@article {pmid35879542,
year = {2022},
author = {Ní Leathlobhair, M and Lenski, RE},
title = {Population genetics of clonally transmissible cancers.},
journal = {Nature ecology & evolution},
volume = {6},
number = {8},
pages = {1077-1089},
pmid = {35879542},
issn = {2397-334X},
support = {DEB-1951307//National Science Foundation (NSF)/ ; MICL02253//U.S. Department of Agriculture (United States Department of Agriculture)/ ; },
mesh = {Animals ; Biological Evolution ; *Genetics, Population ; Genome ; *Neoplasms/genetics ; Population Dynamics ; },
abstract = {Populations of cancer cells are subject to the same core evolutionary processes as asexually reproducing, unicellular organisms. Transmissible cancers are particularly striking examples of these processes. These unusual cancers are clonal lineages that can spread through populations via physical transfer of living cancer cells from one host individual to another, and they have achieved long-term success in the colonization of at least eight different host species. Population genetic theory provides a useful framework for understanding the shift from a multicellular sexual animal into a unicellular asexual clone and its long-term effects on the genomes of these cancers. In this Review, we consider recent findings from transmissible cancer research with the goals of developing an evolutionarily informed perspective on transmissible cancers, examining possible implications for their long-term fate and identifying areas for future research on these exceptional lineages.},
}

Animals
Biological Evolution
*Genetics, Population
Genome
*Neoplasms/genetics
Population Dynamics

@article {pmid35894230,
year = {2022},
author = {Le Gloanec, C and Collet, L and Silveira, SR and Wang, B and Routier-Kierzkowska, AL and Kierzkowski, D},
title = {Cell type-specific dynamics underlie cellular growth variability in plants.},
journal = {Development (Cambridge, England)},
volume = {149},
number = {14},
pages = {},
doi = {10.1242/dev.200783},
pmid = {35894230},
issn = {1477-9129},
support = {NFRFE-2018-00953//Government of Canada/ ; RGPIN-2018-05762//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Arabidopsis ; *Arabidopsis Proteins/genetics ; Cell Differentiation/genetics ; Cell Proliferation ; Plant Leaves ; Plant Stomata ; },
abstract = {Coordination of growth, patterning and differentiation is required for shaping organs in multicellular organisms. In plants, cell growth is controlled by positional information, yet the behavior of individual cells is often highly heterogeneous. The origin of this variability is still unclear. Using time-lapse imaging, we determined the source and relevance of cellular growth variability in developing organs of Arabidopsis thaliana. We show that growth is more heterogeneous in the leaf blade than in the midrib and petiole, correlating with higher local differences in growth rates between neighboring cells in the blade. This local growth variability coincides with developing stomata. Stomatal lineages follow a specific, time-dependent growth program that is different from that of their surroundings. Quantification of cellular dynamics in the leaves of a mutant lacking stomata, as well as analysis of floral organs, supports the idea that growth variability is mainly driven by stomata differentiation. Thus, the cell-autonomous behavior of specialized cells is the main source of local growth variability in otherwise homogeneously growing tissue. Those growth differences are buffered by the immediate neighbors of stomata and trichomes to achieve robust organ shapes.},
}

*Arabidopsis
*Arabidopsis Proteins/genetics
Cell Differentiation/genetics
Cell Proliferation
Plant Leaves
Plant Stomata

@article {pmid35838349,
year = {2022},
author = {Meléndez García, R and Haccard, O and Chesneau, A and Narassimprakash, H and Roger, J and Perron, M and Marheineke, K and Bronchain, O},
title = {A non-transcriptional function of Yap regulates the DNA replication program in Xenopus laevis.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
doi = {10.7554/eLife.75741},
pmid = {35838349},
issn = {2050-084X},
support = {NA//Association pour la Recherche sur le Cancer/ ; NA//Retina France/ ; NA//Fondation Valentin Haüy/ ; NA//UNADEV/ ; 439641//Conacyt/ ; },
mesh = {Animals ; DNA Replication ; DNA Replication Timing ; *Replication Origin ; S Phase/genetics ; *Telomere-Binding Proteins/genetics ; Xenopus laevis/genetics/metabolism ; },
abstract = {In multicellular eukaryotic organisms, the initiation of DNA replication occurs asynchronously throughout S-phase according to a regulated replication timing program. Here, using Xenopus egg extracts, we showed that Yap (Yes-associated protein 1), a downstream effector of the Hippo signalling pathway, is required for the control of DNA replication dynamics. We found that Yap is recruited to chromatin at the start of DNA replication and identified Rif1, a major regulator of the DNA replication timing program, as a novel Yap binding protein. Furthermore, we show that either Yap or Rif1 depletion accelerates DNA replication dynamics by increasing the number of activated replication origins. In Xenopus embryos, using a Trim-Away approach during cleavage stages devoid of transcription, we found that either Yap or Rif1 depletion triggers an acceleration of cell divisions, suggesting a shorter S-phase by alterations of the replication program. Finally, our data show that Rif1 knockdown leads to defects in the partitioning of early versus late replication foci in retinal stem cells, as we previously showed for Yap. Altogether, our findings unveil a non-transcriptional role for Yap in regulating replication dynamics. We propose that Yap and Rif1 function as brakes to control the DNA replication program in early embryos and post-embryonic stem cells.},
}

Animals
DNA Replication
DNA Replication Timing
*Replication Origin
S Phase/genetics
*Telomere-Binding Proteins/genetics
Xenopus laevis/genetics/metabolism

@article {pmid35893123,
year = {2022},
author = {Dijkwel, Y and Tremethick, DJ},
title = {The Role of the Histone Variant H2A.Z in Metazoan Development.},
journal = {Journal of developmental biology},
volume = {10},
number = {3},
pages = {},
doi = {10.3390/jdb10030028},
pmid = {35893123},
issn = {2221-3759},
support = {1142399//National Health and Medical Research Council/ ; },
abstract = {During the emergence and radiation of complex multicellular eukaryotes from unicellular ancestors, transcriptional systems evolved by becoming more complex to provide the basis for this morphological diversity. The way eukaryotic genomes are packaged into a highly complex structure, known as chromatin, underpins this evolution of transcriptional regulation. Chromatin structure is controlled by a variety of different epigenetic mechanisms, including the major mechanism for altering the biochemical makeup of the nucleosome by replacing core histones with their variant forms. The histone H2A variant H2A.Z is particularly important in early metazoan development because, without it, embryos cease to develop and die. However, H2A.Z is also required for many differentiation steps beyond the stage that H2A.Z-knockout embryos die. H2A.Z can facilitate the activation and repression of genes that are important for pluripotency and differentiation, and acts through a variety of different molecular mechanisms that depend upon its modification status, its interaction with histone and nonhistone partners, and where it is deposited within the genome. In this review, we discuss the current knowledge about the different mechanisms by which H2A.Z regulates chromatin function at various developmental stages and the chromatin remodeling complexes that determine when and where H2A.Z is deposited.},
}

@article {pmid35862435,
year = {2022},
author = {Howe, J and Rink, JC and Wang, B and Griffin, AS},
title = {Multicellularity in animals: The potential for within-organism conflict.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {32},
pages = {e2120457119},
doi = {10.1073/pnas.2120457119},
pmid = {35862435},
issn = {1091-6490},
support = {94818//Volkswagen Foundation (VolkswagenStiftung)/ ; CF20_0541//Carlsbergfondet (Carlsberg Foundation)/ ; },
mesh = {Animals ; *Biological Evolution ; *Cell Lineage ; Clone Cells ; Developmental Biology ; *Insecta/growth & development ; Reproduction ; },
abstract = {Metazoans function as individual organisms but also as "colonies" of cells whose single-celled ancestors lived and reproduced independently. Insights from evolutionary biology about multicellular group formation help us understand the behavior of cells: why they cooperate, and why cooperation sometimes breaks down. Current explanations for multicellularity focus on two aspects of development which promote cooperation and limit conflict among cells: a single-cell bottleneck, which creates organisms composed of clones, and a separation of somatic and germ cell lineages, which reduces the selective advantage of cheating. However, many obligately multicellular organisms thrive with neither, creating the potential for within-organism conflict. Here, we argue that the prevalence of such organisms throughout the Metazoa requires us to refine our preconceptions of conflict-free multicellularity. Evolutionary theory must incorporate developmental mechanisms across a broad range of organisms-such as unusual reproductive strategies, totipotency, and cell competition-while developmental biology must incorporate evolutionary principles. To facilitate this cross-disciplinary approach, we provide a conceptual overview from evolutionary biology for developmental biologists, using analogous examples in the well-studied social insects.},
}

Animals
*Biological Evolution
*Cell Lineage
Clone Cells
Developmental Biology
*Insecta/growth & development
Reproduction

@article {pmid35858311,
year = {2022},
author = {Belcher, LJ and Madgwick, PG and Kuwana, S and Stewart, B and Thompson, CRL and Wolf, JB},
title = {Developmental constraints enforce altruism and avert the tragedy of the commons in a social microbe.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {29},
pages = {e2111233119},
doi = {10.1073/pnas.2111233119},
pmid = {35858311},
issn = {1091-6490},
support = {GW4+ PhD Studentship//UKRI | Natural Environment Research Council (NERC)/ ; SWBio PhD Studentship//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/M01035X/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/M007146/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; NE/V012002/1//UKRI | Natural Environment Research Council (NERC)/ ; WT095643AIA//Wellcome Trust (WT)/ ; },
mesh = {*Altruism ; Biological Evolution ; Cooperative Behavior ; *Dictyostelium ; Humans ; Motivation ; },
abstract = {Organisms often cooperate through the production of freely available public goods. This can greatly benefit the group but is vulnerable to the "tragedy of the commons" if individuals lack the motivation to make the necessary investment into public goods production. Relatedness to groupmates can motivate individual investment because group success ultimately benefits their genes' own self-interests. However, systems often lack mechanisms that can reliably ensure that relatedness is high enough to promote cooperation. Consequently, groups face a persistent threat from the tragedy unless they have a mechanism to enforce investment when relatedness fails to provide adequate motivation. To understand the real threat posed by the tragedy and whether groups can avert its impact, we determine how the social amoeba Dictyostelium discoideum responds as relatedness decreases to levels that should induce the tragedy. We find that, while investment in public goods declines as overall within-group relatedness declines, groups avert the expected catastrophic collapse of the commons by continuing to invest, even when relatedness should be too low to incentivize any contribution. We show that this is due to a developmental buffering system that generates enforcement because insufficient cooperation perturbs the balance of a negative feedback system controlling multicellular development. This developmental constraint enforces investment under the conditions expected to be most tragic, allowing groups to avert a collapse in cooperation. These results help explain how mechanisms that suppress selfishness and enforce cooperation can arise inadvertently as a by-product of constraints imposed by selection on different traits.},
}

*Altruism
Biological Evolution
Cooperative Behavior
*Dictyostelium
Humans
Motivation

@article {pmid35713948,
year = {2022},
author = {Passer, AR and Clancey, SA and Shea, T and David-Palma, M and Averette, AF and Boekhout, T and Porcel, BM and Nowrousian, M and Cuomo, CA and Sun, S and Heitman, J and Coelho, MA},
title = {Obligate sexual reproduction of a homothallic fungus closely related to the Cryptococcus pathogenic species complex.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35713948},
issn = {2050-084X},
support = {AI50113-17//National Institute of Allergy and Infectious Diseases/ ; AI39115-24//National Institute of Allergy and Infectious Diseases/ ; AI33654-04//National Institute of Allergy and Infectious Diseases/ ; U54HG003067/NH/NIH HHS/United States ; U54HG003067/NH/NIH HHS/United States ; NO407/7-2//German Research Foundation/ ; },
mesh = {Biological Evolution ; *Cryptococcus neoformans/genetics ; *Genes, Mating Type, Fungal/genetics ; Humans ; Reproduction ; Saccharomyces cerevisiae/genetics ; },
abstract = {.

Fungi are enigmatic organisms that flourish in soil, on decaying plants, or during infection of animals or plants. Growing in myriad forms, from single-celled yeast to multicellular molds and mushrooms, fungi have also evolved a variety of strategies to reproduce. Normally, fungi reproduce in one of two ways: either they reproduce asexually, with one individual producing a new individual identical to itself, or they reproduce sexually, with two individuals of different 'mating types' contributing to produce a new individual. However, individuals of some species exhibit 'homothallism' or self-fertility: these individuals can produce reproductive cells that are universally compatible, and therefore can reproduce sexually with themselves or with any other cell in the population.

Homothallism has evolved multiple times throughout the fungal kingdom, suggesting it confers advantage when population numbers are low or mates are hard to find. Yet some homothallic fungi been overlooked compared to heterothallic species, whose mating types have been well characterised. Understanding the genetic basis of homothallism and how it evolved in different species can provide insights into pathogenic species that cause fungal disease.

With that in mind, Passer, Clancey et al. explored the genetic basis of homothallism in Cryptococcus depauperatus, a close relative of C. neoformans, a species that causes fungal infections in humans. A combination of genetic sequencing techniques and experiments were applied to analyse, compare, and manipulate C. depauperatus' genome to see how this species evolved self-fertility.

Passer, Clancey et al. showed that C. depauperatus evolved the ability to reproduce sexually by itself via a unique evolutionary pathway. The result is a form of homothallism never reported in fungi before. C. depauperatus lost some of the genes that control mating in other species of fungi, and acquired genes from the opposing mating types of a heterothallic ancestor to become self-fertile.

Passer, Clancey et al. also found that, unlike other Cryptococcus species that switch between asexual and sexual reproduction, C. depauperatus grows only as long, branching filaments called hyphae, a sexual form. The species reproduces sexually with itself throughout its life cycle and is unable to produce a yeast (asexual) form, in contrast to other closely related species.

This work offers new insights into how different modes of sexual reproduction have evolved in fungi. It also provides another interesting case of how genome plasticity and evolutionary pressures can produce similar outcomes, homothallism, via different evolutionary paths. Lastly, assembling the complete genome of C. depauperatus will foster comparative studies between pathogenic and non-pathogenic Cryptococcus species.},
}

Biological Evolution
*Cryptococcus neoformans/genetics
*Genes, Mating Type, Fungal/genetics
Humans
Reproduction
Saccharomyces cerevisiae/genetics

@article {pmid35726057,
year = {2022},
author = {Kaufmann, M and Schaupp, AL and Sun, R and Coscia, F and Dendrou, CA and Cortes, A and Kaur, G and Evans, HG and Mollbrink, A and Navarro, JF and Sonner, JK and Mayer, C and DeLuca, GC and Lundeberg, J and Matthews, PM and Attfield, KE and Friese, MA and Mann, M and Fugger, L},
title = {Identification of early neurodegenerative pathways in progressive multiple sclerosis.},
journal = {Nature neuroscience},
volume = {25},
number = {7},
pages = {944-955},
pmid = {35726057},
issn = {1546-1726},
support = {NNF14CC0001 and NNF15CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 686547//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 100308/Z/12/Z//Wellcome Trust (Wellcome)/ ; OCAY-15-520//Oak Foundation/ ; },
mesh = {*Central Nervous System Diseases/complications ; Disease Progression ; Humans ; *Multiple Sclerosis/pathology ; Neurons/metabolism ; Proteomics ; },
abstract = {Progressive multiple sclerosis (MS) is characterized by unrelenting neurodegeneration, which causes cumulative disability and is refractory to current treatments. Drug development to prevent disease progression is an urgent clinical need yet is constrained by an incomplete understanding of its complex pathogenesis. Using spatial transcriptomics and proteomics on fresh-frozen human MS brain tissue, we identified multicellular mechanisms of progressive MS pathogenesis and traced their origin in relation to spatially distributed stages of neurodegeneration. By resolving ligand-receptor interactions in local microenvironments, we discovered defunct trophic and anti-inflammatory intercellular communications within areas of early neuronal decline. Proteins associated with neuronal damage in patient samples showed mechanistic concordance with published in vivo knockdown and central nervous system (CNS) disease models, supporting their causal role and value as potential therapeutic targets in progressive MS. Our findings provide a new framework for drug development strategies, rooted in an understanding of the complex cellular and signaling dynamics in human diseased tissue that facilitate this debilitating disease.},
}

*Central Nervous System Diseases/complications
Disease Progression
Humans
*Multiple Sclerosis/pathology
Neurons/metabolism
Proteomics

@article {pmid35678467,
year = {2022},
author = {Northey, JJ and Weaver, VM},
title = {Mechanosensitive Steroid Hormone Signaling and Cell Fate.},
journal = {Endocrinology},
volume = {163},
number = {8},
pages = {},
doi = {10.1210/endocr/bqac085},
pmid = {35678467},
issn = {1945-7170},
support = {/NH/NIH HHS/United States ; R01CA192914/CA/NCI NIH HHS/United States ; },
mesh = {Cell Differentiation ; Hormones/physiology ; Humans ; *Neoplasms/pathology ; *Receptors, Steroid ; Signal Transduction ; Steroids ; },
abstract = {Mechanical forces collaborate across length scales to coordinate cell fate during development and the dynamic homeostasis of adult tissues. Similarly, steroid hormones interact with their nuclear and nonnuclear receptors to regulate diverse physiological processes necessary for the appropriate development and function of complex multicellular tissues. Aberrant steroid hormone action is associated with tumors originating in hormone-sensitive tissues and its disruption forms the basis of several therapeutic interventions. Prolonged perturbations to mechanical forces may further foster tumor initiation and the evolution of aggressive metastatic disease. Recent evidence suggests that steroid hormone and mechanical signaling intersect to direct cell fate during development and tumor progression. Potential mechanosensitive steroid hormone signaling pathways along with their molecular effectors will be discussed in this context.},
}

Cell Differentiation
Hormones/physiology
Humans
*Neoplasms/pathology
*Receptors, Steroid
Signal Transduction
Steroids

@article {pmid35790840,
year = {2022},
author = {Beljan, S and Dominko, K and Talajić, A and Hloušek-Kasun, A and Škrobot Vidaček, N and Herak Bosnar, M and Vlahoviček, K and Ćetković, H},
title = {Structure and function of cancer-related developmentally regulated GTP-binding protein 1 (DRG1) is conserved between sponges and humans.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {11379},
pmid = {35790840},
issn = {2045-2322},
mesh = {Animals ; GTP-Binding Proteins ; Genomics ; Humans ; *Neoplasms/genetics ; *Oncogenes ; RNA ; Transcription Factors ; },
abstract = {Cancer is a disease caused by errors within the multicellular system and it represents a major health issue in multicellular organisms. Although cancer research has advanced substantially, new approaches focusing on fundamental aspects of cancer origin and mechanisms of spreading are necessary. Comparative genomic studies have shown that most genes linked to human cancer emerged during the early evolution of Metazoa. Thus, basal animals without true tissues and organs, such as sponges (Porifera), might be an innovative model system for understanding the molecular mechanisms of proteins involved in cancer biology. One of these proteins is developmentally regulated GTP-binding protein 1 (DRG1), a GTPase stabilized by interaction with DRG family regulatory protein 1 (DFRP1). This study reveals a high evolutionary conservation of DRG1 gene/protein in metazoans. Our biochemical analysis and structural predictions show that both recombinant sponge and human DRG1 are predominantly monomers that form complexes with DFRP1 and bind non-specifically to RNA and DNA. We demonstrate the conservation of sponge and human DRG1 biological features, including intracellular localization and DRG1:DFRP1 binding, function of DRG1 in α-tubulin dynamics, and its role in cancer biology demonstrated by increased proliferation, migration and colonization in human cancer cells. These results suggest that the ancestor of all Metazoa already possessed DRG1 that is structurally and functionally similar to the human DRG1, even before the development of real tissues or tumors, indicating an important function of DRG1 in fundamental cellular pathways.},
}

Animals
GTP-Binding Proteins
Genomics
Humans
*Neoplasms/genetics
*Oncogenes
RNA
Transcription Factors

@article {pmid35728616,
year = {2022},
author = {Cameron-Pack, ME and König, SG and Reyes-Guevara, A and Reyes-Prieto, A and Nedelcu, AM},
title = {A personal cost of cheating can stabilize reproductive altruism during the early evolution of clonal multicellularity.},
journal = {Biology letters},
volume = {18},
number = {6},
pages = {20220059},
doi = {10.1098/rsbl.2022.0059},
pmid = {35728616},
issn = {1744-957X},
mesh = {*Altruism ; Biological Evolution ; Reproduction ; *Volvox/genetics ; },
abstract = {Understanding how cooperation evolved and is maintained remains an important and often controversial topic because cheaters that reap the benefits of cooperation without paying the costs can threaten the evolutionary stability of cooperative traits. Cooperation-and especially reproductive altruism-is particularly relevant to the evolution of multicellularity, as somatic cells give up their reproductive potential in order to contribute to the fitness of the newly emerged multicellular individual. Here, we investigated cheating in a simple multicellular species-the green alga Volvox carteri, in the context of the mechanisms that can stabilize reproductive altruism during the early evolution of clonal multicellularity. We found that the benefits cheater mutants can gain in terms of their own reproduction are pre-empted by a cost in survival due to increased sensitivity to stress. This personal cost of cheating reflects the antagonistic pleiotropic effects that the gene coding for reproductive altruism-regA-has at the cell level. Specifically, the expression of regA in somatic cells results in the suppression of their reproduction potential but also confers them with increased resistance to stress. Since regA evolved from a life-history trade-off gene, we suggest that co-opting trade-off genes into cooperative traits can provide a built-in safety system against cheaters in other clonal multicellular lineages.},
}

*Altruism
Biological Evolution
Reproduction
*Volvox/genetics

@article {pmid35725583,
year = {2022},
author = {Mori, G and Delfino, D and Pibiri, P and Rivetti, C and Percudani, R},
title = {Origin and significance of the human DNase repertoire.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10364},
pmid = {35725583},
issn = {2045-2322},
support = {FFC#9/2018//Fondazione Ricerca Fibrosi Cistica (FFC)/ ; },
mesh = {Animals ; DNA/genetics ; Deoxyribonuclease I/genetics ; *Deoxyribonucleases/genetics ; *Evolution, Molecular ; Fishes/genetics ; Gene Duplication ; Humans ; Phylogeny ; Synteny ; Vertebrates/genetics ; },
abstract = {The human genome contains four DNase1 and two DNase2 genes. The origin and functional specialization of this repertoire are not fully understood. Here we use genomics and transcriptomics data to infer the evolutionary history of DNases and investigate their biological significance. Both DNase1 and DNase2 families have expanded in vertebrates since ~ 650 million years ago before the divergence of jawless and jawed vertebrates. DNase1, DNase1L1, and DNase1L3 co-existed in jawless fish, whereas DNase1L2 originated in amniotes by tandem duplication of DNase1. Among the non-human DNases, DNase1L4 and newly identified DNase1L5 derived from early duplications that were lost in terrestrial vertebrates. The ancestral gene of the DNase2 family, DNase2b, has been conserved in synteny with the Uox gene across 700 million years of animal evolution,while DNase2 originated in jawless fish. DNase1L1 acquired a GPI-anchor for plasma membrane attachment in bony fishes, and DNase1L3 acquired a C-terminal basic peptide for the degradation of microparticle DNA in jawed vertebrates. The appearance of DNase1L2, with a distinct low pH optimum and skin localization, is among the amniote adaptations to life on land. The expansion of the DNase repertoire in vertebrates meets the diversified demand for DNA debris removal in complex multicellular organisms.},
}

Animals
DNA/genetics
Deoxyribonuclease I/genetics
*Deoxyribonucleases/genetics
*Evolution, Molecular
Fishes/genetics
Gene Duplication
Humans
Phylogeny
Synteny
Vertebrates/genetics

@article {pmid35681485,
year = {2022},
author = {Minelli, A and Valero-Gracia, A},
title = {Spatially and Temporally Distributed Complexity-A Refreshed Framework for the Study of GRN Evolution.},
journal = {Cells},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/cells11111790},
pmid = {35681485},
issn = {2073-4409},
mesh = {Animals ; *Gene Regulatory Networks ; Genotype ; Phenotype ; },
abstract = {Irrespective of the heuristic value of interpretations of developmental processes in terms of gene regulatory networks (GRNs), larger-angle views often suffer from: (i) an inadequate understanding of the relationship between genotype and phenotype; (ii) a predominantly zoocentric vision; and (iii) overconfidence in a putatively hierarchical organization of animal body plans. Here, we constructively criticize these assumptions. First, developmental biology is pervaded by adultocentrism, but development is not necessarily egg to adult. Second, during development, many unicells undergo transcriptomic profile transitions that are comparable to those recorded in pluricellular organisms; thus, their study should not be neglected from the GRN perspective. Third, the putatively hierarchical nature of the animal body is mirrored in the GRN logic, but in relating genotype to phenotype, independent assessments of the dynamics of the regulatory machinery and the animal's architecture are required, better served by a combinatorial than by a hierarchical approach. The trade-offs between spatial and temporal aspects of regulation, as well as their evolutionary consequences, are also discussed. Multicellularity may derive from a unicell's sequential phenotypes turned into different but coexisting, spatially arranged cell types. In turn, polyphenism may have been a crucial mechanism involved in the origin of complex life cycles.},
}

