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

Biological Evolution
Phenotype
Saccharomyces cerevisiae/*physiology

@article {pmid30912270,
year = {2019},
author = {Hamant, O and Bhat, R and Nanjundiah, V and Newman, SA},
title = {Does resource availability help determine the evolutionary route to multicellularity?.},
journal = {Evolution & development},
volume = {21},
number = {3},
pages = {115-119},
pmid = {30912270},
issn = {1525-142X},
support = {ICTS/Prog-LivingMatter2018/04//International Centre for Theoretical Sciences (ICTS)/International ; ERC-2013-CoG-615739 "MechanoDevo"/ERC_/European Research Council/International ; 0412//CSIR/International ; 1586//SERB DST Early Career Grant/International ; },
mesh = {Animals ; *Biological Evolution ; *Gene Expression Regulation, Developmental ; *Genetic Variation ; },
abstract = {Genetic heterogeneity and homogeneity are associated with distinct sets of adaptive advantages and bottlenecks, both in developmental biology and population genetics. Whereas populations of individuals are usually genetically heterogeneous, most multicellular metazoans are genetically homogeneous. Observing that resource scarcity fuels genetic heterogeneity in populations, we propose that monoclonal development is compatible with the resource-rich and stable internal environments that complex multicellular bodies offer. In turn, polyclonal development persists in tumors and in certain metazoans, both exhibiting a closer dependence on external resources. This eco-evo-devo approach also suggests that multicellularity may originally have emerged through polyclonal development in early metazoans, because of their reduced shielding from environmental fluctuations.},
}

Animals
*Biological Evolution
*Gene Expression Regulation, Developmental
*Genetic Variation

@article {pmid31055860,
year = {2019},
author = {Singer, D and Mitchell, EAD and Payne, RJ and Blandenier, Q and Duckert, C and Fernández, LD and Fournier, B and Hernández, CE and Granath, G and Rydin, H and Bragazza, L and Koronatova, NG and Goia, I and Harris, LI and Kajukało, K and Kosakyan, A and Lamentowicz, M and Kosykh, NP and Vellak, K and Lara, E},
title = {Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists.},
journal = {Molecular ecology},
volume = {28},
number = {12},
pages = {3089-3100},
doi = {10.1111/mec.15117},
pmid = {31055860},
issn = {1365-294X},
mesh = {Amoeba/*genetics ; Animals ; Butterflies/genetics ; Ecosystem ; Eukaryota/genetics ; Genetic Speciation ; Genetic Variation/*genetics ; North America ; *Phylogeny ; Plants/genetics ; Sphagnopsida/growth & development ; },
abstract = {Recent studies show that soil eukaryotic diversity is immense and dominated by micro-organisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to micro-organisms. Major diversification events in multicellular organisms have often been attributed to long-term climatic and geological processes, but the impact of such processes on protist diversity has received much less attention as their distribution has often been believed to be largely cosmopolitan. Here, we quantified phylogeographical patterns in Hyalosphenia papilio, a large testate amoeba restricted to Holarctic Sphagnum-dominated peatlands, to test if the current distribution of its genetic diversity can be explained by historical factors or by the current distribution of suitable habitats. Phylogenetic diversity was higher in Western North America, corresponding to the inferred geographical origin of the H. papilio complex, and was lower in Eurasia despite extensive suitable habitats. These results suggest that patterns of phylogenetic diversity and distribution can be explained by the history of Holarctic Sphagnum peatland range expansions and contractions in response to Quaternary glaciations that promoted cladogenetic range evolution, rather than the contemporary distribution of suitable habitats. Species distributions were positively correlated with climatic niche breadth, suggesting that climatic tolerance is key to dispersal ability in H. papilio. This implies that, at least for large and specialized terrestrial micro-organisms, propagule dispersal is slow enough that historical processes may contribute to their diversification and phylogeographical patterns and may partly explain their very high overall diversity.},
}

Amoeba/*genetics
Animals
Butterflies/genetics
Ecosystem
Eukaryota/genetics
Genetic Speciation
Genetic Variation/*genetics
North America
*Phylogeny
Plants/genetics
Sphagnopsida/growth & development

@article {pmid32462426,
year = {2020},
author = {Casanova, JL and Abel, L},
title = {The human genetic determinism of life-threatening infectious diseases: genetic heterogeneity and physiological homogeneity?.},
journal = {Human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00439-020-02184-w},
pmid = {32462426},
issn = {1432-1203},
abstract = {Multicellular eukaryotes emerged late in evolution from an ocean of viruses, bacteria, archaea, and unicellular eukaryotes. These macroorganisms are exposed to and infected by a tremendous diversity of microorganisms. Those that are large enough can even be infected by multicellular fungi and parasites. Each interaction is unique, if only because it operates between two unique living organisms, in an infinite diversity of circumstances. This is neatly illustrated by the extraordinarily high level of interindividual clinical variability in human infections, even for a given pathogen, ranging from a total absence of clinical manifestations to death. We discuss here the idea that the determinism of human life-threatening infectious diseases can be governed by single-gene inborn errors of immunity, which are rarely Mendelian and frequently display incomplete penetrance. We briefly review the evidence in support of this notion obtained over the last two decades, referring to a number of focused and thorough reviews published by eminent colleagues in this issue of Human Genetics. It seems that almost any life-threatening infectious disease can be driven by at least one, and, perhaps, a great many diverse monogenic inborn errors, which may nonetheless be immunologically related. While the proportions of monogenic cases remain unknown, a picture in which genetic heterogeneity is combined with physiological homogeneity is emerging from these studies. A preliminary sketch of the human genetic architecture of severe infectious diseases is perhaps in sight.},
}

@article {pmid31088261,
year = {2019},
author = {Pichugin, Y and Park, HJ and Traulsen, A},
title = {Evolution of simple multicellular life cycles in dynamic environments.},
journal = {Journal of the Royal Society, Interface},
volume = {16},
number = {154},
pages = {20190054},
pmid = {31088261},
issn = {1742-5662},
mesh = {Animals ; *Biological Evolution ; *Environment ; *Life Cycle Stages ; *Models, Biological ; Reproduction ; *Selection, Genetic ; },
abstract = {The mode of reproduction is a critical characteristic of any species, as it has a strong effect on its evolution. As any other trait, the reproduction mode is subject to natural selection and may adapt to the environment. When the environment varies over time, different reproduction modes could be optimal at different times. The natural response to a dynamic environment seems to be bet hedging, where multiple reproductive strategies are stochastically executed. Here, we develop a framework for the evolution of simple multicellular life cycles in a dynamic environment. We use a matrix population model of undifferentiated multicellular groups undergoing fragmentation and ask which mode maximizes the population growth rate. Counterintuitively, we find that natural selection in dynamic environments generally tends to promote deterministic, not stochastic, reproduction modes.},
}

Animals
*Biological Evolution
*Environment
*Life Cycle Stages
*Models, Biological
Reproduction
*Selection, Genetic

@article {pmid32455487,
year = {2020},
author = {Kumler, WE and Jorge, J and Kim, PM and Iftekhar, N and Koehl, MAR},
title = {Does Formation of Multicellular Colonies by Choanoflagellates Affect Their Susceptibility to Capture by Passive Protozoan Predators?.},
journal = {The Journal of eukaryotic microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jeu.12808},
pmid = {32455487},
issn = {1550-7408},
abstract = {Microbial eukaryotes, critical links in aquatic food webs, are unicellular, but some, such as choanoflagellates, form multicellular colonies. Are there consequences to predator avoidance of being unicellular versus forming larger colonies? Choanoflagellates share a common ancestor with animals and are used as model organisms to study the evolution of multicellularity. Escape in size from protozoan predators is suggested as a selective factor favoring evolution of multicellularity. Heterotrophic protozoans are categorized as suspension feeders, motile raptors, or passive predators that eat swimming prey which bump into them. We focused on passive predation and measured the mechanisms responsible for the susceptibility of unicellular versus multicellular choanoflagellates, Salpingoeca helianthica, to capture by passive heliozoan predators, Actinosphaerium nucleofilum, which trap prey on axopodia radiating from the cell body. Microvideography showed that unicellular and colonial choanoflagellates entered the predator's capture zone at similar frequencies, but a greater proportion of colonies contacted axopodia. However, more colonies than single cells were lost during transport by axopodia to the cell body. Thus, feeding efficiency (proportion of prey entering the capture zone that were engulfed in phagosomes) was the same for unicellular and multicellular prey, suggesting that colony formation is not an effective defense against such passive predators.},
}

@article {pmid32355003,
year = {2020},
author = {Lazzaro, BP and Zasloff, M and Rolff, J},
title = {Antimicrobial peptides: Application informed by evolution.},
journal = {Science (New York, N.Y.)},
volume = {368},
number = {6490},
pages = {},
doi = {10.1126/science.aau5480},
pmid = {32355003},
issn = {1095-9203},
support = {R01 AI141385/AI/NIAID NIH HHS/United States ; /ERC_/European Research Council/International ; },
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Antimicrobial Cationic Peptides/chemistry/*genetics/*pharmacology ; Drosophila Proteins/genetics/pharmacology ; *Drug Resistance, Bacterial ; Drug Synergism ; *Evolution, Molecular ; Humans ; Polymorphism, Genetic ; Translational Medical Research ; },
abstract = {Antimicrobial peptides (AMPs) are essential components of immune defenses of multicellular organisms and are currently in development as anti-infective drugs. AMPs have been classically assumed to have broad-spectrum activity and simple kinetics, but recent evidence suggests an unexpected degree of specificity and a high capacity for synergies. Deeper evaluation of the molecular evolution and population genetics of AMP genes reveals more evidence for adaptive maintenance of polymorphism in AMP genes than has previously been appreciated, as well as adaptive loss of AMP activity. AMPs exhibit pharmacodynamic properties that reduce the evolution of resistance in target microbes, and AMPs may synergize with one another and with conventional antibiotics. Both of these properties make AMPs attractive for translational applications. However, if AMPs are to be used clinically, it is crucial to understand their natural biology in order to lessen the risk of collateral harm and avoid the crisis of resistance now facing conventional antibiotics.},
}

Animals
Anti-Bacterial Agents/*pharmacology
Antimicrobial Cationic Peptides/chemistry/*genetics/*pharmacology
Drosophila Proteins/genetics/pharmacology
*Drug Resistance, Bacterial
Drug Synergism
*Evolution, Molecular
Humans
Polymorphism, Genetic
Translational Medical Research

