@article {pmid30220504,
year = {2018},
author = {De Clerck, O and Kao, SM and Bogaert, KA and Blomme, J and Foflonker, F and Kwantes, M and Vancaester, E and Vanderstraeten, L and Aydogdu, E and Boesger, J and Califano, G and Charrier, B and Clewes, R and Del Cortona, A and D'Hondt, S and Fernandez-Pozo, N and Gachon, CM and Hanikenne, M and Lattermann, L and Leliaert, F and Liu, X and Maggs, CA and Popper, ZA and Raven, JA and Van Bel, M and Wilhelmsson, PKI and Bhattacharya, D and Coates, JC and Rensing, SA and Van Der Straeten, D and Vardi, A and Sterck, L and Vandepoele, K and Van de Peer, Y and Wichard, T and Bothwell, JH},
title = {Insights into the Evolution of Multicellularity from the Sea Lettuce Genome.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2018.08.015},
pmid = {30220504},
issn = {1879-0445},
abstract = {We report here the 98.5 Mbp haploid genome (12,924 protein coding genes) of Ulva mutabilis, a ubiquitous and iconic representative of the Ulvophyceae or green seaweeds. Ulva's rapid and abundant growth makes it a key contributor to coastal biogeochemical cycles; its role in marine sulfur cycles is particularly important because it produces high levels of dimethylsulfoniopropionate (DMSP), the main precursor of volatile dimethyl sulfide (DMS). Rapid growth makes Ulva attractive biomass feedstock but also increasingly a driver of nuisance "green tides." Ulvophytes are key to understanding the evolution of multicellularity in the green lineage, and Ulva morphogenesis is dependent on bacterial signals, making it an important species with which to study cross-kingdom communication. Our sequenced genome informs these aspects of ulvophyte cell biology, physiology, and ecology. Gene family expansions associated with multicellularity are distinct from those of freshwater algae. Candidate genes, including some that arose following horizontal gene transfer from chromalveolates, are present for the transport and metabolism of DMSP. The Ulva genome offers, therefore, new opportunities to understand coastal and marine ecosystems and the fundamental evolution of the green lineage.},
}

@article {pmid30218496,
year = {2018},
author = {Kulkarni, P and Uversky, VN},
title = {Intrinsically Disordered Proteins: The Dark Horse of the Dark Proteome.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e1800061},
doi = {10.1002/pmic.201800061},
pmid = {30218496},
issn = {1615-9861},
abstract = {A good portion of the 'protein universe' embodies the 'dark proteome'. The latter comprises proteins not amenable to experimental structure determination by existing means and inaccessible to homology modeling. Hence, the dark proteome has remained largely unappreciated. Intrinsically disordered proteins (IDPs) that lack rigid 3D structure are a major component of this dark proteome across all three kingdoms of life. Despite lack of structure, IDPs play critical roles in numerous important biological processes. Furthermore, IDPs serve as crucial constituents of proteinaceous membrane-less organelles (PMLOs), where they often serve as drivers and controllers of biological liquid-liquid phase transitions responsible for the PMLO biogenesis. In this perspective, we discuss the role of IDPs in i) the origin of prebiotic life and the evolution of the first independent primordial living unit akin to Tibor Gánti's chemoton, which preceded the Last Universal Common Ancestor (LUCA), ii) role in multicellularity and hence, in major evolutionary transitions, and iii), their role in phenotypic switching, and the emergence of new traits and adaptive opportunities via non-genetic, protein-based, mechanisms. The emerging picture suggests that, despite being major constituents of the dark matter, IDPs may be the dark horse in the protein universe. This article is protected by copyright. All rights reserved.},
}

@article {pmid30214674,
year = {2018},
author = {Baluška, F and Miller, WB},
title = {Senomic view of the cell: Senome versus Genome.},
journal = {Communicative & integrative biology},
volume = {11},
number = {3},
pages = {1-9},
doi = {10.1080/19420889.2018.1489184},
pmid = {30214674},
issn = {1942-0889},
abstract = {In the legacy of Thomas Henry Huxley, and his 'epigenetic' philosophy of biology, cells are proposed to represent a trinity of three memory-storing media: Senome, Epigenome, and Genome that together comprise a cell-wide informational architecture. Our current preferential focus on the Genome needs to be complemented by a similar focus on the Epigenome and a here proposed Senome, representing the sum of all the sensory experiences of the cognitive cell and its sensing apparatus. Only then will biology be in a position to embrace the whole complexity of the eukaryotic cell, understanding its true nature which allows the communicative assembly of cells in the form of sentient multicellular organisms.},
}

@article {pmid30212236,
year = {2018},
author = {Zhang, L and Vijg, J},
title = {Somatic Mutagenesis in Mammals and Its Implications for Human Disease and Aging.},
journal = {Annual review of genetics},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-genet-120417-031501},
pmid = {30212236},
issn = {1545-2948},
abstract = {DNA mutations as a consequence of errors during DNA damage repair, replication, or mitosis are the substrate for evolution. In multicellular organisms, mutations can occur in the germline and also in somatic tissues, where they are associated with cancer and other chronic diseases and possibly with aging. Recent advances in high-throughput sequencing have made it relatively easy to study germline de novo mutations, but in somatic cells, the vast majority of mutations are low-abundant and can be detected only in clonal lineages, such as tumors, or single cells. Here we review recent results on somatic mutations in normal human and animal tissues with a focus on their possible functional consequences. Expected final online publication date for the Annual Review of Genetics Volume 52 is November 23, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid30183198,
year = {2016},
author = {Savostyanov, GA},
title = {EMERGENCE OF STEM CELLS. THE DEVELOPMENT OF MULTICELLULARITY AND ITS QUANTITATIVE CHARACTERISTICS.},
journal = {Tsitologiia},
volume = {58},
number = {8},
pages = {577-593},
pmid = {30183198},
issn = {0041-3771},
}

@article {pmid30177944,
year = {2018},
author = {Yruela, I and Contreras-Moreira, B and Dunker, AK and Niklas, KJ},
title = {Evolution of Protein Ductility in Duplicated Genes of Plants.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1216},
doi = {10.3389/fpls.2018.01216},
pmid = {30177944},
issn = {1664-462X},
abstract = {Previous work has shown that ductile/intrinsically disordered proteins (IDPs) and residues (IDRs) are found in all unicellular and multicellular organisms, wherein they are essential for basic cellular functions and complement the function of rigid proteins. In addition, computational studies of diverse phylogenetic lineages have revealed: (1) that protein ductility increases in concert with organismic complexity, and (2) that distributions of IDPs and IDRs along the chromosomes of plant species are non-random and correlate with variations in the rates of the genetic recombination and chromosomal rearrangement. Here, we show that approximately 50% of aligned residues in paralogs across a spectrum of algae, bryophytes, monocots, and eudicots are IDRs and that a high proportion (ca. 60%) are in disordered segments greater than 30 residues. When three types of IDRs are distinguished (i.e., identical, similar and variable IDRs) we find that species with large numbers of chromosome and endoduplicated genes exhibit paralogous sequences with a higher frequency of identical IDRs, whereas species with small chromosomes numbers exhibit paralogous sequences with a higher frequency of similar and variable IDRs. These results are interpreted to indicate that genome duplication events influence the distribution of IDRs along protein sequences and likely favor the presence of identical IDRs (compared to similar IDRs or variable IDRs). We discuss the evolutionary implications of gene duplication events in the context of ductile/disordered residues and segments, their conservation, and their effects on functionality.},
}

@article {pmid30172691,
year = {2018},
author = {Olejarz, J and Kaveh, K and Veller, C and Nowak, MA},
title = {Selection for synchronized cell division in simple multicellular organisms.},
journal = {Journal of theoretical biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtbi.2018.08.038},
pmid = {30172691},
issn = {1095-8541},
abstract = {The evolution of multicellularity was a major transition in the history of life on earth. Conditions under which multicellularity is favored have been studied theoretically and experimentally. But since the construction of a multicellular organism requires multiple rounds of cell division, a natural question is whether these cell divisions should be synchronous or not. We study a population model in which there compete simple multicellular organisms that grow by either synchronous or asynchronous cell divisions. We demonstrate that natural selection can act differently on synchronous and asynchronous cell division, and we offer intuition for why these phenotypes are generally not neutral variants of each other.},
}

@article {pmid30170750,
year = {2018},
author = {Atkinson, SD and Bartholomew, JL and Lotan, T},
title = {Myxozoans: Ancient metazoan parasites find a home in phylum Cnidaria.},
journal = {Zoology (Jena, Germany)},
volume = {129},
number = {},
pages = {66-68},
doi = {10.1016/j.zool.2018.06.005},
pmid = {30170750},
issn = {1873-2720},
abstract = {Myxozoans are endoparasites with complex life cycles that alternate between invertebrate and vertebrate hosts. Though considered protozoans for over 150 years, they are now recognized as metazoans, given their multicellularity and ultrastructural features. In recognition of synapomorphies and cnidarian-specific genes, myxozoans were placed recently within the phylum Cnidaria. Although they have lost genetic and structural complexity on the path to parasitism, myxozoans have retained characteristic cnidarian cnidocysts, but use them for initiating host infection. Myxozoans represent at least 20% of phylum Cnidaria, but as a result of rapid evolution, extensive diversification and host specialization, they are probably at least as diverse as their free-living relatives. The ability of myxozoans to infect freshwater, marine and terrestrial hosts implies that Cnidaria are no longer constrained to the aquatic environment.},
}

@article {pmid30159848,
year = {2018},
author = {Chi, C and Wang, L and Lan, W and Zhao, L and Su, Y},
title = {PpV, acting via the JNK pathway, represses apoptosis during normal development of Drosophila wing.},
journal = {Apoptosis : an international journal on programmed cell death},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10495-018-1479-2},
pmid = {30159848},
issn = {1573-675X},
support = {201612010//Fundamental Research Funds for the Central Universities/ ; 201762003//Fundamental Research Funds for the Central Universities/ ; 201562029//Fundamental Research Funds for the Central Universities/ ; 31701274//National Natural Science Foundation of China/ ; 2017M612349//China Postdoctoral Science Foundation/ ; },
abstract = {Apoptosis is one of the main fundamental biological processes required for development of multicellular organisms. Inappropriate regulation of apoptosis can lead to severe developmental abnormalities and diseases. Therefore, the control of apoptosis, not only for its activation but also for its inhibition, is critically important during development. In contrast to the extensive studies of apoptosis induction, its inhibitory mechanisms that are even more vital in certain populations of cells actually are very far from being well understood. Here we report an inhibitory role of protein phosphatase V (PpV), a serine/threonine protein phosphatase, in controlling the apoptosis during Drosophila wing development. We observed that inhibition of ppv by RNAi in wing imaginal discs induced ectopic cell death and caspase activation, thus, resulted in a defective adult wing. Moreover, knocking-down ppv triggered the activation of c-Jun N-terminal kinase (JNK) signal, an evolutionarily conserved intracellular signaling that has been implicated to modulate the apoptotic machinery in many biological and experimental systems. Disrupting the JNK signal transduction was adequate to suppress the ppv effects for wing development. Together, we provided the evidence to demonstrate that ppv is required for normal wing development in maintaining the silence of apoptotic signal possibly through JNK pathway.},
}

@article {pmid30149856,
year = {2018},
author = {Strauss, J and Wilkinson, C and Vidilaseris, K and Harborne, SPD and Goldman, A},
title = {A Simple Strategy to Determine the Dependence of Membrane-Bound Pyrophosphatases on K+ as a Cofactor.},
journal = {Methods in enzymology},
volume = {607},
number = {},
pages = {131-156},
doi = {10.1016/bs.mie.2018.04.018},
pmid = {30149856},
issn = {1557-7988},
abstract = {Membrane-bound pyrophosphatases (mPPases) couple pyrophosphate hydrolysis to H+ and/or Na+ pumping across membranes and are found in all domains of life except for multicellular animals including humans. They are important for development and stress resistance in plants. Furthermore, mPPases play a role in virulence of human pathogens that cause severe diseases such as malaria and African sleeping sickness. Sequence analysis, functional studies, and recently solved crystal structures have contributed to the understanding of the mPPase catalytic cycle. However, several key mechanistic features remain unknown. During evolution, several subgroups of mPPases differing in their pumping specificity and cofactor dependency arose. mPPases are classified into one of five subgroups, usually by sequence analysis. However, classification based solely on sequence has been inaccurate in several instances due to our limited understanding of the molecular mechanism of mPPases. Thus, pumping specificity and cofactor dependency of mPPases require experimental confirmation. Here, we describe a simple method for the determination of K+ dependency in mPPases using a hydrolytic activity assay. By coupling these dependency studies with site-directed mutagenesis, we have begun to build a better understanding of the molecular mechanisms of mPPases. We optimized the assay for thermostable mPPases that are commonly used as model systems in our lab, but the method is equally applicable to mesophilic mPPases with minor modifications.},
}

@article {pmid29198427,
year = {2018},
author = {Kenny, NJ and de Goeij, JM and de Bakker, DM and Whalen, CG and Berezikov, E and Riesgo, A},
title = {Towards the identification of ancestrally shared regenerative mechanisms across the Metazoa: A Transcriptomic case study in the Demosponge Halisarca caerulea.},
journal = {Marine genomics},
volume = {37},
number = {},
pages = {135-147},
doi = {10.1016/j.margen.2017.11.001},
pmid = {29198427},
issn = {1876-7478},
mesh = {Animals ; *Evolution, Molecular ; Porifera/genetics/*physiology ; Regeneration/*genetics ; Time Factors ; *Transcriptome ; },
abstract = {Regeneration is an essential process for all multicellular organisms, allowing them to recover effectively from internal and external injury. This process has been studied extensively in a medical context in vertebrates, with pathways often investigated mechanistically, both to derive increased understanding and as potential drug targets for therapy. Several species from other parts of the metazoan tree of life, including Hydra, planarians and echinoderms, noted for their regenerative capabilities, have previously been targeted for study. Less well-documented for their regenerative abilities are sponges. This is surprising, as they are both one of the earliest-branching extant metazoan phyla on Earth, and are rapidly able to respond to injury. Their sessile lifestyle, lack of an external protective layer, inability to respond to predation and filter-feeding strategy all mean that regeneration is often required. In particular the demosponge genus Halisarca has been noted for its fast cell turnover and ability to quickly adjust its cell kinetic properties to repair damage through regeneration. However, while the rate and structure of regeneration in sponges has begun to be investigated, the molecular mechanisms behind this ability are yet to be catalogued. Here we describe the assembly of a reference transcriptome for Halisarca caerulea, along with additional transcriptomes noting response to injury before, shortly following (2h post-), and 12h after trauma. RNAseq reads were assembled using Trinity, annotated, and samples compared, to allow initial insight into the transcriptomic basis of sponge regenerative processes. These resources are deep, with our reference assembly containing >92.6% of the BUSCO Metazoa set of genes, and well-assembled (N50s of 836, 957, 1688 and 2032 for untreated, 2h, 12h and reference transcriptomes respectively), and therefore represent excellent qualitative resources as a bedrock for future study. The generation of transcriptomic resources from sponges before and following deliberate damage has allowed us to study particular pathways within this species responsible for repairing damage. We note particularly the involvement of the Wnt cascades in this process in this species, and detail the contents of this cascade, along with cell cycle, extracellular matrix and apoptosis-linked genes in this work. This resource represents an initial starting point for the continued development of this knowledge, given H. caerulea's ability to regenerate and position as an outgroup for comparing the process of regeneration across metazoan lineages. With this resource in place, we can begin to infer the regenerative capacity of the common ancestor of all extant animal life, and unravel the elements of regeneration in an often-overlooked clade.},
}

Animals
*Evolution, Molecular
Porifera/genetics/*physiology
Regeneration/*genetics
Time Factors
*Transcriptome

@article {pmid29954963,
year = {2018},
author = {Pennisi, E},
title = {Is cancer a breakdown of multicellularity?.},
journal = {Science (New York, N.Y.)},
volume = {360},
number = {6396},
pages = {1391},
doi = {10.1126/science.360.6396.1391},
pmid = {29954963},
issn = {1095-9203},
mesh = {*Biological Evolution ; Carcinogenesis/genetics/*pathology ; Gene Regulatory Networks ; Humans ; Neoplasms/genetics/*pathology ; },
}

*Biological Evolution
Carcinogenesis/genetics/*pathology
Gene Regulatory Networks
Humans
Neoplasms/genetics/*pathology

@article {pmid30134151,
year = {2018},
author = {Stone, R and Portegys, T and Mikhailovsky, G and Alicea, B},
title = {Origins of the Embryo: Self-organization through cybernetic regulation.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biosystems.2018.08.005},
pmid = {30134151},
issn = {1872-8324},
abstract = {The construction of an embryo from a single cell precursor is a highly complex process. Evolutionary emergence of the first embryos is even more complex, and involves both a transition to multicellularity along with the establishment of developmental mechanisms. We propose that embryogenesis relies on a community of cells conforming to a regulatory model of emergent multicellularity. This model draws together multiple threads in the scientific literature, from complexity theory to cybernetics, and from thermodynamic entropy to artificial life. All of these strands come together to inform a model of goal-oriented regulation for emergent structures in early life. This is an important step in the evolution of early life, as well as the emergence of complex life in the earliest habitats. Our model, called the cybernetic embryo, allows for a systems-level view of the embryogenetic process.},
}

@article {pmid30125231,
year = {2018},
author = {Hanschen, ER and Herron, MD and Wiens, JJ and Nozaki, H and Michod, RE},
title = {Multicellularity Drives the Evolution of Sexual Traits.},
journal = {The American naturalist},
volume = {192},
number = {3},
pages = {E93-E105},
doi = {10.1086/698301},
pmid = {30125231},
issn = {1537-5323},
abstract = {From the male peacock's tail plumage to the floral displays of flowering plants, traits related to sexual reproduction are often complex and exaggerated. Why has sexual reproduction become so complicated? Why have such exaggerated sexual traits evolved? Early work posited a connection between multicellularity and sexual traits such as anisogamy (i.e., the evolution of small sperm and large eggs). Anisogamy then drives the evolution of other forms of sexual dimorphism. Yet the relationship between multicellularity and the evolution of sexual traits has not been empirically tested. Given their extensive variation in both multicellular complexity and sexual systems, the volvocine green algae offer a tractable system for understanding the interrelationship of multicellular complexity and sex. Here we show that species with greater multicellular complexity have a significantly larger number of derived sexual traits, including anisogamy, internal fertilization, and secondary sexual dimorphism. Our results demonstrate that anisogamy repeatedly evolved from isogamous multicellular ancestors and that anisogamous species are larger and produce larger zygotes than isogamous species. In the volvocine algae, the evolution of multicellularity likely drives the evolution of anisogamy, and anisogamy subsequently drives secondary sexual dimorphism. Multicellularity may set the stage for the overall diversity of sexual complexity throughout the Tree of Life.},
}

