@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},
doi = {10.1038/s41598-020-57494-w},
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 = {2019},
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 = {},
number = {},
pages = {},
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 = {},
doi = {10.12688/f1000research.20942.1},
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},
doi = {10.1038/s41467-019-14141-x},
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 = {2019},
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 = {},
number = {},
pages = {},
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},
doi = {10.1002/advs.201901850},
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},
doi = {10.3389/fpsyg.2019.02688},
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 = {},
number = {},
pages = {},
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 {pmid30794780,
year = {2019},
author = {Tucci, V and Isles, AR and Kelsey, G and Ferguson-Smith, AC and , },
title = {Genomic Imprinting and Physiological Processes in Mammals.},
journal = {Cell},
volume = {176},
number = {5},
pages = {952-965},
doi = {10.1016/j.cell.2019.01.043},
pmid = {30794780},
issn = {1097-4172},
support = {MR/K011332/1/MRC_/Medical Research Council/United Kingdom ; MR/L010305/1/MRC_/Medical Research Council/United Kingdom ; 210757/Z/18/WT_/Wellcome Trust/United Kingdom ; MR/R009791/1/MRC_/Medical Research Council/United Kingdom ; MR/S000437/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/B/000C0426/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P008623/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P002307/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Alleles ; Animals ; Biological Evolution ; Chromosomes ; DNA Methylation ; Epigenesis, Genetic/genetics/physiology ; Genomic Imprinting/*genetics/*physiology ; Mammals/*genetics/metabolism ; Physiological Phenomena ; },
abstract = {Complex multicellular organisms, such as mammals, express two complete sets of chromosomes per nucleus, combining the genetic material of both parents. However, epigenetic studies have demonstrated violations to this rule that are necessary for mammalian physiology; the most notable parental allele expression phenomenon is genomic imprinting. With the identification of endogenous imprinted genes, genomic imprinting became well-established as an epigenetic mechanism in which the expression pattern of a parental allele influences phenotypic expression. The expanding study of genomic imprinting is revealing a significant impact on brain functions and associated diseases. Here, we review key milestones in the field of imprinting and discuss mechanisms and systems in which imprinted genes exert a significant role.},
}

Alleles
Animals
Biological Evolution
Chromosomes
DNA Methylation
Epigenesis, Genetic/genetics/physiology
Genomic Imprinting/*genetics/*physiology
Mammals/*genetics/metabolism
Physiological Phenomena

@article {pmid30350947,
year = {2019},
author = {Budin, I and Keasling, JD},
title = {Synthetic Biology for Fundamental Biochemical Discovery.},
journal = {Biochemistry},
volume = {58},
number = {11},
pages = {1464-1469},
doi = {10.1021/acs.biochem.8b00915},
pmid = {30350947},
issn = {1520-4995},
mesh = {Biological Evolution ; Gene Regulatory Networks ; Protein Engineering/methods/*trends ; Research/trends ; Research Design/trends ; Synthetic Biology/*methods/*trends ; },
abstract = {Synthetic biologists have developed sophisticated molecular and genetic tools to engineer new biochemical functions in cells. Applications for these tools have focused on important problems in energy and medicine, but they can also be applied to address basic science topics that cannot be easily accessed by classical approaches. We focus on recent work that has utilized synthetic biology approaches, ranging from promoter engineering to the de novo synthesis of cellular parts, to investigate a wide range of biochemical and cellular questions. Insights obtained by these efforts include how fatty acid composition mediates cellular metabolism, how transcriptional circuits act to stabilize multicellular networks, and fitness trade-offs involved in the selection of genetic regulatory elements. We also highlight common themes about how "discovery by synthesis" approaches can aid fundamental research. For example, rewiring of native metabolism through metabolic engineering is a powerful tool for investigating biological molecules whose exact composition and abundance are key for function. Meanwhile, endeavors to synthesize cells and their components allow scientists to address evolutionary questions that are otherwise constrained by extant laboratory models.},
}

Biological Evolution
Gene Regulatory Networks
Protein Engineering/methods/*trends
Research/trends
Research Design/trends
Synthetic Biology/*methods/*trends

@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},
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 towards integrating the fields studying the GPM. This article is protected by copyright. All rights reserved.},
}

@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 = {},
number = {},
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 magnetotactic bacteria. We propose that deltaproteobacterial magnetotactic bacteria 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 = {2019},
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 = {},
number = {},
pages = {},
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 = {},
doi = {10.3390/ijms20246290},
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 {pmid30919490,
year = {2019},
author = {Marshall, RC and Whitworth, DE},
title = {Is "Wolf-Pack" Predation by Antimicrobial Bacteria Cooperative? Cell Behaviour and Predatory Mechanisms Indicate Profound Selfishness, Even when Working Alongside Kin.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {41},
number = {4},
pages = {e1800247},
doi = {10.1002/bies.201800247},
pmid = {30919490},
issn = {1521-1878},
mesh = {Anti-Bacterial Agents/*metabolism ; Biological Evolution ; Models, Biological ; Myxococcales/*cytology ; Time Factors ; },
abstract = {For decades, myxobacteria have been spotlighted as exemplars of social "wolf-pack" predation, communally secreting antimicrobial substances into the shared public milieu. This behavior has been described as cooperative, becoming more efficient if performed by more cells. However, laboratory evidence for cooperativity is limited and of little relevance to predation in a natural setting. In contrast, there is accumulating evidence for predatory mechanisms promoting "selfish" behavior during predation, which together with conflicting definitions of cooperativity, casts doubt on whether microbial "wolf-pack" predation really is cooperative. Here, it is hypothesized that public-goods-mediated predation is not cooperative, and it is argued that a holistic model of microbial predation is needed, accounting for predator and prey relatedness, social phenotypes, spatial organization, activity/specificity/transport of secreted toxins, and prey resistance mechanisms. Filling such gaps in our knowledge is vital if the evolutionary benefits of potentially costly microbial behaviors mediated by public goods are to be properly understood.},
}

Anti-Bacterial Agents/*metabolism
Biological Evolution
Models, Biological
Myxococcales/*cytology
Time Factors

@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},
doi = {10.1371/journal.pgen.1008520},
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},
doi = {10.1387/ijdb.190239gs},
pmid = {31840777},
issn = {1696-3547},
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},
doi = {10.1387/ijdb.190108ps},
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 {pmid31589468,
year = {2019},
author = {Blutt, SE and Klein, OD and Donowitz, M and Shroyer, N and Guha, C and Estes, MK},
title = {Use of organoids to study regenerative responses to intestinal damage.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {317},
number = {6},
pages = {G845-G852},
doi = {10.1152/ajpgi.00346.2018},
pmid = {31589468},
issn = {1522-1547},
abstract = {Intestinal organoid cultures provide an in vitro model system for studying pathways and mechanisms involved in epithelial damage and repair. Derived from either embryonic or induced pluripotent stem cells or adult intestinal stem cells or tissues, these self-organizing, multicellular structures contain polarized mature cells that recapitulate both the physiology and heterogeneity of the intestinal epithelium. These cultures provide a cutting-edge technology for defining regenerative pathways that are induced following radiation or chemical damage, which directly target the cycling intestinal stem cell, or damage resulting from viral, bacterial, or parasitic infection of the epithelium. Novel signaling pathways or biological mechanisms identified from organoid studies that mediate regeneration of the epithelium following damage are likely to be important targets of preventive or therapeutic modalities to mitigate intestinal injury. The evolution of these cultures to include more components of the intestinal wall and the ability to genetically modify them are key components for defining the mechanisms that modulate epithelial regeneration.},
}

@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 = {2019},
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 = {},
number = {},
pages = {},
doi = {10.1080/15476286.2019.1697548},
pmid = {31814500},
issn = {1555-8584},
abstract = {How have the branchpoints 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' splice site G3/A3 co-vary with the G4. However, corresponding increase of the G4-complementary GCAGTA-U2 gene is rare, suggesting wobble-base pairing between the branchpoint motif and U2 in most species. Interestingly, the G4/A4 ratio correlates well with the abundance of alternative splicing in the two phyla, and G4 enriched significantly in the alternative splice sites of genes in RNA metabolism, kinases and membrane proteins. Similar wobble nucleotides also enriched in the splice sites 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-U2 interaction and/or branchpoint A protrusion for alternative splicing. This implies an important role of the relaxation of 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},
doi = {10.1371/journal.pbio.3000565},
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},
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},
doi = {10.1186/s13100-019-0189-9},
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 {pmid30633408,
year = {2019},
author = {Škaloud, P and Škaloudová, M and Doskočilová, P and Kim, JI and Shin, W and Dvořák, P},
title = {Speciation in protists: Spatial and ecological divergence processes cause rapid species diversification in a freshwater chrysophyte.},
journal = {Molecular ecology},
volume = {28},
number = {5},
pages = {1084-1095},
doi = {10.1111/mec.15011},
pmid = {30633408},
issn = {1365-294X},
support = {17-13254S//Czech Science Foundation/International ; NRF-2015R1A2A2A01003192//National Research Foundation of Korea/International ; },
mesh = {Biodiversity ; *Biological Evolution ; Chrysophyta/*genetics/growth & development ; DNA, Mitochondrial/genetics ; *Ecosystem ; Fresh Water ; *Genetic Speciation ; Haplotypes/genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Although eukaryotic microorganisms are extremely numerous, diverse and essential to global ecosystem functioning, they are largely understudied by evolutionary biologists compared to multicellular macroscopic organisms. In particular, very little is known about the speciation mechanisms which may give rise to the diversity of microscopic eukaryotes. It was postulated that the enormous population sizes and ubiquitous distribution of these organisms could lead to a lack of population differentiation and therefore very low speciation rates. However, such assumptions have traditionally been based on morphospecies, which may not accurately reflect the true diversity, missing cryptic taxa. In this study, we aim to articulate the major diversification mechanisms leading to the contemporary molecular diversity by using a colonial freshwater flagellate, Synura sphagnicola, as an example. Phylogenetic analysis of five sequenced loci showed that S. sphagnicola differentiated into two morphologically distinct lineages approximately 15.4 million years ago, which further diverged into several evolutionarily recent haplotypes during the late Pleistocene. The most recent haplotypes are ecologically and biogeographically much more differentiated than the old lineages, presumably because of their persistent differentiation after the allopatric speciation events. Our study shows that in microbial eukaryotes, species diversification via the colonization of new geographical regions or ecological resources occurs much more readily than was previously thought. Consequently, divergence times of microorganisms in some lineages may be equivalent to the estimated times of speciation in plants and animals.},
}

Biodiversity
*Biological Evolution
Chrysophyta/*genetics/growth & development
DNA, Mitochondrial/genetics
*Ecosystem
Fresh Water
*Genetic Speciation
Haplotypes/genetics
Phylogeny
Sequence Analysis, DNA
Species Specificity

@article {pmid30846531,
year = {2019},
author = {Sequeira-Mendes, J and Vergara, Z and Peiró, R and Morata, J and Aragüez, I and Costas, C and Mendez-Giraldez, R and Casacuberta, JM and Bastolla, U and Gutierrez, C},
title = {Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins.},
journal = {Genome research},
volume = {29},
number = {5},
pages = {784-797},
doi = {10.1101/gr.240986.118},
pmid = {30846531},
issn = {1549-5469},
mesh = {Arabidopsis/*genetics/growth & development ; Base Composition/genetics ; Cells, Cultured ; Chromatin/metabolism ; *DNA Replication ; Heterochromatin/*genetics ; Replication Origin/*genetics ; Retroelements/genetics ; Transcription Initiation Site ; Transcription, Genetic ; },
abstract = {Eukaryotic genome replication depends on thousands of DNA replication origins (ORIs). A major challenge is to learn ORI biology in multicellular organisms in the context of growing organs to understand their developmental plasticity. We have identified a set of ORIs of Arabidopsis thaliana and their chromatin landscape at two stages of post-embryonic development. ORIs associate with multiple chromatin signatures including transcription start sites (TSS) but also proximal and distal regulatory regions and heterochromatin, where ORIs colocalize with retrotransposons. In addition, quantitative analysis of ORI activity led us to conclude that strong ORIs have high GC content and clusters of GGN trinucleotides. Development primarily influences ORI firing strength rather than ORI location. ORIs that preferentially fire at early developmental stages colocalize with GC-rich heterochromatin, but at later stages with transcribed genes, perhaps as a consequence of changes in chromatin features associated with developmental processes. Our study provides the set of ORIs active in an organism at the post-embryo stage that should allow us to study ORI biology in response to development, environment, and mutations with a quantitative approach. In a wider scope, the computational strategies developed here can be transferred to other eukaryotic systems.},
}