@article {pmid30520011,
year = {2019},
author = {Rebolleda-Gómez, M and Travisano, M},
title = {Adaptation, chance, and history in experimental evolution reversals to unicellularity.},
journal = {Evolution; international journal of organic evolution},
volume = {73},
number = {1},
pages = {73-83},
pmid = {30520011},
issn = {1558-5646},
support = {//John Templeton Foundation/International ; 1051115//Division of Environmental Biology/International ; },
mesh = {*Adaptation, Biological ; *Biological Evolution ; Saccharomyces cerevisiae/*physiology ; },
abstract = {Evolution is often deemed irreversible. The evolution of complex traits that require many mutations makes their reversal unlikely. Even in simpler traits, reversals might become less likely as neutral or beneficial mutations, with deleterious effects in the ancestral context, become fixed in the novel background. This is especially true in changes that involve large reorganizations of the organism and its interactions with the environment. The evolution of multicellularity involves the reorganization of previously autonomous cells into a more complex organism; despite the complexity of this change, single cells have repeatedly evolved from multicellular ancestors. These repeated reversals to unicellularity undermine the generality of Dollo's law. In this article, we evaluated the dynamics of reversals to unicellularity from recently evolved multicellular phenotypes of the brewers yeast Saccharomyces cerevisae. Even though multicellularity in this system evolved recently, it involves the evolution of new levels of selection. Strong selective pressures against multicellularity lead to rapid reversibility to single cells in all of our replicate lines, whereas counterselection favoring multicellularity led to minimal reductions to the rates of reversal. History and chance played an important role in the tempo and mode of reversibility, highlighting the interplay of deterministic and stochastic events in evolutionary reversals.},
}

*Adaptation, Biological
*Biological Evolution
Saccharomyces cerevisiae/*physiology

@article {pmid32415185,
year = {2020},
author = {Hörandl, E and Hadacek, F},
title = {Oxygen, life forms, and the evolution of sexes in multicellular eukaryotes.},
journal = {Heredity},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41437-020-0317-9},
pmid = {32415185},
issn = {1365-2540},
abstract = {The evolutionary advantage of different sexual systems in multicellular eukaryotes is still not well understood, because the differentiation into male and female individuals halves offspring production compared with asexuality. Here we propose that various physiological adaptations to oxidative stress could have forged sessility versus motility, and consequently the evolution of sexual systems in multicellular animals, plants, and fungi. Photosynthesis causes substantial amounts of oxidative stress in photoautotrophic plants and, likewise, oxidative chemistry of polymer breakdown, cellulose and lignin, for saprotrophic fungi. In both cases, its extent precludes motility, an additional source of oxidative stress. Sessile life form and the lack of neuronal systems, however, limit options for mate recognition and adult sexual selection, resulting in inefficient mate-searching systems. Hence, sessility requires that all individuals can produce offspring, which is achieved by hermaphroditism in plants and/or by multiple mating types in fungi. In animals, motility requires neuronal systems, and muscle activity, both of which are highly sensitive to oxidative damage. As a consequence, motility has evolved in animals as heterotrophic organisms that (1) are not photosynthetically active, and (2) are not primary decomposers. Adaptations to motility provide prerequisites for an active mating behavior and efficient mate-searching systems. These benefits compensate for the "cost of males", and may explain the early evolution of sex chromosomes in metazoans. We conclude that different sexual systems evolved under the indirect physiological constraints of lifestyles.},
}

@article {pmid31006855,
year = {2019},
author = {Sudianto, E},
title = {Digest: Banding together to battle adversaries has its consequences.},
journal = {Evolution; international journal of organic evolution},
volume = {73},
number = {6},
pages = {1320-1321},
doi = {10.1111/evo.13750},
pmid = {31006855},
issn = {1558-5646},
mesh = {Animals ; *Biological Evolution ; *Chlorella ; Cost-Benefit Analysis ; Predatory Behavior ; },
abstract = {Why did life evolve from single-celled to multicellular organisms? Could there be advantages to this transition? What about associated fitness costs? Kapsetaki and West found that although multicellularity allows Chlorella sorokiniana to avoid predation from similarly-sized predators, it also reduces their competitiveness when resources are limited.},
}

Animals
*Biological Evolution
*Chlorella
Cost-Benefit Analysis
Predatory Behavior

@article {pmid30839008,
year = {2019},
author = {Ruiz, MC and Kljun, J and Turel, I and Di Virgilio, AL and León, IE},
title = {Comparative antitumor studies of organoruthenium complexes with 8-hydroxyquinolines on 2D and 3D cell models of bone, lung and breast cancer.},
journal = {Metallomics : integrated biometal science},
volume = {11},
number = {3},
pages = {666-675},
doi = {10.1039/c8mt00369f},
pmid = {30839008},
issn = {1756-591X},
mesh = {Antineoplastic Agents/chemistry/*pharmacology ; Apoptosis/drug effects ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Cell Survival/drug effects ; Cisplatin/chemistry/pharmacology ; Humans ; Models, Biological ; Neoplasms/*metabolism ; Organometallic Compounds/chemistry/*pharmacology ; Oxyquinoline/chemistry/*pharmacology ; Ruthenium/pharmacology ; Ruthenium Compounds/chemistry/*pharmacology ; },
abstract = {The purpose of this work was to screen the antitumor actions of two metal organoruthenium-8-hydroxyquinolinato (Ru-hq) complexes to find a potential novel agent for bone, lung and breast chemotherapies. We showed that ruthenium compounds (1 and 2) impaired the cell viability of human bone (MG-63), lung (A549) and breast (MCF7) cancer cells with greater selectivity and specificity than cisplatin. Besides, complexes 1 and 2 decreased proliferation, migration and invasion on cell monolayers at lower concentrations (2.5-10 μM). In addition, both compounds induced genotoxicity revealed by the micronucleus test, which led to G2/M cell cycle arrest and induced the tumor cells to undergo apoptosis. On the other hand, in multicellular 3D models (multicellular spheroids; MCS), 1 and 2 overcame CDDP presenting lower IC50 values only in MCS of lung origin. Moreover, 1 outperformed 2 in MCS of bone and breast origin. Finally, our findings revealed that both compounds inhibited the cell invasion of multicellular spheroids, showing that complex 1 exhibited the most important antimetastatic action. Taken together, these results indicate that compound 1 is an interesting candidate to be tested on in vivo models as a novel strategy for anticancer therapy.},
}

Antineoplastic Agents/chemistry/*pharmacology
Apoptosis/drug effects
Cell Line, Tumor
Cell Proliferation/drug effects
Cell Survival/drug effects
Cisplatin/chemistry/pharmacology
Humans
Models, Biological
Neoplasms/*metabolism
Organometallic Compounds/chemistry/*pharmacology
Oxyquinoline/chemistry/*pharmacology
Ruthenium/pharmacology
Ruthenium Compounds/chemistry/*pharmacology

@article {pmid32399193,
year = {2020},
author = {Zardoya, R},
title = {Recent advances in understanding mitochondrial genome diversity.},
journal = {F1000Research},
volume = {9},
number = {},
pages = {},
doi = {10.12688/f1000research.21490.1},
pmid = {32399193},
issn = {2046-1402},
abstract = {Ever since its discovery, the double-stranded DNA contained in the mitochondria of eukaryotes has fascinated researchers because of its bacterial endosymbiotic origin, crucial role in encoding subunits of the respiratory complexes, compact nature, and specific inheritance mechanisms. In the last few years, high-throughput sequencing techniques have accelerated the sequencing of mitochondrial genomes (mitogenomes) and uncovered the great diversity of organizations, gene contents, and modes of replication and transcription found in living eukaryotes. Some early divergent lineages of unicellular eukaryotes retain certain synteny and gene content resembling those observed in the genomes of alphaproteobacteria (the inferred closest living group of mitochondria), whereas others adapted to anaerobic environments have drastically reduced or even lost the mitogenome. In the three main multicellular lineages of eukaryotes, mitogenomes have pursued diverse evolutionary trajectories in which different types of molecules (circular versus linear and single versus multipartite), gene structures (with or without self-splicing introns), gene contents, gene orders, genetic codes, and transfer RNA editing mechanisms have been selected. Whereas animals have evolved a rather compact mitochondrial genome between 11 and 50 Kb in length with a highly conserved gene content in bilaterians, plants exhibit large mitochondrial genomes of 66 Kb to 11.3 Mb with large intergenic repetitions prone to recombination, and fungal mitogenomes have intermediate sizes of 12 to 236 Kb.},
}

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

Animals
Breast Neoplasms/*genetics
*Epithelial-Mesenchymal Transition
Female
Humans
Receptors, Notch/*genetics
Signal Transduction

@article {pmid30281390,
year = {2018},
author = {Booth, DS and Szmidt-Middleton, H and King, N},
title = {Transfection of choanoflagellates illuminates their cell biology and the ancestry of animal septins.},
journal = {Molecular biology of the cell},
volume = {29},
number = {25},
pages = {3026-3038},
doi = {10.1091/mbc.E18-08-0514},
pmid = {30281390},
issn = {1939-4586},
mesh = {Choanoflagellata/*genetics/physiology ; Evolution, Molecular ; Fluorescent Dyes ; Genetic Markers ; Plasmids ; Septins/genetics/*physiology ; Transfection/*methods ; },
abstract = {As the closest living relatives of animals, choanoflagellates offer unique insights into animal origins and core mechanisms underlying animal cell biology. However, unlike traditional model organisms, such as yeast, flies, and worms, choanoflagellates have been refractory to DNA delivery methods for expressing foreign genes. Here we report a robust method for expressing transgenes in the choanoflagellate Salpingoeca rosetta, overcoming barriers that have previously hampered DNA delivery and expression. To demonstrate how this method accelerates the study of S. rosetta cell biology, we engineered a panel of fluorescent protein markers that illuminate key features of choanoflagellate cells. We then investigated the localization of choanoflagellate septins, a family of GTP-binding cytoskeletal proteins that are hypothesized to regulate multicellular rosette development in S. rosetta. Fluorescently tagged septins localized to the basal poles of S. rosetta single cells and rosettes in a pattern resembling septin localization in animal epithelia. The establishment of transfection in S. rosetta and its application to the study of septins represent critical advances in the use of S. rosetta as an experimental model for investigating choanoflagellate cell biology, core mechanisms underlying animal cell biology, and the origin of animals.},
}