@article {pmid29385672,
year = {2018},
author = {Park, B and Shin, DY and Jeon, TJ},
title = {CBP7 Interferes with the Multicellular Development of Dictyostelium Cells by Inhibiting Chemoattractant-Mediated Cell Aggregation.},
journal = {Molecules and cells},
volume = {41},
number = {2},
pages = {103-109},
doi = {10.14348/molcells.2018.2170},
pmid = {29385672},
issn = {0219-1032},
mesh = {Calcium/metabolism ; Calcium-Binding Proteins/classification/genetics/*metabolism ; Chemotactic Factors/genetics/metabolism ; *Chemotaxis ; Cyclic AMP/metabolism ; Dictyostelium/cytology/genetics/*metabolism ; Movement ; Phylogeny ; *Signal Transduction ; },
abstract = {Calcium ions are involved in the regulation of diverse cellular processes. Fourteen genes encoding calcium binding proteins have been identified in Dictyostelium. CBP7, one of the 14 CBPs, is composed of 169 amino acids and contains four EF-hand motifs. Here, we investigated the roles of CBP7 in the development and cell migration of Dictyostelium cells and found that high levels of CBP7 exerted a negative effect on cells aggregation during development, possibly by inhibiting chemoattractant-directed cell migration. While cells lacking CBP7 exhibited normal development and chemotaxis similar that of wild-type cells, CBP7 overexpressing cells completely lost their chemotactic abilities to move toward increasing cAMP concentrations. This resulted in inhibition of cellular aggregation, a process required for forming multicellular organisms during development. Low levels of cytosolic free calcium were observed in CBP7 overexpressing cells, which was likely the underlying cause of their lack of chemotaxis. Our results demonstrate that CBP7 plays an important role in cell spreading and cell-substrate adhesion. cbp7 null cells showed decreased cell size and cell-substrate adhesion. The present study contributes to further understanding the role of calcium signaling in regulation of cell migration and development.},
}

Calcium/metabolism
Calcium-Binding Proteins/classification/genetics/*metabolism
Chemotactic Factors/genetics/metabolism
*Chemotaxis
Cyclic AMP/metabolism
Dictyostelium/cytology/genetics/*metabolism
Movement
Phylogeny
*Signal Transduction

@article {pmid30109121,
year = {2018},
author = {Wang, X and Zhu, W and Chang, P and Wu, H and Liu, H and Chen, J},
title = {Merge and separation of NuA4 and SWR1 complexes control cell fate plasticity in Candida albicans.},
journal = {Cell discovery},
volume = {4},
number = {},
pages = {45},
doi = {10.1038/s41421-018-0043-0},
pmid = {30109121},
issn = {2056-5968},
abstract = {Phenotypic plasticity is common in development. Candida albicans, a polymorphic fungal pathogen of humans, possesses the unique ability to achieve rapid and reversible cell fate between unicellular form (yeast) and multicellular form (hypha) in response to environmental cues. The NuA4 histone acetyltransferase activity and Hda1 histone deacetylase activity have been reported to be required for hyphal initiation and maintenance. However, how Hda1 and NuA4 regulate hyphal elongation is not clear. NuA4 histone acetyltransferase and SWR1 chromatin remodeling complexes are conserved from yeast to human, which may have merged together to form a larger TIP60 complex since the origin of metazoan. In this study, we show a dynamic merge and separation of NuA4 and SWR1 complexes in C. albicans. NuA4 and SWR1 merge together in yeast state and separate into two distinct complexes in hyphal state. We demonstrate that acetylation of Eaf1 K173 controls the interaction between the two complexes. The YEATS domain of Yaf9 in C. albicans can recognize an acetyl-lysine of the Eaf1 and mediate the Yaf9-Eaf1 interaction. The reversible acetylation and deacetylation of Eaf1 by Esa1 and Hda1 control the merge and separation of NuA4 and SWR1, and this regulation is triggered by Brg1 recruitment of Hda1 to chromatin in response nutritional signals that sustain hyphal elongation. We have also observed an orchestrated promoter association of Esa1, Hda1, Swr1, and H2A.Z during the reversible yeast-hyphae transitions. This is the first discovery of a regulated merge of the NuA4 and SWR1 complexes that controls cell fate determination and this regulation may be conserved in polymorphic fungi.},
}

@article {pmid30103474,
year = {2018},
author = {Mattick, JS},
title = {The State of Long Non-Coding RNA Biology.},
journal = {Non-coding RNA},
volume = {4},
number = {3},
pages = {},
doi = {10.3390/ncrna4030017},
pmid = {30103474},
issn = {2311-553X},
abstract = {Transcriptomic studies have demonstrated that the vast majority of the genomes of mammals and other complex organisms is expressed in highly dynamic and cell-specific patterns to produce large numbers of intergenic, antisense and intronic long non-protein-coding RNAs (lncRNAs). Despite well characterized examples, their scaling with developmental complexity, and many demonstrations of their association with cellular processes, development and diseases, lncRNAs are still to be widely accepted as major players in gene regulation. This may reflect an underappreciation of the extent and precision of the epigenetic control of differentiation and development, where lncRNAs appear to have a central role, likely as organizational and guide molecules: most lncRNAs are nuclear-localized and chromatin-associated, with some involved in the formation of specialized subcellular domains. I suggest that a reassessment of the conceptual framework of genetic information and gene expression in the 4-dimensional ontogeny of spatially organized multicellular organisms is required. Together with this and further studies on their biology, the key challenges now are to determine the structure⁻function relationships of lncRNAs, which may be aided by emerging evidence of their modular structure, the role of RNA editing and modification in enabling epigenetic plasticity, and the role of RNA signaling in transgenerational inheritance of experience.},
}

@article {pmid30102347,
year = {2018},
author = {Gaouda, H and Hamaji, T and Yamamoto, K and Kawai-Toyooka, H and Suzuki, M and Noguchi, H and Minakuchi, Y and Toyoda, A and Fujiyama, A and Nozaki, H and Smith, DR},
title = {Exploring the limits and causes of plastid genome expansion in volvocine green algae.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evy175},
pmid = {30102347},
issn = {1759-6653},
abstract = {Plastid genomes are not normally celebrated for being large. But researchers are steadily uncovering algal lineages with big and, in rare cases, enormous plastid DNAs (ptDNAs), such as volvocine green algae. Plastome sequencing of five different volvocine species has revealed some of the largest, most repeat-dense plastomes on record, including that of Volvox carteri (∼525 kb). Volvocine algae have also been used as models for testing leading hypotheses on organelle genome evolution (e.g., the mutational hazard hypothesis), and it has been suggested that ptDNA inflation within this group might be a consequence of low mutation rates and/or the transition from a unicellular to multicellular existence. Here, we further our understanding of plastome size variation in the volvocine line by examining the ptDNA sequences of the colonial species Yamagishiella unicocca and Eudorina sp. NIES-3984 and the multicellular Volvox africanus, which are phylogenetically situated between species with known ptDNA sizes. Although V. africanus is closely related and similar in multicellular organization to V. carteri, its ptDNA was much less inflated than that of V. carteri. Synonymous- and noncoding-site nucleotide substitution rate analyses of these two Volvox ptDNAs suggest that there are drastically different plastid mutation rates operating in the coding versus intergenic regions, supporting the idea that error-prone DNA repair in repeat-rich intergenic spacers is contributing to genome expansion. Our results reinforce the idea that the volvocine line harbours extremes in plastome size but ultimately shed doubt on some of the previously proposed hypotheses for ptDNA inflation within the lineage.},
}

@article {pmid30099198,
year = {2018},
author = {Lazzari, G and Nicolas, V and Matsusaki, M and Akashi, M and Couvreur, P and Mura, S},
title = {Multicellular spheroid based on a triple co-culture: a novel 3D model to mimic pancreatic tumor complexity.},
journal = {Acta biomaterialia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.actbio.2018.08.008},
pmid = {30099198},
issn = {1878-7568},
abstract = {The preclinical drug screening of pancreatic cancer treatments suffers from the absence of appropriate models capable to reproduce in vitro the heterogeneous tumor microenvironment and its stiff desmoplasia. Driven by this pressing need, we describe in this paper the conception and the characterization of a novel 3D tumor model, consisting of a triple co-culture of pancreatic cancer cells (PANC-1), fibroblasts (MRC-5) and endothelial cells (HUVEC), which assembled to form a hetero-type multicellular tumor spheroid (MCTS). By histological analyses and Selective Plain Illumination Microscopy (SPIM) we have monitored the spatial distribution of each cell type and the evolution of the spheroid composition. Results revealed the presence of a core rich in fibroblasts and fibronectin in which endothelial cells were homogeneously distributed. The integration of the three cell types enabled to reproduce in vitro with fidelity the influence of the surrounding environment on the sensitivity of cancer cells to chemotherapy. To our knowledge, this is the first time that a scaffold-free pancreatic cancer spheroid model combining both tumor and multiple stromal components has been designed. It holds the possibility to become an advantageous tool for a pertinent assessment of the efficacy of various therapeutic strategies.

STATEMENT OF SIGNIFICANCE: Pancreatic tumor microenvironment is characterized by abundant fibrosis and aberrant vasculature. Aiming to reproduce in vitro these features, cancer cells have been already co-cultured with fibroblasts or endothelial cells separately but the integration of both these essential components of the pancreatic tumor microenvironment in a unique system, although urgently needed, was still missing. In this study, we successfully integrated cellular and acellular microenvironment components (i.e., fibroblasts, endothelial cells, fibronectin) in a hetero-type scaffold-free multicellular tumor spheroid. This new 3D triple co-culture model closely mimicked the resistance to treatments observed in vivo, resulting in a reduction of cancer cell sensitivity to the anticancer treatment.},
}

@article {pmid30089142,
year = {2018},
author = {Tverskoi, D and Makarenkov, V and Aleskerov, F},
title = {Modeling functional specialization of a cell colony under different fecundity and viability rates and resource constraint.},
journal = {PloS one},
volume = {13},
number = {8},
pages = {e0201446},
doi = {10.1371/journal.pone.0201446},
pmid = {30089142},
issn = {1932-6203},
abstract = {The emergence of functional specialization is a core problem in biology. In this work we focus on the emergence of reproductive (germ) and vegetative viability-enhancing (soma) cell functions (or germ-soma specialization). We consider a group of cells and assume that they contribute to two different evolutionary tasks, fecundity and viability. The potential of cells to contribute to fitness components is traded off. As embodied in current models, the curvature of the trade-off between fecundity and viability is concave in small-sized organisms and convex in large-sized multicellular organisms. We present a general mathematical model that explores how the division of labor in a cell colony depends on the trade-off curvatures, a resource constraint and different fecundity and viability rates. Moreover, we consider the case of different trade-off functions for different cells. We describe the set of all possible solutions of the formulated mathematical programming problem and show some interesting examples of optimal specialization strategies found for our objective fitness function. Our results suggest that the transition to specialized organisms can be achieved in several ways. The evolution of Volvocalean green algae is considered to illustrate the application of our model. The proposed model can be generalized to address a number of important biological issues, including the evolution of specialized enzymes and the emergence of complex organs.},
}

@article {pmid30086318,
year = {2018},
author = {Furumizu, C and Hirakawa, Y and Bowman, JL and Sawa, S},
title = {3D Body Evolution: Adding a New Dimension to Colonize the Land.},
journal = {Current biology : CB},
volume = {28},
number = {15},
pages = {R838-R840},
doi = {10.1016/j.cub.2018.06.040},
pmid = {30086318},
issn = {1879-0445},
abstract = {Complex multicellular plant bodies evolved in both generations of land plants. A new study demonstrates that CLAVATA3-like peptides function via conserved receptors in Physcomitrella patens as key molecules for morphological innovation of 3D growth in land plants.},
}

@article {pmid30082786,
year = {2018},
author = {Li, Z and Fu, X and Wang, Y and Liu, R and He, Y},
title = {Polycomb-mediated gene silencing by the BAH-EMF1 complex in plants.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41588-018-0190-0},
pmid = {30082786},
issn = {1546-1718},
abstract = {Polycomb proteins implement genome-wide transcriptional repression in multicellular organisms. The evolutionarily conserved Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) that is read and effected by Polycomb repressive complex 1 (PRC1) in animals, but the interpretation of this mark remains unclear in plants. Here we report that in the eudicot Arabidopsis thaliana two homologous BAH (Bromo adjacent homology) domain-containing proteins form a plant-specific complex with EMBRYONIC FLOWER 1 (EMF1), and that the BAH-EMF1 complex (BAH-EMF1c) reads and effects the H3K27me3 mark and mediates genome-wide transcriptional repression. Furthermore, in the monocot rice a homolog of the Arabidopsis BAH-domain proteins also binds methylated H3K27 and forms a complex with the rice homolog of EMF1, suggesting that BAH-EMF1c is conserved in flowering plants. Therefore, our results show that the plant-specific BAH-EMF1c fulfills PRC1-like functions in higher plants, suggesting a convergent evolution of PRC1 activity in plants and animals.},
}

@article {pmid29415511,
year = {2018},
author = {Henderson, SW and Wege, S and Gilliham, M},
title = {Plant Cation-Chloride Cotransporters (CCC): Evolutionary Origins and Functional Insights.},
journal = {International journal of molecular sciences},
volume = {19},
number = {2},
pages = {},
doi = {10.3390/ijms19020492},
pmid = {29415511},
issn = {1422-0067},
mesh = {Biological Evolution ; Gene Expression ; Homeostasis ; Ions/metabolism ; Phenotype ; Plant Development/genetics ; Plant Proteins/genetics/*metabolism ; Plants/classification/drug effects/genetics/*metabolism ; Sodium-Potassium-Chloride Symporters/genetics/*metabolism ; Water/metabolism ; },
abstract = {Genomes of unicellular and multicellular green algae, mosses, grasses and dicots harbor genes encoding cation-chloride cotransporters (CCC). CCC proteins from the plant kingdom have been comparatively less well investigated than their animal counterparts, but proteins from both plants and animals have been shown to mediate ion fluxes, and are involved in regulation of osmotic processes. In this review, we show that CCC proteins from plants form two distinct phylogenetic clades (CCC1 and CCC2). Some lycophytes and bryophytes possess members from each clade, most land plants only have members of the CCC1 clade, and green algae possess only the CCC2 clade. It is currently unknown whether CCC1 and CCC2 proteins have similar or distinct functions, however they are both more closely related to animal KCC proteins compared to NKCCs. Existing heterologous expression systems that have been used to functionally characterize plant CCC proteins, namely yeast and Xenopus laevis oocytes, have limitations that are discussed. Studies from plants exposed to chemical inhibitors of animal CCC protein function are reviewed for their potential to discern CCC function in planta. Thus far, mutations in plant CCC genes have been evaluated only in two species of angiosperms, and such mutations cause a diverse array of phenotypes-seemingly more than could simply be explained by localized disruption of ion transport alone. We evaluate the putative roles of plant CCC proteins and suggest areas for future investigation.},
}

Biological Evolution
Gene Expression
Homeostasis
Ions/metabolism
Phenotype
Plant Development/genetics
Plant Proteins/genetics/*metabolism
Plants/classification/drug effects/genetics/*metabolism
Sodium-Potassium-Chloride Symporters/genetics/*metabolism
Water/metabolism

@article {pmid29292130,
year = {2018},
author = {López, JL and Alvarez, F and Príncipe, A and Salas, ME and Lozano, MJ and Draghi, WO and Jofré, E and Lagares, A},
title = {Isolation, taxonomic analysis, and phenotypic characterization of bacterial endophytes present in alfalfa (Medicago sativa) seeds.},
journal = {Journal of biotechnology},
volume = {267},
number = {},
pages = {55-62},
doi = {10.1016/j.jbiotec.2017.12.020},
pmid = {29292130},
issn = {1873-4863},
mesh = {Actinobacteria/genetics/isolation & purification ; Bacteroidetes/genetics/isolation & purification ; Endophytes/classification/*genetics ; Firmicutes/genetics/isolation & purification ; Medicago sativa/genetics/*microbiology ; Microbiota/*genetics ; *Phylogeny ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Seedlings/microbiology ; Seeds/microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {A growing body of evidence has reinforced the central role of microbiomes in the life of sound multicellular eukaryotes, thus more properly described as true holobionts. Though soil was considered a main source of plant microbiomes, seeds have been shown to be endophytically colonized by microorganisms thus representing natural carriers of a selected microbial inoculum to the young seedlings. In this work we have investigated the type of culturable endophytic bacteria that are carried within surface-sterilized alfalfa seeds. MALDI-TOF analysis revealed the presence of bacteria that belonged to 40 separate genera, distributed within four taxa (Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes). Nonsymbiotic members of the Rhizobiaceae family were also found. The evaluation of nine different in-vitro biochemical activities demonstrated isolates with complex combinations of traits that, upon a Principal-Component-Analysis, could be classified into four phenotypic groups. That isolates from nearly half of the genera identified had been able to colonize alfalfa plants grown under axenic conditions was remarkable. Further analyses should be addressed to investigating the colonization mechanisms of the alfalfa seeds, the evolutionary significance of the alfalfa-seed endophytes, and also how after germination the seed microbiome competes with spermospheric and rhizospheric soil bacteria to colonize newly emerging seedlings.},
}

Actinobacteria/genetics/isolation & purification
Bacteroidetes/genetics/isolation & purification
Endophytes/classification/*genetics
Firmicutes/genetics/isolation & purification
Medicago sativa/genetics/*microbiology
Microbiota/*genetics
*Phylogeny
Proteobacteria/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Seedlings/microbiology
Seeds/microbiology
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

@article {pmid30078827,
year = {2018},
author = {Oka, M and Yoneda, Y},
title = {Importin α: functions as a nuclear transport factor and beyond.},
journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences},
volume = {94},
number = {7},
pages = {259-274},
doi = {10.2183/pjab.94.018},
pmid = {30078827},
issn = {1349-2896},
abstract = {Nucleocytoplasmic transport is an essential process in eukaryotes. The molecular mechanisms underlying nuclear transport that involve the nuclear transport receptor, small GTPase Ran, and the nuclear pore complex are highly conserved from yeast to humans. On the other hand, it has become clear that the nuclear transport system diverged during evolution to achieve various physiological functions in multicellular eukaryotes. In this review, we first summarize the molecular mechanisms of nuclear transport and how these were elucidated. Then, we focus on the diverse functions of importin α, which acts not merely an import factor but also as a multi-functional protein contributing to a variety of cellular functions in higher eukaryotes.},
}

@article {pmid30072980,
year = {2018},
author = {Sharma, G and Burrows, LL and Singer, M},
title = {Diversity and Evolution of Myxobacterial Type IV Pilus Systems.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1630},
doi = {10.3389/fmicb.2018.01630},
pmid = {30072980},
issn = {1664-302X},
abstract = {Type IV pili (T4P) are surface-exposed protein fibers that play key roles in the bacterial life cycle via surface attachment/adhesion, biofilm formation, motility, and development. The order Myxococcales (myxobacteria) are members of the class Deltaproteobacteria and known for their large genome size and complex social behaviors, including gliding motility, fruiting body formation, biofilm production, and prey hunting. Myxococcus xanthus, the best-characterized member of the order, relies on the appropriate expression of 17 type IVa (T4aP) genes organized in a single cluster plus additional genes (distributed throughout the genome) for social motility and development. Here, we compared T4aP genes organization within the myxobacteria to understand their evolutionary origins and diversity. We found that T4aP genes are organized as large clusters in suborder Cystobacterineae, whereas in other two suborders Sorangiineae and Nannocystineae, these genes are dispersed throughout the genome. Based on the genomic organization, the phylogeny of conserved proteins, and synteny studies among 28 myxobacterial and 66 Proteobacterial genomes, we propose an evolutionary model for the origin of myxobacterial T4aP genes independently from other orders in class Deltaproteobacteria. Considering a major role for T4P, this study further proposes the origins and evolution of social motility in myxobacteria and provides a foundation for understanding how complex-behavioral traits, such as gliding motility, multicellular development, etc., might have evolved in this diverse group of complex organisms.},
}