Arabidopsis/*genetics/growth & development
Base Composition/genetics
Cells, Cultured
Chromatin/metabolism
*DNA Replication
Heterochromatin/*genetics
Replication Origin/*genetics
Retroelements/genetics
Transcription Initiation Site
Transcription, Genetic

@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 = {},
doi = {10.3390/genes10120961},
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 {pmid30860988,
year = {2019},
author = {Riahi, H and Brekelmans, C and Foriel, S and Merkling, SH and Lyons, TA and Itskov, PM and Kleefstra, T and Ribeiro, C and van Rij, RP and Kramer, JM and Schenck, A},
title = {The histone methyltransferase G9a regulates tolerance to oxidative stress-induced energy consumption.},
journal = {PLoS biology},
volume = {17},
number = {3},
pages = {e2006146},
doi = {10.1371/journal.pbio.2006146},
pmid = {30860988},
issn = {1545-7885},
mesh = {Animals ; Antioxidants/metabolism ; Energy Metabolism/genetics/physiology ; Epigenesis, Genetic/genetics ; Glycogen Phosphorylase/genetics/metabolism ; Histone Methyltransferases/genetics/*metabolism ; Histone-Lysine N-Methyltransferase/genetics/metabolism ; Humans ; Male ; Oxidative Stress/genetics/physiology ; Phylogeny ; Sequence Analysis, RNA ; },
abstract = {Stress responses are crucial processes that require activation of genetic programs that protect from the stressor. Stress responses are also energy consuming and can thus be deleterious to the organism. The mechanisms coordinating energy consumption during stress response in multicellular organisms are not well understood. Here, we show that loss of the epigenetic regulator G9a in Drosophila causes a shift in the transcriptional and metabolic responses to oxidative stress (OS) that leads to decreased survival time upon feeding the xenobiotic paraquat. During OS exposure, G9a mutants show overactivation of stress response genes, rapid depletion of glycogen, and inability to access lipid energy stores. The OS survival deficiency of G9a mutants can be rescued by a high-sugar diet. Control flies also show improved OS survival when fed a high-sugar diet, suggesting that energy availability is generally a limiting factor for OS tolerance. Directly limiting access to glycogen stores by knocking down glycogen phosphorylase recapitulates the OS-induced survival defects of G9a mutants. We propose that G9a mutants are sensitive to stress because they experience a net reduction in available energy due to (1) rapid glycogen use, (2) an inability to access lipid energy stores, and (3) an overinduced transcriptional response to stress that further exacerbates energy demands. This suggests that G9a acts as a critical regulatory hub between the transcriptional and metabolic responses to OS. Our findings, together with recent studies that established a role for G9a in hypoxia resistance in cancer cell lines, suggest that G9a is of wide importance in controlling the cellular and organismal response to multiple types of stress.},
}

Animals
Antioxidants/metabolism
Energy Metabolism/genetics/physiology
Epigenesis, Genetic/genetics
Glycogen Phosphorylase/genetics/metabolism
Histone Methyltransferases/genetics/*metabolism
Histone-Lysine N-Methyltransferase/genetics/metabolism
Humans
Male
Oxidative Stress/genetics/physiology
Phylogeny
Sequence Analysis, RNA

@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},
doi = {10.1186/s12864-019-6239-3},
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 = {2019},
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 = {},
number = {},
pages = {103559},
doi = {10.1016/j.dci.2019.103559},
pmid = {31751628},
issn = {1879-0089},
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.},
}

@article {pmid30113099,
year = {2018},
author = {Stelbrink, B and Jovanovska, E and Levkov, Z and Ognjanova-Rumenova, N and Wilke, T and Albrecht, C},
title = {Diatoms do radiate: evidence for a freshwater species flock.},
journal = {Journal of evolutionary biology},
volume = {31},
number = {12},
pages = {1969-1975},
doi = {10.1111/jeb.13368},
pmid = {30113099},
issn = {1420-9101},
mesh = {Diatoms/*genetics/*physiology ; *Evolution, Molecular ; Fossils ; *Fresh Water ; *Genetic Variation ; *Phylogeny ; Time Factors ; },
abstract = {Due to the ubiquity and high dispersal capacity of unicellular eukaryotes, their often extraordinary diversity found in isolated and long-lived ecosystems such as ancient lakes is typically attributed to multiple colonization events rather than to in situ speciation. However, respective evolutionary studies are very scarce and the often high number of species flocks in ancient lakes across multicellular taxa raises the question whether unicellular species, such as diatoms, may radiate as well. Here, we use an integrative approach that includes molecular data from benthic diatom species of the genus Aneumastus endemic to ancient Lake Ohrid, fossil data obtained from the sediment record of a recent deep-drilling project and biogeographical information to test if this group, indeed, constitutes a species flock. Molecular-clock and phylogenetic analyses indicate a young monophyletic group of several endemic species. Molecular, fossil and biogeographical data strongly suggest a rapid intralacustrine diversification, which was possibly triggered by the emergence of novel habitats. This finding is the first evidence for a species flock in diatoms and suggests that in situ speciation is also a relevant evolutionary process for unicellular eukaryotes in isolated ecosystems.},
}

Diatoms/*genetics/*physiology
*Evolution, Molecular
Fossils
*Fresh Water
*Genetic Variation
*Phylogeny
Time Factors

@article {pmid31743442,
year = {2019},
author = {Brenneis, G and Beltz, BS},
title = {Adult neurogenesis in crayfish: origin, expansion and migration of neural progenitor lineages in a pseudostratified neuroepithelium.},
journal = {The Journal of comparative neurology},
volume = {},
number = {},
pages = {},
doi = {10.1002/cne.24820},
pmid = {31743442},
issn = {1096-9861},
abstract = {Two decades after the discovery of adult-born neurons in the brains of decapod crustaceans, the deutocerebral proliferative system (DPS) producing these neural lineages has become a model of adult neurogenesis in invertebrates. Studies on crayfish have provided substantial insights into the anatomy, cellular dynamics and regulation of the DPS. Contrary to traditional thinking, recent evidence suggests that the neurogenic niche in the crayfish DPS lacks self-renewing stem cells, its cell pool being instead sustained via integration of hemocytes generated by the innate immune system. Here, we investigated the origin, division and migration patterns of the adult-born neural progenitor (NP) lineages in detail. We show that the niche cell pool is not only replenished by hemocyte integration but also by limited numbers of symmetric cell divisions with some characteristics reminiscent of interkinetic nuclear migration. Once specified in the niche, 1st generation NPs act as transit-amplifying intermediate NPs which eventually exit and produce multicellular clones as they move along migratory streams toward target brain areas. Different clones may migrate simultaneously in the streams but occupy separate tracks and show spatio-temporally flexible division patterns. Based on this, we propose an extended DPS model that emphasizes structural similarities to pseudostratified neuroepithelia in other arthropods and vertebrates. This model includes hemocyte integration and intrinsic cell proliferation to synergistically counteract niche cell pool depletion during the animal's lifespan. Further, we discuss parallels to recent findings on mammalian adult neurogenesis, as both systems seem to exhibit a similar decoupling of proliferative replenishment divisions and consuming neurogenic divisions. This article is protected by copyright. All rights reserved.},
}

@article {pmid31736534,
year = {2019},
author = {Chen, J and Wang, N},
title = {Tissue cell differentiation and multicellular evolution via cytoskeletal stiffening in mechanically stressed microenvironments.},
journal = {Acta mechanica Sinica = Li xue xue bao},
volume = {35},
number = {2},
pages = {270-274},
doi = {10.1007/s10409-018-0814-8},
pmid = {31736534},
issn = {0567-7718},
abstract = {Evolution of eukaryotes from simple cells to complex multicellular organisms remains a mystery. Our postulate is that cytoskeletal stiffening is a necessary condition for evolution of complex multicellular organisms from early simple eukaryotes. Recent findings show that embryonic stem cells are as soft as primitive eukaryotes-amoebae and that differentiated tissue cells can be two orders of magnitude stiffer than embryonic stem cells. Soft embryonic stem cells become stiff as they differentiate into tissue cells of the complex multicellular organisms to match their microenvironment stiffness. We perhaps see in differentiation of embryonic stem cells (derived from inner cell mass cells) the echo of those early evolutionary events. Early soft unicellular organisms might have evolved to stiffen their cytoskeleton to protect their structural integrity from external mechanical stresses while being able to maintain form, to change shape, and to move.},
}

@article {pmid31723354,
year = {2018},
author = {Jacobeen, S and Pentz, JT and Graba, EC and Brandys, CG and Ratcliff, WC and Yunker, PJ},
title = {Cellular packing, mechanical stress and the evolution of multicellularity.},
journal = {Nature physics},
volume = {14},
number = {},
pages = {286-290},
doi = {10.1038/s41567-017-0002-y},
pmid = {31723354},
issn = {1745-2473},
abstract = {The evolution of multicellularity set the stage for sustained increases in organismal complexity1-5. However, a fundamental aspect of this transition remains largely unknown: how do simple clusters of cells evolve increased size when confronted by forces capable of breaking intracellular bonds? Here we show that multicellular snowflake yeast clusters6-8 fracture due to crowding-induced mechanical stress. Over seven weeks (~291 generations) of daily selection for large size, snowflake clusters evolve to increase their radius 1.7-fold by reducing the accumulation of internal stress. During this period, cells within the clusters evolve to be more elongated, concomitant with a decrease in the cellular volume fraction of the clusters. The associated increase in free space reduces the internal stress caused by cellular growth, thus delaying fracture and increasing cluster size. This work demonstrates how readily natural selection finds simple, physical solutions to spatial constraints that limit the evolution of group size-a fundamental step in the evolution of multicellularity.},
}

@article {pmid31724951,
year = {2019},
author = {Thattai, M},
title = {How contraction has shaped evolution.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
doi = {10.7554/eLife.52805},
pmid = {31724951},
issn = {2050-084X},
abstract = {Two unicellular relatives of animals reveal that coordinated contractions of groups of cells using actomyosin predated animal multicellularity during evolution.},
}

@article {pmid31647412,
year = {2019},
author = {Dudin, O and Ondracka, A and Grau-Bové, X and Haraldsen, AA and Toyoda, A and Suga, H and Bråte, J and Ruiz-Trillo, I},
title = {A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
doi = {10.7554/eLife.49801},
pmid = {31647412},
issn = {2050-084X},
support = {Consolidator Grant ERC-2012-Co-616960/ERC_/European Research Council/International ; MEXT KAKENHI 221S0002//Ministry of Education, Culture, Sports, Science and Technology/ ; MEXT KAKENHI 26891021//Ministry of Education, Culture, Sports, Science and Technology/ ; Young Research Talents grant 240284//Research Council of Norway/ ; P2LAP3_171815/SNSF_/Swiss National Science Foundation/Switzerland ; Individual fellowship MSCA-IF 746044//H2020 Marie Skłodowska-Curie Actions/ ; Individual fellowship MSCA-IF 747086//H2020 Marie Skłodowska-Curie Actions/ ; ERC-2012-Co -616960//European Research Council Consolidator Grant/ ; 221S0002//MEXT KAKENHI/ ; 26891021//MEXT KAKENHI/ ; 240284//Young Research Talents grant from the Research Council of Norway/ ; MSCA-IF 746044//Marie Sklodowska-Curie individual fellowship/ ; MSCA-IF 747086//Marie Sklodowska-Curie individual fellowship/ ; },
abstract = {In animals, cellularization of a coenocyte is a specialized form of cytokinesis that results in the formation of a polarized epithelium during early embryonic development. It is characterized by coordinated assembly of an actomyosin network, which drives inward membrane invaginations. However, whether coordinated cellularization driven by membrane invagination exists outside animals is not known. To that end, we investigate cellularization in the ichthyosporean Sphaeroforma arctica, a close unicellular relative of animals. We show that the process of cellularization involves coordinated inward plasma membrane invaginations dependent on an actomyosin network and reveal the temporal order of its assembly. This leads to the formation of a polarized layer of cells resembling an epithelium. We show that this stage is associated with tightly regulated transcriptional activation of genes involved in cell adhesion. Hereby we demonstrate the presence of a self-organized, clonally-generated, polarized layer of cells in a unicellular relative of animals.},
}