Choanoflagellata/*genetics/physiology
Evolution, Molecular
Fluorescent Dyes
Genetic Markers
Plasmids
Septins/genetics/*physiology
Transfection/*methods

@article {pmid31267819,
year = {2019},
author = {Etxebeste, O and Otamendi, A and Garzia, A and Espeso, EA and Cortese, MS},
title = {Rewiring of transcriptional networks as a major event leading to the diversity of asexual multicellularity in fungi.},
journal = {Critical reviews in microbiology},
volume = {45},
number = {5-6},
pages = {548-563},
doi = {10.1080/1040841X.2019.1630359},
pmid = {31267819},
issn = {1549-7828},
mesh = {Fungal Proteins/genetics/*metabolism ; Fungi/genetics/*growth & development/physiology ; *Gene Expression Regulation, Fungal ; Gene Regulatory Networks ; Reproduction, Asexual ; Spores, Fungal/genetics/growth & development/metabolism ; Transcription Factors/genetics/*metabolism ; },
abstract = {Complex multicellularity (CM) is characterized by the generation of three-dimensional structures that follow a genetically controlled program. CM emerged at least five times in evolution, one of them in fungi. There are two types of CM programs in fungi, leading, respectively, to the formation of sexual or asexual spores. Asexual spores foment the spread of mycoses, as they are the main vehicle for dispersion. In spite of this key dependence, there is great morphological diversity of asexual multicellular structures in fungi. To advance the understanding of the mechanisms that control initiation and progression of asexual CM and how they can lead to such a remarkable morphological diversification, we studied 503 fungal proteomes, representing all phyla and subphyla, and most known classes. Conservation analyses of 33 regulators of asexual development suggest stepwise emergence of transcription factors. While velvet proteins constitute one of the most ancient systems, the central regulator BrlA emerged late in evolution (with the class Eurotiomycetes). Some factors, such as MoConX4, seem to be species-specific. These observations suggest that the emergence and evolution of transcriptional regulators rewire transcriptional networks. This process could reach the species level, resulting in a vast diversity of morphologies.},
}

Fungal Proteins/genetics/*metabolism
Fungi/genetics/*growth & development/physiology
*Gene Expression Regulation, Fungal
Gene Regulatory Networks
Reproduction, Asexual
Spores, Fungal/genetics/growth & development/metabolism
Transcription Factors/genetics/*metabolism

@article {pmid32084159,
year = {2020},
author = {Finoshin, AD and Adameyko, KI and Mikhailov, KV and Kravchuk, OI and Georgiev, AA and Gornostaev, NG and Kosevich, IA and Mikhailov, VS and Gazizova, GR and Shagimardanova, EI and Gusev, OA and Lyupina, YV},
title = {Iron metabolic pathways in the processes of sponge plasticity.},
journal = {PloS one},
volume = {15},
number = {2},
pages = {e0228722},
pmid = {32084159},
issn = {1932-6203},
mesh = {Animals ; Computational Biology ; Gene Expression Profiling ; Iron/*metabolism ; Iron-Regulatory Proteins/genetics/metabolism ; Molecular Sequence Annotation ; Phylogeny ; Porifera/genetics/*metabolism ; RNA-Seq ; },
abstract = {The ability to regulate oxygen consumption evolved in ancestral animals and is intrinsically linked to iron metabolism. The iron pathways have been intensively studied in mammals, whereas data on distant invertebrates are limited. Sea sponges represent the oldest animal phylum and have unique structural plasticity and capacity to reaggregate after complete dissociation. We studied iron metabolic factors and their expression during reaggregation in the White Sea cold-water sponges Halichondria panicea and Halisarca dujardini. De novo transcriptomes were assembled using RNA-Seq data, and evolutionary trends were analyzed with bioinformatic tools. Differential expression during reaggregation was studied for H. dujardini. Enzymes of the heme biosynthesis pathway and transport globins, neuroglobin (NGB) and androglobin (ADGB), were identified in sponges. The globins mutate at higher evolutionary rates than the heme synthesis enzymes. Highly conserved iron-regulatory protein 1 (IRP1) presumably interacts with the iron-responsive elements (IREs) found in mRNAs of ferritin (FTH1) and a putative transferrin receptor NAALAD2. The reaggregation process is accompanied by increased expression of IRP1, the antiapoptotic factor BCL2, the inflammation factor NFκB (p65), FTH1 and NGB, as well as by an increase in mitochondrial density. Our data indicate a complex mechanism of iron regulation in sponge structural plasticity and help to better understand general mechanisms of morphogenetic processes in multicellular species.},
}

Animals
Computational Biology
Gene Expression Profiling
Iron/*metabolism
Iron-Regulatory Proteins/genetics/metabolism
Molecular Sequence Annotation
Phylogeny
Porifera/genetics/*metabolism
RNA-Seq

@article {pmid30720904,
year = {2019},
author = {Xiong, F and Ren, JJ and Yu, Q and Wang, YY and Kong, LJ and Otegui, MS and Wang, XL},
title = {AtBUD13 affects pre-mRNA splicing and is essential for embryo development in Arabidopsis.},
journal = {The Plant journal : for cell and molecular biology},
volume = {98},
number = {4},
pages = {714-726},
doi = {10.1111/tpj.14268},
pmid = {30720904},
issn = {1365-313X},
mesh = {Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/classification/genetics/*metabolism ; Embryonic Development/genetics/*physiology ; Gene Expression Regulation, Developmental/genetics ; Gene Expression Regulation, Plant/genetics ; Genes, Plant/genetics ; Introns ; Mutation ; Nuclear Proteins/classification/genetics/*metabolism ; Phylogeny ; Plants, Genetically Modified ; Protein Domains ; RNA Precursors/genetics ; RNA Splicing ; RNA Splicing Factors/classification/genetics/*metabolism ; Sequence Alignment ; Sequence Analysis ; },
abstract = {Pre-mRNA splicing is an important step for gene expression regulation. Yeast Bud13p (bud-site selection protein 13) regulates the budding pattern and pre-mRNA splicing in yeast cells; however, no Bud13p homologs have been identified in plants. Here, we isolated two mutants that carry T-DNA insertions at the At1g31870 locus and shows early embryo lethality and seed abortion. At1g31870 encodes an Arabidopsis homolog of yeast Bud13p, AtBUD13. Although AtBUD13 homologs are widely distributed in eukaryotic organisms, phylogenetic analysis revealed that their protein domain organization is more complex in multicellular species. AtBUD13 is expressed throughout plant development including embryogenesis and AtBUD13 proteins is localized in the nucleus in Arabidopsis. RNA-seq analysis revealed that AtBUD13 mutation predominantly results in the intron retention, especially for shorter introns (≤100 bases). Within this group of genes, we identified 52 genes involved in embryogenesis, out of which 22 are involved in nucleic acid metabolism. Our results demonstrate that AtBUD13 plays critical roles in early embryo development by effecting pre-mRNA splicing.},
}

Arabidopsis/genetics/*metabolism
Arabidopsis Proteins/classification/genetics/*metabolism
Embryonic Development/genetics/*physiology
Gene Expression Regulation, Developmental/genetics
Gene Expression Regulation, Plant/genetics
Genes, Plant/genetics
Introns
Mutation
Nuclear Proteins/classification/genetics/*metabolism
Phylogeny
Plants, Genetically Modified
Protein Domains
RNA Precursors/genetics
RNA Splicing
RNA Splicing Factors/classification/genetics/*metabolism
Sequence Alignment
Sequence Analysis

@article {pmid30989827,
year = {2019},
author = {Hehmeyer, J},
title = {Two potential evolutionary origins of the fruiting bodies of the dictyostelid slime moulds.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {94},
number = {5},
pages = {1591-1604},
doi = {10.1111/brv.12516},
pmid = {30989827},
issn = {1469-185X},
mesh = {*Biological Evolution ; Dictyostelium/classification/genetics/*physiology ; Fruiting Bodies, Fungal/genetics/*physiology ; Phylogeny ; Spores, Fungal/genetics/physiology ; },
abstract = {Dictyostelium discoideum and the other dictyostelid slime moulds ('social amoebae') are popular model organisms best known for their demonstration of sorocarpic development. In this process, many cells aggregate to form a multicellular unit that ultimately becomes a fruiting body bearing asexual spores. Several other unrelated microorganisms undergo comparable processes, and in some it is evident that their multicellular development evolved from the differentiation process of encystation. While it has been argued that the dictyostelid fruiting body had similar origins, it has also been proposed that dictyostelid sorocarpy evolved from the unicellular fruiting process found in other amoebozoan slime moulds. This paper reviews the developmental biology of the dictyostelids and other relevant organisms and reassesses the two hypotheses on the evolutionary origins of dictyostelid development. Recent advances in phylogeny, genetics, and genomics and transcriptomics indicate that further research is necessary to determine whether or not the fruiting bodies of the dictyostelids and their closest relatives, the myxomycetes and protosporangids, are homologous.},
}

*Biological Evolution
Dictyostelium/classification/genetics/*physiology
Fruiting Bodies, Fungal/genetics/*physiology
Phylogeny
Spores, Fungal/genetics/physiology

@article {pmid32353148,
year = {2020},
author = {Hoffman, SK and Seitz, KW and Havird, JC and Weese, DA and Santos, SR},
title = {Phenotypic Comparability from Genotypic Variability among Physically Structured Microbial Consortia.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaa022},
pmid = {32353148},
issn = {1557-7023},
abstract = {Microbiomes represent the collective bacteria, archaea, protist, fungi, and virus communities living in or on individual organisms that are typically multicellular eukaryotes. Such consortia have become recognized as having significant impacts on the development, health, and disease status of their hosts. Since understanding the mechanistic connections between an individual's genetic makeup and their complete set of traits (i.e., genome to phenome) requires consideration at different levels of biological organization, this should include interactions with, and the organization of, microbial consortia. To understand microbial consortia organization, we elucidated the genetic constituents amongst phenotypically similar (and hypothesized functionally-analogous) layers (i.e., top orange, second orange, pink, and green layers) in the unique laminated orange cyanobacterial-bacterial crusts endemic to Hawaii's anchialine ecosystem. High-throughput amplicon sequencing of ribosomal RNA hypervariable regions (i.e., Bacteria-specific V6 and Eukarya-biased V9) revealed microbial richness increasing by crust layer depth, with samples of a given layer more similar to different layers from the same geographic site than to their phenotypically-analogous layer from different sites. Furthermore, samples from sites on the same island were more similar to each other, regardless of which layer they originated from, than to analogous layers from another island. However, cyanobacterial and algal taxa were abundant in all surface and bottom layers, with anaerobic and chemoautotrophic taxa concentrated in the middle two layers, suggesting crust oxygenation from both above and below. Thus, the arrangement of oxygenated vs. anoxygenated niches in these orange crusts are functionally distinct relative to other laminated cyanobacterial-bacterial communities examined to date, with convergent evolution due to similar environmental conditions a likely driver for these phenotypically comparable but genetically distinct microbial consortia.},
}

