroRNAs/genetics ; Phylogeny ; *Evolution, Molecular ; *RNA, Protozoan/genetics ; Conserved Sequence/genetics ; RNA Interference ; },
abstract = {MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, expanding the total number of protists harbouring miRNAs from 7 to 15. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. This shows rapid gain and/or loss of miRNAs in Amoebozoa, further illustrated by a detailed comparison between two evolutionary closely related dictyostelids. Additionally, loss of miRNAs in the Dictyostelium discoideum drnB mutant did not seem to affect multicellular development and, hence, demonstrates that the presence of miRNAs does not appear to be a strict requirement for the transition from uni- to multicellular life.},
}

*Amoebozoa/classification/genetics
Dictyostelium/genetics
*MicroRNAs/genetics
Phylogeny
*Evolution, Molecular
*RNA, Protozoan/genetics
Conserved Sequence/genetics
RNA Interference

@article {pmid38352462,
year = {2024},
author = {Kidner, RQ and Goldstone, EB and Laidemitt, MR and Sanchez, MC and Gerdt, C and Brokaw, LP and Ros-Rocher, N and Morris, J and Davidson, WS and Gerdt, JP},
title = {Host lipids regulate multicellular behavior of a predator of a human pathogen.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38352462},
issn = {2692-8205},
support = {R37 AI101438/AI/NIAID NIH HHS/United States ; R01 HL062542/HL/NHLBI NIH HHS/United States ; T32 GM131994/GM/NIGMS NIH HHS/United States ; S10 OD024988/OD/NIH HHS/United States ; P30 GM110907/GM/NIGMS NIH HHS/United States ; R35 GM138376/GM/NIGMS NIH HHS/United States ; HHSN272201700014C/AI/NIAID NIH HHS/United States ; },
abstract = {As symbionts of animals, microbial eukaryotes benefit and harm their hosts in myriad ways. A model microeukaryote (Capsaspora owczarzaki) is a symbiont of Biomphalaria glabrata snails and may prevent transmission of parasitic schistosomes from snails to humans. However, it is unclear which host factors determine Capsaspora's ability to colonize snails. Here, we discovered that Capsaspora forms multicellular aggregates when exposed to snail hemolymph. We identified a molecular cue for aggregation: a hemolymph-derived phosphatidylcholine, which becomes elevated in schistosome-infected snails. Therefore, Capsaspora aggregation may be a response to the physiological state of its host, and it may determine its ability to colonize snails and exclude parasitic schistosomes. Furthermore, Capsaspora is an evolutionary model organism whose aggregation may be ancestral to animals. This discovery, that a prevalent lipid induces Capsaspora multicellularity, suggests that this aggregation phenotype may be ancient. Additionally, the specific lipid will be a useful tool for further aggregation studies.},
}

@article {pmid38333966,
year = {2024},
author = {Bowles, AMC and Williamson, CJ and Williams, TA and Donoghue, PCJ},
title = {Cryogenian Origins of Multicellularity in Archaeplastida.},
journal = {Genome biology and evolution},
volume = {16},
number = {2},
pages = {},
pmid = {38333966},
issn = {1759-6653},
support = {RPG-2020-199//Leverhulme Trust/ ; NE/P013678/1//Natural Environment Research Council/ ; //Biosphere Evolution, Transitions and Resilience/ ; //Natural Science Foundation of China/ ; 62220//John Templeton Foundation/ ; GBMF9741//Gordon and Betty Moore Foundation/ ; URF\R\201024//University Research Fellowship to T.W/ ; },
mesh = {Phylogeny ; Biological Evolution ; Plants ; *Embryophyta ; *Chlorophyta ; Fossils ; Evolution, Molecular ; },
abstract = {Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the phylogeny and timescale of archaeplastid evolution. We infer a time-calibrated phylogeny of early archaeplastid evolution based on a revised molecular dataset and reappraisal of the fossil record. Phylogenetic topology testing resolves deep archaeplastid relationships, identifying two clades of Viridiplantae and placing Bryopsidales as sister to the Chlorophyceae. Our molecular clock analysis infers an origin of Archaeplastida in the late-Paleoproterozoic to early-Mesoproterozoic (1712 to 1387 Ma). Ancestral state reconstruction of cytomorphological traits on this time-calibrated tree reveals many of the independent origins of multicellularity span the Cryogenian, consistent with the Cryogenian multicellularity hypothesis. Multicellular rhodophytes emerged 902 to 655 Ma while crown-Anydrophyta (Zygnematophyceae and Embryophyta) originated 796 to 671 Ma, broadly compatible with the Cryogenian plant terrestrialization hypothesis. Our analyses resolve the timetree of Archaeplastida with age estimates for ancestral multicellular archaeplastids coinciding with the Cryogenian, compatible with hypotheses that propose a role of Snowball Earth in plant evolution.},
}

Phylogeny
Biological Evolution
Plants
*Embryophyta
*Chlorophyta
Fossils
Evolution, Molecular

@article {pmid38320478,
year = {2024},
author = {Donoghue, PCJ and Clark, JW},
title = {Plant evolution: Streptophyte multicellularity, ecology, and the acclimatisation of plants to life on land.},
journal = {Current biology : CB},
volume = {34},
number = {3},
pages = {R86-R89},
doi = {10.1016/j.cub.2023.12.036},
pmid = {38320478},
issn = {1879-0445},
support = {BB/T012773/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Plants ; Biological Evolution ; Phylogeny ; *Embryophyta ; Acclimatization ; },
abstract = {Land plants are celebrated as one of the three great instances of complex multicellularity, but new phylogenomic and phenotypic analyses are revealing deep evolutionary roots of multicellularity among algal relatives, prompting questions about the causal basis of this major evolutionary transition.},
}

*Plants
Biological Evolution
Phylogeny
*Embryophyta
Acclimatization

@article {pmid38315855,
year = {2024},
author = {Bingham, EP and Ratcliff, WC},
title = {A nonadaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {7},
pages = {e2319840121},
pmid = {38315855},
issn = {1091-6490},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; T32 GM142616/GM/NIGMS NIH HHS/United States ; },
mesh = {*Biological Evolution ; *Genetic Drift ; Eukaryota/genetics ; Genome ; Gene Expression Regulation ; },
abstract = {"Complex multicellularity," conventionally defined as large organisms with many specialized cell types, has evolved five times independently in eukaryotes, but never within prokaryotes. A number of hypotheses have been proposed to explain this phenomenon, most of which posit that eukaryotes evolved key traits (e.g., dynamic cytoskeletons, alternative mechanisms of gene regulation, or subcellular compartments) which were a necessary prerequisite for the evolution of complex multicellularity. Here, we propose an alternative, nonadaptive hypothesis for this broad macroevolutionary pattern. By binning cells into groups with finite genetic bottlenecks between generations, the evolution of multicellularity greatly reduces the effective population size (Ne) of cellular populations, increasing the role of genetic drift in evolutionary change. While both prokaryotes and eukaryotes experience this phenomenon, they have opposite responses to drift: eukaryotes tend to undergo genomic expansion, providing additional raw genetic material for subsequent multicellular innovation, while prokaryotes generally face genomic erosion. Taken together, we hypothesize that these idiosyncratic lineage-specific evolutionary dynamics play a fundamental role in the long-term divergent evolution of complex multicellularity across the tree of life.},
}