@article {pmid30068565,
year = {2018},
author = {Bornens, M},
title = {Cell polarity: having and making sense of direction-on the evolutionary significance of the primary cilium/centrosome organ in Metazoa.},
journal = {Open biology},
volume = {8},
number = {8},
pages = {},
doi = {10.1098/rsob.180052},
pmid = {30068565},
issn = {2046-2441},
abstract = {Cell-autonomous polarity in Metazoans is evolutionarily conserved. I assume that permanent polarity in unicellular eukaryotes is required for cell motion and sensory reception, integration of these two activities being an evolutionarily constrained function. Metazoans are unique in making cohesive multicellular organisms through complete cell divisions. They evolved a primary cilium/centrosome (PC/C) organ, ensuring similar functions to the basal body/flagellum of unicellular eukaryotes, but in different cells, or in the same cell at different moments. The possibility that this innovation contributed to the evolution of individuality, in being instrumental in the early specification of the germ line during development, is further discussed. Then, using the example of highly regenerative organisms like planarians, which have lost PC/C organ in dividing cells, I discuss the possibility that part of the remodelling necessary to reach a new higher-level unit of selection in multi-cellular organisms has been triggered by conflicts among individual cell polarities to reach an organismic polarity. Finally, I briefly consider organisms with a sensorimotor organ like the brain that requires exceedingly elongated polarized cells for its activity. I conclude that beyond critical consequences for embryo development, the conservation of cell-autonomous polarity in Metazoans had far-reaching implications for the evolution of individuality.},
}

@article {pmid30066215,
year = {2018},
author = {Stencel, A and Wloch-Salamon, DM},
title = {Some theoretical insights into the hologenome theory of evolution and the role of microbes in speciation.},
journal = {Theory in biosciences = Theorie in den Biowissenschaften},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12064-018-0268-3},
pmid = {30066215},
issn = {1611-7530},
support = {2018/28/T/HS1/00201//Narodowe Centrum Nauki/ ; Opus 2017/25/B/NZ8/01035//Narodowe Centrum Nauki/ ; DS/762 - K/ZDS/007338//Uniwersytet Jagielloński w Krakowie/ ; },
abstract = {Research on symbiotic communities (microbiomes) of multicellular organisms seems to be changing our understanding of how species of plants and animals have evolved over millions of years. The quintessence of these discoveries is the emergence of the hologenome theory of evolution, founded on the concept that a holobiont (a host along with all of its associated symbiotic microorganisms) acts a single unit of selection in the process of evolution. Although the hologenome theory has become very popular among certain scientific circles, its principles are still being debated. In this paper, we argue, firstly, that only a very small number of symbiotic microorganisms are sufficiently integrated into multicellular organisms to act in concert with them as units of selection, thus rendering claims that holobionts are units of selection invalid. Secondly, even though holobionts are not units of selection, they can still constitute genuine units from an evolutionary perspective, provided we accept certain constraints: mainly, they should be considered units of co-operation. Thirdly, we propose a reconciliation of the role of symbiotic microorganisms with the theory of speciation through the use of a developed framework. Mainly, we will argue that, in order to understand the role of microorganisms in the speciation of multicellular organisms, it is not necessary to consider holobionts units of selection; it is sufficient to consider them units of co-operation.},
}

@article {pmid30065707,
year = {2018},
author = {Chen, H and Zhang, SD and Chen, L and Cai, Y and Zhang, WJ and Song, T and Wu, LF},
title = {Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1569},
doi = {10.3389/fmicb.2018.01569},
pmid = {30065707},
issn = {1664-302X},
abstract = {Magnetotactic bacteria (MTB) are a diverse group of microorganisms capable of using geomagnetic fields for navigation. This magnetotactic behavior can help microorganisms move toward favorable habitats for optimal growth and reproduction. A comprehensive understanding of the magnetotactic mechanism at molecular levels requires highly efficient genomic editing tools, which remain underdeveloped in MTB. Here, we adapted an engineered CRISPR-Cas9 system for efficient inactivation of genes in a widely used MTB model strain, Magnetospirillum magneticum AMB-1. By combining a nuclease-deficient Cas9 (dCas9) and single-guide RNA (sgRNA), a CRISPR interference system was successfully developed to repress amb0994 expression. Furthermore, we constructed an in-frame deletion mutant of amb0994 by developing a CRISPR-Cas9 system. This mutant produces normal magnetosomes; however, its response to abrupt magnetic field reversals is faster than wild-type strain. This behavioral difference is probably a consequence of altered flagella function, as suggested with our dynamics simulation study by modeling M. magneticum AMB-1 cell as an ellipsoid. These data indicate that, Amb0994 is involved in the cellular response to magnetic torque changes via controlling flagella. In summary, this study, besides contributing to a better understanding of magnetotaxis mechanism, demonstrated the CRISPR-(d)Cas9 system as a useful genetic tool for efficient genome editing in MTB.},
}

@article {pmid30061903,
year = {2018},
author = {Benítez, M and Hernández-Hernández, V and Newman, SA and Niklas, KJ},
title = {Dynamical Patterning Modules, Biogeneric Materials, and the Evolution of Multicellular Plants.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {871},
doi = {10.3389/fpls.2018.00871},
pmid = {30061903},
issn = {1664-462X},
abstract = {Comparative analyses of developmental processes across a broad spectrum of organisms are required to fully understand the mechanisms responsible for the major evolutionary transitions among eukaryotic photosynthetic lineages (defined here as the polyphyletic algae and the monophyletic land plants). The concepts of dynamical patterning modules (DPMs) and biogeneric materials provide a framework for studying developmental processes in the context of such comparative analyses. In the context of multicellularity, DPMs are defined as sets of conserved gene products and molecular networks, in conjunction with the physical morphogenetic and patterning processes they mobilize. A biogeneric material is defined as mesoscale matter with predictable morphogenetic capabilities that arise from complex cellular conglomerates. Using these concepts, we outline some of the main events and transitions in plant evolution, and describe the DPMs and biogeneric properties associated with and responsible for these transitions. We identify four primary DPMs that played critical roles in the evolution of multicellularity (i.e., the DPMs responsible for cell-to-cell adhesion, identifying the future cell wall, cell differentiation, and cell polarity). Three important conclusions emerge from a broad phyletic comparison: (1) DPMs have been achieved in different ways, even within the same clade (e.g., phycoplastic cell division in the Chlorophyta and phragmoplastic cell division in the Streptophyta), (2) DPMs had their origins in the co-option of molecular species present in the unicellular ancestors of multicellular plants, and (3) symplastic transport mediated by intercellular connections, particularly plasmodesmata, was critical for the evolution of complex multicellularity in plants.},
}

@article {pmid30061561,
year = {2018},
author = {Stewart, AD and Rice, WR},
title = {Arrest of sex-specific adaptation during the evolution of sexual dimorphism in Drosophila.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-018-0613-4},
pmid = {30061561},
issn = {2397-334X},
abstract = {Sexually antagonistic selection arises when a trait expressed in both sexes (a shared trait) is selected towards different, sex-specific optima. Sex-discordant selection causes different alleles to be favoured in each sex (intralocus sexual conflict). A key parameter responsible for generating this conflict is the intersexual genetic correlation (rMF), which determines the degree to which heritable genetic variation for the shared trait produces a similar phenotype in both sexes. A strong, positive rMF interferes with adaptation when there is sex-discordant selection. In principle, the rMF can evolve in response to sex-discordant selection: the faster it declines, the faster the resolution of intralocus sexual conflict. Here, we use Drosophila melanogaster to quantify the time scale over which a strong, positive rMF impedes a response to sex-discordant selection for a canonical quantitative trait (body size) with an exceptionally long (250 generations) selection experiment for a complex multicellular organism. We found that, compared with rapid and substantial evolution under sex-concordant selection, a high rMF arrested sex-specific adaptation for 100 generations in females and a minimum of 250 generations in males. Our study demonstrates that a high rMF can lead to a protracted period of adaptive stalemate during the evolution of sexual dimorphism.},
}

@article {pmid30059538,
year = {2018},
author = {Waldron, FM and Stone, GN and Obbard, DJ},
title = {Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes.},
journal = {PLoS genetics},
volume = {14},
number = {7},
pages = {e1007533},
doi = {10.1371/journal.pgen.1007533},
pmid = {30059538},
issn = {1553-7404},
abstract = {RNA interference (RNAi)-related pathways target viruses and transposable element (TE) transcripts in plants, fungi, and ecdysozoans (nematodes and arthropods), giving protection against infection and transmission. In each case, this produces abundant TE and virus-derived 20-30nt small RNAs, which provide a characteristic signature of RNAi-mediated defence. The broad phylogenetic distribution of the Argonaute and Dicer-family genes that mediate these pathways suggests that defensive RNAi is ancient, and probably shared by most animal (metazoan) phyla. Indeed, while vertebrates had been thought an exception, it has recently been argued that mammals also possess an antiviral RNAi pathway, although its immunological relevance is currently uncertain and the viral small RNAs (viRNAs) are not easily detectable. Here we use a metagenomic approach to test for the presence of viRNAs in five species from divergent animal phyla (Porifera, Cnidaria, Echinodermata, Mollusca, and Annelida), and in a brown alga-which represents an independent origin of multicellularity from plants, fungi, and animals. We use metagenomic RNA sequencing to identify around 80 virus-like contigs in these lineages, and small RNA sequencing to identify viRNAs derived from those viruses. We identified 21U small RNAs derived from an RNA virus in the brown alga, reminiscent of plant and fungal viRNAs, despite the deep divergence between these lineages. However, contrary to our expectations, we were unable to identify canonical (i.e. Drosophila- or nematode-like) viRNAs in any of the animals, despite the widespread presence of abundant micro-RNAs, and somatic transposon-derived piwi-interacting RNAs. We did identify a distinctive group of small RNAs derived from RNA viruses in the mollusc. However, unlike ecdysozoan viRNAs, these had a piRNA-like length distribution but lacked key signatures of piRNA biogenesis. We also identified primary piRNAs derived from putatively endogenous copies of DNA viruses in the cnidarian and the echinoderm, and an endogenous RNA virus in the mollusc. The absence of canonical virus-derived small RNAs from our samples may suggest that the majority of animal phyla lack an antiviral RNAi response. Alternatively, these phyla could possess an antiviral RNAi response resembling that reported for vertebrates, with cryptic viRNAs not detectable through simple metagenomic sequencing of wild-type individuals. In either case, our findings show that the antiviral RNAi responses of arthropods and nematodes, which are highly divergent from each other and from that of plants and fungi, are also highly diverged from the most likely ancestral metazoan state.},
}

@article {pmid30028958,
year = {2018},
author = {Campbell, FC and Loughrey, MB and McClements, J and Deevi, RK and Javadi, A and Rainey, L},
title = {Mechanistic insights into colorectal cancer phenomics from fundamental and organotypic model studies.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2018.05.021},
pmid = {30028958},
issn = {1525-2191},
abstract = {Colorectal cancer (CRC) diagnosis and prognostic stratification are based on histopathological assessment of cell or nuclear pleomorphism, aberrant mitotic figures, altered glandular architecture, and other phenomic abnormalities. This complexity is driven by oncogenic perturbation of tightly coordinated spatiotemporal signaling to disrupt multiple scales of tissue organization. This review clarifies molecular and cellular mechanisms underlying common CRC histological features and help understand how the CRC genome controls core aspects of tumor aggressiveness. It further explores a spatiotemporal framework for CRC phenomics based on regulation of living cells in fundamental and organotypic model systems. The review also discusses tissue homeostasis, considers distinct classes of oncogenic perturbations, and evolution of cellular or multicellular cancer phenotypes. It further explores the molecular controls of cribriform, micropapillary, and high-grade CRC morphology in organotypic culture models and assesses relevant translational studies. In addition, the review delves into complexities of morphological plasticity whereby a single molecular signature generates heterogeneous cancer phenotypes, and conversely, morphologically homogeneous tumors show substantive molecular diversity. Principles outlined may aid mechanistic interpretation of OMICs data in a setting of cancer pathology, provide insight into CRC consensus molecular subtypes, and better define principles for CRC prognostic stratification.},
}

@article {pmid29992410,
year = {2018},
author = {Leong, SP and Aktipis, A and Maley, C},
title = {Cancer initiation and progression within the cancer microenvironment.},
journal = {Clinical & experimental metastasis},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10585-018-9921-y},
pmid = {29992410},
issn = {1573-7276},
abstract = {Within the cancer microenvironment, the growth and proliferation of cancer cells in the primary site as well as in the metastatic site represent a global biological phenomenon. To understand the growth, proliferation and progression of cancer either by local expansion and/or metastasis, it is important to understand the cancer microenvironment and host response to cancer growth. Melanoma is an excellent model to study the interaction of cancer initiation and growth in relationship to its microenvironment. Social evolution with cooperative cellular groups within an organism is what gives rise to multicellularity in the first place. Cancer cells evolve to exploit their cellular environment. The foundations of multicellular cooperation break down in cancer because those cells that misbehave have an evolutionary advantage over their normally behaving neighbors. It is important to classify evolutionary and ecological aspects of cancer growth, thus, data for cancer growth and outcomes need to be collected to define these parameters so that accurate predictions of how cancer cells may proliferate and metastasize can be developed.},
}

@article {pmid29968903,
year = {2018},
author = {Veronesi, F and Pagani, S and Torricelli, P and Filardo, G and Cavallo, C and Grigolo, B and Fini, M},
title = {PRP and MSCs on tenocytes artificial wound healing: an in vitro study comparing fresh and frozen PRP.},
journal = {Histology and histopathology},
volume = {},
number = {},
pages = {18018},
doi = {10.14670/HH-18-018},
pmid = {29968903},
issn = {1699-5848},
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.Tendon tissue has poor regenerative capacity due to its low vascularization, cell density and extracellular matrix (ECM) production. Therefore, tendon injuries are an increasing clinical problem because of the formation of scar tissue with traditional therapies. Regenerative medicine aims at triggering a healing response through the use of biological treatments such as mesenchymal stromal cells (MSCs) and growth factors (GFs). MSCs show several advantages in tendon clinical setting, while platelet rich plasma (PRP) has gained popularity because of its high GF concentration, although its applications in the tendon clinical setting are still controversial. The aim of the present study was to evaluate a combined treatment of MSCs and PRP in an in vitro microwound model of tendon injuries. In addition, fresh and frozen PRP were compared. Single human tenocytes cultures or co-cultures with bone marrow derived MSCs (BMSCs) were set up with or without human PRP, fresh or frozen. After 24 hours of culture, it was observed that MSCs alone significantly increased tenocyte migration speed, microwound healing rate, fibronectin, collagen I and aggrecan production. These effects were enhanced by the combination with PRP, fresh being more effective than frozen PRP. In addition, the number of MSCs and tenocytes inside the microwound was significantly increased, especially with fresh PRP. In conclusion, the combination of MSCs and PRP, especially the fresh one, increases tenocytes and MSC migration speed, as well as ECM protein production compared to the use of MSCs alone.},
}

@article {pmid29966484,
year = {2018},
author = {Liao, Z and Kjellin, J and Hoeppner, MP and Grabherr, M and Söderbom, F},
title = {Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.},
journal = {RNA biology},
volume = {},
number = {},
pages = {},
doi = {10.1080/15476286.2018.1481697},
pmid = {29966484},
issn = {1555-8584},
abstract = {Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3'-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.},
}

@article {pmid29961831,
year = {2018},
author = {Zhao, J and Yuan, S and Gao, B and Zhu, S},
title = {Molecular diversity of fungal inhibitor cystine knot peptides evolved by domain repeat and fusion.},
journal = {FEMS microbiology letters},
volume = {365},
number = {15},
pages = {},
doi = {10.1093/femsle/fny158},
pmid = {29961831},
issn = {1574-6968},
abstract = {Peptides with the inhibitor cystine knot (ICK) motif are extensively present in animals and plants where they exert a diversity of biological functions. However, few studies have been undertaken on this class of peptides in fungi. In this work, we identify a total of 386 fungal ICK peptides and proteins containing this motif by computational data mining of fungal genome databases, which exhibit 14 different exon-intron structures. According to their domain architectures, these proteins are classified into three distinct structural types, including single domains, tandem repeat domains and fusion domains, in which six families belonging to single or tandem repeat domains show remarkable sequence similarity to those from animals and plants, suggesting their orthologous relationship. Extremely high molecular diversity in fungal ICKs might be attributable to different genetic mechanisms, such as gene/domain duplication and fusion. This work not only enlarges the number of ICK peptides in multicellular organisms, but also uncovers their complex evolutionary history in a specific lineage.},
}

@article {pmid29942020,
year = {2018},
author = {Sebé-Pedrós, A and Chomsky, E and Pang, K and Lara-Astiaso, D and Gaiti, F and Mukamel, Z and Amit, I and Hejnol, A and Degnan, BM and Tanay, A},
title = {Early metazoan cell type diversity and the evolution of multicellular gene regulation.},
journal = {Nature ecology & evolution},
volume = {2},
number = {7},
pages = {1176-1188},
doi = {10.1038/s41559-018-0575-6},
pmid = {29942020},
issn = {2397-334X},
abstract = {A hallmark of metazoan evolution is the emergence of genomic mechanisms that implement cell-type-specific functions. However, the evolution of metazoan cell types and their underlying gene regulatory programmes remains largely uncharacterized. Here, we use whole-organism single-cell RNA sequencing to map cell-type-specific transcription in Porifera (sponges), Ctenophora (comb jellies) and Placozoa species. We describe the repertoires of cell types in these non-bilaterian animals, uncovering diverse instances of previously unknown molecular signatures, such as multiple types of peptidergic cells in Placozoa. Analysis of the regulatory programmes of these cell types reveals variable levels of complexity. In placozoans and poriferans, sequence motifs in the promoters are predictive of cell-type-specific programmes. By contrast, the generation of a higher diversity of cell types in ctenophores is associated with lower specificity of promoter sequences and the existence of distal regulatory elements. Our findings demonstrate that metazoan cell types can be defined by networks of transcription factors and proximal promoters, and indicate that further genome regulatory complexity may be required for more diverse cell type repertoires.},
}

@article {pmid29939836,
year = {2018},
author = {Pashov, A and Hernandez Puente, CV and Ibrahim, SM and Monzavi-Karbassi, B and Makhoul, I and Kieber-Emmons, T},
title = {Thinking Cancer.},
journal = {Monoclonal antibodies in immunodiagnosis and immunotherapy},
volume = {37},
number = {3},
pages = {117-125},
doi = {10.1089/mab.2018.0014},
pmid = {29939836},
issn = {2167-9436},
abstract = {Evolutionary theories are necessarily invoked for understanding cancer development at the level of species, at the level of cells and tissues, and for developing effective therapies. It is crucial to view cancer in a Darwinian light, where the differential survival of individual cells is based on heritable variations. In the process of this somatic evolution, multicellularity controls are overridden by cancer cells, which become increasingly autonomous. Ecological epigenetics also helps understand how rogue cells that have basically the same DNA as their normal cell counterpart overcome the tissue homeostasis. As we struggle to wrap our minds around the complexity of these phenomena, we apply often times anthropomorphic terms, such as subversion, hijacking, or hacking, to describe especially the most complex among them-the interaction of tumors with the immune system. In this commentary we highlight examples of the anthropomorphic thinking of cancer and try to put into context the relative meaning of terms and the mechanisms that are oftentimes invoked to justify those terms.},
}