@article {pmid31430180,
year = {2019},
author = {D'Ario, M and Sablowski, R},
title = {Cell Size Control in Plants.},
journal = {Annual review of genetics},
volume = {53},
number = {},
pages = {45-65},
doi = {10.1146/annurev-genet-112618-043602},
pmid = {31430180},
issn = {1545-2948},
support = {BBS/E/J/00000594/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P013511/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M003825/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Cell Size ; DNA Replication ; Eukaryotic Cells/cytology ; Meristem/*cytology/growth & development ; Mitosis ; Models, Biological ; Plant Cells/*physiology ; Plant Development/genetics ; *Ploidies ; Yeasts/cytology/genetics ; },
abstract = {The genetic control of the characteristic cell sizes of different species and tissues is a long-standing enigma. Plants are convenient for studying this question in a multicellular context, as their cells do not move and are easily tracked and measured from organ initiation in the meristems to subsequent morphogenesis and differentiation. In this article, we discuss cell size control in plants compared with other organisms. As seen from yeast cells to mammalian cells, size homeostasis is maintained cell autonomously in the shoot meristem. In developing organs, vacuolization contributes to cell size heterogeneity and may resolve conflicts between growth control at the cellular and organ levels. Molecular mechanisms for cell size control have implications for how cell size responds to changes in ploidy, which are particularly important in plant development and evolution. We also discuss comparatively the functional consequences of cell size and their potential repercussions at higher scales, including genome evolution.},
}

Cell Size
DNA Replication
Eukaryotic Cells/cytology
Meristem/*cytology/growth & development
Mitosis
Models, Biological
Plant Cells/*physiology
Plant Development/genetics
*Ploidies
Yeasts/cytology/genetics

@article {pmid31069269,
year = {2019},
author = {Erkenbrack, EM and Thompson, JR},
title = {Cell type phylogenetics informs the evolutionary origin of echinoderm larval skeletogenic cell identity.},
journal = {Communications biology},
volume = {2},
number = {},
pages = {160},
pmid = {31069269},
issn = {2399-3642},
mesh = {Animal Shells/anatomy & histology/cytology/growth & development/*metabolism ; Animals ; Bayes Theorem ; Biological Evolution ; Echinodermata/classification/*genetics ; Embryo, Nonmammalian ; Extinction, Biological ; Gene Expression Regulation, Developmental ; *Gene Regulatory Networks ; Larva/cytology/growth & development/*metabolism ; Mesoderm/cytology/growth & development/metabolism ; *Phylogeny ; Stem Cells/cytology/metabolism ; },
abstract = {The multiplicity of cell types comprising multicellular organisms begs the question as to how cell type identities evolve over time. Cell type phylogenetics informs this question by comparing gene expression of homologous cell types in distantly related taxa. We employ this approach to inform the identity of larval skeletogenic cells of echinoderms, a clade for which there are phylogenetically diverse datasets of spatial gene expression patterns. We determined ancestral spatial expression patterns of alx1, ets1, tbr, erg, and vegfr, key components of the skeletogenic gene regulatory network driving identity of the larval skeletogenic cell. Here we show ancestral state reconstructions of spatial gene expression of extant eleutherozoan echinoderms support homology and common ancestry of echinoderm larval skeletogenic cells. We propose larval skeletogenic cells arose in the stem lineage of eleutherozoans during a cell type duplication event that heterochronically activated adult skeletogenic cells in a topographically distinct tissue in early development.},
}

Animal Shells/anatomy & histology/cytology/growth & development/*metabolism
Animals
Bayes Theorem
Biological Evolution
Echinodermata/classification/*genetics
Embryo, Nonmammalian
Extinction, Biological
Gene Expression Regulation, Developmental
*Gene Regulatory Networks
Larva/cytology/growth & development/*metabolism
Mesoderm/cytology/growth & development/metabolism
*Phylogeny
Stem Cells/cytology/metabolism

@article {pmid30857590,
year = {2019},
author = {Sicard, A and Pirolles, E and Gallet, R and Vernerey, MS and Yvon, M and Urbino, C and Peterschmitt, M and Gutierrez, S and Michalakis, Y and Blanc, S},
title = {A multicellular way of life for a multipartite virus.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {30857590},
issn = {2050-084X},
support = {ANR-14-CE02-0014//Agence Nationale de la Recherche/International ; },
mesh = {DNA Viruses ; DNA, Viral/*genetics ; *Genome, Viral ; In Situ Hybridization, Fluorescence ; Microscopy, Confocal ; Nanovirus/*genetics/physiology ; Plant Diseases/*virology ; Regression Analysis ; Vicia faba/*virology ; Virion/*genetics ; Virus Replication ; },
abstract = {A founding paradigm in virology is that the spatial unit of the viral replication cycle is an individual cell. Multipartite viruses have a segmented genome where each segment is encapsidated separately. In this situation the viral genome is not recapitulated in a single virus particle but in the viral population. How multipartite viruses manage to efficiently infect individual cells with all segments, thus with the whole genome information, is a long-standing but perhaps deceptive mystery. By localizing and quantifying the genome segments of a nanovirus in host plant tissues we show that they rarely co-occur within individual cells. We further demonstrate that distinct segments accumulate independently in different cells and that the viral system is functional through complementation across cells. Our observation deviates from the classical conceptual framework in virology and opens an alternative possibility (at least for nanoviruses) where the infection can operate at a level above the individual cell level, defining a viral multicellular way of life.},
}

DNA Viruses
DNA, Viral/*genetics
*Genome, Viral
In Situ Hybridization, Fluorescence
Microscopy, Confocal
Nanovirus/*genetics/physiology
Plant Diseases/*virology
Regression Analysis
Vicia faba/*virology
Virion/*genetics
Virus Replication

@article {pmid30644818,
year = {2019},
author = {Arun, A and Coelho, SM and Peters, AF and Bourdareau, S and Pérès, L and Scornet, D and Strittmatter, M and Lipinska, AP and Yao, H and Godfroy, O and Montecinos, GJ and Avia, K and Macaisne, N and Troadec, C and Bendahmane, A and Cock, JM},
title = {Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {30644818},
issn = {2050-084X},
support = {ANR-10-BLAN-1727//Agence Nationale de la Recherche/International ; Marinexus//Interreg Program France (Channel)-England/International ; 638240/ERC_/European Research Council/International ; European Erasmus Mundus program//European Commission/International ; ANR-10-BTBR-04-01//Agence Nationale de la Recherche/International ; ANR-10-LABX-40//Agence Nationale de la Recherche/International ; ERC-SEXYPARTH/ERC_/European Research Council/International ; Marinexus//Interreg Program France -England/International ; },
mesh = {Amino Acid Sequence ; Embryophyta/genetics/*growth & development/*metabolism ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Homeodomain Proteins/chemistry/genetics/*metabolism ; Mutation/genetics ; Phaeophyta/genetics/*growth & development/*metabolism ; Phenotype ; Plant Proteins/*metabolism ; Protein Binding ; Protein Domains ; RNA, Messenger/genetics/metabolism ; Transcription Factors/chemistry/genetics ; },
abstract = {Three amino acid loop extension homeodomain transcription factors (TALE HD TFs) act as life cycle regulators in green algae and land plants. In mosses these regulators are required for the deployment of the sporophyte developmental program. We demonstrate that mutations in either of two TALE HD TF genes, OUROBOROS or SAMSARA, in the brown alga Ectocarpus result in conversion of the sporophyte generation into a gametophyte. The OUROBOROS and SAMSARA proteins heterodimerise in a similar manner to TALE HD TF life cycle regulators in the green lineage. These observations demonstrate that TALE-HD-TF-based life cycle regulation systems have an extremely ancient origin, and that these systems have been independently recruited to regulate sporophyte developmental programs in at least two different complex multicellular eukaryotic supergroups, Archaeplastida and Chromalveolata.},
}

Amino Acid Sequence
Embryophyta/genetics/*growth & development/*metabolism
Evolution, Molecular
Gene Expression Regulation, Plant
Homeodomain Proteins/chemistry/genetics/*metabolism
Mutation/genetics
Phaeophyta/genetics/*growth & development/*metabolism
Phenotype
Plant Proteins/*metabolism
Protein Binding
Protein Domains
RNA, Messenger/genetics/metabolism
Transcription Factors/chemistry/genetics

@article {pmid32283732,
year = {2020},
author = {Annenkova, NV and Giner, CR and Logares, R},
title = {Tracing the Origin of Planktonic Protists in an Ancient Lake.},
journal = {Microorganisms},
volume = {8},
number = {4},
pages = {},
doi = {10.3390/microorganisms8040543},
pmid = {32283732},
issn = {2076-2607},
support = {18-74-00054//Russian Science Foundation/ ; 0345-2016-0009//Russian state assignment/ ; RYC-2013-12554//Ministerio de Economía y Competitividad/ ; },
abstract = {Ancient lakes are among the most interesting models for evolution studies because their biodiversity is the result of a complex combination of migration and speciation. Here, we investigate the origin of single celled planktonic eukaryotes from the oldest lake in the world-Lake Baikal (Russia). By using 18S rDNA metabarcoding, we recovered 1414 Operational Taxonomic Units (OTUs) belonging to protists populating surface waters (1-50 m) and representing pico/nano-sized cells. The recovered communities resembled other lacustrine freshwater assemblages found elsewhere, especially the taxonomically unclassified protists. However, our results suggest that a fraction of Baikal protists could belong to glacial relicts and have close relationships with marine/brackish species. Moreover, our results suggest that rapid radiation may have occurred among some protist taxa, partially mirroring what was already shown for multicellular organisms in Lake Baikal. We found 16% of the OTUs belonging to potential species flocks in Stramenopiles, Alveolata, Opisthokonta, Archaeplastida, Rhizaria, and Hacrobia. Putative flocks predominated in Chrysophytes, which are highly diverse in Lake Baikal. Also, the 18S rDNA of a number of species (7% of the total) differed >10% from other known sequences. These taxa as well as those belonging to the flocks may be endemic to Lake Baikal. Overall, our study points to novel diversity of planktonic protists in Lake Baikal, some of which may have emerged in situ after evolutionary diversification.},
}