*Biological Evolution
*Genetic Drift
Eukaryota/genetics
Genome
Gene Expression Regulation

@article {pmid38306281,
year = {2024},
author = {Siljestam, M and Martinossi-Allibert, I},
title = {Anisogamy Does Not Always Promote the Evolution of Mating Competition Traits in Males.},
journal = {The American naturalist},
volume = {203},
number = {2},
pages = {230-253},
doi = {10.1086/727968},
pmid = {38306281},
issn = {1537-5323},
mesh = {Male ; Female ; Humans ; *Models, Biological ; *Biological Evolution ; Semen ; Reproduction ; Fertilization ; },
abstract = {AbstractAnisogamy has evolved in most sexually reproducing multicellular organisms allowing the definition of male and female sexes, producing small and large gametes. Anisogamy, as the initial sexual dimorphism, is a good starting point to understand the evolution of further sexual dimorphisms. For instance, it is generally accepted that anisogamy sets the stage for more intense mating competition in males than in females. We argue that this idea stems from a restrictive assumption on the conditions under which anisogamy evolved in the first place: the absence of sperm limitation (assuming that all female gametes are fertilized). Here, we relax this assumption and present a model that considers the coevolution of gamete size with a mating competition trait, starting in a population without dimorphism. We vary gamete density to produce different scenarios of gamete limitation. We show that while at high gamete density the evolution of anisogamy always results in male investment in competition, gamete limitation at intermediate gamete densities allows for either females or males to invest more into mating competition. Our results thus suggest that anisogamy does not always promote mating competition among males. The conditions under which anisogamy evolves matter, as does the competition trait.},
}

Male
Female
Humans
*Models, Biological
*Biological Evolution
Semen
Reproduction
Fertilization

@article {pmid38277698,
year = {2024},
author = {Krämer, U},
title = {Metal Homeostasis in Land Plants: A Perpetual Balancing Act Beyond the Fulfilment of Metalloproteome Cofactor Demands.},
journal = {Annual review of plant biology},
volume = {75},
number = {1},
pages = {27-65},
doi = {10.1146/annurev-arplant-070623-105324},
pmid = {38277698},
issn = {1545-2123},
mesh = {*Homeostasis ; *Metals/metabolism ; *Embryophyta/metabolism/physiology ; *Metalloproteins/metabolism ; Plant Proteins/metabolism ; },
abstract = {One of life's decisive innovations was to harness the catalytic power of metals for cellular chemistry. With life's expansion, global atmospheric and biogeochemical cycles underwent dramatic changes. Although initially harmful, they permitted the evolution of multicellularity and the colonization of land. In land plants as primary producers, metal homeostasis faces heightened demands, in part because soil is a challenging environment for nutrient balancing. To avoid both nutrient metal limitation and metal toxicity, plants must maintain the homeostasis of metals within tighter limits than the homeostasis of other minerals. This review describes the present model of protein metalation and sketches its transfer from unicellular organisms to land plants as complex multicellular organisms. The inseparable connection between metal and redox homeostasis increasingly draws our attention to more general regulatory roles of metals. Mineral co-option, the use of nutrient or other metals for functions other than nutrition, is an emerging concept beyond that of nutritional immunity.},
}

*Homeostasis
*Metals/metabolism
*Embryophyta/metabolism/physiology
*Metalloproteins/metabolism
Plant Proteins/metabolism

@article {pmid38271513,
year = {2024},
author = {Pennisi, E},
title = {Tiny fossils upend timeline of multicellular life.},
journal = {Science (New York, N.Y.)},
volume = {383},
number = {6681},
pages = {352-353},
doi = {10.1126/science.ado2396},
pmid = {38271513},
issn = {1095-9203},
mesh = {*Biological Evolution ; *Eukaryota ; *Fossils ; },
abstract = {Eukaryotes organized into multicellular forms 1.6 billion years ago.},
}

*Biological Evolution
*Eukaryota
*Fossils

@article {pmid38262417,
year = {2024},
author = {Choi, SW and Graf, L and Choi, JW and Jo, J and Boo, GH and Kawai, H and Choi, CG and Xiao, S and Knoll, AH and Andersen, RA and Yoon, HS},
title = {Ordovician origin and subsequent diversification of the brown algae.},
journal = {Current biology : CB},
volume = {34},
number = {4},
pages = {740-754.e4},
doi = {10.1016/j.cub.2023.12.069},
pmid = {38262417},
issn = {1879-0445},
mesh = {Phylogeny ; Eukaryota/genetics ; Plants ; *Rhodophyta/genetics ; Plastids/genetics ; *Phaeophyceae/genetics ; Evolution, Molecular ; },
abstract = {Brown algae are the only group of heterokont protists exhibiting complex multicellularity. Since their origin, brown algae have adapted to various marine habitats, evolving diverse thallus morphologies and gamete types. However, the evolutionary processes behind these transitions remain unclear due to a lack of a robust phylogenetic framework and problems with time estimation. To address these issues, we employed plastid genome data from 138 species, including heterokont algae, red algae, and other red-derived algae. Based on a robust phylogeny and new interpretations of algal fossils, we estimated the geological times for brown algal origin and diversification. The results reveal that brown algae first evolved true multicellularity, with plasmodesmata and reproductive cell differentiation, during the late Ordovician Period (ca. 450 Ma), coinciding with a major diversification of marine fauna (the Great Ordovician Biodiversification Event) and a proliferation of multicellular green algae. Despite its early Paleozoic origin, the diversification of major orders within this brown algal clade accelerated only during the Mesozoic Era, coincident with both Pangea rifting and the diversification of other heterokont algae (e.g., diatoms), coccolithophores, and dinoflagellates, with their red algal-derived plastids. The transition from ancestral isogamy to oogamy was followed by three simultaneous reappearances of isogamy during the Cretaceous Period. These are concordant with a positive character correlation between parthenogenesis and isogamy. Our new brown algal timeline, combined with a knowledge of past environmental conditions, shed new light on brown algal diversification and the intertwined evolution of multicellularity and sexual reproduction.},
}