@article {pmid29938763,
year = {2018},
author = {Funayama, N},
title = {The cellular and molecular bases of the sponge stem cell systems underlying reproduction, homeostasis and regeneration.},
journal = {The International journal of developmental biology},
volume = {62},
number = {6-7-8},
pages = {513-525},
doi = {10.1387/ijdb.180016nf},
pmid = {29938763},
issn = {1696-3547},
abstract = {The evolution of multicellular organisms is generally thought (and seems likely) to have been accompanied by the evolution of a stem cell system. Sponges, some of the early-evolved metazoans, have totipotent/pluripotent stem cells. Thus, uncovering the cellular and molecular bases of the sponge stem cells will not only be crucial for understanding the ancestral gene repertoire of animal stem cells, but will also give us clues to understanding the evolution of molecular mechanisms for maintaining multipotency (pluripotency) and differentiation ability during animal evolution. Sponges (Porifera) are a large phylum that includes an enormous number of species, whose cellular compositions and life cycles show striking variations. In the last decade, methodologies for molecular studies and sequencing resources have dramatically advanced and made it possible to clearly define stem cells in sponges in cellular and molecular terms. In this review, together with recent studies of sponges in various classes, the following issues will be discussed: i) recent findings that revealed that the previously proposed model that "archeocytes and choanocytes are the two types of stem cells" originally based on work in demosponges can be applied as a unified view of the stem cell system in sponges that have various cellular organizations, ii) the fact that sponge cells are more plastic than previously thought, as shown by recent studies of sponge regeneration both from dissociated cells and upon injury, and iii) the importance of transdifferentiation in sponge stem cell systems and regeneration.},
}

@article {pmid29930939,
year = {2018},
author = {Fiore, APZP and Ribeiro, PF and Bruni-Cardoso, A},
title = {Sleeping Beauty and the Microenvironment Enchantment: Microenvironmental Regulation of the Proliferation-Quiescence Decision in Normal Tissues and in Cancer Development.},
journal = {Frontiers in cell and developmental biology},
volume = {6},
number = {},
pages = {59},
doi = {10.3389/fcell.2018.00059},
pmid = {29930939},
issn = {2296-634X},
abstract = {Cells from prokaryota to the more complex metazoans cease proliferating at some point in their lives and enter a reversible, proliferative-dormant state termed quiescence. The appearance of quiescence in the course of evolution was essential to the acquisition of multicellular specialization and compartmentalization and is also a central aspect of tissue function and homeostasis. But what makes a cell cease proliferating even in the presence of nutrients, growth factors, and mitogens? And what makes some cells "wake up" when they should not, as is the case in cancer? Here, we summarize and discuss evidence showing how microenvironmental cues such as those originating from metabolism, extracellular matrix (ECM) composition and arrangement, neighboring cells and tissue architecture control the cellular proliferation-quiescence decision, and how this complex regulation is corrupted in cancer.},
}

@article {pmid29914363,
year = {2018},
author = {Dunning Hotopp, JC},
title = {Grafting or pruning in the animal tree: lateral gene transfer and gene loss?.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {470},
doi = {10.1186/s12864-018-4832-5},
pmid = {29914363},
issn = {1471-2164},
support = {R01 CA206188/CA/NCI NIH HHS/United States ; ABI-1457957//National Science Foundation/ ; 1-R01-CA206188//National Cancer Institute/ ; },
abstract = {BACKGROUND: Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted LGTs in vertebrates/chordates than invertebrates, but there is still evidence of LGT into chordates, including humans. More recently, a reanalysis of a subset of these putative LGTs into vertebrates concluded that there is not horizontal gene transfer in the human genome. One of the genes in dispute is an N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which encodes ACY3. This gene was initially identified as a putative bacteria-chordate LGT but was later debunked as it has a significant BLAST match to a more recently deposited genome of Saccoglossus kowalevskii, a flatworm, Metazoan, and hemichordate.

RESULTS: Using BLAST searches, HMM searches, and phylogenetics to assess the evidence for LGT, gene loss, and rate variation in ACY3/ASPA homologues, the most parsimonious explanation for the distribution of ACY3/ASPA genes in eukaryotes involves both gene loss and bacteria-animal LGT, albeit LGT that occurred hundreds of millions of years ago prior to the divergence of gnathostomes.

CONCLUSIONS: ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these time scales in the ancestors of humans are not unexpected given the many known, well-characterized, and adaptive LGTs from bacteria to insects and nematodes.},
}

@article {pmid29906914,
year = {2018},
author = {Kang, C and Aguilar, B and Shmulevich, I},
title = {Emergence of diversity in homogeneous coupled Boolean networks.},
journal = {Physical review. E},
volume = {97},
number = {5-1},
pages = {052415},
doi = {10.1103/PhysRevE.97.052415},
pmid = {29906914},
issn = {2470-0053},
abstract = {The origin of multicellularity in metazoa is one of the fundamental questions of evolutionary biology. We have modeled the generic behaviors of gene regulatory networks in isogenic cells as stochastic nonlinear dynamical systems-coupled Boolean networks with perturbation. Model simulations under a variety of dynamical regimes suggest that the central characteristic of multicellularity, permanent spatial differentiation (diversification), indeed can arise. Additionally, we observe that diversification is more likely to occur near the critical regime of Lyapunov stability.},
}

@article {pmid29906891,
year = {2018},
author = {Jacobeen, S and Graba, EC and Brandys, CG and Day, TC and Ratcliff, WC and Yunker, PJ},
title = {Geometry, packing, and evolutionary paths to increased multicellular size.},
journal = {Physical review. E},
volume = {97},
number = {5-1},
pages = {050401},
doi = {10.1103/PhysRevE.97.050401},
pmid = {29906891},
issn = {2470-0053},
abstract = {The evolutionary transition to multicellularity transformed life on earth, heralding the evolution of large, complex organisms. Recent experiments demonstrated that laboratory-evolved multicellular "snowflake yeast" readily overcome the physical barriers that limit cluster size by modifying cellular geometry [Jacobeen et al., Nat. Phys. 14, 286 (2018)10.1038/s41567-017-0002-y]. However, it is unclear why this route to large size is observed, rather than an evolved increase in intercellular bond strength. Here, we use a geometric model of the snowflake yeast growth form to examine the geometric efficiency of increasing size by modifying geometry and bond strength. We find that changing geometry is a far more efficient route to large size than evolving increased intercellular adhesion. In fact, increasing cellular aspect ratio is on average ∼13 times more effective than increasing bond strength at increasing the number of cells in a cluster. Modifying other geometric parameters, such as the geometric arrangement of mother and daughter cells, also had larger effects on cluster size than increasing bond strength. Simulations reveal that as cells reproduce, internal stress in the cluster increases rapidly; thus, increasing bond strength provides diminishing returns in cluster size. Conversely, as cells become more elongated, cellular packing density within the cluster decreases, which substantially decreases the rate of internal stress accumulation. This suggests that geometrically imposed physical constraints may have been a key early selective force guiding the emergence of multicellular complexity.},
}

@article {pmid29891718,
year = {2018},
author = {Smith, CCR and Tittes, S and Mendieta, JP and Collier-Zans, E and Rowe, HC and Rieseberg, LH and Kane, NC},
title = {Genetics of alternative splicing evolution during sunflower domestication.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {26},
pages = {6768-6773},
doi = {10.1073/pnas.1803361115},
pmid = {29891718},
issn = {1091-6490},
abstract = {Alternative splicing enables organisms to produce the diversity of proteins necessary for multicellular life by using relatively few protein-coding genes. Although differences in splicing have been identified among divergent taxa, the shorter-term evolution of splicing is understudied. The origins of novel splice forms, and the contributions of alternative splicing to major evolutionary transitions, are largely unknown. This study used transcriptomes of wild and domesticated sunflowers to examine splice differentiation and regulation during domestication. We identified substantial splicing divergence between wild and domesticated sunflowers, mainly in the form of intron retention. Transcripts with divergent splicing were enriched for seed-development functions, suggesting that artificial selection impacted splicing patterns. Mapping of quantitative trait loci (QTLs) associated with 144 differential splicing cases revealed primarily trans-acting variation affecting splicing patterns. A large proportion of identified QTLs contain known spliceosome proteins and are associated with splicing variation in multiple genes. Examining a broader set of wild and domesticated sunflower genotypes revealed that most differential splicing patterns in domesticated sunflowers likely arose from standing variation in wild Helianthus annuus and gained frequency during the domestication process. However, several domesticate-associated splicing patterns appear to be introgressed from other Helianthus species. These results suggest that sunflower domestication involved selection on pleiotropic regulatory alleles. More generally, our findings indicate that substantial differences in isoform abundances arose rapidly during a recent evolutionary transition and appear to contribute to adaptation and population divergence.},
}

@article {pmid29889237,
year = {2018},
author = {Leys, SP and Kahn, AS},
title = {Oxygen and the energetic requirements of the first multicellular animals.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icy051},
pmid = {29889237},
issn = {1557-7023},
abstract = {The appearance of multicellular animals during the Neoproterozoic Era is thought to have coincided with oxygenation of the oceans, however we know little about the physiological needs of early animals or about the environment they lived in. Approaches using biomarkers, fossils, and phylogenomics have provided some hints of the types of animals that may have been present during the Neoproterozoic, but extant animals are our best modern links to the theoretical ancestors of animals. Neoproterozoic oceans were low energy habitats, with low oxygen concentrations and sparse food availability for the first animals. We examined tolerance of extant ctenophores and sponges - as representatives of extant lineages of the earliest known metazoan groups - to feeding and oxygen use. A review of respiration rates in species across several phyla suggests that suspension feeders in general have a wide range of metabolic rates, but sponges have some of the highest of invertebrates and ctenophores some of the lowest. Our own studies on the metabolism of two groups of deep water sponges show sponges have different approaches to deal with the cost of filtration and low food availability. We also confirmed that deep water sponges tolerate periods of hypoxia, but at the cost of filtration, indicating that normal feeding is energetically expensive. Predictions of oxygen levels in the Neoproterozoic suggest the last common ancestor (LCA) of multicellular animals was unlikely to have filtered like modern sponges. Getting enough food at low oxygen would have been a more important driver of the evolution of early body plans.},
}

@article {pmid29880641,
year = {2018},
author = {Miller, PW and Pokutta, S and Mitchell, JM and Chodaparambil, JV and Clarke, DN and Nelson, W and Weis, WI and Nichols, SA},
title = {Analysis of a vinculin homolog in a sponge (phylum Porifera) reveals that vertebrate-like cell adhesions emerged early in animal evolution.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.RA117.001325},
pmid = {29880641},
issn = {1083-351X},
abstract = {The evolution of cell adhesion mechanisms in animals facilitated the assembly of organized multicellular tissues. Studies in traditional animal models have revealed two predominant adhesion structures, the adherens junction (AJ) and focal adhesions (FAs), which are involved in the attachment of neighboring cells to each other and to the secreted extracellular matrix (ECM), respectively. The AJ (containing cadherins and catenins) and FAs (comprising integrins, talin, and paxillin) differ in protein composition, but both junctions contain the actin-binding protein vinculin. The near ubiquity of these structures in animals suggests that AJ and FAs evolved early, possibly coincident with multicellularity. However, a challenge to this perspective is that previous studies of sponges-a divergent animal lineage-indicate that their tissues are organized primarily by an alternative, sponge-specific cell adhesion mechanism called "aggregation factor." In this study, we examined the structure, biochemical properties, and tissue localization of a vinculin ortholog in the sponge Oscarella pearsei (Op). Our results indicate that Op vinculin localizes to both cell-cell and cell-ECM contacts and has biochemical and structural properties similar to those of vertebrate vinculin. We propose that Op vinculin played a role in cell adhesion and tissue organization in the last common ancestor of sponges and other animals. These findings provide compelling evidence that sponge tissues are indeed organized like epithelia in other animals and support the notion that AJ- and FA-like structures extend to the earliest periods of animal evolution.},
}

@article {pmid29866913,
year = {2018},
author = {Grüter, C and Jongepier, E and Foitzik, S},
title = {Insect societies fight back: the evolution of defensive traits against social parasites.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {373},
number = {1751},
pages = {},
doi = {10.1098/rstb.2017.0200},
pmid = {29866913},
issn = {1471-2970},
abstract = {Insect societies face many social parasites that exploit their altruistic behaviours or their resources. Due to the fitness costs these social parasites incur, hosts have evolved various behavioural, chemical, architectural and morphological defence traits. Similar to bacteria infecting multicellular hosts, social parasites have to successfully go through several steps to exploit their hosts. Here, we review how social insects try to interrupt this sequence of events. They can avoid parasite contact by choosing to nest in parasite-free locales or evade attacks by adapting their colony structure. Once social parasites attack, hosts attempt to detect them, which can be facilitated by adjustments in colony odour. If social parasites enter the nest, hosts can either aggressively defend their colony or take their young and flee. Nest structures are often shaped to prevent social parasite invasion or to safeguard host resources. Finally, if social parasites successfully establish themselves in host nests, hosts can rebel by killing the parasite brood or by reproducing in the parasites' presence. Hosts of social parasites can therefore develop multiple traits, leading to the evolution of complex defence portfolios of co-dependent traits. Social parasites can respond to these multi-level defences with counter-adaptations, potentially leading to geographical mosaics of coevolution.This article is part of the Theo Murphy meeting issue 'Evolution of pathogen and parasite avoidance behaviours'.},
}

@article {pmid29860723,
year = {2018},
author = {Mustafin, RN and Khusnutdinova, EK},
title = {[Epigenetic hypothesis of the role of peptides in aging.].},
journal = {Advances in gerontology = Uspekhi gerontologii},
volume = {31},
number = {1},
pages = {10-20},
pmid = {29860723},
issn = {1561-9125},
abstract = {In regulation of gene expression in the ontogenesis of multicellular eukaryotes, in addition to transcription factors, an important role is played by epigenetic factors that control the release of genetic information in each cell division. Many binding sites for the transcription factors were derived from transposons sequences. Mobile elements are also important sources of non-coding RNA. Due to this, transposons have an indirect effect on gene expression and genome methylation. In evolution, transposons serve as important sources for the origin of new protein and proteins domains. A number of studies have identified that long non-coding RNAs and microRNAs can be translated into functional peptides. At the same time, transposons remain active in the hypothalamus of adult humans, which is consistent with the transcription of non-coding RNAs in these structures, which may be key in aging.},
}

@article {pmid29856957,
year = {2018},
author = {Sebé-Pedrós, A and Saudemont, B and Chomsky, E and Plessier, F and Mailhé, MP and Renno, J and Loe-Mie, Y and Lifshitz, A and Mukamel, Z and Schmutz, S and Novault, S and Steinmetz, PRH and Spitz, F and Tanay, A and Marlow, H},
title = {Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq.},
journal = {Cell},
volume = {173},
number = {6},
pages = {1520-1534.e20},
doi = {10.1016/j.cell.2018.05.019},
pmid = {29856957},
issn = {1097-4172},
abstract = {The emergence and diversification of cell types is a leading factor in animal evolution. So far, systematic characterization of the gene regulatory programs associated with cell type specificity was limited to few cell types and few species. Here, we perform whole-organism single-cell transcriptomics to map adult and larval cell types in the cnidarian Nematostella vectensis, a non-bilaterian animal with complex tissue-level body-plan organization. We uncover eight broad cell classes in Nematostella, including neurons, cnidocytes, and digestive cells. Each class comprises different subtypes defined by the expression of multiple specific markers. In particular, we characterize a surprisingly diverse repertoire of neurons, which comparative analysis suggests are the result of lineage-specific diversification. By integrating transcription factor expression, chromatin profiling, and sequence motif analysis, we identify the regulatory codes that underlie Nematostella cell-specific expression. Our study reveals cnidarian cell type complexity and provides insights into the evolution of animal cell-specific genomic regulation.},
}

@article {pmid29853554,
year = {2018},
author = {Toda, S and Blauch, LR and Tang, SKY and Morsut, L and Lim, WA},
title = {Programming self-organizing multicellular structures with synthetic cell-cell signaling.},
journal = {Science (New York, N.Y.)},
volume = {361},
number = {6398},
pages = {156-162},
doi = {10.1126/science.aat0271},
pmid = {29853554},
issn = {1095-9203},
support = {K99 EB021030/EB/NIBIB NIH HHS/United States ; P50 GM081879/GM/NIGMS NIH HHS/United States ; T32 GM008412/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
abstract = {A common theme in the self-organization of multicellular tissues is the use of cell-cell signaling networks to induce morphological changes. We used the modular synNotch juxtacrine signaling platform to engineer artificial genetic programs in which specific cell-cell contacts induced changes in cadherin cell adhesion. Despite their simplicity, these minimal intercellular programs were sufficient to yield assemblies with hallmarks of natural developmental systems: robust self-organization into multidomain structures, well-choreographed sequential assembly, cell type divergence, symmetry breaking, and the capacity for regeneration upon injury. The ability of these networks to drive complex structure formation illustrates the power of interlinking cell signaling with cell sorting: Signal-induced spatial reorganization alters the local signals received by each cell, resulting in iterative cycles of cell fate branching. These results provide insights into the evolution of multicellularity and demonstrate the potential to engineer customized self-organizing tissues or materials.},
}

@article {pmid29851258,
year = {2018},
author = {Schaefke, B and Sun, W and Li, YS and Fang, L and Chen, W},
title = {The evolution of posttranscriptional regulation.},
journal = {Wiley interdisciplinary reviews. RNA},
volume = {},
number = {},
pages = {e1485},
doi = {10.1002/wrna.1485},
pmid = {29851258},
issn = {1757-7012},
abstract = {"DNA makes RNA makes protein." After transcription, mRNAs undergo a series of intertwining processes to be finally translated into functional proteins. The "posttranscriptional" regulation (PTR) provides cells an extended option to fine-tune their proteomes. To meet the demands of complex organism development and the appropriate response to environmental stimuli, every step in these processes needs to be finely regulated. Moreover, changes in these regulatory processes are important driving forces underlying the evolution of phenotypic differences across different species. The major PTR mechanisms discussed in this review include the regulation of splicing, polyadenylation, decay, and translation. For alternative splicing and polyadenylation, we mainly discuss their evolutionary dynamics and the genetic changes underlying the regulatory differences in cis-elements versus trans-factors. For mRNA decay and translation, which, together with transcription, determine the cellular RNA or protein abundance, we focus our discussion on how their divergence coordinates with transcriptional changes to shape the evolution of gene expression. Then to highlight the importance of PTR in the evolution of higher complexity, we focus on their roles in two major phenomena during eukaryotic evolution: the evolution of multicellularity and the division of labor between different cell types and tissues; and the emergence of diverse, often highly specialized individual phenotypes, especially those concerning behavior in eusocial insects. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution Translation > Translation Regulation RNA Processing > Splicing Regulation/Alternative Splicing.},
}

@article {pmid29846592,
year = {2018},
author = {Paps, J},
title = {What makes an animal? The molecular quest for the origin of the Animal Kingdom.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icy036},
pmid = {29846592},
issn = {1557-7023},
abstract = {SYNOPSIS: What makes an animal? To find the answer we need to integrate data from disciplines such as phylogenetics, palaeontology, ecology, development, anatomy and physiology, as well as molecular biology and genomics. Knowledge of which groups branched before and after the origin of animals is essential. Recent advances in molecular phylogenetics, together with the discovery of new eukaryotic lineages, have drawn a new picture of the ancestry of animals. The nature of the early diverging animal lineages and the timing of the transition are in a state of flux. Various factors have been linked to this striking transition to multicellularity, including changes in environmental conditions and the ecological interactions between unicellular eukaryotes. The current wealth of genomic data has also shed new light on this question. The analysis of the genome of various close relatives of animals has revealed the importance that recycling of ancient genes into metazoan biological functions played into animal origins. A recent study reconstructing the genome of the last common ancestor of extant animals has unveiled an unprecedented emergence of new genes, highlighting the role of genomic novelty in the origin of metazoans.},
}