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

Actomyosin/metabolism
Animals
Biological Evolution
Choanoflagellata/cytology/*physiology
Cyclic GMP/metabolism
*Light
Microvilli/physiology
Movement
Phosphoric Diester Hydrolases/metabolism
Protozoan Proteins/metabolism
Sensory Rhodopsins/metabolism

@article {pmid31589468,
year = {2019},
author = {Blutt, SE and Klein, OD and Donowitz, M and Shroyer, N and Guha, C and Estes, MK},
title = {Use of organoids to study regenerative responses to intestinal damage.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {317},
number = {6},
pages = {G845-G852},
doi = {10.1152/ajpgi.00346.2018},
pmid = {31589468},
issn = {1522-1547},
support = {P30 DK089502/DK/NIDDK NIH HHS/United States ; },
mesh = {*Adult Stem Cells ; Animals ; Cells, Cultured/physiology/transplantation ; Humans ; *Intestinal Diseases/etiology/metabolism/therapy ; *Intestines/drug effects/radiation effects ; Models, Biological ; *Organoids/physiology/transplantation ; Regeneration/*physiology ; Tissue Engineering/methods ; },
abstract = {Intestinal organoid cultures provide an in vitro model system for studying pathways and mechanisms involved in epithelial damage and repair. Derived from either embryonic or induced pluripotent stem cells or adult intestinal stem cells or tissues, these self-organizing, multicellular structures contain polarized mature cells that recapitulate both the physiology and heterogeneity of the intestinal epithelium. These cultures provide a cutting-edge technology for defining regenerative pathways that are induced following radiation or chemical damage, which directly target the cycling intestinal stem cell, or damage resulting from viral, bacterial, or parasitic infection of the epithelium. Novel signaling pathways or biological mechanisms identified from organoid studies that mediate regeneration of the epithelium following damage are likely to be important targets of preventive or therapeutic modalities to mitigate intestinal injury. The evolution of these cultures to include more components of the intestinal wall and the ability to genetically modify them are key components for defining the mechanisms that modulate epithelial regeneration.},
}

*Adult Stem Cells
Animals
Cells, Cultured/physiology/transplantation
Humans
*Intestinal Diseases/etiology/metabolism/therapy
*Intestines/drug effects/radiation effects
Models, Biological
*Organoids/physiology/transplantation
Regeneration/*physiology
Tissue Engineering/methods

@article {pmid31012964,
year = {2019},
author = {Gunaratne, PH and Pan, Y and Rao, AK and Lin, C and Hernandez-Herrera, A and Liang, K and Rait, AS and Venkatanarayan, A and Benham, AL and Rubab, F and Kim, SS and Rajapakshe, K and Chan, CK and Mangala, LS and Lopez-Berestein, G and Sood, AK and Rowat, AC and Coarfa, C and Pirollo, KF and Flores, ER and Chang, EH},
title = {Activating p53 family member TAp63: A novel therapeutic strategy for targeting p53-altered tumors.},
journal = {Cancer},
volume = {125},
number = {14},
pages = {2409-2422},
pmid = {31012964},
issn = {1097-0142},
support = {R00 DK094981/DK/NIDDK NIH HHS/United States ; R01 CA132012/CA/NCI NIH HHS/United States ; T32 CA009686/CA/NCI NIH HHS/United States ; R01 CA160394/CA/NCI NIH HHS/United States ; R01 CA218025/CA/NCI NIH HHS/United States ; R35 CA197452/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Antineoplastic Agents/pharmacology/therapeutic use ; Binding Sites ; Cell Line, Tumor ; Cell Movement/drug effects ; Cisplatin/pharmacology/therapeutic use ; Drug Resistance, Neoplasm/drug effects ; Female ; Humans ; Liposomes ; Mice ; Mice, Nude ; MicroRNAs/administration & dosage/genetics/metabolism/*therapeutic use ; *Mutation, Missense ; Neoplasm Invasiveness/prevention & control ; Ovarian Neoplasms/*drug therapy/*genetics ; Protein Isoforms/genetics ; Signal Transduction/drug effects ; Transcription Factors/*genetics/metabolism ; Transcriptional Activation/*genetics ; Transfection ; Tumor Suppressor Protein p53/*genetics/metabolism ; Tumor Suppressor Proteins/*genetics/metabolism ; Xenograft Model Antitumor Assays ; },
abstract = {BACKGROUND: Over 96% of high-grade ovarian carcinomas and 50% of all cancers are characterized by alterations in the p53 gene. Therapeutic strategies to restore and/or reactivate the p53 pathway have been challenging. By contrast, p63, which shares many of the downstream targets and functions of p53, is rarely mutated in cancer.

METHODS: A novel strategy is presented for circumventing alterations in p53 by inducing the tumor-suppressor isoform TAp63 (transactivation domain of tumor protein p63) through its direct downstream target, microRNA-130b (miR-130b), which is epigenetically silenced and/or downregulated in chemoresistant ovarian cancer.

RESULTS: Treatment with miR-130b resulted in: 1) decreased migration/invasion in HEYA8 cells (p53 wild-type) and disruption of multicellular spheroids in OVCAR8 cells (p53-mutant) in vitro, 2) sensitization of HEYA8 and OVCAR8 cells to cisplatin (CDDP) in vitro and in vivo, and 3) transcriptional activation of TAp63 and the B-cell lymphoma (Bcl)-inhibitor B-cell lymphoma 2-like protein 11 (BIM). Overexpression of TAp63 was sufficient to decrease cell viability, suggesting that it is a critical downstream effector of miR-130b. In vivo, combined miR-130b plus CDDP exhibited greater therapeutic efficacy than miR-130b or CDDP alone. Mice that carried OVCAR8 xenograft tumors and were injected with miR-130b in 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) liposomes had a significant decrease in tumor burden at rates similar to those observed in CDDP-treated mice, and 20% of DOPC-miR-130b plus CDDP-treated mice were living tumor free. Systemic injections of scL-miR-130b plus CDDP in a clinically tested, tumor-targeted nanocomplex (scL) improved survival in 60% and complete remissions in 40% of mice that carried HEYA8 xenografts.

CONCLUSIONS: The miR-130b/TAp63 axis is proposed as a new druggable pathway that has the potential to uncover broad-spectrum therapeutic options for the majority of p53-altered cancers.},
}

Animals
Antineoplastic Agents/pharmacology/therapeutic use
Binding Sites
Cell Line, Tumor
Cell Movement/drug effects
Cisplatin/pharmacology/therapeutic use
Drug Resistance, Neoplasm/drug effects
Female
Humans
Liposomes
Mice
Mice, Nude
MicroRNAs/administration & dosage/genetics/metabolism/*therapeutic use
*Mutation, Missense
Neoplasm Invasiveness/prevention & control
Ovarian Neoplasms/*drug therapy/*genetics
Protein Isoforms/genetics
Signal Transduction/drug effects
Transcription Factors/*genetics/metabolism
Transcriptional Activation/*genetics
Transfection
Tumor Suppressor Protein p53/*genetics/metabolism
Tumor Suppressor Proteins/*genetics/metabolism
Xenograft Model Antitumor Assays

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

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

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

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

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

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

Amoebozoa/classification/*genetics/growth & development/metabolism
Dictyostelium/genetics
*Evolution, Molecular
Gene Expression Regulation, Developmental
Phenotype
Phylogeny
Protein Domains
Transcription Factors/chemistry/*genetics/metabolism
Transcriptome

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

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

@article {pmid31380606,
year = {2019},
author = {Newman, SA},
title = {Inherent forms and the evolution of evolution.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {332},
number = {8},
pages = {331-338},
doi = {10.1002/jez.b.22895},
pmid = {31380606},
issn = {1552-5015},
mesh = {Animals ; *Biological Evolution ; Chlorophyta ; Developmental Biology ; Dictyosteliida ; Morphogenesis ; },
abstract = {John Bonner presented a provocative conjecture that the means by which organisms evolve has itself evolved. The elements of his postulated nonuniformitarianism in the essay under discussion-the emergence of sex, the enhanced selection pressures on larger multicellular forms-center on a presumed close mapping of genotypic to phenotypic change. A different view emerges from delving into earlier work of Bonner's in which he proposed the concept of "neutral phenotypes" and "neutral morphologies" allied to D'Arcy Thompson's analysis of physical determinants of form and studied the conditional elicitation of intrinsic organizational properties of cell aggregates in social amoebae. By comparing the shared and disparate mechanistic bases of morphogenesis and developmental outcomes in the embryos of metazoans (animals), closely related nonmetazoan holozoans, more distantly related dictyostelids, and very distantly related volvocine algae, I conclude, in agreement with Bonner's earlier proposals, that understanding the evolution of multicellular evolution requires knowledge of the inherent forms of diversifying lineages, and that the relevant causative factors extend beyond genes and adaptation to the physics of materials.},
}

Animals
*Biological Evolution
Chlorophyta
Developmental Biology
Dictyosteliida
Morphogenesis

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

Animals
*Biological Evolution
Drug Resistance, Neoplasm
Energy Metabolism
Humans
Metabolic Diseases/*etiology
Mitochondria/metabolism
Neoplasms/*etiology

@article {pmid31077747,
year = {2019},
author = {Vinogradov, AE and Anatskaya, OV},
title = {Evolutionary framework of the human interactome: Unicellular and multicellular giant clusters.},
journal = {Bio Systems},
volume = {181},
number = {},
pages = {82-87},
doi = {10.1016/j.biosystems.2019.05.004},
pmid = {31077747},
issn = {1872-8324},
mesh = {*Biological Evolution ; Cluster Analysis ; *Databases, Genetic ; Evolution, Molecular ; Humans ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping/*methods ; Protein Interaction Maps/*genetics ; },
abstract = {The main contradiction of multicellularity (MCM) is between the unicellular (UC) and multicellular (MC) levels. In human interactome we revealed two giant clusters with MC and UC medians (and several smaller ones with MC medians). The enrichment of these clusters by phylostrata and by functions support the MC versus UC division. The total interactome and the giant clusters show a core-periphery evolutionary growth. From viewpoint of the MCM, the most important is the placement of genes, appearing at UC evolutionary stage, in the MC clusters. Thus, genes involved in vesicle-mediated transport, cell cycle, cellular responses to stress, post-translational modifications and many diseases appeared at UC evolutionary stage but are placed mostly in MC clusters. Genes downregulated with age are enriched in UC cluster, whereas the upregulated genes are preferentially placed in MC giant cluster. The tumor suppressor and pluripotency regulating pathways are also enriched in MC giant cluster. Therefore, this cluster probably operates as 'internal manager' constraining runaway unicellularity. The clusters have denser interactions within than between them, therefore they can serve as attractors (stable states of dynamic systems) of cellular programs. Importantly, the UC cluster have a higher inside/outside connection ratio compared with MC clusters, which suggests a stronger attractor effect and may explain why cells of MC organisms are prone to oncogenesis. The evolutionary clustering of human interactome elucidates the MC control over functions appearing at UC evolutionary stage and can build a framework for biosystems studies focusing on the interplay between UC and MC levels.},
}