Phylogeny
Eukaryota/genetics
Plants
*Rhodophyta/genetics
Plastids/genetics
*Phaeophyceae/genetics
Evolution, Molecular

@article {pmid38230926,
year = {2024},
author = {Corrales, J and Ramos-Alonso, L and González-Sabín, J and Ríos-Lombardía, N and Trevijano-Contador, N and Engen Berg, H and Sved Skottvoll, F and Moris, F and Zaragoza, O and Chymkowitch, P and Garcia, I and Enserink, JM},
title = {Characterization of a selective, iron-chelating antifungal compound that disrupts fungal metabolism and synergizes with fluconazole.},
journal = {Microbiology spectrum},
volume = {12},
number = {2},
pages = {e0259423},
pmid = {38230926},
issn = {2165-0497},
support = {182524, 208012//Kreftforeningen (NCS)/ ; 2017064, 2018012, 2019096//Ministry of Health and Care Services | Helse Sør-Øst RHF (sorost)/ ; 2017072//Ministry of Health and Care Services | Helse Sør-Øst RHF (sorost)/ ; 261936, 301268, 262652//Norges Forskningsråd (Forskningsrådet)/ ; PID2020-114546RB//Ministerio de Ciencia e Innovación (MCIN)/ ; },
mesh = {Animals ; Humans ; Antifungal Agents/pharmacology ; Fluconazole/pharmacology ; Iron ; Candida ; *Mycoses/microbiology ; Candida albicans ; *Anti-Infective Agents/pharmacology ; Azoles/pharmacology ; Candida glabrata ; Iron Chelating Agents/pharmacology ; Drug Resistance, Fungal ; Microbial Sensitivity Tests ; Mammals ; },
abstract = {Fungal infections are a growing global health concern due to the limited number of available antifungal therapies as well as the emergence of fungi that are resistant to first-line antimicrobials, particularly azoles and echinocandins. Development of novel, selective antifungal therapies is challenging due to similarities between fungal and mammalian cells. An attractive source of potential antifungal treatments is provided by ecological niches co-inhabited by bacteria, fungi, and multicellular organisms, where complex relationships between multiple organisms have resulted in evolution of a wide variety of selective antimicrobials. Here, we characterized several analogs of one such natural compound, collismycin A. We show that NR-6226C has antifungal activity against several pathogenic Candida species, including C. albicans and C. glabrata, whereas it only has little toxicity against mammalian cells. Mechanistically, NR-6226C selectively chelates iron, which is a limiting factor for pathogenic fungi during infection. As a result, NR-6226C treatment causes severe mitochondrial dysfunction, leading to formation of reactive oxygen species, metabolic reprogramming, and a severe reduction in ATP levels. Using an in vivo model for fungal infections, we show that NR-6226C significantly increases survival of Candida-infected Galleria mellonella larvae. Finally, our data indicate that NR-6226C synergizes strongly with fluconazole in inhibition of C. albicans. Taken together, NR-6226C is a promising antifungal compound that acts by chelating iron and disrupting mitochondrial functions.IMPORTANCEDrug-resistant fungal infections are an emerging global threat, and pan-resistance to current antifungal therapies is an increasing problem. Clearly, there is a need for new antifungal drugs. In this study, we characterized a novel antifungal agent, the collismycin analog NR-6226C. NR-6226C has a favorable toxicity profile for human cells, which is essential for further clinical development. We unraveled the mechanism of action of NR-6226C and found that it disrupts iron homeostasis and thereby depletes fungal cells of energy. Importantly, NR-6226C strongly potentiates the antifungal activity of fluconazole, thereby providing inroads for combination therapy that may reduce or prevent azole resistance. Thus, NR-6226C is a promising compound for further development into antifungal treatment.},
}

Animals
Humans
Antifungal Agents/pharmacology
Fluconazole/pharmacology
Iron
Candida
*Mycoses/microbiology
Candida albicans
*Anti-Infective Agents/pharmacology
Azoles/pharmacology
Candida glabrata
Iron Chelating Agents/pharmacology
Drug Resistance, Fungal
Microbial Sensitivity Tests
Mammals

@article {pmid38196363,
year = {2024},
author = {Howe, J and Cornwallis, CK and Griffin, AS},
title = {Conflict-reducing innovations in development enable increased multicellular complexity.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2014},
pages = {20232466},
pmid = {38196363},
issn = {1471-2954},
mesh = {Animals ; Phylogeny ; *Cognition ; Cell Division ; *Stem Cells ; },
abstract = {Obligately multicellular organisms, where cells can only reproduce as part of the group, have evolved multiple times across the tree of life. Obligate multicellularity has only evolved when clonal groups form by cell division, rather than by cells aggregating, as clonality prevents internal conflict. Yet obligately multicellular organisms still vary greatly in 'multicellular complexity' (the number of cells and cell types): some comprise a few cells and cell types, while others have billions of cells and thousands of types. Here, we test whether variation in multicellular complexity is explained by two conflict-suppressing mechanisms, namely a single-cell bottleneck at the start of development, and a strict separation of germline and somatic cells. Examining the life cycles of 129 lineages of plants, animals, fungi and algae, we show using phylogenetic comparative analyses that an early segregation of the germline stem-cell lineage is key to the evolution of more cell types, driven by a strong correlation in the Metazoa. By contrast, the presence of a strict single-cell bottleneck was not related to either the number of cells or the number of cell types, but was associated with early germline segregation. Our results suggest that segregating the germline earlier in development enabled greater evolutionary innovation, although whether this is a consequence of conflict reduction or other non-conflict effects, such as developmental flexibility, is unclear.},
}

Animals
Phylogeny
*Cognition
Cell Division
*Stem Cells

@article {pmid38196360,
year = {2024},
author = {Pequeno, PACL},
title = {Resource adaptation drives the size-complexity rule in termites.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2014},
pages = {20232363},
pmid = {38196360},
issn = {1471-2954},
mesh = {Animals ; *Isoptera ; Food ; *Infertility ; Phenotype ; Phylogeny ; },
abstract = {The size-complexity rule posits that the evolution of larger cooperative groups should favour more division of labour. Examples include more cell types in larger multicellular organisms, and more polymorphic castes in larger eusocial colonies. However, a correlation between division of labour and group size may reflect a shared response of both traits to resource availability and/or profitability. Here, this possibility was addressed by investigating the evolution of sterile caste number (worker and soldier morphotypes) in termites, a major clade of eusocial insects in which the drivers of caste polymorphism are poorly understood. A novel dataset on 90 termite species was compiled from the published literature. The analysis showed that sterile caste number did increase markedly with colony size. However, after controlling for resource adaptations and phylogeny, there was no evidence for this relationship. Rather, sterile caste number increased with increasing nest-food separation and decreased with soil-feeding, through changes in worker (but not soldier) morphotype number. Further, colony size increased with nest-food separation, thus driving the false correlation between sterile caste number and colony size. These findings support adaptation to higher energy acquisition as key to the rise of complex insect societies, with larger size being a by-product.},
}

