@article {pmid32260425,
year = {2020},
author = {Simeone, P and Bologna, G and Lanuti, P and Pierdomenico, L and Guagnano, MT and Pieragostino, D and Del Boccio, P and Vergara, D and Marchisio, M and Miscia, S and Mariani-Costantini, R},
title = {Extracellular Vesicles as Signaling Mediators and Disease Biomarkers across Biological Barriers.},
journal = {International journal of molecular sciences},
volume = {21},
number = {7},
pages = {},
doi = {10.3390/ijms21072514},
pmid = {32260425},
issn = {1422-0067},
abstract = {Extracellular vesicles act as shuttle vectors or signal transducers that can deliver specific biological information and have progressively emerged as key regulators of organized communities of cells within multicellular organisms in health and disease. Here, we survey the evolutionary origin, general characteristics, and biological significance of extracellular vesicles as mediators of intercellular signaling, discuss the various subtypes of extracellular vesicles thus far described and the principal methodological approaches to their study, and review the role of extracellular vesicles in tumorigenesis, immunity, non-synaptic neural communication, vascular-neural communication through the blood-brain barrier, renal pathophysiology, and embryo-fetal/maternal communication through the placenta.},
}

@article {pmid32253306,
year = {2020},
author = {Shao, S and Koh, M and Schultz, PG},
title = {Expanding the genetic code of the human hematopoietic system.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1914408117},
pmid = {32253306},
issn = {1091-6490},
abstract = {The genetic incorporation of noncanonical amino acids (ncAAs) into proteins has been realized in bacteria, yeast, and mammalian cells, and recently, in multicellular organisms including plants and animals. However, the addition of new building blocks to the genetic code of tissues from human origin has not yet been achieved. To this end, we report a self-replicating Epstein-Barr virus-based episomal vector for the long-term encoding of ncAAs in human hematopoietic stem cells and reconstitution of this genetically engineered hematopoietic system in mice.},
}

@article {pmid32251406,
year = {2020},
author = {Kazer, SW and Aicher, TP and Muema, DM and Carroll, SL and Ordovas-Montanes, J and Miao, VN and Tu, AA and Ziegler, CGK and Nyquist, SK and Wong, EB and Ismail, N and Dong, M and Moodley, A and Berger, B and Love, JC and Dong, KL and Leslie, A and Ndhlovu, ZM and Ndung'u, T and Walker, BD and Shalek, AK},
title = {Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-020-0799-2},
pmid = {32251406},
issn = {1546-170X},
support = {Beckman Young Investigator Program//Arnold and Mabel Beckman Foundation/ ; Pew-Stewart Scholars for Cancer Research//Pew Charitable Trusts/ ; Sloan Fellowship in Chemistry//Alfred P. Sloan Foundation/ ; 2U19AI089992//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2P01AI039671//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 5U24AI118672//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1R01AI138546//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; K08AI118538//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1R01AI145305//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1R37AI067073//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01HL095791//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; 1R01HL134539//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; 1U54CA217377//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; 2RM1HG006193//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; 1R01DA046277//U.S. Department of Health & Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; Graduate Student Fellowship Award//National Science Foundation (NSF)/ ; HHMI Fellow DRG-2274-16//Damon Runyon Cancer Research Foundation (Cancer Research Fund of the Damon Runyon-Walter Winchell Foundation)/ ; 107752/Z/15/Z//Wellcome Trust (Wellcome)/ ; 210662/Z/18/Z//Wellcome Trust (Wellcome)/ ; UKZNRSA1001//International AIDS Vaccine Initiative (International AIDS Vaccine Initiative, Inc.)/ ; 00406//Gilead Sciences (Gilead)/ ; OPP1066973//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; OPP1146433//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; P30AI060354//Harvard University Center for AIDS Research (HU CFAR)/ ; },
abstract = {Cellular immunity is critical for controlling intracellular pathogens, but individual cellular dynamics and cell-cell cooperativity in evolving human immune responses remain poorly understood. Single-cell RNA-sequencing (scRNA-seq) represents a powerful tool for dissecting complex multicellular behaviors in health and disease1,2 and nominating testable therapeutic targets3. Its application to longitudinal samples could afford an opportunity to uncover cellular factors associated with the evolution of disease progression without potentially confounding inter-individual variability4. Here, we present an experimental and computational methodology that uses scRNA-seq to characterize dynamic cellular programs and their molecular drivers, and apply it to HIV infection. By performing scRNA-seq on peripheral blood mononuclear cells from four untreated individuals before and longitudinally during acute infection5, we were powered within each to discover gene response modules that vary by time and cell subset. Beyond previously unappreciated individual- and cell-type-specific interferon-stimulated gene upregulation, we describe temporally aligned gene expression responses obscured in bulk analyses, including those involved in proinflammatory T cell differentiation, prolonged monocyte major histocompatibility complex II upregulation and persistent natural killer (NK) cell cytolytic killing. We further identify response features arising in the first weeks of infection, for example proliferating natural killer cells, which potentially may associate with future viral control. Overall, our approach provides a unified framework for characterizing multiple dynamic cellular responses and their coordination.},
}

@article {pmid32246828,
year = {2020},
author = {Zheng, W and Chen, J and Doak, TG and Song, W and Yan, Y},
title = {ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaa226},
pmid = {32246828},
issn = {1367-4811},
abstract = {MOTIVATION: Programmed DNA elimination plays a crucial role in the transitions between germline and somatic genomes in diverse organisms ranging from unicellular ciliates to multicellular nematodes. However, software specific to the detection of DNA splicing events is scarce. In this paper, we describe ADFinder, an efficient detector of programmed DNA eliminations using NGS high-throughput sequencing data. ADFinder can predict programmed DNA eliminations with relatively low sequencing coverage, detect multiple alternative splicing forms in the same genomic location, and calculate the frequency for each splicing event. This software will facilitate research of programmed DNA eliminations and all down-stream analyses.

RESULTS: By analyzing genome-wide DNA splicing events in two micronuclear genomes of Oxytricha trifallax and Tetrahymena thermophila we prove that ADFinder is effective in predicting large scale programmed DNA eliminations.

AVAILABILITY: The source codes and manual of ADFinder are available in our GitHub website: https://github.com/weibozheng/ADFinder.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid32244231,
year = {2020},
author = {Copley, SD},
title = {The physical basis and practical consequences of biological promiscuity.},
journal = {Physical biology},
volume = {},
number = {},
pages = {},
doi = {10.1088/1478-3975/ab8697},
pmid = {32244231},
issn = {1478-3975},
abstract = {Proteins interact with metabolites, nucleic acids, and other proteins to orchestrate the myriad catalytic, structural and regulatory functions that support life from the simplest microbes to the most complex multicellular organisms. These molecular interactions are often exquisitely specific, but never perfectly so. Adventitious "promiscuous" interactions are ubiquitous due to the thousands of macromolecules and small molecules crowded together in cells. Such interactions may perturb protein function at the molecular level, but as long as they do not compromise organismal fitness, they will not be removed by natural selection. Although promiscuous interactions are physiologically irrelevant, they are important because they can provide a vast reservoir of potential functions that can provide the starting point for evolution of new functions, both in nature and in the laboratory.},
}

@article {pmid32234827,
year = {2020},
author = {Pienta, KJ and Hammarlund, EU and Axelrod, R and Amend, SR and Brown, JS},
title = {Convergent evolution, evolving evolvability, and the origins of lethal cancer.},
journal = {Molecular cancer research : MCR},
volume = {},
number = {},
pages = {},
doi = {10.1158/1541-7786.MCR-19-1158},
pmid = {32234827},
issn = {1557-3125},
abstract = {Advances in curative treatment to remove the primary tumor have increased survival of localized cancers for most solid tumor types, yet cancers that have spread are typically incurable and account for >90% of cancer-related deaths. Metastatic disease remains incurable because, somehow, tumors evolve resistance to all known compounds, including therapies. In all of these incurable patients, de novo lethal cancer evolves capacities for both metastasis and resistance. Therefore, cancers in different patients appear to follow the same eco-evolutionary path that independently manifests in affected patients. This convergent outcome that always includes the ability to metastasize and exhibit resistance demands an explanation beyond the slow and steady accrual of stochastic mutations. The common denominator may be that cancer starts as a speciation event when a unicellular protist breaks away from its multicellular host and initiates a cancer clade within the patient. As the cancer cells speciate and diversify further, some evolve the capacity to evolve: evolvability. Evolvability becomes a heritable trait that influences the available variation of other phenotypes that can then be acted upon by natural selection. Evolving evolvability may be an adaptation for cancer cells. By generating and maintaining considerable heritable variation, the cancer clade can with high certainty serendipitously produce cells resistant to therapy and cells capable of metastasizing. Understanding that cancer cells can swiftly evolve responses to novel and varied stressors create opportunities for adaptive therapy, double-bind therapies, and extinction therapies; all involving strategic decision making that steers and anticipates the convergent co-evolutionary responses of the cancers.},
}

@article {pmid32234519,
year = {2020},
author = {Nelson, WJ},
title = {The Glue that Binds Us: The Hunt for the Molecular Basis for Multicellularity.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2020.03.017},
pmid = {32234519},
issn = {1097-4172},
abstract = {This year's Canada Gairdner International Prize is shared by Rolf Kemler and Masatoshi Takeichi for the discovery of the cadherin family of Ca2+-dependent cell-cell adhesion proteins, which play essential roles in animal evolution, tissue development, and homeostasis, and are disrupted in human cancers.},
}

@article {pmid31212208,
year = {2019},
author = {Masuyama, N and Mori, H and Yachie, N},
title = {DNA barcodes evolve for high-resolution cell lineage tracing.},
journal = {Current opinion in chemical biology},
volume = {52},
number = {},
pages = {63-71},
doi = {10.1016/j.cbpa.2019.05.014},
pmid = {31212208},
issn = {1879-0402},
mesh = {Animals ; Biomarkers ; *Cell Lineage ; Clustered Regularly Interspaced Short Palindromic Repeats ; *DNA Barcoding, Taxonomic ; Evolution, Molecular ; Humans ; Mutation ; Single-Cell Analysis ; },
abstract = {Mammalian development involves continuous dynamic processes in which cells propagate, differentiate, orchestrate, and decease to produce high-order functions. Although accurate cell lineage information can provide a strong foundation to understand such complex processes, the cell lineages involved in development of the whole mammalian body remain largely unclear, except for in early embryogenesis, which is observable under a microscope. With CRISPR genome editing, the concept of 'evolving DNA barcodes' has rapidly emerged for large-scale, high-resolution cell lineage tracing, where cell-embedded DNA barcodes continuously accumulate random mutations that are inherited from mother to daughter cells. Similar to evolutionary tree reconstruction using species' DNA sequences, cell lineages can be reconstructed using shared mutation patterns in the DNA barcodes identified using massively parallel sequencing. The dramatic developments of single-cell and imaging technologies have enabled analyses of the molecular and spatial architecture of heterogeneous cells. The evolving DNA barcodes can also consolidate this information on a reconstructed cell lineage tree and accelerate our understanding of multicellular organisms.},
}

Animals
Biomarkers
*Cell Lineage
Clustered Regularly Interspaced Short Palindromic Repeats
*DNA Barcoding, Taxonomic
Evolution, Molecular
Humans
Mutation
Single-Cell Analysis

@article {pmid31744876,
year = {2019},
author = {Vassallo, CN and Wall, D},
title = {Self-identity barcodes encoded by six expansive polymorphic toxin families discriminate kin in myxobacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {49},
pages = {24808-24818},
pmid = {31744876},
issn = {1091-6490},
mesh = {Alleles ; Bacterial Outer Membrane Proteins/genetics/metabolism ; Bacterial Toxins/classification/*genetics/immunology/*isolation & purification ; Cation Transport Proteins/genetics/metabolism ; Lipoproteins ; Myxococcales/*genetics/*metabolism ; Myxococcus xanthus/genetics/metabolism ; Phylogeny ; Receptors, Cell Surface/*metabolism ; Sequence Analysis ; },
abstract = {Myxobacteria are an example of how single-cell individuals can transition into multicellular life by an aggregation strategy. For these and all organisms that consist of social groups of cells, discrimination against, and exclusion of, nonself is critical. In myxobacteria, TraA is a polymorphic cell surface receptor that identifies kin by homotypic binding, and in so doing exchanges outer membrane (OM) proteins and lipids between cells with compatible receptors. However, TraA variability alone is not sufficient to discriminate against all cells, as traA allele diversity is not necessarily high among local strains. To increase discrimination ability, myxobacteria include polymorphic OM lipoprotein toxins called SitA in their delivered cargo, which poison recipient cells that lack the cognate, allele-specific SitI immunity protein. We previously characterized 3 SitAI toxin/immunity pairs that belong to 2 families. Here, we discover 4 additional SitA families. Each family is unique in sequence, but share the characteristic features of SitA: OM-associated toxins delivered by TraA. We demonstrate that, within a SitA family, C-terminal nuclease domains are polymorphic and often modular. Remarkably, sitA loci are strikingly numerous and diverse, with most genomes possessing >30 and up to 83 distinct sitAI loci. Interestingly, all SitA protein families are serially transferred between cells, allowing a SitA inhibitor cell to poison multiple targets, including cells that never made direct contact. The expansive suites of sitAI loci thus serve as identify barcodes to exquisitely discriminate against nonself to ensure populations are genetically homogenous to conduct cooperative behaviors.},
}

Alleles
Bacterial Outer Membrane Proteins/genetics/metabolism
Bacterial Toxins/classification/*genetics/immunology/*isolation & purification
Cation Transport Proteins/genetics/metabolism
Lipoproteins
Myxococcales/*genetics/*metabolism
Myxococcus xanthus/genetics/metabolism
Phylogeny
Receptors, Cell Surface/*metabolism
Sequence Analysis

@article {pmid32226593,
year = {2020},
author = {Xu, H and Zhang, S and Yi, X and Plewczynski, D and Li, MJ},
title = {Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {558-570},
doi = {10.1016/j.csbj.2020.02.013},
pmid = {32226593},
issn = {2001-0370},
abstract = {Mechanisms underlying gene regulation are key to understand how multicellular organisms with various cell types develop from the same genetic blueprint. Dynamic interactions between enhancers and genes are revealed to play central roles in controlling gene transcription, but the determinants to link functional enhancer-promoter pairs remain elusive. A major challenge is the lack of reliable approach to detect and verify functional enhancer-promoter interactions (EPIs). In this review, we summarized the current methods for detecting EPIs and described how developing techniques facilitate the identification of EPI through assessing the merits and drawbacks of these methods. We also reviewed recent state-of-art EPI prediction methods in terms of their rationale, data usage and characterization. Furthermore, we briefly discussed the evolved strategies for validating functional EPIs.},
}

@article {pmid32224105,
year = {2020},
author = {Mikhailovsky, G and Gordon, R},
title = {Shuffling type of biological evolution based on horizontal gene transfer and the biosphere gene pool hypothesis.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {104131},
doi = {10.1016/j.biosystems.2020.104131},
pmid = {32224105},
issn = {1872-8324},
abstract = {Widespread horizontal gene transfer (HGT) may appear a significant factor that accelerates biological evolution. Here we look at HGT primarily from the point of view of prokaryote clones, which we take as the descendants of a single cell, all of whom have exactly the same nucleotide sequence. Any novelty that emerges as a random mutation, creating a new clone, could either disappear before its first HGT, or survive for a period and be transferred to another clone. Due to the chain character of HGT, each gene with an adaptive mutation is thus spread among numerous existing clones, creating further new clones in the process. This makes propagation far faster than elimination, and such genes become practically immortal and form a kind of "biosphere gene pool" (BGP). Not all of these genes exist in every clone, and moreover not all of them are expressed. A significant fraction of the BGP includes of genes repressed by regulatory genes. However, these genes express often enough to be subject to natural selection. In a changing environment, both repressed and expressed genes, after transferring to another clone, may prove useful in an alternative environment, and this will give rise to new clones. This mechanism for testing repressed genes for adaptability can be thought as a "shuffle of a deck of genes" by analogy with shuffling a deck of cards. In the Archean and Proterozoic eons, both BGP and the operational part of each genome were rather poor, and the probability of incorporation of randomly expressed genes into the operational part of each genome was very small. Accordingly, biological evolution during these eons was slow due to rare adaptive mutations. This explains why the realm of prokaryotes as the sole organisms on Earth lasted so long. However, over about 3.5 billion years before the Phanerozoic eon, the BGP gradually accumulated a huge number of genes. Each of them was useful in a certain environment of past eras. We suggest that multicellular eukaryotes that appeared at the end of the Proterozoic eon could shuffle these genes accumulated in BGP via HGT from prokaryotes that live in these multicellular organisms. Perhaps this was the cause of the "Cambrian explosion" and the high (and increasing) rate of evolution in the Phanerozoic eon compared with the Archean and Proterozoic.},
}

@article {pmid31633482,
year = {2019},
author = {Murphy, DP and Hughes, AE and Lawrence, KA and Myers, CA and Corbo, JC},
title = {Cis-regulatory basis of sister cell type divergence in the vertebrate retina.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {31633482},
issn = {2050-084X},
support = {T32 EY013360/EY/NEI NIH HHS/United States ; T32EY013360/EY/NEI NIH HHS/United States ; R01EY024958/EY/NEI NIH HHS/United States ; R01EY025196/EY/NEI NIH HHS/United States ; R01EY026672/EY/NEI NIH HHS/United States ; F32EY029571/EY/NEI NIH HHS/United States ; },
mesh = {Animals ; Binding Sites ; Chromatin/metabolism ; *Evolution, Molecular ; Gene Expression Profiling ; *Gene Regulatory Networks ; Mice ; Photoreceptor Cells/*physiology ; Regulatory Sequences, Nucleic Acid/*genetics ; Retinal Bipolar Cells/*physiology ; },
abstract = {Multicellular organisms evolved via repeated functional divergence of transcriptionally related sister cell types, but the mechanisms underlying sister cell type divergence are not well understood. Here, we study a canonical pair of sister cell types, retinal photoreceptors and bipolar cells, to identify the key cis-regulatory features that distinguish them. By comparing open chromatin maps and transcriptomic profiles, we found that while photoreceptor and bipolar cells have divergent transcriptomes, they share remarkably similar cis-regulatory grammars, marked by enrichment of K50 homeodomain binding sites. However, cell class-specific enhancers are distinguished by enrichment of E-box motifs in bipolar cells, and Q50 homeodomain motifs in photoreceptors. We show that converting K50 motifs to Q50 motifs represses reporter expression in bipolar cells, while photoreceptor expression is maintained. These findings suggest that partitioning of Q50 motifs within cell type-specific cis-regulatory elements was a critical step in the evolutionary divergence of the bipolar transcriptome from that of photoreceptors.},
}

Animals
Binding Sites
Chromatin/metabolism
*Evolution, Molecular
Gene Expression Profiling
*Gene Regulatory Networks
Mice
Photoreceptor Cells/*physiology
Regulatory Sequences, Nucleic Acid/*genetics
Retinal Bipolar Cells/*physiology

@article {pmid32220299,
year = {2020},
author = {Aich, M and Chakraborty, D},
title = {Role of lncRNAs in stem cell maintenance and differentiation.},
journal = {Current topics in developmental biology},
volume = {138},
number = {},
pages = {73-112},
doi = {10.1016/bs.ctdb.2019.11.003},
pmid = {32220299},
issn = {1557-8933},
abstract = {Embryonic Stem cells are widely studied to elucidate the disease and developmental processes because of their capability to differentiate into cells of any lineage, Pervasive transcription is a distinct feature of all multicellular organisms and genomic elements such as enhancers and bidirectional or unidirectional promoters regulate these processes. Thousands of loci in each species produce a class of transcripts called noncoding RNAs (ncRNAs), that are well known for their influential regulatory roles in multiple biological processes including stem cell pluripotency and differentiation. The number of lncRNA species increases in more complex organisms highlighting the importance of RNA-based control in the evolution of multicellular organisms. Over the past decade, numerous studies have shed light on lncRNA biogenesis and functional significance in the cell and the organism. In this review, we focus primarily on lncRNAs affecting the stem cell state and developmental pathways.},
}