*Biological Evolution
Cluster Analysis
*Databases, Genetic
Evolution, Molecular
Humans
Protein Interaction Domains and Motifs
Protein Interaction Mapping/*methods
Protein Interaction Maps/*genetics

@article {pmid30803482,
year = {2019},
author = {Trigos, AS and Pearson, RB and Papenfuss, AT and Goode, DL},
title = {Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {30803482},
issn = {2050-084X},
mesh = {Carcinogenesis ; Cell Differentiation ; Cell Line, Tumor ; Cell Proliferation ; *Cell Transformation, Neoplastic ; Gene Dosage ; *Gene Regulatory Networks ; *Genes, Regulator ; Humans ; Neoplasms/*pathology ; *Point Mutation ; Transcription, Genetic ; },
abstract = {Extensive transcriptional alterations are observed in cancer, many of which activate core biological processes established in unicellular organisms or suppress differentiation pathways formed in metazoans. Through rigorous, integrative analysis of genomics data from a range of solid tumors, we show many transcriptional changes in tumors are tied to mutations disrupting regulatory interactions between unicellular and multicellular genes within human gene regulatory networks (GRNs). Recurrent point mutations were enriched in regulator genes linking unicellular and multicellular subnetworks, while copy-number alterations affected downstream target genes in distinctly unicellular and multicellular regions of the GRN. Our results depict drivers of tumourigenesis as genes that created key regulatory links during the evolution of early multicellular life, whose dysfunction creates widespread dysregulation of primitive elements of the GRN. Several genes we identified as important in this process were associated with drug response, demonstrating the potential clinical value of our approach.},
}

Carcinogenesis
Cell Differentiation
Cell Line, Tumor
Cell Proliferation
*Cell Transformation, Neoplastic
Gene Dosage
*Gene Regulatory Networks
*Genes, Regulator
Humans
Neoplasms/*pathology
*Point Mutation
Transcription, Genetic

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

Amino Acid Sequence
Animals
Carboxypeptidases/chemistry/genetics/*metabolism
Phylogeny
Porifera/classification/genetics/*metabolism
Proprotein Convertases/chemistry/genetics/*metabolism
Protein Subunits/chemistry/*metabolism
*Signal Transduction

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

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

Adaptation, Physiological/*physiology
Animals
Biological Evolution
Female
Humans
Menopause/metabolism/*physiology
Neoplasms/physiopathology/*prevention & control
Reproduction/physiology

@article {pmid32032743,
year = {2020},
author = {Dokanehiifard, S and Soltani, BM and Ghiasi, P and Baharvand, H and Reza Ganjali, M and Hosseinkhani, S},
title = {hsa-miR-766-5p as a new regulator of mitochondrial apoptosis pathway for discriminating of cell death from cardiac differentiation.},
journal = {Gene},
volume = {736},
number = {},
pages = {144448},
doi = {10.1016/j.gene.2020.144448},
pmid = {32032743},
issn = {1879-0038},
mesh = {Apoptosis/*genetics ; Cell Death/*genetics ; Cell Differentiation/*genetics ; Cell Line ; Computational Biology/methods ; Down-Regulation/genetics ; HEK293 Cells ; Human Embryonic Stem Cells/physiology ; Humans ; MicroRNAs/*genetics ; Mitochondria/*genetics ; Myocytes, Cardiac/*physiology ; },
abstract = {Dispose of unnecessary cells in multicellular organism take place through apoptosis as a mode of programmed cell death (PCD). This process is triggered through two main pathway including extrinsic pathway or death receptor pathway and intrinsic or mitochondrial pathway. An alternative role for mitochondrial pathway of cell death is its involvement in cell differentiation. Biochemistry of cell differentiation indicates a common origin for differentiation and apoptosis. miRNAs are a group of small non coding mediator RNAs in regulation of many routes such as apoptosis and differentiation. By using bioinformatics tools hsa-miR-766-5p was predicted to target the BAX, BAK and BOK genes involved in mitochondrial apoptosis pathway. RT-qPCR and dual luciferase assay showed targeting of BAX, BAK and BOK 3'UTRs via hsa-miR-766, detected in SW480 and HEK293T cell lines. Caspases 3/7 and 9 activity assay revealed the involvement of hsa-miR-766-5p in mitochondrial apoptosis pathway regulation detected following overexpression and downregulation of this miRNA, detected in SW480 cells treated with 1 μM doxorubicin. Flow cytometry and MTT assay indicated cell death reduction and viability elevation effect of hsa-miR-766 in SW480 cells after its overexpression. Endogenous expression of hsa-miR-766 during the course of human embryonic stem cells (hESCs) differentiation into cardiomyocytes revealed an inverse expression status of this miRNA with BOK. However, the expression of this miRNA was inversely related to BAX and BAK for some time points of differentiation. Overall this results show the involvement of hsa-miR-766 in regulation of mitochondrial apoptosis pathway.},
}

Apoptosis/*genetics
Cell Death/*genetics
Cell Differentiation/*genetics
Cell Line
Computational Biology/methods
Down-Regulation/genetics
HEK293 Cells
Human Embryonic Stem Cells/physiology
Humans
MicroRNAs/*genetics
Mitochondria/*genetics
Myocytes, Cardiac/*physiology

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

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

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

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

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

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

@article {pmid31325911,
year = {2019},
author = {Perez-Lamarque, B and Morlon, H},
title = {Characterizing symbiont inheritance during host-microbiota evolution: Application to the great apes gut microbiota.},
journal = {Molecular ecology resources},
volume = {19},
number = {6},
pages = {1659-1671},
doi = {10.1111/1755-0998.13063},
pmid = {31325911},
issn = {1755-0998},
support = {Programme Bettencourt//Ecole Doctorale FIRE/ ; //Ecole normale supérieure/ ; //Centre National de la Recherche Scientifique/ ; PANDA/ERC_/European Research Council/International ; /ERC_/European Research Council/International ; //École Normale Supérieure/ ; },
mesh = {Animals ; Bacteria/genetics ; DNA Barcoding, Taxonomic/methods ; Disease Transmission, Infectious ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Hominidae/*microbiology ; Infectious Disease Transmission, Vertical ; Microbiota/*genetics ; Phylogeny ; Symbiosis/*genetics ; },
abstract = {Microbiota play a central role in the functioning of multicellular life, yet understanding their inheritance during host evolutionary history remains an important challenge. Symbiotic microorganisms are either acquired from the environment during the life of the host (i.e. environmental acquisition), transmitted across generations with a faithful association with their hosts (i.e. strict vertical transmission), or transmitted with occasional host switches (i.e. vertical transmission with horizontal switches). These different modes of inheritance affect microbes' diversification, which at the two extremes can be independent from that of their associated host or follow host diversification. The few existing quantitative tools for investigating the inheritance of symbiotic organisms rely on cophylogenetic approaches, which require knowledge of both host and symbiont phylogenies, and are therefore often not well adapted to DNA metabarcoding microbial data. Here, we develop a model-based framework for identifying vertically transmitted microbial taxa. We consider a model for the evolution of microbial sequences on a fixed host phylogeny that includes vertical transmission and horizontal host switches. This model allows estimating the number of host switches and testing for strict vertical transmission and independent evolution. We test our approach using simulations. Finally, we illustrate our framework on gut microbiota high-throughput sequencing data of the family Hominidae and identify several microbial taxonomic units, including fibrolytic bacteria involved in carbohydrate digestion, that tend to be vertically transmitted.},
}

Animals
Bacteria/genetics
DNA Barcoding, Taxonomic/methods
Disease Transmission, Infectious
Evolution, Molecular
Gastrointestinal Microbiome/*genetics
Hominidae/*microbiology
Infectious Disease Transmission, Vertical
Microbiota/*genetics
Phylogeny
Symbiosis/*genetics

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

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

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

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

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

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

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

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

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

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

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

@article {pmid31841515,
year = {2019},
author = {Lamelza, P and Young, JM and Noble, LM and Caro, L and Isakharov, A and Palanisamy, M and Rockman, MV and Malik, HS and Ailion, M},
title = {Hybridization promotes asexual reproduction in Caenorhabditis nematodes.},
journal = {PLoS genetics},
volume = {15},
number = {12},
pages = {e1008520},
pmid = {31841515},
issn = {1553-7404},
support = {T32 GM007270/GM/NIGMS NIH HHS/United States ; R01 GM121828/GM/NIGMS NIH HHS/United States ; R01 GM074108/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Caenorhabditis/genetics/*physiology ; Female ; Fertility ; *Hybridization, Genetic ; Male ; Maternal Inheritance ; Parthenogenesis ; Paternal Inheritance ; *Reproduction, Asexual ; Whole Genome Sequencing ; },
abstract = {Although most unicellular organisms reproduce asexually, most multicellular eukaryotes are obligately sexual. This implies that there are strong barriers that prevent the origin or maintenance of asexuality arising from an obligately sexual ancestor. By studying rare asexual animal species we can gain a better understanding of the circumstances that facilitate their evolution from a sexual ancestor. Of the known asexual animal species, many originated by hybridization between two ancestral sexual species. The balance hypothesis predicts that genetic incompatibilities between the divergent genomes in hybrids can modify meiosis and facilitate asexual reproduction, but there are few instances where this has been shown. Here we report that hybridizing two sexual Caenorhabditis nematode species (C. nouraguensis females and C. becei males) alters the normal inheritance of the maternal and paternal genomes during the formation of hybrid zygotes. Most offspring of this interspecies cross die during embryogenesis, exhibiting inheritance of a diploid C. nouraguensis maternal genome and incomplete inheritance of C. becei paternal DNA. However, a small fraction of offspring develop into viable adults that can be either fertile or sterile. Fertile offspring are produced asexually by sperm-dependent parthenogenesis (also called gynogenesis or pseudogamy); these progeny inherit a diploid maternal genome but fail to inherit a paternal genome. Sterile offspring are hybrids that inherit both a diploid maternal genome and a haploid paternal genome. Whole-genome sequencing of individual viable worms shows that diploid maternal inheritance in both fertile and sterile offspring results from an altered meiosis in C. nouraguensis oocytes and the inheritance of two randomly selected homologous chromatids. We hypothesize that hybrid incompatibility between C. nouraguensis and C. becei modifies maternal and paternal genome inheritance and indirectly induces gynogenetic reproduction. This system can be used to dissect the molecular mechanisms by which hybrid incompatibilities can facilitate the emergence of asexual reproduction.},
}