Animals
*Isoptera
Food
*Infertility
Phenotype
Phylogeny

@article {pmid38185860,
year = {2024},
author = {Roggenbuck, EC and Hall, EA and Hanson, IB and Roby, AA and Zhang, KK and Alkatib, KA and Carter, JA and Clewner, JE and Gelfius, AL and Gong, S and Gordon, FR and Iseler, JN and Kotapati, S and Li, M and Maysun, A and McCormick, EO and Rastogi, G and Sengupta, S and Uzoma, CU and Wolkov, MA and Clowney, EJ},
title = {Let's talk about sex: Mechanisms of neural sexual differentiation in Bilateria.},
journal = {WIREs mechanisms of disease},
volume = {16},
number = {2},
pages = {e1636},
doi = {10.1002/wsbm.1636},
pmid = {38185860},
issn = {2692-9368},
support = {//McKnight Scholar Award/ ; //Pew Biomedical Scholar Award/ ; //Rita Allen Foundation Scholar Award/ ; },
mesh = {Male ; Animals ; *Sex Differentiation ; *Semen ; Reproduction ; Germ Cells ; Spermatozoa ; },
abstract = {In multicellular organisms, sexed gonads have evolved that facilitate release of sperm versus eggs, and bilaterian animals purposefully combine their gametes via mating behaviors. Distinct neural circuits have evolved that control these physically different mating events for animals producing eggs from ovaries versus sperm from testis. In this review, we will describe the developmental mechanisms that sexually differentiate neural circuits across three major clades of bilaterian animals-Ecdysozoa, Deuterosomia, and Lophotrochozoa. While many of the mechanisms inducing somatic and neuronal sex differentiation across these diverse organisms are clade-specific rather than evolutionarily conserved, we develop a common framework for considering the developmental logic of these events and the types of neuronal differences that produce sex-differentiated behaviors. This article is categorized under: Congenital Diseases > Stem Cells and Development Neurological Diseases > Stem Cells and Development.},
}

Male
Animals
*Sex Differentiation
*Semen
Reproduction
Germ Cells
Spermatozoa

@article {pmid38175037,
year = {2024},
author = {Lyman, GH and Lyman, CH and Kuderer, NM},
title = {The Nature, Origin, and Evolution of Life: Part IV Cellular Differentiation and the Emergence of Multicellular Life.},
journal = {Cancer investigation},
volume = {42},
number = {4},
pages = {275-277},
doi = {10.1080/07357907.2024.2302201},
pmid = {38175037},
issn = {1532-4192},
mesh = {*Cell Differentiation ; Humans ; Biological Evolution ; Origin of Life ; Animals ; },
}

*Cell Differentiation
Humans
Biological Evolution
Origin of Life
Animals

@article {pmid38154271,
year = {2024},
author = {Kong, Z and Zhu, L and Liu, Y and Liu, Y and Chen, G and Jiang, T and Wang, H},
title = {Effects of azithromycin exposure during pregnancy at different stages, doses and courses on testicular development in fetal mice.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {170},
number = {},
pages = {116063},
doi = {10.1016/j.biopha.2023.116063},
pmid = {38154271},
issn = {1950-6007},
mesh = {Mice ; Male ; Female ; Pregnancy ; Animals ; *Azithromycin/toxicity ; *Testis ; Leydig Cells ; Sertoli Cells ; Fetus ; },
abstract = {Azithromycin is a commonly used antibiotic during pregnancy, but some studies have suggested its potential developmental toxicity. Currently, the effects and mechanisms of prenatal azithromycin exposure (PAzE) on fetal testicular development are still unclear. The effects of prenatal exposure to the same drug on fetal testicular development could vary depending on different stages, doses, and courses. Hence, in this study, based on clinical medication characteristics, Kunming mice was administered intragastrically with azithromycin at different stages (mid-/late-pregnancy), doses (50, 100, 200 mg/kg·d), and courses (single-/multi-course). Fetal blood and testicular samples were collected on GD18 for relevant assessments. The results indicated that PAzE led to changes in fetal testicular morphology, reduced cell proliferation, increased apoptosis, and decreased expression of markers related to Leydig cells (Star), Sertoli cells (Wt1), and spermatogonia (Plzf). Further investigation revealed that the effects of PAzE on fetal testicular development were characterized by mid-pregnancy, high dose (clinical dose), and single course having more pronounced effects. Additionally, the TGFβ/Smad and Nrf2 signaling pathways may be involved in the changes in fetal testicular development induced by PAzE. In summary, this study confirmed that PAzE influences fetal testicular morphological development and multicellular function. It provided theoretical and experimental evidence for guiding the rational use of azithromycin during pregnancy and further exploring the mechanisms underlying its developmental toxicity on fetal testicles.},
}

Mice
Male
Female
Pregnancy
Animals
*Azithromycin/toxicity
*Testis
Leydig Cells
Sertoli Cells
Fetus

@article {pmid38151680,
year = {2023},
author = {Bich, L},
title = {Integrating Multicellular Systems: Physiological Control and Degrees of Biological Individuality.},
journal = {Acta biotheoretica},
volume = {72},
number = {1},
pages = {1},
pmid = {38151680},
issn = {1572-8358},
mesh = {Animals ; *Biological Evolution ; *Biofilms ; },
abstract = {This paper focuses on physiological integration in multicellular systems, a notion often associated with biological individuality, but which has not received enough attention and needs a thorough theoretical treatment. Broadly speaking, physiological integration consists in how different components come together into a cohesive unit in which they are dependent on one another for their existence and activity. This paper argues that physiological integration can be understood by considering how the components of a biological multicellular system are controlled and coordinated in such a way that their activities can contribute to the maintenance of the system. The main implication of this perspective is that different ways of controlling their parts may give rise to multicellular organizations with different degrees of integration. After defining control, this paper analyses how control is realized in two examples of multicellular systems located at different ends of the spectrum of multicellularity: biofilms and animals. It focuses on differences in control ranges, and it argues that a high degree of integration implies control exerted at both medium and long ranges, and that insofar as biofilms lack long-range control (relative to their size) they can be considered as less integrated than other multicellular systems. It then discusses the implication of this account for the debate on physiological individuality and the idea that degrees of physiological integration imply degrees of individuality.},
}