Animals
*Gene Regulatory Networks
Genotype
Phenotype

@article {pmid35484218,
year = {2022},
author = {Farkas, Z and Kovács, K and Sarkadi, Z and Kalapis, D and Fekete, G and Birtyik, F and Ayaydin, F and Molnár, C and Horváth, P and Pál, C and Papp, B},
title = {Gene loss and compensatory evolution promotes the emergence of morphological novelties in budding yeast.},
journal = {Nature ecology & evolution},
volume = {6},
number = {6},
pages = {763-773},
pmid = {35484218},
issn = {2397-334X},
mesh = {Mutation ; Phenotype ; Saccharomyces cerevisiae/genetics ; *Saccharomycetales/genetics ; },
abstract = {Deleterious mutations are generally considered to be irrelevant for morphological evolution. However, they could be compensated by conditionally beneficial mutations, thereby providing access to new adaptive paths. Here we use high-dimensional phenotyping of laboratory-evolved budding yeast lineages to demonstrate that new cellular morphologies emerge exceptionally rapidly as a by-product of gene loss and subsequent compensatory evolution. Unexpectedly, the capacities for invasive growth, multicellular aggregation and biofilm formation also spontaneously evolve in response to gene loss. These multicellular phenotypes can be achieved by diverse mutational routes and without reactivating the canonical regulatory pathways. These ecologically and clinically relevant traits originate as pleiotropic side effects of compensatory evolution and have no obvious utility in the laboratory environment. The extent of morphological diversity in the evolved lineages is comparable to that of natural yeast isolates with diverse genetic backgrounds and lifestyles. Finally, we show that both the initial gene loss and subsequent compensatory mutations contribute to new morphologies, with their synergistic effects underlying specific morphological changes. We conclude that compensatory evolution is a previously unrecognized source of morphological diversity and phenotypic novelties.},
}

Mutation
Phenotype
Saccharomyces cerevisiae/genetics
*Saccharomycetales/genetics

@article {pmid35514085,
year = {2022},
author = {Yuan, F and Wang, X and Zhao, B and Xu, X and Shi, M and Leng, B and Dong, X and Lu, C and Feng, Z and Guo, J and Han, G and Zhang, H and Huang, J and Chen, M and Wang, BS},
title = {The genome of the recretohalophyte Limonium bicolor provides insights into salt gland development and salinity adaptation during terrestrial evolution.},
journal = {Molecular plant},
volume = {15},
number = {6},
pages = {1024-1044},
doi = {10.1016/j.molp.2022.04.011},
pmid = {35514085},
issn = {1752-9867},
mesh = {Animals ; *Arabidopsis ; Plant Leaves/genetics ; *Plumbaginaceae/genetics ; Salinity ; Salt Gland ; Salt Tolerance/genetics ; Salt-Tolerant Plants/genetics ; },
abstract = {Halophytes have evolved specialized strategies to cope with high salinity. The extreme halophyte sea lavender (Limonium bicolor) lacks trichomes but possesses salt glands on its epidermis that can excrete harmful ions, such as sodium, to avoid salt damage. Here, we report a high-quality, 2.92-Gb, chromosome-scale L. bicolor genome assembly based on a combination of Illumina short reads, single-molecule, real-time long reads, chromosome conformation capture (Hi-C) data, and Bionano genome maps, greatly enriching the genomic information on recretohalophytes with multicellular salt glands. Although the L. bicolor genome contains genes that show similarity to trichome fate genes from Arabidopsis thaliana, it lacks homologs of the decision fate genes GLABRA3, ENHANCER OF GLABRA3, GLABRA2, TRANSPARENT TESTA GLABRA2, and SIAMESE, providing a molecular explanation for the absence of trichomes in this species. We identified key genes (LbHLH and LbTTG1) controlling salt gland development among classical trichome homologous genes and confirmed their roles by showing that their mutations markedly disrupted salt gland initiation, salt secretion, and salt tolerance, thus offering genetic support for the long-standing hypothesis that salt glands and trichomes may share a common origin. In addition, a whole-genome duplication event occurred in the L. bicolor genome after its divergence from Tartary buckwheat and may have contributed to its adaptation to high salinity. The L. bicolor genome resource and genetic evidence reported in this study provide profound insights into plant salt tolerance mechanisms that may facilitate the engineering of salt-tolerant crops.},
}

Animals
*Arabidopsis
Plant Leaves/genetics
*Plumbaginaceae/genetics
Salinity
Salt Gland
Salt Tolerance/genetics
Salt-Tolerant Plants/genetics

@article {pmid35504284,
year = {2022},
author = {Reyes-Rivera, J and Wu, Y and Guthrie, BGH and Marletta, MA and King, N and Brunet, T},
title = {Nitric oxide signaling controls collective contractions in a colonial choanoflagellate.},
journal = {Current biology : CB},
volume = {32},
number = {11},
pages = {2539-2547.e5},
doi = {10.1016/j.cub.2022.04.017},
pmid = {35504284},
issn = {1879-0445},
mesh = {Animals ; *Choanoflagellata/metabolism ; Cyclic GMP/metabolism ; Guanylate Cyclase/genetics ; Nitric Oxide/metabolism ; Nitric Oxide Synthase/genetics/metabolism ; Signal Transduction/physiology ; },
abstract = {Although signaling by the gaseous molecule nitric oxide (NO) regulates key physiological processes in animals, including contractility,1-3 immunity,4,5 development,6-9 and locomotion,10,11 the early evolution of animal NO signaling remains unclear. To reconstruct the role of NO in the animal stem lineage, we set out to study NO signaling in choanoflagellates, the closest living relatives of animals.12 In animals, NO produced by the nitric oxide synthase (NOS) canonically signals through cGMP by activating soluble guanylate cyclases (sGCs).13,14 We surveyed the distribution of the NO signaling pathway components across the diversity of choanoflagellates and found three species that express NOS (of either bacterial or eukaryotic origin), sGCs, and downstream genes previously shown to be involved in the NO/cGMP pathway. One of the species coexpressing sGCs and a bacterial-type NOS, Choanoeca flexa, forms multicellular sheets that undergo collective contractions controlled by cGMP.15 We found that treatment with NO induces cGMP synthesis and contraction in C. flexa. Biochemical assays show that NO directly binds C. flexa sGC1 and stimulates its cyclase activity. The NO/cGMP pathway acts independently from other inducers of C. flexa contraction, including mechanical stimuli and heat, but sGC activity is required for contractions induced by light-to-dark transitions. The output of NO signaling in C. flexa-contractions resulting in a switch from feeding to swimming-resembles the effect of NO in sponges1-3 and cnidarians,11,16,17 where it interrupts feeding and activates contractility. These data provide insights into the biology of the first animals and the evolution of NO signaling.},
}

Animals
*Choanoflagellata/metabolism
Cyclic GMP/metabolism
Guanylate Cyclase/genetics
Nitric Oxide/metabolism
Nitric Oxide Synthase/genetics/metabolism
Signal Transduction/physiology

@article {pmid35659869,
year = {2022},
author = {Phillips, JE and Santos, M and Konchwala, M and Xing, C and Pan, D},
title = {Genome editing in the unicellular holozoan Capsaspora owczarzaki suggests a premetazoan role for the Hippo pathway in multicellular morphogenesis.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
doi = {10.7554/eLife.77598},
pmid = {35659869},
issn = {2050-084X},
support = {EY015708/NH/NIH HHS/United States ; Investigator/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Eukaryota/genetics ; *Evolution, Molecular ; *Gene Editing ; Hippo Signaling Pathway ; Morphogenesis ; },
abstract = {Animal development is mediated by a surprisingly small set of canonical signaling pathways such as Wnt, Hedgehog, TGF-beta, Notch, and Hippo pathways. Although once thought to be present only in animals, recent genome sequencing has revealed components of these pathways in the closest unicellular relatives of animals. These findings raise questions about the ancestral functions of these developmental pathways and their potential role in the emergence of animal multicellularity. Here, we provide the first functional characterization of any of these developmental pathways in unicellular organisms by developing techniques for genetic manipulation in Capsaspora owczarzaki, a close unicellular relative of animals that displays aggregative multicellularity. We then use these tools to characterize the Capsaspora ortholog of the Hippo signaling nuclear effector YAP/TAZ/Yorkie (coYki), a key regulator of tissue size in animals. In contrast to what might be expected based on studies in animals, we show that coYki is dispensable for cell proliferation but regulates cytoskeletal dynamics and the three-dimensional (3D) shape of multicellular structures. We further demonstrate that the cytoskeletal abnormalities of individual coYki mutant cells underlie the abnormal 3D shape of coYki mutant aggregates. Taken together, these findings implicate an ancestral role for the Hippo pathway in cytoskeletal dynamics and multicellular morphogenesis predating the origin of animal multicellularity, which was co-opted during evolution to regulate cell proliferation.},
}

Animals
Eukaryota/genetics
*Evolution, Molecular
*Gene Editing
Hippo Signaling Pathway
Morphogenesis

@article {pmid35651757,
year = {2022},
author = {Díaz, E and Febres, A and Giammarresi, M and Silva, A and Vanegas, O and Gomes, C and Ponte-Sucre, A},
title = {G Protein-Coupled Receptors as Potential Intercellular Communication Mediators in Trypanosomatidae.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {812848},
doi = {10.3389/fcimb.2022.812848},
pmid = {35651757},
issn = {2235-2988},
mesh = {*Calcitonin Gene-Related Peptide/pharmacology ; Cell Communication ; Humans ; *Leishmania/metabolism ; Receptor Activity-Modifying Proteins/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Substance P/pharmacology ; },
abstract = {Detection and transduction of environmental signals, constitute a prerequisite for successful parasite invasion; i.e., Leishmania transmission, survival, pathogenesis and disease manifestation and dissemination, with diverse molecules functioning as inter-cellular signaling ligands. Receptors [i.e., G protein-coupled receptors (GPCRs)] and their associated transduction mechanisms, well conserved through evolution, specialize in this function. However, canonical GPCR-related signal transduction systems have not been described in Leishmania, although orthologs, with reduced domains and function, have been identified in Trypanosomatidae. These inter-cellular communication means seem to be essential for multicellular and unicellular organism's survival. GPCRs are flexible in their molecular architecture and may interact with the so-called receptor activity-modifying proteins (RAMPs), which modulate their function, changing GPCRs pharmacology, acting as chaperones and regulating signaling and/or trafficking in a receptor-dependent manner. In the skin, vasoactive- and neuro- peptides released in response to the noxious stimuli represented by the insect bite may trigger parasite physiological responses, for example, chemotaxis. For instance, in Leishmania (V.) braziliensis, sensory [Substance P, SP, chemoattractant] and autonomic [Vasoactive Intestinal Peptide, VIP, and Neuropeptide Y, NPY, chemorepellent] neuropeptides at physiological levels stimulate in vitro effects on parasite taxis. VIP and NPY chemotactic effects are impaired by their corresponding receptor antagonists, suggesting that the stimulated responses might be mediated by putative GPCRs (with essential conserved receptor domains); the effect of SP is blocked by [(D-Pro 2, D-Trp7,9]-Substance P (10-6 M)] suggesting that it might be mediated by neurokinin-1 transmembrane receptors. Additionally, vasoactive molecules like Calcitonin Gene-Related Peptide [CGRP] and Adrenomedullin [AM], exert a chemorepellent effect and increase the expression of a 24 kDa band recognized in western blot analysis by (human-)-RAMP-2 antibodies. In-silico search oriented towards GPCRs-like receptors and signaling cascades detected a RAMP-2-aligned sequence corresponding to Leishmania folylpolyglutamate synthase and a RAMP-3 aligned protein, a hypothetical Leishmania protein with yet unknown function, suggesting that in Leishmania, CGRP and AM activities may be modulated by RAMP- (-2) and (-3) homologs. The possible presence of proteins and molecules potentially involved in GPCRs cascades, i.e., RAMPs, signpost conservation of ancient signaling systems associated with responses, fundamental for cell survival, (i.e., taxis and migration) and may constitute an open field for description of pharmacophores against Leishmania parasites.},
}

*Calcitonin Gene-Related Peptide/pharmacology
Cell Communication
Humans
*Leishmania/metabolism
Receptor Activity-Modifying Proteins/metabolism
Receptors, G-Protein-Coupled/metabolism
Substance P/pharmacology

@article {pmid35588907,
year = {2022},
author = {Udayantha, HMV and Samaraweera, AV and Liyanage, DS and Sandamalika, WMG and Lim, C and Yang, H and Lee, JH and Lee, S and Lee, J},
title = {Molecular characterization, antiviral activity, and UV-B damage responses of Caspase-9 from Amphiprion clarkii.},
journal = {Fish & shellfish immunology},
volume = {125},
number = {},
pages = {247-257},
doi = {10.1016/j.fsi.2022.05.023},
pmid = {35588907},
issn = {1095-9947},
mesh = {Animals ; Antiviral Agents ; Caspase 3 ; Caspase 9 ; *Cyprinidae ; *Perciformes ; Phylogeny ; Poly I-C/pharmacology ; },
abstract = {Apoptosis plays a vital role in maintaining cellular homeostasis in multicellular organisms. Caspase-9 (casp-9) is one of the major initiator caspases that induces apoptosis by activating downstream intrinsic apoptosis pathway genes. Here, we isolated the cDNA sequence (1992 bp) of caspase-9 from Amphiprion clarkii (Accasp-9) that consists of a 1305 bp coding region and encodes a 434 aa protein. In silico analysis showed that Accasp-9 has a theoretical isoelectric point of 5.81 and a molecular weight of 48.45 kDa. Multiple sequence alignment revealed that the CARD domain is located at the N-terminus, whereas the large P-20 and small P-10 domains are located at the C-terminus. Moreover, a highly conserved pentapeptide active site (296QACGG301), as well as histidine and cysteine active sites, are also retained at the C-terminus. In phylogenetic analysis, Accasp-9 formed a clade with casp-9 from different species, distinct from other caspases. Accasp-9 was highly expressed in the gill and intestine compared with other tissues analyzed in healthy A. clarkii. Accasp-9 expression was significantly elevated in the blood after stimulation with Vibrio harveyi and polyinosinic:polycytidylic acid (poly I:C; 12-48 h), but not with lipopolysaccharide. The nucleoprotein expression of the viral hemorrhagic septicemia virus was significantly reduced in Accasp-9 overexpressed fathead minnow (FHM) cells compared with that in the control. In addition, other in vitro assays revealed that cell apoptosis was significantly elevated in poly I:C and UV-B-treated Accasp-9 transfected FHM cells. However, H248P or C298S mutated Accasp-9 significantly reduced apoptosis in UV-B irradiated cells. Collectively, our results show that Accasp-9 might play a defensive role against invading pathogens and UV-B radiation and H248 and C298 active residues are significantly involved in apoptosis in teleosts.},
}

Animals
Antiviral Agents
Caspase 3
Caspase 9
*Cyprinidae
*Perciformes
Phylogeny
Poly I-C/pharmacology

@article {pmid35483597,
year = {2022},
author = {Wang, B and Zhu, F and Shi, Z and Huang, Z and Sun, R and Wang, Q and Ouyang, G and Ji, W},
title = {Molecular characteristics, polymorphism and expression analysis of mhc Ⅱ in yellow catfish(pelteobagrus fulvidraco)responding to Flavobacterium columnare infection.},
journal = {Fish & shellfish immunology},
volume = {125},
number = {},
pages = {90-100},
doi = {10.1016/j.fsi.2022.04.036},
pmid = {35483597},
issn = {1095-9947},
mesh = {Animals ; *Catfishes ; Fish Proteins/chemistry ; Flavobacterium/genetics ; Phylogeny ; RNA, Messenger/metabolism ; },
abstract = {The major histocompatibility complex (MHC) is an important component of the immune system of vertebrates, which plays a vital role in presenting extrinsic antigens. In this study, we cloned and characterized the mhc ⅡA and mhc ⅡB genes of yellow catfish Pelteobagrus fulvidraco. The open reading frames (ORFs) of mhc ⅡA and mhc ⅡB genes were 708 bp and 747bp in length, encoding 235 and 248 amino acids, respectively. The structure of mhc ⅡA and mhc ⅡB includes a signal peptide, an α1/β1 domain, an α2/β2 domain, a transmembrane region and a cytoplasmic region. Homologous identity analysis revealed that both mhc ⅡA and mhc ⅡB shared high protein sequence similarity with that of Chinese longsnout catfish Leiocassis longirostris. mhc ⅡA and mhc ⅡB showed similar expression patterns in different tissues, with the higher expression level in spleen, head kidney and gill and lower expression in liver, stomach, gall bladder and heart. The mRNA expression level of mhc ⅡA and mhc ⅡB in different embryonic development stages also showed the similar trends. The higher expression was detected from fertilized egg to 32 cell stage, low expression from multicellular period to 3 days post hatching (dph), and then the expression increased to a higher level from 4 dph to 14 dph. The mRNA expression levels of mhc ⅡA and mhc ⅡB were significantly up-regulated not only in the body kidney and spleen, but also in the midgut, hindgut, liver and gill after challenge of Flavobacterium columnare. The results suggest that Mhc Ⅱ plays an important role in the anti-infection process of yellow catfish P. fulvidraco.},
}

Animals
*Catfishes
Fish Proteins/chemistry
Flavobacterium/genetics
Phylogeny
RNA, Messenger/metabolism

@article {pmid35626631,
year = {2022},
author = {Paul, B and Sterner, ZR and Buchholz, DR and Shi, YB and Sachs, LM},
title = {Thyroid and Corticosteroid Signaling in Amphibian Metamorphosis.},
journal = {Cells},
volume = {11},
number = {10},
pages = {},
doi = {10.3390/cells11101595},
pmid = {35626631},
issn = {2073-4409},
support = {825753//ERGO a European Union's Horizon 2020 research and innovation program/ ; },
mesh = {Adrenal Cortex Hormones ; Amphibians ; Animals ; *Metamorphosis, Biological/physiology ; *Thyroid Gland/metabolism ; Thyroid Hormones/metabolism ; Vertebrates/metabolism ; },
abstract = {In multicellular organisms, development is based in part on the integration of communication systems. Two neuroendocrine axes, the hypothalamic-pituitary-thyroid and the hypothalamic-pituitary-adrenal/interrenal axes, are central players in orchestrating body morphogenesis. In all vertebrates, the hypothalamic-pituitary-thyroid axis controls thyroid hormone production and release, whereas the hypothalamic-pituitary-adrenal/interrenal axis regulates the production and release of corticosteroids. One of the most salient effects of thyroid hormones and corticosteroids in post-embryonic developmental processes is their critical role in metamorphosis in anuran amphibians. Metamorphosis involves modifications to the morphological and biochemical characteristics of all larval tissues to enable the transition from one life stage to the next life stage that coincides with an ecological niche switch. This transition in amphibians is an example of a widespread phenomenon among vertebrates, where thyroid hormones and corticosteroids coordinate a post-embryonic developmental transition. The review addresses the functions and interactions of thyroid hormone and corticosteroid signaling in amphibian development (metamorphosis) as well as the developmental roles of these two pathways in vertebrate evolution.},
}

Adrenal Cortex Hormones
Amphibians
Animals
*Metamorphosis, Biological/physiology
*Thyroid Gland/metabolism
Thyroid Hormones/metabolism
Vertebrates/metabolism

@article {pmid35486699,
year = {2022},
author = {Staps, M and Tarnita, CE},
title = {When being flexible matters: Ecological underpinnings for the evolution of collective flexibility and task allocation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {18},
pages = {e2116066119},
doi = {10.1073/pnas.2116066119},
pmid = {35486699},
issn = {1091-6490},
mesh = {Animals ; Ants ; *Behavior, Animal ; *Biological Evolution ; Ecology ; Humans ; *Social Behavior ; },
abstract = {Task allocation is a central feature of collective organization. Living collective systems, such as multicellular organisms or social insect colonies, have evolved diverse ways to allocate individuals to different tasks, ranging from rigid, inflexible task allocation that is not adjusted to changing circumstances to more fluid, flexible task allocation that is rapidly adjusted to the external environment. While the mechanisms underlying task allocation have been intensely studied, it remains poorly understood whether differences in the flexibility of task allocation can be viewed as adaptive responses to different ecological contexts—for example, different degrees of temporal variability. Motivated by this question, we develop an analytically tractable mathematical framework to explore the evolution of task allocation in dynamic environments. We find that collective flexibility is not necessarily always adaptive, and fails to evolve in environments that change too slowly (relative to how long tasks can be left unattended) or too quickly (relative to how rapidly task allocation can be adjusted). We further employ the framework to investigate how environmental variability impacts the internal organization of task allocation, which allows us to propose adaptive explanations for some puzzling empirical observations, such as seemingly unnecessary task switching under constant environmental conditions, apparent task specialization without efficiency benefits, and high levels of individual inactivity. Altogether, this work provides a general framework for probing the evolved diversity of task allocation strategies in nature and reinforces the idea that considering a system’s ecology is crucial to explaining its collective organization.},
}

Animals
Ants
*Behavior, Animal
*Biological Evolution
Ecology
Humans
*Social Behavior

@article {pmid35621103,
year = {2022},
author = {Puzakov, MV and Puzakova, LV},
title = {[Prevalence, Diversity, and Evolution of L18 (DD37E) Transposons in the Genomes of Cnidarians].},
journal = {Molekuliarnaia biologiia},
volume = {56},
number = {3},
pages = {476-490},
doi = {10.31857/S0026898422030120},
pmid = {35621103},
issn = {0026-8984},
mesh = {Animals ; *Cnidaria/genetics ; *DNA Transposable Elements/genetics ; Prevalence ; },
abstract = {Transposable elements have a significant impact on the structure and functioning of multicellular genomes, and also serve as a source of new genes. Studying the diversity and evolution of transposable elements in different taxa is necessary for the fundamental understanding of their role in genomes. The Tc1/mariner elements are one of the most widespread and diverse groups of DNA transposons. In this work, the structure, distribution, diversity, and evolution of the L18 (DD37E) elements in the genomes of cnidarians (Cnidaria) were studied for the first time. As a result, it was found that the L18 group is an independent family (and not a subfamily of the TLE family, as previously thought) in the Tc1/mariner superfamily. Of the 51 detected elements, only four had potentially functional copies. It is assumed that the L18 transposons are of ancient origin, and, in addition, the elements found in the genomes of organisms of the Anthozoa and Hydrozoa classes do not come from a common ancestral transposon within the Cnidaria phylum. In organisms of the Hydrozoa class, L18 transposons appeared as a result of horizontal transfer at a later time period. An intraspecies comparison of the diversity of the L18 elements demonstrates high homogeneity with respect to "old" transposons, which have already lost their activity. At the same time, distant populations, as in the case of Hydra viridissima, have differences in the representation of DNA transposons and the number of copies. These data supplement the knowledge on the diversity and evolution of Tc1/mariner transposons and contribute to the study of the influence of mobile genetic elements on the evolution of multicellular organisms.},
}

Animals
*Cnidaria/genetics
*DNA Transposable Elements/genetics
Prevalence

@article {pmid35574025,
year = {2022},
author = {Ritch, SJ and Telleria, CM},
title = {The Transcoelomic Ecosystem and Epithelial Ovarian Cancer Dissemination.},
journal = {Frontiers in endocrinology},
volume = {13},
number = {},
pages = {886533},
pmid = {35574025},
issn = {1664-2392},
mesh = {Carcinoma, Ovarian Epithelial ; *Ecosystem ; Epithelial Cells/metabolism ; Female ; Humans ; Neoplasm Recurrence, Local ; *Ovarian Neoplasms/therapy ; Tumor Microenvironment ; },
abstract = {Epithelial ovarian cancer (EOC) is considered the deadliest gynecological disease and is normally diagnosed at late stages, at which point metastasis has already occurred. Throughout disease progression, EOC will encounter various ecosystems and the communication between cancer cells and these microenvironments will promote the survival and dissemination of EOC. The primary tumor is thought to develop within the ovaries or the fallopian tubes, both of which provide a microenvironment with high risk of causing DNA damage and enhanced proliferation. EOC disseminates by direct extension from the primary tumors, as single cells or multicellular aggregates. Under the influence of cellular and non-cellular factors, EOC spheroids use the natural flow of peritoneal fluid to reach distant organs within the peritoneal cavity. These cells can then implant and seed distant organs or tissues, which develop rapidly into secondary tumor nodules. The peritoneal tissue and the omentum are two common sites of EOC metastasis, providing a microenvironment that supports EOC invasion and survival. Current treatment for EOC involves debulking surgery followed by platinum-taxane combination chemotherapy; however, most patients will relapse with a chemoresistant disease with tumors developed within the peritoneum. Therefore, understanding the role of the unique microenvironments that promote EOC transcoelomic dissemination is important in improving patient outcomes from this disease. In this review article, we address the process of ovarian cancer cellular fate at the site of its origin in the secretory cells of the fallopian tube or in the ovarian surface epithelial cells, their detachment process, how the cells survive in the peritoneal fluid avoiding cell death triggers, and how cancer- associated cells help them in the process. Finally, we report the mechanisms used by the ovarian cancer cells to adhere and migrate through the mesothelial monolayer lining the peritoneum. We also discuss the involvement of the transcoelomic ecosystem on the development of chemoresistance of EOC.},
}

Carcinoma, Ovarian Epithelial
*Ecosystem
Epithelial Cells/metabolism
Female
Humans
Neoplasm Recurrence, Local
*Ovarian Neoplasms/therapy
Tumor Microenvironment

@article {pmid35572413,
year = {2022},
author = {Zhang, J and Shen, N and Li, C and Xiang, X and Liu, G and Gui, Y and Patev, S and Hibbett, DS and Barry, K and Andreopoulos, W and Lipzen, A and Riley, R and He, G and Yan, M and Grigoriev, IV and Shan Kwan, H and Kit Cheung, M and Bian, Y and Xiao, Y},
title = {Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes.},
journal = {Journal of advanced research},
volume = {38},
number = {},
pages = {91-106},
doi = {10.1016/j.jare.2021.09.008},
pmid = {35572413},
issn = {2090-1224},
mesh = {*Agaricales/genetics ; Genome ; Genome-Wide Association Study ; Metagenomics ; *Shiitake Mushrooms/genetics ; },
abstract = {Introduction: Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi.