@article {pmid31714927,
year = {2019},
author = {Hammond, MJ and Wang, T and Cummins, SF},
title = {Characterisation of early metazoan secretion through associated signal peptidase complex subunits, prohormone convertases and carboxypeptidases of the marine sponge (Amphimedon queenslandica).},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0225227},
doi = {10.1371/journal.pone.0225227},
pmid = {31714927},
issn = {1932-6203},
abstract = {Efficient communication between cells requires the ability to process precursor proteins into their mature and biologically active forms, prior to secretion into the extracellular space. Eukaryotic cells achieve this via a suite of enzymes that involve a signal peptidase complex, prohormone convertases and carboxypeptidases. Using genome and transcriptome data of the demosponge Amphimedon queenslandica, a universal ancestor to metazoan multicellularity, we endeavour to bridge the evolution of precursor processing machinery from single-celled eukaryotic ancestors through to the complex multicellular organisms that compromise Metazoa. The precursor processing repertoire as defined in this study of A. queenslandica consists of 3 defined signal peptidase subunits, 6 prohormone convertases and 1 carboxypeptidase, with 2 putative duplicates identified for signal peptidase complex subunits. Analysis of their gene expression levels throughout the sponge development enabled us to predict levels of activity. Some A. queenslandica precursor processing components belong to established functional clades while others were identified as having novel, yet to be discovered roles. These findings have clarified the presence of precursor processing machinery in the poriferans, showing the necessary machinery for the removal of precursor sequences, a critical post-translational modification required by multicellular organisms, and further sets a foundation towards understanding the molecular mechanism for ancient protein processing.},
}

@article {pmid30851154,
year = {2019},
author = {Kalsoom, N and Zafar, M and Ahmad, M and Sultana, S and Usma, A and Jabeen, A},
title = {Investigating Schizocarp morphology as a taxonomic tool in study of Apiaceae family by utilizing LM and SEM techniques.},
journal = {Microscopy research and technique},
volume = {82},
number = {7},
pages = {1012-1020},
doi = {10.1002/jemt.23248},
pmid = {30851154},
issn = {1097-0029},
mesh = {Apiaceae/*anatomy & histology/*classification ; Fruit/*anatomy & histology/ultrastructure ; *Microscopy ; *Microscopy, Electron, Scanning ; Phylogeny ; Pollen ; },
abstract = {In present study, the schizocarp morphology of 14 species belonging to Apiaceae family has been investigated. Light microscopy (LM) and scanning electron microscopy (SEM) have been utilized to highlight qualitative and quantitative features of studied species. Variations have been observed in macro- and micro-morphological features such as color, shape, symmetry, length, width, apex, epicuticular projections, surface patterns, anticlinal, and periclinal wall patterns. Schizocarp shapes observed were oval, round, triangular, linear, elliptic, and globose. Fruit was either homomorphic or heteromorphic. Crystalloids, stellate hair, multicellular spines, and platelets were mostly observed epicuticular projections. Surface patterns on the fruit surface were striate, rugulate-striate, reticulate, and striato-knotted. Both macro- and micro-morphological characters can serve as an important tool in classifying Apiaceae family at various taxonomic ranks. Substantial variations observed can assist as useful constraints at various taxonomic levels as they provide reliable and constant details. Disparities observed in schizocarp features can pave a path for Apiaceae family classification based on phylogenetic and molecular studies.},
}

Apiaceae/*anatomy & histology/*classification
Fruit/*anatomy & histology/ultrastructure
*Microscopy
*Microscopy, Electron, Scanning
Phylogeny
Pollen

@article {pmid31709760,
year = {2019},
author = {Collens, A and Kelley, E and Katz, LA},
title = {The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.b.22915},
pmid = {31709760},
issn = {1552-5015},
support = {1541511//Division of Environmental Biology/ ; 1651908//Division of Environmental Biology/ ; R15HG010409/GM/NIGMS NIH HHS/United States ; R15HG010409/GF/NIH HHS/United States ; },
abstract = {John Tyler Bonner's call to re-evaluate evolutionary theory in light of major transitions in life on Earth (e.g., from the first origins of microbial life to the evolution of sex, and the origins of multicellularity) resonate with recent discoveries on epigenetics and the concept of the hologenome. Current studies of genome evolution often mistakenly focus only on the inheritance of DNA between parent and offspring. These are in line with the widely accepted Neo-Darwinian framework that pairs Mendelian genetics with an emphasis on natural selection as explanations for the evolution of biodiversity on Earth. Increasing evidence for widespread symbioses complicates this narrative, as is seen in Scott Gilbert's discussion of the concept of the holobiont in this series: Organisms across the tree of life coexist with substantial influence on one another through endosymbiosis, symbioses, and host-associated microbiomes. The holobiont theory, coupled with observations from molecular studies, also requires us to understand genomes in a new way-by considering the interactions underlain by the genome of a host plus its associated microbes, a conglomerate entity referred to as the hologenome. We argue that the complex patterns of inheritance of these genomes coupled with the influence of symbionts on host gene expression make the concept of the hologenome an epigenetic phenomenon. We further argue that the aspects of the hologenome challenge of the modern evolutionary synthesis, which requires updating to remain consistent with Darwin's intent of providing natural laws that underlie the evolution of life on Earth.},
}

@article {pmid31707219,
year = {2019},
author = {Stubbendieck, RM and Li, H and Currie, CR},
title = {Convergent evolution of signal-structure interfaces for maintaining symbioses.},
journal = {Current opinion in microbiology},
volume = {50},
number = {},
pages = {71-78},
doi = {10.1016/j.mib.2019.10.001},
pmid = {31707219},
issn = {1879-0364},
abstract = {Symbiotic microbes are essential to the ecological success and evolutionary diversification of multicellular organisms. The establishment and stability of bipartite symbioses are shaped by mechanisms ensuring partner fidelity between host and symbiont. In this minireview, we demonstrate how the interface of chemical signals and host structures influences fidelity between legume root nodules and rhizobia, Hawaiian bobtail squid light organs and Allivibrio fischeri, and fungus-growing ant crypts and Pseudonocardia. Subsequently, we illustrate the morphological diversity and widespread phylogenetic distribution of specialized structures used by hosts to house microbial symbionts, indicating the importance of signal-structure interfaces across the history of multicellular life. These observations, and the insights garnered from well-studied bipartite associations, demonstrate the need to concentrate on the signal-structure interface in complex and multipartite systems, including the human microbiome.},
}

@article {pmid31702845,
year = {2019},
author = {Grall, E and Tschopp, P},
title = {A sense of place, many times over - pattern formation and evolution of repetitive morphological structures.},
journal = {Developmental dynamics : an official publication of the American Association of Anatomists},
volume = {},
number = {},
pages = {},
doi = {10.1002/dvdy.131},
pmid = {31702845},
issn = {1097-0177},
abstract = {50 years ago, Lewis Wolpert introduced the concept of 'positional information' to explain how patterns form in a multicellular embryonic field. Using morphogen gradients, whose continuous distributions of positional values are discretized via thresholds into distinct cellular states, he provided, at the theoretical level, an elegant solution to the 'French Flag problem'. In the intervening years, many experimental studies have lent support to Wolpert's ideas. However, the embryonic patterning of highly repetitive morphological structures, as often occurring in nature, can reveal limitations in the strict implementation of his initial theory, given the number of distinct threshold values that would have to be specified. Here, we review how positional information is complemented to circumvent these inadequacies, to accommodate tissue growth and pattern periodicity. In particular, we focus on functional anatomical assemblies composed of such structures, like the vertebrate spine or tetrapod digits, where the resulting segmented architecture is intrinsically linked to periodic pattern formation and unidirectional growth. These systems integrate positional information and growth with additional patterning cues that, we suggest, increase robustness and evolvability. We discuss different experimental and theoretical models to study such patterning systems, and how the underlying processes are modulated over evolutionary timescales to enable morphological diversification. This article is protected by copyright. All rights reserved.},
}

@article {pmid31700531,
year = {2019},
author = {Raven, N and Bramwell, G and Hamede, R and Thomas, F and Ujvari, B},
title = {Fifth International Biannual Evolution and Ecology of Cancer Conference (Cooperation, Conflict and Parasitism) meeting report-Wellcome Genome Campus, Hinxton, UK.},
journal = {Evolutionary applications},
volume = {12},
number = {10},
pages = {1863-1867},
doi = {10.1111/eva.12862},
pmid = {31700531},
issn = {1752-4571},
abstract = {The fifth biannual conference of the International Society of Evolution and Ecology of Cancer (ISEEC) was held between the 17th and 19th of July 2019 in Hinxton (UK) at the Wellcome Genome Campus. The main theme of the conference: cooperation, conflict and parasitism reflected our growing understanding of the role cancer has played in the evolution of multicellular organisms, as well as the urgent need of translating these Darwinian processes to treatment strategies. Below we provide a brief summary of each plenary sessions and other oral presentations, to bring the conference to the broader audience of evolutionary biology and applications.},
}

@article {pmid31689405,
year = {2019},
author = {Coudert, Y and Harris, S and Charrier, B},
title = {Design Principles of Branching Morphogenesis in Filamentous Organisms.},
journal = {Current biology : CB},
volume = {29},
number = {21},
pages = {R1149-R1162},
doi = {10.1016/j.cub.2019.09.021},
pmid = {31689405},
issn = {1879-0445},
abstract = {The radiation of life on Earth was accompanied by the diversification of multicellular body plans in the eukaryotic kingdoms Animalia, Plantae, Fungi and Chromista. Branching forms are ubiquitous in nature and evolved repeatedly in the above lineages. The developmental and genetic basis of branch formation is well studied in the three-dimensional shoot and root systems of land plants, and in animal organs such as the lung, kidney, mammary gland, vasculature, etc. Notably, recent thought-provoking studies combining experimental analysis and computational modeling of branching patterns in whole animal organs have identified global patterning rules and proposed unifying principles of branching morphogenesis. Filamentous branching forms represent one of the simplest expressions of the multicellular body plan and constitute a key step in the evolution of morphological complexity. Similarities between simple and complex branching forms distantly related in evolution are compelling, raising the question whether shared mechanisms underlie their development. Here, we focus on filamentous branching organisms that represent major study models from three distinct eukaryotic kingdoms, including the moss Physcomitrella patens (Plantae), the brown alga Ectocarpus sp. (Chromista), and the ascomycetes Neurospora crassa and Aspergillus nidulans (Fungi), and bring to light developmental regulatory mechanisms and design principles common to these lineages. Throughout the review we explore how the regulatory mechanisms of branching morphogenesis identified in other models, and in particular animal organs, may inform our thinking on filamentous systems and thereby advance our understanding of the diverse strategies deployed across the eukaryotic tree of life to evolve similar forms.},
}

@article {pmid31687086,
year = {2019},
author = {Poljsak, B and Kovac, V and Dahmane, R and Levec, T and Starc, A},
title = {Cancer Etiology: A Metabolic Disease Originating from Life's Major Evolutionary Transition?.},
journal = {Oxidative medicine and cellular longevity},
volume = {2019},
number = {},
pages = {7831952},
doi = {10.1155/2019/7831952},
pmid = {31687086},
issn = {1942-0994},
abstract = {A clear understanding of the origins of cancer is the basis of successful strategies for effective cancer prevention and management. The origin of cancer at the molecular and cellular levels is not well understood. Is the primary cause of the origin of cancer the genomic instability or impaired energy metabolism? An attempt was made to present cancer etiology originating from life's major evolutionary transition. The first evolutionary transition went from simple to complex cells when eukaryotic cells with glycolytic energy production merged with the oxidative mitochondrion (The Endosymbiosis Theory first proposed by Lynn Margulis in the 1960s). The second transition went from single-celled to multicellular organisms once the cells obtained mitochondria, which enabled them to obtain a higher amount of energy. Evidence will be presented that these two transitions, as well as the decline of NAD+ and ATP levels, are the root of cancer diseases. Restoring redox homeostasis and reactivation of mitochondrial oxidative metabolism are important factors in cancer prevention.},
}