Animals
*Biological Evolution
*Biofilms

@article {pmid38103995,
year = {2024},
author = {Yu, Y and Li, YP and Ren, K and Hao, X and Fru, EC and Rønn, R and Rivera, WL and Becker, K and Feng, R and Yang, J and Rensing, C},
title = {A brief history of metal recruitment in protozoan predation.},
journal = {Trends in microbiology},
volume = {32},
number = {5},
pages = {465-476},
doi = {10.1016/j.tim.2023.11.008},
pmid = {38103995},
issn = {1878-4380},
mesh = {*Metals/metabolism ; *Phagocytosis ; *Dictyostelium/metabolism/physiology ; Biological Evolution ; Acanthamoeba ; Animals ; Phagosomes/metabolism ; Zinc/metabolism ; Metalloids/metabolism ; Copper/metabolism ; Biological Availability ; Mitochondria/metabolism ; },
abstract = {Metals and metalloids are used as weapons for predatory feeding by unicellular eukaryotes on prokaryotes. This review emphasizes the role of metal(loid) bioavailability over the course of Earth's history, coupled with eukaryogenesis and the evolution of the mitochondrion to trace the emergence and use of the metal(loid) prey-killing phagosome as a feeding strategy. Members of the genera Acanthamoeba and Dictyostelium use metals such as zinc (Zn) and copper (Cu), and possibly metalloids, to kill their bacterial prey after phagocytosis. We provide a potential timeline on when these capacities first evolved and how they correlate with perceived changes in metal(loid) bioavailability through Earth's history. The origin of phagotrophic eukaryotes must have postdated the Great Oxidation Event (GOE) in agreement with redox-dependent modification of metal(loid) bioavailability for phagotrophic poisoning. However, this predatory mechanism is predicted to have evolved much later - closer to the origin of the multicellular metazoans and the evolutionary development of the immune systems.},
}

*Metals/metabolism
*Phagocytosis
*Dictyostelium/metabolism/physiology
Biological Evolution
Acanthamoeba
Animals
Phagosomes/metabolism
Zinc/metabolism
Metalloids/metabolism
Copper/metabolism
Biological Availability
Mitochondria/metabolism

@article {pmid38060007,
year = {2023},
author = {Romei, M and Carpentier, M and Chomilier, J and Lecointre, G},
title = {Origins and Functional Significance of Eukaryotic Protein Folds.},
journal = {Journal of molecular evolution},
volume = {91},
number = {6},
pages = {854-864},
pmid = {38060007},
issn = {1432-1432},
support = {IPV program of Sorbonne University, PhD grant//Sorbonne Université/ ; },
mesh = {Animals ; Phylogeny ; *Bacteria/genetics ; *Archaea/genetics ; Proteins ; Eukaryota/genetics ; Biological Evolution ; },
abstract = {Folds are the architecture and topology of a protein domain. Categories of folds are very few compared to the astronomical number of sequences. Eukaryotes have more protein folds than Archaea and Bacteria. These folds are of two types: shared with Archaea and/or Bacteria on one hand and specific to eukaryotic clades on the other hand. The first kind of folds is inherited from the first endosymbiosis and confirms the mixed origin of eukaryotes. In a dataset of 1073 folds whose presence or absence has been evidenced among 210 species equally distributed in the three super-kingdoms, we have identified 28 eukaryotic folds unambiguously inherited from Bacteria and 40 eukaryotic folds unambiguously inherited from Archaea. Compared to previous studies, the repartition of informational function is higher than expected for folds originated from Bacteria and as high as expected for folds inherited from Archaea. The second type of folds is specifically eukaryotic and associated with an increase of new folds within eukaryotes distributed in particular clades. Reconstructed ancestral states coupled with dating of each node on the tree of life provided fold appearance rates. The rate is on average twice higher within Eukaryota than within Bacteria or Archaea. The highest rates are found in the origins of eukaryotes, holozoans, metazoans, metazoans stricto sensu, and vertebrates: the roots of these clades correspond to bursts of fold evolution. We could correlate the functions of some of the fold synapomorphies within eukaryotes with significant evolutionary events. Among them, we find evidence for the rise of multicellularity, adaptive immune system, or virus folds which could be linked to an ecological shift made by tetrapods.},
}

Animals
Phylogeny
*Bacteria/genetics
*Archaea/genetics
Proteins
Eukaryota/genetics
Biological Evolution

@article {pmid38039969,
year = {2023},
author = {Mulvey, H and Dolan, L},
title = {RHO of plant signaling was established early in streptophyte evolution.},
journal = {Current biology : CB},
volume = {33},
number = {24},
pages = {5515-5525.e4},
doi = {10.1016/j.cub.2023.11.007},
pmid = {38039969},
issn = {1879-0445},
mesh = {Phylogeny ; *Chlorophyta ; Plants ; *Embryophyta/genetics ; *Streptophyta/physiology ; },
abstract = {The algal ancestors of land plants underwent a transition from a unicellular to a multicellular body plan.[1] This transition likely took place early in streptophyte evolution, sometime after the divergence of the Chlorokybophyceae/Mesostigmatophyceae lineage, but before the divergence of the Klebsormidiophyceae lineage.[2] How this transition was brought about is unknown; however, it was likely facilitated by the evolution of novel mechanisms to spatially regulate morphogenesis. In land plants, RHO of plant (ROP) signaling plays a conserved role in regulating polarized cell growth and cell division orientation to orchestrate morphogenesis.[3][,][4][,][5][,][6][,][7][,][8] ROP constitutes a plant-specific subfamily of the RHO GTPases, which are more widely conserved throughout eukaryotes.[9][,][10] Although the RHO family originated in early eukaryotes,[11][,][12] how and when the ROP subfamily originated had remained elusive. Here, we demonstrate that ROP signaling was established early in the streptophyte lineage, sometime after the divergence of the Chlorokybophyceae/Mesostigmatophyceae lineage, but before the divergence of the Klebsormidiophyceae lineage. This period corresponds to when the unicellular-to-multicellular transition likely took place in the streptophytes. In addition to being critical for the complex morphogenesis of extant land plants, we speculate that ROP signaling contributed to morphological evolution in early streptophytes.},
}