Objectives: This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution.

Methods: We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution.

Results: We detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation.

Conclusion: Adaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.},
}

*Agaricales/genetics
Genome
Genome-Wide Association Study
Metagenomics
*Shiitake Mushrooms/genetics

@article {pmid35570706,
year = {2022},
author = {Heinz, MC and Peters, NA and Oost, KC and Lindeboom, RGH and van Voorthuijsen, L and Fumagalli, A and van der Net, MC and de Medeiros, G and Hageman, JH and Verlaan-Klink, I and Borel Rinkes, IHM and Liberali, P and Gloerich, M and van Rheenen, J and Vermeulen, M and Kranenburg, O and Snippert, HJG},
title = {Liver Colonization by Colorectal Cancer Metastases Requires YAP-Controlled Plasticity at the Micrometastatic Stage.},
journal = {Cancer research},
volume = {82},
number = {10},
pages = {1953-1968},
doi = {10.1158/0008-5472.CAN-21-0933},
pmid = {35570706},
issn = {1538-7445},
support = {UU 2013-6070//Dutch Cancer Society/ ; 803608//ERC Starting Grant/ ; },
mesh = {Animals ; *Colorectal Neoplasms/pathology ; Humans ; *Liver Neoplasms/metabolism ; Mice ; Neoplasm Micrometastasis/pathology ; Neoplastic Stem Cells/pathology ; },
abstract = {Micrometastases of colorectal cancer can remain dormant for years prior to the formation of actively growing, clinically detectable lesions (i.e., colonization). A better understanding of this step in the metastatic cascade could help improve metastasis prevention and treatment. Here we analyzed liver specimens of patients with colorectal cancer and monitored real-time metastasis formation in mouse livers using intravital microscopy to reveal that micrometastatic lesions are devoid of cancer stem cells (CSC). However, lesions that grow into overt metastases demonstrated appearance of de novo CSCs through cellular plasticity at a multicellular stage. Clonal outgrowth of patient-derived colorectal cancer organoids phenocopied the cellular and transcriptomic changes observed during in vivo metastasis formation. First, formation of mature CSCs occurred at a multicellular stage and promoted growth. Conversely, failure of immature CSCs to generate more differentiated cells arrested growth, implying that cellular heterogeneity is required for continuous growth. Second, early-stage YAP activity was required for the survival of organoid-forming cells. However, subsequent attenuation of early-stage YAP activity was essential to allow for the formation of cell type heterogeneity, while persistent YAP signaling locked micro-organoids in a cellularly homogenous and growth-stalled state. Analysis of metastasis formation in mouse livers using single-cell RNA sequencing confirmed the transient presence of early-stage YAP activity, followed by emergence of CSC and non-CSC phenotypes, irrespective of the initial phenotype of the metastatic cell of origin. Thus, establishment of cellular heterogeneity after an initial YAP-controlled outgrowth phase marks the transition to continuously growing macrometastases.

SIGNIFICANCE: Characterization of the cell type dynamics, composition, and transcriptome of early colorectal cancer liver metastases reveals that failure to establish cellular heterogeneity through YAP-controlled epithelial self-organization prohibits the outgrowth of micrometastases. See related commentary by LeBleu, p. 1870.},
}

Animals
*Colorectal Neoplasms/pathology
Humans
*Liver Neoplasms/metabolism
Mice
Neoplasm Micrometastasis/pathology
Neoplastic Stem Cells/pathology

@article {pmid35563757,
year = {2022},
author = {Stange, K and Keric, A and Friese, A and Röntgen, M},
title = {Preparation of Spheroids from Primary Pig Cells in a Mid-Scale Bioreactor Retaining Their Myogenic Potential.},
journal = {Cells},
volume = {11},
number = {9},
pages = {},
pmid = {35563757},
issn = {2073-4409},
support = {IBÖ-07, 031B1041//Federal Ministry of Education and Research/ ; },
mesh = {Animals ; Bioreactors ; Cell Differentiation ; *Muscle Development ; *Muscle Fibers, Skeletal ; Swine ; },
abstract = {Three-dimensional cell culture techniques mimic the in vivo cell environment more adequately than flat surfaces. Spheroids are multicellular aggregates and we aimed to produce scaffold-free spheroids of myogenic origin, called myospheres, using a mid-scale incubator and bioreactor hybrid. For the first time, we obtained spheroids from primary porcine muscle cells (PMCs) with this technology and compared their morphology and growth parameters, marker expression, and myogenic potential to C2C12-derived spheroids. Both cell types were able to form round-shaped spheroids in the bioreactor already after 24 h. The mean diameter of the C2C12 spheroids (44.6 µm) was larger than that of the PMCs (32.7 µm), and the maximum diameter exceeded 1 mm. C2C12 cells formed less aggregates than PMCs with a higher packing density (cell nuclei/mm2). After dissociation from the spheroids, C2C12 cells and PMCs started to proliferate again and were able to differentiate into the myogenic lineage, as shown by myotube formation and the expression of F-Actin, Desmin, MyoG, and Myosin. For C2C12, multinucleated syncytia and Myosin expression were observed in spheroids, pointing to accelerated myogenic differentiation. In conclusion, the mid-scale incubator and bioreactor system is suitable for spheroid formation and cultivation from primary muscle cells while preserving their myogenic potential.},
}

Animals
Bioreactors
Cell Differentiation
*Muscle Development
*Muscle Fibers, Skeletal
Swine

@article {pmid35551578,
year = {2022},
author = {Eskandari, E and Eaves, CJ},
title = {Paradoxical roles of caspase-3 in regulating cell survival, proliferation, and tumorigenesis.},
journal = {The Journal of cell biology},
volume = {221},
number = {6},
pages = {},
doi = {10.1083/jcb.202201159},
pmid = {35551578},
issn = {1540-8140},
support = {21296//Canadian Cancer Society Research Institute/ ; //University of British Columbia/ ; },
mesh = {*Apoptosis/genetics ; Carcinogenesis/genetics ; Caspase 3 ; Caspase 8/genetics ; Caspase 9 ; Cell Proliferation ; Cell Survival/genetics ; Cell Transformation, Neoplastic ; Humans ; *Saccharomyces cerevisiae ; },
abstract = {Caspase-3 is a widely expressed member of a conserved family of proteins, generally recognized for their activated proteolytic roles in the execution of apoptosis in cells responding to specific extrinsic or intrinsic inducers of this mode of cell death. However, accumulating evidence indicates that caspase-3 also plays key roles in regulating the growth and homeostatic maintenance of both normal and malignant cells and tissues in multicellular organisms. Given that yeast possess an ancestral caspase-like gene suggests that the caspase-3 protein may have acquired different functions later during evolution to better meet the needs of more complex multicellular organisms, but without necessarily losing all of the functions of its ancestral yeast precursor. This review provides an update on what has been learned about these interesting dichotomous roles of caspase-3, their evolution, and their potential relevance to malignant as well as normal cell biology.},
}

*Apoptosis/genetics
Carcinogenesis/genetics
Caspase 3
Caspase 8/genetics
Caspase 9
Cell Proliferation
Cell Survival/genetics
Cell Transformation, Neoplastic
Humans
*Saccharomyces cerevisiae

@article {pmid35135345,
year = {2022},
author = {La Richelière, F and Muñoz, G and Guénard, B and Dunn, RR and Economo, EP and Powell, S and Sanders, NJ and Weiser, MD and Abouheif, E and Lessard, JP},
title = {Warm and arid regions of the world are hotspots of superorganism complexity.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1968},
pages = {20211899},
pmid = {35135345},
issn = {1471-2954},
mesh = {Animals ; *Ants/genetics ; Desert Climate ; Neurons ; Phenotype ; Social Class ; },
abstract = {Biologists have long been fascinated by the processes that give rise to phenotypic complexity of organisms, yet whether there exist geographical hotspots of phenotypic complexity remains poorly explored. Phenotypic complexity can be readily observed in ant colonies, which are superorganisms with morphologically differentiated queen and worker castes analogous to the germline and soma of multicellular organisms. Several ant species have evolved 'worker polymorphism', where workers in a single colony show quantifiable differences in size and head-to-body scaling. Here, we use 256 754 occurrence points from 8990 ant species to investigate the geography of worker polymorphism. We show that arid regions of the world are the hotspots of superorganism complexity. Tropical savannahs and deserts, which are typically species-poor relative to tropical or even temperate forests, harbour the highest densities of polymorphic ants. We discuss the possible adaptive advantages that worker polymorphism provides in arid environments. Our work may provide a window into the environmental conditions that promote the emergence of highly complex phenotypes.},
}

Animals
*Ants/genetics
Desert Climate
Neurons
Phenotype
Social Class

@article {pmid35349792,
year = {2022},
author = {Toret, C and Picco, A and Boiero-Sanders, M and Michelot, A and Kaksonen, M},
title = {The cellular slime mold Fonticula alba forms a dynamic, multicellular collective while feeding on bacteria.},
journal = {Current biology : CB},
volume = {32},
number = {9},
pages = {1961-1973.e4},
doi = {10.1016/j.cub.2022.03.018},
pmid = {35349792},
issn = {1879-0445},
mesh = {Animals ; Bacteria ; *Dictyosteliida ; Eukaryota ; Fungi ; Phylogeny ; },
abstract = {Multicellularity evolved in fungi and animals, or the opisthokonts, from their common amoeboflagellate ancestor but resulted in strikingly distinct cellular organizations. The origins of this multicellularity divergence are not known. The stark mechanistic differences that underlie the two groups and the lack of information about ancestral cellular organizations limits progress in this field. We discovered a new type of invasive multicellular behavior in Fonticula alba, a unique species in the opisthokont tree, which has a simple, bacteria-feeding sorocarpic amoeba lifestyle. This invasive multicellularity follows germination dependent on the bacterial culture state, after which amoebae coalesce to form dynamic collectives that invade virgin bacterial resources. This bacteria-dependent social behavior emerges from amoeba density and allows for rapid and directed invasion. The motile collectives have animal-like properties but also hyphal-like search and invasive behavior. These surprising findings enrich the diverse multicellularities present within the opisthokont lineage and offer a new perspective on fungal origins.},
}

Animals
Bacteria
*Dictyosteliida
Eukaryota
Fungi
Phylogeny

@article {pmid35470227,
year = {2022},
author = {Mulcahey, PJ and Chen, Y and Driscoll, N and Murphy, BB and Dickens, OO and Johnson, ATC and Vitale, F and Takano, H},
title = {Multimodal, Multiscale Insights into Hippocampal Seizures Enabled by Transparent, Graphene-Based Microelectrode Arrays.},
journal = {eNeuro},
volume = {9},
number = {3},
pages = {},
doi = {10.1523/ENEURO.0386-21.2022},
pmid = {35470227},
issn = {2373-2822},
mesh = {Animals ; *Epilepsy, Temporal Lobe ; *Graphite ; Hippocampus ; Mice ; Microelectrodes ; Seizures ; },
abstract = {Hippocampal seizures are a defining feature of mesial temporal lobe epilepsy (MTLE). Area CA1 of the hippocampus is commonly implicated in the generation of seizures, which may occur because of the activity of endogenous cell populations or of inputs from other regions within the hippocampal formation. Simultaneously observing activity at the cellular and network scales in vivo remains challenging. Here, we present a novel technology for simultaneous electrophysiology and multicellular calcium imaging of CA1 pyramidal cells (PCs) in mice enabled by a transparent graphene-based microelectrode array (Gr MEA). We examine PC firing at seizure onset, oscillatory coupling, and the dynamics of the seizure traveling wave as seizures evolve. Finally, we couple features derived from both modalities to predict the speed of the traveling wave using bootstrap aggregated regression trees. Analysis of the most important features in the regression trees suggests a transition among states in the evolution of hippocampal seizures.},
}

Animals
*Epilepsy, Temporal Lobe
*Graphite
Hippocampus
Mice
Microelectrodes
Seizures

@article {pmid35530508,
year = {2022},
author = {de la Fuente, M and Novo, M},
title = {Understanding Diversity, Evolution, and Structure of Small Heat Shock Proteins in Annelida Through in Silico Analyses.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {817272},
doi = {10.3389/fphys.2022.817272},
pmid = {35530508},
issn = {1664-042X},
abstract = {Small heat shock proteins (sHsps) are oligomeric stress proteins characterized by an α-crystallin domain (ACD). These proteins are localized in different subcellular compartments and play critical roles in the stress physiology of tissues, organs, and whole multicellular eukaryotes. They are ubiquitous proteins found in all living organisms, from bacteria to mammals, but they have never been studied in annelids. Here, a data set of 23 species spanning the annelid tree of life, including mostly transcriptomes but also two genomes, was interrogated and 228 novel putative sHsps were identified and manually curated. The analysis revealed very high protein diversity and showed that a significant number of sHsps have a particular dimeric architecture consisting of two tandemly repeated ACDs. The phylogenetic analysis distinguished three main clusters, two of them containing both monomeric sHsps, and ACDs located downstream in the dimeric sHsps, and the other one comprising the upstream ACDs from those dimeric forms. Our results support an evolutionary history of these proteins based on duplication events prior to the Spiralia split. Monomeric sHsps 76) were further divided into five subclusters. Physicochemical properties, subcellular location predictions, and sequence conservation analyses provided insights into the differentiating elements of these putative functional groups. Strikingly, three of those subclusters included sHsps with features typical of metazoans, while the other two presented characteristics resembling non-metazoan proteins. This study provides a solid background for further research on the diversity, evolution, and function in the family of the sHsps. The characterized annelid sHsps are disclosed as essential for improving our understanding of this important family of proteins and their pleotropic functions. The features and the great diversity of annelid sHsps position them as potential powerful molecular biomarkers of environmental stress for acting as prognostic tool in a diverse range of environments.},
}

@article {pmid34147034,
year = {2022},
author = {Caipa Garcia, AL and Arlt, VM and Phillips, DH},
title = {Organoids for toxicology and genetic toxicology: applications with drugs and prospects for environmental carcinogenesis.},
journal = {Mutagenesis},
volume = {37},
number = {2},
pages = {143-154},
pmid = {34147034},
issn = {1464-3804},
support = {MR/N013700/1//UK Medical Research Council/ ; //National Institute for Health Research/ ; },
mesh = {Animals ; Carcinogenesis ; Cell Culture Techniques ; Humans ; Mammals ; Models, Biological ; *Organoids ; *Pluripotent Stem Cells ; },
abstract = {Advances in three-dimensional (3D) cell culture technology have led to the development of more biologically and physiologically relevant models to study organ development, disease, toxicology and drug screening. Organoids have been derived from many mammalian tissues, both normal and tumour, from adult stem cells and from pluripotent stem cells. Tissue organoids can retain many of the cell types and much of the structure and function of the organ of origin. Organoids derived from pluripotent stem cells display increased complexity compared with organoids derived from adult stem cells. It has been shown that organoids express many functional xenobiotic-metabolising enzymes including cytochrome P450s (CYPs). This has benefitted the drug development field in facilitating pre-clinical testing of more personalised treatments and in developing large toxicity and efficacy screens for a range of compounds. In the field of environmental and genetic toxicology, treatment of organoids with various compounds has generated responses that are close to those obtained in primary tissues and in vivo models, demonstrating the biological relevance of these in vitro multicellular 3D systems. Toxicological investigations of compounds in different tissue organoids have produced promising results indicating that organoids will refine future studies on the effects of environmental exposures and carcinogenic risk to humans. With further development and standardised procedures, advancing our understanding on the metabolic capabilities of organoids will help to validate their use to investigate the modes of action of environmental carcinogens.},
}

Animals
Carcinogenesis
Cell Culture Techniques
Humans
Mammals
Models, Biological
*Organoids
*Pluripotent Stem Cells

@article {pmid35472432,
year = {2022},
author = {Chaigne, A and Brunet, T},
title = {Incomplete abscission and cytoplasmic bridges in the evolution of eukaryotic multicellularity.},
journal = {Current biology : CB},
volume = {32},
number = {8},
pages = {R385-R397},
doi = {10.1016/j.cub.2022.03.021},
pmid = {35472432},
issn = {1879-0445},
abstract = {The textbook view of cell division terminates with the final separation of the two daughter cells in the process called abscission. However, in contrast to this classical view, a variety of cell types in multicellular organisms are connected through cytoplasmic bridges, which most often form by incomplete abscission or - more rarely - by local fusion of plasma membranes. In this review, we survey the distribution, function, and formation of cytoplasmic bridges across the eukaryotic tree of life. We find that cytoplasmic bridges are widespread, and were likely ancestrally present, in almost all lineages of eukaryotes with clonal multicellularity - including the five 'complex multicellular' lineages: animals, fungi, land plants, red algae, and brown algae. In animals, cytoplasmic bridges resulting from incomplete abscission are ubiquitous in the germline and common in pluripotent cell types. Although cytoplasmic bridges have been less studied than other structural mediators of multicellularity (such as adhesion proteins and extracellular matrix), we propose that they have played a pivotal role in the repeated evolution of eukaryotic clonal multicellularity - possibly by first performing a structural role and later by allowing exchange of nutrients and/or intercellular communication, which notably buffered cell-cell competition by averaging gene expression. Bridges were eventually lost from many animal tissues in concert with the evolution of spatial cell differentiation, cell motility within the organism, and other mechanisms for intercellular distribution of signals and metabolites. Finally, we discuss the molecular basis for the evolution of incomplete abscission and examine the alternative hypotheses of single or multiple origins.},
}

@article {pmid34716098,
year = {2022},
author = {Bogaert, KA and Blomme, J and Beeckman, T and De Clerck, O},
title = {Auxin's origin: do PILS hold the key?.},
journal = {Trends in plant science},
volume = {27},
number = {3},
pages = {227-236},
doi = {10.1016/j.tplants.2021.09.008},
pmid = {34716098},
issn = {1878-4372},
mesh = {Biological Transport ; *Indoleacetic Acids/metabolism ; *Membrane Transport Proteins/genetics/metabolism ; Plants/genetics/metabolism ; },
abstract = {Auxin is a key regulator of many developmental processes in land plants and plays a strikingly similar role in the phylogenetically distant brown seaweeds. Emerging evidence shows that the PIN and PIN-like (PILS) auxin transporter families have preceded the evolution of the canonical auxin response pathway. A wide conservation of PILS-mediated auxin transport, together with reports of auxin function in unicellular algae, would suggest that auxin function preceded the advent of multicellularity. We find that PIN and PILS transporters form two eukaryotic subfamilies within a larger bacterial family. We argue that future functional characterisation of algal PIN and PILS transporters can shed light on a common origin of an auxin function followed by independent co-option in a multicellular context.},
}

Biological Transport
*Indoleacetic Acids/metabolism
*Membrane Transport Proteins/genetics/metabolism
Plants/genetics/metabolism

@article {pmid35205423,
year = {2022},
author = {Alfieri, JM and Wang, G and Jonika, MM and Gill, CA and Blackmon, H and Athrey, GN},
title = {A Primer for Single-Cell Sequencing in Non-Model Organisms.},
journal = {Genes},
volume = {13},
number = {2},
pages = {},
pmid = {35205423},
issn = {2073-4425},
support = {R35 GM138098/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Genotype ; *Phenotype ; },
abstract = {Single-cell sequencing technologies have led to a revolution in our knowledge of the diversity of cell types, connections between biological levels of organization, and relationships between genotype and phenotype. These advances have mainly come from using model organisms; however, using single-cell sequencing in non-model organisms could enable investigations of questions inaccessible with typical model organisms. This primer describes a general workflow for single-cell sequencing studies and considerations for using non-model organisms (limited to multicellular animals). Importantly, single-cell sequencing, when further applied in non-model organisms, will allow for a deeper understanding of the mechanisms between genotype and phenotype and the basis for biological variation.},
}

Animals
Genotype
*Phenotype

@article {pmid35421922,
year = {2022},
author = {Nozaki, H and Mori, F and Tanaka, Y and Matsuzaki, R and Yamaguchi, H and Kawachi, M},
title = {Cryopreservation of vegetative cells and zygotes of the multicellular volvocine green alga Gonium pectorale.},
journal = {BMC microbiology},
volume = {22},
number = {1},
pages = {103},
pmid = {35421922},
issn = {1471-2180},
support = {19K22446//Japan Society for the Promotion of Science/ ; National BioResource Project for Algae//Ministry of Education, Culture, Sports, Science and Technology/ ; National BioResource Project for Algae//Ministry of Education, Culture, Sports, Science and Technology/ ; },
mesh = {*Chlorophyta ; Cryopreservation ; Nitrogen ; Phylogeny ; *Zygote ; },
abstract = {BACKGROUND: Colonial and multicellular volvocine green algae have been extensively studied recently in various fields of the biological sciences. However, only one species (Pandorina morum) has been cryopreserved in public culture collections.

RESULTS: Here, we investigated conditions for cryopreservation of the multicellular volvocine alga Gonium pectorale using vegetative colonies or cells and zygotes. Rates of vegetative cell survival in a G. pectorale strain after two-step cooling and freezing in liquid nitrogen were compared between different concentrations (3% and 6%) of the cryoprotectant N,N-dimethylformamide (DMF) and two types of tubes (0.2-mL polymerase chain reaction tubes and 2-mL cryotubes) used for cryopreservation. Among the four conditions investigated, the highest rate of survival [2.7 ± 3.6% (0.54-10%) by the most probable number (MPN) method] was obtained when 2.0-mL cryotubes containing 1.0 mL of culture samples with 6% DMF were subjected to cryogenic treatment. Using these optimized cryopreservation conditions, survival rates after freezing in liquid nitrogen were examined for twelve other strains of G. pectorale and twelve strains of five other Gonium species. We obtained ≥ 0.1% MPN survival in nine of the twelve G. pectorale strains tested. However, < 0.1% MPN survival was detected in eleven of twelve strains of five other Gonium species. In total, ten cryopreserved strains of G. pectorale were newly established in the Microbial Culture Collection at the National Institute for Environmental Studies. Although the cryopreservation of zygotes of volvocine algae has not been previously reported, high rates (approximately 60%) of G. pectorale zygote germination were observed after thawing zygotes that had been cryopreserved with 5% or 10% methanol as the cryoprotectant during two-step cooling and freezing in liquid nitrogen.