@article {pmid32206719,
year = {2020},
author = {Guo, Z and Richardson, JJ and Kong, B and Liang, K},
title = {Nanobiohybrids: Materials approaches for bioaugmentation.},
journal = {Science advances},
volume = {6},
number = {12},
pages = {eaaz0330},
doi = {10.1126/sciadv.aaz0330},
pmid = {32206719},
issn = {2375-2548},
abstract = {Nanobiohybrids, synthesized by integrating functional nanomaterials with living systems, have emerged as an exciting branch of research at the interface of materials engineering and biological science. Nanobiohybrids use synthetic nanomaterials to impart organisms with emergent properties outside their scope of evolution. Consequently, they endow new or augmented properties that are either innate or exogenous, such as enhanced tolerance against stress, programmed metabolism and proliferation, artificial photosynthesis, or conductivity. Advances in new materials design and processing technologies made it possible to tailor the physicochemical properties of the nanomaterials coupled with the biological systems. To date, many different types of nanomaterials have been integrated with various biological systems from simple biomolecules to complex multicellular organisms. Here, we provide a critical overview of recent developments of nanobiohybrids that enable new or augmented biological functions that show promise in high-tech applications across many disciplines, including energy harvesting, biocatalysis, biosensing, medicine, and robotics.},
}

@article {pmid32118436,
year = {2020},
author = {Xu, L and Wang, J},
title = {Curl Flux as a Dynamical Origin of the Bifurcations/Phase Transitions of Nonequilibrium Systems: Cell Fate Decision Making.},
journal = {The journal of physical chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jpcb.9b11998},
pmid = {32118436},
issn = {1520-5207},
abstract = {The underlying interactions in physical and biological systems often lead to a variety of behaviors and emergent states or phases. Under certain conditions, these phases can be transformed from one to another. The phase transition behaviors can be described by the bifurcation or catastrophe where different stable/unstable states can branch out or meet together with the birth of the new and death of the old states. Despite significant efforts, how the bifurcation and catastrophe actually occur dynamically and the associated mechanisms for nonequilibrium systems are still not very clear. As an example, we study the underlying mechanism of cell differentiation through bifurcations. Cell differentiation is one of the key fate decision-making processes that a cell faces. It is crucial for the development of multicellular organisms. Under induction, gene regulation changes, or stochastic fluctuations, the cell fate decision-making processes can exhibit different types of bifurcations or phase transitions. In order to understand the underlying mechanism, it is crucial to find out where and how the bifurcation occurs. However, this is still largely unknown. In this study, we found that the average of the curl flux as a major component of the driving force for the dynamics in addition to the landscape gradient and the associated entropy production rate both reach maximum near the bifurcation. This indicates that the curl flux and entropy production rate may provide the dynamical and thermodynamic origins of the bifurcation/catastrophe or phase transitions for cell differentiation and this possibly applies to many other nonequilibrium active systems.},
}

@article {pmid32198827,
year = {2020},
author = {Koehl, MAR},
title = {Selective factors in the evolution of multicellularity in choanoflagellates.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.b.22941},
pmid = {32198827},
issn = {1552-5015},
support = {IOS-1147215//National Science Foundation/ ; IOS-1655318//National Science Foundation/ ; },
abstract = {Choanoflagellates, unicellular eukaryotes that can form multicellular colonies by cell division and that share a common ancestor with animals, are used as a model system to study functional consequences of being unicellular versus colonial. This review examines performance differences between unicellular and multicellular choanoflagellates in swimming, feeding, and avoiding predation, to provide insights about possible selective advantages of being multicellular for the protozoan ancestors of animals. Each choanoflagellate cell propels water by beating a single flagellum and captures bacterial prey on a collar of microvilli around the flagellum. Formation of multicellular colonies does not improve the swimming performance, but the flux of prey-bearing water to the collars of some of the cells in colonies of certain configurations can be greater than for single cells. Colony geometry appears to affect whether cells in colonies catch more prey per cell per time than do unicellular choanoflagellates. Although multicellular choanoflagellates show chemokinetic behavior in response to oxygen, only the unicellular dispersal stage (fast swimmers without collars) use pH signals to aggregate in locations where bacterial prey might be abundant. Colonies produce larger hydrodynamic signals than do single cells, and raptorial protozoan predators capture colonies while ignoring single cells. In contrast, ciliate predators entrain both single cells and colonies in their feeding currents, but reject larger colonies, whereas passive heliozoan predators show no preference. Thus, the ability of choanoflagellate cells to differentiate into different morphotypes, including multicellular forms, in response to variable aquatic environments might have provided a selective advantage to the ancestors of animals.},
}

@article {pmid32191325,
year = {2020},
author = {Merényi, Z and Prasanna, AN and Wang, Z and Kovács, K and Hegedüs, B and Bálint, B and Papp, B and Townsend, JP and Nagy, LG},
title = {Unmatched level of molecular convergence among deeply divergent complex multicellular fungi.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaa077},
pmid = {32191325},
issn = {1537-1719},
abstract = {Convergent evolution is pervasive in nature, but it is poorly understood how various constraints and natural selection limit the diversity of evolvable phenotypes. Here, we analyze the transcriptome across fruiting body development to understand the independent evolution of complex multicellularity in the two largest clades of fungi-the Agarico- and Pezizomycotina. Despite >650 million years of divergence between these clades, we find that very similar sets of genes have convergently been co-opted for complex multicellularity, followed by expansions of their gene families by duplications. Over 82% of shared multicellularity-related gene families were expanding in both clades, indicating a high prevalence of convergence also at the gene-family level. This convergence is coupled with a rich inferred repertoire of multicellularity-related genes in the most recent common ancestor of the Agarico- and Pezizomycotina, consistent with the hypothesis that the coding capacity of ancestral fungal genomes might have promoted the repeated evolution of complex multicellularity. We interpret this repertoire as an indication of evolutionary predisposition of fungal ancestors for evolving complex multicellular fruiting bodies. Our work suggests that evolutionary convergence may happen not only when organisms are closely related or are under similar selection pressures, but also when ancestral genomic repertoires render certain evolutionary trajectories more likely than others, even across large phylogenetic distances.},
}

@article {pmid32188162,
year = {2020},
author = {Zhang, WJ and Wu, LF},
title = {Flagella and Swimming Behavior of Marine Magnetotactic Bacteria.},
journal = {Biomolecules},
volume = {10},
number = {3},
pages = {},
doi = {10.3390/biom10030460},
pmid = {32188162},
issn = {2218-273X},
support = {A-M-AAP-EI-17-07-170301-07.50-WU-ENV//Fondation Aix-Marseille Universite/ ; LIA-MagMC//Centre National de la Recherche Scientifique/ ; 91751202//National Natural Science Foundation of China/ ; 91751108//National Natural Science Foundation of China/ ; },
abstract = {Marine environments are generally characterized by low bulk concentrations of nutrients that are susceptible to steady or intermittent motion driven by currents and local turbulence. Marine bacteria have therefore developed strategies, such as very fast-swimming and the exploitation of multiple directional sensing-response systems in order to efficiently migrate towards favorable places in nutrient gradients. The magnetotactic bacteria (MTB) even utilize Earth's magnetic field to facilitate downward swimming into the oxic-anoxic interface, which is the most favorable place for their persistence and proliferation, in chemically stratified sediments or water columns. To ensure the desired flagella-propelled motility, marine MTBs have evolved an exquisite flagellar apparatus, and an extremely high number (tens of thousands) of flagella can be found on a single entity, displaying a complex polar, axial, bounce, and photosensitive magnetotactic behavior. In this review, we describe gene clusters, the flagellar apparatus architecture, and the swimming behavior of marine unicellular and multicellular magnetotactic bacteria. The physiological significance and mechanisms that govern these motions are discussed.},
}

@article {pmid32188032,
year = {2020},
author = {Goyeneche, A and Lisio, MA and Fu, L and Srinivasan, R and Valdez Capuccino, J and Gao, ZH and Telleria, C},
title = {The Capacity of High-Grade Serous Ovarian Cancer Cells to Form Multicellular Structures Spontaneously along Disease Progression Correlates with Their Orthotopic Tumorigenicity in Immunosuppressed Mice.},
journal = {Cancers},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/cancers12030699},
pmid = {32188032},
issn = {2072-6694},
support = {35635//Canada Foundation for Innovation/ ; 164222/CA/NCI NIH HHS/United States ; },
abstract = {Many studies have examined the biology, genetics, and chemotherapeutic response of ovarian cancer's solid component; its liquid facet, however, remains critically underinvestigated. Floating within peritoneal effusions known as ascites, ovarian cancer cells form multicellular structures, creating a cancer niche in suspension. This study explores the pathobiology of spontaneously formed, multicellular, ovarian cancer structures derived from serous ovarian cancer cells isolated along disease evolution. It also tests their capacity to cause peritoneal disease in immunosuppressed mice. Results stem from an analysis of cell lines representing the most frequently diagnosed ovarian cancer histotype (high-grade serous ovarian cancer), derived from ascites of the same patient at distinct stages of disease progression. When cultured under adherent conditions, in addition to forming cellular monolayers, the cultures developed areas in which the cells grew upwards, forming densely packed multilayers that ultimately detached from the bottom of the plates and lived as free-floating, multicellular structures. The capacity to form foci and to develop multicellular structures was proportional to disease progression at the time of ascites extraction. Self-assembled in culture, these structures varied in size, were either compact or hollow, irregular, or spheroidal, and exhibited replicative capacity and an epithelial nature. Furthermore, they fully recreated ovarian cancer disease in immunosuppressed mice: accumulation of malignant ascites and pleural effusions; formation of discrete, solid, macroscopic, peritoneal tumors; and microscopic growths in abdominal organs. They also reproduced the histopathological features characteristic of high-grade serous ovarian cancer when diagnosed in patients. The following results encourage the development of therapeutic interventions to interrupt the formation and/or survival of multicellular structures that constitute a floating niche in the peritoneal fluid, which in turn halts disease progression and prevents recurrence.},
}

@article {pmid32129607,
year = {2020},
author = {Han, X and Tomaszewski, EJ and Sorwat, J and Pan, Y and Kappler, A and Byrne, JM},
title = {Effect of Microbial Biomass and Humic Acids on Abiotic and Biotic Magnetite Formation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.9b07095},
pmid = {32129607},
issn = {1520-5851},
abstract = {Magnetite (Fe3O4) is an environmentally ubiquitous mixed-valent iron (Fe) mineral, which can form via biotic or abiotic transformation of Fe(III) (oxyhydr)oxides such as ferrihydrite (Fh). It is currently unclear whether environmentally relevant biogenic Fh from Fe(II)-oxidizing bacteria, containing cell-derived organic matter, can transform to magnetite. We compared abiotic and biotic transformation: (1) abiogenic Fh (aFh); (2) abiogenic Fh coprecipitated with humic acids (aFh-HA); (3) biogenic Fh produced by phototrophic Fe(II)-oxidizer Rhodobacter ferrooxidans SW2 (bFh); and (4) biogenic Fh treated with bleach to remove biogenic organic matter (bFh-bleach). Abiotic or biotic transformation of Fh was promoted by Feaq2+ or Fe(III)-reducing bacteria. Feaq2+-catalyzed abiotic reaction with aFh and bFh-bleach led to complete transformation to magnetite. In contrast, aFh-HA only partially (68%) transformed to magnetite, and bFh (17%) transformed to goethite. We hypothesize that microbial biomass stabilized bFh against reaction with Feaq2+. All four Fh substrates were transformed into magnetite during biotic reduction, suggesting that Fh remains bioavailable even when associated with microbial biomass. Additionally, there were poorly ordered magnetic components detected in the biogenic end products for aFh and aFh-HA. Nevertheless, abiotic transformation was much faster than biotic transformation, implying that initial Feaq2+ concentration, passivation of Fh, and/or sequestration of Fe(II) by bacterial cells and associated biomass play major roles in the rate of magnetite formation from Fh. These results improve our understanding of factors influencing secondary mineralization of Fh in the environment.},
}

@article {pmid31818732,
year = {2020},
author = {Shuryak, I},
title = {Review of resistance to chronic ionizing radiation exposure under environmental conditions in multicellular organisms.},
journal = {Journal of environmental radioactivity},
volume = {212},
number = {},
pages = {106128},
doi = {10.1016/j.jenvrad.2019.106128},
pmid = {31818732},
issn = {1879-1700},
mesh = {Animals ; Humans ; Phylogeny ; *Radiation Exposure ; *Radiation Monitoring ; Radiation, Ionizing ; Radioisotopes ; },
abstract = {Ionizing radiation resistance occurs among many phylogenetic groups and its mechanisms remain incompletely understood. Tolerances to acute and chronic irradiation do not always correlate because different mechanisms may be involved. The radioresistance phenomenon becomes even more complex in the field than in the laboratory because the effects of radioactive contamination on natural populations are intertwined with those of other factors, such as bioaccumulation of radionuclides, interspecific competition, seasonal variations in environmental conditions, and land use changes due to evacuation of humans from contaminated areas. Previous reviews of studies performed in radioactive sites like the Kyshtym, Chernobyl, and Fukushima accident regions, and of protracted irradiation experiments, often focused on detecting radiation effects at low doses in radiosensitive organisms. Here we review the literature with a different purpose: to identify organisms with high tolerance to chronic irradiation under environmental conditions, which maintained abundant populations and/or outcompeted more radiosensitive species at high dose rates. Taxa for which consistent evidence for radioresistance came from multiple studies conducted in different locations and at different times were found among plants (e.g. willow and birch trees, sedges), invertebrate and vertebrate animals (e.g. rotifers, some insects, crustaceans and freshwater fish). These organisms are not specialized "extremophiles", but tend to tolerate broad ranges of environmental conditions and stresses, have small genomes, reproduce quickly and/or disperse effectively over long distances. Based on these findings, resistance to radioactive contamination can be examined in a more broad context of chronic stress responses.},
}

Animals
Humans
Phylogeny
*Radiation Exposure
*Radiation Monitoring
Radiation, Ionizing
Radioisotopes

@article {pmid31581262,
year = {2019},
author = {Garud, A and Carrillo, AJ and Collier, LA and Ghosh, A and Kim, JD and Lopez-Lopez, B and Ouyang, S and Borkovich, KA},
title = {Genetic relationships between the RACK1 homolog cpc-2 and heterotrimeric G protein subunit genes in Neurospora crassa.},
journal = {PloS one},
volume = {14},
number = {10},
pages = {e0223334},
pmid = {31581262},
issn = {1932-6203},
support = {T34 GM062756/GM/NIGMS NIH HHS/United States ; },
mesh = {Genes, Fungal ; Heterotrimeric GTP-Binding Proteins/chemistry/*genetics/metabolism ; Models, Biological ; Mutation ; Neurospora crassa/classification/*genetics/immunology ; Phenotype ; Phylogeny ; Protein Binding ; Recombinant Proteins ; rho-Associated Kinases/chemistry/*genetics/metabolism ; },
abstract = {Receptor for Activated C Kinase-1 (RACK1) is a multifunctional eukaryotic scaffolding protein with a seven WD repeat structure. Among their many cellular roles, RACK1 homologs have been shown to serve as alternative Gβ subunits during heterotrimeric G protein signaling in many systems. We investigated genetic interactions between the RACK1 homolog cpc-2, the previously characterized Gβ subunit gnb-1 and other G protein signaling components in the multicellular filamentous fungus Neurospora crassa. Results from cell fractionation studies and from fluorescent microscopy of a strain expressing a CPC-2-GFP fusion protein revealed that CPC-2 is a cytoplasmic protein. Genetic epistasis experiments between cpc-2, the three Gα genes (gna-1, gna-2 and gna-3) and gnb-1 demonstrated that cpc-2 is epistatic to gna-2 with regards to basal hyphae growth rate and aerial hyphae height, while deletion of cpc-2 mitigates the increased macroconidiation on solid medium observed in Δgnb-1 mutants. Δcpc-2 mutants inappropriately produce conidiophores during growth in submerged culture and mutational activation of gna-3 alleviates this defect. Δcpc-2 mutants are female-sterile and fertility could not be restored by mutational activation of any of the three Gα genes. With the exception of macroconidiation on solid medium, double mutants lacking cpc-2 and gnb-1 exhibited more severe defects for all phenotypic traits, supporting a largely synergistic relationship between GNB-1 and CPC-2 in N. crassa.},
}

Genes, Fungal
Heterotrimeric GTP-Binding Proteins/chemistry/*genetics/metabolism
Models, Biological
Mutation
Neurospora crassa/classification/*genetics/immunology
Phenotype
Phylogeny
Protein Binding
Recombinant Proteins
rho-Associated Kinases/chemistry/*genetics/metabolism

@article {pmid32168596,
year = {2020},
author = {de Maleprade, H and Moisy, F and Ishikawa, T and Goldstein, RE},
title = {Motility and phototaxis of Gonium, the simplest differentiated colonial alga.},
journal = {Physical review. E},
volume = {101},
number = {2-1},
pages = {022416},
doi = {10.1103/PhysRevE.101.022416},
pmid = {32168596},
issn = {2470-0053},
abstract = {Green algae of the Volvocine lineage, spanning from unicellular Chlamydomonas to vastly larger Volvox, are models for the study of the evolution of multicellularity, flagellar dynamics, and developmental processes. Phototactic steering in these organisms occurs without a central nervous system, driven solely by the response of individual cells. All such algae spin about a body-fixed axis as they swim; directional photosensors on each cell thus receive periodic signals when that axis is not aligned with the light. The flagella of Chlamydomonas and Volvox both exhibit an adaptive response to such signals in a manner that allows for accurate phototaxis, but in the former the two flagella have distinct responses, while the thousands of flagella on the surface of spherical Volvox colonies have essentially identical behavior. The planar 16-cell species Gonium pectorale thus presents a conundrum, for its central 4 cells have a Chlamydomonas-like beat that provide propulsion normal to the plane, while its 12 peripheral cells generate rotation around the normal through a Volvox-like beat. Here we combine experiment, theory, and computations to reveal how Gonium, perhaps the simplest differentiated colonial organism, achieves phototaxis. High-resolution cell tracking, particle image velocimetry of flagellar driven flows, and high-speed imaging of flagella on micropipette-held colonies show how, in the context of a recently introduced model for Chlamydomonas phototaxis, an adaptive response of the peripheral cells alone leads to photoreorientation of the entire colony. The analysis also highlights the importance of local variations in flagellar beat dynamics within a given colony, which can lead to enhanced reorientation dynamics.},
}

@article {pmid31943343,
year = {2020},
author = {Wang, Y and Wang, F and Hong, DK and Gao, SJ and Wang, R and Wang, JD},
title = {Molecular characterization of DNA methyltransferase 1 and its role in temperature change of armyworm Mythimna separata Walker.},
journal = {Archives of insect biochemistry and physiology},
volume = {103},
number = {4},
pages = {e21651},
doi = {10.1002/arch.21651},
pmid = {31943343},
issn = {1520-6327},
support = {2017J01422//National Key R&D Program of China/ ; CARS-17//Sugar Crop Research System/ ; 31601363//National Natural Science Foundation of China/ ; 2017J01422//Nature Science Foundation of Fujian/ ; },
mesh = {Amino Acid Sequence ; Animals ; Body Temperature ; DNA (Cytosine-5-)-Methyltransferase 1/chemistry/*genetics/metabolism ; Insect Proteins/chemistry/*genetics/metabolism ; Larva/genetics/growth & development/physiology ; Moths/genetics/growth & development/*physiology ; Ovum/growth & development/physiology ; Phylogeny ; Pupa/genetics/growth & development/physiology ; Sequence Alignment ; },
abstract = {DNA methylation refers to the addition of cytosine residues in a CpG context (5'-cytosine-phosphate-guanine-3'). As one of the most common mechanisms of epigenetic modification, it plays a crucial role in regulating gene expression and in a diverse range of biological processes across all multicellular organisms. The relationship between temperature and DNA methylation and how it acts on the adaptability of migratory insects remain unknown. In the present work, a 5,496 bp full-length complementary DNA encoding 1,436 amino acids (named MsDnmt1) was cloned from the devastating migratory pest oriental armyworm, Mythimna separata Walker. The protein shares 36.8-84.4% identity with other insect Dnmt1 isoforms. Spatial and temporal expression analysis revealed that MsDnmt1 was highly expressed in adult stages and head tissue. The changing temperature decreased the expression of MsDnmt1 in both high and low temperature condition. Besides, we found that M. separata exhibited the shortest duration time from the last instar to pupae under 36°C environment when injected with DNA methylation inhibitor. Therefore, our data highlight a potential role for DNA methylation in thermal resistance, which help us to understand the biological role adaptability and colonization of migratory pest in various environments.},
}