@article {pmid31681764,
year = {2019},
author = {Naumann, B and Burkhardt, P},
title = {Spatial Cell Disparity in the Colonial Choanoflagellate Salpingoeca rosetta.},
journal = {Frontiers in cell and developmental biology},
volume = {7},
number = {},
pages = {231},
doi = {10.3389/fcell.2019.00231},
pmid = {31681764},
issn = {2296-634X},
abstract = {Choanoflagellates are the closest unicellular relatives of animals (Metazoa). These tiny protists display complex life histories that include sessile as well as different pelagic stages. Some choanoflagellates have the ability to form colonies as well. Up until recently, these colonies have been described to consist of mostly identical cells showing no spatial cell differentiation, which supported the traditional view that spatial cell differentiation, leading to the co-existence of specific cell types in animals, evolved after the split of the last common ancestor of the Choanoflagellata and Metazoa. The recent discovery of single cells in colonies of the choanoflagellate Salpingoeca rosetta that exhibit unique cell morphologies challenges this traditional view. We have now reanalyzed TEM serial sections, aiming to determine the degree of similarity of S. rosetta cells within a rosette colony. We investigated cell morphologies and nuclear, mitochondrial, and food vacuole volumes of 40 individual cells from four different S. rosetta rosette colonies and compared our findings to sponge choanocytes. Our analysis shows that cells in a choanoflagellate colony differ from each other in respect to cell morphology and content ratios of nuclei, mitochondria, and food vacuoles. Furthermore, cell disparity within S. rosetta colonies is slightly higher compared to cell disparity within sponge choanocytes. Moreover, we discovered the presence of plasma membrane contacts between colonial cells in addition to already described intercellular bridges and filo-/pseudopodial contacts. Our findings indicate that the last common ancestor of Choanoflagellata and Metazoa might have possessed plasma membrane contacts and spatial cell disparity during colonial life history stages.},
}

@article {pmid31680996,
year = {2019},
author = {Arnellos, A and Keijzer, F},
title = {Bodily Complexity: Integrated Multicellular Organizations for Contraction-Based Motility.},
journal = {Frontiers in physiology},
volume = {10},
number = {},
pages = {1268},
doi = {10.3389/fphys.2019.01268},
pmid = {31680996},
issn = {1664-042X},
abstract = {Compared to other forms of multicellularity, the animal case is unique. Animals-barring some exceptions-consist of collections of cells that are connected and integrated to such an extent that these collectives act as unitary, large free-moving entities capable of sensing macroscopic properties and events. This animal configuration is so well-known that it is often taken as a natural one that 'must' have evolved, given environmental conditions that make large free-moving units 'obviously' adaptive. Here we question the seemingly evolutionary inevitableness of animals and introduce a thesis of bodily complexity: The multicellular organization characteristic for typical animals requires the integration of a multitude of intrinsic bodily features between its sensorimotor, physiological, and developmental aspects, and the related contraction-based tissue- and cellular-level events and processes. The evolutionary road toward this bodily complexity involves, we argue, various intermediate organizational steps that accompany and support the wider transition from cilia-based to contraction/muscle-based motility, and which remain insufficiently acknowledged. Here, we stress the crucial and specific role played by muscle-based and myoepithelial tissue contraction-acting as a physical platform for organizing both the multicellular transmission of mechanical forces and multicellular signaling-as key foundation of animal motility, sensing and maintenance, and development. We illustrate and discuss these bodily features in the context of the four basal animal phyla-Porifera, Ctenophores, Placozoans, and Cnidarians-that split off before the bilaterians, a supergroup that incorporates all complex animals.},
}

@article {pmid30177778,
year = {2018},
author = {Waters, AJ and Capriotti, P and Gaboriau, DCA and Papathanos, PA and Windbichler, N},
title = {Rationally-engineered reproductive barriers using CRISPR & CRISPRa: an evaluation of the synthetic species concept in Drosophila melanogaster.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {13125},
pmid = {30177778},
issn = {2045-2322},
support = {335724//European Research Council/International ; },
mesh = {Animals ; Base Sequence ; CRISPR-Associated Protein 9/genetics/metabolism ; *CRISPR-Cas Systems ; Drosophila Proteins/*genetics ; Drosophila melanogaster/*genetics ; Female ; Gene Editing/*methods ; *Genes, Insect ; Genes, Lethal ; Genetic Fitness ; Genetic Loci ; *Genome, Insect ; Homeodomain Proteins/*genetics ; INDEL Mutation ; Male ; Population Control/methods ; Promoter Regions, Genetic ; RNA, Guide/genetics/metabolism ; Reproductive Isolation ; Sequence Alignment ; Transcription Factors/*genetics ; Transcriptional Activation ; },
abstract = {The ability to erect rationally-engineered reproductive barriers in animal or plant species promises to enable a number of biotechnological applications such as the creation of genetic firewalls, the containment of gene drives or novel population replacement and suppression strategies for genetic control. However, to date no experimental data exist that explores this concept in a multicellular organism. Here we examine the requirements for building artificial reproductive barriers in the metazoan model Drosophila melanogaster by combining CRISPR-based genome editing and transcriptional transactivation (CRISPRa) of the same loci. We directed 13 single guide RNAs (sgRNAs) to the promoters of 7 evolutionary conserved genes and used 11 drivers to conduct a misactivation screen. We identify dominant-lethal activators of the eve locus and find that they disrupt development by strongly activating eve outside its native spatio-temporal context. We employ the same set of sgRNAs to isolate, by genome editing, protective INDELs that render these loci resistant to transactivation without interfering with target gene function. When these sets of genetic components are combined we find that complete synthetic lethality, a prerequisite for most applications, is achievable using this approach. However, our results suggest a steep trade-off between the level and scope of dCas9 expression, the degree of genetic isolation achievable and the resulting impact on fly fitness. The genetic engineering strategy we present here allows the creation of single or multiple reproductive barriers and could be applied to other multicellular organisms such as disease vectors or transgenic organisms of economic importance.},
}

Animals
Base Sequence
CRISPR-Associated Protein 9/genetics/metabolism
*CRISPR-Cas Systems
Drosophila Proteins/*genetics
Drosophila melanogaster/*genetics
Female
Gene Editing/*methods
*Genes, Insect
Genes, Lethal
Genetic Fitness
Genetic Loci
*Genome, Insect
Homeodomain Proteins/*genetics
INDEL Mutation
Male
Population Control/methods
Promoter Regions, Genetic
RNA, Guide/genetics/metabolism
Reproductive Isolation
Sequence Alignment
Transcription Factors/*genetics
Transcriptional Activation

@article {pmid31667165,
year = {2019},
author = {Fortunato, A and Aktipis, A},
title = {Social feeding behavior of Trichoplax adhaerens.},
journal = {Frontiers in ecology and evolution},
volume = {7},
number = {},
pages = {},
doi = {10.3389/fevo.2019.00019},
pmid = {31667165},
issn = {2296-701X},
abstract = {Animals have evolved different foraging strategies in which some animals forage independently and others forage in groups. The evolution of social feeding does not necessarily require cooperation; social feeding can be a beneficial individual-level strategy if it provides mutualistic benefits, for example though increasing the efficiency of resource extraction or processing. We found that Trichoplax adhaerens, the simplest multicellular animal ever described, engages in social feeding behavior. T. adhaerens lacks muscle tissue, nervous and digestive systems - yet is capable of aggregating and forming groups of closely connected individuals who collectively feed. The tight physical interactions between the animals are transitory and appear to serve the goal of staying connected to neighbors during the external digestion of algae when enzymes are released on the biofilm and nutrients are absorbed through the ventral epithelium. We found that T. adhaerens are more likely to engage in social feeding when the concentrations of algae are high - both in a semi-natural conditions and in vitro. It is surprising that T. adhaerens - an organism without a nervous system - is able to engage in this social feeding behavior. Whether this behavior is cooperative is still an open question. Nevertheless, the social feeding behavior of T. adhaerens, an early multicellular animal, suggests that sociality may have played an important role in the early evolution of animals. It also suggests that T. adhaerens could be used as a simple model organism for exploring questions regarding ecology and sociobiology.},
}

@article {pmid31662428,
year = {2019},
author = {Du, H and Zhang, W and Zhang, W and Zhang, W and Pan, H and Pan, Y and Bazylinski, DA and Wu, LF and Xiao, T and Lin, W},
title = {Magnetosome Gene Duplication as an Important Driver in the Evolution of Magnetotaxis in the Alphaproteobacteria.},
journal = {mSystems},
volume = {4},
number = {5},
pages = {},
doi = {10.1128/mSystems.00315-19},
pmid = {31662428},
issn = {2379-5077},
abstract = {The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth's geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely unstudied. Here we report the isolation, cultivation, and sequencing of a novel magnetotactic spirillum belonging to the genus Terasakiella (Terasakiella sp. strain SH-1) within the class Alphaproteobacteria The complete genome sequence of Terasakiella sp. strain SH-1 revealed an unexpected duplication event of magnetosome genes within the mamAB operon, a group of genes essential for magnetosome biomineralization and magnetotaxis. Intriguingly, further comparative genomic analysis suggests that the duplication of mamAB genes is a common feature in the genomes of alphaproteobacterial MTB. Taken together, with the additional finding that gene duplication appears to have also occurred in some magnetotactic members of the Deltaproteobacteria, our results indicate that gene duplication plays an important role in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain BacteriaIMPORTANCE A diversity of organisms can sense the geomagnetic field for the purpose of navigation. Magnetotactic bacteria are the most primitive magnetism-sensing organisms known thus far and represent an excellent model system for the study of the origin, evolution, and mechanism of microbial magnetoreception (or magnetotaxis). The present study is the first report focused on magnetosome gene cluster duplication in the Alphaproteobacteria, which suggests the important role of gene duplication in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria A novel scenario for the evolution of magnetotaxis in the Alphaproteobacteria is proposed and may provide new insights into evolution of magnetoreception of higher species.},
}

@article {pmid31209289,
year = {2019},
author = {Morrissey, EM and Mau, RL and Hayer, M and Liu, XA and Schwartz, E and Dijkstra, P and Koch, BJ and Allen, K and Blazewicz, SJ and Hofmockel, K and Pett-Ridge, J and Hungate, BA},
title = {Evolutionary history constrains microbial traits across environmental variation.},
journal = {Nature ecology & evolution},
volume = {3},
number = {7},
pages = {1064-1069},
doi = {10.1038/s41559-019-0918-y},
pmid = {31209289},
issn = {2397-334X},
mesh = {Biological Evolution ; Carbon ; *Ecosystem ; Nitrogen ; *Soil ; },
abstract = {Organisms influence ecosystems, from element cycling to disturbance regimes, to trophic interactions and to energy partitioning. Microorganisms are part of this influence, and understanding their ecology in nature requires studying the traits of these organisms quantitatively in their natural habitats-a challenging task, but one which new approaches now make possible. Here, we show that growth rate and carbon assimilation rate of soil microorganisms are influenced more by evolutionary history than by climate, even across a broad climatic gradient spanning major temperate life zones, from mixed conifer forest to high-desert grassland. Most of the explained variation (~50% to ~90%) in growth rate and carbon assimilation rate was attributable to differences among taxonomic groups, indicating a strong influence of evolutionary history, and taxonomic groupings were more predictive for organisms responding to resource addition. With added carbon and nitrogen substrates, differences among taxonomic groups explained approximately eightfold more variance in growth rate than did differences in ecosystem type. Taxon-specific growth and carbon assimilation rates were highly intercorrelated across the four ecosystems, constrained by the taxonomic identity of the organisms, such that plasticity driven by environment was limited across ecosystems varying in temperature, precipitation and dominant vegetation. Taken together, our results suggest that, similar to multicellular life, the traits of prokaryotes in their natural habitats are constrained by evolutionary history to a greater degree than environmental variation.},
}

Biological Evolution
Carbon
*Ecosystem
Nitrogen
*Soil

@article {pmid31649660,
year = {2019},
author = {Smith, NC and Rise, ML and Christian, SL},
title = {A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {2292},
doi = {10.3389/fimmu.2019.02292},
pmid = {31649660},
issn = {1664-3224},
abstract = {The immune system is composed of two subsystems-the innate immune system and the adaptive immune system. The innate immune system is the first to respond to pathogens and does not retain memory of previous responses. Innate immune responses are evolutionarily older than adaptive responses and elements of innate immunity can be found in all multicellular organisms. If a pathogen persists, the adaptive immune system will engage the pathogen with specificity and memory. Several components of the adaptive system including immunoglobulins (Igs), T cell receptors (TCR), and major histocompatibility complex (MHC), are assumed to have arisen in the first jawed vertebrates-the Gnathostomata. This review will discuss and compare components of both the innate and adaptive immune systems in Gnathostomes, particularly in Chondrichthyes (cartilaginous fish) and in Osteichthyes [bony fish: the Actinopterygii (ray-finned fish) and the Sarcopterygii (lobe-finned fish)]. While many elements of both the innate and adaptive immune systems are conserved within these species and with higher level vertebrates, some elements have marked differences. Components of the innate immune system covered here include physical barriers, such as the skin and gastrointestinal tract, cellular components, such as pattern recognition receptors and immune cells including macrophages and neutrophils, and humoral components, such as the complement system. Components of the adaptive system covered include the fundamental cells and molecules of adaptive immunity: B lymphocytes (B cells), T lymphocytes (T cells), immunoglobulins (Igs), and major histocompatibility complex (MHC). Comparative studies in fish such as those discussed here are essential for developing a comprehensive understanding of the evolution of the immune system.},
}