CONCLUSIONS: The present study demonstrated that cryopreservation of G. pectorale is possible with 6% DMF as a cryoprotectant and 1.0-mL culture samples in 2.0-mL cryotubes subjected to two-step cooling in a programmable freezer.},
}

*Chlorophyta
Cryopreservation
Nitrogen
Phylogeny
*Zygote

@article {pmid35417559,
year = {2022},
author = {Kambayashi, C and Kakehashi, R and Sato, Y and Mizuno, H and Tanabe, H and Rakotoarison, A and Künzel, S and Furuno, N and Ohshima, K and Kumazawa, Y and Nagy, ZT and Mori, A and Allison, A and Donnellan, SC and Ota, H and Hoso, M and Yanagida, T and Sato, H and Vences, M and Kurabayashi, A},
title = {Geography-Dependent Horizontal Gene Transfer from Vertebrate Predators to Their Prey.},
journal = {Molecular biology and evolution},
volume = {39},
number = {4},
pages = {},
pmid = {35417559},
issn = {1537-1719},
mesh = {Animals ; Cattle ; *Gene Transfer, Horizontal ; Geography ; *Parasites/genetics ; Phylogeny ; Predatory Behavior ; Retroelements ; Vertebrates/genetics ; },
abstract = {Horizontal transfer (HT) of genes between multicellular animals, once thought to be extremely rare, is being more commonly detected, but its global geographic trend and transfer mechanism have not been investigated. We discovered a unique HT pattern of Bovine-B (BovB) LINE retrotransposons in vertebrates, with a bizarre transfer direction from predators (snakes) to their prey (frogs). At least 54 instances of BovB HT were detected, which we estimate to have occurred across time between 85 and 1.3 Ma. Using comprehensive transcontinental sampling, our study demonstrates that BovB HT is highly prevalent in one geographical region, Madagascar, suggesting important regional differences in the occurrence of HTs. We discovered parasite vectors that may plausibly transmit BovB and found that the proportion of BovB-positive parasites is also high in Madagascar where BovB thus might be physically transported by parasites to diverse vertebrates, potentially including humans. Remarkably, in two frog lineages, BovB HT occurred after migration from a non-HT area (Africa) to the HT hotspot (Madagascar). These results provide a novel perspective on how the prevalence of parasites influences the occurrence of HT in a region, similar to pathogens and their vectors in some endemic diseases.},
}

Animals
Cattle
*Gene Transfer, Horizontal
Geography
*Parasites/genetics
Phylogeny
Predatory Behavior
Retroelements
Vertebrates/genetics

@article {pmid35189700,
year = {2022},
author = {Simon-Soro, A and Ren, Z and Krom, BP and Hoogenkamp, MA and Cabello-Yeves, PJ and Daniel, SG and Bittinger, K and Tomas, I and Koo, H and Mira, A},
title = {Polymicrobial Aggregates in Human Saliva Build the Oral Biofilm.},
journal = {mBio},
volume = {13},
number = {1},
pages = {e0013122},
pmid = {35189700},
issn = {2150-7511},
support = {R01 DE025220/DE/NIDCR NIH HHS/United States ; 834.13.006//NWO Earth and Life Sciences (ALW)/ ; BIO2015-68711-R//Spanish Ministry of Economy and Competitiveness/ ; },
mesh = {Bacteria ; Biofilms ; *Ecosystem ; Humans ; Phylogeny ; *Saliva/microbiology ; },
abstract = {Biofilm community development has been established as a sequential process starting from the attachment of single cells on a surface. However, microorganisms are often found as aggregates in the environment and in biological fluids. Here, we conduct a comprehensive analysis of the native structure and composition of aggregated microbial assemblages in human saliva and investigate their spatiotemporal attachment and biofilm community development. Using multiscale imaging, cell sorting, and computational approaches combined with sequencing analysis, a diverse mixture of aggregates varying in size, structure, and microbial composition, including bacteria associated with host epithelial cells, can be found in saliva in addition to a few single-cell forms. Phylogenetic analysis reveals a mixture of complex consortia of aerobes and anaerobes in which bacteria traditionally considered early and late colonizers are found mixed together. When individually tracked during colonization and biofilm initiation, aggregates rapidly proliferate and expand tridimensionally, modulating population growth, spatial organization, and community scaffolding. In contrast, most single cells remain static or are incorporated by actively growing aggregates. These results suggest an alternative biofilm development process whereby aggregates containing different species or associated with human cells collectively adhere to the surface as "growth nuclei" to build the biofilm and shape polymicrobial communities at various spatial and taxonomic scales. IMPORTANCE Microbes in biological fluids can be found as aggregates. How these multicellular structures bind to surfaces and initiate the biofilm life cycle remains understudied. Here, we investigate the structural organization of microbial aggregates in human saliva and their role in biofilm formation. We found diverse mixtures of aggregates with different sizes, structures, and compositions in addition to free-living cells. When individually tracked during binding and growth on tooth-like surfaces, most aggregates developed into structured biofilm communities, whereas most single cells remained static or were engulfed by the growing aggregates. Our results reveal that preformed microbial consortia adhere as "buds of growth," governing biofilm initiation without specific taxonomic order or cell-by-cell succession, which provide new insights into spatial and population heterogeneity development in complex ecosystems.},
}

Bacteria
Biofilms
*Ecosystem
Humans
Phylogeny
*Saliva/microbiology

@article {pmid34878516,
year = {2022},
author = {Suissa, JS},
title = {Fern fronds that move like pine cones: humidity-driven motion of fertile leaflets governs the timing of spore dispersal in a widespread fern species.},
journal = {Annals of botany},
volume = {129},
number = {5},
pages = {519-528},
pmid = {34878516},
issn = {1095-8290},
support = {//Harvard University Department of Organismic and Evolutionary Biology Graduate Student Fellowship/ ; },
mesh = {*Ferns/physiology ; Germ Cells, Plant ; Humidity ; Plant Cone ; Spores/physiology ; Spores, Fungal ; },
abstract = {BACKGROUND AND AIMS: The sensitive fern, Onoclea sensibilis, is a widespread species in eastern North America and has an atypical timing of spore dispersal among temperate ferns. During early summer, this dimorphic species produces heavily modified spore-bearing fronds with leaflets tightly enveloping their sporangia and spores. These fronds senesce and persist above ground as dead mature structures until the following early spring when the leaflets finally open and spores are dispersed. While this timing of spore dispersal has been observed for over 120 years, the structural mechanisms underpinning this phenology have remained elusive.

METHODS: Based on field observations, growth chamber manipulations and scanning electron microscopy, the mechanisms underlying this distinctive timing of spore dispersal in the sensitive fern were investigated.

KEY RESULTS: I show that fertile leaflets of the sensitive fern move in direct response to changes in humidity, exhibiting structural and functional parallels with multicellular hygromorphic structures in seed plants, such as pine cones. These parallels include differences in cellulose microfibril orientation in cells on the abaxial and adaxial sides of the leaflet. The dynamics of this hygroscopic movement concomitant with regular abscission zones along the pinnules and coordinated senescence lead to the specific timing of early spring spore dispersal in the sensitive fern.

CONCLUSIONS: While hygroscopic movement is common in seed-free plants, it mostly occurs in small structures that are either one or a few cells in size, such as the leptosporangium. Given its multicellular structure and integration across many cells and tissues, the movement and construction of the sensitive fern pinnules are more similar to structures in seed plants. The evolution of this complex trait in the sensitive fern efficiently regulates the timing of spore release, leading to early spring dispersal. This phenology likely gives gametophytes and subsequent sporophytes an advantage with early germination and growth.},
}

*Ferns/physiology
Germ Cells, Plant
Humidity
Plant Cone
Spores/physiology
Spores, Fungal

@article {pmid35420439,
year = {2022},
author = {Rohkin Shalom, S and Weiss, B and Lalzar, M and Kaltenpoth, M and Chiel, E},
title = {Abundance and Localization of Symbiotic Bacterial Communities in the Fly Parasitoid Spalangia cameroni.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0254921},
doi = {10.1128/aem.02549-21},
pmid = {35420439},
issn = {1098-5336},
abstract = {Multicellular eukaryotes often host multiple microbial symbionts that may cooperate or compete for host resources, such as space and nutrients. Here, we studied the abundances and localization of four bacterial symbionts, Rickettsia, Wolbachia, Sodalis, and Arsenophonus, in the parasitic wasp Spalangia cameroni. Using quantitative PCR (qPCR), we measured the symbionts' titers in wasps that harbor different combinations of these symbionts. We found that the titer of each symbiont decreased as the number of symbiont species in the community increased. Symbionts' titers were higher in females than in males. Rickettsia was the most abundant symbiont in all the communities, followed by Sodalis and Wolbachia. The titers of these three symbionts were positively correlated in some of the colonies. Fluorescence in situ hybridization was in line with the qPCR results: Rickettsia, Wolbachia, and Sodalis were observed in high densities in multiple organs, including brain, muscles, gut, Malpighian tubules, fat body, ovaries, and testes, while Arsenophonus was localized to fewer organs and in lower densities. Sodalis and Arsenophonus were observed in ovarian follicle cells but not within oocytes or laid eggs. This study highlights the connection between symbionts' abundance and localization. We discuss the possible connections between our findings to symbiont transmission success. IMPORTANCE Many insects carry intracellular bacterial symbionts (bacteria that reside within the cells of the insect). When multiple symbiont species cohabit in a host, they may compete or cooperate for space, nutrients, and transmission, and the nature of such interactions would be reflected in the abundance of each symbiont species. Given the widespread occurrence of coinfections with maternally transmitted symbionts in insects, it is important to learn more about how they interact, where they are localized, and how these two aspects affect their co-occurrence within individual insects. Here, we studied the abundance and the localization of four symbionts, Rickettsia, Wolbachia, Sodalis, and Arsenophonus, that cohabit the parasitic wasp Spalangia cameroni. We found that symbionts' titers differed between symbiotic communities. These results were corroborated by microscopy, which shows differential localization patterns. We discuss the findings in the contexts of community ecology, possible symbiont-symbiont interactions, and host control mechanisms that may shape the symbiotic community structure.},
}

@article {pmid35409376,
year = {2022},
author = {Kasperski, A},
title = {Life Entrapped in a Network of Atavistic Attractors: How to Find a Rescue.},
journal = {International journal of molecular sciences},
volume = {23},
number = {7},
pages = {},
doi = {10.3390/ijms23074017},
pmid = {35409376},
issn = {1422-0067},
mesh = {Cell Physiological Phenomena ; Cell Transformation, Neoplastic/metabolism ; *Energy Metabolism ; Humans ; Mitochondria/metabolism ; *Neoplasms/metabolism ; },
abstract = {In view of unified cell bioenergetics, cell bioenergetic problems related to cell overenergization can cause excessive disturbances in current cell fate and, as a result, lead to a change of cell-fate. At the onset of the problem, cell overenergization of multicellular organisms (especially overenergization of mitochondria) is solved inter alia by activation and then stimulation of the reversible Crabtree effect by cells. Unfortunately, this apparently good solution can also lead to a much bigger problem when, despite the activation of the Crabtree effect, cell overenergization persists for a long time. In such a case, cancer transformation, along with the Warburg effect, may occur to further reduce or stop the charging of mitochondria by high-energy molecules. Understanding the phenomena of cancer transformation and cancer development has become a real challenge for humanity. To date, many models have been developed to understand cancer-related mechanisms. Nowadays, combining all these models into one coherent universal model of cancer transformation and development can be considered a new challenge. In this light, the aim of this article is to present such a potentially universal model supported by a proposed new model of cellular functionality evolution. The methods of fighting cancer resulting from unified cell bioenergetics and the two presented models are also considered.},
}

Cell Physiological Phenomena
Cell Transformation, Neoplastic/metabolism
*Energy Metabolism
Humans
Mitochondria/metabolism
*Neoplasms/metabolism

@article {pmid35406795,
year = {2022},
author = {Zschüntzsch, J and Meyer, S and Shahriyari, M and Kummer, K and Schmidt, M and Kummer, S and Tiburcy, M},
title = {The Evolution of Complex Muscle Cell In Vitro Models to Study Pathomechanisms and Drug Development of Neuromuscular Disease.},
journal = {Cells},
volume = {11},
number = {7},
pages = {},
doi = {10.3390/cells11071233},
pmid = {35406795},
issn = {2073-4409},
support = {101034427-2//IMI2-2020-23-05/ ; SFB 1002 TP C04//German Research Foundation/ ; 413501650//German Research Foundation/ ; },
mesh = {Coculture Techniques ; Drug Development ; Humans ; Muscle Cells ; *Neuromuscular Diseases/drug therapy ; *Organoids ; },
abstract = {Many neuromuscular disease entities possess a significant disease burden and therapeutic options remain limited. Innovative human preclinical models may help to uncover relevant disease mechanisms and enhance the translation of therapeutic findings to strengthen neuromuscular disease precision medicine. By concentrating on idiopathic inflammatory muscle disorders, we summarize the recent evolution of the novel in vitro models to study disease mechanisms and therapeutic strategies. A particular focus is laid on the integration and simulation of multicellular interactions of muscle tissue in disease phenotypes in vitro. Finally, the requirements of a neuromuscular disease drug development workflow are discussed with a particular emphasis on cell sources, co-culture systems (including organoids), functionality, and throughput.},
}

Coculture Techniques
Drug Development
Humans
Muscle Cells
*Neuromuscular Diseases/drug therapy
*Organoids

@article {pmid35358607,
year = {2022},
author = {Shapiro, JA},
title = {What we have learned about evolutionary genome change in the past 7 decades.},
journal = {Bio Systems},
volume = {215-216},
number = {},
pages = {104669},
doi = {10.1016/j.biosystems.2022.104669},
pmid = {35358607},
issn = {1872-8324},
mesh = {Animals ; *Biological Evolution ; *DNA Transposable Elements/genetics ; Eukaryota/genetics ; Evolution, Molecular ; Genomics ; Hybridization, Genetic ; },
abstract = {Cytogenetics and genomics have completely transformed our understanding of evolutionary genome change since the early 1950s. The point of this paper is to outline some of the empirical findings responsible for that transformation. The discovery of transposable elements (TEs) in maize by McClintock, and their subsequent rediscovery in all forms of life, tell us that organisms have the inherent capacity to evolve dispersed genomic networks encoding complex cellular and multicellular adaptations. Genomic analysis confirms the role of TEs in wiring novel networks at major evolutionary transitions. TEs and other forms of repetitive DNA are also important contributors to genome regions that serve as transcriptional templates for regulatory and other biologically functional noncoding ncRNAs. The many functions documented for ncRNAs shows the concept of abundant "selfish" or "junk" DNA in complex genomes is mistaken. Natural and artificial speciation by interspecific hybridization demonstrates that TEs and other biochemical systems of genome restructuring are subject to rapid activation and can generate changes throughout the genomes of the novel species that emerge. In addition to TEs and hybrid species, cancer cells have taught us important lessons about chromothripsis, chromoplexy and other forms of non-random multisite genome restructuring. In many of these restructured genomes, alternative end-joining processes display the capacities of eukaryotes to generate novel combinations of templated and untemplated DNA sequences at the sites of break repair. Sequence innovation by alternative end-joining is widespread among eukaryotes from single cells to advanced plants and animals. In sum, the cellular and genomic capacities of eukaryotic cells have proven to be capable of executing rapid macroevolutionary change under a variety of conditions.},
}

Animals
*Biological Evolution
*DNA Transposable Elements/genetics
Eukaryota/genetics
Evolution, Molecular
Genomics
Hybridization, Genetic

@article {pmid35167804,
year = {2022},
author = {Davis, JR and Ainslie, AP and Williamson, JJ and Ferreira, A and Torres-Sánchez, A and Hoppe, A and Mangione, F and Smith, MB and Martin-Blanco, E and Salbreux, G and Tapon, N},
title = {ECM degradation in the Drosophila abdominal epidermis initiates tissue growth that ceases with rapid cell-cycle exit.},
journal = {Current biology : CB},
volume = {32},
number = {6},
pages = {1285-1300.e4},
doi = {10.1016/j.cub.2022.01.045},
pmid = {35167804},
issn = {1879-0445},
support = {201358/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 107885/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; FC001317/CRUK_/Cancer Research UK/United Kingdom ; FC001175/CRUK_/Cancer Research UK/United Kingdom ; FC001317/MRC_/Medical Research Council/United Kingdom ; FC001175/MRC_/Medical Research Council/United Kingdom ; FC001317/WT_/Wellcome Trust/United Kingdom ; FC001175/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Cell Cycle ; Cell Division ; *Drosophila ; *Epidermal Cells ; Epidermis ; Mice ; },
abstract = {During development, multicellular organisms undergo stereotypical patterns of tissue growth in space and time. How developmental growth is orchestrated remains unclear, largely due to the difficulty of observing and quantitating this process in a living organism. Drosophila histoblast nests are small clusters of progenitor epithelial cells that undergo extensive growth to give rise to the adult abdominal epidermis and are amenable to live imaging. Our quantitative analysis of histoblast proliferation and tissue mechanics reveals that tissue growth is driven by cell divisions initiated through basal extracellular matrix degradation by matrix metalloproteases secreted by the neighboring larval epidermal cells. Laser ablations and computational simulations show that tissue mechanical tension does not decrease as the histoblasts fill the abdominal epidermal surface. During tissue growth, the histoblasts display oscillatory cell division rates until growth termination occurs through the rapid emergence of G0/G1 arrested cells, rather than a gradual increase in cell-cycle time as observed in other systems such as the Drosophila wing and mouse postnatal epidermis. Different developing tissues can therefore achieve their final size using distinct growth termination strategies. Thus, adult abdominal epidermal development is characterized by changes in the tissue microenvironment and a rapid exit from the cell cycle.},
}

Animals
Cell Cycle
Cell Division
*Drosophila
*Epidermal Cells
Epidermis
Mice

@article {pmid35396623,
year = {2022},
author = {Koide, RT},
title = {On Holobionts, Holospecies, and Holoniches: the Role of Microbial Symbioses in Ecology and Evolution.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35396623},
issn = {1432-184X},
abstract = {My goal in writing this is to increase awareness of the roles played by microbial symbionts in eukaryote ecology and evolution. Most eukaryotes host one or more species of symbiotic microorganisms, including prokaryotes and fungi. Many of these have profound impacts on the biology of their hosts. For example, microbial symbionts may expand the niches of their hosts, cause rapid adaptation of the host to the environment and re-adaptation to novel conditions via symbiont swapping, facilitate speciation, and fundamentally alter our concept of the species. In some cases, microbial symbionts and multicellular eukaryote hosts have a mutual dependency, which has obvious conservation implications. Hopefully, this contribution will stimulate a reevaluation of important ecological and evolutionary concepts including niche, adaptation, the species, speciation, and conservation of multicellular eukaryotes.},
}

@article {pmid35159213,
year = {2022},
author = {Ribba, AS and Fraboulet, S and Sadoul, K and Lafanechère, L},
title = {The Role of LIM Kinases during Development: A Lens to Get a Glimpse of Their Implication in Pathologies.},
journal = {Cells},
volume = {11},
number = {3},
pages = {},
pmid = {35159213},
issn = {2073-4409},
support = {R18LAFANECHERE//Ligue contre le Cancer, comité de l'Isère/ ; },
mesh = {Actin Depolymerizing Factors/metabolism ; Animals ; *Lim Kinases/metabolism ; Phosphorylation ; Phylogeny ; *Protein Kinases/metabolism ; },
abstract = {The organization of cell populations within animal tissues is essential for the morphogenesis of organs during development. Cells recognize three-dimensional positions with respect to the whole organism and regulate their cell shape, motility, migration, polarization, growth, differentiation, gene expression and cell death according to extracellular signals. Remodeling of the actin filaments is essential to achieve these cell morphological changes. Cofilin is an important binding protein for these filaments; it increases their elasticity in terms of flexion and torsion and also severs them. The activity of cofilin is spatiotemporally inhibited via phosphorylation by the LIM domain kinases 1 and 2 (LIMK1 and LIMK2). Phylogenetic analysis indicates that the phospho-regulation of cofilin has evolved as a mechanism controlling the reorganization of the actin cytoskeleton during complex multicellular processes, such as those that occur during embryogenesis. In this context, the main objective of this review is to provide an update of the respective role of each of the LIM kinases during embryonic development.},
}

Actin Depolymerizing Factors/metabolism
Animals
*Lim Kinases/metabolism
Phosphorylation
Phylogeny
*Protein Kinases/metabolism

@article {pmid35311270,
year = {2022},
author = {Chen, C and Wang, P and Chen, H and Wang, X and Halgamuge, MN and Chen, C and Song, T},
title = {Smart Magnetotactic Bacteria Enable the Inhibition of Neuroblastoma under an Alternating Magnetic Field.},
journal = {ACS applied materials & interfaces},
volume = {14},
number = {12},
pages = {14049-14058},
doi = {10.1021/acsami.1c24154},
pmid = {35311270},
issn = {1944-8252},
mesh = {Animals ; *Hyperthermia, Induced ; Magnetic Fields ; *Magnetosomes/metabolism ; Mice ; Mice, Nude ; *Neuroblastoma/metabolism/therapy ; },
abstract = {Magnetotactic bacteria are ubiquitous microorganisms in nature that synthesize intracellular magnetic nanoparticles called magnetosomes in a gene-controlled way and arrange them in chains. From in vitro to in vivo, we demonstrate that the intact body of Magnetospirillum magneticum AMB-1 has potential as a natural magnetic hyperthermia material for cancer therapy. Compared to chains of magnetosomes and individual magnetosomes, the entire AMB-1 cell exhibits superior heating capability under an alternating magnetic field. When incubating with tumor cells, the intact AMB-1 cells disperse better than the other two types of magnetosomes, decreasing cellular viability under the control of an alternating magnetic field. Furthermore, in vivo experiments in nude mice with neuroblastoma found that intact AMB-1 cells had the best antitumor activity with magnetic hyperthermia therapy compared to other treatment groups. These findings suggest that the intact body of magnetotactic bacteria has enormous promise as a natural material for tumor magnetic hyperthermia. In biomedical applications, intact and living magnetotactic bacteria play an increasingly essential function as a targeting robot due to their magnetotaxis.},
}

Animals
*Hyperthermia, Induced
Magnetic Fields
*Magnetosomes/metabolism
Mice
Mice, Nude
*Neuroblastoma/metabolism/therapy

@article {pmid34752334,
year = {2021},
author = {Pereira, PHS and Garcia, CRS and Bouvier, M},
title = {Identifying Plasmodium falciparum receptor activation using bioluminescence resonance energy transfer (BRET)-based biosensors in HEK293 cells.},
journal = {Methods in cell biology},
volume = {166},
number = {},
pages = {223-233},
doi = {10.1016/bs.mcb.2021.06.018},
pmid = {34752334},
issn = {0091-679X},
mesh = {*Biosensing Techniques ; Energy Transfer ; HEK293 Cells ; Humans ; *Plasmodium falciparum/metabolism ; Receptors, G-Protein-Coupled/genetics/metabolism ; },
abstract = {Throughout evolution the need for unicellular organisms to associate and form a single cluster of cells had several evolutionary advantages. G protein coupled receptors (GPCRs) are responsible for a large part of the senses that allow this clustering to succeed, playing a fundamental role in the perception of cell's external environment, enabling the interaction and coordinated development between each cell of a multicellular organism. GPCRs are not exclusive to complex multicellular organisms. In single-celled organisms, GPCRs are also present and have a similar function of detecting changes in the external environment and transforming them into a biological response. There are no reports of GPCRs in parasitic protozoa, such as the Plasmodium genus, and the identification of a protein of this family in P. falciparum would have a significant impact both on the understanding of the basic biology of the parasite and on the history of the evolution of GPCRs. The protocol described here was successfully applied to study a GPCR candidate in P. falciparum for the first time, and we hope that it helps other groups to use the same approach to study this deadly parasite.},
}

*Biosensing Techniques
Energy Transfer
HEK293 Cells
Humans
*Plasmodium falciparum/metabolism
Receptors, G-Protein-Coupled/genetics/metabolism