Amino Acid Sequence
Animals
Body Temperature
DNA (Cytosine-5-)-Methyltransferase 1/chemistry/*genetics/metabolism
Insect Proteins/chemistry/*genetics/metabolism
Larva/genetics/growth & development/physiology
Moths/genetics/growth & development/*physiology
Ovum/growth & development/physiology
Phylogeny
Pupa/genetics/growth & development/physiology
Sequence Alignment

@article {pmid32163611,
year = {2020},
author = {Nedelcu, AM and Michod, RE},
title = {Stress Responses Co-Opted for Specialized Cell Types During the Early Evolution of Multicellularity: The Role of Stress in the Evolution of Cell Types Can Be Traced Back to the Early Evolution of Multicellularity.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e2000029},
doi = {10.1002/bies.202000029},
pmid = {32163611},
issn = {1521-1878},
support = {//Natural Sciences and Engineering Research Council (NSERC) of Canada and Harrison McCain Foundation/ ; NNX13AH41G/NASA/NASA/United States ; MCB-1412395//National Science Foundation/ ; //Natural Sciences and Engineering Research Council of Canada/ ; },
}

@article {pmid32163413,
year = {2020},
author = {Rodríguez-Rojas, A and Kim, JJ and Johnston, P and Makarova, O and Eravci, M and Weise, C and Hengge, R and Rolff, J},
title = {Non-lethal exposure to H2O2 boosts bacterial survival and evolvability against oxidative stress.},
journal = {PLoS genetics},
volume = {16},
number = {3},
pages = {e1008649},
doi = {10.1371/journal.pgen.1008649},
pmid = {32163413},
issn = {1553-7404},
abstract = {Unicellular organisms have the prevalent challenge to survive under oxidative stress of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2). ROS are present as by-products of photosynthesis and aerobic respiration. These reactive species are even employed by multicellular organisms as potent weapons against microbes. Although bacterial defences against lethal and sub-lethal oxidative stress have been studied in model bacteria, the role of fluctuating H2O2 concentrations remains unexplored. It is known that sub-lethal exposure of Escherichia coli to H2O2 results in enhanced survival upon subsequent exposure. Here we investigate the priming response to H2O2 at physiological concentrations. The basis and the duration of the response (memory) were also determined by time-lapse quantitative proteomics. We found that a low level of H2O2 induced several scavenging enzymes showing a long half-life, subsequently protecting cells from future exposure. We then asked if the phenotypic resistance against H2O2 alters the evolution of resistance against oxygen stress. Experimental evolution of H2O2 resistance revealed faster evolution and higher levels of resistance in primed cells. Several mutations were found to be associated with resistance in evolved populations affecting different loci but, counterintuitively, none of them was directly associated with scavenging systems. Our results have important implications for host colonisation and infections where microbes often encounter reactive oxygen species in gradients.},
}

@article {pmid32146616,
year = {2020},
author = {Fuchs, M and Lohmann, JU},
title = {Aiming for the top: non-cell autonomous control of shoot stem cells in Arabidopsis.},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10265-020-01174-3},
pmid = {32146616},
issn = {1618-0860},
support = {SFB873//Deutsche Forschungsgemeinschaft/ ; },
abstract = {In multicellular organisms, not all cells are created equal. Instead, organismal complexity is achieved by specialisation and division of labour between distinct cell types. Therefore, the organism depends on the presence, correct proportion and function of all cell types. It follows that early development is geared towards setting up the basic body plan and to specify cell lineages. Since plants employ a post-embryonic mode of development, the continuous growth and addition of new organs require a source of new cells, as well as a strict regulation of cellular composition throughout the entire life-cycle. To meet these demands, evolution has brought about complex regulatory systems to maintain and control continuously active stem cell systems. Here, we review recent work on the mechanisms of non cell-autonomous control of shoot stem cells in the model plant Arabidopsis thaliana with a strong focus on the cell-to-cell mobility and function of the WUSCHEL homeodomain transcription factor.},
}

@article {pmid32143753,
year = {2020},
author = {Klesen, S and Hill, K and Timmermans, MCP},
title = {Small RNAs as plant morphogens.},
journal = {Current topics in developmental biology},
volume = {137},
number = {},
pages = {455-480},
doi = {10.1016/bs.ctdb.2019.11.001},
pmid = {32143753},
issn = {1557-8933},
abstract = {The coordination of cell fate decisions within complex multicellular structures rests on intercellular communication. To generate ordered patterns, cells need to know their relative positions within the growing structure. This is commonly achieved via the production and perception of mobile signaling molecules. In animal systems, such positional signals often act as morphogens and subdivide a field of cells into domains of discrete cell identities using a threshold-based readout of their mobility gradient. Reflecting the independent origin of multicellularity, plants evolved distinct signaling mechanisms to drive cell fate decisions. Many of the basic principles underlying developmental patterning are, however, shared between animals and plants, including the use of signaling gradients to provide positional information. In plant development, small RNAs can act as mobile instructive signals, and similar to classical morphogens in animals, employ a threshold-based readout of their mobility gradient to generate precisely defined cell fate boundaries. Given the distinctive nature of peptide morphogens and small RNAs, how might mechanisms underlying the function of traditionally morphogens be adapted to create morphogen-like behavior using small RNAs? In this review, we highlight the contributions of mobile small RNAs to pattern formation in plants and summarize recent studies that have advanced our understanding regarding the formation, stability, and interpretation of small RNA gradients.},
}

@article {pmid32133683,
year = {2020},
author = {Horton, MB and Hawkins, ED and Heinzel, S and Hodgkin, PD},
title = {Speculations on the evolution of humoral adaptive immunity.},
journal = {Immunology and cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imcb.12323},
pmid = {32133683},
issn = {1440-1711},
abstract = {The protection of a multicellular organism from infection, at both a cell and humoral level has been a tremendous driver of gene selection and cellular response strategies. Here we focus on a critical event in the development of humoral immunity: The transition from principally innate responses, to a system of adaptive cell selection, with all the attendant mechanical problems that must be solved in order for it to work effectively. Here we review recent advances, but our major goal is to highlight that the development of adaptive immunity resulted from the adoption, reuse and repurposing of an ancient, autonomous cellular programme, that combines and exploits three titratable cellular fate timers. We illustrate how this common cell machinery recurs and appears throughout biology, and has been essential for the evolution of complex organisms, at many levels of scale.},
}

@article {pmid31451789,
year = {2019},
author = {Bruno, L and Ramlall, V and Studer, RA and Sauer, S and Bradley, D and Dharmalingam, G and Carroll, T and Ghoneim, M and Chopin, M and Nutt, SL and Elderkin, S and Rueda, DS and Fisher, AG and Siggers, T and Beltrao, P and Merkenschlager, M},
title = {Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system.},
journal = {Nature immunology},
volume = {20},
number = {10},
pages = {1372-1380},
doi = {10.1038/s41590-019-0471-5},
pmid = {31451789},
issn = {1529-2916},
support = {099276/WT_/Wellcome Trust/United Kingdom ; MC_U120027516/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; R01 AI116829/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Cell Differentiation ; Cell Lineage ; Conserved Sequence ; Core Binding Factor alpha Subunits/*genetics ; Evolution, Molecular ; Gene Duplication ; Humans ; Immune System/*physiology ; Langerhans Cells/*physiology ; Mammals ; Organ Specificity/*genetics ; Signal Transduction ; T-Lymphocytes, Regulatory/*physiology ; Transcriptome ; },
abstract = {In multicellular organisms, duplicated genes can diverge through tissue-specific gene expression patterns, as exemplified by highly regulated expression of RUNX transcription factor paralogs with apparent functional redundancy. Here we asked what cell-type-specific biologies might be supported by the selective expression of RUNX paralogs during Langerhans cell and inducible regulatory T cell differentiation. We uncovered functional nonequivalence between RUNX paralogs. Selective expression of native paralogs allowed integration of transcription factor activity with extrinsic signals, while non-native paralogs enforced differentiation even in the absence of exogenous inducers. DNA binding affinity was controlled by divergent amino acids within the otherwise highly conserved RUNT domain and evolutionary reconstruction suggested convergence of RUNT domain residues toward submaximal strength. Hence, the selective expression of gene duplicates in specialized cell types can synergize with the acquisition of functional differences to enable appropriate gene expression, lineage choice and differentiation in the mammalian immune system.},
}

Animals
Cell Differentiation
Cell Lineage
Conserved Sequence
Core Binding Factor alpha Subunits/*genetics
Evolution, Molecular
Gene Duplication
Humans
Immune System/*physiology
Langerhans Cells/*physiology
Mammals
Organ Specificity/*genetics
Signal Transduction
T-Lymphocytes, Regulatory/*physiology
Transcriptome

@article {pmid30967090,
year = {2019},
author = {Cotter, SC and Pincheira-Donoso, D and Thorogood, R},
title = {Defences against brood parasites from a social immunity perspective.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {374},
number = {1769},
pages = {20180207},
doi = {10.1098/rstb.2018.0207},
pmid = {30967090},
issn = {1471-2970},
mesh = {Animals ; Biological Evolution ; *Birds/parasitology/physiology ; *Cues ; *Host-Parasite Interactions ; *Insecta/parasitology/physiology ; *Recognition, Psychology ; *Social Behavior ; },
abstract = {Parasitic interactions are so ubiquitous that all multicellular organisms have evolved a system of defences to reduce their costs, whether the parasites they encounter are the classic parasites which feed on the individual, or brood parasites which usurp parental care. Many parallels have been drawn between defences deployed against both types of parasite, but typically, while defences against classic parasites have been selected to protect survival, those against brood parasites have been selected to protect the parent's inclusive fitness, suggesting that the selection pressures they impose are fundamentally different. However, there is another class of defences against classic parasites that have specifically been selected to protect an individual's inclusive fitness, known as social immunity. Social immune responses include the anti-parasite defences typically provided for others in kin-structured groups, such as the antifungal secretions produced by termite workers to protect the brood. Defences against brood parasites, therefore, are more closely aligned with social immune responses. Much like social immunity, host defences against brood parasitism are employed by a donor (a parent) for the benefit of one or more recipients (typically kin), and as with social defences against classic parasites, defences have therefore evolved to protect the donor's inclusive fitness, not the survival or ultimately the fitness of individual recipients This can lead to severe conflicts between the different parties, whose interests are not always aligned. Here, we consider defences against brood parasitism in the light of social immunity, at different stages of parasite encounter, addressing where conflicts occur and how they might be resolved. We finish with considering how this approach could help us to address longstanding questions in our understanding of brood parasitism. This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.},
}

Animals
Biological Evolution
*Birds/parasitology/physiology
*Cues
*Host-Parasite Interactions
*Insecta/parasitology/physiology
*Recognition, Psychology
*Social Behavior

@article {pmid32130880,
year = {2020},
author = {González, A and Hall, MN and Lin, SC and Hardie, DG},
title = {AMPK and TOR: The Yin and Yang of Cellular Nutrient Sensing and Growth Control.},
journal = {Cell metabolism},
volume = {31},
number = {3},
pages = {472-492},
doi = {10.1016/j.cmet.2020.01.015},
pmid = {32130880},
issn = {1932-7420},
abstract = {The AMPK (AMP-activated protein kinase) and TOR (target-of-rapamycin) pathways are interlinked, opposing signaling pathways involved in sensing availability of nutrients and energy and regulation of cell growth. AMPK (Yin, or the "dark side") is switched on by lack of energy or nutrients and inhibits cell growth, while TOR (Yang, or the "bright side") is switched on by nutrient availability and promotes cell growth. Genes encoding the AMPK and TOR complexes are found in almost all eukaryotes, suggesting that these pathways arose very early during eukaryotic evolution. During the development of multicellularity, an additional tier of cell-extrinsic growth control arose that is mediated by growth factors, but these often act by modulating nutrient uptake so that AMPK and TOR remain the underlying regulators of cellular growth control. In this review, we discuss the evolution, structure, and regulation of the AMPK and TOR pathways and the complex mechanisms by which they interact.},
}

@article {pmid32122349,
year = {2020},
author = {Gray, MW and Burger, G and Derelle, R and Klimeš, V and Leger, MM and Sarrasin, M and Vlček, Č and Roger, AJ and Eliáš, M and Lang, BF},
title = {The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome.},
journal = {BMC biology},
volume = {18},
number = {1},
pages = {22},
doi = {10.1186/s12915-020-0741-6},
pmid = {32122349},
issn = {1741-7007},
support = {RGPIN-2014-05286//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN- 2017-05411//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2016-06792//Natural Sciences and Engineering Research Council of Canada/ ; AFR grant PHD-08-001//Fonds National de la Recherche Luxembourg/ ; 18-13458S//Czech Science Foundation/ ; OPVVV 16_019/0000759//ERD Funds/ ; },
abstract = {BACKGROUND: Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes discovered to date.

RESULTS: In this study, we assembled the draft nuclear genome sequence for the jakobid Andalucia godoyi and used a comprehensive in silico approach to infer the nucleus-encoded portion of the mitochondrial proteome of this protist, identifying 864 candidate mitochondrial proteins. The A. godoyi mitochondrial proteome has a complexity that parallels that of other eukaryotes, while exhibiting an unusually large number of ancestral features that have been lost particularly in opisthokont (animal and fungal) mitochondria. Notably, we find no evidence that the A. godoyi nuclear genome has or had a gene encoding a single-subunit, T3/T7 bacteriophage-like RNA polymerase, which functions as the mitochondrial transcriptase in all eukaryotes except the jakobids.

CONCLUSIONS: As genome and mitochondrial proteome data have become more widely available, a strikingly punctuate phylogenetic distribution of different mitochondrial components has been revealed, emphasizing that the pathways of mitochondrial proteome evolution are likely complex and lineage-specific. Unraveling this complexity will require comprehensive comparative analyses of mitochondrial proteomes from a phylogenetically broad range of eukaryotes, especially protists. The systematic in silico approach described here offers a valuable adjunct to direct proteomic analysis (e.g., via mass spectrometry), particularly in cases where the latter approach is constrained by sample limitation or other practical considerations.},
}

@article {pmid32109395,
year = {2020},
author = {Tan, Y and Barnbrook, M and Wilson, Y and Molnár, A and Bukys, A and Hudson, A},
title = {Shared Mutations in a Novel Glutaredoxin Repressor of Multicellular Trichome Fate Underlie Parallel Evolution of Antirrhinum Species.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2020.01.060},
pmid = {32109395},
issn = {1879-0445},
abstract = {Most angiosperms produce trichomes-epidermal hairs that have protective or more specialized roles. Trichomes are multicellular in almost all species and, in the majority, secretory. Despite the importance of multicellular trichomes for plant protection and as a source of high-value products, the mechanisms that control their development are only poorly understood. Here, we investigate the control of multicellular trichome patterns using natural variation within the genus Antirrhinum (snapdragons), which has evolved hairy alpine-adapted species or lowland species with a restricted trichome pattern multiple times in parallel. We find that a single gene, Hairy (H), which is needed to repress trichome fate, underlies variation in trichome patterns between all Antirrhinum species except one. We show that H encodes a novel epidermis-specific glutaredoxin and that the pattern of trichome distribution within individuals reflects the location of H expression. Phylogenetic and functional tests suggest that H gained its trichome-repressing role late in the history of eudicots and that the ancestral Antirrhinum had an active H gene and restricted trichome distribution. Loss of H function was involved in an early divergence of alpine and lowland Antirrhinum lineages, and the alleles underlying this split were later reused in parallel evolution of alpines from lowland ancestors, and vice versa. We also find evidence for an evolutionary reversal from a widespread to restricted trichome distribution involving a suppressor mutation and for a pleiotropic effect of H on plant growth that might constrain the evolution of trichome pattern.},
}

@article {pmid32102937,
year = {2020},
author = {Elliott, L and Moore, I and Kirchhelle, C},
title = {Spatio-temporal control of post-Golgi exocytic trafficking in plants.},
journal = {Journal of cell science},
volume = {133},
number = {4},
pages = {},
doi = {10.1242/jcs.237065},
pmid = {32102937},
issn = {1477-9137},
abstract = {A complex and dynamic endomembrane system is a hallmark of eukaryotic cells and underpins the evolution of specialised cell types in multicellular organisms. Endomembrane system function critically depends on the ability of the cell to (1) define compartment and pathway identity, and (2) organise compartments and pathways dynamically in space and time. Eukaryotes possess a complex molecular machinery to control these processes, including small GTPases and their regulators, SNAREs, tethering factors, motor proteins, and cytoskeletal elements. Whereas many of the core components of the eukaryotic endomembrane system are broadly conserved, there have been substantial diversifications within different lineages, possibly reflecting lineage-specific requirements of endomembrane trafficking. This Review focusses on the spatio-temporal regulation of post-Golgi exocytic transport in plants. It highlights recent advances in our understanding of the elaborate network of pathways transporting different cargoes to different domains of the cell surface, and the molecular machinery underpinning them (with a focus on Rab GTPases, their interactors and the cytoskeleton). We primarily focus on transport in the context of growth, but also highlight how these pathways are co-opted during plant immunity responses and at the plant-pathogen interface.},
}

@article {pmid31512055,
year = {2019},
author = {Alcorta, J and Vergara-Barros, P and Antonaru, LA and Alcamán-Arias, ME and Nürnberg, DJ and Díez, B},
title = {Fischerella thermalis: a model organism to study thermophilic diazotrophy, photosynthesis and multicellularity in cyanobacteria.},
journal = {Extremophiles : life under extreme conditions},
volume = {23},
number = {6},
pages = {635-647},
pmid = {31512055},
issn = {1433-4909},
support = {1150171//Fondo de Fomento al Desarrollo Científico y Tecnológico/ ; 1190998//Fondo de Fomento al Desarrollo Científico y Tecnológico/ ; },
mesh = {Acclimatization/*physiology ; *Biological Evolution ; Cyanobacteria/*physiology ; Hot Springs/*microbiology ; *Hot Temperature ; *Models, Biological ; Trichomes/physiology ; },
abstract = {The true-branching cyanobacterium Fischerella thermalis (also known as Mastigocladus laminosus) is widely distributed in hot springs around the world. Morphologically, it has been described as early as 1837. However, its taxonomic placement remains controversial. F. thermalis belongs to the same genus as mesophilic Fischerella species but forms a monophyletic clade of thermophilic Fischerella strains and sequences from hot springs. Their recent divergence from freshwater or soil true-branching species and the ongoing process of specialization inside the thermal gradient make them an interesting evolutionary model to study. F. thermalis is one of the most complex prokaryotes. It forms a cellular network in which the main trichome and branches exchange metabolites and regulators via septal junctions. This species can adapt to a variety of environmental conditions, with its photosynthetic apparatus remaining active in a temperature range from 15 to 58 °C. Together with its nitrogen-fixing ability, this allows it to dominate in hot spring microbial mats and contribute significantly to the de novo carbon and nitrogen input. Here, we review the current knowledge on the taxonomy and distribution of F. thermalis, its morphological complexity, and its physiological adaptations to an extreme environment.},
}

Acclimatization/*physiology
*Biological Evolution
Cyanobacteria/*physiology
Hot Springs/*microbiology
*Hot Temperature
*Models, Biological
Trichomes/physiology