Phylogeny
*Chlorophyta
Plants
*Embryophyta/genetics
*Streptophyta/physiology

@article {pmid38014282,
year = {2023},
author = {Bingham, EP and Ratcliff, WC},
title = {A non-adaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38014282},
issn = {2692-8205},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; T32 GM142616/GM/NIGMS NIH HHS/United States ; },
abstract = {"Complex multicellularity", conventionally defined as large organisms with many specialized cell types, has evolved five times independently in eukaryotes, but never within prokaryotes. A number hypotheses have been proposed to explain this phenomenon, most of which posit that eukaryotes evolved key traits (e.g., dynamic cytoskeletons, alternative mechanisms of gene regulation, or subcellular compartments) which were a necessary prerequisite for the evolution of complex multicellularity. Here we propose an alternative, non-adaptive hypothesis for this broad macroevolutionary pattern. By binning cells into groups with finite genetic bottlenecks between generations, the evolution of multicellularity greatly reduces the effective population size (Ne) of cellular populations, increasing the role of genetic drift in evolutionary change. While both prokaryotes and eukaryotes experience this phenomenon, they have opposite responses to drift: mutational biases in eukaryotes tend to drive genomic expansion, providing additional raw genetic material for subsequent multicellular innovation, while prokaryotes generally face genomic erosion. These effects become more severe as organisms evolve larger size and more stringent genetic bottlenecks between generations- both of which are hallmarks of complex multicellularity. Taken together, we hypothesize that it is these idiosyncratic lineage-specific mutational biases, rather than cell-biological innovations within eukaryotes, that underpins the long-term divergent evolution of complex multicellularity across the tree of life.},
}

@article {pmid37996670,
year = {2024},
author = {Spradling, AC},
title = {The Ancient Origin and Function of Germline Cysts.},
journal = {Results and problems in cell differentiation},
volume = {71},
number = {},
pages = {3-21},
pmid = {37996670},
issn = {0080-1844},
mesh = {Female ; Animals ; Male ; Mice ; *Semen ; *Oocytes ; Germ Cells ; Spermatozoa ; Organelles ; },
abstract = {Gamete production in most animal species is initiated within an evolutionarily ancient multicellular germline structure, the germline cyst, whose interconnected premeiotic cells synchronously develop from a single progenitor arising just downstream from a stem cell. Cysts in mice, Drosophila, and many other animals protect developing sperm, while in females, cysts generate nurse cells that guard sister oocytes from transposons (TEs) and help them grow and build a Balbiani body. However, the origin and extreme evolutionary conservation of germline cysts remains a mystery. We suggest that cysts arose in ancestral animals like Hydra and Planaria whose multipotent somatic and germline stem cells (neoblasts) express genes conserved in all animal germ cells and frequently begin differentiation in cysts. A syncytial state is proposed to help multipotent stem cell chromatin transition to an epigenetic state with heterochromatic domains suitable for TE repression and specialized function. Most modern animals now lack neoblasts but have retained stem cells and cysts in their early germlines, which continue to function using this ancient epigenetic strategy.},
}

Female
Animals
Male
Mice
*Semen
*Oocytes
Germ Cells
Spermatozoa
Organelles

@article {pmid37993452,
year = {2023},
author = {Nicolas, E and Simion, P and Guérineau, M and Terwagne, M and Colinet, M and Virgo, J and Lingurski, M and Boutsen, A and Dieu, M and Hallet, B and Van Doninck, K},
title = {Horizontal acquisition of a DNA ligase improves DNA damage tolerance in eukaryotes.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7638},
pmid = {37993452},
issn = {2041-1723},
mesh = {Animals ; Humans ; *Eukaryota/genetics ; Phylogeny ; DNA Ligases/genetics/metabolism ; Ligases/metabolism ; Proteomics ; *Rotifera/genetics ; DNA Damage ; DNA Ligase ATP/genetics/metabolism ; },
abstract = {Bdelloid rotifers are part of the restricted circle of multicellular animals that can withstand a wide range of genotoxic stresses at any stage of their life cycle. In this study, bdelloid rotifer Adineta vaga is used as a model to decipher the molecular basis of their extreme tolerance. Proteomic analysis shows that a specific DNA ligase, different from those usually involved in DNA repair in eukaryotes, is strongly over-represented upon ionizing radiation. A phylogenetic analysis reveals its orthology to prokaryotic DNA ligase E, and its horizontal acquisition by bdelloid rotifers and plausibly other eukaryotes. The fungus Mortierella verticillata, having a single copy of this DNA Ligase E homolog, also exhibits an increased radiation tolerance with an over-expression of this DNA ligase E following X-ray exposure. We also provide evidence that A. vaga ligase E is a major contributor of DNA breaks ligation activity, which is a common step of all important DNA repair pathways. Consistently, its heterologous expression in human cell lines significantly improves their radio-tolerance. Overall, this study highlights the potential of horizontal gene transfers in eukaryotes, and their contribution to the adaptation to extreme conditions.},
}

Animals
Humans
*Eukaryota/genetics
Phylogeny
DNA Ligases/genetics/metabolism
Ligases/metabolism
Proteomics
*Rotifera/genetics
DNA Damage
DNA Ligase ATP/genetics/metabolism

@article {pmid37981028,
year = {2024},
author = {Rossi, SA and García-Barbazán, I and Chamorro-Herrero, I and Taborda, CP and Zaragoza, Ó and Zambrano, A},
title = {Use of 2D minilungs from human embryonic stem cells to study the interaction of Cryptococcus neoformans with the respiratory tract.},
journal = {Microbes and infection},
volume = {26},
number = {3},
pages = {105260},
doi = {10.1016/j.micinf.2023.105260},
pmid = {37981028},
issn = {1769-714X},
mesh = {Humans ; *Cryptococcus neoformans/physiology ; *Human Embryonic Stem Cells ; *Cryptococcosis/microbiology ; Lung/microbiology ; Cell Culture Techniques ; },
abstract = {Organoids can meet the needs between the use of cell culture and in vivo work, bringing together aspects of multicellular tissues, providing a more similar in vitro system for the study of various components, including host-interactions with pathogens and drug response. Organoids are structures that resemble organs in vivo, originating from pluripotent stem cells (PSCs) or adult stem cells (ASCs). There is great interest in deepening the understanding of the use of this technology to produce information about fungal infections and their treatments. This work aims the use 2D human lung organoid derived from human embryonic stem cells (hESCs), to investigate Cryptococcus neoformans-host interactions. C. neoformans is an opportunistic fungus acquired by inhalation that causes systemic mycosis mainly in immunocompromised individuals. Our work highlights the suitability of human minilungs for the study of C. neoformans infection (adhesion, invasion and replication), the interaction with the surfactant and induction of the host's alveolar pro-inflammatory response.},
}

Humans
*Cryptococcus neoformans/physiology
*Human Embryonic Stem Cells
*Cryptococcosis/microbiology
Lung/microbiology
Cell Culture Techniques