@article {pmid34275698,
year = {2022},
author = {Verdonck, R and Legrand, D and Jacob, S and Philippe, H},
title = {Phenotypic plasticity through disposable genetic adaptation in ciliates.},
journal = {Trends in microbiology},
volume = {30},
number = {2},
pages = {120-130},
doi = {10.1016/j.tim.2021.06.007},
pmid = {34275698},
issn = {1878-4380},
mesh = {Adaptation, Physiological/genetics ; Biological Evolution ; *Ciliophora/genetics ; *Paramecium/genetics ; },
abstract = {Ciliates have an extraordinary genetic system in which each cell harbors two distinct kinds of nucleus, a transcriptionally active somatic nucleus and a quiescent germline nucleus. The latter undergoes classical, heritable genetic adaptation, while adaptation of the somatic nucleus is only short-term and thus disposable. The ecological and evolutionary relevance of this nuclear dimorphism have never been well formalized, which is surprising given the long history of using ciliates such as Tetrahymena and Paramecium as model organisms. We present a novel, alternative explanation for ciliate nuclear dimorphism which, we argue, should be considered an instrument of phenotypic plasticity by somatic selection on the level of the ciliate clone, as if it were a diffuse multicellular organism. This viewpoint helps to put some enigmatic aspects of ciliate biology into perspective and presents the diversity of ciliates as a large natural experiment that we can exploit to study phenotypic plasticity and organismality.},
}

Adaptation, Physiological/genetics
Biological Evolution
*Ciliophora/genetics
*Paramecium/genetics

@article {pmid35359304,
year = {2022},
author = {Ramon-Mateu, J and Edgar, A and Mitchell, D and Martindale, MQ},
title = {Studying Ctenophora WBR Using Mnemiopsis leidyi.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2450},
number = {},
pages = {95-119},
pmid = {35359304},
issn = {1940-6029},
mesh = {Animals ; Cell Lineage ; *Ctenophora/genetics ; Genome ; Phylogeny ; },
abstract = {Ctenophores, also known as comb jellies, are a clade of fragile holopelagic, carnivorous marine invertebrates, that represent one of the most ancient extant groups of multicellular animals. Ctenophores show a remarkable ability to regenerate in the adult form, being capable of replacing all body parts (i.e., whole-body regeneration) after loss/amputation. With many favorable experimental features (optical clarity, stereotyped cell lineage, multiple cell types), a full genome sequence available and their early branching phylogenetic position, ctenophores are well placed to provide information about the evolution of regenerative ability throughout the Metazoa. Here, we provide a collection of detailed protocols for use of the lobate ctenophore Mnemiopsis leidyi to study whole-body regeneration, including specimen collection, husbandry, surgical manipulation, and imaging techniques.},
}

Animals
Cell Lineage
*Ctenophora/genetics
Genome
Phylogeny

@article {pmid35018470,
year = {2022},
author = {von der Heyde, EL and Hallmann, A},
title = {Molecular and cellular dynamics of early embryonic cell divisions in Volvox carteri.},
journal = {The Plant cell},
volume = {34},
number = {4},
pages = {1326-1353},
doi = {10.1093/plcell/koac004},
pmid = {35018470},
issn = {1532-298X},
support = {//Bielefeld University/ ; },
mesh = {Animals ; Cell Division/genetics ; *Volvox/genetics ; },
abstract = {Cell division is fundamental to all organisms and the green alga used here exhibits both key animal and plant functions. Specifically, we analyzed the molecular and cellular dynamics of early embryonic divisions of the multicellular green alga Volvox carteri (Chlamydomonadales). Relevant proteins related to mitosis and cytokinesis were identified in silico, the corresponding genes were cloned, fused to yfp, and stably expressed in Volvox, and the tagged proteins were studied by live-cell imaging. We reveal rearrangements of the microtubule cytoskeleton during centrosome separation, spindle formation, establishment of the phycoplast, and generation of previously unknown structures. The centrosomes participate in initiation of spindle formation and determination of spindle orientation. Although the nuclear envelope does not break down during early mitosis, intermixing of cytoplasm and nucleoplasm results in loss of nuclear identity. Finally, we present a model for mitosis in Volvox. Our study reveals enormous dynamics, clarifies spatio-temporal relationships of subcellular structures, and provides insight into the evolution of cell division.},
}

Animals
Cell Division/genetics
*Volvox/genetics

@article {pmid35349578,
year = {2022},
author = {Dudin, O and Wielgoss, S and New, AM and Ruiz-Trillo, I},
title = {Regulation of sedimentation rate shapes the evolution of multicellularity in a close unicellular relative of animals.},
journal = {PLoS biology},
volume = {20},
number = {3},
pages = {e3001551},
pmid = {35349578},
issn = {1545-7885},
mesh = {Animals ; Cell Size ; *Cytokinesis ; Phenotype ; },
abstract = {Significant increases in sedimentation rate accompany the evolution of multicellularity. These increases should lead to rapid changes in ecological distribution, thereby affecting the costs and benefits of multicellularity and its likelihood to evolve. However, how genetic and cellular traits control this process, their likelihood of emergence over evolutionary timescales, and the variation in these traits as multicellularity evolves are still poorly understood. Here, using isolates of the ichthyosporean genus Sphaeroforma-close unicellular relatives of animals with brief transient multicellular life stages-we demonstrate that sedimentation rate is a highly variable and evolvable trait affected by at least 2 distinct physical mechanisms. First, we find extensive (>300×) variation in sedimentation rates for different Sphaeroforma species, mainly driven by size and density during the unicellular-to-multicellular life cycle transition. Second, using experimental evolution with sedimentation rate as a focal trait, we readily obtained, for the first time, fast settling and multicellular Sphaeroforma arctica isolates. Quantitative microscopy showed that increased sedimentation rates most often arose by incomplete cellular separation after cell division, leading to clonal "clumping" multicellular variants with increased size and density. Strikingly, density increases also arose by an acceleration of the nuclear doubling time relative to cell size. Similar size- and density-affecting phenotypes were observed in 4 additional species from the Sphaeroforma genus, suggesting that variation in these traits might be widespread in the marine habitat. By resequencing evolved isolates to high genomic coverage, we identified mutations in regulators of cytokinesis, plasma membrane remodeling, and chromatin condensation that may contribute to both clump formation and the increase in the nuclear number-to-volume ratio. Taken together, this study illustrates how extensive cellular control of density and size drive sedimentation rate variation, likely shaping the onset and further evolution of multicellularity.},
}

Animals
Cell Size
*Cytokinesis
Phenotype

@article {pmid35032334,
year = {2022},
author = {Nemec-Venza, Z and Madden, C and Stewart, A and Liu, W and Novák, O and Pěnčík, A and Cuming, AC and Kamisugi, Y and Harrison, CJ},
title = {CLAVATA modulates auxin homeostasis and transport to regulate stem cell identity and plant shape in a moss.},
journal = {The New phytologist},
volume = {234},
number = {1},
pages = {149-163},
doi = {10.1111/nph.17969},
pmid = {35032334},
issn = {1469-8137},
mesh = {*Arabidopsis Proteins/genetics/metabolism ; *Bryophyta/metabolism ; *Bryopsida/genetics/metabolism ; Gene Expression Regulation, Plant ; Homeostasis ; Indoleacetic Acids/metabolism ; Stem Cells/metabolism ; },
abstract = {The CLAVATA pathway is a key regulator of stem cell function in the multicellular shoot tips of Arabidopsis, where it acts via the WUSCHEL transcription factor to modulate hormone homeostasis. Broad-scale evolutionary comparisons have shown that CLAVATA is a conserved regulator of land plant stem cell function, but CLAVATA acts independently of WUSCHEL-like (WOX) proteins in bryophytes. The relationship between CLAVATA, hormone homeostasis and the evolution of land plant stem cell functions is unknown. Here we show that in the moss, Physcomitrella (Physcomitrium patens), CLAVATA affects stem cell activity by modulating hormone homeostasis. CLAVATA pathway genes are expressed in the tip cells of filamentous tissues, regulating cell identity, filament branching, plant spread and auxin synthesis. The receptor-like kinase PpRPK2 plays the major role, and Pprpk2 mutants have abnormal responses to cytokinin, auxin and auxin transport inhibition, and show reduced expression of PIN auxin transporters. We propose a model whereby PpRPK2 modulates auxin gradients in filaments to determine stem cell identity and overall plant form. Our data indicate that CLAVATA-mediated auxin homeostasis is a fundamental property of plant stem cell function, probably exhibited by the last shared common ancestor of land plants.},
}

*Arabidopsis Proteins/genetics/metabolism
*Bryophyta/metabolism
*Bryopsida/genetics/metabolism
Gene Expression Regulation, Plant
Homeostasis
Indoleacetic Acids/metabolism
Stem Cells/metabolism

@article {pmid34998872,
year = {2022},
author = {Kulkarni, P and Behal, A and Mohanty, A and Salgia, R and Nedelcu, AM and Uversky, VN},
title = {Co-opting disorder into order: Intrinsically disordered proteins and the early evolution of complex multicellularity.},
journal = {International journal of biological macromolecules},
volume = {201},
number = {},
pages = {29-36},
doi = {10.1016/j.ijbiomac.2021.12.182},
pmid = {34998872},
issn = {1879-0003},
mesh = {*Intrinsically Disordered Proteins ; *Volvox ; },
abstract = {Intrinsically disordered proteins (IDPs) are proteins that lack rigid structures yet play important roles in myriad biological phenomena. A distinguishing feature of IDPs is that they often mediate specific biological outcomes via multivalent weak cooperative interactions with multiple partners. Here, we show that several proteins specifically associated with processes that were key in the evolution of complex multicellularity in the lineage leading to the multicellular green alga Volvox carteri are IDPs. We suggest that, by rewiring cellular protein interaction networks, IDPs facilitated the co-option of ancestral pathways for specialized multicellular functions, underscoring the importance of IDPs in the early evolution of complex multicellularity.},
}

*Intrinsically Disordered Proteins
*Volvox

@article {pmid34838795,
year = {2022},
author = {Tverskoi, D and Gavrilets, S},
title = {The evolution of germ-soma specialization under different genetic and environmental effects.},
journal = {Journal of theoretical biology},
volume = {534},
number = {},
pages = {110964},
doi = {10.1016/j.jtbi.2021.110964},
pmid = {34838795},
issn = {1095-8541},
mesh = {*Biological Evolution ; Cell Differentiation ; Climate ; Fertility ; Humans ; *Models, Biological ; },
abstract = {Division of labor exists at different levels of biological organization - from cell colonies to human societies. One of the simplest examples of the division of labor in multicellular organisms is germ-soma specialization, which plays a key role in the evolution of organismal complexity. Here we formulate and study a general mathematical model exploring the emergence of germ-soma specialization in colonies of cells. We consider a finite population of colonies competing for resources. Colonies are of the same size and are composed by asexually reproducing haploid cells. Each cell can contribute to activity and fecundity of the colony, these contributions are traded-off. We assume that all cells within a colony are genetically identical but gene effects on fecundity and activity are influenced by variation in the microenvironment experienced by individual cells. Through analytical theory and evolutionary agent-based modeling we show that the shape of the trade-off relation between somatic and reproductive functions, the type and extent of variation in within-colony microenvironment, and, in some cases, the number of genes involved, are important predictors of the extent of germ-soma specialization. Specifically, increasing convexity of the trade-off relation, the number of different environmental gradients acting within a colony, and the number of genes (in the case of random microenvironmental effects) promote the emergence of germ-soma specialization. Overall our results contribute towards a better understanding of the role of genetic, environmental, and microenvironmental factors in the evolution of germ-soma specialization.},
}

*Biological Evolution
Cell Differentiation
Climate
Fertility
Humans
*Models, Biological

@article {pmid34814752,
year = {2021},
author = {Irisarri, I and Darienko, T and Pröschold, T and Fürst-Jansen, JMR and Jamy, M and de Vries, J},
title = {Unexpected cryptic species among streptophyte algae most distant to land plants.},
journal = {Proceedings. Biological sciences},
volume = {288},
number = {1963},
pages = {20212168},
pmid = {34814752},
issn = {1471-2954},
mesh = {*Chlorophyta/genetics ; *Embryophyta/genetics ; Evolution, Molecular ; Genome ; Phylogeny ; Plants/genetics ; },
abstract = {Streptophytes are one of the major groups of the green lineage (Chloroplastida or Viridiplantae). During one billion years of evolution, streptophytes have radiated into an astounding diversity of uni- and multicellular green algae as well as land plants. Most divergent from land plants is a clade formed by Mesostigmatophyceae, Spirotaenia spp. and Chlorokybophyceae. All three lineages are species-poor and the Chlorokybophyceae consist of a single described species, Chlorokybus atmophyticus. In this study, we used phylogenomic analyses to shed light into the diversity within Chlorokybus using a sampling of isolates across its known distribution. We uncovered a consistent deep genetic structure within the Chlorokybus isolates, which prompted us to formally extend the Chlorokybophyceae by describing four new species. Gene expression differences among Chlorokybus species suggest certain constitutive variability that might influence their response to environmental factors. Failure to account for this diversity can hamper comparative genomic studies aiming to understand the evolution of stress response across streptophytes. Our data highlight that future studies on the evolution of plant form and function can tap into an unknown diversity at key deep branches of the streptophytes.},
}

*Chlorophyta/genetics
*Embryophyta/genetics
Evolution, Molecular
Genome
Phylogeny
Plants/genetics

@article {pmid33950183,
year = {2021},
author = {Li, X and Hou, Z and Xu, C and Shi, X and Yang, L and Lewis, LA and Zhong, B},
title = {Large Phylogenomic Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae.},
journal = {Genome biology and evolution},
volume = {13},
number = {7},
pages = {},
pmid = {33950183},
issn = {1759-6653},
mesh = {*Chlorophyta/genetics ; Evolution, Molecular ; Genetic Code ; Phylogeny ; },
abstract = {The chlorophyte green algae (Chlorophyta) are species-rich ancient groups ubiquitous in various habitats with high cytological diversity, ranging from microscopic to macroscopic organisms. However, the deep phylogeny within core Chlorophyta remains unresolved, in part due to the relatively sparse taxon and gene sampling in previous studies. Here we contribute new transcriptomic data and reconstruct phylogenetic relationships of core Chlorophyta based on four large data sets up to 2,698 genes of 70 species, representing 80% of extant orders. The impacts of outgroup choice, missing data, bootstrap-support cutoffs, and model misspecification in phylogenetic inference of core Chlorophyta are examined. The species tree topologies of core Chlorophyta from different analyses are highly congruent, with strong supports at many relationships (e.g., the Bryopsidales and the Scotinosphaerales-Dasycladales clade). The monophyly of Chlorophyceae and of Trebouxiophyceae as well as the uncertain placement of Chlorodendrophyceae and Pedinophyceae corroborate results from previous studies. The reconstruction of ancestral scenarios illustrates the evolution of the freshwater-sea and microscopic-macroscopic transition in the Ulvophyceae, and the transformation of unicellular→colonial→multicellular in the chlorophyte green algae. In addition, we provided new evidence that serine is encoded by both canonical codons and noncanonical TAG code in Scotinosphaerales, and stop-to-sense codon reassignment in the Ulvophyceae has originated independently at least three times. Our robust phylogenetic framework of core Chlorophyta unveils the evolutionary history of phycoplast, cyto-morphology, and noncanonical genetic codes in chlorophyte green algae.},
}

*Chlorophyta/genetics
Evolution, Molecular
Genetic Code
Phylogeny

@article {pmid35295942,
year = {2022},
author = {Jiménez-Marín, B and Olson, BJSC},
title = {The Curious Case of Multicellularity in the Volvocine Algae.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {787665},
pmid = {35295942},
issn = {1664-8021},
abstract = {The evolution of multicellularity is a major evolutionary transition that underlies the radiation of many species in all domains of life, especially in eukaryotes. The volvocine green algae are an unconventional model system that holds great promise in the field given its genetic tractability, late transition to multicellularity, and phenotypic diversity. Multiple efforts at linking multicellularity-related developmental landmarks to key molecular changes, especially at the genome level, have provided key insights into the molecular innovations or lack thereof that underlie multicellularity. Twelve developmental changes have been proposed to explain the evolution of complex differentiated multicellularity in the volvocine algae. Co-option of key genes, such as cell cycle and developmental regulators has been observed, but with few exceptions, known co-option events do not seem to coincide with most developmental features observed in multicellular volvocines. The apparent lack of "master multicellularity genes" combined with no apparent correlation between gene gains for developmental processes suggest the possibility that many multicellular traits might be the product gene-regulatory and functional innovations; in other words, multicellularity can arise from shared genomic repertoires that undergo regulatory and functional overhauls.},
}

@article {pmid35251134,
year = {2022},
author = {Palazzo, AF and Kejiou, NS},
title = {Non-Darwinian Molecular Biology.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {831068},
pmid = {35251134},
issn = {1664-8021},
abstract = {With the discovery of the double helical structure of DNA, a shift occurred in how biologists investigated questions surrounding cellular processes, such as protein synthesis. Instead of viewing biological activity through the lens of chemical reactions, this new field used biological information to gain a new profound view of how biological systems work. Molecular biologists asked new types of questions that would have been inconceivable to the older generation of researchers, such as how cellular machineries convert inherited biological information into functional molecules like proteins. This new focus on biological information also gave molecular biologists a way to link their findings to concepts developed by genetics and the modern synthesis. However, by the late 1960s this all changed. Elevated rates of mutation, unsustainable genetic loads, and high levels of variation in populations, challenged Darwinian evolution, a central tenant of the modern synthesis, where adaptation was the main driver of evolutionary change. Building on these findings, Motoo Kimura advanced the neutral theory of molecular evolution, which advocates that selection in multicellular eukaryotes is weak and that most genomic changes are neutral and due to random drift. This was further elaborated by Jack King and Thomas Jukes, in their paper "Non-Darwinian Evolution", where they pointed out that the observed changes seen in proteins and the types of polymorphisms observed in populations only become understandable when we take into account biochemistry and Kimura's new theory. Fifty years later, most molecular biologists remain unaware of these fundamental advances. Their adaptionist viewpoint fails to explain data collected from new powerful technologies which can detect exceedingly rare biochemical events. For example, high throughput sequencing routinely detects RNA transcripts being produced from almost the entire genome yet are present less than one copy per thousand cells and appear to lack any function. Molecular biologists must now reincorporate ideas from classical biochemistry and absorb modern concepts from molecular evolution, to craft a new lens through which they can evaluate the functionality of transcriptional units, and make sense of our messy, intricate, and complicated genome.},
}

@article {pmid35235070,
year = {2022},
author = {Kwantes, M and Wichard, T},
title = {The APAF1_C/WD40 repeat domain-encoding gene from the sea lettuce Ulva mutabilis sheds light on the evolution of NB-ARC domain-containing proteins in green plants.},
journal = {Planta},
volume = {255},
number = {4},
pages = {76},
pmid = {35235070},
issn = {1432-2048},
support = {SFB 1127/2 ChemBioSys//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Ecosystem ; Phylogeny ; Plant Proteins/metabolism ; Proteins/genetics ; *Ulva/genetics ; WD40 Repeats ; },
abstract = {MAIN CONCLUSION: We advance Ulva's genetic tractability and highlight its value as a model organism by characterizing its APAF1_C/WD40 domain-encoding gene, which belongs to a family that bears homology to R genes. The multicellular chlorophyte alga Ulva mutabilis (Ulvophyceae, Ulvales) is native to coastal ecosystems worldwide and attracts both high socio-economic and scientific interest. To further understand the genetic mechanisms that guide its biology, we present a protocol, based on adapter ligation-mediated PCR, for retrieving flanking sequences in U. mutabilis vector-insertion mutants. In the created insertional library, we identified a null mutant with an insertion in an apoptotic protease activating factor 1 helical domain (APAF1_C)/WD40 repeat domain-encoding gene. Protein domain architecture analysis combined with phylogenetic analysis revealed that this gene is a member of a subfamily that arose early in the evolution of green plants (Viridiplantae) through the acquisition of a gene that also encoded N-terminal nucleotide-binding adaptor shared by APAF-1, certain R-gene products and CED-4 (NB-ARC) and winged helix-like (WH-like) DNA-binding domains. Although phenotypic analysis revealed no mutant phenotype, gene expression levels in control plants correlated to the presence of bacterial symbionts, which U. mutabilis requires for proper morphogenesis. In addition, our analysis led to the discovery of a putative Ulva nucleotide-binding site and leucine-rich repeat (NBS-LRR) Resistance protein (R-protein), and we discuss how the emergence of these R proteins in green plants may be linked to the evolution of the APAF1_C/WD40 protein subfamily.},
}

Ecosystem
Phylogeny
Plant Proteins/metabolism
Proteins/genetics
*Ulva/genetics
WD40 Repeats

@article {pmid35218347,
year = {2022},
author = {Spang, A and Mahendrarajah, TA and Offre, P and Stairs, CW},
title = {Evolving perspective on the origin and diversification of cellular life and the virosphere.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evac034},
pmid = {35218347},
issn = {1759-6653},
abstract = {The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed in part due to profound methodological advances which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of this data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity as well as the origin and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.},
}

@article {pmid35194081,
year = {2022},
author = {Lin, HK and Cheng, JH and Wu, CC and Hsieh, FS and Dunlap, C and Chen, SH},
title = {Functional buffering via cell-specific gene expression promotes tissue homeostasis and cancer robustness.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {2974},
pmid = {35194081},
issn = {2045-2322},
mesh = {*Databases, Nucleic Acid ; *Gene Expression Regulation, Neoplastic ; *Homeostasis ; Humans ; *Neoplasms/genetics/metabolism ; Organ Specificity ; },
abstract = {Functional buffering that ensures biological robustness is critical for maintaining tissue homeostasis, organismal survival, and evolution of novelty. However, the mechanism underlying functional buffering, particularly in multicellular organisms, remains largely elusive. Here, we proposed that functional buffering can be mediated via expression of buffering genes in specific cells and tissues, by which we named Cell-specific Expression-BUffering (CEBU). We developed an inference index (C-score) for CEBU by computing C-scores across 684 human cell lines using genome-wide CRISPR screens and transcriptomic RNA-seq. We report that C-score-identified putative buffering gene pairs are enriched for members of the same duplicated gene family, pathway, and protein complex. Furthermore, CEBU is especially prevalent in tissues of low regenerative capacity (e.g., bone and neuronal tissues) and is weakest in highly regenerative blood cells, linking functional buffering to tissue regeneration. Clinically, the buffering capacity enabled by CEBU can help predict patient survival for multiple cancers. Our results suggest CEBU as a potential buffering mechanism contributing to tissue homeostasis and cancer robustness in humans.},
}

*Databases, Nucleic Acid
*Gene Expression Regulation, Neoplastic
*Homeostasis
Humans
*Neoplasms/genetics/metabolism
Organ Specificity

@article {pmid35188101,
year = {2022},
author = {Day, TC and Höhn, SS and Zamani-Dahaj, SA and Yanni, D and Burnetti, A and Pentz, J and Honerkamp-Smith, AR and Wioland, H and Sleath, HR and Ratcliff, WC and Goldstein, RE and Yunker, PJ},
title = {Cellular organization in lab-evolved and extant multicellular species obeys a maximum entropy law.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35188101},
issn = {2050-084X},
support = {/WT_/Wellcome Trust/United Kingdom ; R35 GM138030/GM/NIGMS NIH HHS/United States ; R35 GM138354/GM/NIGMS NIH HHS/United States ; 207510/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Cell Size ; *Directed Molecular Evolution ; Phylogeny ; Volvox/cytology/*genetics/physiology ; Yeasts/cytology/*genetics/physiology ; },
abstract = {The prevalence of multicellular organisms is due in part to their ability to form complex structures. How cells pack in these structures is a fundamental biophysical issue, underlying their functional properties. However, much remains unknown about how cell packing geometries arise, and how they are affected by random noise during growth - especially absent developmental programs. Here, we quantify the statistics of cellular neighborhoods of two different multicellular eukaryotes: lab-evolved 'snowflake' yeast and the green alga Volvox carteri. We find that despite large differences in cellular organization, the free space associated with individual cells in both organisms closely fits a modified gamma distribution, consistent with maximum entropy predictions originally developed for granular materials. This 'entropic' cellular packing ensures a degree of predictability despite noise, facilitating parent-offspring fidelity even in the absence of developmental regulation. Together with simulations of diverse growth morphologies, these results suggest that gamma-distributed cell neighborhood sizes are a general feature of multicellularity, arising from conserved statistics of cellular packing.},
}

Cell Size
*Directed Molecular Evolution
Phylogeny
Volvox/cytology/*genetics/physiology
Yeasts/cytology/*genetics/physiology