@article {pmid31152521,
year = {2019},
author = {Odendall, C and Kagan, JC},
title = {Host-Encoded Sensors of Bacteria: Our Windows into the Microbial World.},
journal = {Microbiology spectrum},
volume = {7},
number = {3},
pages = {},
doi = {10.1128/microbiolspec.BAI-0011-2019},
pmid = {31152521},
issn = {2165-0497},
support = {R01 AI093589/AI/NIAID NIH HHS/United States ; R01 AI116550/AI/NIAID NIH HHS/United States ; U19 AI133524/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Bacteria/*immunology/pathogenicity ; Bacterial Infections/*immunology/microbiology ; Evolution, Molecular ; Germ-Free Life ; Host-Pathogen Interactions/*immunology/*physiology ; Humans ; Neutrophil Infiltration ; Receptors, Pattern Recognition/immunology/*physiology ; Virulence Factors ; },
abstract = {Bacterial pathogens can be very efficient at causing disease and are the cause of some of the worst epidemics that have affected humanity. However, most infections are prevented by the actions of our immune system. Immune activation depends on the rapid detection of bacteria by a diverse family of sensory proteins known as pattern recognition receptors. These receptors detect conserved features of bacteria that are not found in humans but are often necessary for survival within the host or environment. In this review, we discuss the strategies used by pattern recognition receptors to detect bacteria and their products. We also discuss emerging evidence that some pattern recognition receptors can be activated by bacterial pathogens specifically, through the surveillance of host activities that are commonly targeted by virulence factors. This collection of surveillance mechanisms provides an interconnected network of defense, which is important to maintain the germ-free environment of the inner organs of humans and other multicellular organisms.},
}

Animals
Bacteria/*immunology/pathogenicity
Bacterial Infections/*immunology/microbiology
Evolution, Molecular
Germ-Free Life
Host-Pathogen Interactions/*immunology/*physiology
Humans
Neutrophil Infiltration
Receptors, Pattern Recognition/immunology/*physiology
Virulence Factors

@article {pmid32097591,
year = {2020},
author = {Greyson-Gaito, CJ and Bartley, TJ and Cottenie, K and Jarvis, WMC and Newman, AEM and Stothart, MR},
title = {Into the wild: microbiome transplant studies need broader ecological reality.},
journal = {Proceedings. Biological sciences},
volume = {287},
number = {1921},
pages = {20192834},
doi = {10.1098/rspb.2019.2834},
pmid = {32097591},
issn = {1471-2954},
abstract = {Gut microbial communities (microbiomes) profoundly shape the ecology and evolution of multicellular life. Interactions between host and microbiome appear to be reciprocal, and ecological theory is now being applied to better understand how hosts and their microbiome influence each other. However, some ecological processes that underlie reciprocal host-microbiome interactions may be obscured by the current convention of highly controlled transplantation experiments. Although these approaches have yielded invaluable insights, there is a need for a broader array of approaches to fully understand host-microbiome reciprocity. Using a directed review, we surveyed the breadth of ecological reality in the current literature on gut microbiome transplants with non-human recipients. For 55 studies, we categorized nine key experimental conditions that impact the ecological reality (EcoReality) of the transplant, including host taxon match and donor environment. Using these categories, we rated the EcoReality of each transplant. Encouragingly, the breadth of EcoReality has increased over time, but some components of EcoReality are still relatively unexplored, including recipient host environment and microbiome state. The conceptual framework we develop here maps the landscape of possible EcoReality to highlight where fundamental ecological processes can be considered in future transplant experiments.},
}

@article {pmid32095969,
year = {2020},
author = {Moody, LA},
title = {Three-dimensional growth: a developmental innovation that facilitated plant terrestrialization.},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10265-020-01173-4},
pmid = {32095969},
issn = {1618-0860},
support = {BB/M020517/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; University Research Fellowship//Royal Society/ ; },
abstract = {One of the most transformative events in the history of life on earth was the transition of plants from water to land approximately 470 million years ago. Within the Charophyte green algae, the closest living relatives of land plants, body plans have evolved from those that comprise simple unicells to those that are morphologically complex, large and multicellular. The Charophytes developed these broad ranging body plans by exploiting a range of one-dimensional and two-dimensional growth strategies to produce filaments, mats and branches. When plants were confronted with harsh conditions on land, they were required to make significant changes to the way they shaped their body plans. One of the fundamental developmental transitions that occurred was the evolution of three-dimensional growth and the acquisition of apical cells with three or more cutting faces. Plants subsequently developed a range of morphological adaptations (e.g. vasculature, roots, flowers, seeds) that enabled them to colonise progressively drier environments. 3D apical growth also evolved convergently in the brown algae, completely independently of the green lineage. This review summarises the evolving developmental complexities observed in the early divergent Charophytes all the way through to the earliest conquerors of land, and investigates 3D apical growth in the brown algae.},
}

@article {pmid32094536,
year = {2020},
author = {Tang, Q and Pang, K and Yuan, X and Xiao, S},
title = {A one-billion-year-old multicellular chlorophyte.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-020-1122-9},
pmid = {32094536},
issn = {2397-334X},
support = {41602007//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41602007//National Natural Science Foundation of China (National Science Foundation of China)/ ; 80NSSC18K1086/NASA/NASA/United States ; },
abstract = {Chlorophytes (representing a clade within the Viridiplantae and a sister group of the Streptophyta) probably dominated marine export bioproductivity and played a key role in facilitating ecosystem complexity before the Mesozoic diversification of phototrophic eukaryotes such as diatoms, coccolithophorans and dinoflagellates. Molecular clock and biomarker data indicate that chlorophytes diverged in the Mesoproterozoic or early Neoproterozoic, followed by their subsequent phylogenetic diversification, multicellular evolution and ecological expansion in the late Neoproterozoic and Palaeozoic. This model, however, has not been rigorously tested with palaeontological data because of the scarcity of Proterozoic chlorophyte fossils. Here we report abundant millimetre-sized, multicellular and morphologically differentiated macrofossils from rocks approximately 1,000 million years ago. These fossils are described as Proterocladus antiquus new species and are interpreted as benthic siphonocladalean chlorophytes, suggesting that chlorophytes acquired macroscopic size, multicellularity and cellular differentiation nearly a billion years ago, much earlier than previously thought.},
}

@article {pmid32094163,
year = {2020},
author = {Yahalomi, D and Atkinson, SD and Neuhof, M and Chang, ES and Philippe, H and Cartwright, P and Bartholomew, JL and Huchon, D},
title = {A cnidarian parasite of salmon (Myxozoa: Henneguya) lacks a mitochondrial genome.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1909907117},
pmid = {32094163},
issn = {1091-6490},
abstract = {Although aerobic respiration is a hallmark of eukaryotes, a few unicellular lineages, growing in hypoxic environments, have secondarily lost this ability. In the absence of oxygen, the mitochondria of these organisms have lost all or parts of their genomes and evolved into mitochondria-related organelles (MROs). There has been debate regarding the presence of MROs in animals. Using deep sequencing approaches, we discovered that a member of the Cnidaria, the myxozoan Henneguya salminicola, has no mitochondrial genome, and thus has lost the ability to perform aerobic cellular respiration. This indicates that these core eukaryotic features are not ubiquitous among animals. Our analyses suggest that H. salminicola lost not only its mitochondrial genome but also nearly all nuclear genes involved in transcription and replication of the mitochondrial genome. In contrast, we identified many genes that encode proteins involved in other mitochondrial pathways and determined that genes involved in aerobic respiration or mitochondrial DNA replication were either absent or present only as pseudogenes. As a control, we used the same sequencing and annotation methods to show that a closely related myxozoan, Myxobolus squamalis, has a mitochondrial genome. The molecular results are supported by fluorescence micrographs, which show the presence of mitochondrial DNA in M. squamalis, but not in H. salminicola. Our discovery confirms that adaptation to an anaerobic environment is not unique to single-celled eukaryotes, but has also evolved in a multicellular, parasitic animal. Hence, H. salminicola provides an opportunity for understanding the evolutionary transition from an aerobic to an exclusive anaerobic metabolism.},
}

@article {pmid32032743,
year = {2020},
author = {Dokanehiifard, S and Soltani, BM and Ghiasi, P and Baharvand, H and Reza Ganjali, M and Hosseinkhani, S},
title = {hsa-miR-766-5p as a new regulator of mitochondrial apoptosis pathway for discriminating of cell death from cardiac differentiation.},
journal = {Gene},
volume = {736},
number = {},
pages = {144448},
doi = {10.1016/j.gene.2020.144448},
pmid = {32032743},
issn = {1879-0038},
abstract = {Dispose of unnecessary cells in multicellular organism take place through apoptosis as a mode of programmed cell death (PCD). This process is triggered through two main pathway including extrinsic pathway or death receptor pathway and intrinsic or mitochondrial pathway. An alternative role for mitochondrial pathway of cell death is its involvement in cell differentiation. Biochemistry of cell differentiation indicates a common origin for differentiation and apoptosis. miRNAs are a group of small non coding mediator RNAs in regulation of many routes such as apoptosis and differentiation. By using bioinformatics tools hsa-miR-766-5p was predicted to target the BAX, BAK and BOK genes involved in mitochondrial apoptosis pathway. RT-qPCR and dual luciferase assay showed targeting of BAX, BAK and BOK 3'UTRs via hsa-miR-766, detected in SW480 and HEK293T cell lines. Caspases 3/7 and 9 activity assay revealed the involvement of hsa-miR-766-5p in mitochondrial apoptosis pathway regulation detected following overexpression and downregulation of this miRNA, detected in SW480 cells treated with 1 μM doxorubicin. Flow cytometry and MTT assay indicated cell death reduction and viability elevation effect of hsa-miR-766 in SW480 cells after its overexpression. Endogenous expression of hsa-miR-766 during the course of human embryonic stem cells (hESCs) differentiation into cardiomyocytes revealed an inverse expression status of this miRNA with BOK. However, the expression of this miRNA was inversely related to BAX and BAK for some time points of differentiation. Overall this results show the involvement of hsa-miR-766 in regulation of mitochondrial apoptosis pathway.},
}

@article {pmid31722397,
year = {2020},
author = {López, EH and Palumbi, SR},
title = {Somatic Mutations and Genome Stability Maintenance in Clonal Coral Colonies.},
journal = {Molecular biology and evolution},
volume = {37},
number = {3},
pages = {828-838},
doi = {10.1093/molbev/msz270},
pmid = {31722397},
issn = {1537-1719},
abstract = {One challenge for multicellular organisms is maintaining genome stability in the face of mutagens across long life spans. Imperfect genome maintenance leads to mutation accumulation in somatic cells, which is associated with tumors and senescence in vertebrates. Colonial reef-building corals are often large, can live for hundreds of years, rarely develop recognizable tumors, and are thought to convert somatic cells into gamete producers, so they are a pivotal group in which to understand long-term genome maintenance. To measure rates and patterns of somatic mutations, we analyzed transcriptomes from 17 to 22 branches from each of four Acropora hyacinthus colonies, determined putative single nucleotide variants, and verified them with Sanger resequencing. Unlike for human skin carcinomas, there is no signature of mutations caused by UV damage, indicating either higher efficiency of repair than in vertebrates, or strong sunscreen protection in these shallow water tropical animals. The somatic mutation frequency per nucleotide in A. hyacinthus is on the same order of magnitude (10-7) as noncancerous human somatic cells, and accumulation of mutations with age is similar. Loss of heterozygosity variants outnumber gain of heterozygosity mutations ∼2:1. Although the mutation frequency is similar in mammals and corals, the preponderance of loss of heterozygosity changes and potential selection may reduce the frequency of deleterious mutations in colonial animals like corals. This may limit the deleterious effects of somatic mutations on the coral organism as well as potential offspring.},
}

@article {pmid32079678,
year = {2020},
author = {Erwin, DH},
title = {The origin of animal body plans: a view from fossil evidence and the regulatory genome.},
journal = {Development (Cambridge, England)},
volume = {147},
number = {4},
pages = {},
doi = {10.1242/dev.182899},
pmid = {32079678},
issn = {1477-9129},
abstract = {The origins and the early evolution of multicellular animals required the exploitation of holozoan genomic regulatory elements and the acquisition of new regulatory tools. Comparative studies of metazoans and their relatives now allow reconstruction of the evolution of the metazoan regulatory genome, but the deep conservation of many genes has led to varied hypotheses about the morphology of early animals and the extent of developmental co-option. In this Review, I assess the emerging view that the early diversification of animals involved small organisms with diverse cell types, but largely lacking complex developmental patterning, which evolved independently in different bilaterian clades during the Cambrian Explosion.},
}

@article {pmid32078984,
year = {2020},
author = {Moreau, CS},
title = {Symbioses among ants and microbes.},
journal = {Current opinion in insect science},
volume = {39},
number = {},
pages = {1-5},
doi = {10.1016/j.cois.2020.01.002},
pmid = {32078984},
issn = {2214-5753},
abstract = {Ants have been shown to engage in symbiosis across the tree of life, although our knowledge is far from complete. These interactions range from mutualistic to parasitic with several instances of manipulation of host behavior. Nutrient contributions in these symbioses include both farming for food and nitrogen recycling by gut-associated microbes. Interestingly, the ants that are mostly likely to host diverse and likely functional gut microbial communities are those that feed on extreme diets. Although we do see many instances of symbiosis between ants and microbes, there are also examples of species without a functional gut microbiome. Symbiosis among microbes and eukaryotic hosts is common and often considered a hallmark of multicellular evolution [1]. This is true among many of the over 13000 species of ants, although symbiosis between ants and microbes are not ubiquitous. These microbial-ant symbiotic interactions span the tree of life and include microbial eukaryotes, fungi, viruses, and bacteria. These interactions range from pathogenic to mutualistic, with many relationships still not well understood. Although our knowledge of the diversity of these microbes in ants is growing rapidly, and in some cases we know the function and interaction with the host, we still have much to learn about - the little things that run the little things that run the world!},
}

@article {pmid32076502,
year = {2020},
author = {Noh, S and Christopher, L and Strassmann, JE and Queller, DC},
title = {Wild Dictyostelium discoideum social amoebae show plastic responses to the presence of nonrelatives during multicellular development.},
journal = {Ecology and evolution},
volume = {10},
number = {3},
pages = {1119-1134},
doi = {10.1002/ece3.5924},
pmid = {32076502},
issn = {2045-7758},
abstract = {When multiple strains of microbes form social groups, such as the multicellular fruiting bodies of Dictyostelium discoideum, conflict can arise regarding cell fate. Both fixed and plastic differences among strains can contribute to cell fate, and plastic responses may be particularly important if social environments frequently change. We used RNA-sequencing and photographic time series analysis to detect possible conflict-induced plastic differences between wild D. discoideum aggregates formed by single strains compared with mixed pairs of strains (chimeras). We found one hundred and two differentially expressed genes that were enriched for biological processes including cytoskeleton organization and cyclic AMP response (up-regulated in chimeras), and DNA replication and cell cycle (down-regulated in chimeras). In addition, our data indicate that in reference to a time series of multicellular development in the laboratory strain AX4, chimeras may be slightly behind clonal aggregates in their development. Finally, phenotypic analysis supported slower splitting of aggregates and a nonsignificant trend for larger group sizes in chimeras. The transcriptomic comparison and phenotypic analyses support discoordination among aggregate group members due to social conflict. These results are consistent with previously observed factors that affect cell fate decision in D. discoideum and provide evidence for plasticity in cAMP signaling and phenotypic coordination during development in response to social conflict in D. discoideum and similar microbial social groups.},
}

@article {pmid32075388,
year = {2020},
author = {Raudenská, M and Svobodová, M and Gumulec, J and Falk, M and Masařík, M},
title = {The Importance of Cancer-Associated Fibroblasts in the Pathogenesis of Head and Neck Cancers.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {33},
number = {1},
pages = {39-48},
doi = {10.14735/amko202039},
pmid = {32075388},
issn = {1802-5307},
abstract = {BACKGROUND: Despite progress in anticancer therapies, head and neck squamous cell carcinoma (HNSCC) has still a low survival rate. Recent studies have shown that tumour stroma may play an important role in the pathogenesis of this malignant disease. Fibroblasts are a major component of the tumour microenvironment and may significantly influence HNSCC progression as indicated by the contribution they make to important hallmarks of cancer, such as inflammation, non-restricted growth, angiogenesis, invasion, metastasis, and therapy resistance. It is well known that tumour cells can confer a cancer-associated fibroblast (CAF) phenotype that supports the growth and dissemination of cancer cells. CAFs can stimulate cancer progression through cell-cell contacts and communication, remodelling of extracellular matrix, and production of many signal molecules and matrix metalloproteinases. Consequently, genetic changes in epithelial cells are probably not the only factor that drives HNSCC carcinogenesis. Non-genetic changes in the tumour stroma can also be significantly involved. Stress-induced signals can induce a multicellular program, creating a field of tissue that is predisposed to malignant transformation. The “field cancerization” concept represents a process of active evolution of intercellular interactions and feedback loops between tumour and stromal cells. This model paves the way to study cancer from a new perspective and identify new therapeutic targets.

PURPOSE: In this review, we discuss current knowledge about CAFs, such as their cellular origin, phenotypical plasticity and functional heterogeneity, and stress their contribution to HNSCC progression. This article was supported by the project AZV 16-29835A. The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers. Submitted: 18. 6. 2019 Accepted: 9. 9. 2019.},
}

@article {pmid32072723,
year = {2020},
author = {Kulanthaivelu, K and Bhat, MD and Prasad, C and Srinivas, D and Mhatre, R and Nandeesh, BN},
title = {Brain MRI Findings in Coenurosis: A Helminth Infection.},
journal = {Journal of neuroimaging : official journal of the American Society of Neuroimaging},
volume = {},
number = {},
pages = {},
doi = {10.1111/jon.12696},
pmid = {32072723},
issn = {1552-6569},
abstract = {BACKGROUND AND PURPOSE: Parasitic neuroinfections in humans have etiological agents spanning a broad spectrum from unicellular (protozoan) to multicellular helminthic (metazoan) organisms. Cerebral coenurosis is a rare cestodal helminthic infection caused by Taenia multiceps. The neuroimaging features of this entity were reviewed to discern an imaging phenotype.

METHODS: Retrospective analysis was performed on 6 cases of cerebral coenurosis, whose diagnoses were confirmed by histopathology. The clinical, imaging, and histopathological features were recorded for analysis.

RESULTS: Clinical expressions included focal neurological deficit due to mass effect (n = 4), intraventricular obstruction with features of raised intracranial tension (n = 1), headache (n = 3), seizures (n = 3), and incidental lesions (n = 1). One patient presented with recurrence 1 year after surgical excision. Neuroimaging revealed cystic thin-walled lesions with clustered eccentric internal nodules corresponding to the plenitude of protoscolices of the tapeworm. Three of the lesions showed a multilocular cystic morphology. Spectroscopic metabolite signature of alanine and succinate commensurate with the parasitic etiology was remarkable in the lesions. Enhancement and edema inversely correlated with the signal suppression on fluid-attenuated inversion recovery (FLAIR) imaging. The lesions had a predominantly juxtacortical distribution.