@article {pmid29844338,
year = {2018},
author = {Pinhal, D and Bovolenta, LA and Moxon, S and Oliveira, AC and Nachtigall, PG and Acencio, ML and Patton, JG and Hilsdorf, AWS and Lemke, N and Martins, C},
title = {Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs' transcription, sex-biased arm switching and increasing complexity of expression throughout development.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {8248},
doi = {10.1038/s41598-018-26607-x},
pmid = {29844338},
issn = {2045-2322},
abstract = {MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic organisms, as the fast-evolving cichlid fishes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus), an emergent model organism to investigate evo-devo mechanisms. Five hundred known miRNAs and almost one hundred putative novel vertebrate miRNAs have been identified, many of which seem to be teleost-specific, cichlid-specific or tilapia-specific. Abundant miRNA isoforms (isomiRs) were identified with modifications in both 5p and 3p miRNA transcripts. Changes in arm usage (arm switching) of nine miRNAs were detected in early development, adult stage and even between male and female samples. We found an increasing complexity of miRNA expression during ontogenetic development, revealing a remarkable synchronism between the rate of new miRNAs recruitment and morphological changes. Overall, our results enlarge vertebrate miRNA collection and reveal a notable differential ratio of miRNA arms and isoforms influenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs.},
}

@article {pmid29807994,
year = {2018},
author = {Cooper, GA and West, SA},
title = {Division of labour and the evolution of extreme specialization.},
journal = {Nature ecology & evolution},
volume = {2},
number = {7},
pages = {1161-1167},
doi = {10.1038/s41559-018-0564-9},
pmid = {29807994},
issn = {2397-334X},
abstract = {Division of labour is a common feature of social groups, from biofilms to complex animal societies. However, we lack a theoretical framework that can explain why division of labour has evolved on certain branches of the tree of life but not others. Here, we model the division of labour over a cooperative behaviour, considering both when it should evolve and the extent to which the different types should become specialized. We found that: (1) division of labour is usually-but not always-favoured by high efficiency benefits to specialization and low within-group conflict; and (2) natural selection favours extreme specialization, where some individuals are completely dependent on the helping behaviour of others. We make a number of predictions, several of which are supported by the existing empirical data, from microbes and animals, while others suggest novel directions for empirical work. More generally, we show how division of labour can lead to mutual dependence between different individuals and hence drive major evolutionary transitions, such as those to multicellularity and eusociality.},
}

@article {pmid29802408,
year = {2018},
author = {Reeves, MQ and Kandyba, E and Harris, S and Del Rosario, R and Balmain, A},
title = {Multicolour lineage tracing reveals clonal dynamics of squamous carcinoma evolution from initiation to metastasis.},
journal = {Nature cell biology},
volume = {20},
number = {6},
pages = {699-709},
doi = {10.1038/s41556-018-0109-0},
pmid = {29802408},
issn = {1476-4679},
abstract = {Tumour cells are subjected to evolutionary selection pressures during progression from initiation to metastasis. We analysed the clonal evolution of squamous skin carcinomas induced by DMBA/TPA treatment using the K5CreER-Confetti mouse and stage-specific lineage tracing. We show that benign tumours are polyclonal, but only one population contains the Hras driver mutation. Thus, benign papillomas are monoclonal in origin but recruit neighbouring epithelial cells during growth. Papillomas that never progress to malignancy retain several distinct clones, whereas progression to carcinoma is associated with a clonal sweep. Newly generated clones within carcinomas demonstrate intratumoural invasion and clonal intermixing, often giving rise to metastases containing two or more distinct clones derived from the matched primary tumour. These data demonstrate that late-stage tumour progression and dissemination are governed by evolutionary selection pressures that operate at a multicellular level and, therefore, differ from the clonal events that drive initiation and the benign-malignant transition.},
}

@article {pmid29797026,
year = {2018},
author = {Hauser, CJ and Otterbein, LE},
title = {Danger signals from mitochondrial DAMPS in trauma and post-injury sepsis.},
journal = {European journal of trauma and emergency surgery : official publication of the European Trauma Society},
volume = {44},
number = {3},
pages = {317-324},
doi = {10.1007/s00068-018-0963-2},
pmid = {29797026},
issn = {1863-9941},
support = {W81XWH-16-1-0464//U.S. Department of Defense/ ; },
abstract = {In all multicellular organisms, immediate host responses to both sterile and infective threat are initiated by very primitive systems now grouped together under the general term 'danger responses'. Danger signals are generated when primitive 'pattern recognition receptors' (PRR) encounter activating 'alarmins'. These molecular species may be of pathogenic infective origin (pathogen-associated molecular patterns) or of sterile endogenous origin (danger-associated molecular patterns). There are many sterile and infective alarmins and there is considerable overlap in their ability to activate PRR, but in all cases the end result is inflammation. It is the overlap between sterile and infective signals acting via a relatively limited number of PRR that generally underlies the great clinical similarity we see between sterile and infective systemic inflammatory responses. Mitochondria (MT) are evolutionarily derived from bacteria, and thus they sit at the crossroads between sterile and infective danger signal pathways. Many of the molecular species in mitochondria are alarmins, and so the release of MT from injured cells results in a wide variety of inflammatory events. This paper discusses the known participation of MT in inflammation and reviews what is known about how the major.},
}

@article {pmid29789717,
year = {2018},
author = {Al Habyan, S and Kalos, C and Szymborski, J and McCaffrey, L},
title = {Multicellular detachment generates metastatic spheroids during intra-abdominal dissemination in epithelial ovarian cancer.},
journal = {Oncogene},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41388-018-0317-x},
pmid = {29789717},
issn = {1476-5594},
abstract = {Ovarian cancer is the most lethal gynecological cancer, where survival rates have had modest improvement over the last 30 years. Metastasis of cancer cells is a major clinical problem, and patient mortality occurs when ovarian cancer cells spread beyond the confinement of ovaries. Disseminated ovarian cancer cells typically spread within the abdomen, where ascites accumulation aids in their transit. Metastatic ascites contain multicellular spheroids, which promote chemo-resistance and recurrence. However, little is known about the origin and mechanisms through which spheroids arise. Using live-imaging of 3D culture models and animal models, we report that epithelial ovarian cancer (EOC) cells, the most common type of ovarian cancer, can spontaneously detach as either single cells or clusters. We report that clusters are more resistant to anoikis and have a potent survival advantage over single cells. Using in vivo lineage tracing, we found that multicellular spheroids arise preferentially from collective detachment, rather than aggregation in the abdomen. Finally, we report that multicellular spheroids from collective detachment are capable of seeding intra-abdominal metastases that retain intra-tumoral heterogeneity from the primary tumor.},
}

@article {pmid29788279,
year = {2018},
author = {Tarver, JE and Taylor, RS and Puttick, MN and Lloyd, GT and Pett, W and Fromm, B and Schirrmeister, BE and Pisani, D and Peterson, KJ and Donoghue, PCJ},
title = {Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss.},
journal = {Genome biology and evolution},
volume = {10},
number = {6},
pages = {1457-1470},
doi = {10.1093/gbe/evy096},
pmid = {29788279},
issn = {1759-6653},
abstract = {microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.},
}

@article {pmid29775683,
year = {2018},
author = {Dechristé, G and Fehrenbach, J and Griseti, E and Lobjois, V and Poignard, C},
title = {Viscoelastic modeling of the fusion of multicellular tumor spheroids in growth phase.},
journal = {Journal of theoretical biology},
volume = {454},
number = {},
pages = {102-109},
doi = {10.1016/j.jtbi.2018.05.005},
pmid = {29775683},
issn = {1095-8541},
abstract = {BACKGROUND: Since several decades, the experiments have highlighted the analogy of fusing cell aggregates with liquid droplets. The physical macroscopic models have been derived under incompressible assumptions. The aim of this paper is to provide a 3D model of growing spheroids, which is more relevant regarding embryo cell aggregates or tumor cell spheroids.

METHODS: We extend the past approach to a compressible 3D framework in order to account for the tumor spheroid growth. We exhibit the crucial importance of the effective surface tension, and of the inner pressure of the spheroid to describe precisely the fusion. The experimental data were obtained on spheroids of colon carcinoma human cells (HCT116 cell line). After 3 or 6 days of culture, two identical spheroids were transferred in one well and their fusion was monitored by live videomicroscopy acquisition each 2 h during 72 h. From these images the neck radius and the diameter of the assembly of the fusing spheroids are extracted.

RESULTS: The numerical model is fitted with the experiments. It is worth noting that the time evolution of both neck radius and spheroid diameter are quantitatively obtained. The interesting feature lies in the fact that such measurements characterise the macroscopic rheological properties of the tumor spheroids.

CONCLUSIONS: The experimental determination of the kinetics of neck radius and overall diameter during spheroids fusion characterises the rheological properties of the spheroids. The consistency of the model is shown by fitting the model with two different experiments, enhancing the importance of both surface tension and cell proliferation.

GENERAL SIGNIFICANCE: The paper sheds new light on the macroscopic rheological properties of tumor spheroids. It emphasizes the role of the surface tension and the inner pressure in the fusion of growing spheroid. Under geometrical assumptions, the model reduces to a 2-parameter differential equation fit with experimental measurements. The 3-D partial differential system makes it possible to study the fusion of spheroids in non-symmetrical or more general frameworks.},
}

@article {pmid29760902,
year = {2018},
author = {Quintero-Galvis, JF and Paleo-López, R and Solano-Iguaran, JJ and Poupin, MJ and Ledger, T and Gaitan-Espitia, JD and Antoł, A and Travisano, M and Nespolo, RF},
title = {Exploring the evolution of multicellularity in Saccharomyces cerevisiae under bacteria environment: An experimental phylogenetics approach.},
journal = {Ecology and evolution},
volume = {8},
number = {9},
pages = {4619-4630},
doi = {10.1002/ece3.3979},
pmid = {29760902},
issn = {2045-7758},
abstract = {There have been over 25 independent unicellular to multicellular evolutionary transitions, which have been transformational in the complexity of life. All of these transitions likely occurred in communities numerically dominated by unicellular organisms, mostly bacteria. Hence, it is reasonable to expect that bacteria were involved in generating the ecological conditions that promoted the stability and proliferation of the first multicellular forms as protective units. In this study, we addressed this problem by analyzing the occurrence of multicellularity in an experimental phylogeny of yeasts (Sacharomyces cerevisiae) a model organism that is unicellular but can generate multicellular clusters under some conditions. We exposed a single ancestral population to periodic divergences, coevolving with a cocktail of environmental bacteria that were inoculated to the environment of the ancestor, and compared to a control (no bacteria). We quantified culturable microorganisms to the level of genera, finding up to 20 taxa (all bacteria) that competed with the yeasts during diversification. After 600 generations of coevolution, the yeasts produced two types of multicellular clusters: clonal and aggregative. Whereas clonal clusters were present in both treatments, aggregative clusters were only present under the bacteria treatment and showed significant phylogenetic signal. However, clonal clusters showed different properties if bacteria were present as follows: They were more abundant and significantly smaller than in the control. These results indicate that bacteria are important modulators of the occurrence of multicellularity, providing support to the idea that they generated the ecological conditions-promoting multicellularity.},
}

@article {pmid29755113,
year = {2018},
author = {Jézéquel, P and Campone, M},
title = {Comment on "How the evolution of multicellularity set the stage for cancer".},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41416-018-0091-0},
pmid = {29755113},
issn = {1532-1827},
}

@article {pmid29752387,
year = {2018},
author = {Parra-Acero, H and Ros-Rocher, N and Perez-Posada, A and Kożyczkowska, A and Sánchez-Pons, N and Nakata, A and Suga, H and Najle, SR and Ruiz-Trillo, I},
title = {Transfection of Capsaspora owczarzaki, a close unicellular relative of animals.},
journal = {Development (Cambridge, England)},
volume = {145},
number = {10},
pages = {},
doi = {10.1242/dev.162107},
pmid = {29752387},
issn = {1477-9129},
mesh = {Animals ; Biological Evolution ; DNA/*genetics ; Evolution, Molecular ; Gene Expression Regulation/genetics ; Genome, Protozoan/*genetics ; Mesomycetozoea/*genetics ; Plasmids/*genetics ; Transfection/*methods ; },
abstract = {How animals emerged from their unicellular ancestor remains a major evolutionary question. New genome data from the closest unicellular relatives of animals have provided important insights into the evolution of animal multicellularity. We know that the unicellular ancestor of animals had an unexpectedly complex genetic repertoire, including many genes that are key to animal development and multicellularity. Thus, assessing the function of these genes among unicellular relatives of animals is key to understanding how they were co-opted at the onset of the Metazoa. However, such analyses have been hampered by the lack of genetic tools. Progress has been made in choanoflagellates and teretosporeans, two of the three lineages closely related to animals, whereas no tools are yet available for functional analysis in the third lineage: the filastereans. Importantly, filastereans have a striking repertoire of genes involved in transcriptional regulation and other developmental processes. Here, we describe a reliable transfection method for the filasterean Capsaspora owczarzaki We also provide a set of constructs for visualising subcellular structures in live cells. These tools convert Capsaspora into a unique experimentally tractable organism to use to investigate the origin and evolution of animal multicellularity.},
}

Animals
Biological Evolution
DNA/*genetics
Evolution, Molecular
Gene Expression Regulation/genetics
Genome, Protozoan/*genetics
Mesomycetozoea/*genetics
Plasmids/*genetics
Transfection/*methods

@article {pmid29738987,
year = {2018},
author = {Tasic, B},
title = {Single cell transcriptomics in neuroscience: cell classification and beyond.},
journal = {Current opinion in neurobiology},
volume = {50},
number = {},
pages = {242-249},
doi = {10.1016/j.conb.2018.04.021},
pmid = {29738987},
issn = {1873-6882},
abstract = {Biology has been facing a daunting problem since the cell was understood to be the building block of metazoans: how do we study multicellular systems, when a universal approach to characterize their building blocks and classify them does not exist? Metazoan diversity has not helped: there are many model and non-model organisms, developmental and adult stages, healthy and diseased states. Here, I review the application of single cell transcriptomics to cell classification in neuroscience and its corollaries: the differentially expressed genes discovered in this process are a treasure trove for understanding cell type function and enabling specific access to those types. The advancements and widespread adoption of single-cell transcriptomics are bound to transform our understanding of neural system development, function, pathology and evolution.},
}

@article {pmid29735660,
year = {2018},
author = {Elsner, D and Meusemann, K and Korb, J},
title = {Longevity and transposon defense, the case of termite reproductives.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {21},
pages = {5504-5509},
doi = {10.1073/pnas.1804046115},
pmid = {29735660},
issn = {1091-6490},
abstract = {Social insects are promising new models in aging research. Within single colonies, longevity differences of several magnitudes exist that can be found elsewhere only between different species. Reproducing queens (and, in termites, also kings) can live for several decades, whereas sterile workers often have a lifespan of a few weeks only. We studied aging in the wild in a highly social insect, the termite Macrotermes bellicosus, which has one of the most pronounced longevity differences between reproductives and workers. We show that gene-expression patterns differed little between young and old reproductives, implying negligible aging. By contrast, old major workers had many genes up-regulated that are related to transposable elements (TEs), which can cause aging. Strikingly, genes from the PIWI-interacting RNA (piRNA) pathway, which are generally known to silence TEs in the germline of multicellular animals, were down-regulated only in old major workers but not in reproductives. Continued up-regulation of the piRNA defense commonly found in the germline of animals can explain the long life of termite reproductives, implying somatic cooption of germline defense during social evolution. This presents a striking germline/soma analogy as envisioned by the superorganism concept: the reproductives and workers of a colony reflect the germline and soma of multicellular animals, respectively. Our results provide support for the disposable soma theory of aging.},
}

@article {pmid29731304,
year = {2018},
author = {Maclean, AE and Hertle, AP and Ligas, J and Bock, R and Balk, J and Meyer, EH},
title = {Absence of Complex I Is Associated with Diminished Respiratory Chain Function in European Mistletoe.},
journal = {Current biology : CB},
volume = {28},
number = {10},
pages = {1614-1619.e3},
doi = {10.1016/j.cub.2018.03.036},
pmid = {29731304},
issn = {1879-0445},
abstract = {Parasitism is a life history strategy found across all domains of life whereby nutrition is obtained from a host. It is often associated with reductive evolution of the genome, including loss of genes from the organellar genomes [1, 2]. In some unicellular parasites, the mitochondrial genome (mitogenome) has been lost entirely, with far-reaching consequences for the physiology of the organism [3, 4]. Recently, mitogenome sequences of several species of the hemiparasitic plant mistletoe (Viscum sp.) have been reported [5, 6], revealing a striking loss of genes not seen in any other multicellular eukaryotes. In particular, the nad genes encoding subunits of respiratory complex I are all absent and other protein-coding genes are also lost or highly diverged in sequence, raising the question what remains of the respiratory complexes and mitochondrial functions. Here we show that oxidative phosphorylation (OXPHOS) in European mistletoe, Viscum album, is highly diminished. Complex I activity and protein subunits of complex I could not be detected. The levels of complex IV and ATP synthase were at least 5-fold lower than in the non-parasitic model plant Arabidopsis thaliana, whereas alternative dehydrogenases and oxidases were higher in abundance. Carbon flux analysis indicates that cytosolic reactions including glycolysis are greater contributors to ATP synthesis than the mitochondrial tricarboxylic acid (TCA) cycle. Our results describe the extreme adjustments in mitochondrial functions of the first reported multicellular eukaryote without complex I.},
}

@article {pmid29730580,
year = {2018},
author = {Vijay, K},
title = {Toll-like receptors in immunity and inflammatory diseases: Past, present, and future.},
journal = {International immunopharmacology},
volume = {59},
number = {},
pages = {391-412},
doi = {10.1016/j.intimp.2018.03.002},
pmid = {29730580},
issn = {1878-1705},
abstract = {The immune system is a very diverse system of the host that evolved during evolution to cope with various pathogens present in the vicinity of environmental surroundings inhabited by multicellular organisms ranging from achordates to chordates (including humans). For example, cells of immune system express various pattern recognition receptors (PRRs) that detect danger via recognizing specific pathogen-associated molecular patterns (PAMPs) and mount a specific immune response. Toll-like receptors (TLRs) are one of these PRRs expressed by various immune cells. However, they were first discovered in the Drosophila melanogaster (common fruit fly) as genes/proteins important in embryonic development and dorso-ventral body patterning/polarity. Till date, 13 different types of TLRs (TLR1-TLR13) have been discovered and described in mammals since the first discovery of TLR4 in humans in late 1997. This discovery of TLR4 in humans revolutionized the field of innate immunity and thus the immunology and host-pathogen interaction. Since then TLRs are found to be expressed on various immune cells and have been targeted for therapeutic drug development for various infectious and inflammatory diseases including cancer. Even, Single nucleotide polymorphisms (SNPs) among various TLR genes have been identified among the different human population and their association with susceptibility/resistance to certain infections and other inflammatory diseases. Thus, in the present review the current and future importance of TLRs in immunity, their pattern of expression among various immune cells along with TLR based therapeutic approach is reviewed.},
}