@article {pmid31649059,
year = {2019},
author = {Duttke, SH and Chang, MW and Heinz, S and Benner, C},
title = {Identification and dynamic quantification of regulatory elements using total RNA.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.253492.119},
pmid = {31649059},
issn = {1549-5469},
abstract = {The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSSs) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than does RNA-seq. Interrogating tissues from species across the eukaryotic kingdoms identified unstable transcripts resembling enhancer RNAs, pri-miRNAs, antisense transcripts, and promoter upstream transcripts in multicellular animals, plants, and fungi spanning 1.6 million years of evolution. Integration of epigenomic data from these organisms revealed that histone H3 trimethylation (H3K4me3) was largely confined to TSSs of stable transcripts, whereas H3K27ac marked nucleosomes downstream from all active TSSs, suggesting an ancient role for posttranslational histone modifications in transcription. Our findings show that total RNA is sufficient to identify transcribed regulatory elements and capture the dynamics of initiated stable and unstable transcripts at single-nucleotide resolution in eukaryotes.},
}

@article {pmid30270182,
year = {2018},
author = {Thomas, GWC and Wang, RJ and Puri, A and Harris, RA and Raveendran, M and Hughes, DST and Murali, SC and Williams, LE and Doddapaneni, H and Muzny, DM and Gibbs, RA and Abee, CR and Galinski, MR and Worley, KC and Rogers, J and Radivojac, P and Hahn, MW},
title = {Reproductive Longevity Predicts Mutation Rates in Primates.},
journal = {Current biology : CB},
volume = {28},
number = {19},
pages = {3193-3197.e5},
pmid = {30270182},
issn = {1879-0445},
support = {HHSN272201200031C/AI/NIAID NIH HHS/United States ; P40 OD010938/OD/NIH HHS/United States ; },
mesh = {Animals ; Aotidae/genetics ; Genetic Fitness/*genetics ; Genetics, Population/methods ; Genome/genetics ; Humans ; Longevity/*genetics ; Mutation ; *Mutation Rate ; Pedigree ; Population Density ; Primates/genetics ; Reproduction ; },
abstract = {Mutation rates vary between species across several orders of magnitude, with larger organisms having the highest per-generation mutation rates. Hypotheses for this pattern typically invoke physiological or population-genetic constraints imposed on the molecular machinery preventing mutations [1]. However, continuing germline cell division in multicellular eukaryotes means that organisms with longer generation times and of larger size will leave more mutations to their offspring simply as a byproduct of their increased lifespan [2, 3]. Here, we deeply sequence the genomes of 30 owl monkeys (Aotus nancymaae) from six multi-generation pedigrees to demonstrate that paternal age is the major factor determining the number of de novo mutations in this species. We find that owl monkeys have an average mutation rate of 0.81 × 10-8 per site per generation, roughly 32% lower than the estimate in humans. Based on a simple model of reproductive longevity that does not require any changes to the mutational machinery, we show that this is the expected mutation rate in owl monkeys. We further demonstrate that our model predicts species-specific mutation rates in other primates, including study-specific mutation rates in humans based on the average paternal age. Our results suggest that variation in life history traits alone can explain variation in the per-generation mutation rate among primates, and perhaps among a wide range of multicellular organisms.},
}

Animals
Aotidae/genetics
Genetic Fitness/*genetics
Genetics, Population/methods
Genome/genetics
Humans
Longevity/*genetics
Mutation
*Mutation Rate
Pedigree
Population Density
Primates/genetics
Reproduction

@article {pmid31624206,
year = {2019},
author = {Brunet, T and Larson, BT and Linden, TA and Vermeij, MJA and McDonald, K and King, N},
title = {Light-regulated collective contractility in a multicellular choanoflagellate.},
journal = {Science (New York, N.Y.)},
volume = {366},
number = {6463},
pages = {326-334},
doi = {10.1126/science.aay2346},
pmid = {31624206},
issn = {1095-9203},
abstract = {Collective cell contractions that generate global tissue deformations are a signature feature of animal movement and morphogenesis. However, the origin of collective contractility in animals remains unclear. While surveying the Caribbean island of Curaçao for choanoflagellates, the closest living relatives of animals, we isolated a previously undescribed species (here named Choanoeca flexa sp. nov.) that forms multicellular cup-shaped colonies. The colonies rapidly invert their curvature in response to changing light levels, which they detect through a rhodopsin-cyclic guanosine monophosphate pathway. Inversion requires actomyosin-mediated apical contractility and allows alternation between feeding and swimming behavior. C. flexa thus rapidly converts sensory inputs directly into multicellular contractions. These findings may inform reconstructions of hypothesized animal ancestors that existed before the evolution of specialized sensory and contractile cells.},
}

@article {pmid31617664,
year = {2019},
author = {Nanjundiah, V},
title = {Many roads lead to Rome: Neutral phenotypes in microorganisms.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.b.22909},
pmid = {31617664},
issn = {1552-5015},
abstract = {John Bonner pointed out that microorganisms differ in several ways, some of which may reflect neutral phenotypic evolution. For making his case, Bonner referred to interspecies differences and morphological traits. Here we consider intraspecies differences and physiological traits. As a case-study, we examine the production of an extracellular cyclic 3 ' ,5 ' monophosphate phosphodiesterase in the cellular slime mold Dictyostelium discoideum. Temporal profiles of phosphodiesterase activity differ significantly between wild-type strains. From that we argue that the inference drawn initially from studies on a single wild-type, namely that the profile displayed by it pointed to an adaptive role, was mistaken. We generalize the conclusion to suggest that physiological differences exhibited by microorganisms of the same species may, but need not, reflect adaptations to different environments. Rather, the differences could be related to the fact that microorganisms live in groups whose composition can vary between homogeneous (clonal) and heterogeneous (polyclonal). More than one physiological profile is consistent with the normal development of the group in a given environment; the alternatives are neutral. When studying microbial physiology and behavior, it is expected that the observations are made on a clonal population; genetic (and so phenotypic) heterogeneity is carefully guarded against. As the example from D. discoideum shows, an unintended consequence of overlooking phenotypic heterogeneity is that one can fall into the trap of accepting a seemingly plausible, but possibly erroneous, adaptive explanation for a "normal" wild-type phenotype.},
}

@article {pmid31617575,
year = {2019},
author = {Wan, TM and Iyer, DN and Ng, L},
title = {Roles of microRNAs as non-invasive biomarker and therapeutic target in colorectal cancer.},
journal = {Histology and histopathology},
volume = {},
number = {},
pages = {18171},
doi = {10.14670/HH-18-171},
pmid = {31617575},
issn = {1699-5848},
support = {-//-/ ; },
abstract = {Evolutionary medicine has proven helpful to understand the origin of human disease, e.g. in identifying causal roles of recent environmental changes impacting on human physiology (environment-phenotype mismatch). In contrast, diseases affecting only a limited number of members of a species often originate from evolutionary trade-offs for usually physiologic adaptations assuring reproductive success in the context of extrinsic threats. For example, the G1 and G2 variants of the APOL1 gene supporting control of Trypanosoma infection come with the trade-off that they promote the progression of kidney disease. In this review we extend the concept of evolutionary nephrology by discussing how the physiologic adaptations (danger responses) to tissue injury create evolutionary trade-offs that drive histopathological changes underlying acute and chronic kidney diseases. The evolution of multicellular organisms positively selected a number of danger response programs for their overwhelming benefits in assuring survival such as clotting, inflammation, epithelial healing and mesenchymal healing, i.e. fibrosis and sclerosis. Upon kidney injury these danger programs often present as pathomechanisms driving persistent nephron loss and renal failure. We explore how classic kidney disease entities involve insufficient or overshooting activation of these danger response programs for which the underlying genetic basis remains largely to be defined. Dissecting the causative and hierarchical relationships between danger programs should help to identify molecular targets to control kidney injury and to improve disease outcomes.},
}

@article {pmid29487180,
year = {2018},
author = {Cardon, ZG and Peredo, EL and Dohnalkova, AC and Gershone, HL and Bezanilla, M},
title = {A model suite of green algae within the Scenedesmaceae for investigating contrasting desiccation tolerance and morphology.},
journal = {Journal of cell science},
volume = {131},
number = {7},
pages = {},
doi = {10.1242/jcs.212233},
pmid = {29487180},
issn = {1477-9137},
mesh = {Cell Nucleus/chemistry/genetics/ultrastructure ; Chlorophyceae/classification/*genetics/growth & development ; Chlorophyta/*genetics/growth & development/ultrastructure ; Cytokinesis/genetics ; Ecosystem ; Golgi Apparatus/chemistry/ultrastructure ; Light ; Photosynthesis/*genetics ; *Phylogeny ; Reactive Oxygen Species/metabolism ; Time-Lapse Imaging ; },
abstract = {Microscopic green algae inhabiting desert microbiotic crusts are remarkably diverse phylogenetically, and many desert lineages have independently evolved from aquatic ancestors. Here we worked with five desert and aquatic species within the family Scenedesmaceae to examine mechanisms that underlie desiccation tolerance and release of unicellular versus multicellular progeny. Live cell staining and time-lapse confocal imaging coupled with transmission electron microscopy established that the desert and aquatic species all divide by multiple (rather than binary) fission, although progeny were unicellular in three species and multicellular (joined in a sheet-like coenobium) in two. During division, Golgi complexes were localized near nuclei, and all species exhibited dynamic rotation of the daughter cell mass within the mother cell wall at cytokinesis. Differential desiccation tolerance across the five species, assessed from photosynthetic efficiency during desiccation/rehydration cycles, was accompanied by differential accumulation of intracellular reactive oxygen species (ROS) detected using a dye sensitive to intracellular ROS. Further comparative investigation will aim to understand the genetic, ultrastructural and physiological characteristics supporting unicellular versus multicellular coenobial morphology, and the ability of representatives in the Scenedesmaceae to colonize ecologically diverse, even extreme, habitats.},
}

Cell Nucleus/chemistry/genetics/ultrastructure
Chlorophyceae/classification/*genetics/growth & development
Chlorophyta/*genetics/growth & development/ultrastructure
Cytokinesis/genetics
Ecosystem
Golgi Apparatus/chemistry/ultrastructure
Light
Photosynthesis/*genetics
*Phylogeny
Reactive Oxygen Species/metabolism
Time-Lapse Imaging

@article {pmid31613422,
year = {2019},
author = {Love, AC},
title = {Evolution evolving? Reflections on big questions.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.b.22907},
pmid = {31613422},
issn = {1552-5015},
abstract = {John Bonner managed a long and productive career that balanced specialized inquiry into cellular slime molds with general investigations of big questions in evolutionary biology, such as the origins of multicellular development and the evolution of complexity. This commentary engages with his final paper ("The evolution of evolution"), which argues that the evolutionary process has changed through the history of life. In particular, Bonner emphasizes the possibility that natural selection plays different roles at different size scales. I identify some underlying assumptions in his argument and evaluate its cogency to both foster future discussion and emulate the intellectual example set by Bonner over a lifetime. This endeavor is important beyond Bonner's own theoretical disposition because similar issues are visible in controversies about the possibility of an extended evolutionary synthesis.},
}

@article {pmid31604443,
year = {2019},
author = {Ramon-Mateu, J and Ellison, ST and Angelini, TE and Martindale, MQ},
title = {Regeneration in the ctenophore Mnemiopsis leidyi occurs in the absence of a blastema, requires cell division, and is temporally separable from wound healing.},
journal = {BMC biology},
volume = {17},
number = {1},
pages = {80},
doi = {10.1186/s12915-019-0695-8},
pmid = {31604443},
issn = {1741-7007},
support = {IOS-1755364//National Science Foundation (NSF)/ ; },
abstract = {BACKGROUND: The ability to regenerate is a widely distributed but highly variable trait among metazoans. A variety of modes of regeneration has been described for different organisms; however, many questions regarding the origin and evolution of these strategies remain unanswered. Most species of ctenophore (or "comb jellies"), a clade of marine animals that branch off at the base of the animal tree of life, possess an outstanding capacity to regenerate. However, the cellular and molecular mechanisms underlying this ability are unknown. We have used the ctenophore Mnemiopsis leidyi as a system to study wound healing and adult regeneration and provide some first-time insights of the cellular mechanisms involved in the regeneration of one of the most ancient extant group of multicellular animals.