CONCLUSIONS: In an appropriate clinical setting, a cystic lesion with clustered eccentric internal nodular foci ought to raise the suspicion of this rare infection. Magnetic resonance spectroscopic signature of succinate and alanine, if present, further strengthens the likelihood of coenurosis. Signal characteristics, wall enhancement, and perilesional edema may vary, possibly determined by the stage in the evolution of the parasite.},
}

@article {pmid32067938,
year = {2020},
author = {Agosti, A and Marchesi, S and Scita, G and Ciarletta, P},
title = {Modelling cancer cell budding in-vitro as a self-organised, non-equilibrium growth process.},
journal = {Journal of theoretical biology},
volume = {},
number = {},
pages = {110203},
doi = {10.1016/j.jtbi.2020.110203},
pmid = {32067938},
issn = {1095-8541},
abstract = {Tissue self-organization into defined and well-controlled three-dimensional structures is essential during development for the generation of organs. A similar, but highly deranged process might also occur during the aberrant growth of cancers, which frequently display a loss of the orderly structures of the tissue of origin, but retain a multicellular organization in the form of spheroids, strands, and buds. The latter structures are often seen when tumors masses switch to an invasive behavior into surrounding tissues. However, the general physical principles governing the self-organized architectures of tumor cell populations remain by and large unclear. In this work, we perform in-vitro experiments to characterize the growth properties of glioblastoma budding emerging from monolayers. We further propose a theoretical model and its finite element implementation to characterize such a topological transition, that is modelled as a self-organised, non-equilibrium phenomenon driven by the trade-off of mechanical forces and physical interactions exerted at cell-cell and cell-substrate adhesions. Notably, the unstable disorder states of uncontrolled cellular proliferation macroscopically emerge as complex spatio-temporal patterns that evolve statistically correlated by a universal law.},
}

@article {pmid32061337,
year = {2020},
author = {Ishibashi, K and Tanaka, Y and Morishita, Y},
title = {Perspectives on the evolution of aquaporin superfamily.},
journal = {Vitamins and hormones},
volume = {112},
number = {},
pages = {1-27},
doi = {10.1016/bs.vh.2019.08.001},
pmid = {32061337},
issn = {0083-6729},
abstract = {Aquaporins (AQPs) belong to a transmembrane protein superfamily composed of an internal repeat of a three membrane-spanning domain and each has a highly conserved NPA box. Based on the more variable carboxyl-terminal NPA box, AQPs can be divided into three subfamilies: (1) glycerol-channel aquaglyceroporin (gAQP) (2) water-selective AQP (wAQP), and (3) deviated superaquaporin (sAQP) in the order of passible evolution. This classification has functional and localization relevance: most wAQPs transports water selectively whereas gAQPs and sAQPs also transport small molecules with sAQPs mostly localized inside the cell. As this classification is not based on the function, some wAQPs functioning as glycerol channels will not be included in gAQPs. AQP ancestors may have first originated in eubacteria as gAQPs to transport small molecules such as glycerol. Later some of them may have acquired a water-selective filter to become wAQPs. Although AQPs are absent in many bacteria, especially in archaea, both gAQPs and wAQPs may have been carried over to eukaryotes or horizontally transferred. Finally, multicellular organisms have obtained new sAQPs, which are curiously absent in fungi and plants. Interestingly, both plants and higher insects independently have lost gAQPs, whose functions, however, have been taken over by functionally modified wAQPs partly obtained by horizontal gene transfers from bacteria. This evolutionary viewpoints on AQPs will facilitate further functional analysis of AQP-like sequences and expand our viewpoints on AQP superfamily.},
}

@article {pmid32045589,
year = {2020},
author = {Duan, H and Ni, S and Yang, S and Zhou, Y and Zhang, Y and Zhang, S},
title = {Conservation of eATP perception throughout multicellular animal evolution: Identification and functional characterization of coral and amphioxus P2X7-like receptors and flounder P2X7 receptor.},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {103641},
doi = {10.1016/j.dci.2020.103641},
pmid = {32045589},
issn = {1879-0089},
abstract = {Perception of extracellular ATP (eATP), a common endogenous damage-associated molecular pattern, is through its receptor P2X7R. If eATP/P2X7R signaling is conserved throughout animal evolution is unknown. Moreover, little information is currently available regarding P2X7R in invertebrates. Here we demonstrated that the coral P2X7-like receptor, AdP2X7RL, the amphioxus P2X7-like receptor, BjP2X7RL and the flounder P2X7 receptor, PoP2X7R, shared common features characteristic of mammalian P2X7R, and their 3D structures displayed high resemblance to that of human P2X7R. Expression of Adp2x7rl, Bjp2x7rl and Pop2x7r was all subjected to the regulation by LPS and ATP. We also showed that AdP2X7RL, BjP2X7RL and PoP2X7R were distributed on the plasma membrane in AdP2X7RL-, BjP2X7RL- and PoP2X7R-expressing HEK cells, and had strong affinity to eATP. Importantly, the binding of AdP2X7RL, BjP2X7RL and PoP2X7R to eATP all induced similar downstream responses, including induction of cytokines (IL-1β, IL-6, IL-8 and CCL-2), enhancement of phagocytosis and activation of AKT/ERK-associated signaling pathway observed for mammalian P2X7R. Collectively, our results indicate for the first time that both coral and amphioxus P2X7RL as well as flounder P2X7R can interact with eATP, and induce events that trigger mammalian mechanisms, suggesting the high conservation of eATP perception throughout multicellular animal evolution.},
}

@article {pmid32044287,
year = {2020},
author = {Kuwabara, T and Igarashi, K},
title = {Thermotogales origin scenario of eukaryogenesis.},
journal = {Journal of theoretical biology},
volume = {},
number = {},
pages = {110192},
doi = {10.1016/j.jtbi.2020.110192},
pmid = {32044287},
issn = {1095-8541},
abstract = {How eukaryotes were generated is an enigma of evolutionary biology. Widely accepted archaeal-origin eukaryogenesis scenarios, based on similarities of genes and related characteristics between archaea and eukaryotes, cannot explain several eukaryote-specific features of the last eukaryotic common ancestor, such as glycerol-3-phosphate-type membrane lipids, large cells and genomes, and endomembrane formation. Thermotogales spheroids, having multicopy-integrated large nucleoids and producing progeny in periplasm, may explain all of these features as well as endoplasmic reticulum-type signal cleavage sites, although they cannot divide. We hypothesize that the progeny chromosome is formed by random joining small DNAs in immature progeny, followed by reorganization by mechanisms including homologous recombination enabled with multicopy-integrated large genome (MILG). We propose that Thermotogales ancestor spheroids came to divide owing to the archaeal cell division genes horizontally transferred via virus-related particles, forming the first eukaryotic common ancestor (FECA). Referring to the hypothesis, the archaeal information-processing system would have been established in FECA by random joining DNAs excised from the MILG, which contained horizontally transferred archaeal and bacterial DNAs, followed by reorganization by the MILG-enabled homologous recombination. Thus, the large genome may have been a prerequisite, but not a consequence, of eukaryogenesis. The random joining of DNAs likely provided the basic mechanisms for eukaryotic evolution: producing the diversity by the formations of supergroups, novel genes, and introns, which are involved in exon shuffling.},
}

@article {pmid32042121,
year = {2020},
author = {Black, AJ and Bourrat, P and Rainey, PB},
title = {Ecological scaffolding and the evolution of individuality.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-019-1086-9},
pmid = {32042121},
issn = {2397-334X},
abstract = {Evolutionary transitions in individuality are central to the emergence of biological complexity. Recent experiments provide glimpses of processes underpinning the transition from single cells to multicellular life and draw attention to the critical role of ecology. Here, we emphasize this ecological dimension and argue that its current absence from theoretical frameworks hampers development of general explanatory solutions. Using mechanistic mathematical models, we show how a minimal ecological structure comprising patchily distributed resources and between-patch dispersal can scaffold Darwinian-like properties on collectives of cells. This scaffolding causes cells to participate directly in the process of evolution by natural selection as if they were members of multicellular collectives, with collectives participating in a death-birth process arising from the interplay between the timing of dispersal events and the rate of resource use by cells. When this timescale is sufficiently long and new collectives are founded by single cells, collectives experience conditions that favour evolution of a reproductive division of labour. Together our simple model makes explicit key events in the major evolutionary transition to multicellularity. It also makes predictions concerning the life history of certain pathogens and serves as an ecological recipe for experimental realization of evolutionary transitions.},
}

@article {pmid32039188,
year = {2020},
author = {Li, R and Hornberger, K and Dutton, JR and Hubel, A},
title = {Cryopreservation of Human iPS Cell Aggregates in a DMSO-Free Solution-An Optimization and Comparative Study.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {8},
number = {},
pages = {1},
doi = {10.3389/fbioe.2020.00001},
pmid = {32039188},
issn = {2296-4185},
abstract = {Human induced pluripotent stem cells (hiPSCs) are an important cell source for regenerative medicine products. Effective methods of preservation are critical to their clinical and commercial applications. The use of a dimethyl sulfoxide (DMSO)-free solution containing all non-toxic molecules offers an effective alternative to the conventional DMSO and alleviates pain points associated with the use of DMSO in the cryopreservation of hiPSCs. Both hiPSCs and cells differentiated from them are commonly multicellular systems, which are more sensitive to stresses of freezing and thawing than single cells. In this investigation, low-temperature Raman spectroscopy visualized freezing behaviors of hiPSC aggregates in different solutions. These aggregates exhibited sensitivity to undercooling in DMSO-containing solutions. We demonstrated the ability to replace DMSO with non-toxic molecules, improve post-thaw cell survival, and reduce sensitivity to undercooling. An accelerated optimization process capitalized on the positive synergy among multiple DMSO-free molecules, which acted in concert to influence ice formation and protect cells during freezing and thawing. A differential evolution algorithm was used to optimize the multi-variable, DMSO-free preservation protocol in 8 experiments. hiPSC aggregates frozen in the optimized solution did not exhibit the same sensitivity to undercooling as those frozen in non-optimized solutions or DMSO, indicating superior adaptability of the optimized solution to different freezing modalities and unplanned deviations. This investigation shows the importance of optimization, explains the mechanisms and advantages of a DMSO-free solution, and enables not only improved cryopreservation of hiPSCs but potentially other cell types for translational regenerative medicine.},
}

@article {pmid32027371,
year = {2020},
author = {Posada, D},
title = {CellCoal: coalescent simulation of single-cell sequencing samples.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaa025},
pmid = {32027371},
issn = {1537-1719},
abstract = {Our capacity to study individual cells has enabled a new level of resolution for understanding complex biological systems like multicellular organisms or microbial communities. Not surprisingly, several methods have been developed in recent years with a formidable potential to investigate the somatic evolution of single cells in both healthy and pathological tissues. However, single-cell genomic data can be quite noisy due to different technical biases, so inferences resulting from these new methods need to be carefully contrasted. Here I introduce CellCoal, a software tool for the coalescent simulation of single-cell genotypes. CellCoal simulates the history of single-cell samples obtained from somatic cell populations with different demographic histories and produces single-nucleotide variants under a variety of mutation models, sequencing read counts and genotype likelihoods, considering allelic imbalance, allelic dropout, amplification and sequencing errors, typical of this type of data. CellCoal is a flexible tool that can be used to understand the implications of different somatic evolutionary processes at the single-cell level, and to benchmark dedicated bioinformatic tools for the analysis of single-cell genotypes.},
}

@article {pmid32024776,
year = {2020},
author = {Munke, A and Kimura, K and Tomaru, Y and Okamoto, K},
title = {Capsid structure of a marine algae virus of the order Picornavirales.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JVI.01855-19},
pmid = {32024776},
issn = {1098-5514},
abstract = {The order Picornavirales includes viruses that infect different kinds of eukaryotes and that share similar properties. The capsid proteins (CPs) of viruses in the order that infect unicellular organisms, such as algae, presumably possess certain characteristics that have changed little over the course of evolution, and thus these viruses may resemble the Picornavirales ancestor in some respects. Herein, we present the capsid structure of Chaetoceros tenuissimus RNA virus type II (CtenRNAV-II) determined using cryo-electron microscopy at a resolution of 3.1 Å, the first of an algae virus belonging to the family Marnaviridae of the order Picornavirales A structural comparison to related invertebrate and vertebrate viruses revealed a unique surface loop of the major CP VP1 that had not been observed previously, and further, that another VP1 loop obscures the so-called canyon, which is a host-receptor binding site for many of the mammalian Picornavirales viruses. VP2 has an N-terminal tail, which has previously been reported as a primordial feature of Picornavirales viruses. Based on the above-mentioned and other critical structural features, the acquired traits among Picornavirales viruses were categorized for profound discussions. The observations afford new insights on three long-standing theories among Picornavirales: the canyon hypothesis, the primordial VP2 domain swap, and the hypothesis that algae picorna-like viruses could share characteristics with the Picornavirales ancestor.ImportanceIdentifying the acquired structural traits in virus capsids is important for elucidating what functions are essential among viruses that infect different hosts. The Picornavirales viruses infect a broad spectrum of hosts, ranging from unicellular algae to insects and mammals, and include many human pathogens. Those viruses that infect unicellular protists, such as algae, are likely to have undergone fewer structural changes during the course of evolution compared to those viruses that infect multicellular eukaryotes, and thus still share some characteristics with the Picornavirales ancestor. This manuscript describes the first atomic capsid structure of an alga Marnavirus, CtenRNAV-II. A comparison to capsid structures of the related invertebrate and vertebrate viruses identified a number of structural traits that have been functionally acquired or lost during the course of evolution. These observations provide new insights on past theories on the viability and evolution of Picornavirales viruses.},
}

@article {pmid32020592,
year = {2020},
author = {Nishino, J and Watanabe, S and Miya, F and Kamatani, T and Sugawara, T and Boroevich, KA and Tsunoda, T},
title = {Quantification of multicellular colonization in tumor metastasis using exome sequencing data.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.32910},
pmid = {32020592},
issn = {1097-0215},
abstract = {Metastasis is a major cause of cancer-related mortality, and it is essential to understand how metastasis occurs in order to overcome it. One relevant question is the origin of a metastatic tumor cell population. Although the hypothesis of a single-cell origin for metastasis from a primary tumor has long been prevalent, several recent studies using mouse models have supported a multi-cellular origin of metastasis. Human bulk whole-exome sequencing (WES) studies also have demonstrated a multiple 'clonal' origin of metastasis, with different mutational compositions. Specifically, there has not yet been strong research to determine how many founder cells colonize a metastatic tumor. To address this question, under the metastatic model of 'single bottleneck followed by rapid growth', we developed a method to quantify the 'founder cell population size' in a metastasis using paired WES data from primary and metachronous metastatic tumors. Simulation studies demonstrated the proposed method gives unbiased results with sufficient accuracy in the range of realistic settings. Applying the proposed method to real WES data from four colorectal cancer patients, all samples supported a multi-cellular origin of metastasis and the founder size was quantified, ranging from 3 to 17 cells. Such a wide-range of founder sizes estimated by the proposed method suggests that there are large variations in genetic similarity between primary and metastatic tumors in the same subjects, which may explain the observed (dis)similarity of drug responses between tumors. This article is protected by copyright. All rights reserved.},
}

@article {pmid32016363,
year = {2020},
author = {Alsufyani, T and Califano, G and Deicke, M and Grueneberg, J and Weiss, A and Engelen, AH and Kwantes, M and Mohr, JF and Ulrich, JF and Wichard, T},
title = {Macroalgal-bacterial interactions: Identification and role of thallusin in morphogenesis of the seaweed Ulva (Chlorophyta).},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraa066},
pmid = {32016363},
issn = {1460-2431},
abstract = {Macroalgal microbiomes have core functions related to biofilm formation, growth, and morphogenesis of seaweeds. In particular, the growth and development of the sea lettuce Ulva spp. (Chlorophyta) depends on bacteria releasing morphogenetic compounds. Under axenic conditions, the macroalga Ulva mutabilis develops a callus-like phenotype with cell wall protrusions. However, coculturing with Roseovarius sp. (MS2) and Maribacter sp. (MS6), which produce various stimulatory chemical mediators, completely recovers morphogenesis. This ecological reconstruction forms a tripartite community which can be further studied for its role in cross-kingdom interactions. Hence, our study sought to identify algal growth- and morphogenesis-promoting factors (AGMPFs) capable of phenocopying the activity of Maribacter spp. We performed bioassay-guided solid-phase extraction in water samples collected from U. mutabilis aquaculture systems. We uncovered novel ecophysiological functions of thallusin, a sesquiterpenoid morphogen, identified for the first time in algal aquaculture. Thallusin, released by Maribacter sp., induced rhizoid and cell wall formation at a concentration of 11 pmol L-1. We further demonstrated that gametes acquired the iron complex of thallusin, thereby linking morphogenetic processes with intracellular iron homeostasis. Understanding macroalgae-bacteria interactions permits further elucidation of the evolution of multicellularity and cellular differentiation and development of new applications in microbiome-mediated aquaculture systems.},
}

@article {pmid32003151,
year = {2020},
author = {Rimskaya-Korsakova, N and Dyachuk, V and Temereva, E},
title = {Parapodial glandular organs in Owenia borealis (Annelida: Oweniidae) and their possible relationship with nephridia.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.b.22928},
pmid = {32003151},
issn = {1552-5015},
support = {18-14-00082//Russian Science Foundation/ ; },
abstract = {Oweniidae is a basal group of recent annelids and nowadays it attracts the attention of researchers of many biological fields. Surprisingly, details of their anatomy, like the adult excretory system, remain obscure. Researchers recently suggested that the paired organs of tubeworms in the family Oweniidae are related to nephridia. In the current study of Owenia borealis adults, we determined that these structures are parapodial glandular organs (PGOs) and are located in the first two segments of adults. The PGOs are complex subepidermal multicellular glands that contain secretory cells, that is, goblet cells, which are differentiated by the type of the producing tube matter. The goblet cells are surrounded by muscles that are used to extrude material stored in the PGO's lumen into the external environment. The anterior pair of PGOs have very well-developed rough endoplasmatic reticulum in the proximal cells, spacious Golgi complexes, numerous nail-shaped microvilli, and apocrine secretory processes in the goblet cells of the distal parts. The posterior pair of PGOs only consists of cells, which probably produce proteinaceous fibrils. We discuss the homology of goblet cells with specific nail-shaped microvilli that produce β-chitin within annelids. We also discuss the possibility that PGOs and nephridia have a common origin. This study provides new information on the ultrastructure of cells that secrete the organic material used to form the tubes inhabited by tube-dwelling annelids.},
}

@article {pmid31983537,
year = {2020},
author = {Yao, M and Ventura, PB and Jiang, Y and Rodriguez, FJ and Wang, L and Perry, JSA and Yang, Y and Wahl, K and Crittenden, RB and Bennett, ML and Qi, L and Gong, CC and Li, XN and Barres, BA and Bender, TP and Ravichandran, KS and Janes, KA and Eberhart, CG and Zong, H},
title = {Astrocytic trans-Differentiation Completes a Multicellular Paracrine Feedback Loop Required for Medulloblastoma Tumor Growth.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2019.12.024},
pmid = {31983537},
issn = {1097-4172},
abstract = {The tumor microenvironment (TME) is critical for tumor progression. However, the establishment and function of the TME remain obscure because of its complex cellular composition. Using a mouse genetic system called mosaic analysis with double markers (MADMs), we delineated TME evolution at single-cell resolution in sonic hedgehog (SHH)-activated medulloblastomas that originate from unipotent granule neuron progenitors in the brain. First, we found that astrocytes within the TME (TuAstrocytes) were trans-differentiated from tumor granule neuron precursors (GNPs), which normally never differentiate into astrocytes. Second, we identified that TME-derived IGF1 promotes tumor progression. Third, we uncovered that insulin-like growth factor 1 (IGF1) is produced by tumor-associated microglia in response to interleukin-4 (IL-4) stimulation. Finally, we found that IL-4 is secreted by TuAstrocytes. Collectively, our studies reveal an evolutionary process that produces a multi-lateral network within the TME of medulloblastoma: a fraction of tumor cells trans-differentiate into TuAstrocytes, which, in turn, produce IL-4 that stimulates microglia to produce IGF1 to promote tumor progression.},
}