@article {pmid29718307,
year = {2018},
author = {Tarhan, LG and Droser, ML and Cole, DB and Gehling, JG},
title = {Ecological Expansion and Extinction in the Late Ediacaran: Weighing the Evidence for Environmental and Biotic Drivers.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icy020},
pmid = {29718307},
issn = {1557-7023},
abstract = {The Ediacara Biota, Earth's earliest communities of complex, macroscopic, multicellular organisms, appeared during the late Ediacaran Period, just prior to the Cambrian Explosion. Ediacara fossil assemblages consist of exceptionally preserved soft-bodied forms of enigmatic morphology and affinity which nonetheless represent a critical stepping-stone in the evolution of complex animal ecosystems. The Ediacara Biota has historically been divided into three successive Assemblages-the Avalon, the White Sea and the Nama. Although the oldest (Avalon) Assemblage documents the initial appearance of several groups of Ediacara taxa, the two younger (White Sea and Nama) Assemblages record a particularly striking suite of ecological innovations, including the appearance of diverse Ediacara body plans-in tandem with the rise of bilaterian animals-as well as the emergence of novel ecological strategies such as movement, sexual reproduction, biomineralization and the development of dense, heterogeneous benthic communities. Many of these ecological innovations appear to be linked to adaptations to heterogeneous substrates and shallow and energetic marine settings. In spite of these innovations, the majority of Ediacara taxa disappear by the end of the Ediacaran, with interpretations for this disappearance historically ranging from the closing of preservational windows to environmentally or biotically mediated extinction. However, in spite of the unresolved affinity and eventual extinction of individual Ediacara taxa, these distinctive ecological strategies persist across the Ediacaran-Cambrian boundary and are characteristic of younger animal-dominated communities of the Phanerozoic. The late Ediacaran emergence of these strategies may, therefore, have facilitated subsequent radiations of the Cambrian. In this light, the Ediacaran and Cambrian Periods, although traditionally envisioned as separate worlds, are likely to have been part of an ecological and evolutionary continuum.},
}

@article {pmid29688518,
year = {2018},
author = {Lee, J and Yang, EC and Graf, L and Yang, JH and Qiu, H and Zel Zion, U and Chan, CX and Stephens, TG and Weber, APM and Boo, GH and Boo, SM and Kim, KM and Shin, Y and Jung, M and Lee, SJ and Yim, HS and Lee, JH and Bhattacharya, D and Yoon, HS},
title = {Analysis of the draft genome of the red seaweed Gracilariopsis chorda provides insights into genome size evolution in Rhodophyta.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msy081},
pmid = {29688518},
issn = {1537-1719},
abstract = {Red algae (Rhodophyta) underwent two phases of large-scale genome reduction during their early evolution. The red seaweeds did not attain genome sizes or gene inventories typical of other multicellular eukaryotes. We generated a high quality 92.1 Mbp draft genome assembly from the red seaweed Gracilariopsis chorda, including methylation and small (s)RNA data. We analyzed these and other Archaeplastida genomes to address three questions: 1) what is the role of repeats and transposable elements (TEs) in explaining Rhodophyta genome size variation, 2) what is the history of genome duplication and gene family expansion/reduction in these taxa, and 3) is there evidence for TE suppression in red algae? We find the number of predicted genes in red algae is relatively small (4,803-13,125 genes), particularly when compared to land plants, with no evidence of polyploidization. Genome size variation is primarily explained by TE expansion with the red seaweeds having the largest genomes. Long terminal repeat elements and DNA repeats are the major contributors to genome size growth. About 8.3% of the G. chorda genome undergoes cytosine methylation among gene-bodies, promoters, and TEs, and 71.5% of TEs contain methylated-DNA with 57% of these regions associated with sRNAs. These latter results suggest a role for TE-associated sRNAs in RNA-dependent DNA methylation to facilitate silencing. We postulate that the evolution of genome size in red algae is the result of the combined action of TE spread and the concomitant emergence of its epigenetic suppression, together with other important factors such as changes in population size.},
}

@article {pmid29687636,
year = {2018},
author = {Liu, J and Zhang, W and Du, H and Leng, X and Li, JH and Pan, H and Xu, J and Wu, LF and Xiao, T},
title = {Seasonal changes in the vertical distribution of two types of multicellular magnetotactic prokaryotes in the sediment of Lake Yuehu, China.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12652},
pmid = {29687636},
issn = {1758-2229},
abstract = {There are two genetically distinct morphological types of multicellular magnetotactic prokaryotes (MMPs) in the intertidal zone of Lake Yuehu (China): ellipsoidal MMPs (eMMPs) and spherical MMPs (sMMPs). We studied the vertical distribution of both types of MMPs in the sediment at Lake Yuehu during 1 year. Both types of MMPs were observed at sediment depths ranging from 1 to 34 cm, depending on the seasons. The eMMPs distributed at depths of 2-34 cm during spring, 1-11 cm during summer, 2-21 cm during autumn and 9-32 cm during winter. The eMMP species Candidatus Magnetananas rongchenensis, with magnetite magnetosomes, dominated at all distribution depths. These results suggested that Ca. M. rongchenensis migrated vertically during four seasons. The vertical profiles of oxidation-reduction potential (ORP) in Lake Yuehu changed seasonally, and these changes coincided with the seasonal distribution of MMPs, suggesting that the ORP affected the vertical distribution of MMPs. In addition, high concentrations of ammonium and silicate were associated with low abundances of MMPs.},
}

@article {pmid29686411,
year = {2018},
author = {Marín, I},
title = {Origin and evolution of fungal HECT ubiquitin ligases.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {6419},
doi = {10.1038/s41598-018-24914-x},
pmid = {29686411},
issn = {2045-2322},
abstract = {Ubiquitin ligases (E3s) are basic components of the eukaryotic ubiquitination system. In this work, the emergence and diversification of fungal HECT ubiquitin ligases is described. Phylogenetic and structural data indicate that six HECT subfamilies (RSP5, TOM1, UFD4, HUL4, HUL4A and HUL5) existed in the common ancestor of all fungi. These six subfamilies have evolved very conservatively, with only occasional losses and duplications in particular fungal lineages. However, an early, drastic reduction in the number of HECT genes occurred in microsporidians, in parallel to the reduction of their genomes. A significant correlation between the total number of genes and the number of HECT-encoding genes present in fungi has been observed. However, transitions from unicellularity to multicellularity or vice versa apparently had no effect on the evolution of this family. Likely orthologs or co-orthologs of all fungal HECT genes have been detected in animals. Four genes are deduced to be present in the common ancestor of fungi, animals and plants. Protein-protein interactions detected in both the yeast Saccharomyces cerevisiae and humans suggest that some ancient functions of HECT proteins have been conserved since the animals/fungi split.},
}

@article {pmid29686139,
year = {2018},
author = {Wang, Y and Gao, Y and Li, C and Gao, H and Zhang, CC and Xu, X},
title = {Three Substrains of the Cyanobacterium Anabaena sp. Strain PCC 7120 Display Divergence in Genomic Sequences and hetC Function.},
journal = {Journal of bacteriology},
volume = {200},
number = {13},
pages = {},
doi = {10.1128/JB.00076-18},
pmid = {29686139},
issn = {1098-5530},
}

@article {pmid29685747,
year = {2018},
author = {Miller, WB and Torday, JS},
title = {Four domains: The fundamental unicell and Post-Darwinian Cognition-Based Evolution.},
journal = {Progress in biophysics and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pbiomolbio.2018.04.006},
pmid = {29685747},
issn = {1873-1732},
abstract = {Contemporary research supports the viewpoint that self-referential cognition is the proper definition of life. From that initiating platform, a cohesive alternative evolutionary narrative distinct from standard Neodarwinism can be presented. Cognition-Based Evolution contends that biological variation is a product of a self-reinforcing information cycle that derives from self-referential attachment to biological information space-time with its attendant ambiguities. That information cycle is embodied through obligatory linkages among energy, biological information, and communication. Successive reiterations of the information cycle enact the informational architectures of the basic unicellular forms. From that base, inter-domain and cell-cell communications enable genetic and cellular variations through self-referential natural informational engineering and cellular niche construction. Holobionts are the exclusive endpoints of that self-referential cellular engineering as obligatory multicellular combinations of the essential Four Domains: Prokaryota, Archaea, Eukaryota and the Virome. Therefore, it is advocated that these Four Domains represent the perpetual object of the living circumstance rather than the visible macroorganic forms. In consequence, biology and its evolutionary development can be appraised as the continual defense of instantiated cellular self-reference. As the survival of cells is as dependent upon limitations and boundaries as upon any freedom of action, it is proposed that selection represents only one of many forms of cellular constraint that sustain self-referential integrity.},
}

@article {pmid29675836,
year = {2018},
author = {Nagy, LG and Kovács, GM and Krizsán, K},
title = {Complex multicellularity in fungi: evolutionary convergence, single origin, or both?.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.12418},
pmid = {29675836},
issn = {1469-185X},
abstract = {Complex multicellularity represents the most advanced level of biological organization and it has evolved only a few times: in metazoans, green plants, brown and red algae and fungi. Compared to other lineages, the evolution of multicellularity in fungi follows different principles; both simple and complex multicellularity evolved via unique mechanisms not found in other lineages. Herein we review ecological, palaeontological, developmental and genomic aspects of complex multicellularity in fungi and discuss general principles of the evolution of complex multicellularity in light of its fungal manifestations. Fungi represent the only lineage in which complex multicellularity shows signatures of convergent evolution: it appears 8-11 times in distinct fungal lineages, which show a patchy phylogenetic distribution yet share some of the genetic mechanisms underlying complex multicellular development. To explain the patchy distribution of complex multicellularity across the fungal phylogeny we identify four key observations: the large number of apparently independent complex multicellular clades; the lack of documented phenotypic homology between these clades; the conservation of gene circuits regulating the onset of complex multicellular development; and the existence of clades in which the evolution of complex multicellularity is coupled with limited gene family diversification. We discuss how these patterns and known genetic aspects of fungal development can be reconciled with the genetic theory of convergent evolution to explain the pervasive occurrence of complex multicellularity across the fungal tree of life.},
}

@article {pmid29675831,
year = {2018},
author = {Kauko, A and Lehto, K},
title = {Eukaryote specific folds: Part of the whole.},
journal = {Proteins},
volume = {},
number = {},
pages = {},
doi = {10.1002/prot.25517},
pmid = {29675831},
issn = {1097-0134},
abstract = {The origin of eukaryotes is one of the central transitions in the history of life; without eukaryotes there would be no complex multicellular life. The most accepted scenarios suggest the endosymbiosis of a mitochondrial ancestor with a complex archaeon, even though the details regarding the host and the triggering factors are still being discussed. Accordingly, phylogenetic analyses have demonstrated archaeal affiliations with key informational systems, while metabolic genes are often related to bacteria, mostly to the mitochondrial ancestor. Despite of this, there exists a large number of protein families and folds found only in eukaryotes. In this study, we have analyzed structural superfamilies and folds that probably appeared during eukaryogenesis. These folds typically represent relatively small binding domains of larger multidomain proteins. They are commonly involved in biological processes that are particularly complex in eukaryotes, such as signaling, trafficking/cytoskeleton, ubiquitination, transcription and RNA processing, but according to recent studies, these processes also have prokaryotic roots. Thus the folds originating from an eukaryotic stem seem to represent accessory parts that have contributed in the expansion of several prokaryotic processes to a new level of complexity. This might have taken place as a co-evolutionary process where increasing complexity and fold innovations have supported each other.},
}

@article {pmid29663630,
year = {2018},
author = {Albuquerque, TAF and Drummond do Val, L and Doherty, A and de Magalhães, JP},
title = {From humans to hydra: patterns of cancer across the tree of life.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {93},
number = {3},
pages = {1715-1734},
doi = {10.1111/brv.12415},
pmid = {29663630},
issn = {1469-185X},
abstract = {Cancer is a disease of multicellularity; it originates when cells become dysregulated due to mutations and grow out of control, invading other tissues and provoking discomfort, disability, and eventually death. Human life expectancy has greatly increased in the last two centuries, and consequently so has the incidence of cancer. However, how cancer patterns in humans compare to those of other species remains largely unknown. In this review, we search for clues about cancer and its evolutionary underpinnings across the tree of life. We discuss data from a wide range of species, drawing comparisons with humans when adequate, and interpret our findings from an evolutionary perspective. We conclude that certain cancers are uniquely common in humans, such as lung, prostate, and testicular cancer; while others are common across many species. Lymphomas appear in almost every animal analysed, including in young animals, which may be related to pathogens imposing selection on the immune system. Cancers unique to humans may be due to our modern environment or may be evolutionary accidents: random events in the evolution of our species. Finally, we find that cancer-resistant animals such as whales and mole-rats have evolved cellular mechanisms that help them avoid neoplasia, and we argue that there are multiple natural routes to cancer resistance.},
}

@article {pmid29662839,
year = {2018},
author = {Dhakshinamoorthy, R and Bitzhenner, M and Cosson, P and Soldati, T and Leippe, M},
title = {The Saposin-Like Protein AplD Displays Pore-Forming Activity and Participates in Defense Against Bacterial Infection During a Multicellular Stage of Dictyostelium discoideum.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {73},
doi = {10.3389/fcimb.2018.00073},
pmid = {29662839},
issn = {2235-2988},
abstract = {Due to their archaic life style and microbivor behavior, amoebae may represent a source of antimicrobial peptides and proteins. The amoebic protozoon Dictyostelium discoideum has been a model organism in cell biology for decades and has recently also been used for research on host-pathogen interactions and the evolution of innate immunity. In the genome of D. discoideum, genes can be identified that potentially allow the synthesis of a variety of antimicrobial proteins. However, at the protein level only very few antimicrobial proteins have been characterized that may interact directly with bacteria and help in fighting infection of D. discoideum with potential pathogens. Here, we focus on a large group of gene products that structurally belong to the saposin-like protein (SAPLIP) family and which members we named provisionally Apls (amoebapore-like peptides) according to their similarity to a comprehensively studied antimicrobial and cytotoxic pore-forming protein of the protozoan parasite Entamoeba histolytica. We focused on AplD because it is the only Apl gene that is reported to be primarily transcribed further during the multicellular stages such as the mobile slug stage. Upon knock-out (KO) of the gene, aplD- slugs became highly vulnerable to virulent Klebsiella pneumoniae. AplD- slugs harbored bacterial clumps in their interior and were unable to slough off the pathogen in their slime sheath. Re-expression of AplD in aplD- slugs rescued the susceptibility toward K. pneumoniae. The purified recombinant protein rAplD formed pores in liposomes and was also capable of permeabilizing the membrane of live Bacillus megaterium. We propose that the multifarious Apl family of D. discoideum comprises antimicrobial effector polypeptides that are instrumental to interact with bacteria and their phospholipid membranes. The variety of its members would allow a complementary and synergistic action against a variety of microbes, which the amoeba encounters in its environment.},
}

@article {pmid29644800,
year = {2018},
author = {Mincarelli, L and Lister, A and Lipscombe, J and Macaulay, IC},
title = {Defining Cell Identity with Single-Cell Omics.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e1700312},
doi = {10.1002/pmic.201700312},
pmid = {29644800},
issn = {1615-9861},
abstract = {Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic, and metabolomic) exhibit dramatic heterogeneity between and within the different cell types and states underlying cellular functional diversity. Cell genotypes can also display heterogeneity throughout an organism, in the form of somatic genetic variation-most notably in the emergence and evolution of tumors. Recent technical advances in single-cell isolation and the development of omics approaches sensitive enough to reveal these aspects of cell identity have enabled a revolution in the study of multicellular systems. In this review, we discuss the technologies available to resolve the genomes, epigenomes, transcriptomes, proteomes, and metabolomes of single cells from a wide variety of living systems.},
}

@article {pmid29641448,
year = {2018},
author = {Zheng, S and Long, J and Liu, Z and Tao, W and Wang, D},
title = {Identification and Evolution of TGF-β Signaling Pathway Members in Twenty-Four Animal Species and Expression in Tilapia.},
journal = {International journal of molecular sciences},
volume = {19},
number = {4},
pages = {},
doi = {10.3390/ijms19041154},
pmid = {29641448},
issn = {1422-0067},
abstract = {Transforming growth factor β (TGF-β) signaling controls diverse cellular processes during embryogenesis as well as in mature tissues of multicellular animals. Here we carried out a comprehensive analysis of TGF-β pathway members in 24 representative animal species. The appearance of the TGF-β pathway was intrinsically linked to the emergence of metazoan. The total number of TGF-β ligands, receptors, and smads changed slightly in all invertebrates and jawless vertebrates analyzed. In contrast, expansion of the pathway members, especially ligands, was observed in jawed vertebrates most likely due to the second round of whole genome duplication (2R) and additional rounds in teleosts. Duplications of TGFB2, TGFBR2, ACVR1, SMAD4 and SMAD6, which were resulted from 2R, were first isolated. Type II receptors may be originated from the ACVR2-like ancestor. Interestingly, AMHR2 was not identified in Chimaeriformes and Cypriniformes even though they had the ligand AMH. Based on transcriptome data, TGF-β ligands exhibited a tissue-specific expression especially in the heart and gonads. However, most receptors and smads were expressed in multiple tissues indicating they were shared by different ligands. Spatial and temporal expression profiles of 8 genes in gonads of different developmental stages provided a fundamental clue for understanding their important roles in sex determination and reproduction. Taken together, our findings provided a global insight into the phylogeny and expression patterns of the TGF-β pathway genes, and hence contribute to the greater understanding of their biological roles in the organism especially in teleosts.},
}

@article {pmid29632050,
year = {2018},
author = {Fidler, AL and Boudko, SP and Rokas, A and Hudson, BG},
title = {The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution.},
journal = {Journal of cell science},
volume = {131},
number = {7},
pages = {},
doi = {10.1242/jcs.203950},
pmid = {29632050},
issn = {1477-9137},
support = {R01 DK018381/DK/NIDDK NIH HHS/United States ; R37 DK018381/DK/NIDDK NIH HHS/United States ; },
abstract = {The cellular microenvironment, characterized by an extracellular matrix (ECM), played an essential role in the transition from unicellularity to multicellularity in animals (metazoans), and in the subsequent evolution of diverse animal tissues and organs. A major ECM component are members of the collagen superfamily -comprising 28 types in vertebrates - that exist in diverse supramolecular assemblies ranging from networks to fibrils. Each assembly is characterized by a hallmark feature, a protein structure called a triple helix. A current gap in knowledge is understanding the mechanisms of how the triple helix encodes and utilizes information in building scaffolds on the outside of cells. Type IV collagen, recently revealed as the evolutionarily most ancient member of the collagen superfamily, serves as an archetype for a fresh view of fundamental structural features of a triple helix that underlie the diversity of biological activities of collagens. In this Opinion, we argue that the triple helix is a protein structure of fundamental importance in building the extracellular matrix, which enabled animal multicellularity and tissue evolution.},
}

@article {pmid29625658,
year = {2018},
author = {Padder, SA and Prasad, R and Shah, AH},
title = {Quorum sensing: A less known mode of communication among fungi.},
journal = {Microbiological research},
volume = {210},
number = {},
pages = {51-58},
doi = {10.1016/j.micres.2018.03.007},
pmid = {29625658},
issn = {1618-0623},
abstract = {Quorum sensing (QS), a density-dependent signaling mechanism of microbial cells, involves an exchange and sense of low molecular weight signaling compounds called autoinducers. With the increase in population density, the autoinducers accumulate in the extracellular environment and once their concentration reaches a threshold, many genes are either expressed or repressed. This cell density-dependent signaling mechanism enables single cells to behave as multicellular organisms and regulates different microbial behaviors like morphogenesis, pathogenesis, competence, biofilm formation, bioluminescence, etc guided by environmental cues. Initially, QS was regarded to be a specialized system of certain bacteria. The discovery of filamentation control in pathogenic polymorphic fungus Candida albicans by farnesol revealed the phenomenon of QS in fungi as well. Pathogenic microorganisms primarily regulate the expression of virulence genes using QS systems. The indirect role of QS in the emergence of multiple drug resistance (MDR) in microbial pathogens necessitates the finding of alternative antimicrobial therapies that target QS and inhibit the same. A related phenomenon of quorum sensing inhibition (QSI) performed by small inhibitor molecules called quorum sensing inhibitors (QSIs) has an ability for efficient reduction of gene expression regulated by quorum sensing. In the present review, recent advancements in the study of different fungal quorum sensing molecules (QSMs) and quorum sensing inhibitors (QSIs) of fungal origin along with their mechanism of action and/or role/s are discussed.},
}