RESULTS: We show that cell proliferation is activated at the wound site and is indispensable for whole-body regeneration. Wound healing occurs normally in the absence of cell proliferation forming a scar-less wound epithelium. No blastema-like structure is generated at the cut site, and pulse-chase experiments and surgical intervention show that cells originating in the main regions of cell proliferation (the tentacle bulbs) do not seem to contribute to the formation of new structures after surgical challenge, suggesting a local source of cells during regeneration. While exposure to cell-proliferation blocking treatment inhibits regeneration, the ability to regenerate is recovered when the treatment ends (days after the original cut), suggesting that ctenophore regenerative capabilities are constantly ready to be triggered and they are somehow separable of the wound healing process.

CONCLUSIONS: Ctenophore regeneration takes place through a process of cell proliferation-dependent non-blastemal-like regeneration and is temporally separable of the wound healing process. We propose that undifferentiated cells assume the correct location of missing structures and differentiate in place. The remarkable ability to replace missing tissue, the many favorable experimental features (e.g., optical clarity, high fecundity, rapid regenerative performance, stereotyped cell lineage, sequenced genome), and the early branching phylogenetic position in the animal tree, all point to the emergence of ctenophores as a new model system to study the evolution of animal regeneration.},
}

@article {pmid31601898,
year = {2019},
author = {Agić, H and Högström, AES and Moczydłowska, M and Jensen, S and Palacios, T and Meinhold, G and Ebbestad, JOR and Taylor, WL and Høyberget, M},
title = {Organically-preserved multicellular eukaryote from the early Ediacaran Nyborg Formation, Arctic Norway.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {14659},
doi = {10.1038/s41598-019-50650-x},
pmid = {31601898},
issn = {2045-2322},
support = {VR2016-06810//Vetenskapsrådet (Swedish Research Council)/ ; },
abstract = {Eukaryotic multicellularity originated in the Mesoproterozoic Era and evolved multiple times since, yet early multicellular fossils are scarce until the terminal Neoproterozoic and often restricted to cases of exceptional preservation. Here we describe unusual organically-preserved fossils from mudrocks, that provide support for the presence of organisms with differentiated cells (potentially an epithelial layer) in the late Neoproterozoic. Cyathinema digermulense gen. et sp. nov. from the Nyborg Formation, Vestertana Group, Digermulen Peninsula in Arctic Norway, is a new carbonaceous organ-taxon which consists of stacked tubes with cup-shaped ends. It represents parts of a larger organism (multicellular eukaryote or a colony), likely with greater preservation potential than its other elements. Arrangement of open-ended tubes invites comparison with cells of an epithelial layer present in a variety of eukaryotic clades. This tissue may have benefitted the organism in: avoiding overgrowth, limiting fouling, reproduction, or water filtration. C. digermulense shares characteristics with extant and fossil groups including red algae and their fossils, demosponge larvae and putative sponge fossils, colonial protists, and nematophytes. Regardless of its precise affinity, C. digermulense was a complex and likely benthic marine eukaryote exhibiting cellular differentiation, and a rare occurrence of early multicellularity outside of Konservat-Lagerstätten.},
}

@article {pmid31521503,
year = {2019},
author = {Kieninger, AK and Forchhammer, K and Maldener, I},
title = {A nanopore array in the septal peptidoglycan hosts gated septal junctions for cell-cell communication in multicellular cyanobacteria.},
journal = {International journal of medical microbiology : IJMM},
volume = {},
number = {},
pages = {151303},
doi = {10.1016/j.ijmm.2019.03.007},
pmid = {31521503},
issn = {1618-0607},
abstract = {Some filamentous cyanobacteria are phototrophic bacteria with a true multicellular life style. They show patterned cell differentiation with the distribution of metabolic tasks between different cell types. This life style requires a system of cell-cell communication and metabolite exchange along the filament. During our study of the cell wall of species Nostoc punctiforme and Anabaena sp. PCC 7120 we discovered regular perforations in the septum between neighboring cells, which we called nanopore array. AmiC-like amidases are drilling the nanopores with a diameter of 20 nm, and are essential for communication and cell differentiation. NlpD-like regulators of AmiC activity and septum localized proteins SepJ, FraC and FraD are also involved in correct nanopore formation. By focused ion beam (FIB) milling and electron cryotomography we could visualize the septal junctions, which connect adjacent cells and pass thru the nanopores. They consist of cytoplasmic caps, which are missing in the fraD mutant, a plug inside the cytoplasmic membrane and a tube like conduit. A destroyed membrane potential and other stress factors lead to a conformational change in the cap structure and loss of cell-cell communication. These gated septal junctions of cyanobacteria are ancient structures that represent an example of convergent evolution, predating metazoan gap junctions.},
}

@article {pmid31339482,
year = {2019},
author = {Guo, JS and Zhang, Z and Qiao, M and Yu, ZF},
title = {Phalangispora sinensis sp. nov. from Yunnan, China and two new members of Wiesneriomycetaceae.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {69},
number = {10},
pages = {3207-3213},
doi = {10.1099/ijsem.0.003612},
pmid = {31339482},
issn = {1466-5034},
mesh = {Ascomycota/*classification/isolation & purification ; China ; DNA, Fungal/genetics ; Mycological Typing Techniques ; *Phylogeny ; Sequence Analysis, DNA ; Spores, Fungal ; *Water Microbiology ; },
abstract = {Phalangispora sinensis, an aquatic hyphomycete collected from south-western PR China, is described as a new species. This new species is characterized by having multicellular branched conidia composed of a curved main axis and one or two laterals, with the laterals arising from the third or fourth cell of the base of the main axis. Combined analyses of the LSU, SSU, RPB2 and TEF1 gene sequence data revealed that Phalangispora and another aquatic hyphomycete genus, Setosynnema, belonged to Wiesneriomycetaceae, Tubeufiales, Dothideomycetes, Ascomycota.},
}

Ascomycota/*classification/isolation & purification
China
DNA, Fungal/genetics
Mycological Typing Techniques
*Phylogeny
Sequence Analysis, DNA
Spores, Fungal
*Water Microbiology

@article {pmid31589243,
year = {2019},
author = {Arcas, A and Wilkinson, DG and Nieto, MÁ},
title = {The evolutionary history of Ephs and ephrins: towards multicellular organisms.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz222},
pmid = {31589243},
issn = {1537-1719},
abstract = {Eph receptor (Eph) and ephrin signalling regulates fundamental developmental processes through both forward and reverse signalling triggered upon cell-cell contact. In vertebrates, they are both classified into classes A and B, and some representatives have been identified in many metazoan groups, where their expression and functions have been well studied. We have extended previous phylogenetic analyses and examined the presence of Eph and ephrins in the tree of life to determine their origin and evolution. We have found that (i) premetazoan choanoflagellates may already have rudimental Eph/ephrin signalling as they have an Eph-/ephrin-like pair and homologues of downstream signalling genes; (ii) both forward and reverse downstream signalling might already occur in Porifera since sponges have most genes involved in these types of signalling; (iii) the non-vertebrate metazoan Eph is a type-B receptor that can bind ephrins regardless of their membrane anchoring structure, glycosylphosphatidylinositol or transmembrane; (iv) Eph/ephrin cross-class binding is specific to Gnathostomata and (v) kinase-dead Eph receptors can be traced back to Gnathostomata. We conclude that Eph/ephrin signalling is of older origin than previously believed. We also examined the presence of protein domains associated with functional characteristics and the appearance and conservation of downstream signalling pathways to understand the original and derived functions of Ephs and ephrins. We find that the evolutionary history of these gene families points to an ancestral function in cell-cell interactions that could contribute to the emergence of multicellularity and, in particular, to the required segregation of cell populations.},
}

@article {pmid31587642,
year = {2019},
author = {López-Escardó, D and Grau-Bové, X and Guillaumet-Adkins, A and Gut, M and Sieracki, ME and Ruiz-Trillo, I},
title = {Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {374},
number = {1786},
pages = {20190088},
doi = {10.1098/rstb.2019.0088},
pmid = {31587642},
issn = {1471-2970},
abstract = {Understanding the origins of animal multicellularity is a fundamental biological question. Recent genome data have unravelled the role that co-option of pre-existing genes played in the origin of animals. However, there were also some important genetic novelties at the onset of Metazoa. To have a clear understanding of the specific genetic innovations and how they appeared, we need the broadest taxon sampling possible, especially among early-branching animals and their unicellular relatives. Here, we take advantage of single-cell genomics to expand our understanding of the genomic diversity of choanoflagellates, the sister-group to animals. With these genomes, we have performed an updated and taxon-rich reconstruction of protein evolution from the Last Eukaryotic Common Ancestor (LECA) to animals. Our novel data re-defines the origin of some genes previously thought to be metazoan-specific, like the POU transcription factor, which we show appeared earlier in evolution. Moreover, our data indicate that the acquisition of new genes at the stem of Metazoa was mainly driven by duplications and protein domain rearrangement processes at the stem of Metazoa. Furthermore, our analysis allowed us to reveal protein domains that are essential to the maintenance of animal multicellularity. Our analyses also demonstrate the utility of single-cell genomics from uncultured taxa to address evolutionary questions. This article is part of a discussion meeting issue 'Single cell ecology'.},
}

@article {pmid31568885,
year = {2019},
author = {Thakur, R and Shiratori, T and Ishida, KI},
title = {Taxon-rich Multigene Phylogenetic Analyses Resolve the Phylogenetic Relationship Among Deep-branching Stramenopiles.},
journal = {Protist},
volume = {170},
number = {5},
pages = {125682},
doi = {10.1016/j.protis.2019.125682},
pmid = {31568885},
issn = {1618-0941},
abstract = {Stramenopiles are one of the major eukaryotic assemblages. This group comprises a wide range of species including photosynthetic unicellular and multicellular algae, fungus-like osmotrophic organisms and many free-living phagotrophic flagellates. However, the phylogeny of the Stramenopiles, especially relationships among deep-branching heterotrophs, has not yet been resolved because of a lack of adequate transcriptomic data for representative lineages. In this study, we performed multigene phylogenetic analyses of deep-branching Stramenopiles with improved taxon sampling. We sequenced transcriptomes of three deep-branching Stramenopiles: Incisomonas marina, Pseudophyllomitus vesiculosus and Platysulcus tardus. Phylogenetic analyses using 120 protein-coding genes and 56 taxa indicated that Pl. tardus is sister to all other Stramenopiles while Ps. vesiculosus is sister to MAST-4 and form a robust clade with the Labyrinthulea. The resolved phylogenetic relationships of deep-branching Stramenopiles provide insights into the ancestral traits of the Stramenopiles.},
}

@article {pmid31568790,
year = {2019},
author = {Newman, SA},
title = {Cell differentiation: what have we learned in 50 years?.},
journal = {Journal of theoretical biology},
volume = {},
number = {},
pages = {110031},
doi = {10.1016/j.jtbi.2019.110031},
pmid = {31568790},
issn = {1095-8541},
abstract = {I revisit two theories of cell differentiation in multicellular organisms published a half-century ago, Stuart Kauffman's global gene regulatory dynamics (GGRD) model and Roy Britten's and Eric Davidson's modular gene regulatory network (MGRN) model, in light of newer knowledge of mechanisms of gene regulation in the metazoans (animals). The two models continue to inform hypotheses and computational studies of differentiation of lineage-adjacent cell types. However, their shared notion (based on bacterial regulatory systems) of gene switches and networks built from them, have constrained progress in understanding the dynamics and evolution of differentiation. Recent work has described unique write-read-rewrite chromatin-based expression encoding in eukaryotes, as well metazoan-specific processes of gene activation and silencing in condensed-phase, enhancer-recruiting regulatory hubs, employing disordered proteins, including transcription factors, with context-dependent identities. These findings suggest an evolutionary scenario in which the origination of differentiation in animals, rather than depending exclusively on adaptive natural selection, emerged as a consequence of a type of multicellularity in which the novel metazoan gene regulatory apparatus was readily mobilized to amplify and exaggerate inherent cell functions of unicellular ancestors. The plausibility of this hypothesis is illustrated by the evolution of the developmental role of Grainyhead-like in the formation of epithelium.},
}