@article {pmid35154170,
year = {2021},
author = {Žárský, J and Žárský, V and Hanáček, M and Žárský, V},
title = {Cryogenian Glacial Habitats as a Plant Terrestrialisation Cradle - The Origin of the Anydrophytes and Zygnematophyceae Split.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {735020},
pmid = {35154170},
issn = {1664-462X},
abstract = {For tens of millions of years (Ma), the terrestrial habitats of Snowball Earth during the Cryogenian period (between 720 and 635 Ma before present-Neoproterozoic Era) were possibly dominated by global snow and ice cover up to the equatorial sublimative desert. The most recent time-calibrated phylogenies calibrated not only on plants but on a comprehensive set of eukaryotes indicate that within the Streptophyta, multicellular charophytes (Phragmoplastophyta) evolved in the Mesoproterozoic to the early Neoproterozoic. At the same time, Cryogenian is the time of the likely origin of the common ancestor of Zygnematophyceae and Embryophyta and later, also of the Zygnematophyceae-Embryophyta split. This common ancestor is proposed to be called Anydrophyta; here, we use anydrophytes. Based on the combination of published phylogenomic studies and estimated diversification time comparisons, we deem it highly likely that anydrophytes evolved in response to Cryogenian cooling. Also, later in the Cryogenian, secondary simplification of multicellular anydrophytes and loss of flagella resulted in Zygnematophyceae diversification as an adaptation to the extended cold glacial environment. We propose that the Marinoan geochemically documented expansion of first terrestrial flora has been represented not only by Chlorophyta but also by Streptophyta, including the anydrophytes, and later by Zygnematophyceae, thriving on glacial surfaces until today. It is possible that multicellular early Embryophyta survived in less abundant (possibly relatively warmer) refugia, relying more on mineral substrates, allowing the retention of flagella-based sexuality. The loss of flagella and sexual reproduction by conjugation evolved in Zygnematophyceae and zygomycetous fungi during the Cryogenian in a remarkably convergent way. Thus, we support the concept that the important basal cellular adaptations to terrestrial environments were exapted in streptophyte algae for terrestrialization and propose that this was stimulated by the adaptation to glacial habitats dominating the Cryogenian Snowball Earth. Including the glacial lifestyle when considering the rise of land plants increases the parsimony of connecting different ecological, phylogenetic, and physiological puzzles of the journey from aquatic algae to terrestrial floras.},
}

@article {pmid35143488,
year = {2022},
author = {Yaguchi, S and Taniguchi, Y and Suzuki, H and Kamata, M and Yaguchi, J},
title = {Planktonic sea urchin larvae change their swimming direction in response to strong photoirradiation.},
journal = {PLoS genetics},
volume = {18},
number = {2},
pages = {e1010033},
pmid = {35143488},
issn = {1553-7404},
mesh = {Animals ; Cilia/metabolism ; Larva/metabolism ; Light ; Locomotion/physiology ; Movement/*physiology ; Muscles/physiology ; Opsins/genetics/metabolism ; Photoreceptor Cells/*metabolism ; Plankton ; Sea Urchins/*metabolism ; },
abstract = {To survive, organisms need to precisely respond to various environmental factors, such as light and gravity. Among these, light is so important for most life on Earth that light-response systems have become extraordinarily developed during evolution, especially in multicellular animals. A combination of photoreceptors, nervous system components, and effectors allows these animals to respond to light stimuli. In most macroscopic animals, muscles function as effectors responding to light, and in some microscopic aquatic animals, cilia play a role. It is likely that the cilia-based response was the first to develop and that it has been substituted by the muscle-based response along with increases in body size. However, although the function of muscle appears prominent, it is poorly understood whether ciliary responses to light are present and/or functional, especially in deuterostomes, because it is possible that these responses are too subtle to be observed, unlike muscle responses. Here, we show that planktonic sea urchin larvae reverse their swimming direction due to the inhibitory effect of light on the cholinergic neuron signaling>forward swimming pathway. We found that strong photoirradiation of larvae that stay on the surface of seawater immediately drives the larvae away from the surface due to backward swimming. When Opsin2, which is expressed in mesenchymal cells in larval arms, is knocked down, the larvae do not show backward swimming under photoirradiation. Although Opsin2-expressing cells are not neuronal cells, immunohistochemical analysis revealed that they directly attach to cholinergic neurons, which are thought to regulate forward swimming. These data indicate that light, through Opsin2, inhibits the activity of cholinergic signaling, which normally promotes larval forward swimming, and that the light-dependent ciliary response is present in deuterostomes. These findings shed light on how light-responsive tissues/organelles have been conserved and diversified during evolution.},
}

Animals
Cilia/metabolism
Larva/metabolism
Light
Locomotion/physiology
Movement/*physiology
Muscles/physiology
Opsins/genetics/metabolism
Photoreceptor Cells/*metabolism
Plankton
Sea Urchins/*metabolism

@article {pmid35014399,
year = {2021},
author = {Klein, S and Distel, LVR and Neuhuber, W},
title = {X-ray Dose-Enhancing Impact of Functionalized Au-Fe3O4 Nanoheterodimers on MCF-7 and A549 Multicellular Tumor Spheroids.},
journal = {ACS applied bio materials},
volume = {4},
number = {4},
pages = {3113-3123},
doi = {10.1021/acsabm.0c01494},
pmid = {35014399},
issn = {2576-6422},
mesh = {Biocompatible Materials/chemistry/*pharmacology ; Cell Survival/drug effects ; Ferric Compounds/chemistry/*pharmacology ; Gold/chemistry/*pharmacology ; Humans ; MCF-7 Cells ; Materials Testing ; Nanoparticles/*chemistry ; Particle Size ; Spheroids, Cellular/*drug effects ; *X-Rays ; },
abstract = {The efficiency of nanoparticle-enhanced radiotherapy was studied by loading MCF-7 and A549 multicellular tumor spheroids (MCTSs) with caffeic acid- and nitrosonium-functionalized Au-Fe3O4 nanoheterodimers (Au-Fe3O4 NHDs). Transmission electron microscope images of MCTS cross-sectional sections visualized the invasion and distribution of the nitrosonium- and caffeic acid-functionalized Au-Fe3O4 NHDs (NO- and CA-NHDs) in the A549 and MCF-7 MCTSs, whereas the iron content of the MCTSs were quantified using the ferrozine assay. The synergistic impact of intracellular NO- and CA-NHDs and X-ray irradiation on the growth dynamics of the A549 and MCF-7 MCTSs was surveyed by monitoring their temporal evolution under a light microscope over a period of 14 days. The emergence of hypoxia during the spheroid growth was followed by detecting the lactate efflux of MCTSs without and with NO- and CA-NHDs. The performance of the NO- and CA-NHDs as X-ray dose-enhancing agents in the A549 and MCF-7 MCTSs was clarified by performing clonogenic cell survival assays and determining the respective dose-modifying factors for X-ray doses of 0, 2, 4, and 6 Gy. The NO- and CA-NHDs were shown to perform as potent X-ray dose-enhancing agents in A549 and MCF-7 MCTSs. Moreover, the CA-NHDs boosted their radio-sensitizing efficacy by inhibiting the lactate efflux as impairing metabolic reprogramming. A synergistic effect on the MCTS destruction was observed for the combination of both NHDs since the surfactants differ in their antitumor effect.},
}

Biocompatible Materials/chemistry/*pharmacology
Cell Survival/drug effects
Ferric Compounds/chemistry/*pharmacology
Gold/chemistry/*pharmacology
Humans
MCF-7 Cells
Materials Testing
Nanoparticles/*chemistry
Particle Size
Spheroids, Cellular/*drug effects
*X-Rays

@article {pmid35013306,
year = {2022},
author = {Sforna, MC and Loron, CC and Demoulin, CF and François, C and Cornet, Y and Lara, YJ and Grolimund, D and Ferreira Sanchez, D and Medjoubi, K and Somogyi, A and Addad, A and Fadel, A and Compère, P and Baudet, D and Brocks, JJ and Javaux, EJ},
title = {Intracellular bound chlorophyll residues identify 1 Gyr-old fossils as eukaryotic algae.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {146},
pmid = {35013306},
issn = {2041-1723},
mesh = {Biological Evolution ; Chlorophyll/*chemistry/history ; Chlorophyta/anatomy & histology/classification/physiology/*ultrastructure ; Coordination Complexes/*chemistry ; Democratic Republic of the Congo ; Ecosystem ; Eukaryotic Cells ; *Fossils ; Geologic Sediments/analysis ; History, Ancient ; Microscopy, Electron, Transmission ; Nickel/chemistry ; Photosynthesis/*physiology ; Phylogeny ; Plant Cells/physiology/ultrastructure ; Tetrapyrroles/chemistry ; X-Ray Absorption Spectroscopy ; },
abstract = {The acquisition of photosynthesis is a fundamental step in the evolution of eukaryotes. However, few phototrophic organisms are unambiguously recognized in the Precambrian record. The in situ detection of metabolic byproducts in individual microfossils is the key for the direct identification of their metabolisms. Here, we report a new integrative methodology using synchrotron-based X-ray fluorescence and absorption. We evidence bound nickel-geoporphyrins moieties in low-grade metamorphic rocks, preserved in situ within cells of a ~1 Gyr-old multicellular eukaryote, Arctacellularia tetragonala. We identify these moieties as chlorophyll derivatives, indicating that A. tetragonala was a phototrophic eukaryote, one of the first unambiguous algae. This new approach, applicable to overmature rocks, creates a strong new proxy to understand the evolution of phototrophy and diversification of early ecosystems.},
}

Biological Evolution
Chlorophyll/*chemistry/history
Chlorophyta/anatomy & histology/classification/physiology/*ultrastructure
Coordination Complexes/*chemistry
Democratic Republic of the Congo
Ecosystem
Eukaryotic Cells
*Fossils
Geologic Sediments/analysis
History, Ancient
Microscopy, Electron, Transmission
Nickel/chemistry
Photosynthesis/*physiology
Phylogeny
Plant Cells/physiology/ultrastructure
Tetrapyrroles/chemistry
X-Ray Absorption Spectroscopy

@article {pmid34937533,
year = {2021},
author = {Shilovsky, GA and Putyatina, TS and Markov, AV},
title = {Altruism and Phenoptosis as Programs Supported by Evolution.},
journal = {Biochemistry. Biokhimiia},
volume = {86},
number = {12},
pages = {1540-1552},
pmid = {34937533},
issn = {1608-3040},
mesh = {*Altruism ; Animals ; *Apoptosis ; *Biological Evolution ; *COVID-19 ; Humans ; Insecta/physiology ; *SARS-CoV-2 ; },
abstract = {Phenoptosis is a programmed death that has emerged in the process of evolution, sometimes taking the form of an altruistic program. In particular, it is believed to be a weapon against the spread of pandemics in the past and an obstacle in fighting pandemics in the present (COVID). However, on the evolutionary scale, deterministic death is not associated with random relationships (for example, bacteria with a particular mutation), but is a product of higher nervous activity or a consequence of established hierarchy that reaches its maximal expression in eusocial communities of Hymenoptera and highly social communities of mammals. Unlike a simple association of individuals, eusociality is characterized by the appearance of non-reproductive individuals as the highest form of altruism. In contrast to primitive programs for unicellular organisms, higher multicellular organisms are characterized by the development of behavior-based phenoptotic programs, especially in the case of reproduction-associated limitation of lifespan. Therefore, we can say that the development of altruism in the course of evolution of sociality leads in its extreme manifestation to phenoptosis. Development of mathematical models for the emergence of altruism and programmed death contributes to our understanding of mechanisms underlying these paradoxical counterproductive (harmful) programs. In theory, this model can be applied not only to insects, but also to other social animals and even to the human society. Adaptive death is an extreme form of altruism. We consider altruism and programmed death as programmed processes in the mechanistic and adaptive sense, respectively. Mechanistically, this is a program existing as a predetermined chain of certain responses, regardless of its adaptive value. As to its adaptive value (regardless of the degree of "phenoptoticity"), this is a characteristic of organisms that demonstrate high levels of kinship, social organization, and physical association typical for higher-order individuals, e.g., unicellular organisms forming colonies with some characteristics of multicellular animals or colonies of multicellular animals displaying features of supraorganisms.},
}

*Altruism
Animals
*Apoptosis
*Biological Evolution
*COVID-19
Humans
Insecta/physiology
*SARS-CoV-2

@article {pmid34932575,
year = {2021},
author = {Maltseva, AL and Varfolomeeva, MA and Gafarova, ER and Panova, MAZ and Mikhailova, NA and Granovitch, AI},
title = {Divergence together with microbes: A comparative study of the associated microbiomes in the closely related Littorina species.},
journal = {PloS one},
volume = {16},
number = {12},
pages = {e0260792},
pmid = {34932575},
issn = {1932-6203},
mesh = {Animals ; Bacteria/classification/genetics/*isolation & purification ; Environmental Microbiology ; *Genetic Variation ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Snails/classification/*microbiology ; Species Specificity ; },
abstract = {Any multicellular organism during its life is involved in relatively stable interactions with microorganisms. The organism and its microbiome make up a holobiont, possessing a unique set of characteristics and evolving as a whole system. This study aimed to evaluate the degree of the conservativeness of microbiomes associated with intertidal gastropods. We studied the composition and the geographic and phylogenetic variability of the gut and body surface microbiomes of five closely related sympatric Littorina (Neritrema) spp. and a more distant species, L. littorea, from the sister subgenus Littorina (Littorina). Although snail-associated microbiomes included many lineages (207-603), they were dominated by a small number of OTUs of the genera Psychromonas, Vibrio, and Psychrilyobacter. The geographic variability was greater than the interspecific differences at the same collection site. While the microbiomes of the six Littorina spp. did not differ at the high taxonomic level, the OTU composition differed between groups of cryptic species and subgenera. A few species-specific OTUs were detected within the collection sites; notably, such OTUs never dominated microbiomes. We conclude that the composition of the high-rank taxa of the associated microbiome ("scaffolding enterotype") is more evolutionarily conserved than the composition of the low-rank individual OTUs, which may be site- and / or species-specific.},
}

Animals
Bacteria/classification/genetics/*isolation & purification
Environmental Microbiology
*Genetic Variation
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics
Snails/classification/*microbiology
Species Specificity

@article {pmid34890552,
year = {2021},
author = {Brückner, A and Badroos, JM and Learsch, RW and Yousefelahiyeh, M and Kitchen, SA and Parker, J},
title = {Evolutionary assembly of cooperating cell types in an animal chemical defense system.},
journal = {Cell},
volume = {184},
number = {25},
pages = {6138-6156.e28},
doi = {10.1016/j.cell.2021.11.014},
pmid = {34890552},
issn = {1097-4172},
mesh = {Animals ; Benzoquinones/*metabolism ; Biological Evolution ; Biosynthetic Pathways ; Coleoptera/*metabolism ; Drosophila melanogaster/*metabolism ; Pheromones/*metabolism ; },
abstract = {How the functions of multicellular organs emerge from the underlying evolution of cell types is poorly understood. We deconstructed evolution of an organ novelty: a rove beetle gland that secretes a defensive cocktail. We show how gland function arose via assembly of two cell types that manufacture distinct compounds. One cell type, comprising a chemical reservoir within the abdomen, produces alkane and ester compounds. We demonstrate that this cell type is a hybrid of cuticle cells and ancient pheromone and adipocyte-like cells, executing its function via a mosaic of enzymes from each parental cell type. The second cell type synthesizes benzoquinones using a chimera of conserved cellular energy and cuticle formation pathways. We show that evolution of each cell type was shaped by coevolution between the two cell types, yielding a potent secretion that confers adaptive value. Our findings illustrate how cooperation between cell types arises, generating new, organ-level behaviors.},
}

Animals
Benzoquinones/*metabolism
Biological Evolution
Biosynthetic Pathways
Coleoptera/*metabolism
Drosophila melanogaster/*metabolism
Pheromones/*metabolism

@article {pmid34870903,
year = {2021},
author = {Prostak, SM and Fritz-Laylin, LK},
title = {Laboratory Maintenance of the Chytrid Fungus Batrachochytrium dendrobatidis.},
journal = {Current protocols},
volume = {1},
number = {12},
pages = {e309},
doi = {10.1002/cpz1.309},
pmid = {34870903},
issn = {2691-1299},
support = {//National Science Foundation/ ; },
mesh = {Amphibians ; Animals ; Batrachochytrium ; *Chytridiomycota ; Ecosystem ; Laboratories ; },
abstract = {The chytrid fungus Batrachochytrium dendrobatidis (Bd) is a causative agent of chytridiomycosis, a skin disease associated with amphibian population declines around the world. Despite the major impact Bd is having on global ecosystems, much of Bd's basic biology remains unstudied. In addition to revealing mechanisms driving the spread of chytridiomycosis, studying Bd can shed light on the evolution of key fungal traits because chytrid fungi, including Bd, diverged before the radiation of the Dikaryotic fungi (multicellular fungi and yeast). Studying Bd in the laboratory is, therefore, of growing interest to a wide range of scientists, ranging from herpetologists and disease ecologists to molecular, cell, and evolutionary biologists. This protocol describes how to maintain developmentally synchronized liquid cultures of Bd for use in the laboratory, how to grow Bd on solid media, as well as cryopreservation and revival of frozen stocks. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Reviving cryopreserved Bd cultures Basic Protocol 2: Establishing synchronized liquid cultures of Bd Basic Protocol 3: Regular maintenance of synchronous Bd in liquid culture Alternate Protocol 1: Regular maintenance of asynchronous Bd in liquid culture Basic Protocol 4: Regular maintenance of synchronous Bd on solid medium Alternate Protocol 2: Starting a culture on solid medium from a liquid culture Basic Protocol 5: Cryopreservation of Bd.},
}

Amphibians
Animals
Batrachochytrium
*Chytridiomycota
Ecosystem
Laboratories

@article {pmid34857936,
year = {2021},
author = {Liu, K and Deng, S and Ye, C and Yao, Z and Wang, J and Gong, H and Liu, L and He, X},
title = {Mapping single-cell-resolution cell phylogeny reveals cell population dynamics during organ development.},
journal = {Nature methods},
volume = {18},
number = {12},
pages = {1506-1514},
pmid = {34857936},
issn = {1548-7105},
mesh = {Alleles ; Animals ; Animals, Genetically Modified ; Cell Division ; Cell Lineage ; Computational Biology/*methods ; DNA Replication ; Drosophila melanogaster/embryology/*metabolism ; Endonucleases/metabolism ; Likelihood Functions ; Male ; Microscopy/*methods ; Mutagenesis ; *Mutation ; Phenotype ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Single-Cell Analysis ; },
abstract = {Mapping the cell phylogeny of a complex multicellular organism relies on somatic mutations accumulated from zygote to adult. Available cell barcoding methods can record about three mutations per barcode, enabling only low-resolution mapping of the cell phylogeny of complex organisms. Here we developed SMALT, a substitution mutation-aided lineage-tracing system that outperforms the available cell barcoding methods in mapping cell phylogeny. We applied SMALT to Drosophila melanogaster and obtained on average more than 20 mutations on a three-kilobase-pair barcoding sequence in early-adult cells. Using the barcoding mutations, we obtained high-quality cell phylogenetic trees, each comprising several thousand internal nodes with 84-93% median bootstrap support. The obtained cell phylogenies enabled a population genetic analysis that estimates the longitudinal dynamics of the number of actively dividing parental cells (Np) in each organ through development. The Np dynamics revealed the trajectory of cell births and provided insight into the balance of symmetric and asymmetric cell division.},
}

Alleles
Animals
Animals, Genetically Modified
Cell Division
Cell Lineage
Computational Biology/*methods
DNA Replication
Drosophila melanogaster/embryology/*metabolism
Endonucleases/metabolism
Likelihood Functions
Male
Microscopy/*methods
Mutagenesis
*Mutation
Phenotype
Phylogeny
Saccharomyces cerevisiae/genetics
Single-Cell Analysis

@article {pmid34853303,
year = {2021},
author = {Pennemann, FL and Mussabekova, A and Urban, C and Stukalov, A and Andersen, LL and Grass, V and Lavacca, TM and Holze, C and Oubraham, L and Benamrouche, Y and Girardi, E and Boulos, RE and Hartmann, R and Superti-Furga, G and Habjan, M and Imler, JL and Meignin, C and Pichlmair, A},
title = {Cross-species analysis of viral nucleic acid interacting proteins identifies TAOKs as innate immune regulators.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {7009},
pmid = {34853303},
issn = {2041-1723},
mesh = {Animals ; Antiviral Agents ; Drosophila melanogaster ; Evolution, Molecular ; Humans ; *Immunity, Innate ; Mice ; Nucleic Acids/*chemistry/*immunology ; Protein Serine-Threonine Kinases ; Proteomics ; RNA Interference ; RNA, Double-Stranded ; Species Specificity ; THP-1 Cells ; Viral Proteins/*chemistry/*immunology ; },
abstract = {The cell intrinsic antiviral response of multicellular organisms developed over millions of years and critically relies on the ability to sense and eliminate viral nucleic acids. Here we use an affinity proteomics approach in evolutionary distant species (human, mouse and fly) to identify proteins that are conserved in their ability to associate with diverse viral nucleic acids. This approach shows a core of orthologous proteins targeting viral genetic material and species-specific interactions. Functional characterization of the influence of 181 candidates on replication of 6 distinct viruses in human cells and flies identifies 128 nucleic acid binding proteins with an impact on virus growth. We identify the family of TAO kinases (TAOK1, -2 and -3) as dsRNA-interacting antiviral proteins and show their requirement for type-I interferon induction. Depletion of TAO kinases in mammals or flies leads to an impaired response to virus infection characterized by a reduced induction of interferon stimulated genes in mammals and impaired expression of srg1 and diedel in flies. Overall, our study shows a larger set of proteins able to mediate the interaction between viral genetic material and host factors than anticipated so far, attesting to the ancestral roots of innate immunity and to the lineage-specific pressures exerted by viruses.},
}

Animals
Antiviral Agents
Drosophila melanogaster
Evolution, Molecular
Humans
*Immunity, Innate
Mice
Nucleic Acids/*chemistry/*immunology
Protein Serine-Threonine Kinases
Proteomics
RNA Interference
RNA, Double-Stranded
Species Specificity
THP-1 Cells
Viral Proteins/*chemistry/*immunology

@article {pmid34849891,
year = {2021},
author = {Varahan, S and Laxman, S},
title = {Bend or break: how biochemically versatile molecules enable metabolic division of labor in clonal microbial communities.},
journal = {Genetics},
volume = {219},
number = {2},
pages = {},
pmid = {34849891},
issn = {1943-2631},
mesh = {Evolution, Molecular ; *Microbial Consortia ; *Microbial Interactions ; Yeasts/genetics/metabolism/physiology ; },
abstract = {In fluctuating nutrient environments, isogenic microbial cells transition into "multicellular" communities composed of phenotypically heterogeneous cells, showing functional specialization. In fungi (such as budding yeast), phenotypic heterogeneity is often described in the context of cells switching between different morphotypes (e.g., yeast to hyphae/pseudohyphae or white/opaque transitions in Candida albicans). However, more fundamental forms of metabolic heterogeneity are seen in clonal Saccharomyces cerevisiae communities growing in nutrient-limited conditions. Cells within such communities exhibit contrasting, specialized metabolic states, and are arranged in distinct, spatially organized groups. In this study, we explain how such an organization can stem from self-organizing biochemical reactions that depend on special metabolites. These metabolites exhibit plasticity in function, wherein the same metabolites are metabolized and utilized for distinct purposes by different cells. This in turn allows cell groups to function as specialized, interdependent cross-feeding systems which support distinct metabolic processes. Exemplifying a system where cells exhibit either gluconeogenic or glycolytic states, we highlight how available metabolites can drive favored biochemical pathways to produce new, limiting resources. These new resources can themselves be consumed or utilized distinctly by cells in different metabolic states. This thereby enables cell groups to sustain contrasting, even apparently impossible metabolic states with stable transcriptional and metabolic signatures for a given environment, and divide labor in order to increase community fitness or survival. We speculate on possible evolutionary implications of such metabolic specialization and division of labor in isogenic microbial communities.},
}

Evolution, Molecular
*Microbial Consortia
*Microbial Interactions
Yeasts/genetics/metabolism/physiology