@article {pmid31975241,
year = {2020},
author = {Puzakov, MV and Puzakova, LV and Cheresiz, SV},
title = {The Tc1-like elements with the spliceosomal introns in mollusk genomes.},
journal = {Molecular genetics and genomics : MGG},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00438-020-01645-1},
pmid = {31975241},
issn = {1617-4623},
abstract = {Transposable elements (TEs) are DNA sequences capable of transpositions within the genome and thus exerting a considerable influence on the genome functioning and structure and serving as a source of new genes. TE biodiversity studies in previously unexplored species are important for the fundamental understanding of the TE influence on eukaryotic genomes. TEs are classified into retrotransposons and DNA transposons. IS630/Tc1/mariner (ITm) superfamily of DNA transposons is one of the most diverse groups broadly represented among the eukaryotes. The study of 19 mollusk genomes revealed a new group of ITm superfamily elements, which we henceforth refer to as TLEWI. These TEs are characterized by the low copy number, the lack of terminal inverted repeats, the catalytic domain with DD36E signature and the presence of spliceosomal introns in transposase coding sequence. Their prevalence among the mollusks is limited to the class Bivalvia. Since TLEWI possess the features of domesticated TE and structures similar to the eukaryotic genes which are not typical for the DNA transposons, we consider the hypothesis of co-optation of TLEWI gene by the bivalves. The results of our study will fill the gap of knowledge about the prevalence, activity, and evolution of the ITm DNA transposons in multicellular genomes and will facilitate our understanding of the mechanisms of TE domestication by the host genome.},
}

@article {pmid31973071,
year = {2020},
author = {Auboeuf, D},
title = {Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.},
journal = {Life (Basel, Switzerland)},
volume = {10},
number = {2},
pages = {},
doi = {10.3390/life10020007},
pmid = {31973071},
issn = {2075-1729},
support = {Salary//Institut National de la Santé et de la Recherche Médicale/ ; },
abstract = {The current framework of evolutionary theory postulates that evolution relies on random mutations generating a diversity of phenotypes on which natural selection acts. This framework was established using a top-down approach as it originated from Darwinism, which is based on observations made of complex multicellular organisms and, then, modified to fit a DNA-centric view. In this article, it is argued that based on a bottom-up approach starting from the physicochemical properties of nucleic and amino acid polymers, we should reject the facts that (i) natural selection plays a dominant role in evolution and (ii) the probability of mutations is independent of the generated phenotype. It is shown that the adaptation of a phenotype to an environment does not correspond to organism fitness, but rather corresponds to maintaining the genome stability and integrity. In a stable environment, the phenotype maintains the stability of its originating genome and both (genome and phenotype) are reproduced identically. In an unstable environment (i.e., corresponding to variations in physicochemical parameters above a physiological range), the phenotype no longer maintains the stability of its originating genome, but instead influences its variations. Indeed, environment- and cellular-dependent physicochemical parameters define the probability of mutations in terms of frequency, nature, and location in a genome. Evolution is non-deterministic because it relies on probabilistic physicochemical rules, and evolution is driven by a bidirectional interplay between genome and phenotype in which the phenotype ensures the stability of its originating genome in a cellular and environmental physicochemical parameter-depending manner.},
}

@article {pmid31971511,
year = {2020},
author = {Narasimhan, M and Johnson, A and Prizak, R and Kaufmann, WA and Tan, S and Casillas-Pérez, B and Friml, J},
title = {Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
doi = {10.7554/eLife.52067},
pmid = {31971511},
issn = {2050-084X},
support = {742985//H2020 European Research Council/ ; I3630B25//Austrian Science Fund/ ; ALTF 723-2015//European Molecular Biology Organization/ ; },
abstract = {In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the surface but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes.},
}

@article {pmid31965986,
year = {2020},
author = {Reddy, PC and Pradhan, SJ and Karmodiya, K and Galande, S},
title = {Origin of RNA Polymerase II pause in eumetazoans: Insights from Hydra.},
journal = {Journal of biosciences},
volume = {45},
number = {},
pages = {},
pmid = {31965986},
issn = {0973-7138},
abstract = {Multicellular organisms have evolved sophisticated mechanisms for responding to various developmental, environmental and physical stimuli by regulating transcription. The correlation of distribution of RNA Polymerase II (RNA Pol II) with transcription is well established in higher metazoans, however genome-wide information about its distribution in early metazoans, such as Hydra, is virtually absent. To gain insights into RNA Pol II-mediated transcription and chromatin organization in Hydra, we performed chromatin immunoprecipitation (ChIP)-coupled high-throughput sequencing (ChIP-seq) for RNA Pol II and Histone H3. Strikingly, we found that Hydra RNA Pol II is uniformly distributed across the entire gene body, as opposed to its counterparts in bilaterians such as human and mouse. Furthermore, correlation with transcriptome data revealed that the levels of RNA Pol II correlate with the magnitude of gene expression. Strikingly, the characteristic peak of RNA Pol II pause typically observed in bilaterians at the transcription start sites (TSSs) was not observed in Hydra. The RNA Pol II traversing ratio in Hydra was found to be intermediate to yeast and bilaterians. The search for factors involved in RNA Pol II pause revealed that RNA Pol II pausing machinery was most likely acquired first in Cnidaria. However, only a small subset of genes exhibited the promoter proximal RNP Pol II pause. Interestingly, the nucleosome occupancy is highest over the subset of paused genes as compared to total Hydra genes, which is another indication of paused RNA Pol II at these genes. Thus, this study provides evidence for the molecular basis of RNA Pol II pause early during the evolution of multicellular organisms.},
}

@article {pmid31959809,
year = {2020},
author = {Oña, L and Lachmann, M},
title = {Signalling architectures can prevent cancer evolution.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {674},
pmid = {31959809},
issn = {2045-2322},
abstract = {Cooperation between cells in multicellular organisms is preserved by an active regulation of growth through the control of cell division. Molecular signals used by cells for tissue growth are usually present during developmental stages, angiogenesis, wound healing and other processes. In this context, the use of molecular signals triggering cell division is a puzzle, because any molecule inducing and aiding growth can be exploited by a cancer cell, disrupting cellular cooperation. A significant difference is that normal cells in a multicellular organism have evolved in competition between high-level organisms to be altruistic, being able to send signals even if it is to their detriment. Conversely, cancer cells evolve their abuse over the cancer's lifespan by out-competing their neighbours. A successful mutation leading to cancer must evolve to be adaptive, enabling a cancer cell to send a signal that results in higher chances to be selected. Using a mathematical model of such molecular signalling mechanism, this paper argues that a signal mechanism would be effective against abuse by cancer if it affects the cell that generates the signal as well as neighbouring cells that would receive a benefit without any cost, resulting in a selective disadvantage for a cancer signalling cell. We find that such molecular signalling mechanisms normally operate in cells as exemplified by growth factors. In scenarios of global and local competition between cells, we calculate how this process affects the fixation probability of a mutant cell generating such a signal, and find that this process can play a key role in limiting the emergence of cancer.},
}

@article {pmid31956023,
year = {2020},
author = {Bowles, AMC and Bechtold, U and Paps, J},
title = {The Origin of Land Plants Is Rooted in Two Bursts of Genomic Novelty.},
journal = {Current biology : CB},
volume = {30},
number = {3},
pages = {530-536.e2},
doi = {10.1016/j.cub.2019.11.090},
pmid = {31956023},
issn = {1879-0445},
abstract = {Over the last 470 Ma, plant evolution has seen major evolutionary transitions, such as the move from water to land and the origins of vascular tissues, seeds, and flowers [1]. These have resulted in the evolution of terrestrial flora that has shaped modern ecosystems and the diversification of the Plant Kingdom, Viridiplantae, into over 374,000 described species [2]. Each of these transitions was accompanied by the gain and loss of genes in plant genomes. For example, whole-genome duplications are known to be fundamental to the origins of both seed and flowering plants [3, 4]. With the ever-increasing quality and quantity of whole-genome data, evolutionary insight into origins of distinct plant groups using comparative genomic techniques is now feasible. Here, using an evolutionary genomics pipeline to compare 208 complete genomes, we analyze the gene content of the ancestral genomes of the last common ancestor of land plants and all other major groups of plant. This approach reveals an unprecedented level of fundamental genomic novelties in two nodes related to the origin of land plants: the first in the origin of streptophytes during the Ediacaran and another in the ancestor of land plants in the Ordovician. Our findings highlight the biological processes that evolved with the origin of land plants and emphasize the importance of conserved gene novelties in plant diversification. Comparisons to other eukaryotic studies suggest a separation of the genomic origins of multicellularity and terrestrialization in plants.},
}

@article {pmid31942240,
year = {2019},
author = {Green, KJ and Jaiganesh, A and Broussard, JA},
title = {Desmosomes: Essential contributors to an integrated intercellular junction network.},
journal = {F1000Research},
volume = {8},
number = {},
pages = {},
pmid = {31942240},
issn = {2046-1402},
abstract = {The development of adhesive connections between cells was critical for the evolution of multicellularity and for organizing cells into complex organs with discrete compartments. Four types of intercellular junction are present in vertebrates: desmosomes, adherens junctions, tight junctions, and gap junctions. All are essential for the development of the embryonic layers and organs as well as adult tissue homeostasis. While each junction type is defined as a distinct entity, it is now clear that they cooperate physically and functionally to create a robust and functionally diverse system. During evolution, desmosomes first appeared in vertebrates as highly specialized regions at the plasma membrane that couple the intermediate filament cytoskeleton at points of strong cell-cell adhesion. Here, we review how desmosomes conferred new mechanical and signaling properties to vertebrate cells and tissues through their interactions with the existing junctional and cytoskeletal network.},
}

@article {pmid31932592,
year = {2020},
author = {Li, Q and Li, S and Zhang, X and Xu, W and Han, X},
title = {Programmed magnetic manipulation of vesicles into spatially coded prototissue architectures arrays.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {232},
pmid = {31932592},
issn = {2041-1723},
support = {21773050//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {In nature, cells self-assemble into spatially coded tissular configurations to execute higher-order biological functions as a collective. This mechanism has stimulated the recent trend in synthetic biology to construct tissue-like assemblies from protocell entities, with the aim to understand the evolution mechanism of multicellular mechanisms, create smart materials or devices, and engineer tissue-like biomedical implant. However, the formation of spatially coded and communicating micro-architectures from large quantity of protocell entities, especially for lipid vesicle-based systems that mostly resemble cells, is still challenging. Herein, we magnetically assemble giant unilamellar vesicles (GUVs) or cells into various microstructures with spatially coded configurations and spatialized cascade biochemical reactions using a stainless steel mesh. GUVs in these tissue-like aggregates exhibit uncustomary osmotic stability that cannot be achieved by individual GUVs suspensions. This work provides a versatile and cost-effective strategy to form robust tissue-mimics and indicates a possible superiority of protocell colonies to individual protocells.},
}

@article {pmid31928871,
year = {2020},
author = {Miller, SR and Longley, R and Hutchins, PR and Bauersachs, T},
title = {Cellular Innovation of the Cyanobacterial Heterocyst by the Adaptive Loss of Plasticity.},
journal = {Current biology : CB},
volume = {30},
number = {2},
pages = {344-350.e4},
doi = {10.1016/j.cub.2019.11.056},
pmid = {31928871},
issn = {1879-0445},
abstract = {Cellular innovation is central to biological diversification, yet its underlying mechanisms remain poorly understood [1]. One potential source of new cellular traits is environmentally induced phenotypic variation, or phenotypic plasticity. The plasticity-first hypothesis [2-4] proposes that natural selection can improve upon an ancestrally plastic phenotype to produce a locally adaptive trait, but the role of plasticity for adaptive evolution is still unclear [5-10]. Here, we show that a structurally novel form of the heterocyst, the specialized nitrogen-fixing cell of the multicellular cyanobacterium Fischerella thermalis, has evolved multiple times from ancestrally plastic developmental variation during adaptation to high temperature. Heterocyst glycolipids (HGs) provide an extracellular gas diffusion barrier that protects oxygen-sensitive nitrogenase [11, 12], and cyanobacteria typically exhibit temperature-induced plasticity in HG composition that modulates heterocyst permeability [13, 14]. By contrast, high-temperature specialists of F. thermalis constitutively overproduce glycolipid isomers associated with high temperature to levels unattained by plastic strains. This results in a less-permeable heterocyst, which is advantageous at high temperature but deleterious at low temperature for both nitrogen fixation activity and fitness. Our study illustrates how the origin of a novel cellular phenotype by the genetic assimilation and adaptive refinement of a plastic trait can be a source of biological diversity and contribute to ecological specialization.},
}

@article {pmid31925005,
year = {2019},
author = {Erkenbrack, EM and Thompson, JR},
title = {Cell type phylogenetics informs the evolutionary origin of echinoderm larval skeletogenic cell identity.},
journal = {Communications biology},
volume = {2},
number = {1},
pages = {160},
doi = {10.1038/s42003-019-0417-3},
pmid = {31925005},
issn = {2399-3642},
abstract = {The multiplicity of cell types comprising multicellular organisms begs the question as to how cell type identities evolve over time. Cell type phylogenetics informs this question by comparing gene expression of homologous cell types in distantly related taxa. We employ this approach to inform the identity of larval skeletogenic cells of echinoderms, a clade for which there are phylogenetically diverse datasets of spatial gene expression patterns. We determined ancestral spatial expression patterns of alx1, ets1, tbr, erg, and vegfr, key components of the skeletogenic gene regulatory network driving identity of the larval skeletogenic cell. Here we show ancestral state reconstructions of spatial gene expression of extant eleutherozoan echinoderms support homology and common ancestry of echinoderm larval skeletogenic cells. We propose larval skeletogenic cells arose in the stem lineage of eleutherozoans during a cell type duplication event that heterochronically activated adult skeletogenic cells in a topographically distinct tissue in early development.},
}

@article {pmid31921561,
year = {2020},
author = {Liang, Z and Geng, Y and Ji, C and Du, H and Wong, CE and Zhang, Q and Zhang, Y and Zhang, P and Riaz, A and Chachar, S and Ding, Y and Wen, J and Wu, Y and Wang, M and Zheng, H and Wu, Y and Demko, V and Shen, L and Han, X and Zhang, P and Gu, X and Yu, H},
title = {Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {7},
number = {1},
pages = {1901850},
pmid = {31921561},
issn = {2198-3844},
abstract = {The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants is a major evolutionary event that has transformed the planet. So far, lack of genome information on unicellular charophyte algae hinders the understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta. This work reports the high-quality reference genome and transcriptome of Mesostigma viride, a single-celled charophyte alga with a position at the base of Streptophyta. There are abundant segmental duplications and transposable elements in M. viride, which contribute to a relatively large genome with high gene content compared to other algae and early diverging land plants. This work identifies the origin of genetic tools that multicellular Streptophyta have inherited and key genetic innovations required for the evolution of land plants from unicellular aquatic ancestors. The findings shed light on the age-old questions of the evolution of multicellularity and the origin of land plants.},
}

@article {pmid31920779,
year = {2019},
author = {Levin, M},
title = {The Computational Boundary of a "Self": Developmental Bioelectricity Drives Multicellularity and Scale-Free Cognition.},
journal = {Frontiers in psychology},
volume = {10},
number = {},
pages = {2688},
pmid = {31920779},
issn = {1664-1078},
abstract = {All epistemic agents physically consist of parts that must somehow comprise an integrated cognitive self. Biological individuals consist of subunits (organs, cells, and molecular networks) that are themselves complex and competent in their own native contexts. How do coherent biological Individuals result from the activity of smaller sub-agents? To understand the evolution and function of metazoan creatures' bodies and minds, it is essential to conceptually explore the origin of multicellularity and the scaling of the basal cognition of individual cells into a coherent larger organism. In this article, I synthesize ideas in cognitive science, evolutionary biology, and developmental physiology toward a hypothesis about the origin of Individuality: "Scale-Free Cognition." I propose a fundamental definition of an Individual based on the ability to pursue goals at an appropriate level of scale and organization and suggest a formalism for defining and comparing the cognitive capacities of highly diverse types of agents. Any Self is demarcated by a computational surface - the spatio-temporal boundary of events that it can measure, model, and try to affect. This surface sets a functional boundary - a cognitive "light cone" which defines the scale and limits of its cognition. I hypothesize that higher level goal-directed activity and agency, resulting in larger cognitive boundaries, evolve from the primal homeostatic drive of living things to reduce stress - the difference between current conditions and life-optimal conditions. The mechanisms of developmental bioelectricity - the ability of all cells to form electrical networks that process information - suggest a plausible set of gradual evolutionary steps that naturally lead from physiological homeostasis in single cells to memory, prediction, and ultimately complex cognitive agents, via scale-up of the basic drive of infotaxis. Recent data on the molecular mechanisms of pre-neural bioelectricity suggest a model of how increasingly sophisticated cognitive functions emerge smoothly from cell-cell communication used to guide embryogenesis and regeneration. This set of hypotheses provides a novel perspective on numerous phenomena, such as cancer, and makes several unique, testable predictions for interdisciplinary research that have implications not only for evolutionary developmental biology but also for biomedicine and perhaps artificial intelligence and exobiology.},
}

@article {pmid31911467,
year = {2020},
author = {Del Cortona, A and Jackson, CJ and Bucchini, F and Van Bel, M and D'hondt, S and Škaloud, P and Delwiche, CF and Knoll, AH and Raven, JA and Verbruggen, H and Vandepoele, K and De Clerck, O and Leliaert, F},
title = {Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {5},
pages = {2551-2559},
doi = {10.1073/pnas.1910060117},
pmid = {31911467},
issn = {1091-6490},
abstract = {The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified in benthic environments that became increasingly available as ice retreated. An increased supply of nutrients and biotic interactions, such as grazing pressure, likely triggered the independent evolution of macroscopic growth via different strategies, including true multicellularity, and multiple types of giant-celled forms.},
}

@article {pmid31883344,
year = {2019},
author = {Milocco, L and Salazar-Ciudad, I},
title = {Is evolution predictable? Quantitative genetics under complex genotype-phenotype maps.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1111/evo.13907},
pmid = {31883344},
issn = {1558-5646},
support = {PGC2018-096802-B-I00//Ministerio de Ciencia, Innovación y Universidades/ ; //Suomalainen Tiedeakatemia/ ; },
abstract = {A fundamental aim of post-genomic 21st century biology is to understand the genotype-phenotype map (GPM) or how specific genetic variation relates to specific phenotypic variation. Quantitative genetics approximates such maps using linear models, and has developed methods to predict the response to selection in a population. The other major field of research concerned with the GPM, developmental evolutionary biology, or evo-devo, has found the GPM to be highly nonlinear and complex. Here, we quantify how the predictions of quantitative genetics are affected by a complex, nonlinear map based on the development of a multicellular organ. We compared the predicted change in mean phenotype for a single generation using the multivariate breeder's equation, with the change observed from the model of development. We found that there are frequent disagreements between predicted and observed responses to selection due to the nonlinear nature of the genotype-phenotype map. Our results are a step toward integrating the fields studying the GPM.},
}

@article {pmid31880593,
year = {2019},
author = {Wang, DG and Huang, FR and Chen, W and Zhou, Y and Wang, CY and Zhu, F and Shao, BJ and Luo, D},
title = {Clinicopathological Analysis of Acquired Melanocytic Nevi and a Preliminary Study on the Possible Origin of Nevus Cells.},
journal = {The American Journal of dermatopathology},
volume = {},
number = {},
pages = {},
doi = {10.1097/DAD.0000000000001599},
pmid = {31880593},
issn = {1533-0311},
abstract = {BACKGROUND: The pathogenesis of acquired melanocytic nevi (AMN) is still unclear, and the origin of nevus cells has not been clarified.

OBJECTIVE: To analyze the clinical features and pathological types of AMN and identify the possible origin of nevus cells.

METHODS: A retrospective study of 2929 cases of AMN was conducted, and 96 specimens of intradermal and junctional nevi were selected. Immunohistochemical assays were performed to detect the expression of basement membrane component receptor DDR-1 and the molecular markers on epidermal melanocytes, dermal stem cells (DSCs), and hair follicle stem cells.

RESULTS: Junctional nevi and compound nevi were prone to occur on glabrous skin, such as the palms, soles, and vulva, and on the extremities in children, whereas intradermal nevi tended to develop on the trunk, head, and face of adults. The immunohistochemical data revealed that both junctional nevi and intradermal nevi expressed the epidermal melanocyte surface markers E-cadherin, DDR-1, and integrin α6 and the DSC molecular markers NGFRp-75 and nestin. CD34 was expressed only in junctional nevi, whereas K19 was not expressed in any type of melanocytic nevi. There was no significant difference in molecular expression at different sites or in different ages of onset. Nestin expression was markedly stronger in the intradermal nevi than in the junctional nevi, but there was no difference between the superficial and deep nevus cell nests of intradermal nevi.