@article {pmid37963956,
year = {2023},
author = {Tissot, S and Guimard, L and Meliani, J and Boutry, J and Dujon, AM and Capp, JP and Tökölyi, J and Biro, PA and Beckmann, C and Fontenille, L and Do Khoa, N and Hamede, R and Roche, B and Ujvari, B and Nedelcu, AM and Thomas, F},
title = {The impact of food availability on tumorigenesis is evolutionarily conserved.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {19825},
pmid = {37963956},
issn = {2045-2322},
mesh = {Animals ; Humans ; *Cnidaria ; Biological Evolution ; *Hydra ; Carcinogenesis ; *Neoplasms/etiology ; },
abstract = {The inability to control cell proliferation results in the formation of tumors in many multicellular lineages. Nonetheless, little is known about the extent of conservation of the biological traits and ecological factors that promote or inhibit tumorigenesis across the metazoan tree. Particularly, changes in food availability have been linked to increased cancer incidence in humans, as an outcome of evolutionary mismatch. Here, we apply evolutionary oncology principles to test whether food availability, regardless of the multicellular lineage considered, has an impact on tumorigenesis. We used two phylogenetically unrelated model systems, the cnidarian Hydra oligactis and the fish Danio rerio, to investigate the impact of resource availability on tumor occurrence and progression. Individuals from healthy and tumor-prone lines were placed on four diets that differed in feeding frequency and quantity. For both models, frequent overfeeding favored tumor emergence, while lean diets appeared more protective. In terms of tumor progression, high food availability promoted it, whereas low resources controlled it, but without having a curative effect. We discuss our results in light of current ideas about the possible conservation of basic processes governing cancer in metazoans (including ancestral life history trade-offs at the cell level) and in the framework of evolutionary medicine.},
}

Animals
Humans
*Cnidaria
Biological Evolution
*Hydra
Carcinogenesis
*Neoplasms/etiology

@article {pmid37947621,
year = {2023},
author = {Wang, X and Xu, X and Wang, Z},
title = {The Post-Translational Role of UFMylation in Physiology and Disease.},
journal = {Cells},
volume = {12},
number = {21},
pages = {},
pmid = {37947621},
issn = {2073-4409},
support = {32090031, 32000911//NSFC/ ; },
mesh = {Animals ; Humans ; *Proteins/metabolism ; *Protein Processing, Post-Translational ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitin/metabolism ; Ubiquitins/metabolism ; Mammals/metabolism ; },
abstract = {Ubiquitin-fold modifier 1 (UFM1) is a newly identified ubiquitin-like protein that has been conserved during the evolution of multicellular organisms. In a similar manner to ubiquitin, UFM1 can become covalently linked to the lysine residue of a substrate via a dedicated enzymatic cascade. Although a limited number of substrates have been identified so far, UFM1 modification (UFMylation) has been demonstrated to play a vital role in a variety of cellular activities, including mammalian development, ribosome biogenesis, the DNA damage response, endoplasmic reticulum stress responses, immune responses, and tumorigenesis. In this review, we summarize what is known about the UFM1 enzymatic cascade and its biological functions, and discuss its recently identified substrates. We also explore the pathological role of UFMylation in human disease and the corresponding potential therapeutic targets and strategies.},
}

Animals
Humans
*Proteins/metabolism
*Protein Processing, Post-Translational
Ubiquitin-Protein Ligases/metabolism
Ubiquitin/metabolism
Ubiquitins/metabolism
Mammals/metabolism

@article {pmid37931037,
year = {2023},
author = {Dupouy, G and Cashell, R and Brychkova, G and Tuteja, R and McKeown, PC and Spillane, C},
title = {PICKLE RELATED 2 is a Neofunctionalized Gene Duplicate Under Positive Selection With Antagonistic Effects to the Ancestral PICKLE Gene on the Seed Transcriptome.},
journal = {Genome biology and evolution},
volume = {15},
number = {11},
pages = {},
pmid = {37931037},
issn = {1759-6653},
mesh = {*Arabidopsis/genetics ; *Arabidopsis Proteins/genetics ; Gene Expression Regulation, Plant ; Seeds/genetics ; Transcription Factors/genetics ; Transcriptome ; Gene Duplication ; },
abstract = {The evolution and diversification of proteins capable of remodeling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodeling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis thaliana, yet the basis of this functional divergence remains unknown. In this study, we demonstrate that genes encoding the CHD3 proteins PICKLE (PKL) and PICKLE-RELATED 2 (PKR2) originated from a duplication event during the diversification of crown Brassicaceae, and that these homologs have undergone distinct evolutionary trajectories since this duplication, with PKR2 fast evolving under positive selection, while PKL is subject to purifying selection. We find that the rapid evolution of PKR2 under positive selection reduces the encoded protein's intrinsic disorder, possibly suggesting a tertiary structure configuration which differs from that of PKL. Our whole genome transcriptome analysis in seeds of pkr2 and pkl mutants reveals that they act antagonistically on the expression of specific sets of genes, providing a basis for their differing roles in seed development. Our results provide insights into how gene duplication and neofunctionalization can lead to differing and antagonistic selective pressures on transcriptomes during plant reproduction, as well as on the evolutionary diversification of the CHD3 family within seed plants.},
}

*Arabidopsis/genetics
*Arabidopsis Proteins/genetics
Gene Expression Regulation, Plant
Seeds/genetics
Transcription Factors/genetics
Transcriptome
Gene Duplication

@article {pmid37925718,
year = {2023},
author = {Fung, L and Konkol, A and Ishikawa, T and Larson, BT and Brunet, T and Goldstein, RE},
title = {Swimming, Feeding, and Inversion of Multicellular Choanoflagellate Sheets.},
journal = {Physical review letters},
volume = {131},
number = {16},
pages = {168401},
pmid = {37925718},
issn = {1079-7114},
support = {/WT_/Wellcome Trust/United Kingdom ; 207510/WT_/Wellcome Trust/United Kingdom ; 207510/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Choanoflagellata/metabolism ; Swimming ; Biological Evolution ; },
abstract = {The recent discovery of the striking sheetlike multicellular choanoflagellate species Choanoeca flexa that dynamically interconverts between two hemispherical forms of opposite orientation raises fundamental questions in cell and evolutionary biology, as choanoflagellates are the closest living relatives of animals. It similarly motivates questions in fluid and solid mechanics concerning the differential swimming speeds in the two states and the mechanism of curvature inversion triggered by changes in the geometry of microvilli emanating from each cell. Here we develop fluid dynamical and mechanical models to address these observations and show that they capture the main features of the swimming, feeding, and inversion of C. flexa colonies, which can be viewed as active, shape-shifting polymerized membranes.},
}