@article {pmid34848727,
year = {2021},
author = {Benaissa, H and Ounoughi, K and Aujard, I and Fischer, E and Goïame, R and Nguyen, J and Tebo, AG and Li, C and Le Saux, T and Bertolin, G and Tramier, M and Danglot, L and Pietrancosta, N and Morin, X and Jullien, L and Gautier, A},
title = {Engineering of a fluorescent chemogenetic reporter with tunable color for advanced live-cell imaging.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {6989},
pmid = {34848727},
issn = {2041-1723},
mesh = {Animals ; Biocompatible Materials ; Biosensing Techniques ; Color ; Coloring Agents ; Diagnostic Imaging/*methods ; Electronics ; Female ; *Fluorescence ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes ; Green Fluorescent Proteins ; Male ; Neurons ; Protein Engineering/*methods ; Rats ; Rats, Sprague-Dawley ; },
abstract = {Biocompatible fluorescent reporters with spectral properties spanning the entire visible spectrum are indispensable tools for imaging the biochemistry of living cells and organisms in real time. Here, we report the engineering of a fluorescent chemogenetic reporter with tunable optical and spectral properties. A collection of fluorogenic chromophores with various electronic properties enables to generate bimolecular fluorescent assemblies that cover the visible spectrum from blue to red using a single protein tag engineered and optimized by directed evolution and rational design. The ability to tune the fluorescence color and properties through simple molecular modulation provides a broad experimental versatility for imaging proteins in live cells, including neurons, and in multicellular organisms, and opens avenues for optimizing Förster resonance energy transfer (FRET) biosensors in live cells. The ability to tune the spectral properties and fluorescence performance enables furthermore to match the specifications and requirements of advanced super-resolution imaging techniques.},
}

Animals
Biocompatible Materials
Biosensing Techniques
Color
Coloring Agents
Diagnostic Imaging/*methods
Electronics
Female
*Fluorescence
Fluorescence Resonance Energy Transfer
Fluorescent Dyes
Green Fluorescent Proteins
Male
Neurons
Protein Engineering/*methods
Rats
Rats, Sprague-Dawley

@article {pmid34841798,
year = {2021},
author = {Yu, D and Cao, H and Wang, X},
title = {[Advances and applications of organoids: a review].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {37},
number = {11},
pages = {3961-3974},
doi = {10.13345/j.cjb.200764},
pmid = {34841798},
issn = {1872-2075},
mesh = {*Gene Editing ; Humans ; Models, Biological ; *Organoids ; Regenerative Medicine ; Stem Cells ; },
abstract = {Novel model systems have provided powerful tools for the research of human biology. Despite of being widely used, the conventional research models could not precisely describe the human physiological phenomenon. Organoids are three-dimensional multicellular aggregates derived from stem cells or organ progenitors that could differentiate and self-organize to recapitulate some specific functionalities and architectures of their in vivo counterpart organs. Organoids can be used to simulate organogenesis because of their human origin. In addition, the genomic stability of organoids could be well maintained during long-term amplification in vitro. Moreover, organoids can be cryopreserved as a live biobank for high-throughput screening. Combinatorial use of organoids with other emerging technologies (e.g. gene editing, organ-on-a-chip and single-cell RNA sequencing) could overcome the bottlenecks of conventional models and provide valuable information for disease modelling, pharmaceutical research, precision medicine and regenerative medicine at the organ level. This review summarizes the classifications, characteristics, current applications, combined use with other technologies and future prospects of organoids.},
}

*Gene Editing
Humans
Models, Biological
*Organoids
Regenerative Medicine
Stem Cells

@article {pmid34830470,
year = {2021},
author = {Kertmen, A and Petrenko, I and Schimpf, C and Rafaja, D and Petrova, O and Sivkov, V and Nekipelov, S and Fursov, A and Stelling, AL and Heimler, K and Rogoll, A and Vogt, C and Ehrlich, H},
title = {Calcite Nanotuned Chitinous Skeletons of Giant Ianthella basta Marine Demosponge.},
journal = {International journal of molecular sciences},
volume = {22},
number = {22},
pages = {},
pmid = {34830470},
issn = {1422-0067},
support = {HE 394/3.//DFG/ ; },
mesh = {Animals ; Aquatic Organisms/*chemistry ; Biomineralization ; Calcium Carbonate/*chemistry ; Chitin/chemistry ; Porifera/*chemistry ; Skeleton/*chemistry ; Spectroscopy, Fourier Transform Infrared ; Tissue Scaffolds/chemistry ; X-Ray Diffraction ; },
abstract = {Marine sponges were among the first multicellular organisms on our planet and have survived to this day thanks to their unique mechanisms of chemical defense and the specific design of their skeletons, which have been optimized over millions of years of evolution to effectively inhabit the aquatic environment. In this work, we carried out studies to elucidate the nature and nanostructural organization of three-dimensional skeletal microfibers of the giant marine demosponge Ianthella basta, the body of which is a micro-reticular, durable structure that determines the ideal filtration function of this organism. For the first time, using the battery of analytical tools including three-dimensional micro-X-ray Fluorescence (3D-µXRF), X-ray diffraction (XRD), infra-red (FTIR), Raman and Near Edge X-ray Fine Structure (NEXAFS) spectroscopy, we have shown that biomineral calcite is responsible for nano-tuning the skeletal fibers of this sponge species. This is the first report on the presence of a calcitic mineral phase in representatives of verongiid sponges which belong to the class Demospongiae. Our experimental data suggest a possible role for structural amino polysaccharide chitin as a template for calcification. Our study suggests further experiments to elucidate both the origin of calcium carbonate inside the skeleton of this sponge and the mechanisms of biomineralization in the surface layers of chitin microfibers saturated with bromotyrosines, which have effective antimicrobial properties and are responsible for the chemical defense of this organism. The discovery of the calcified phase in the chitinous template of I. basta skeleton is expected to broaden the knowledge in biomineralization science where the calcium carbonate is regarded as a valuable material for applications in biomedicine, environmental science, and even in civil engineering.},
}

Animals
Aquatic Organisms/*chemistry
Biomineralization
Calcium Carbonate/*chemistry
Chitin/chemistry
Porifera/*chemistry
Skeleton/*chemistry
Spectroscopy, Fourier Transform Infrared
Tissue Scaffolds/chemistry
X-Ray Diffraction

@article {pmid34830263,
year = {2021},
author = {Pereira, PHS and Garcia, CRS},
title = {Evidence of G-Protein-Coupled Receptors (GPCR) in the Parasitic Protozoa Plasmodium falciparum-Sensing the Host Environment and Coupling within Its Molecular Signaling Toolkit.},
journal = {International journal of molecular sciences},
volume = {22},
number = {22},
pages = {},
pmid = {34830263},
issn = {1422-0067},
support = {2017/08684-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
mesh = {Animals ; Antimalarials/pharmacology/therapeutic use ; Calcium/metabolism ; Calcium Signaling/drug effects/*physiology ; Host-Parasite Interactions/*physiology ; Humans ; Malaria, Falciparum/drug therapy/*metabolism/parasitology ; Molecular Targeted Therapy/methods ; Perception/drug effects/*physiology ; Plasmodium falciparum/*metabolism ; Protein Binding ; Protozoan Proteins/*metabolism ; Receptors, G-Protein-Coupled/antagonists & inhibitors/*metabolism ; },
abstract = {Throughout evolution, the need for single-celled organisms to associate and form a single cluster of cells has had several evolutionary advantages. In complex, multicellular organisms, each tissue or organ has a specialty and function that make life together possible, and the organism as a whole needs to act in balance and adapt to changes in the environment. Sensory organs are essential for connecting external stimuli into a biological response, through the senses: sight, smell, taste, hearing, and touch. The G-protein-coupled receptors (GPCRs) are responsible for many of these senses and therefore play a key role in the perception of the cells' external environment, enabling interaction and coordinated development between each cell of a multicellular organism. The malaria-causing protozoan parasite, Plasmodium falciparum, has a complex life cycle that is extremely dependent on a finely regulated cellular signaling machinery. In this review, we summarize strong evidence and the main candidates of GPCRs in protozoan parasites. Interestingly, one of these GPCRs is a sensor for K+ shift in Plasmodium falciparum, PfSR25. Studying this family of proteins in P. falciparum could have a significant impact, both on understanding the history of the evolution of GPCRs and on finding new targets for antimalarials.},
}

Animals
Antimalarials/pharmacology/therapeutic use
Calcium/metabolism
Calcium Signaling/drug effects/*physiology
Host-Parasite Interactions/*physiology
Humans
Malaria, Falciparum/drug therapy/*metabolism/parasitology
Molecular Targeted Therapy/methods
Perception/drug effects/*physiology
Plasmodium falciparum/*metabolism
Protein Binding
Protozoan Proteins/*metabolism
Receptors, G-Protein-Coupled/antagonists & inhibitors/*metabolism

@article {pmid34811380,
year = {2021},
author = {Yamashita, S and Yamamoto, K and Matsuzaki, R and Suzuki, S and Yamaguchi, H and Hirooka, S and Minakuchi, Y and Miyagishima, SY and Kawachi, M and Toyoda, A and Nozaki, H},
title = {Genome sequencing of the multicellular alga Astrephomene provides insights into convergent evolution of germ-soma differentiation.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {22231},
pmid = {34811380},
issn = {2045-2322},
support = {17J03439//Japan Society for the Promotion of Science/ ; 16H06279//Japan Society for the Promotion of Science/ ; 16H02518//Japan Society for the Promotion of Science/ ; 20H03299//Japan Society for the Promotion of Science/ ; },
mesh = {Algal Proteins/genetics/metabolism ; *Biological Evolution ; Cell Differentiation/*genetics ; Chlorophyceae/*genetics ; Chlorophyta/*genetics ; Germ Cells ; Volvox/genetics ; Whole Genome Sequencing ; },
abstract = {Germ-soma differentiation evolved independently in many eukaryotic lineages and contributed to complex multicellular organizations. However, the molecular genetic bases of such convergent evolution remain unresolved. Two multicellular volvocine green algae, Volvox and Astrephomene, exhibit convergent evolution of germ-soma differentiation. The complete genome sequence is now available for Volvox, while genome information is scarce for Astrephomene. Here, we generated the de novo whole genome sequence of Astrephomene gubernaculifera and conducted RNA-seq analysis of isolated somatic and reproductive cells. In Volvox, tandem duplication and neofunctionalization of the ancestral transcription factor gene (RLS1/rlsD) might have led to the evolution of regA, the master regulator for Volvox germ-soma differentiation. However, our genome data demonstrated that Astrephomene has not undergone tandem duplication of the RLS1/rlsD homolog or acquisition of a regA-like gene. Our RNA-seq analysis revealed the downregulation of photosynthetic and anabolic gene expression in Astrephomene somatic cells, as in Volvox. Among genes with high expression in somatic cells of Astrephomene, we identified three genes encoding putative transcription factors, which may regulate somatic cell differentiation. Thus, the convergent evolution of germ-soma differentiation in the volvocine algae may have occurred by the acquisition of different regulatory circuits that generate a similar division of labor.},
}

Algal Proteins/genetics/metabolism
*Biological Evolution
Cell Differentiation/*genetics
Chlorophyceae/*genetics
Chlorophyta/*genetics
Germ Cells
Volvox/genetics
Whole Genome Sequencing

@article {pmid34789585,
year = {2021},
author = {Miller, EA and Leidholt, S and Galvin, T and Norton, A and Van Houtan, KS and Vega Thurber, R and Boustany, A},
title = {Electron microscopy reveals viral-like particles and mitochondrial degradation in scombrid puffy snout syndrome.},
journal = {Diseases of aquatic organisms},
volume = {147},
number = {},
pages = {25-31},
doi = {10.3354/dao03634},
pmid = {34789585},
issn = {0177-5103},
mesh = {Animals ; Eukaryota ; Fishes ; Microscopy, Electron/veterinary ; *Mitophagy ; *Perciformes ; },
abstract = {Aquaculture is an increasingly important food resource, but its sustainability is often limited by disease. In Scombridae fishes, puffy snout syndrome (PSS) is a debilitating condition where tumor-like collagenous growths form around the eyes, nares, and mandibles which impair vision and feeding and frequently lead to mortality. While PSS is considered an infectious or metabolic disease, no disease agents or promoters have been identified. Here, we used electron microscopy (EM) to describe the cellular pathology and search for etiological agents of PSS in Pacific mackerel Scomber japonicus, the first use of this approach for PSS. We examined aquaculture specimens across a range of apparent PSS severity, comparing the results to both wild and aquaculture asymptomatic mackerel. EM imagery consistently revealed viral-like particles in PSS samples, as well as the uniform absence of bacteria, protists, fungi, and other multicellular parasites. In addition to viral-like particles, symptomatic fish had a higher mean percentage of swollen and disintegrating mitochondria than both asymptomatic aquaculture and wild mackerel. This suggests that degraded mitochondria may be related to PSS and could be important to further understanding the origin, promoters, and prevention of PSS. This study serves as a first step in identifying the etiological agents of PSS.},
}

Animals
Eukaryota
Fishes
Microscopy, Electron/veterinary
*Mitophagy
*Perciformes

@article {pmid34788294,
year = {2021},
author = {Fortunato, A and Fleming, A and Aktipis, A and Maley, CC},
title = {Upregulation of DNA repair genes and cell extrusion underpin the remarkable radiation resistance of Trichoplax adhaerens.},
journal = {PLoS biology},
volume = {19},
number = {11},
pages = {e3001471},
pmid = {34788294},
issn = {1545-7885},
support = {U54 CA217376/CA/NCI NIH HHS/United States ; R01 CA185138/CA/NCI NIH HHS/United States ; U2C CA233254/CA/NCI NIH HHS/United States ; P01 CA091955/CA/NCI NIH HHS/United States ; R01 CA170595/CA/NCI NIH HHS/United States ; R01 CA140657/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; DNA Damage/genetics/radiation effects ; DNA Repair/*genetics/radiation effects ; Gene Expression Regulation/radiation effects ; Placozoa/anatomy & histology/*genetics/radiation effects ; Radiation Exposure ; Radiation Tolerance/*genetics ; Sequence Analysis, DNA ; Up-Regulation/*genetics/radiation effects ; Whole Genome Sequencing ; X-Rays ; },
abstract = {Trichoplax adhaerens is the simplest multicellular animal with tissue differentiation and somatic cell turnover. Like all other multicellular organisms, it should be vulnerable to cancer, yet there have been no reports of cancer in T. adhaerens or any other placozoan. We investigated the cancer resistance of T. adhaerens, discovering that they are able to tolerate high levels of radiation damage (218.6 Gy). To investigate how T. adhaerens survive levels of radiation that are lethal to other animals, we examined gene expression after the X-ray exposure, finding overexpression of genes involved in DNA repair and apoptosis including the MDM2 gene. We also discovered that T. adhaerens extrudes clusters of inviable cells after X-ray exposure. T. adhaerens is a valuable model organism for studying the molecular, genetic, and tissue-level mechanisms underlying cancer suppression.},
}

Animals
DNA Damage/genetics/radiation effects
DNA Repair/*genetics/radiation effects
Gene Expression Regulation/radiation effects
Placozoa/anatomy & histology/*genetics/radiation effects
Radiation Exposure
Radiation Tolerance/*genetics
Sequence Analysis, DNA
Up-Regulation/*genetics/radiation effects
Whole Genome Sequencing
X-Rays

@article {pmid34769394,
year = {2021},
author = {Marijuán, PC and Navarro, J},
title = {From Molecular Recognition to the "Vehicles" of Evolutionary Complexity: An Informational Approach.},
journal = {International journal of molecular sciences},
volume = {22},
number = {21},
pages = {},
pmid = {34769394},
issn = {1422-0067},
mesh = {Animals ; *Biological Evolution ; Computational Biology/*methods ; Humans ; *Metabolic Networks and Pathways ; *Mutation ; Signal Transduction ; },
abstract = {Countless informational proposals and models have explored the singular characteristics of biological systems: from the initial choice of information terms in the early days of molecular biology to the current bioinformatic avalanche in this "omic" era. However, this was conducted, most often, within partial, specialized scopes or just metaphorically. In this paper, we attempt a consistent informational discourse, initially based on the molecular recognition paradigm, which addresses the main stages of biological organization in a new way. It considers the interconnection between signaling systems and information flows, between informational architectures and biomolecular codes, between controlled cell cycles and multicellular complexity. It also addresses, in a new way, a central issue: how new evolutionary paths are opened by the cumulated action of multiple variation engines or mutational 'vehicles' evolved for the genomic exploration of DNA sequence space. Rather than discussing the possible replacement, extension, or maintenance of traditional neo-Darwinian tenets, a genuine informational approach to evolutionary phenomena is advocated, in which systemic variation in the informational architectures may induce differential survival (self-construction, self-maintenance, and reproduction) of biological agents within their open ended environment.},
}

Animals
*Biological Evolution
Computational Biology/*methods
Humans
*Metabolic Networks and Pathways
*Mutation
Signal Transduction

@article {pmid34769071,
year = {2021},
author = {Vinogradov, AE and Anatskaya, OV},
title = {Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome.},
journal = {International journal of molecular sciences},
volume = {22},
number = {21},
pages = {},
pmid = {34769071},
issn = {1422-0067},
mesh = {Animals ; Epigenesis, Genetic ; *Evolution, Molecular ; *Gene Regulatory Networks ; *Genome, Human ; Hominidae/genetics ; Humans ; Multigene Family ; Oncogenes ; Prokaryotic Cells/metabolism ; Transcription Factors/genetics ; },
abstract = {The growth of complexity in evolution is a most intriguing phenomenon. Using gene phylostratigraphy, we showed this growth (as reflected in regulatory mechanisms) in the human genome, tracing the path from prokaryotes to hominids. Generally, the different regulatory gene families expanded at different times, yet only up to the Euteleostomi (bony vertebrates). The only exception was the expansion of transcription factors (TF) in placentals; however, we argue that this was not related to increase in general complexity. Surprisingly, although TF originated in the Prokaryota while chromatin appeared only in the Eukaryota, the expansion of epigenetic factors predated the expansion of TF. Signaling receptors, tumor suppressors, oncogenes, and aging- and disease-associated genes (indicating vulnerabilities in terms of complex organization and strongly enrichment in regulatory genes) also expanded only up to the Euteleostomi. The complexity-related gene properties (protein size, number of alternative splicing mRNA, length of untranslated mRNA, number of biological processes per gene, number of disordered regions in a protein, and density of TF-TF interactions) rose in multicellular organisms and declined after the Euteleostomi, and possibly earlier. At the same time, the speed of protein sequence evolution sharply increased in the genes that originated after the Euteleostomi. Thus, several lines of evidence indicate that molecular mechanisms of complexity growth were changing with time, and in the phyletic lineage leading to humans, the most salient shift occurred after the basic vertebrate body plan was fixed with bony skeleton. The obtained results can be useful for evolutionary medicine.},
}

Animals
Epigenesis, Genetic
*Evolution, Molecular
*Gene Regulatory Networks
*Genome, Human
Hominidae/genetics
Humans
Multigene Family
Oncogenes
Prokaryotic Cells/metabolism
Transcription Factors/genetics

@article {pmid34740967,
year = {2021},
author = {Krespach, MKC and Stroe, MC and Flak, M and Komor, AJ and Nietzsche, S and Sasso, S and Hertweck, C and Brakhage, AA},
title = {Bacterial marginolactones trigger formation of algal gloeocapsoids, protective aggregates on the verge of multicellularity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {45},
pages = {},
pmid = {34740967},
issn = {1091-6490},
mesh = {*Cell Aggregation ; Chlamydomonas reinhardtii/*physiology/ultrastructure ; Macrolides/metabolism ; Microbial Interactions ; Streptomyces/metabolism ; },
abstract = {Photosynthetic microorganisms including the green alga Chlamydomonas reinhardtii are essential to terrestrial habitats as they start the carbon cycle by conversion of CO2 to energy-rich organic carbohydrates. Terrestrial habitats are densely populated, and hence, microbial interactions mediated by natural products are inevitable. We previously discovered such an interaction between Streptomyces iranensis releasing the marginolactone azalomycin F in the presence of C. reinhardtii Whether the alga senses and reacts to azalomycin F remained unknown. Here, we report that sublethal concentrations of azalomycin F trigger the formation of a protective multicellular structure by C. reinhardtii, which we named gloeocapsoid. Gloeocapsoids contain several cells which share multiple cell membranes and cell walls and are surrounded by a spacious matrix consisting of acidic polysaccharides. After azalomycin F removal, gloeocapsoid aggregates readily disassemble, and single cells are released. The presence of marginolactone biosynthesis gene clusters in numerous streptomycetes, their ubiquity in soil, and our observation that other marginolactones such as desertomycin A and monazomycin also trigger the formation of gloeocapsoids suggests a cross-kingdom competition with ecological relevance. Furthermore, gloeocapsoids allow for the survival of C. reinhardtii at alkaline pH and otherwise lethal concentrations of azalomycin F. Their structure and polysaccharide matrix may be ancestral to the complex mucilage formed by multicellular members of the Chlamydomonadales such as Eudorina and Volvox Our finding suggests that multicellularity may have evolved to endure the presence of harmful competing bacteria. Additionally, it underlines the importance of natural products as microbial cues, which initiate interesting ecological scenarios of attack and counter defense.},
}

*Cell Aggregation
Chlamydomonas reinhardtii/*physiology/ultrastructure
Macrolides/metabolism
Microbial Interactions
Streptomyces/metabolism

@article {pmid34725037,
year = {2021},
author = {Hakala, SM and Meurville, MP and Stumpe, M and LeBoeuf, AC},
title = {Biomarkers in a socially exchanged /fluid reflect colony maturity, behavior, and distributed metabolism.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34725037},
issn = {2050-084X},
mesh = {Animals ; Ants/metabolism/*physiology ; Biomarkers/*metabolism ; Social Behavior ; },
abstract = {In cooperative systems exhibiting division of labor, such as microbial communities, multicellular organisms, and social insect colonies, individual units share costs and benefits through both task specialization and exchanged materials. Socially exchanged fluids, like seminal fluid and milk, allow individuals to molecularly influence conspecifics. Many social insects have a social circulatory system, where food and endogenously produced molecules are transferred mouth-to-mouth (stomodeal trophallaxis), connecting all the individuals in the society. To understand how these endogenous molecules relate to colony life, we used quantitative proteomics to investigate the trophallactic fluid within colonies of the carpenter ant Camponotus floridanus. We show that different stages of the colony life cycle circulate different types of proteins: young colonies prioritize direct carbohydrate processing; mature colonies prioritize accumulation and transmission of stored resources. Further, colonies circulate proteins implicated in oxidative stress, ageing, and social insect caste determination, potentially acting as superorganismal hormones. Brood-caring individuals that are also closer to the queen in the social network (nurses) showed higher abundance of oxidative stress-related proteins. Thus, trophallaxis behavior could provide a mechanism for distributed metabolism in social insect societies. The ability to thoroughly analyze the materials exchanged between cooperative units makes social insect colonies useful models to understand the evolution and consequences of metabolic division of labor at other scales.},
}

Animals
Ants/metabolism/*physiology
Biomarkers/*metabolism
Social Behavior

@article {pmid34716269,
year = {2021},
author = {Yang, H and Pegoraro, AF and Han, Y and Tang, W and Abeyaratne, R and Bi, D and Guo, M},
title = {Configurational fingerprints of multicellular living systems.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {44},
pages = {},
pmid = {34716269},
issn = {1091-6490},
support = {R01 GM140108/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Biophysical Phenomena/*physiology ; Cell Cycle ; Cell Movement ; Cell Proliferation ; Epithelial Cells/cytology ; Humans ; Image Processing, Computer-Assisted/*methods ; Morphogenesis ; Neoplasms ; Organ Specificity/*physiology ; *Phase Transition ; Spheroids, Cellular/cytology ; Wound Healing ; },
abstract = {Cells cooperate as groups to achieve structure and function at the tissue level, during which specific material characteristics emerge. Analogous to phase transitions in classical physics, transformations in the material characteristics of multicellular assemblies are essential for a variety of vital processes including morphogenesis, wound healing, and cancer. In this work, we develop configurational fingerprints of particulate and multicellular assemblies and extract volumetric and shear order parameters based on this fingerprint to quantify the system disorder. Theoretically, these two parameters form a complete and unique pair of signatures for the structural disorder of a multicellular system. The evolution of these two order parameters offers a robust and experimentally accessible way to map the phase transitions in expanding cell monolayers and during embryogenesis and invasion of epithelial spheroids.},
}

Animals
Biophysical Phenomena/*physiology
Cell Cycle
Cell Movement
Cell Proliferation
Epithelial Cells/cytology
Humans
Image Processing, Computer-Assisted/*methods
Morphogenesis
Neoplasms
Organ Specificity/*physiology
*Phase Transition
Spheroids, Cellular/cytology
Wound Healing