CONCLUSION: AMN may have a multicellular origin that commonly follows the mode of Abtropfung. Furthermore, DSCs may partly or independently participate in the formation of nevus cells.},
}

@article {pmid31879283,
year = {2019},
author = {Erives, A and Fritzsch, B},
title = {A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1534/g3.119.400951},
pmid = {31879283},
issn = {2160-1836},
abstract = {The evolutionary diversification of animals is one of Earth's greatest marvels, yet its earliest steps are shrouded in mystery. Animals, the monophyletic clade known as Metazoa, evolved wildly divergent multicellular life strategies featuring ciliated sensory epithelia. In many lineages epithelial sensoria became coupled to increasingly complex nervous systems. Currently, different phylogenetic analyses of single-copy genes support mutually-exclusive possibilities that either Porifera or Ctenophora is sister to all other animals. Resolving this dilemma would advance the ecological and evolutionary understanding of the first animals and the evolution of nervous systems. Here we describe a comparative phylogenetic approach based on gene duplications. We computationally identify and analyze gene families with early metazoan duplications using an approach that mitigates apparent gene loss resulting from the miscalling of paralogs. In the transmembrane channel-like (TMC) family of mechano-transducing channels, we find ancient duplications that define separate clades for Eumetazoa (Placozoa + Cnidaria + Bilateria) versus Ctenophora, and one duplication that is shared only by Eumetazoa and Porifera. In the Max-like protein X (MLX and MLXIP) family of bHLH-ZIP regulators of metabolism, we find that all major lineages from Eumetazoa and Porifera (sponges) share a duplicated gene pair that is sister to the single-copy gene maintained in Ctenophora. These results suggest a new avenue for deducing deep phylogeny by choosing rather than avoiding ancient gene paralogies.},
}

@article {pmid31866780,
year = {2019},
author = {Durand, PM and Barreto Filho, MM and Michod, RE},
title = {Cell Death in Evolutionary Transitions in Individuality.},
journal = {The Yale journal of biology and medicine},
volume = {92},
number = {4},
pages = {651-662},
pmid = {31866780},
issn = {1551-4056},
abstract = {Programmed cell death (PCD) in cell groups and microbial communities affects population structures, nutrient recycling, and sociobiological interactions. A less explored area is the role played by PCD in the emergence of higher-level individuals. Here, we examine how cell death impacted evolutionary transitions in individuality (ETIs). The focus is on three specific ETIs - the emergence of the eukaryote cell, multicellularity, and social insects - and we review the theoretical and empirical evidence for the role of PCD in these three transitions. We find that PCD likely contributed to many of the processes involved in eukaryogenesis and the transition to multicellularity. PCD is important for the formation of cooperative groups and is a mechanism by which mutual dependencies between individuals evolve. PCD is also a conflict mediator and involved in division of labor in social groups and in the origin of new cell types. In multicellularity, PCD facilitates the transfer of fitness to the higher-level individual. In eusocial insects, PCD of the gonadal cells in workers is the basis for conflict mediation and the division of labor in the colony. In the three ETIs discussed here, PCD likely played an essential role, without which alternate mechanisms would have been necessary for these increases in complexity to occur.},
}

@article {pmid31855240,
year = {2019},
author = {Pan, H and Dong, Y and Teng, Z and Li, J and Zhang, W and Xiao, T and Wu, LF},
title = {A species of magnetotactic deltaproteobacterium was detected at the highest abundance during an algal bloom.},
journal = {FEMS microbiology letters},
volume = {366},
number = {22},
pages = {},
doi = {10.1093/femsle/fnz253},
pmid = {31855240},
issn = {1574-6968},
abstract = {Magnetotactic bacteria (MTB) are a group of microorganisms that have the ability to synthesize intracellular magnetic crystals (magnetosomes). They prefer microaerobic or anaerobic aquatic sediments. Thus, there is growing interest in their ecological roles in various habitats. In this study we found co-occurrence of a large rod-shaped deltaproteobacterial magnetotactic bacterium (tentatively named LR-1) in the sediment of a brackish lagoon with algal bloom. Electron microscopy observations showed that they were ovoid to slightly curved rods having a mean length of 6.3 ± 1.1 μm and a mean width of 4.1 ± 0.4 μm. Each cell had a single polar flagellum. They contained hundreds of bullet-shaped intracellular magnetite magnetosomes. Phylogenetic analysis revealed that they were most closely related to Desulfamplus magnetovallimortis strain BW-1, and belonged to the Deltaproteobacteria. Our findings indicate that LR-1 may be a new species of MTB. We propose that deltaproteobacterial MTB may play an important role in iron cycling and so may represent a reservoir of iron, and be an indicator species for monitoring algal blooms in such eutrophic ecosystems. These observations provide new clues to the cultivation of magnetotactic Deltaproteobacteria and the control of algal blooms, although further studies are needed.},
}

@article {pmid31854473,
year = {2020},
author = {Costa, ML and de Andrade Rosa, I and Andrade, L and Mermelstein, C and C Coutinho, C},
title = {Distinct interactions between epithelial and mesenchymal cells control cell morphology and collective migration during sponge epithelial to mesenchymal transition.},
journal = {Journal of morphology},
volume = {281},
number = {2},
pages = {183-195},
doi = {10.1002/jmor.21090},
pmid = {31854473},
issn = {1097-4687},
support = {//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; },
abstract = {Epithelial and mesenchymal cell types are basic for animal multicellularity and they have complementary functions coordinated by cellular interactions. Sponges are especially important model organisms to address the evolutionary basis of morphogenetic programs for epithelial and mesenchymal organization in animals. Evolutionary studies in sponges can contribute to the understanding of the mechanisms that control tissue maintenance and tumor progression in humans. In the present study, sponge mesenchymal and epithelial cells were isolated from the demosponge Hymeniacidon heliophila, and aggregate formation was observed by video microscopy. Epithelial-mesenchymal interaction, epithelial transition, and cell migration led to sponge cell aggregation after drastic stress. Based on their different morphologies, adhesion specificities, and motilities, we suggest a role for different sponge cell types as well as complementary functions in cell aggregation. Micromanipulation under the microscope and cell tracking were also used to promote specific grafting-host interaction, to further test the effects of cell type interaction. The loss of cell polarity and flattened shape during the epithelial to mesenchymal cell transition generated small immobile aggregates of round/amoeboid cells. The motility of these transited epithelial-cell aggregates was observed by cell tracking using fluorescent dye, but only after interaction with streams of migratory mesenchymal cells. Cell motility occurred independently of morphological changes, indicating a progressive step in the transition toward a migratory mesenchymal state. Our data suggest a two-step signaling process: (a) the lack of interaction between mesenchymal and epithelial cells triggers morphological changes; and (b) migratory mesenchymal cells instruct epithelial cells for directional cell motility. These results could have an impact on the understanding of evolutionary aspects of metastatic cancer cells. HIGHLIGHTS: Morphogenetic movements observed in modern sponges could have a common evolutionary origin with collective cell migration of human metastatic cells. A sponge regenerative model was used here to characterize epithelial and mesenchymal cells, and for the promotion of grafting/host interactions with subsequent cell tracking. The transition from epithelial to mesenchymal cell type can be observed in sponges in two steps: (a) withdrawal of epithelial/mesenchymal cell interactions to trigger morphological changes; (b) migratory mesenchymal cells to induce epithelial cells to a collective migratory state.},
}

@article {pmid31847093,
year = {2019},
author = {Nakamura, T and Fahmi, M and Tanaka, J and Seki, K and Kubota, Y and Ito, M},
title = {Genome-Wide Analysis of Whole Human Glycoside Hydrolases by Data-Driven Analysis in Silico.},
journal = {International journal of molecular sciences},
volume = {20},
number = {24},
pages = {},
pmid = {31847093},
issn = {1422-0067},
support = {NA//MEXT-Supported Program for the Strategic Research Foundation at Private Universities (2015-2019)/ ; NA//Takeda Science Foundation/ ; },
abstract = {Glycans are involved in various metabolic processes via the functions of glycosyltransferases and glycoside hydrolases. Analysing the evolution of these enzymes is essential for improving the understanding of glycan metabolism and function. Based on our previous study of glycosyltransferases, we performed a genome-wide analysis of whole human glycoside hydrolases using the UniProt, BRENDA, CAZy and KEGG databases. Using cluster analysis, 319 human glycoside hydrolases were classified into four clusters based on their similarity to enzymes conserved in chordates or metazoans (Class 1), metazoans (Class 2), metazoans and plants (Class 3) and eukaryotes (Class 4). The eukaryote and metazoan clusters included N- and O-glycoside hydrolases, respectively. The significant abundance of disordered regions within the most conserved cluster indicated a role for disordered regions in the evolution of glycoside hydrolases. These results suggest that the biological diversity of multicellular organisms is related to the acquisition of N- and O-linked glycans.},
}

@article {pmid31845961,
year = {2019},
author = {Majic, P and Payne, JL},
title = {Enhancers facilitate the birth of de novo genes and gene integration into regulatory networks.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz300},
pmid = {31845961},
issn = {1537-1719},
abstract = {Regulatory networks control the spatiotemporal gene expression patterns that give rise to and define the individual cell types of multicellular organisms. In eumetazoa, distal regulatory elements called enhancers play a key role in determining the structure of such networks, particularly the wiring diagram of "who regulates whom." Mutations that affect enhancer activity can therefore rewire regulatory networks, potentially causing adaptive changes in gene expression. Here, we use whole-tissue and single-cell transcriptomic and chromatin accessibility data from mouse to show that enhancers play an additional role in the evolution of regulatory networks: They facilitate network growth by creating transcriptionally active regions of open chromatin that are conducive to de novo gene evolution. Specifically, our comparative transcriptomic analysis with three other mammalian species shows that young, mouse-specific intergenic open reading frames are preferentially located near enhancers, whereas older open reading frames are not. Mouse-specific intergenic open reading frames that are proximal to enhancers are more highly and stably transcribed than those that are not proximal to enhancers or promoters, and they are transcribed in a limited diversity of cellular contexts. Furthermore, we report several instances of mouse-specific intergenic open reading frames proximal to promoters showing evidence of being repurposed enhancers. We also show that open reading frames gradually acquire interactions with enhancers over macro-evolutionary timescales, helping integrate genes - those that have arisen de novo or by other means - into existing regulatory networks. Taken together, our results highlight a dual role of enhancers in expanding and rewiring gene regulatory networks.},
}

@article {pmid31841515,
year = {2019},
author = {Lamelza, P and Young, JM and Noble, LM and Caro, L and Isakharov, A and Palanisamy, M and Rockman, MV and Malik, HS and Ailion, M},
title = {Hybridization promotes asexual reproduction in Caenorhabditis nematodes.},
journal = {PLoS genetics},
volume = {15},
number = {12},
pages = {e1008520},
pmid = {31841515},
issn = {1553-7404},
abstract = {Although most unicellular organisms reproduce asexually, most multicellular eukaryotes are obligately sexual. This implies that there are strong barriers that prevent the origin or maintenance of asexuality arising from an obligately sexual ancestor. By studying rare asexual animal species we can gain a better understanding of the circumstances that facilitate their evolution from a sexual ancestor. Of the known asexual animal species, many originated by hybridization between two ancestral sexual species. The balance hypothesis predicts that genetic incompatibilities between the divergent genomes in hybrids can modify meiosis and facilitate asexual reproduction, but there are few instances where this has been shown. Here we report that hybridizing two sexual Caenorhabditis nematode species (C. nouraguensis females and C. becei males) alters the normal inheritance of the maternal and paternal genomes during the formation of hybrid zygotes. Most offspring of this interspecies cross die during embryogenesis, exhibiting inheritance of a diploid C. nouraguensis maternal genome and incomplete inheritance of C. becei paternal DNA. However, a small fraction of offspring develop into viable adults that can be either fertile or sterile. Fertile offspring are produced asexually by sperm-dependent parthenogenesis (also called gynogenesis or pseudogamy); these progeny inherit a diploid maternal genome but fail to inherit a paternal genome. Sterile offspring are hybrids that inherit both a diploid maternal genome and a haploid paternal genome. Whole-genome sequencing of individual viable worms shows that diploid maternal inheritance in both fertile and sterile offspring results from an altered meiosis in C. nouraguensis oocytes and the inheritance of two randomly selected homologous chromatids. We hypothesize that hybrid incompatibility between C. nouraguensis and C. becei modifies maternal and paternal genome inheritance and indirectly induces gynogenetic reproduction. This system can be used to dissect the molecular mechanisms by which hybrid incompatibilities can facilitate the emergence of asexual reproduction.},
}

@article {pmid31841362,
year = {2019},
author = {Damer, B and Deamer, D},
title = {The Hot Spring Hypothesis for an Origin of Life.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ast.2019.2045},
pmid = {31841362},
issn = {1557-8070},
abstract = {We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first microbial communities. Laboratory and field experiments testing the first steps of the scenario are summarized. The scenario is then placed in a geological setting on the early Earth to suggest a plausible pathway from life's origin in chemically optimal freshwater hot spring pools to the emergence of microbial communities tolerant to more extreme conditions in dilute lakes and salty conditions in marine environments. A continuity is observed for biogenesis beginning with simple protocell aggregates, through the transitional form of the progenote, to robust microbial mats that leave the fossil imprints of stromatolites so representative in the rock record. A roadmap to future testing of the hypothesis is presented. We compare the oceanic vent with land-based pool scenarios for an origin of life and explore their implications for subsequent evolution to multicellular life such as plants. We conclude by utilizing the hypothesis to posit where life might also have emerged in habitats such as Mars or Saturn's icy moon Enceladus. "To postulate one fortuitously catalyzed reaction, perhaps catalyzed by a metal ion, might be reasonable, but to postulate a suite of them is to appeal to magic." -Leslie Orgel.},
}

@article {pmid31840777,
year = {2019},
author = {Kundert, P and Shaulsky, G},
title = {Cellular allorecognition and its roles in Dictyostelium development and social evolution.},
journal = {The International journal of developmental biology},
volume = {63},
number = {8-9-10},
pages = {383-393},
pmid = {31840777},
issn = {1696-3547},
support = {R35 GM118016/GM/NIGMS NIH HHS/United States ; },
abstract = {The social amoeba Dictyostelium discoideum is a tractable model organism to study cellular allorecognition, which is the ability of a cell to distinguish itself and its genetically similar relatives from more distantly related organisms. Cellular allorecognition is ubiquitous across the tree of life and affects many biological processes. Depending on the biological context, these versatile systems operate both within and between individual organisms, and both promote and constrain functional heterogeneity. Some of the most notable allorecognition systems mediate neural self-avoidance in flies and adaptive immunity in vertebrates. D. discoideum's allorecognition system shares several structures and functions with other allorecognition systems. Structurally, its key regulators reside at a single genomic locus that encodes two highly polymorphic proteins, a transmembrane ligand called TgrC1 and its receptor TgrB1. These proteins exhibit isoform-specific, heterophilic binding across cells. Functionally, this interaction determines the extent to which co-developing D. discoideum strains co-aggregate or segregate during the aggregation phase of multicellular development. The allorecognition system thus affects both development and social evolution, as available evidence suggests that the threat of developmental cheating represents a primary selective force acting on it. Other significant characteristics that may inform the study of allorecognition in general include that D. discoideum's allorecognition system is a continuous and inclusive trait, it is pleiotropic, and it is temporally regulated.},
}

@article {pmid31840776,
year = {2019},
author = {Medina, JM and Shreenidhi, PM and Larsen, TJ and Queller, DC and Strassmann, JE},
title = {Cooperation and conflict in the social amoeba Dictyostelium discoideum.},
journal = {The International journal of developmental biology},
volume = {63},
number = {8-9-10},
pages = {371-382},
doi = {10.1387/ijdb.190158jm},
pmid = {31840776},
issn = {1696-3547},
abstract = {The social amoeba Dictyostelium discoideum has provided considerable insight into the evolution of cooperation and conflict. Under starvation, D. discoideum amoebas cooperate to form a fruiting body comprised of hardy spores atop a stalk. The stalk development is altruistic because stalk cells die to aid spore dispersal. The high relatedness of cells in fruiting bodies in nature implies that this altruism often benefits relatives. However, since the fruiting body forms through aggregation there is potential for non-relatives to join the aggregate and create conflict over spore and stalk fates. Cheating is common in chimeras of social amoebas, where one genotype often takes advantage of the other and makes more spores. This social conflict is a significant force in nature as indicated by rapid rates of adaptive evolution in genes involved in cheating and its resistance. However, cheating can be prevented by high relatedness, allorecognition via tgr genes, pleiotropy and evolved resistance. Future avenues for the study of cooperation and conflict in D. discoideum include the sexual cycle as well as the relationship between D. discoideum and its bacterial symbionts. D. discoideum's tractability in the laboratory as well as its uncommon mode of aggregative multicellularity have established it as a promising model for future studies of cooperation and conflict.},
}

@article {pmid31840775,
year = {2019},
author = {Kawabe, Y and Du, Q and Schilde, C and Schaap, P},
title = {Evolution of multicellularity in Dictyostelia.},
journal = {The International journal of developmental biology},
volume = {63},
number = {8-9-10},
pages = {359-369},
pmid = {31840775},
issn = {1696-3547},
abstract = {The well-orchestrated multicellular life cycle of Dictyostelium discoideum has fascinated biologists for over a century. Self-organisation of its amoebas into aggregates, migrating slugs and fruiting structures by pulsatile cAMP signalling and their ability to follow separate differentiation pathways in well-regulated proportions continue to be topics under investigation. A striking aspect of D. discoideum development is the recurrent use of cAMP as chemoattractant, differentiation inducing signal and second messenger for other signals that control the developmental programme. D. discoideum is one of >150 species of Dictyostelia and aggregative life styles similar to those of Dictyostelia evolved many times in eukaryotes. Here we review experimental studies investigating how phenotypic complexity and cAMP signalling co-evolved in Dictyostelia. In addition, we summarize comparative genomic studies of multicellular Dictyostelia and unicellular Amoebozoa aimed to identify evolutionary conservation and change in all genes known to be essential for D. discoideum development.},
}

@article {pmid31830880,
year = {2019},
author = {Heredia-Soto, V and Redondo, A and Kreilinger, JJP and Martínez-Marín, V and Berjón, A and Mendiola, M},
title = {3D culture modelling: An emerging approach for Translational Cancer Research in Sarcomas.},
journal = {Current medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0929867326666191212162102},
pmid = {31830880},
issn = {1875-533X},
abstract = {Sarcomas are tumours of mesenchymal origin, which can arise in bone or soft tissues. They are rare but frequently quite aggressive and with a poor outcome. New approaches are needed to characterise these tumours and their resistance mechanisms to current therapies, responsible for tumour recurrence and treatment failure. This review is focused on the potential of three-dimensional (3D) in vitro models, including multicellular tumour spheroids (MCTS) and organoids, and the latest data about their utility for the study of important properties for tumour development. We also discuss the use of spheroids as a particularly valuable alternative for compound high throughput screening (HTS) in different areas of cancer biology, which enable the identification of new therapeutic opportunities in commonly resistant tumours.},
}