@article {pmid29619014,
year = {2018},
author = {Jani, AJ and Briggs, CJ},
title = {Host and Aquatic Environment Shape the Amphibian Skin Microbiome but Effects on Downstream Resistance to the Pathogen Batrachochytrium dendrobatidis Are Variable.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {487},
doi = {10.3389/fmicb.2018.00487},
pmid = {29619014},
issn = {1664-302X},
abstract = {Symbiotic microbial communities play key roles in the health and development of their multicellular hosts. Understanding why microbial communities vary among different host species or individuals is an important step toward understanding the diversity and function of the microbiome. The amphibian skin microbiome may affect resistance to the fungal pathogen Batrachochytrium dendrobatidis (Bd). Still, the factors that determine the diversity and composition of the amphibian skin microbiome, and therefore may ultimately contribute to disease resistance, are not well understood. We conducted a two-phase experiment to first test how host and environment shape the amphibian skin microbiome, and then test if the microbiome affects or is affected by Bd infection. Most lab experiments testing assembly of the amphibian skin microbiome so far have compared sterile to non-sterile environments or heavily augmented to non-augmented frogs. A goal of this study was to evaluate, in an experimental setting, realistic potential drivers of microbiome assembly that would be relevant to patterns observed in nature. We tested effects of frog genetic background (2 source populations) and 6 natural lake water sources in shaping the microbiome of the frog Rana sierrae. Water in which frogs were housed affected the microbiome in a manner that partially mimicked patterns observed in natural populations. In particular, frogs housed in water from disease-resistant populations had greater bacterial richness than frogs housed in water from populations that died out due to Bd. However, in the experiment this difference in microbiomes did not lead to differences in host mortality or rates of pathogen load increase. Frog source population also affected the microbiome and, although none of the frogs in this study showed true resistance to infection, host source population had a small effect on the rate of pathogen load increase. This difference in infection trajectories could be due to the observed differences in the microbiome, but could also be due to other traits that differ between frogs from the two populations. In addition to examining effects of the microbiome on Bd, we tested the effect of Bd infection severity on the microbiome. Specifically, we studied a time series of the microbiome over the course of infection to test if the effects of Bd on the microbiome are dependent on Bd infection severity. Although limited to a small subset of frogs, time series analysis suggested that relative abundances of several bacterial phylotypes changed as Bd loads increased through time, indicating that Bd-induced disturbance of the R. sierrae microbiome is not a binary effect but instead is dependent on infection severity. We conclude that both host and aquatic environment help shape the R. sierrae skin microbiome, with links to small changes in disease resistance in some cases, but in this study the effect of Bd on the microbiome was greater than the effect of the microbiome on Bd. Assessment of the microbiome differences between more distantly related populations than those studied here is needed to fully understand the role of the microbiome in resistance to Bd.},
}

@article {pmid29616867,
year = {2018},
author = {Gaiti, F and Degnan, BM and Tanurdžić, M},
title = {Long non-coding regulatory RNAs in sponges and insights into the origin of animal multicellularity.},
journal = {RNA biology},
volume = {},
number = {},
pages = {1-7},
doi = {10.1080/15476286.2018.1460166},
pmid = {29616867},
issn = {1555-8584},
abstract = {How animals evolved from a single-celled ancestor over 700 million years ago is poorly understood. Recent transcriptomic and chromatin analyses in the sponge Amphimedon queenslandica, a morphologically-simple representative of one of the oldest animal phyletic lineages, have shed light on what innovations in the genome and its regulation underlie the emergence of animal multicellularity. Comparisons of the regulatory genome of this sponge with those of more complex bilaterian model species and even simpler unicellular relatives have revealed that fundamental changes in genome regulatory complexity accompanied the evolution of animal multicellularity. Here, we review and discuss the results of these recent investigations by specifically focusing on the contribution of long non-coding RNAs to the evolution of the animal regulatory genome.},
}

@article {pmid29608173,
year = {2018},
author = {Clarke, EK and Rivera Gomez, KA and Mustachi, Z and Murph, MC and Schvarzstein, M},
title = {Manipulation of Ploidy in Caenorhabditis elegans.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {133},
pages = {},
doi = {10.3791/57296},
pmid = {29608173},
issn = {1940-087X},
support = {P40 OD010440/OD/NIH HHS/United States ; //CIHR/Canada ; },
mesh = {Animals ; Caenorhabditis elegans/*genetics ; Male ; *Ploidies ; },
abstract = {Mechanisms that involve whole genome polyploidy play important roles in development and evolution; also, an abnormal generation of tetraploid cells has been associated with both the progression of cancer and the development of drug resistance. Until now, it has not been feasible to easily manipulate the ploidy of a multicellular animal without generating mostly sterile progeny. Presented here is a simple and rapid protocol for generating tetraploid Caenorhabditis elegans animals from any diploid strain. This method allows the user to create a bias in chromosome segregation during meiosis, ultimately increasing ploidy in C. elegans. This strategy relies on the transient reduction of expression of the rec-8 gene to generate diploid gametes. A rec-8 mutant produces diploid gametes that can potentially produce tetraploids upon fertilization. This tractable scheme has been used to generate tetraploid strains carrying mutations and chromosome rearrangements to gain insight into chromosomal dynamics and interactions during pairing and synapsis in meiosis. This method is efficient for generating stable tetraploid strains without genetic markers, can be applied to any diploid strain, and can be used to derive triploid C. elegans. This straightforward method is useful for investigating other fundamental biological questions relevant to genome instability, gene dosage, biological scaling, extracellular signaling, adaptation to stress, development of resistance to drugs, and mechanisms of speciation.},
}

Animals
Caenorhabditis elegans/*genetics
Male
*Ploidies

@article {pmid29606595,
year = {2018},
author = {Lherminier, P},
title = {[Informative predation: Towards a new species concept].},
journal = {Comptes rendus biologies},
volume = {341},
number = {4},
pages = {209-218},
doi = {10.1016/j.crvi.2018.02.004},
pmid = {29606595},
issn = {1768-3238},
abstract = {We distinguish two types of predations: the predation of matter-energy equals the food chain, and the informative predation is the capture of the information brought by the sexual partners. The cell or parent consumes energy and matter to grow, multiply and produce offspring. A fixed amount of resources is divided by the number of organisms, so individual growth and numerical multiplication are limited by depletion resources of the environment. Inversely, fertilization does not destroy information, but instead produces news. The information is multiplied by the number of partners and children, since each fertilization gives rise to a new genome following a combinatorial process that continues without exhaustion. The egg does not swallow the sperm to feed, but exchange good food for quality information. With the discovery of sex, that is, 1.5 Ga ago, life added soft predation to hard predation, i.e. information production within each species to matter-energy flow between species. Replicative and informative structures are subject to two competing biological constraints: replicative fidelity promotes proliferation, but limits adaptive evolution. On the contrary, the offspring of a couple obviously cannot be a copy of both partners, they are a new production, a re-production. Sexual recombination allows the exponential enrichment of the genetic diversity, thus promoting indefinite adaptive and evolutionary capacities. Evolutionary history illustrates this: the bacteria proliferate but have remained at the first purely nutritive stage in which most of the sensory functions, mobility, defense, and feeding have experienced almost no significant novelty in three billion years. Another world appeared with the sexual management of information. Sexual reproduction actually combines two functions: multiplicative by "vertical transfer" and informative by "horizontal transfer". This distinction is very common: polypus - medusa alternations, parasite multiplication cycles, the lytochal and deuterotochal parthenogenesis of aphids, and the innumerable para- and pseudo-sexual strategies of plants opportunistically combine the two modes of asexual replication and sexual combination. However, for the majority of animals and multicellular plants that produce many gametes, numerical proliferation by descendants and informative diversity by sexuality are mutually implicated, for example in the seed. The true discovery of eukaryotes may not be the "true nucleus", as their name implies, but an orderly informative function. The field of recombinations circumscribes a class of partners genetically compatible with each other, each simultaneously prey and predator of the DNA of the other. The mythical Maxwell demon capable of tracing entropy by sorting molecules according to their state does exist: each mate is the other's Maxwell's demon. While a sexless bacterium is simply divided into two cells, two sexual parents work together to produce a single offspring a time. Added to this are the burdens involved in meiosis and crossing-over, cellular diploidy, and mating. Sex produces an information gain that is paid for by a cost of energy-material, and this barter must be fair to survive. The domains of sexual intercourse are very diverse: uniparental reproduction, alternation of asexual proliferation and sexual information, self-fertilization, endogamy, exogamy, panmixis, diffuse or structured polymorphism, fertile or sterile hybridization, horizontal transfers. Each species is a recombination field between two domains, cloning and hybridization. Multiplicative descent and informative fertilization are organically distinct, but selectively associated: the information produced by the parents' sexuality favors the predation of matter-energy and therefore the proliferation of offspring, and this proliferation in turn favors the sexed producers of information. The equation specific to each species is: enough energy to proliferate, enough information to diversify. Alternatively, two other reproductive modes obtain or transmit less information at lower cost: not enough recombinations=repetitive clonal proliferation, and too many recombinations=disordered hybridization. But these marginal modes have poor prospects, as the model of the species is successfully attractive. Better discriminate to better inform. In bacteria, the exchanged and incorporated DNA segments are directly identified by the parity of the complementary strands, which determines simultaneously the similarity, the offspring, and the pairing. In eukaryotes, on the contrary, somatic growth and germinal information are segregated. During speciation, adaptive information is compacted, delocalized, codified and published to inform the species about its own state: the prezygotic relationship governs viable mating. Under the effect of sexual selection, the runaway and the reinforcement of the characters related to courtship testifies to their identifying function, which explains the paradox of the singularity and luxuriance of the sexual hypertrophies. The speciation discretizes a balanced recombination field and validates the informative relations. The species is without degree. Mates of a species recognize each other quickly and well because the logic of coding disengages from the ecological game of adaptations. The system of mate recognition has a function of cohesion and its regularity allows the adaptations of the less regular being, it is neither elitist nor normative, it is subjected neither to a level of aptitudes, nor to sexual performances, but permissive; it protects the variability and polymorphism. Two mutually irreducible relationships triggered the debate between the taxonomists who support the phyletic definition of the species by the descendance, and the proponents of the definition by interfertility. Such a taxonomic disagreement is not insurmountable, but the issue is deeper than taxonomic concepts, because these concepts relate to two different modes of evolution. According to the phyletic model, each species is a lineage passively isolated by external circumstances; on the contrary, in the sexual model each species is actively produced by an internal process of adjustment between replicative costs and informative gains. Each species develops a solution of the equation that matches material-energy expenditures with informative gains. A species concept based on a lasting relationship between these two quantities or on the limits of certain values or their equilibrium is therefore legitimate. It is this equilibrium that all couples resolve, without our formulation being as clearly as biology desires and as physics demands. Energy expenditures and informative gains in sexuality are almost impossible to measure, yet observation and experience allow an approximate ranking of the energy/information ratio. For example, endogamy is more economical, but less diversifying than exogamy, polymorphism increases information, the reinforcement of sexual isolation limits the rate of unproductive fertilization, between neighboring species hybridization allows certain genetic contributions, etc. A closed species evolves naturally towards another just as closed. On the contrary, the artificial transfer of DNA opens the species. The natural boundaries that isolate the species are easily trespassed as energy costs and constraints of sexual recognition are easily controlled; and the perspectives of manipulations are visible, whereas natural selection never anticipates and thus works blindly. Informative, artificially directed predation stimulates the evolution of species.},
}

@article {pmid29602367,
year = {2018},
author = {Shingleton, AW and Frankino, WA},
title = {The (ongoing) problem of relative growth.},
journal = {Current opinion in insect science},
volume = {25},
number = {},
pages = {9-19},
doi = {10.1016/j.cois.2017.10.001},
pmid = {29602367},
issn = {2214-5753},
abstract = {Differential growth, the phenomenon where parts of the body grow at different rates, is necessary to generate the complex morphologies of most multicellular organisms. Despite this central importance, how differential growth is regulated remains largely unknown. Recent discoveries, particularly in insects, have started to uncover the molecular-genetic and physiological mechanisms that coordinate growth among different tissues throughout the body and regulate relative growth. These discoveries suggest that growth is coordinated by a network of signals that emanate from growing tissues and central endocrine organs. Here we review these findings and discuss their implications for understanding the regulation of relative growth and the evolution of morphology.},
}

@article {pmid29599012,
year = {2018},
author = {Bang, C and Dagan, T and Deines, P and Dubilier, N and Duschl, WJ and Fraune, S and Hentschel, U and Hirt, H and Hülter, N and Lachnit, T and Picazo, D and Pita, L and Pogoreutz, C and Rädecker, N and Saad, MM and Schmitz, RA and Schulenburg, H and Voolstra, CR and Weiland-Bräuer, N and Ziegler, M and Bosch, TCG},
title = {Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?.},
journal = {Zoology (Jena, Germany)},
volume = {127},
number = {},
pages = {1-19},
doi = {10.1016/j.zool.2018.02.004},
pmid = {29599012},
issn = {1873-2720},
mesh = {*Adaptation, Physiological/physiology ; Animals ; Ecosystem ; *Extreme Environments ; Microbiota/genetics/*physiology ; Phylogeny ; Symbiosis/physiology ; },
abstract = {From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forming a metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms. Research on host-microbe interactions has become an emerging cross-disciplinary field. In both vertebrates and invertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, its disturbance can contribute to the development of disease states. However, the molecular and cellular mechanisms controlling the interactions within a metaorganism are poorly understood and many key interactions between the associated organisms remain unknown. In this perspective article, we outline some of the issues in interspecies interactions and in particular address the question of how metaorganisms react and adapt to inputs from extreme environments such as deserts, the intertidal zone, oligothrophic seas, and hydrothermal vents.},
}

*Adaptation, Physiological/physiology
Animals
Ecosystem
*Extreme Environments
Microbiota/genetics/*physiology
Phylogeny
Symbiosis/physiology

@article {pmid29593113,
year = {2018},
author = {Nair, RR and Fiegna, F and Velicer, GJ},
title = {Indirect evolution of social fitness inequalities and facultative social exploitation.},
journal = {Proceedings. Biological sciences},
volume = {285},
number = {1875},
pages = {},
doi = {10.1098/rspb.2018.0054},
pmid = {29593113},
issn = {1471-2954},
abstract = {Microbial genotypes with similarly high proficiency at a cooperative behaviour in genetically pure groups often exhibit fitness inequalities caused by social interaction in mixed groups. Winning competitors in this scenario have been referred to as 'cheaters' in some studies. Such interaction-specific fitness inequalities, as well as social exploitation (in which interaction between genotypes increases absolute fitness), might evolve due to selection for competitiveness at the focal behaviour or might arise non-adaptively due to pleiotropy, hitchhiking or genetic drift. The bacterium Myxococcus xanthus sporulates during cooperative development of multicellular fruiting bodies. Using M. xanthus lineages that underwent experimental evolution in allopatry without selection on sporulation, we demonstrate that interaction-specific fitness inequalities and facultative social exploitation during development readily evolved indirectly among descendant lineages. Fitness inequalities between evolved genotypes were not caused by divergence in developmental speed, as faster-developing strains were not over-represented among competition winners. In competitions between ancestors and several evolved strains, all evolved genotypes produced more spores than the ancestors, including losers of evolved-versus-evolved competitions, indicating that adaptation in non-developmental contexts pleiotropically increased competitiveness for spore production. Overall, our results suggest that fitness inequalities caused by social interaction during cooperative processes may often evolve non-adaptively in natural populations.},
}

@article {pmid29590089,
year = {2018},
author = {Alemany, A and Florescu, M and Baron, CS and Peterson-Maduro, J and van Oudenaarden, A},
title = {Whole-organism clone tracing using single-cell sequencing.},
journal = {Nature},
volume = {556},
number = {7699},
pages = {108-112},
doi = {10.1038/nature25969},
pmid = {29590089},
issn = {1476-4687},
mesh = {Animal Fins/cytology ; Animals ; Brain/cytology ; CRISPR-Cas Systems/genetics ; *Cell Lineage/genetics ; Cell Tracking/*methods ; Clone Cells/*cytology/*metabolism ; Embryonic Stem Cells/cytology/metabolism ; Eye/cytology ; Female ; Genes, Reporter/genetics ; Hematopoietic Stem Cells/cytology/metabolism ; Male ; Multipotent Stem Cells/cytology/metabolism ; Organ Specificity ; Regeneration ; Sequence Analysis/*methods ; *Single-Cell Analysis ; Transcriptome ; Whole Body Imaging ; Zebrafish/*anatomy & histology/embryology/genetics ; },
abstract = {Embryonic development is a crucial period in the life of a multicellular organism, during which limited sets of embryonic progenitors produce all cells in the adult body. Determining which fate these progenitors acquire in adult tissues requires the simultaneous measurement of clonal history and cell identity at single-cell resolution, which has been a major challenge. Clonal history has traditionally been investigated by microscopically tracking cells during development, monitoring the heritable expression of genetically encoded fluorescent proteins and, more recently, using next-generation sequencing technologies that exploit somatic mutations, microsatellite instability, transposon tagging, viral barcoding, CRISPR-Cas9 genome editing and Cre-loxP recombination. Single-cell transcriptomics provides a powerful platform for unbiased cell-type classification. Here we present ScarTrace, a single-cell sequencing strategy that enables the simultaneous quantification of clonal history and cell type for thousands of cells obtained from different organs of the adult zebrafish. Using ScarTrace, we show that a small set of multipotent embryonic progenitors generate all haematopoietic cells in the kidney marrow, and that many progenitors produce specific cell types in the eyes and brain. In addition, we study when embryonic progenitors commit to the left or right eye. ScarTrace reveals that epidermal and mesenchymal cells in the caudal fin arise from the same progenitors, and that osteoblast-restricted precursors can produce mesenchymal cells during regeneration. Furthermore, we identify resident immune cells in the fin with a distinct clonal origin from other blood cell types. We envision that similar approaches will have major applications in other experimental systems, in which the matching of embryonic clonal origin to adult cell type will ultimately allow reconstruction of how the adult body is built from a single cell.},
}

Animal Fins/cytology
Animals
Brain/cytology
CRISPR-Cas Systems/genetics
*Cell Lineage/genetics
Cell Tracking/*methods
Clone Cells/*cytology/*metabolism
Embryonic Stem Cells/cytology/metabolism
Eye/cytology
Female
Genes, Reporter/genetics
Hematopoietic Stem Cells/cytology/metabolism
Male
Multipotent Stem Cells/cytology/metabolism
Organ Specificity
Regeneration
Sequence Analysis/*methods
*Single-Cell Analysis
Transcriptome
Whole Body Imaging
Zebrafish/*anatomy & histology/embryology/genetics

@article {pmid29587819,
year = {2018},
author = {Dickson, LB and Ghozlane, A and Volant, S and Bouchier, C and Ma, L and Vega-Rúa, A and Dusfour, I and Jiolle, D and Paupy, C and Mayanja, MN and Kohl, A and Lutwama, JJ and Duong, V and Lambrechts, L},
title = {Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome.},
journal = {Parasites & vectors},
volume = {11},
number = {1},
pages = {207},
doi = {10.1186/s13071-018-2780-1},
pmid = {29587819},
issn = {1756-3305},
support = {ANR-16-CE35-0004-01//Agence Nationale de la Recherche/International ; ANR-17-ERC2-0016-01//Agence Nationale de la Recherche/International ; ANR-10-LABX-62-IBEID//Investissement d'Avenir program Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases/International ; 734584//European Union's Horizon 2020 research and innovation programme under ZikaPLAN/International ; 2015-FED-192//Programme Opérationnel FEDER-Guadeloupe-Conseil Régional/International ; MC_UU_12014//Medical Research Council/United Kingdom ; ANR10-INBS-09-08//France Génomique consortium/International ; },
abstract = {BACKGROUND: Host-associated microbes, collectively known as the microbiota, play an important role in the biology of multicellular organisms. In mosquito vectors of human pathogens, the gut bacterial microbiota influences vectorial capacity and has become the subject of intense study. In laboratory studies of vector biology, genetic effects are often inferred from differences between geographically and genetically diverse colonies of mosquitoes that are reared in the same insectary. It is unclear, however, to what extent genetic effects can be confounded by uncontrolled differences in the microbiota composition among mosquito colonies. To address this question, we used 16S metagenomics to compare the midgut bacterial microbiome of six laboratory colonies of Aedes aegypti recently derived from wild populations representing the geographical range and genetic diversity of the species.