@article {pmid34711923,
year = {2021},
author = {Wan, X and Saito, JA and Hou, S and Geib, SM and Yuryev, A and Higa, LM and Womersley, CZ and Alam, M},
title = {The Aphelenchus avenae genome highlights evolutionary adaptation to desiccation.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {1232},
pmid = {34711923},
issn = {2399-3642},
mesh = {Adaptation, Biological/*physiology ; Animals ; Biological Evolution ; *Desiccation ; Gene Duplication/physiology ; Gene Expression Profiling ; Helminth Proteins/*genetics/metabolism ; Humidity ; Phosphotransferases/*genetics/metabolism ; Tylenchida/enzymology/*genetics ; Water/*metabolism ; },
abstract = {Some organisms can withstand complete body water loss (losing up to 99% of body water) and stay in ametabolic state for decades until rehydration, which is known as anhydrobiosis. Few multicellular eukaryotes on their adult stage can withstand life without water. We still have an incomplete understanding of the mechanism for metazoan survival of anhydrobiosis. Here we report the 255-Mb genome of Aphelenchus avenae, which can endure relative zero humidity for years. Gene duplications arose genome-wide and contributed to the expansion and diversification of 763 kinases, which represents the second largest metazoan kinome to date. Transcriptome analyses of ametabolic state of A. avenae indicate the elevation of ATP level for global recycling of macromolecules and enhancement of autophagy in the early stage of anhydrobiosis. We catalogue 74 species-specific intrinsically disordered proteins, which may facilitate A. avenae to survive through desiccation stress. Our findings refine a molecular basis evolving for survival in extreme water loss and open the way for discovering new anti-desiccation strategies.},
}

Adaptation, Biological/*physiology
Animals
Biological Evolution
*Desiccation
Gene Duplication/physiology
Gene Expression Profiling
Helminth Proteins/*genetics/metabolism
Humidity
Phosphotransferases/*genetics/metabolism
Tylenchida/enzymology/*genetics
Water/*metabolism

@article {pmid34699573,
year = {2021},
author = {Tanno, A and Tokutsu, R and Arakaki, Y and Ueki, N and Minagawa, J and Yoshimura, K and Hisabori, T and Nozaki, H and Wakabayashi, KI},
title = {The four-celled Volvocales green alga Tetrabaena socialis exhibits weak photobehavior and high-photoprotection ability.},
journal = {PloS one},
volume = {16},
number = {10},
pages = {e0259138},
pmid = {34699573},
issn = {1932-6203},
mesh = {Chlorophyta/*physiology ; Photic Stimulation ; Phototropism/*physiology ; Volvox/*physiology ; },
abstract = {Photo-induced behavioral responses (photobehaviors) are crucial to the survival of motile phototrophic organisms in changing light conditions. Volvocine green algae are excellent model organisms for studying the regulatory mechanisms of photobehavior. We recently reported that unicellular Chlamydomonas reinhardtii and multicellular Volvox rousseletii exhibit similar photobehaviors, such as phototactic and photoshock responses, via different ciliary regulations. To clarify how the regulatory systems have changed during the evolution of multicellularity, we investigated the photobehaviors of four-celled Tetrabaena socialis. Surprisingly, unlike C. reinhardtii and V. rousseletii, T. socialis did not exhibit immediate photobehaviors after light illumination. Electrophysiological analysis revealed that the T. socialis eyespot does not function as a photoreceptor. Instead, T. socialis exhibited slow accumulation toward the light source in a photosynthesis-dependent manner. Our assessment of photosynthetic activities showed that T. socialis chloroplasts possess higher photoprotection abilities against strong light than C. reinhardtii. These data suggest that C. reinhardtii and T. socialis employ different strategies to avoid high-light stress (moving away rapidly and gaining photoprotection, respectively) despite their close phylogenetic relationship.},
}

Chlorophyta/*physiology
Photic Stimulation
Phototropism/*physiology
Volvox/*physiology

@article {pmid34695730,
year = {2021},
author = {Grochau-Wright, ZI and Ferris, PJ and Tumberger, J and Jiménez-Marin, B and Olson, BJSC and Michod, RE},
title = {Characterization and Transformation of reg Cluster Genes in Volvox powersii Enable Investigation of Convergent Evolution of Cellular Differentiation in Volvox.},
journal = {Protist},
volume = {172},
number = {5-6},
pages = {125834},
doi = {10.1016/j.protis.2021.125834},
pmid = {34695730},
issn = {1618-0941},
support = {GT11065/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Base Sequence ; Cell Differentiation ; *Chlorophyta ; *Volvox/genetics ; },
abstract = {The evolution of germ-soma cellular differentiation represents a key step in the evolution of multicellular individuality. Volvox carteri and its relatives, the volvocine green algae, provide a model system for studying the evolution of cellular differentiation. In V. carteri, the regA gene controls somatic cell differentiation and is found in a group of paralogs called the reg cluster, along with rlsA, rlsB, and rlsC. However, the developmental program of V. carteri is derived compared to other volvocine algae. Here we examine Volvox powersii which possesses an ancestral developmental program and independent evolution of the Volvox body plan. We sequenced the reg cluster from V. powersii wild-type and a mutant with fewer cells and altered germ-soma ratio. We found that the mutant strain's rlsB gene has a deletion predicted to cause a truncated protein product. We developed a genetic transformation procedure to insert wild-type rlsB into the mutant strain. Transformation did not result in phenotypic rescue, suggesting the rlsB mutation is insufficient for generating the mutant phenotype. The transformation techniques and sequences described here provide essential tools to study V. powersii, a species well suited for studying the evolution of cellular differentiation and convergent evolution of Volvox morphology.},
}

Base Sequence
Cell Differentiation
*Chlorophyta
*Volvox/genetics

@article {pmid34685730,
year = {2021},
author = {Ni, Z and Cheng, X},
title = {Origin and Isoform Specific Functions of Exchange Proteins Directly Activated by cAMP: A Phylogenetic Analysis.},
journal = {Cells},
volume = {10},
number = {10},
pages = {},
pmid = {34685730},
issn = {2073-4409},
support = {R35 GM122536/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Conserved Sequence ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Evolution, Molecular ; Guanine Nucleotide Exchange Factors/chemistry/*metabolism ; Humans ; *Phylogeny ; Protein Domains ; Protein Isoforms/chemistry/metabolism ; },
abstract = {Exchange proteins directly activated by cAMP (EPAC1 and EPAC2) are one of the several families of cellular effectors of the prototypical second messenger cAMP. To understand the origin and molecular evolution of EPAC proteins, we performed a comprehensive phylogenetic analysis of EPAC1 and EPAC2. Our study demonstrates that unlike its cousin PKA, EPAC proteins are only present in multicellular Metazoa. Within the EPAC family, EPAC1 is only associated with chordates, while EPAC2 spans the entire animal kingdom. Despite a much more contemporary origin, EPAC1 proteins show much more sequence diversity among species, suggesting that EPAC1 has undergone more selection and evolved faster than EPAC2. Phylogenetic analyses of the individual cAMP binding domain (CBD) and guanine nucleotide exchange (GEF) domain of EPACs, two most conserved regions between the two isoforms, further reveal that EPAC1 and EPAC2 are closely clustered together within both the larger cyclic nucleotide receptor and RAPGEF families. These results support the notion that EPAC1 and EPAC2 share a common ancestor resulting from a fusion between the CBD of PKA and the GEF from RAPGEF1. On the other hand, the two terminal extremities and the RAS-association (RA) domains show the most sequence diversity between the two isoforms. Sequence diversities within these regions contribute significantly to the isoform-specific functions of EPACs. Importantly, unique isoform-specific sequence motifs within the RA domain have been identified.},
}

Amino Acid Motifs
Amino Acid Sequence
Animals
Conserved Sequence
Cyclic AMP-Dependent Protein Kinases/metabolism
Evolution, Molecular
Guanine Nucleotide Exchange Factors/chemistry/*metabolism
Humans
*Phylogeny
Protein Domains
Protein Isoforms/chemistry/metabolism

@article {pmid34681022,
year = {2021},
author = {Luna, SK and Chain, FJJ},
title = {Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development.},
journal = {Genes},
volume = {12},
number = {10},
pages = {},
pmid = {34681022},
issn = {2073-4425},
support = {R15 GM134498/GM/NIGMS NIH HHS/United States ; },
mesh = {Dictyostelium/*genetics/growth & development ; *Evolution, Molecular ; Gene Duplication/genetics ; Gene Expression Regulation, Developmental/genetics ; Genome/genetics ; *Phylogeny ; Species Specificity ; },
abstract = {Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each species and at most developmental time points, suggesting independent functional innovations of new genes throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, consistent with subfunctionalization or neofunctionalization. Lineage-specific expansions in particular had biased genes with both molecular signals of positive selection and high expression, suggesting adaptive genetic and transcriptional diversification following duplication. Our results present insights into the potential contributions of lineage-specific genes and families in generating species-specific phenotypes during multicellular development in dictyostelids.},
}

Dictyostelium/*genetics/growth & development
*Evolution, Molecular
Gene Duplication/genetics
Gene Expression Regulation, Developmental/genetics
Genome/genetics
*Phylogeny
Species Specificity

@article {pmid34680926,
year = {2021},
author = {Cock, JM},
title = {Evolution of Multicellularity.},
journal = {Genes},
volume = {12},
number = {10},
pages = {},
pmid = {34680926},
issn = {2073-4425},
mesh = {Eukaryota/classification/cytology/genetics ; *Evolution, Molecular ; Phylogeny ; },
abstract = {The emergence of multicellular organisms was, perhaps, the most spectacular of the major transitions during the evolutionary history of life on this planet [...].},
}

Eukaryota/classification/cytology/genetics
*Evolution, Molecular
Phylogeny

@article {pmid34671319,
year = {2021},
author = {Quinting, T and Heymann, AK and Bicker, A and Nauth, T and Bernardini, A and Hankeln, T and Fandrey, J and Schreiber, T},
title = {Myoglobin Protects Breast Cancer Cells Due to Its ROS and NO Scavenging Properties.},
journal = {Frontiers in endocrinology},
volume = {12},
number = {},
pages = {732190},
pmid = {34671319},
issn = {1664-2392},
mesh = {Breast Neoplasms/genetics/metabolism/*pathology ; Cell Survival/drug effects/genetics ; Female ; Free Radical Scavengers/metabolism ; Gene Expression Regulation, Neoplastic/drug effects ; Gene Knockdown Techniques ; Humans ; Myoglobin/genetics/metabolism/*physiology ; Nitric Oxide/*metabolism ; Protective Agents/metabolism ; RNA, Small Interfering/pharmacology ; Reactive Oxygen Species/*metabolism ; Signal Transduction/drug effects/genetics ; Tumor Cells, Cultured ; },
abstract = {Myoglobin (MB) is an oxygen-binding protein usually found in cardiac myocytes and skeletal muscle fibers. It may function as a temporary storage and transport protein for O2 but could also have scavenging capacity for reactive oxygen and nitrogen species. In addition, MB has recently been identified as a hallmark in luminal breast cancer and was shown to be robustly induced under hypoxia. Cellular responses to hypoxia are regulated by the transcription factor hypoxia-inducible factor (HIF). For exploring the function of MB in breast cancer, we employed the human cell line MDA-MB-468. Cells were grown in monolayer or as 3D multicellular spheroids, which mimic the in vivo avascular tumor architecture and physiology with a heterogeneous cell population of proliferating cells in the rim and non-cycling or necrotic cells in the core region. This central necrosis was increased after MB knockdown, indicating a role for MB in hypoxic tumor regions. In addition, MB knockdown caused higher levels of HIF-1α protein after treatment with NO, which also plays an important role in cancer cell survival. MB knockdown also led to higher reactive oxygen species (ROS) levels in the cells after treatment with H2O2. To further explore the role of MB in cell survival, we performed RNA-Seq after MB knockdown and NO treatment. 1029 differentially expressed genes (DEGs), including 45 potential HIF-1 target genes, were annotated in regulatory pathways that modulate cellular function and maintenance, cell death and survival, and carbohydrate metabolism. Of these target genes, TMEFF1, TREX2, GLUT-1, MKNK-1, and RAB8B were significantly altered. Consistently, a decreased expression of GLUT-1, MKNK-1, and RAB8B after MB knockdown was confirmed by qPCR. All three genes of interest are often up regulated in cancer and correlate with a poor clinical outcome. Thus, our data indicate that myoglobin might influence the survival of breast cancer cells, possibly due to its ROS and NO scavenging properties and could be a valuable target for cancer therapy.},
}

Breast Neoplasms/genetics/metabolism/*pathology
Cell Survival/drug effects/genetics
Female
Free Radical Scavengers/metabolism
Gene Expression Regulation, Neoplastic/drug effects
Gene Knockdown Techniques
Humans
Myoglobin/genetics/metabolism/*physiology
Nitric Oxide/*metabolism
Protective Agents/metabolism
RNA, Small Interfering/pharmacology
Reactive Oxygen Species/*metabolism
Signal Transduction/drug effects/genetics
Tumor Cells, Cultured

@article {pmid34665225,
year = {2021},
author = {Zagoskin, MV and Wang, J},
title = {Programmed DNA elimination: silencing genes and repetitive sequences in somatic cells.},
journal = {Biochemical Society transactions},
volume = {49},
number = {5},
pages = {1891-1903},
doi = {10.1042/BST20190951},
pmid = {34665225},
issn = {1470-8752},
support = {R01 AI155588/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Chromosomes/genetics ; DNA Transposable Elements/*genetics ; Embryonic Development/genetics ; Evolution, Molecular ; Gene Expression ; Gene Expression Regulation ; *Gene Silencing ; Germ Cells ; Humans ; },
abstract = {In a multicellular organism, the genomes of all cells are in general the same. Programmed DNA elimination is a notable exception to this genome constancy rule. DNA elimination removes genes and repetitive elements in the germline genome to form a reduced somatic genome in various organisms. The process of DNA elimination within an organism is highly accurate and reproducible; it typically occurs during early embryogenesis, coincident with germline-soma differentiation. DNA elimination provides a mechanism to silence selected genes and repeats in somatic cells. Recent studies in nematodes suggest that DNA elimination removes all chromosome ends, resolves sex chromosome fusions, and may also promote the birth of novel genes. Programmed DNA elimination processes are diverse among species, suggesting DNA elimination likely has evolved multiple times in different taxa. The growing list of organisms that undergo DNA elimination indicates that DNA elimination may be more widespread than previously appreciated. These various organisms will serve as complementary and comparative models to study the function, mechanism, and evolution of programmed DNA elimination in metazoans.},
}

Animals
Chromosomes/genetics
DNA Transposable Elements/*genetics
Embryonic Development/genetics
Evolution, Molecular
Gene Expression
Gene Expression Regulation
*Gene Silencing
Germ Cells
Humans

@article {pmid34661335,
year = {2022},
author = {Stüeken, EE and Viehmann, S and Hohl, SV},
title = {Contrasting nutrient availability between marine and brackish waters in the late Mesoproterozoic: Evidence from the Paranoá Group, Brazil.},
journal = {Geobiology},
volume = {20},
number = {2},
pages = {159-174},
doi = {10.1111/gbi.12478},
pmid = {34661335},
issn = {1472-4669},
mesh = {Brazil ; *Ecosystem ; Eukaryota ; Nutrients ; *Seawater ; },
abstract = {Understanding the delayed rise of eukaryotic life on Earth is one of the most fundamental questions about biological evolution. Numerous studies have presented evidence for oxygen and nutrient limitations in seawater during the Mesoproterozoic era, indicating that open marine settings may not have been able to sustain a eukaryotic biosphere with complex, multicellular organisms. However, many of these data sets represent restricted marine basins, which may bias our view of habitability. Furthermore, it remains untested whether rivers could have supplied significant nutrient fluxes to coastal habitats. To better characterize the sources of the major nutrients nitrogen and phosphorus, we turned to the late Mesoproterozoic Paranoá Group in Brazil (~1.1 Ga), which was deposited on a passive margin of the São Francisco craton. We present carbon, nitrogen and sulphur isotope data from an open shelf setting (Fazenda Funil) and from a brackish-water environment with significant riverine input (São Gabriel). Our results show that waters were well-oxygenated and nitrate was bioavailable in the open ocean setting at Fazenda Funil; the redoxcline appears to have been deeper and further offshore compared to restricted marine basins elsewhere in the Mesoproterozoic. In contrast, the brackish site at São Gabriel received only limited input of marine nitrate and sulphate. Nevertheless, previous reports of acritarchs reveal that this brackish-water setting was habitable to eukaryotic life. Paired with previously published cadmium isotope data, which can be used as a proxy for phosphorus cycling, our results suggest that complex organisms were perhaps not strictly dependent on marine nutrient supplies. Riverine influxes of P and possibly other nutrients likely rendered coastal waters perhaps equally habitable to the Mesoproterozoic open ocean. This conclusion supports the notion that eukaryotic organisms may have thrived in brackish or perhaps even freshwater environments.},
}

Brazil
*Ecosystem
Eukaryota
Nutrients
*Seawater

@article {pmid34661162,
year = {2021},
author = {Koya, J and Saito, Y and Kameda, T and Kogure, Y and Yuasa, M and Nagasaki, J and McClure, MB and Shingaki, S and Tabata, M and Tahira, Y and Akizuki, K and Kamiunten, A and Sekine, M and Shide, K and Kubuki, Y and Hidaka, T and Kitanaka, A and Nakano, N and Utsunomiya, A and Togashi, Y and Ogawa, S and Shimoda, K and Kataoka, K},
title = {Single-Cell Analysis of the Multicellular Ecosystem in Viral Carcinogenesis by HTLV-1.},
journal = {Blood cancer discovery},
volume = {2},
number = {5},
pages = {450-467},
pmid = {34661162},
issn = {2643-3249},
mesh = {Animals ; Carcinogenesis/genetics ; Ecosystem ; *Human T-lymphotropic virus 1/genetics ; *Leukemia-Lymphoma, Adult T-Cell/genetics ; Mice ; Single-Cell Analysis ; },
abstract = {Premalignant clonal expansion of human T-cell leukemia virus type-1 (HTLV-1)-infected cells occurs before viral carcinogenesis. Here we characterize premalignant cells and the multicellular ecosystem in HTLV-1 infection with and without adult T-cell leukemia/lymphoma (ATL) by genome sequencing and single-cell simultaneous transcriptome and T/B-cell receptor sequencing with surface protein analysis. We distinguish malignant phenotypes caused by HTLV-1 infection and leukemogenesis and dissect clonal evolution of malignant cells with different clinical behavior. Within HTLV-1-infected cells, a regulatory T-cell phenotype associates with premalignant clonal expansion. We also delineate differences between virus- and tumor-related changes in the nonmalignant hematopoietic pool, including tumor-specific myeloid propagation. In a newly generated conditional knockout mouse model recapitulating T-cell-restricted CD274 (encoding PD-L1) gene lesions found in ATL, we demonstrate that PD-L1 overexpressed by T cells is transferred to surrounding cells, leading to their PD-L1 upregulation. Our findings provide insights into clonal evolution and immune landscape of multistep virus carcinogenesis.

Significance: Our multimodal single-cell analyses comprehensively dissect the cellular and molecular alterations of the peripheral blood in HTLV-1 infection, with and without progression to leukemia. This study not only sheds light on premalignant clonal expansion in viral carcinogenesis, but also helps to devise novel diagnostic and therapeutic strategies for HTLV-1-related disorders.},
}

Animals
Carcinogenesis/genetics
Ecosystem
*Human T-lymphotropic virus 1/genetics
*Leukemia-Lymphoma, Adult T-Cell/genetics
Mice
Single-Cell Analysis

@article {pmid34643506,
year = {2021},
author = {Gao, Y and Park, HJ and Traulsen, A and Pichugin, Y},
title = {Evolution of irreversible somatic differentiation.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34643506},
issn = {2050-084X},
mesh = {Animals ; *Biological Evolution ; *Cell Differentiation ; *Cell Division ; *Cell Lineage ; Gene Expression Regulation ; Germ Cells/*physiology ; *Models, Biological ; Phenotype ; },
abstract = {A key innovation emerging in complex animals is irreversible somatic differentiation: daughters of a vegetative cell perform a vegetative function as well, thus, forming a somatic lineage that can no longer be directly involved in reproduction. Primitive species use a different strategy: vegetative and reproductive tasks are separated in time rather than in space. Starting from such a strategy, how is it possible to evolve life forms which use some of their cells exclusively for vegetative functions? Here, we develop an evolutionary model of development of a simple multicellular organism and find that three components are necessary for the evolution of irreversible somatic differentiation: (i) costly cell differentiation, (ii) vegetative cells that significantly improve the organism's performance even if present in small numbers, and (iii) large enough organism size. Our findings demonstrate how an egalitarian development typical for loose cell colonies can evolve into germ-soma differentiation dominating metazoans.},
}

Animals
*Biological Evolution
*Cell Differentiation
*Cell Division
*Cell Lineage
Gene Expression Regulation
Germ Cells/*physiology
*Models, Biological
Phenotype

@article {pmid34641578,
year = {2021},
author = {Wofford, HA and Myers-Dean, J and Vogel, BA and Alamo, KAE and Longshore-Neate, FA and Jagodzinski, F and Amacher, JF},
title = {Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data.},
journal = {Molecules (Basel, Switzerland)},
volume = {26},
number = {19},
pages = {},
pmid = {34641578},
issn = {1420-3049},
support = {CHE-1904711//National Science Foundation/ ; },
mesh = {Amino Acid Sequence ; Choanoflagellata/*chemistry/*metabolism ; Computational Biology/*methods ; Evolution, Molecular ; Humans ; *PDZ Domains ; Phylogeny ; *Protein Binding ; Protein Conformation ; Signal Transduction ; Software ; Substrate Specificity ; },
abstract = {Choanoflagellates are single-celled eukaryotes with complex signaling pathways. They are considered the closest non-metazoan ancestors to mammals and other metazoans and form multicellular-like states called rosettes. The choanoflagellate Monosiga brevicollis contains over 150 PDZ domains, an important peptide-binding domain in all three domains of life (Archaea, Bacteria, and Eukarya). Therefore, an understanding of PDZ domain signaling pathways in choanoflagellates may provide insight into the origins of multicellularity. PDZ domains recognize the C-terminus of target proteins and regulate signaling and trafficking pathways, as well as cellular adhesion. Here, we developed a computational software suite, Domain Analysis and Motif Matcher (DAMM), that analyzes peptide-binding cleft sequence identity as compared with human PDZ domains and that can be used in combination with literature searches of known human PDZ-interacting sequences to predict target specificity in choanoflagellate PDZ domains. We used this program, protein biochemistry, fluorescence polarization, and structural analyses to characterize the specificity of A9UPE9_MONBE, a M. brevicollis PDZ domain-containing protein with no homology to any metazoan protein, finding that its PDZ domain is most similar to those of the DLG family. We then identified two endogenous sequences that bind A9UPE9 PDZ with <100 μM affinity, a value commonly considered the threshold for cellular PDZ-peptide interactions. Taken together, this approach can be used to predict cellular targets of previously uncharacterized PDZ domains in choanoflagellates and other organisms. Our data contribute to investigations into choanoflagellate signaling and how it informs metazoan evolution.},
}

Amino Acid Sequence
Choanoflagellata/*chemistry/*metabolism
Computational Biology/*methods
Evolution, Molecular
Humans
*PDZ Domains
Phylogeny
*Protein Binding
Protein Conformation
Signal Transduction
Software
Substrate Specificity

@article {pmid34635955,
year = {2021},
author = {Schneider, C},
title = {Tuft cell integration of luminal states and interaction modules in tissues.},
journal = {Pflugers Archiv : European journal of physiology},
volume = {473},
number = {11},
pages = {1713-1722},
pmid = {34635955},
issn = {1432-2013},
mesh = {Animals ; Chemoreceptor Cells/*physiology ; Epithelial Cells/*physiology ; Humans ; Immunity, Innate/physiology ; },
abstract = {Chemosensory processes are integral to the physiology of most organisms. This function is typically performed by specialized cells that are able to detect input signals and to convert them to an output dedicated to a particular group of target cells. Tuft cells are cholinergic chemosensory epithelial cells capable of producing immunologically relevant effector molecules. They are scattered throughout endoderm-derived hollow organs and function as sensors of luminal stimuli, which has been best studied in mucosal barrier epithelia. Given their epithelial origin and broad distribution, and based on their interplay with immune pathways, tuft cells can be considered a prototypical example of how complex multicellular organisms engage innate immune mechanisms to modulate and optimize organ physiology. In this review, I provide a concise overview of tuft cells and discuss how these cells influence organ adaptation to dynamic luminal conditions.},
}

Animals
Chemoreceptor Cells/*physiology
Epithelial Cells/*physiology
Humans
Immunity, Innate/physiology