Animals
Caenorhabditis/genetics/*physiology
Female
Fertility
*Hybridization, Genetic
Male
Maternal Inheritance
Parthenogenesis
Paternal Inheritance
*Reproduction, Asexual
Whole Genome Sequencing

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

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

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

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

@article {pmid31736534,
year = {2019},
author = {Chen, J and Wang, N},
title = {Tissue cell differentiation and multicellular evolution via cytoskeletal stiffening in mechanically stressed microenvironments.},
journal = {Acta mechanica Sinica = Li xue xue bao},
volume = {35},
number = {2},
pages = {270-274},
pmid = {31736534},
issn = {0567-7718},
support = {R01 GM072744/GM/NIGMS NIH HHS/United States ; },
abstract = {Evolution of eukaryotes from simple cells to complex multicellular organisms remains a mystery. Our postulate is that cytoskeletal stiffening is a necessary condition for evolution of complex multicellular organisms from early simple eukaryotes. Recent findings show that embryonic stem cells are as soft as primitive eukaryotes-amoebae and that differentiated tissue cells can be two orders of magnitude stiffer than embryonic stem cells. Soft embryonic stem cells become stiff as they differentiate into tissue cells of the complex multicellular organisms to match their microenvironment stiffness. We perhaps see in differentiation of embryonic stem cells (derived from inner cell mass cells) the echo of those early evolutionary events. Early soft unicellular organisms might have evolved to stiffen their cytoskeleton to protect their structural integrity from external mechanical stresses while being able to maintain form, to change shape, and to move.},
}

@article {pmid31649059,
year = {2019},
author = {Duttke, SH and Chang, MW and Heinz, S and Benner, C},
title = {Identification and dynamic quantification of regulatory elements using total RNA.},
journal = {Genome research},
volume = {29},
number = {11},
pages = {1836-1846},
pmid = {31649059},
issn = {1549-5469},
support = {U19 AI106754/AI/NIAID NIH HHS/United States ; U19 AI135972/AI/NIAID NIH HHS/United States ; },
abstract = {The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSSs) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than does RNA-seq. Interrogating tissues from species across the eukaryotic kingdoms identified unstable transcripts resembling enhancer RNAs, pri-miRNAs, antisense transcripts, and promoter upstream transcripts in multicellular animals, plants, and fungi spanning 1.6 billion years of evolution. Integration of epigenomic data from these organisms revealed that histone H3 trimethylation (H3K4me3) was largely confined to TSSs of stable transcripts, whereas H3K27ac marked nucleosomes downstream from all active TSSs, suggesting an ancient role for posttranslational histone modifications in transcription. Our findings show that total RNA is sufficient to identify transcribed regulatory elements and capture the dynamics of initiated stable and unstable transcripts at single-nucleotide resolution in eukaryotes.},
}

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

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

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

Animals
Body Patterning
Cell Proliferation
Ctenophora/*physiology
Models, Biological
*Regeneration
*Wound Healing

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

*Phylogeny
Stramenopiles/*classification/*genetics
Transcriptome

@article {pmid31568790,
year = {2020},
author = {Newman, SA},
title = {Cell differentiation: What have we learned in 50 years?.},
journal = {Journal of theoretical biology},
volume = {485},
number = {},
pages = {110031},
doi = {10.1016/j.jtbi.2019.110031},
pmid = {31568790},
issn = {1095-8541},
abstract = {I revisit two theories of cell differentiation in multicellular organisms published a half-century ago, Stuart Kauffman's global genome regulatory dynamics (GGRD) model and Roy Britten's and Eric Davidson's modular gene regulatory network (MGRN) model, in light of newer knowledge of mechanisms of gene regulation in the metazoans (animals). The two models continue to inform hypotheses and computational studies of differentiation of lineage-adjacent cell types. However, their shared notion (based on bacterial regulatory systems) of gene switches and networks built from them have constrained progress in understanding the dynamics and evolution of differentiation. Recent work has described unique write-read-rewrite chromatin-based expression encoding in eukaryotes, as well metazoan-specific processes of gene activation and silencing in condensed-phase, enhancer-recruiting regulatory hubs, employing disordered proteins, including transcription factors, with context-dependent identities. These findings suggest an evolutionary scenario in which the origination of differentiation in animals, rather than depending exclusively on adaptive natural selection, emerged as a consequence of a type of multicellularity in which the novel metazoan gene regulatory apparatus was readily mobilized to amplify and exaggerate inherent cell functions of unicellular ancestors. The plausibility of this hypothesis is illustrated by the evolution of the developmental role of Grainyhead-like in the formation of epithelium.},
}

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

Evolution, Molecular
Fungal Proteins/genetics/metabolism
Fungi/*cytology/*genetics
Genes, Fungal
*Genomics
Hyphae/*cytology/*genetics
Morphogenesis/genetics
Multigene Family
Phagocytosis/genetics
Phylogeny
Yeasts/genetics

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

Adenosine Triphosphate/metabolism
Animals
Carcinogenesis/genetics/*metabolism/pathology
*Clonal Evolution
DNA Damage
Glucose/metabolism
Humans
Markov Chains
*Models, Theoretical
Oxygen/metabolism
Spheroids, Cellular/*metabolism/pathology
Tumor Cells, Cultured

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

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

@article {pmid31446445,
year = {2019},
author = {Annunziata, R and Andrikou, C and Perillo, M and Cuomo, C and Arnone, MI},
title = {Development and evolution of gut structures: from molecules to function.},
journal = {Cell and tissue research},
volume = {377},
number = {3},
pages = {445-458},
doi = {10.1007/s00441-019-03093-9},
pmid = {31446445},
issn = {1432-0878},
support = {215781//Marie Curie ITN EVONET/ ; },
mesh = {Animals ; Biological Evolution ; *Gastrointestinal Tract/cytology/physiology ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Larva/physiology ; Sea Urchins/genetics/*physiology ; Starfish/genetics/*physiology ; Vertebrates/genetics/*physiology ; },
abstract = {The emergence of a specialized system for food digestion and nutrient absorption was a crucial innovation for multicellular organisms. Digestive systems with different levels of complexity evolved in different animals, with the endoderm-derived one-way gut of most bilaterians to be the prevailing and more specialized form. While the molecular events regulating the early phases of embryonic tissue specification have been deeply investigated in animals occupying different phylogenetic positions, the mechanisms underlying gut patterning and gut-associated structures differentiation are still mostly obscure. In this review, we describe the main discoveries in gut and gut-associated structures development in echinoderm larvae (mainly for sea urchin and, when available, for sea star) and compare them with existing information in vertebrates. An impressive degree of conservation emerges when comparing the transcription factor toolkits recruited for gut cells and tissue differentiation in animals as diverse as echinoderms and vertebrates, thus suggesting that their function emerged in the deuterostome ancestor.},
}

Animals
Biological Evolution
*Gastrointestinal Tract/cytology/physiology
Gene Expression Regulation, Developmental
Gene Regulatory Networks
Larva/physiology
Sea Urchins/genetics/*physiology
Starfish/genetics/*physiology
Vertebrates/genetics/*physiology

@article {pmid31444229,
year = {2019},
author = {Draper, GW and Shoemark, DK and Adams, JC},
title = {Modelling the early evolution of extracellular matrix from modern Ctenophores and Sponges.},
journal = {Essays in biochemistry},
volume = {63},
number = {3},
pages = {389-405},
doi = {10.1042/EBC20180048},
pmid = {31444229},
issn = {1744-1358},
abstract = {Animals (metazoans) include some of the most complex living organisms on Earth, with regard to their multicellularity, numbers of differentiated cell types, and lifecycles. The metazoan extracellular matrix (ECM) is well-known to have major roles in the development of tissues during embryogenesis and in maintaining homoeostasis throughout life, yet insight into the ECM proteins which may have contributed to the transition from unicellular eukaryotes to multicellular animals remains sparse. Recent phylogenetic studies place either ctenophores or poriferans as the closest modern relatives of the earliest emerging metazoans. Here, we review the literature and representative genomic and transcriptomic databases for evidence of ECM and ECM-affiliated components known to be conserved in bilaterians, that are also present in ctenophores and/or poriferans. Whereas an extensive set of related proteins are identifiable in poriferans, there is a strikingly lack of conservation in ctenophores. From this perspective, much remains to be learnt about the composition of ctenophore mesoglea. The principal ECM-related proteins conserved between ctenophores, poriferans, and bilaterians include collagen IV, laminin-like proteins, thrombospondin superfamily members, integrins, membrane-associated proteoglycans, and tissue transglutaminase. These are candidates for a putative ancestral ECM that may have contributed to the emergence of the metazoans.},
}

@article {pmid31413788,
year = {2019},
author = {Fields, C and Levin, M},
title = {Somatic multicellularity as a satisficing solution to the prediction-error minimization problem.},
journal = {Communicative & integrative biology},
volume = {12},
number = {1},
pages = {119-132},
pmid = {31413788},
issn = {1942-0889},
abstract = {Adaptive success in the biosphere requires the dynamic ability to adjust physiological, transcriptional, and behavioral responses to environmental conditions. From chemical networks to organisms to whole communities, biological entities at all levels of organization seek to optimize their predictive power. Here, we argue that this fundamental drive provides a novel perspective on the origin of multicellularity. One way for unicellular organisms to minimize surprise with respect to external inputs is to be surrounded by reproductively-disabled, i.e. somatic copies of themselves - highly predictable agents which in effect reduce uncertainty in their microenvironments. We show that the transition to multicellularity can be modeled as a phase transition driven by environmental threats. We present modeling results showing how multicellular bodies can arise if non-reproductive somatic cells protect their reproductive parents from environmental lethality. We discuss how a somatic body can be interpreted as a Markov blanket around one or more reproductive cells, and how the transition to somatic multicellularity can be represented as a transition from exposure of reproductive cells to a high-uncertainty environment to their protection from environmental uncertainty by this Markov blanket. This is, effectively, a transition by the Markov blanket from transparency to opacity for the variational free energy of the environment. We suggest that the ability to arrest the cell cycle of daughter cells and redirect their resource utilization from division to environmental threat amelioration is the key innovation of obligate multicellular eukaryotes, that the nervous system evolved to exercise this control over long distances, and that cancer is an escape by somatic cells from the control of reproductive cells. Our quantitative model illustrates the evolutionary dynamics of this system, provides a novel hypothesis for the origin of multicellular animal bodies, and suggests a fundamental link between the architectures of complex organisms and information processing in proto-cognitive cellular agents.},
}