Animals
*Choanoflagellata/metabolism
Swimming
Biological Evolution

@article {pmid37865203,
year = {2023},
author = {Liu, Y and Liu, Y and Chen, S and Kong, Z and Guo, Y and Wang, H},
title = {Prenatal exposure to acetaminophen at different doses, courses and time causes testicular dysplasia in offspring mice and its mechanism.},
journal = {Chemosphere},
volume = {345},
number = {},
pages = {140496},
doi = {10.1016/j.chemosphere.2023.140496},
pmid = {37865203},
issn = {1879-1298},
mesh = {Mice ; Pregnancy ; Humans ; Male ; Female ; Animals ; *Testis/metabolism ; Acetaminophen/toxicity/metabolism ; *Prenatal Exposure Delayed Effects/chemically induced/metabolism ; Leydig Cells/metabolism ; Testosterone/metabolism ; },
abstract = {Epidemiological investigation suggested that the use of acetaminophen during pregnancy may cause offspring testicular dysplasia, but no systematic study has been conducted. In this study, Kunming mice were given acetaminophen at different doses (100/200/400 mg/kg.d), courses (single/multiple), time (second/third trimester) during pregnancy. Fetal blood and testes were collected on gestaional day 18 for detection. The results indicated abnormal testicular development in the PAcE (prenatal acetaminophen exposure) groups. The maximum diameter/cross-sectional area decreased, the interstitial space widened, and decreased proliferation/increased apoptosis were observed, especially in the high-dose, multi-course and second-trimester groups. Meanwhile, the serum testosterone level decreased in PAcE groups, and the steroid synthesis function in Leydig cells, Sertoli and spermatogenic cell function were inhibited, it was more significant in high-dose, multi-course and second-trimester groups. Furthermore, Wnt signal pathway was activated but Notch signal pathway was inhibited in the PAcE groups. Finally, in vitro experiment, acetaminophen could inhibit spermatogonial cell proliferation, enhance apoptosis, and change Wnt/Notch signal pathway. In conclusion, this study confirmed that PAcE can change fetal testicular development in a dose, course and time-dependent manner, and found that multicellular function impaired. This study provides theoretical and experimental basis for systematically elucidating the developmental toxicity of acetaminophen in testis.},
}

Mice
Pregnancy
Humans
Male
Female
Animals
*Testis/metabolism
Acetaminophen/toxicity/metabolism
*Prenatal Exposure Delayed Effects/chemically induced/metabolism
Leydig Cells/metabolism
Testosterone/metabolism

@article {pmid37863060,
year = {2023},
author = {Mishina, T and Chiu, MC and Hashiguchi, Y and Oishi, S and Sasaki, A and Okada, R and Uchiyama, H and Sasaki, T and Sakura, M and Takeshima, H and Sato, T},
title = {Massive horizontal gene transfer and the evolution of nematomorph-driven behavioral manipulation of mantids.},
journal = {Current biology : CB},
volume = {33},
number = {22},
pages = {4988-4994.e5},
doi = {10.1016/j.cub.2023.09.052},
pmid = {37863060},
issn = {1879-0445},
mesh = {Animals ; *Mantodea ; Host-Parasite Interactions/genetics ; Behavior Control ; Gene Transfer, Horizontal ; *Parasites ; },
abstract = {To complete their life cycle, a wide range of parasites must manipulate the behavior of their hosts.[1] This manipulation is a well-known example of the "extended phenotype,[2]" where genes in one organism have phenotypic effects on another organism. Recent studies have explored the parasite genes responsible for such manipulation of host behavior, including the potential molecular mechanisms.[3][,][4] However, little is known about how parasites have acquired the genes involved in manipulating phylogenetically distinct hosts.[4] In a fascinating example of the extended phenotype, nematomorph parasites have evolved the ability to induce their terrestrial insect hosts to enter bodies of water, where the parasite then reproduces. Here, we comprehensively analyzed nematomorphs and their mantid hosts, focusing on the transcriptomic changes associated with host manipulations and sequence similarity between host and parasite genes to test molecular mimicry. The nematomorph's transcriptome changed during host manipulation, whereas no distinct changes were found in mantids. We then discovered numerous possible host-derived genes in nematomorphs, and these genes were frequently up-regulated during host manipulation. Our findings suggest a possible general role of horizontal gene transfer (HGT) in the molecular mechanisms of host manipulation, as well as in the genome evolution of manipulative parasites. The evidence of HGT between multicellular eukaryotes remains scarce but is increasing and, therefore, elucidating its mechanisms will advance our understanding of the enduring influence of HGT on the evolution of the web of life.},
}

Animals
*Mantodea
Host-Parasite Interactions/genetics
Behavior Control
Gene Transfer, Horizontal
*Parasites

@article {pmid37850657,
year = {2024},
author = {Ma, Q and Li, Q and Zheng, X and Pan, J},
title = {CellCommuNet: an atlas of cell-cell communication networks from single-cell RNA sequencing of human and mouse tissues in normal and disease states.},
journal = {Nucleic acids research},
volume = {52},
number = {D1},
pages = {D597-D606},
pmid = {37850657},
issn = {1362-4962},
support = {CSTB2023NSCQ-MSX0289//Chongqing Medical University/ ; //Natural Science Foundation of Chongqing/ ; BJRC202214//Chongqing Medical University/ ; CXQT21016//University Innovation Research Group Project of Chongqing/ ; W0056//Chongqing Medical University/ ; },
mesh = {Animals ; Humans ; Mice ; *Cell Communication ; *Databases, Factual ; *Gene Expression Profiling/methods ; Ligands ; *Sequence Analysis, RNA/methods ; *Single-Cell Analysis/methods ; },
abstract = {Cell-cell communication, as a basic feature of multicellular organisms, is crucial for maintaining the biological functions and microenvironmental homeostasis of cells, organs, and whole organisms. Alterations in cell-cell communication contribute to many diseases, including cancers. Single-cell RNA sequencing (scRNA-seq) provides a powerful method for studying cell-cell communication by enabling the analysis of ligand-receptor interactions. Here, we introduce CellCommuNet (http://www.inbirg.com/cellcommunet/), a comprehensive data resource for exploring cell-cell communication networks in scRNA-seq data from human and mouse tissues in normal and disease states. CellCommuNet currently includes 376 single datasets from multiple sources, and 118 comparison datasets between disease and normal samples originating from the same study. CellCommuNet provides information on the strength of communication between cells and related signalling pathways and facilitates the exploration of differences in cell-cell communication between healthy and disease states. Users can also search for specific signalling pathways, ligand-receptor pairs, and cell types of interest. CellCommuNet provides interactive graphics illustrating cell-cell communication in different states, enabling differential analysis of communication strength between disease and control samples. This comprehensive database aims to be a valuable resource for biologists studying cell-cell communication networks.},
}

Animals
Humans
Mice
*Cell Communication
*Databases, Factual
*Gene Expression Profiling/methods
Ligands
*Sequence Analysis, RNA/methods
*Single-Cell Analysis/methods