@article {pmid31565856,
year = {2019},
author = {Gilbert, SF},
title = {Evolutionary transitions revisited: Holobiont evo-devo.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.b.22903},
pmid = {31565856},
issn = {1552-5015},
support = {//Swarthmore College Faculty Research Grant/ ; },
abstract = {John T. Bonner lists four essential transformations in the evolution of life: the emergence of the eukaryotic cell, meiosis, multicellularity, and the nervous system. This paper analyses the mechanisms for those transitions in light of three of Dr. Bonner's earlier hypotheses: (a) that the organism is its life cycle, (b) that evolution consists of alterations of the life cycle, and (c) that development extends beyond the body and into interactions with other organisms. Using the notion of the holobiont life cycle, this paper attempts to show that these evolutionary transitions can be accomplished through various means of symbiosis. Perceiving the organism both as an interspecies consortium and as a life cycle supports a twofold redefinition of the organism as a holobiont constructed by integrating together the life cycles of several species. These findings highlight the importance of symbiosis and the holobiont development in analyses of evolution.},
}

@article {pmid31563945,
year = {2019},
author = {Hernández-Hernández, V and Benítez, M and Boudaoud, A},
title = {Interplay between turgor pressure and plasmodesmata during plant development.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erz434},
pmid = {31563945},
issn = {1460-2431},
abstract = {Plasmodesmata traverse cell walls, generating connections between neighboring cells. They allow intercellular movement of molecules such as transcription factors, hormones, and sugars, and thus create a symplasmic continuity within a tissue. One important factor that determines plasmodesmal permeability is their aperture which is regulated during developmental and physiological processes. Regulation of aperture has been shown to affect developmental events such as vascular differentiation in the root, initiation of lateral roots, or transition to flowering. Extensive research has unraveled molecular factors involved in the regulation of plasmodesmal permeability. Nevertheless, many plant developmental processes appear to involve feedbacks mediated by mechanical forces, raising the question of whether mechanical forces and plasmodesmal permeability affect each other. Here, we review experimental data on how one of these forces, turgor pressure, and plasmodesmal permeability may mutually influence each other during plant development, and we discuss the questions raised by these data. Addressing such questions will improve our knowledge of how cellular patterns emerge during development, shedding light on the evolution of complex multicellular plants.},
}

@article {pmid31552662,
year = {2020},
author = {Wanninger, A and Wollesen, T},
title = {Methods in Brain Development of Molluscs.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2047},
number = {},
pages = {311-324},
doi = {10.1007/978-1-4939-9732-9_17},
pmid = {31552662},
issn = {1940-6029},
abstract = {Representatives of the phylum Mollusca have long been important models in neurobiological research. Recently, the routine application of immunocytochemistry and gene expression analyses in combination with confocal laserscanning microscopy has allowed fast generation of highly detailed reconstructions of neural structures of even the smallest multicellular animals, including early developmental stages. As a consequence, large-scale comparative analyses of neurogenesis-an important prerequisite for inferences concerning the evolution of animal nervous systems-are now possible in a reasonable amount of time. Herein, we describe immunocytochemical staining and in situ hybridization protocols for both, whole-mount preparations of developmental stages-usually 70-300 μm in size-as well as for vibratome and cryostat sections of complex brains. Although our procedures have been optimized for marine molluscs, they may easily be adapted to other (marine) organisms by the creative neurobiologist.},
}

@article {pmid31542284,
year = {2019},
author = {Barger, SR and James, ML and Pellenz, CD and Krendel, M and Sirotkin, V},
title = {Human myosin 1e tail but not motor domain replaces fission yeast Myo1 domains to support myosin-I function during endocytosis.},
journal = {Experimental cell research},
volume = {},
number = {},
pages = {111625},
doi = {10.1016/j.yexcr.2019.111625},
pmid = {31542284},
issn = {1090-2422},
abstract = {In both unicellular and multicellular organisms, long-tailed class I myosins function in clathrin-mediated endocytosis. Myosin 1e (Myo1e) in vertebrates and Myo1 in fission yeast have similar domain organization, yet whether these proteins or their individual protein domains are functionally interchangeable remains unknown. In an effort to assess functional conservation of class I myosins, we tested whether human Myo1e could replace Myo1 in fission yeast Schizosaccharomyces pombe and found that it was unable to substitute for yeast Myo1. To determine if any individual protein domain is responsible for the inability of Myo1e to function in yeast, we created human-yeast myosin-I chimeras. By functionally testing these chimeric myosins in vivo, we concluded that the Myo1e motor domain is unable to function in yeast, even when combined with the yeast Myo1 tail and a full complement of yeast regulatory light chains. Conversely, the Myo1e tail, when attached to the yeast Myo1 motor domain, supports localization to endocytic actin patches and partially rescues the endocytosis defect in myo1Δ cells. Further dissection showed that both the TH1 and TH2-SH3 domains in the human Myo1e tail are required for localization and function of chimeric myosin-I at endocytic sites. Overall, this study provides insights into the role of individual myosin-I domains, expands the utility of fission yeast as a simple model system to study the effects of disease-associated MYO1E mutations, and supports a model of co-evolution between a myosin motor and its actin track.},
}

@article {pmid31540916,
year = {2019},
author = {Pukhlyakova, EA and Kirillova, AO and Kraus, YA and Zimmermann, B and Technau, U},
title = {Cadherin switch marks germ layer formation in the diploblastic sea anemone Nematostella vectensis.},
journal = {Development (Cambridge, England)},
volume = {},
number = {},
pages = {},
doi = {10.1242/dev.174623},
pmid = {31540916},
issn = {1477-9129},
abstract = {Morphogenesis is a shape-building process during development of multicellular organisms. During this process the establishment and modulation of cell-cell contacts play an important role. Cadherins, the major cell adhesion molecules, form adherens junctions connecting epithelial cells. Numerous studies in Bilateria have shown that cadherins are associated with the regulation of cell differentiation, cell shape changes, cell migration and tissue morphogenesis. To date, the role of Cadherins in non-bilaterians is unknown. Here, we study the expression and the function of two paralogous classical cadherins, cadherin1 and cadherin3, in the diploblastic animal, the sea anemone Nematostella vectensis We show that a cadherin switch is accompanying the formation of germ layers. Using specific antibodies, we show that both cadherins are localized to adherens junctions at apical and basal positions in ectoderm and endoderm. During gastrulation, partial EMT of endodermal cells is marked by a step-wise down-regulation of cadherin3 and up-regulation of cadherin1. Knockdown experiments show that both cadherins are required for maintenance of tissue integrity and tissue morphogenesis. Thus, both sea anemones and bilaterians use independently duplicated cadherins combinatorially for tissue morphogenesis and germ layer differentiation.},
}

@article {pmid31540472,
year = {2019},
author = {Denes, V and Geck, P and Mester, A and Gabriel, R},
title = {Pituitary Adenylate Cyclase-Activating Polypeptide: 30 Years in Research Spotlight and 600 Million Years in Service.},
journal = {Journal of clinical medicine},
volume = {8},
number = {9},
pages = {},
doi = {10.3390/jcm8091488},
pmid = {31540472},
issn = {2077-0383},
abstract = {Emerging from the depths of evolution, pituitary adenylate cyclase-activating polypeptide (PACAP) and its receptors (i.e., PAC1, VPAC1, VPAC2) are present in multicellular organisms from Tunicates to humans and govern a remarkable number of physiological processes. Consequently, the clinical relevance of PACAP systems spans a multifaceted palette that includes more than 40 disorders. We aimed to present the versatility of PACAP1-38 actions with a focus on three aspects: (1) when PACAP1-38 could be a cause of a malfunction, (2) when PACAP1-38 could be the cure for a malfunction, and (3) when PACAP1-38 could either improve or impair biology. PACAP1-38 is implicated in the pathophysiology of migraine and post-traumatic stress disorder whereas an outstanding protective potential has been established in ischemia and in Alzheimer's disease. Lastly, PACAP receptors could mediate opposing effects both in cancers and in inflammation. In the light of the above, the duration and concentrations of PACAP agents must be carefully set at any application to avoid unwanted consequences. An enormous amount of data accumulated since its discovery (1989) and the first clinical trials are dated in 2017. Thus in the field of PACAP research: "this is not the end, not even the beginning of the end, but maybe the end of the beginning."},
}

@article {pmid31534207,
year = {2019},
author = {Moger-Reischer, R and Lennon, JT},
title = {Microbial ageing and longevity.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41579-019-0253-y},
pmid = {31534207},
issn = {1740-1534},
abstract = {Longevity reflects the ability to maintain homeostatic conditions necessary for life as an organism ages. A long-lived organism must contend not only with environmental hazards but also with internal entropy and macromolecular damage that result in the loss of fitness during ageing, a phenomenon known as senescence. Although central to many of the core concepts in biology, ageing and longevity have primarily been investigated in sexually reproducing, multicellular organisms. However, growing evidence suggests that microorganisms undergo senescence, and can also exhibit extreme longevity. In this Review, we integrate theoretical and empirical insights to establish a unified perspective on senescence and longevity. We discuss the evolutionary origins, genetic mechanisms and functional consequences of microbial ageing. In addition to having biomedical implications, insights into microbial ageing shed light on the role of ageing in the origin of life and the upper limits to longevity.},
}

@article {pmid31532063,
year = {2019},
author = {Powell, R and O'Malley, MA},
title = {Metabolic and microbial perspectives on the "evolution of evolution".},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.b.22898},
pmid = {31532063},
issn = {1552-5015},
abstract = {Identifying and theorizing major turning points in the history of life generates insights into not only world-changing evolutionary events but also the processes that bring these events about. In his treatment of these issues, Bonner identifies the evolution of sex, multicellularity, and nervous systems as enabling the "evolution of evolution," which involves fundamental transformations in how evolution occurs. By contextualizing his framework within two decades of theorizing about major transitions in evolution, we identify some basic problems that Bonner's theory shares with much of the prevailing literature. These problems include implicit progressivism, theoretical disunity, and a limited ability to explain major evolutionary transformations. We go on to identify events and processes that are neglected by existing views. In contrast with the "vertical" focus on replication, hierarchy, and morphology that preoccupies most of the literature on major transitions, we propose a "horizontal" dimension in which metabolism and microbial innovations play a central explanatory role in understanding the broad-scale organization of life.},
}

@article {pmid31529373,
year = {2019},
author = {Erwin, DH},
title = {Tempos and modes of collectivity in the history of life.},
journal = {Theory in biosciences = Theorie in den Biowissenschaften},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12064-019-00303-4},
pmid = {31529373},
issn = {1611-7530},
support = {NNA13AA90A//NASA Astrobiology Institute/ ; },
abstract = {Collective integration and processing of information have increased through the history of life, through both the formation of aggregates in which the entities may have very different properties and which jointly coarse-grained environmental variables (ranging from widely varying metabolism in microbial consortia to the ecological diversity of species on reefs) and through collectives of similar entities (such as cells within an organism or social groups). Such increases have been implicated in significant transitions in the history of life, including aspects of the origin of life, the generation of pangenomes among microbes and microbial communities such as stromatolites, multicellularity and social insects. This contribution provides a preliminary overview of the dominant modes of collective information processing in the history of life, their phylogenetic distribution and extent of convergence, and the effects of new modes for integrating and acting upon information on the tempo of evolutionary change.},
}

@article {pmid31521200,
year = {2019},
author = {Rausch, P and Rühlemann, M and Hermes, BM and Doms, S and Dagan, T and Dierking, K and Domin, H and Fraune, S and von Frieling, J and Hentschel, U and Heinsen, FA and Höppner, M and Jahn, MT and Jaspers, C and Kissoyan, KAB and Langfeldt, D and Rehman, A and Reusch, TBH and Roeder, T and Schmitz, RA and Schulenburg, H and Soluch, R and Sommer, F and Stukenbrock, E and Weiland-Bräuer, N and Rosenstiel, P and Franke, A and Bosch, T and Baines, JF},
title = {Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {133},
doi = {10.1186/s40168-019-0743-1},
pmid = {31521200},
issn = {2049-2618},
support = {CRC 1182//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as "metaorganisms." The goal of the Collaborative Research Center "Origin and Function of Metaorganisms" is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants.