@article {pmid31829529,
year = {2020},
author = {Rivera-Yoshida, N and Hernández-Terán, A and Escalante, AE and Benítez, M},
title = {Laboratory biases hinder Eco-Evo-Devo integration: Hints from the microbial world.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {334},
number = {1},
pages = {14-24},
doi = {10.1002/jez.b.22917},
pmid = {31829529},
issn = {1552-5015},
abstract = {How specific environmental contexts contribute to the robustness and variation of developmental trajectories and evolutionary transitions is a central point in Ecological Evolutionary Developmental Biology ("Eco-Evo-Devo"). However, the articulation of ecological, evolutionary and developmental processes into integrative frameworks has been elusive, partly because standard experimental designs neglect or oversimplify ecologically meaningful contexts. Microbial models are useful to expose and discuss two possible sources of bias associated with conventional gene-centered experimental designs: the use of laboratory strains and standard laboratory environmental conditions. We illustrate our point by showing how contrasting developmental phenotypes in Myxococcus xanthus depend on the joint variation of temperature and substrate stiffness. Microorganismal development can provide key information for better understanding the role of environmental conditions in the evolution of developmental variation, and to overcome some of the limitations associated with current experimental approaches.},
}

@article {pmid31819969,
year = {2019},
author = {Niklas, KJ and Newman, SA},
title = {The Many Roads To (and From) Multicellularity.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erz547},
pmid = {31819969},
issn = {1460-2431},
abstract = {The multiple origins of multicellularity had far-reaching consequences ranging from the appearance of phenotypically complex life-forms to their effects on Earth's aquatic and terrestrial ecosystems. Yet, many important but as yet unanswered questions remain. For example, do all lineages and clades share an ancestral developmental predisposition for multicellularity emerging from genomic and biophysical motifs shared from a last common ancestor, or are the multiple origins of multicellularity truly independent evolutionary events? In this review, we highlight recent developments and pitfalls in understanding the evolution of multicellularity with an emphasis on plants (here, defined broadly as "plants" to include the polyphyletic algae), but also draw upon insights from animals and their holozoan relatives, fungi and amoebozoans. Based on our review, we conclude that the evolution of multicellular organisms requires three phases (origination by disparate cell-cell attachment modalities, followed by integration by lineage-specific physiological mechanisms, and autonomization by natural selection) that they have been achieved differently in different lineages.},
}

@article {pmid31818848,
year = {2019},
author = {Lee, MF and Trotman, LC},
title = {PTEN: Bridging Endocytosis and Signaling.},
journal = {Cold Spring Harbor perspectives in medicine},
volume = {},
number = {},
pages = {},
doi = {10.1101/cshperspect.a036103},
pmid = {31818848},
issn = {2157-1422},
abstract = {The transduction of signals in the PTEN/PI3-kinase (PI3K) pathway is built around a phosphoinositide (PIP) lipid messenger, phosphatidylinositol trisphosphate, PI(3,4,5)P3 or PIP3 Another, more ancient role of this family of messengers is the control of endocytosis, where a handful of separate PIPs act like postal codes. Prominent among them is PI(3)P, which helps to ensure that endocytic vesicles, their cargo, and membranes themselves reach their correct destinations. Traditionally, the cancer and the endocytic functions of the PI3K signaling pathway have been studied by cancer and membrane biologists, respectively, with some notable but overall minimal overlap. Modern microscopy has enabled monitoring of the PTEN/PI3K pathway in action. Here, we explore the flurry of groundbreaking concepts emerging from those efforts. The discovery that PTEN contains an autonomous PI(3)P reader domain, fused to the catalytic PIP3 eraser domain has prompted us to explore the relationship between PI3K signaling and endocytosis. This revealed how PTEN can achieve signal termination in a precisely controlled fashion, because endocytosis can package the PIP3 signal into discrete units that PTEN will erase. We explore how PTEN can bridge the worlds of endocytosis and PI3K signaling and discuss progress on how PI3K/AKT signaling can be acting from internal membranes. We discuss how the PTEN/PI3K system for growth control may have emerged from principles of endocytosis, and how this development could have affected the evolution of multicellular organisms.},
}

@article {pmid31814500,
year = {2020},
author = {Nguyen, H and Das, U and Xie, J},
title = {Genome-wide evolution of wobble base-pairing nucleotides of branchpoint motifs with increasing organismal complexity.},
journal = {RNA biology},
volume = {17},
number = {3},
pages = {311-324},
doi = {10.1080/15476286.2019.1697548},
pmid = {31814500},
issn = {1555-8584},
abstract = {How have the branchpoint motifs evolved in organisms of different complexity? Here we identified and examined the consensus motifs (R1C2T3R4A5Y6, R: A or G, Y: C or T) of 898 fungal genomes. In Ascomycota unicellular yeasts, the G4/A4 ratio is mostly (98%) below 0.125 but increases sharply in multicellular species by about 40 times on average, and in the more complex Basidiomycota, it increases further by about 7 times. The global G4 increase is consistent with A4 to G4 transitions in evolution. Of the G4/A4-interacting amino acids of the branchpoint binding protein MSL5 (SF1) and the HSH155 (SF3B1), as well as the 5' splice sites (SS) and U2 snRNA genes, the 5' SS G3/A3 co-vary with the G4 to some extent. However, corresponding increase of the G4-complementary GCAGTA-U2 gene is rare, suggesting wobble-base pairing between the G4-containing branchpoint motif and GTAGTA-U2 in most of these species. Interestingly, the G4/A4 ratio correlates well with the abundance of alternative splicing in the two phyla, and G4 enriched significantly at the alternative 3' SS of genes in RNA metabolism, kinases and membrane proteins. Similar wobble nucleotides also enriched at the 3' SS of multicellular fungi with only thousands of protein-coding genes. Thus, branchpoint motifs have evolved U2-complementarity in unicellular Ascomycota yeasts, but have gradually gained more wobble base-pairing nucleotides in fungi of higher complexity, likely to destabilize branchpoint motif-U2 interaction and/or branchpoint A protrusion for alternative splicing. This implies an important role of relaxing the branchpoint signals in the multicellularity and further complexity of fungi.},
}

@article {pmid31805037,
year = {2019},
author = {Thomas, F and Giraudeau, M and Renaud, F and Ujvari, B and Roche, B and Pujol, P and Raymond, M and Lemaitre, JF and Alvergne, A},
title = {Can postfertile life stages evolve as an anticancer mechanism?.},
journal = {PLoS biology},
volume = {17},
number = {12},
pages = {e3000565},
pmid = {31805037},
issn = {1545-7885},
abstract = {Why a postfertile stage has evolved in females of some species has puzzled evolutionary biologists for over 50 years. We propose that existing adaptive explanations have underestimated in their formulation an important parameter operating both at the specific and the individual levels: the balance between cancer risks and cancer defenses. During their life, most multicellular organisms naturally accumulate oncogenic processes in their body. In parallel, reproduction, notably the pregnancy process in mammals, exacerbates the progression of existing tumors in females. When, for various ecological or evolutionary reasons, anticancer defenses are too weak, given cancer risk, older females could not pursue their reproduction without triggering fatal metastatic cancers, nor even maintain a normal reproductive physiology if the latter also promotes the growth of existing oncogenic processes, e.g., hormone-dependent malignancies. At least until stronger anticancer defenses are selected for in these species, females could achieve higher inclusive fitness by ceasing their reproduction and/or going through menopause (assuming that these traits are easier to select than anticancer defenses), thereby limiting the risk of premature death due to metastatic cancers. Because relatively few species experience such an evolutionary mismatch between anticancer defenses and cancer risks, the evolution of prolonged life after reproduction could also be a rare, potentially transient, anticancer adaptation in the animal kingdom.},
}

@article {pmid31802185,
year = {2019},
author = {Walker, DM and Hill, AJ and Albecker, MA and McCoy, MW and Grisnik, M and Romer, A and Grajal-Puche, A and Camp, C and Kelehear, C and Wooten, J and Rheubert, J and Graham, SP},
title = {Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-019-01456-x},
pmid = {31802185},
issn = {1432-184X},
abstract = {A multicellular host and its microbial communities are recognized as a metaorganism-a composite unit of evolution. Microbial communities have a variety of positive and negative effects on the host life history, ecology, and evolution. This study used high-throughput amplicon sequencing to characterize the complete skin and gut microbial communities, including both bacteria and fungi, of a terrestrial salamander, Plethodon glutinosus (Family Plethodontidae). We assessed salamander populations, representing nine mitochondrial haplotypes ('clades'), for differences in microbial assemblages across 13 geographic locations in the Southeastern United States. We hypothesized that microbial assemblages were structured by both host factors and geographic distance. We found a strong correlation between all microbial assemblages at close geographic distances, whereas, as spatial distance increases, the patterns became increasingly discriminate. Network analyses revealed that gut-bacterial communities have the highest degree of connectedness across geographic space. Host salamander clade was explanatory of skin-bacterial and gut-fungal assemblages but not gut-bacterial assemblages, unless the latter were analyzed within a phylogenetic context. We also inferred the function of gut-fungal assemblages to understand how an understudied component of the gut microbiome may influence salamander life history. We concluded that dispersal limitation may in part describe patterns in microbial assemblages across space and also that the salamander host may select for skin and gut communities that are maintained over time in closely related salamander populations.},
}

@article {pmid31799909,
year = {2020},
author = {Fields, C and Bischof, J and Levin, M},
title = {Morphological Coordination: A Common Ancestral Function Unifying Neural and Non-Neural Signaling.},
journal = {Physiology (Bethesda, Md.)},
volume = {35},
number = {1},
pages = {16-30},
doi = {10.1152/physiol.00027.2019},
pmid = {31799909},
issn = {1548-9221},
abstract = {Nervous systems are traditionally thought of as providing sensing and behavioral coordination functions at the level of the whole organism. What is the evolutionary origin of the mechanisms enabling the nervous systems' information processing ability? Here, we review evidence from evolutionary, developmental, and regenerative biology suggesting a deeper, ancestral function of both pre-neural and neural cell-cell communication systems: the long-distance coordination of cell division and differentiation required to create and maintain body-axis symmetries. This conceptualization of the function of nervous system activity sheds new light on the evolutionary transition from the morphologically rudimentary, non-neural Porifera and Placazoa to the complex morphologies of Ctenophores, Cnidarians, and Bilaterians. It further allows a sharp formulation of the distinction between long-distance axis-symmetry coordination based on external coordinates, e.g., by whole-organism scale trophisms as employed by plants and sessile animals, and coordination based on body-centered coordinates as employed by motile animals. Thus we suggest that the systems that control animal behavior evolved from ancient mechanisms adapting preexisting ionic and neurotransmitter mechanisms to regulate individual cell behaviors during morphogenesis. An appreciation of the ancient, non-neural origins of bioelectrically mediated computation suggests new approaches to the study of embryological development, including embryological dysregulation, cancer, regenerative medicine, and synthetic bioengineering.},
}

@article {pmid31798628,
year = {2019},
author = {Baumgartner, M and Drake, K and Kanadia, RN},
title = {An Integrated Model of Minor Intron Emergence and Conservation.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {1113},
doi = {10.3389/fgene.2019.01113},
pmid = {31798628},
issn = {1664-8021},
support = {R01 NS102538/NS/NINDS NIH HHS/United States ; },
abstract = {Minor introns constitute <0.5% of the introns in the human genome and have remained an enigma since their discovery. These introns are removed by a distinct splicing complex, the minor spliceosome. Both are ancient, tracing back to the last eukaryotic common ancestor (LECA), which is reflected by minor intron enrichment in specific gene families, such as the mitogen activated-protein kinase kinases, voltage-gated sodium and calcium ion channels, and E2F transcription factors. Most minor introns occur as single introns in genes with predominantly major introns. Due to this organization, minor intron-containing gene (MIG) expression requires the coordinated action of two spliceosomes, which increases the probability of missplicing. Thus, one would expect loss of minor introns via purifying selection. This has resulted in complete minor intron loss in at least nine eukaryotic lineages. However, minor introns are highly conserved in land plants and metazoans, where their importance is underscored by embryonic lethality when the minor spliceosome is inactivated. Conditional inactivation of the minor spliceosome has shown that rapidly dividing progenitor cells are highly sensitive to minor spliceosome loss. Indeed, we found that MIGs were significantly enriched in a screen for genes essential for survival in 341 cycling cell lines. Here, we propose that minor introns inserted randomly into genes in LECA or earlier and were subsequently conserved in genes crucial for cycling cell survival. We hypothesize that the essentiality of MIGs allowed minor introns to endure through the unicellularity of early eukaryotic evolution. Moreover, we identified 59 MIGs that emerged after LECA, and that many of these are essential for cycling cell survival, reinforcing our essentiality model for MIG conservation. This suggests that minor intron emergence is dynamic across eukaryotic evolution, and that minor introns should not be viewed as molecular fossils. We also posit that minor intron splicing was co-opted in multicellular evolution as a regulatory switch for en masse control of MIG expression and the biological processes they regulate. Specifically, this mode of regulation could control cell proliferation and thus body size, an idea supported by domestication syndrome, wherein MIGs are enriched in common candidate animal domestication genes.},
}

@article {pmid31794757,
year = {2019},
author = {Jékely, G},
title = {Evolution: How Not to Become an Animal.},
journal = {Current biology : CB},
volume = {29},
number = {23},
pages = {R1240-R1242},
doi = {10.1016/j.cub.2019.10.014},
pmid = {31794757},
issn = {1879-0445},
abstract = {The origin of animals has always fascinated biologists. Studies on choanoflagellates, the closest living relatives of animals, have contributed major insights. The discovery of a multicellular choanoflagellate with light-regulated collective behaviour now provides a new perspective.},
}

@article {pmid31788034,
year = {2019},
author = {Southworth, J and Grace, CA and Marron, AO and Fatima, N and Carr, M},
title = {A genomic survey of transposable elements in the choanoflagellate Salpingoeca rosetta reveals selection on codon usage.},
journal = {Mobile DNA},
volume = {10},
number = {},
pages = {44},
pmid = {31788034},
issn = {1759-8753},
abstract = {Background: Unicellular species make up the majority of eukaryotic diversity, however most studies on transposable elements (TEs) have centred on multicellular host species. Such studies may have therefore provided a limited picture of how transposable elements evolve across eukaryotes. The choanoflagellates, as the sister group to Metazoa, are an important study group for investigating unicellular to multicellular transitions. A previous survey of the choanoflagellate Monosiga brevicollis revealed the presence of only three families of LTR retrotransposons, all of which appeared to be active. Salpingoeca rosetta is the second choanoflagellate to have its whole genome sequenced and provides further insight into the evolution and population biology of transposable elements in the closest relative of metazoans.

Results: Screening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining 13 families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage.

Conclusions: S. rosetta increases the known diversity of choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.},
}

@article {pmid31766724,
year = {2019},
author = {Kar, R and Jha, NK and Jha, SK and Sharma, A and Dholpuria, S and Asthana, N and Chaurasiya, K and Singh, VK and Burgee, S and Nand, P},
title = {A "NOTCH" Deeper into the Epithelial-To-Mesenchymal Transition (EMT) Program in Breast Cancer.},
journal = {Genes},
volume = {10},
number = {12},
pages = {},
pmid = {31766724},
issn = {2073-4425},
abstract = {Notch signaling is a primitive signaling pathway having various roles in the normal origin and development of each multicellular organisms. Therefore, any aberration in the pathway will inevitably lead to deadly outcomes such as cancer. It has now been more than two decades since Notch was acknowledged as an oncogene in mouse mammary tumor virus-infected mice. Since that discovery, activated Notch signaling and consequent up-regulation of tumor-promoting Notch target genes have been observed in human breast cancer. Moreover, consistent over-expression of Notch ligands and receptors has been shown to correlate with poor prognosis in human breast cancer. Notch regulates a number of key processes during breast carcinogenesis, of which, one key phenomenon is epithelial-mesenchymal transition (EMT). EMT is a key process for large-scale cell movement during morphogenesis at the time of embryonic development. Cancer cells aided by transcription factors usurp this developmental program to execute the multi-step process of tumorigenesis and metastasis. In this review, we recapitulate recent progress in breast cancer research that has provided new perceptions into the molecular mechanisms behind Notch-mediated EMT regulation during breast tumorigenesis.},
}

@article {pmid31752673,
year = {2019},
author = {Forbes, G and Chen, ZH and Kin, K and Lawal, HM and Schilde, C and Yamada, Y and Schaap, P},
title = {Phylogeny-wide conservation and change in developmental expression, cell-type specificity and functional domains of the transcriptional regulators of social amoebas.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {890},
pmid = {31752673},
issn = {1471-2164},
support = {100293/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; 742288//H2020 European Research Council/ ; RPG-2016-220//Leverhulme Trust/ ; ALTF 295-2015//European Molecular Biology Organization/ ; H28-1002//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Dictyostelid social amoebas self-organize into fruiting bodies, consisting of spores and up to four supporting cell types in the phenotypically most complex taxon group 4. High quality genomes and stage- and cell-type specific transcriptomes are available for representative species of each of the four taxon groups. To understand how evolution of gene regulation in Dictyostelia contributed to evolution of phenotypic complexity, we analysed conservation and change in abundance, functional domain architecture and developmental regulation of their transcription factors (TFs).

RESULTS: We detected 440 sequence-specific TFs across 33 families, of which 68% were upregulated in multicellular development and about half conserved throughout Dictyostelia. Prespore cells expressed two times more TFs than prestalk cells, but stalk cells expressed more TFs than spores, suggesting that gene expression events that define spores occur earlier than those that define stalk cells. Changes in TF developmental expression, but not in TF abundance or functional domains occurred more frequently between group 4 and groups 1-3, than between the more distant branches formed by groups 1 + 2 and 3 + 4.

CONCLUSIONS: Phenotypic innovation is correlated with changes in TF regulation, rather than functional domain- or TF acquisition. The function of only 34 TFs is known. Of 12 TFs essential for cell differentiation, 9 are expressed in the cell type for which they are required. The information acquired here on conserved cell type specifity of 120 additional TFs can effectively guide further functional analysis, while observed evolutionary change in TF developmental expression may highlight how genotypic change caused phenotypic innovation.},
}

@article {pmid31751628,
year = {2020},
author = {Williams, LM and Inge, MM and Mansfield, KM and Rasmussen, A and Afghani, J and Agrba, M and Albert, C and Andersson, C and Babaei, M and Babaei, M and Bagdasaryants, A and Bonilla, A and Browne, A and Carpenter, S and Chen, T and Christie, B and Cyr, A and Dam, K and Dulock, N and Erdene, G and Esau, L and Esonwune, S and Hanchate, A and Huang, X and Jennings, T and Kasabwala, A and Kehoe, L and Kobayashi, R and Lee, M and LeVan, A and Liu, Y and Murphy, E and Nambiar, A and Olive, M and Patel, D and Pavesi, F and Petty, CA and Samofalova, Y and Sanchez, S and Stejskal, C and Tang, Y and Yapo, A and Cleary, JP and Yunes, SA and Siggers, T and Gilmore, TD},
title = {Transcription factor NF-κB in a basal metazoan, the sponge, has conserved and unique sequences, activities, and regulation.},
journal = {Developmental and comparative immunology},
volume = {104},
number = {},
pages = {103559},
doi = {10.1016/j.dci.2019.103559},
pmid = {31751628},
issn = {1879-0089},
support = {R01 AI116829/AI/NIAID NIH HHS/United States ; },
abstract = {Herein, we characterize transcription factor NF-κB from the demosponge Amphimedon queenslandica (Aq). Aq-NF-κB is most similar to NF-κB p100/p105 among vertebrate proteins, with an N-terminal DNA-binding domain, a C-terminal Ankyrin (ANK) repeat domain, and a DNA binding-site profile akin to human NF-κB proteins. Like mammalian NF-κB p100, C-terminal truncation allows nuclear translocation of Aq-NF-κB and increases its transcriptional activation activity. Expression of IκB kinases (IKKs) induces proteasome-dependent C-terminal processing of Aq-NF-κB in human cells, and processing requires C-terminal serines in Aq-NF-κB. Unlike NF-κB p100, C-terminal sequences of Aq-NF-κB do not inhibit its DNA-binding activity. Tissue of a black encrusting demosponge contains NF-κB site DNA-binding activity, as well as nuclear and processed NF-κB. Treatment of sponge tissue with LPS increases both DNA-binding activity and processing of NF-κB. A. queenslandica transcriptomes contain homologs to upstream NF-κB pathway components. This is first functional characterization of NF-κB in sponge, the most basal multicellular animal.},
}