RESULTS: We found that the diversity, abundance, and community structure of the midgut bacterial microbiome was remarkably similar among the six different colonies of Ae. aegypti, regardless of their geographical origin. We also confirmed the relatively low complexity of bacterial communities inhabiting the mosquito midgut.

CONCLUSIONS: Our finding that geographically diverse colonies of Ae. aegypti reared in the same insectary harbor a similar gut bacterial microbiome supports the conclusion that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype. Thus, uncontrolled differences in microbiota composition are unlikely to represent a significant confounding factor in genetic studies of vector biology.},
}

@article {pmid29581530,
year = {2018},
author = {Lin, W and Zhang, W and Zhao, X and Roberts, AP and Paterson, GA and Bazylinski, DA and Pan, Y},
title = {Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution.},
journal = {The ISME journal},
volume = {12},
number = {6},
pages = {1508-1519},
doi = {10.1038/s41396-018-0098-9},
pmid = {29581530},
issn = {1751-7370},
abstract = {The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth's magnetic field for orientation and navigation, is not well understood in evolutionary biology. The only known prokaryotes capable of sensing the geomagnetic field are magnetotactic bacteria (MTB), motile microorganisms that biomineralize intracellular, membrane-bounded magnetic single-domain crystals of either magnetite (Fe3O4) or greigite (Fe3S4) called magnetosomes. Magnetosomes are responsible for magnetotaxis in MTB. Here we report the first large-scale metagenomic survey of MTB from both northern and southern hemispheres combined with 28 genomes from uncultivated MTB. These genomes expand greatly the coverage of MTB in the Proteobacteria, Nitrospirae, and Omnitrophica phyla, and provide the first genomic evidence of MTB belonging to the Zetaproteobacteria and "Candidatus Lambdaproteobacteria" classes. The gene content and organization of magnetosome gene clusters, which are physically grouped genes that encode proteins for magnetosome biosynthesis and organization, are more conserved within phylogenetically similar groups than between different taxonomic lineages. Moreover, the phylogenies of core magnetosome proteins form monophyletic clades. Together, these results suggest a common ancient origin of iron-based (Fe3O4 and Fe3S4) magnetotaxis in the domain Bacteria that underwent lineage-specific evolution, shedding new light on the origin and evolution of biomineralization and magnetotaxis, and expanding significantly the phylogenomic representation of MTB.},
}

@article {pmid29579574,
year = {2018},
author = {Lower, SS and McGurk, MP and Clark, AG and Barbash, DA},
title = {Satellite DNA evolution: old ideas, new approaches.},
journal = {Current opinion in genetics & development},
volume = {49},
number = {},
pages = {70-78},
doi = {10.1016/j.gde.2018.03.003},
pmid = {29579574},
issn = {1879-0380},
support = {F32 GM126736/GM/NIGMS NIH HHS/United States ; R01 GM119125/GM/NIGMS NIH HHS/United States ; },
abstract = {A substantial portion of the genomes of most multicellular eukaryotes consists of large arrays of tandemly repeated sequence, collectively called satellite DNA. The processes generating and maintaining different satellite DNA abundances across lineages are important to understand as satellites have been linked to chromosome mis-segregation, disease phenotypes, and reproductive isolation between species. While much theory has been developed to describe satellite evolution, empirical tests of these models have fallen short because of the challenges in assessing satellite repeat regions of the genome. Advances in computational tools and sequencing technologies now enable identification and quantification of satellite sequences genome-wide. Here, we describe some of these tools and how their applications are furthering our knowledge of satellite evolution and function.},
}

@article {pmid29575407,
year = {2018},
author = {Radzvilavicius, AL and Blackstone, NW},
title = {The evolution of individuality revisited.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {93},
number = {3},
pages = {1620-1633},
doi = {10.1111/brv.12412},
pmid = {29575407},
issn = {1469-185X},
abstract = {Evolutionary theory is formulated in terms of individuals that carry heritable information and are subject to selective pressures. However, individuality itself is a trait that had to evolve - an individual is not an indivisible entity, but a result of evolutionary processes that necessarily begin at the lower level of hierarchical organisation. Traditional approaches to biological individuality focus on cooperation and relatedness within a group, division of labour, policing mechanisms and strong selection at the higher level. Nevertheless, despite considerable theoretical progress in these areas, a full dynamical first-principles account of how new types of individuals arise is missing. To the extent that individuality is an emergent trait, the problem can be approached by recognising the importance of individuating mechanisms that are present from the very beginning of the transition, when only lower-level selection is acting. Here we review some of the most influential theoretical work on the role of individuating mechanisms in these transitions, and demonstrate how a lower-level, bottom-up evolutionary framework can be used to understand biological complexity involved in the origin of cellular life, early eukaryotic evolution, sexual life cycles and multicellular development. Some of these mechanisms inevitably stem from environmental constraints, population structure and ancestral life cycles. Others are unique to specific transitions - features of the natural history and biochemistry that are co-opted into conflict mediation. Identifying mechanisms of individuation that provide a coarse-grained description of the system's evolutionary dynamics is an important step towards understanding how biological complexity and hierarchical organisation evolves. In this way, individuality can be reconceptualised as an approximate model that with varying degrees of precision applies to a wide range of biological systems.},
}

@article {pmid29575018,
year = {2018},
author = {Revilla-I-Domingo, R and Simakov, O},
title = {The Diversification of Early Emerging Metazoans: A Window into the Evolution of Animal Multicellularity.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {40},
number = {5},
pages = {e1800029},
doi = {10.1002/bies.201800029},
pmid = {29575018},
issn = {1521-1878},
abstract = {The biannual international workshop entitled "The diversification of early emerging metazoans: A window into animal evolution?" took place at the Evangelische Akademie Tutzing, Germany, 11-14. September 2017. It was organized by Thomas Bosch (Kiel), Thomas Holstein (Heidelberg), and Ulrich Technau (Vienna), and it was sponsored by the Deutsche Forschungsgemeinschaft (DFG). The meeting gathered over 140 researchers to discuss the contribution of non-bilaterian metazoan models (Porifera, Ctenophora, Placozoa, and Cnidaria) to our understanding of: a. The evolution of metazoan developmental processes; b. Fundamental molecular mechanisms underlying metazoan features; and c. The complex interactions that animals establish with their environment.},
}

@article {pmid29573204,
year = {2018},
author = {Preisner, H and Habicht, J and Garg, SG and Gould, SB},
title = {Intermediate filament protein evolution and protists.},
journal = {Cytoskeleton (Hoboken, N.J.)},
volume = {75},
number = {6},
pages = {231-243},
doi = {10.1002/cm.21443},
pmid = {29573204},
issn = {1949-3592},
abstract = {Metazoans evolved from a single protist lineage. While all eukaryotes share a conserved actin and tubulin-based cytoskeleton, it is commonly perceived that intermediate filaments (IFs), including lamin, vimentin or keratin among many others, are restricted to metazoans. Actin and tubulin proteins are conserved enough to be detectable across all eukaryotic genomes using standard phylogenetic methods, but IF proteins, in contrast, are notoriously difficult to identify by such means. Since the 1950s, dozens of cytoskeletal proteins in protists have been identified that seemingly do not belong to any of the IF families described for metazoans, yet, from a structural and functional perspective fit criteria that define metazoan IF proteins. Here, we briefly review IF protein discovery in metazoans and the implications this had for the definition of this protein family. We argue that the many cytoskeletal and filament-forming proteins of protists should be incorporated into a more comprehensive picture of IF evolution by aligning it with the recent identification of lamins across the phylogenetic diversity of eukaryotic supergroups. This then brings forth the question of how the diversity of IF proteins has unfolded. The evolution of IF proteins likely represents an example of convergent evolution, which, in combination with the speed with which these cytoskeletal proteins are evolving, generated their current diversity. IF proteins did not first emerge in metazoa, but in protists. Only the emergence of cytosolic IF proteins that appear to stem from a nuclear lamin is unique to animals and coincided with the emergence of true animal multicellularity.},
}

@article {pmid29564400,
year = {2018},
author = {Qin, X and Zhou, C and Zerr, DM and Adler, A and Addetia, A and Yuan, S and Greninger, AL},
title = {Heterogeneous Antimicrobial Susceptibility Characteristics in Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients.},
journal = {mSphere},
volume = {3},
number = {2},
pages = {},
doi = {10.1128/mSphere.00615-17},
pmid = {29564400},
issn = {2379-5042},
abstract = {Clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis (CF) are known to differ from those associated with non-CF hosts by colony morphology, drug susceptibility patterns, and genomic hypermutability. Pseudomonas aeruginosa isolates from CF patients have long been recognized for their overall reduced rate of antimicrobial susceptibility, but their intraclonal MIC heterogeneity has long been overlooked. Using two distinct cohorts of clinical strains (n = 224 from 56 CF patients, n = 130 from 68 non-CF patients) isolated in 2013, we demonstrated profound Etest MIC heterogeneity in CF P. aeruginosa isolates in comparison to non-CF P. aeruginosa isolates. On the basis of whole-genome sequencing of 19 CF P. aeruginosa isolates from 9 patients with heterogeneous MICs, the core genome phylogenetic tree confirmed the within-patient CF P. aeruginosa clonal lineage along with considerable coding sequence variability. No extrachromosomal DNA elements or previously characterized antibiotic resistance mutations could account for the wide divergence in antimicrobial MICs between P. aeruginosa coisolates, though many heterogeneous mutations in efflux and porin genes and their regulators were present. A unique OprD sequence was conserved among the majority of isolates of CF P. aeruginosa analyzed, suggesting a pseudomonal response to selective pressure that is common to the isolates. Genomic sequence data also suggested that CF pseudomonal hypermutability was not entirely due to mutations in mutL, mutS, and uvr. We conclude that the net effect of hundreds of adaptive mutations, both shared between clonally related isolate pairs and unshared, accounts for their highly heterogeneous MIC variances. We hypothesize that this heterogeneity is indicative of the pseudomonal syntrophic-like lifestyle under conditions of being "locked" inside a host focal airway environment for prolonged periods. IMPORTANCE Patients with cystic fibrosis endure "chronic focal infections" with a variety of microorganisms. One microorganism, Pseudomonas aeruginosa, adapts to the host and develops resistance to a wide range of antimicrobials. Interestingly, as the infection progresses, multiple isogenic strains of P. aeruginosa emerge and coexist within the airways of these patients. Despite a common parental origin, the multiple strains of P. aeruginosa develop vastly different susceptibility patterns to actively used antimicrobial agents-a phenomenon we define as "heterogeneous MICs." By sequencing pairs of P. aeruginosa isolates displaying heterogeneous MICs, we observed widespread isogenic gene lesions in drug transporters, DNA mismatch repair machinery, and many other structural or cellular functions. Coupled with the heterogeneous MICs, these genetic lesions demonstrated a symbiotic response to host selection and suggested evolution of a multicellular syntrophic bacterial lifestyle. Current laboratory standard interpretive criteria do not address the emergence of heterogeneous growth and susceptibilities in vitro with treatment implications.},
}

@article {pmid29563281,
year = {2018},
author = {Rodríguez-Rojas, A and Moreno-Morales, J and Mason, AJ and Rolff, J},
title = {Cationic antimicrobial peptides do not change recombination frequency in Escherichia coli.},
journal = {Biology letters},
volume = {14},
number = {3},
pages = {},
doi = {10.1098/rsbl.2018.0006},
pmid = {29563281},
issn = {1744-957X},
abstract = {Cationic antimicrobial peptides are ubiquitous immune effectors of multicellular organisms. We previously reported, that in contrast to most of the classic antibiotics, cationic antimicrobial peptides (AMPs) do not increase mutation rates in E. coli Here, we provide new evidence showing that AMPs do not stimulate or enhance bacterial DNA recombination in the surviving fractions. Recombination accelerates evolution of antibiotic resistance. Our findings have implications for our understanding of host-microbe interactions, the evolution of innate immune defences, and shed new light on the dynamic of antimicrobial-resistance evolution.},
}

@article {pmid29559848,
year = {2018},
author = {Shabardina, V and Kischka, T and Kmita, H and Suzuki, Y and Makałowski, W},
title = {Environmental adaptation of Acanthamoeba castellanii and Entamoeba histolytica at genome level as seen by comparative genomic analysis.},
journal = {International journal of biological sciences},
volume = {14},
number = {3},
pages = {306-320},
doi = {10.7150/ijbs.23869},
pmid = {29559848},
issn = {1449-2288},
abstract = {Amoebozoans are in many aspects interesting research objects, as they combine features of single-cell organisms with complex signaling and defense systems, comparable to multicellular organisms. Acanthamoeba castellanii is a cosmopolitan species and developed diverged feeding abilities and strong anti-bacterial resistance; Entamoeba histolytica is a parasitic amoeba, who underwent massive gene loss and its genome is almost twice smaller than that of A. castellanii. Nevertheless, both species prosper, demonstrating fitness to their specific environments. Here we compare transcriptomes of A. castellanii and E. histolytica with application of orthologs' search and gene ontology to learn how different life strategies influence genome evolution and restructuring of physiology. A. castellanii demonstrates great metabolic activity and plasticity, while E. histolytica reveals several interesting features in its translational machinery, cytoskeleton, antioxidant protection, and nutritional behavior. In addition, we suggest new features in E. histolytica physiology that may explain its successful colonization of human colon and may facilitate medical research.},
}

@article {pmid29556540,
year = {2018},
author = {Hynson, NA and Frank, KL and Alegado, RA and Amend, AS and Arif, M and Bennett, GM and Jani, AJ and Medeiros, MCI and Mileyko, Y and Nelson, CE and Nguyen, NH and Nigro, OD and Prisic, S and Shin, S and Takagi, D and Wilson, ST and Yew, JY},
title = {Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research.},
journal = {mSystems},
volume = {3},
number = {2},
pages = {},
doi = {10.1128/mSystems.00159-17},
pmid = {29556540},
issn = {2379-5077},
support = {P30 GM114737/GM/NIGMS NIH HHS/United States ; R21 AI109293/AI/NIAID NIH HHS/United States ; },
abstract = {Despite increasing acknowledgment that microorganisms underpin the healthy functioning of basically all multicellular life, few cross-disciplinary teams address the diversity and function of microbiota across organisms and ecosystems. Our newly formed consortium of junior faculty spanning fields such as ecology and geoscience to mathematics and molecular biology from the University of Hawai'i at Mānoa aims to fill this gap. We are united in our mutual interest in advancing a new paradigm for biology that incorporates our modern understanding of the importance of microorganisms. As our first concerted research effort, we will assess the diversity and function of microbes across an entire watershed on the island of Oahu, Hawai'i. Due to its high ecological diversity across tractable areas of land and sea, Hawai'i provides a model system for the study of complex microbial communities and the processes they mediate. Owing to our diverse expertise, we will leverage this study system to advance the field of biology.},
}

@article {pmid29547664,
year = {2018},
author = {Zielich, J and Tzima, E and Schröder, EA and Jemel, F and Conradt, B and Lambie, EJ},
title = {Overlapping expression patterns and functions of three paralogous P5B ATPases in Caenorhabditis elegans.},
journal = {PloS one},
volume = {13},
number = {3},
pages = {e0194451},
doi = {10.1371/journal.pone.0194451},
pmid = {29547664},
issn = {1932-6203},
support = {P40 OD010440/OD/NIH HHS/United States ; },
mesh = {Adenosine Triphosphatases/classification/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Caenorhabditis elegans/cytology/enzymology/*genetics ; Caenorhabditis elegans Proteins/*genetics/metabolism ; Cell Movement/genetics ; *Gene Expression Profiling ; *Gene Expression Regulation, Enzymologic ; Luminescent Proteins/genetics/metabolism ; Membrane Proteins/genetics/metabolism ; Mutation ; Organelles/enzymology ; Phylogeny ; Sequence Homology, Amino Acid ; },
abstract = {P5B ATPases are present in the genomes of diverse unicellular and multicellular eukaryotes, indicating that they have an ancient origin, and that they are important for cellular fitness. Inactivation of ATP13A2, one of the four human P5B ATPases, leads to early-onset Parkinson's disease (Kufor-Rakeb Syndrome). The presence of an invariant PPALP motif within the putative substrate interaction pocket of transmembrane segment M4 suggests that all P5B ATPases might have similar transport specificity; however, the identity of the transport substrate(s) remains unknown. Nematodes of the genus Caenorhabditis possess three paralogous P5B ATPase genes, catp-5, catp-6 and catp-7, which probably originated from a single ancestral gene around the time of origin of the Caenorhabditid clade. By using CRISPR/Cas9, we have systematically investigated the expression patterns, subcellular localization and biological functions of each of the P5B ATPases of C. elegans. We find that each gene has a unique expression pattern, and that some tissues express more than one P5B. In some tissues where their expression patterns overlap, different P5Bs are targeted to different subcellular compartments (e.g., early endosomes vs. plasma membrane), whereas in other tissues they localize to the same compartment (plasma membrane). We observed lysosomal co-localization between CATP-6::GFP and LMP-1::RFP in transgenic animals; however, this was an artifact of the tagged LMP-1 protein, since anti-LMP-1 antibody staining of native protein revealed that LMP-1 and CATP-6::GFP occupy different compartments. The nematode P5Bs are at least partially redundant, since we observed synthetic sterility in catp-5(0); catp-6(0) and catp-6(0) catp-7(0) double mutants. The double mutants exhibit defects in distal tip cell migration that resemble those of ina-1 (alpha integrin ortholog) and vab-3 (Pax6 ortholog) mutants, suggesting that the nematode P5Bs are required for ina-1and/or vab-3 function. This is potentially a conserved regulatory interaction, since mammalian ATP13A2, alpha integrin and Pax6 are all required for proper dopaminergic neuron function.},
}

Adenosine Triphosphatases/classification/*genetics/metabolism
Amino Acid Sequence
Animals
Animals, Genetically Modified
Caenorhabditis elegans/cytology/enzymology/*genetics
Caenorhabditis elegans Proteins/*genetics/metabolism
Cell Movement/genetics
*Gene Expression Profiling
*Gene Expression Regulation, Enzymologic
Luminescent Proteins/genetics/metabolism
Membrane Proteins/genetics/metabolism
Mutation
Organelles/enzymology
Phylogeny
Sequence Homology, Amino Acid