METHODS: In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample.

CONCLUSION: While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3 V4 over the V1 V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.},
}

@article {pmid31517991,
year = {2019},
author = {de Araújo Silva-Cardoso, IM and Meira, FS and Gomes, ACMM and Scherwinski-Pereira, JE},
title = {Histology, histochemistry and ultrastructure of pre-embryogenic cells determined for direct somatic embryogenesis in the palm tree Syagrus oleracea.},
journal = {Physiologia plantarum},
volume = {},
number = {},
pages = {},
doi = {10.1111/ppl.13026},
pmid = {31517991},
issn = {1399-3054},
abstract = {Somatic embryogenesis in palm trees is, in general, a slow and highly complex process, with a predominance of the indirect route and, consequently, a lack of knowledge about the direct route. We present new knowledge related to the morphological, histochemical, and ultrastructural aspects of the transition from somatic to embryogenic cells and direct formation of somatic embryos from mature zygotic embryos of Syagrus oleracea, a palm tree. The results support the general concept that 2,4-dichlorophenoxyacetic acid plays a critical role for the formation of somatic embryos of direct and multicellular origin. Seven days in medium with auxin were enough for the identification of embryogenic cells. These cells had a set of characteristics that fit them into the concept of totipotent stem cells. At fourteen days in induction medium, nodular formations were observed in the distal region of inoculated embryos, which evolved into globular somatic embryos. At 120 days in induction medium, the quality of the somatic embryos was compromised. The dynamics of the mobilization of reserve compounds was also demonstrated, with emphasis on starch and protein as energy sources required for the embryogenic process. This study shows for the first time the anatomical and ultrastructural events involved in direct somatic embryogenesis in a palm tree and incites the scientific community to return to the discussion of classical concepts related to direct somatic embryogenesis, especially regarding the characteristics and location of determined pre-embryogenic cells. This article is protected by copyright. All rights reserved.},
}

@article {pmid31501435,
year = {2019},
author = {Kiss, E and Hegedüs, B and Virágh, M and Varga, T and Merényi, Z and Kószó, T and Bálint, B and Prasanna, AN and Krizsán, K and Kocsubé, S and Riquelme, M and Takeshita, N and Nagy, LG},
title = {Comparative genomics reveals the origin of fungal hyphae and multicellularity.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4080},
doi = {10.1038/s41467-019-12085-w},
pmid = {31501435},
issn = {2041-1723},
abstract = {Hyphae represent a hallmark structure of multicellular fungi. The evolutionary origins of hyphae and of the underlying genes are, however, hardly known. By systematically analyzing 72 complete genomes, we here show that hyphae evolved early in fungal evolution probably via diverse genetic changes, including co-option and exaptation of ancient eukaryotic (e.g. phagocytosis-related) genes, the origin of new gene families, gene duplications and alterations of gene structure, among others. Contrary to most multicellular lineages, the origin of filamentous fungi did not correlate with expansions of kinases, receptors or adhesive proteins. Co-option was probably the dominant mechanism for recruiting genes for hypha morphogenesis, while gene duplication was apparently less prevalent, except in transcriptional regulators and cell wall - related genes. We identified 414 novel gene families that show correlated evolution with hyphae and that may have contributed to its evolution. Our results suggest that hyphae represent a unique multicellular organization that evolved by limited fungal-specific innovations and gene duplication but pervasive co-option and modification of ancient eukaryotic functions.},
}

@article {pmid31480977,
year = {2019},
author = {Fisher, RM and Regenberg, B},
title = {Multicellular group formation in Saccharomyces cerevisiae.},
journal = {Proceedings. Biological sciences},
volume = {286},
number = {1910},
pages = {20191098},
doi = {10.1098/rspb.2019.1098},
pmid = {31480977},
issn = {1471-2954},
abstract = {Understanding how and why cells cooperate to form multicellular organisms is a central aim of evolutionary biology. Multicellular groups can form through clonal development (where daughter cells stick to mother cells after division) or by aggregation (where cells aggregate to form groups). These different ways of forming groups directly affect relatedness between individual cells, which in turn can influence the degree of cooperation and conflict within the multicellular group. It is hard to study the evolution of multicellularity by focusing only on obligately multicellular organisms, like complex animals and plants, because the factors that favour multicellular cooperation cannot be disentangled, as cells cannot survive and reproduce independently. We support the use of Saccharomyces cerevisiae as an ideal model for studying the very first stages of the evolution of multicellularity. This is because it can form multicellular groups both clonally and through aggregation and uses a family of proteins called 'flocculins' that determine the way in which groups form, making it particularly amenable to laboratory experiments. We briefly review current knowledge about multicellularity in S. cerevisiae and then propose a framework for making predictions about the evolution of multicellular phenotypes in yeast based on social evolution theory. We finish by explaining how S. cerevisiae is a particularly useful experimental model for the analysis of open questions concerning multicellularity.},
}

@article {pmid31474536,
year = {2019},
author = {Gonçalves, AP and Heller, J and Span, EA and Rosenfield, G and Do, HP and Palma-Guerrero, J and Requena, N and Marletta, MA and Glass, NL},
title = {Allorecognition upon Fungal Cell-Cell Contact Determines Social Cooperation and Impacts the Acquisition of Multicellularity.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2019.07.060},
pmid = {31474536},
issn = {1879-0445},
abstract = {Somatic cell fusion and conspecific cooperation are crucial social traits for microbial unicellular-to-multicellular transitions, colony expansion, and substrate foraging but are also associated with risks of parasitism. We identified a cell wall remodeling (cwr) checkpoint that acts upon cell contact to assess genetic compatibility and regulate cell wall dissolution during somatic cell fusion in a wild population of the filamentous fungus Neurospora crassa. Non-allelic interactions between two linked loci, cwr-1 and cwr-2, were necessary and sufficient to block cell fusion: cwr-1 encodes a polysaccharide monooxygenase (PMO), a class of enzymes associated with extracellular degradative capacities, and cwr-2 encodes a predicted transmembrane protein. Mutations of sites in CWR-1 essential for PMO catalytic activity abolished the block in cell fusion between formerly incompatible strains. In Neurospora, alleles cwr-1 and cwr-2 were highly polymorphic, fell into distinct haplogroups, and showed trans-species polymorphisms. Distinct haplogroups and trans-species polymorphisms at cwr-1 and cwr-2 were also identified in the distantly related genus Fusarium, suggesting convergent evolution. Proteins involved in chemotropic processes showed extended localization at contact sites, suggesting that cwr regulates the transition between chemotropic growth and cell wall dissolution. Our work revealed an allorecognition surveillance system based on kind discrimination that inhibits cooperative behavior in fungi by blocking cell fusion upon contact, contributing to fungal immunity by preventing formation of chimeras between genetically non-identical colonies.},
}

@article {pmid31463010,
year = {2019},
author = {Vostinar, AE and Goldsby, HJ and Ofria, C},
title = {Suicidal selection: Programmed cell death can evolve in unicellular organisms due solely to kin selection.},
journal = {Ecology and evolution},
volume = {9},
number = {16},
pages = {9129-9136},
doi = {10.1002/ece3.5460},
pmid = {31463010},
issn = {2045-7758},
abstract = {Abstract: Unicellular organisms can engage in a process by which a cell purposefully destroys itself, termed programmed cell death (PCD). While it is clear that the death of specific cells within a multicellular organism could increase inclusive fitness (e.g., during development), the origin of PCD in unicellular organisms is less obvious. Kin selection has been shown to help maintain instances of PCD in existing populations of unicellular organisms; however, competing hypotheses exist about whether additional factors are necessary to explain its origin. Those factors could include an environmental shift that causes latent PCD to be expressed, PCD hitchhiking on a large beneficial mutation, and PCD being simply a common pathology. Here, we present results using an artificial life model to demonstrate that kin selection can, in fact, be sufficient to give rise to PCD in unicellular organisms. Furthermore, when benefits to kin are direct-that is, resources provided to nearby kin-PCD is more beneficial than when benefits are indirect-that is, nonkin are injured, thus increasing the relative amount of resources for kin. Finally, when considering how strict organisms are in determining kin or nonkin (in terms of mutations), direct benefits are viable in a narrower range than indirect benefits.

Open Research Badges: This article has been awarded Open Data and Open Materials Badges. All materials and data are publicly accessible via the Open Science Framework at https://github.com/anyaevostinar/SuicidalAltruismDissertation/tree/master/LongTerm.},
}

@article {pmid31462290,
year = {2019},
author = {Romero-Mujalli, D and Jeltsch, F and Tiedemann, R},
title = {Elevated mutation rates are unlikely to evolve in sexual species, not even under rapid environmental change.},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {175},
doi = {10.1186/s12862-019-1494-0},
pmid = {31462290},
issn = {1471-2148},
support = {not applicable//Universität Potsdam/ ; },
abstract = {BACKGROUND: Organisms are expected to respond to changing environmental conditions through local adaptation, range shift or local extinction. The process of local adaptation can occur by genetic changes or phenotypic plasticity, and becomes especially relevant when dispersal abilities or possibilities are somehow constrained. For genetic changes to occur, mutations are the ultimate source of variation and the mutation rate in terms of a mutator locus can be subject to evolutionary change. Recent findings suggest that the evolution of the mutation rate in a sexual species can advance invasion speed and promote adaptation to novel environmental conditions. Following this idea, this work uses an individual-based model approach to investigate if the mutation rate can also evolve in a sexual species experiencing different conditions of directional climate change, under different scenarios of colored stochastic environmental noise, probability of recombination and of beneficial mutations. The color of the noise mimicked investigating the evolutionary dynamics of the mutation rate in different habitats.

RESULTS: The results suggest that the mutation rate in a sexual species experiencing directional climate change scenarios can evolve and reach relatively high values mainly under conditions of complete linkage of the mutator locus and the adaptation locus. In contrast, when they are unlinked, the mutation rate can slightly increase only under scenarios where at least 50% of arising mutations are beneficial and the rate of environmental change is relatively fast. This result is robust under different scenarios of stochastic environmental noise, which supports the observation of no systematic variation in the mutation rate among organisms experiencing different habitats.

CONCLUSIONS: Given that 50% beneficial mutations may be an unrealistic assumption, and that recombination is ubiquitous in sexual species, the evolution of an elevated mutation rate in a sexual species experiencing directional climate change might be rather unlikely. Furthermore, when the percentage of beneficial mutations and the population size are small, sexual species (especially multicellular ones) producing few offspring may be expected to react to changing environments not by adaptive genetic change, but mainly through plasticity. Without the ability for a plastic response, such species may become - at least locally - extinct.},
}

@article {pmid31456065,
year = {2019},
author = {Cleri, F},
title = {Agent-based model of multicellular tumor spheroid evolution including cell metabolism.},
journal = {The European physical journal. E, Soft matter},
volume = {42},
number = {8},
pages = {112},
doi = {10.1140/epje/i2019-11878-7},
pmid = {31456065},
issn = {1292-895X},
abstract = {Computational models aiming at the spatio-temporal description of cancer evolution are a suitable framework for testing biological hypotheses from experimental data, and generating new ones. Building on our recent work (J. Theor. Biol. 389, 146 (2016)) we develop a 3D agent-based model, capable of tracking hundreds of thousands of interacting cells, over time scales ranging from seconds to years. Cell dynamics is driven by a Monte Carlo solver, incorporating partial differential equations to describe chemical pathways and the activation/repression of "genes", leading to the up- or down-regulation of specific cell markers. Each cell-agent of different kind (stem, cancer, stromal etc.) runs through its cycle, undergoes division, can exit to a dormant, senescent, necrotic state, or apoptosis, according to the inputs from its systemic network. The basic network at this stage describes glucose/oxygen/ATP cycling, and can be readily extended to cancer-cell specific markers. Eventual accumulation of chemical/radiation damage to each cell's DNA is described by a Markov chain of internal states, and by a damage-repair network, whose evolution is linked to the cell systemic network. Aimed at a direct comparison with experiments of tumorsphere growth from stem cells, the present model will allow to quantitatively study the role of transcription factors involved in the reprogramming and variable radio-resistance of simulated cancer-stem cells, evolving in a realistic computer simulation of a growing multicellular tumorsphere.},
}