@article {pmid31370870,
year = {2019},
author = {Yeoh, LM and Goodman, CD and Mollard, V and McHugh, E and Lee, VV and Sturm, A and Cozijnsen, A and McFadden, GI and Ralph, SA},
title = {Alternative splicing is required for stage differentiation in malaria parasites.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {151},
pmid = {31370870},
issn = {1474-760X},
mesh = {*Alternative Splicing ; Animals ; Germ Cells/metabolism ; Life Cycle Stages/genetics ; Mice ; Plasmodium berghei/*genetics/growth & development/metabolism ; Transcription, Genetic ; },
abstract = {BACKGROUND: In multicellular organisms, alternative splicing is central to tissue differentiation and identity. Unicellular protists lack multicellular tissue but differentiate into variable cell types during their life cycles. The role of alternative splicing in transitions between cell types and establishing cellular identity is currently unknown in any unicellular organism.

RESULTS: To test whether alternative splicing in unicellular protists plays a role in cellular differentiation, we conduct RNA-seq to compare splicing in female and male sexual stages to asexual intraerythrocytic stages in the rodent malaria parasite Plasmodium berghei. We find extensive changes in alternative splicing between stages and a role for alternative splicing in sexual differentiation. Previously, general gametocyte differentiation was shown to be modulated by specific transcription factors. Here, we show that alternative splicing establishes a subsequent layer of regulation, controlling genes relating to consequent sex-specific differentiation of gametocytes.

CONCLUSIONS: We demonstrate that alternative splicing is reprogrammed during cellular differentiation of a unicellular protist. Disruption of an alternative splicing factor, PbSR-MG, perturbs sex-specific alternative splicing and decreases the ability of the parasites to differentiate into male gametes and oocysts, thereby reducing transmission between vertebrate and insect hosts. Our results reveal alternative splicing as an integral, stage-specific phenomenon in these protists and as a regulator of cellular differentiation that arose early in eukaryotic evolution.},
}

*Alternative Splicing
Animals
Germ Cells/metabolism
Life Cycle Stages/genetics
Mice
Plasmodium berghei/*genetics/growth & development/metabolism
Transcription, Genetic

@article {pmid31367038,
year = {2019},
author = {Olin-Sandoval, V and Yu, JSL and Miller-Fleming, L and Alam, MT and Kamrad, S and Correia-Melo, C and Haas, R and Segal, J and Peña Navarro, DA and Herrera-Dominguez, L and Méndez-Lucio, O and Vowinckel, J and Mülleder, M and Ralser, M},
title = {Lysine harvesting is an antioxidant strategy and triggers underground polyamine metabolism.},
journal = {Nature},
volume = {572},
number = {7768},
pages = {249-253},
pmid = {31367038},
issn = {1476-4687},
support = {200829/WT_/Wellcome Trust/United Kingdom ; FC001134/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 260809/ERC_/European Research Council/International ; FC001134/CRUK_/Cancer Research UK/United Kingdom ; FC001134/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Antioxidants/*metabolism ; Antiporters/metabolism ; Cadaverine/metabolism ; Glutamine/metabolism ; Glutathione/metabolism ; Lysine/*metabolism ; NADP/metabolism ; Organic Cation Transport Proteins/metabolism ; Ornithine Decarboxylase/metabolism ; Oxidants/metabolism ; Polyamines/*metabolism ; Reactive Oxygen Species/metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; },
abstract = {Both single and multicellular organisms depend on anti-stress mechanisms that enable them to deal with sudden changes in the environment, including exposure to heat and oxidants. Central to the stress response are dynamic changes in metabolism, such as the transition from the glycolysis to the pentose phosphate pathway-a conserved first-line response to oxidative insults1,2. Here we report a second metabolic adaptation that protects microbial cells in stress situations. The role of the yeast polyamine transporter Tpo1p3-5 in maintaining oxidant resistance is unknown6. However, a proteomic time-course experiment suggests a link to lysine metabolism. We reveal a connection between polyamine and lysine metabolism during stress situations, in the form of a promiscuous enzymatic reaction in which the first enzyme of the polyamine pathway, Spe1p, decarboxylates lysine and forms an alternative polyamine, cadaverine. The reaction proceeds in the presence of extracellular lysine, which is taken up by cells to reach concentrations up to one hundred times higher than those required for growth. Such extensive harvest is not observed for the other amino acids, is dependent on the polyamine pathway and triggers a reprogramming of redox metabolism. As a result, NADPH-which would otherwise be required for lysine biosynthesis-is channelled into glutathione metabolism, leading to a large increase in glutathione concentrations, lower levels of reactive oxygen species and increased oxidant tolerance. Our results show that nutrient uptake occurs not only to enable cell growth, but when the nutrient availability is favourable it also enables cells to reconfigure their metabolism to preventatively mount stress protection.},
}

Antioxidants/*metabolism
Antiporters/metabolism
Cadaverine/metabolism
Glutamine/metabolism
Glutathione/metabolism
Lysine/*metabolism
NADP/metabolism
Organic Cation Transport Proteins/metabolism
Ornithine Decarboxylase/metabolism
Oxidants/metabolism
Polyamines/*metabolism
Reactive Oxygen Species/metabolism
Saccharomyces cerevisiae/*metabolism
Saccharomyces cerevisiae Proteins/metabolism

@article {pmid31347665,
year = {2019},
author = {Lu, TM and Kanda, M and Furuya, H and Satoh, N},
title = {Dicyemid Mesozoans: A Unique Parasitic Lifestyle and a Reduced Genome.},
journal = {Genome biology and evolution},
volume = {11},
number = {8},
pages = {2232-2243},
pmid = {31347665},
issn = {1759-6653},
mesh = {Animals ; *Evolution, Molecular ; *Gene Expression Regulation, Developmental ; *Genome ; Invertebrates/classification/*genetics/growth & development ; Parasites/*genetics ; Phylogeny ; Proteins/*genetics ; Transcriptome ; },
abstract = {Dicyemids, previously called "mesozoans" (intermediates between unicellular protozoans and multicellular metazoans), are an enigmatic animal group. They have a highly simplified adult body, comprising only ∼30 cells, and they have a unique parasitic lifestyle. Recently, dicyemids were shown to be spiralians, with affinities to the Platyhelminthes. In order to understand molecular mechanisms involved in evolution of this odd animal, we sequenced the genome of Dicyema japonicum and a reference transcriptome assembly using mixed-stage samples. The D. japonicum genome features a high proportion of repetitive sequences that account for 49% of the genome. The dicyemid genome is reduced to ∼67.5 Mb with 5,012 protein-coding genes. Only four Hox genes exist in the genome, with no clustering. Gene distribution in KEGG pathways shows that D. japonicum has fewer genes in most pathways. Instead of eliminating entire critical metabolic pathways, parasitic lineages likely simplify pathways by eliminating pathway-specific genes, while genes with fundamental functions may be retained in multiple pathways. In principle, parasites can stand to lose genes that are unnecessary, in order to conserve energy. However, whether retained genes in incomplete pathways serve intermediate functions and how parasites overcome the physiological needs served by lost genes, remain to be investigated in future studies.},
}

Animals
*Evolution, Molecular
*Gene Expression Regulation, Developmental
*Genome
Invertebrates/classification/*genetics/growth & development
Parasites/*genetics
Phylogeny
Proteins/*genetics
Transcriptome

@article {pmid31339482,
year = {2019},
author = {Guo, JS and Zhang, Z and Qiao, M and Yu, ZF},
title = {Phalangispora sinensis sp. nov. from Yunnan, China and two new members of Wiesneriomycetaceae.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {69},
number = {10},
pages = {3217-3223},
doi = {10.1099/ijsem.0.003612},
pmid = {31339482},
issn = {1466-5034},
mesh = {Ascomycota/*classification/isolation & purification ; China ; DNA, Fungal/genetics ; Mycological Typing Techniques ; *Phylogeny ; Sequence Analysis, DNA ; Spores, Fungal ; *Water Microbiology ; },
abstract = {Phalangispora sinensis, an aquatic hyphomycete collected from south-western PR China, is described as a new species. This new species is characterized by having multicellular branched conidia composed of a curved main axis and one or two laterals, with the laterals arising from the third or fourth cell of the base of the main axis. Combined analyses of the LSU, SSU, RPB2 and TEF1 gene sequence data revealed that Phalangispora and another aquatic hyphomycete genus, Setosynnema, belonged to Wiesneriomycetaceae, Tubeufiales, Dothideomycetes, Ascomycota.},
}

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

@article {pmid31311477,
year = {2019},
author = {Boscaro, V and Husnik, F and Vannini, C and Keeling, PJ},
title = {Symbionts of the ciliate Euplotes: diversity, patterns and potential as models for bacteria-eukaryote endosymbioses.},
journal = {Proceedings. Biological sciences},
volume = {286},
number = {1907},
pages = {20190693},
pmid = {31311477},
issn = {1471-2954},
abstract = {Endosymbioses between bacteria and eukaryotes are enormously important in ecology and evolution, and as such are intensely studied. Despite this, the range of investigated hosts is narrow in the context of the whole eukaryotic tree of life: most of the information pertains to animal hosts, while most of the diversity is found in unicellular protists. A prominent case study is the ciliate Euplotes, which has repeatedly taken up the bacterium Polynucleobacter from the environment, triggering its transformation into obligate endosymbiont. This multiple origin makes the relationship an excellent model to understand recent symbioses, but Euplotes may host bacteria other than Polynucleobacter, and a more detailed knowledge of these additional interactions is needed in order to correctly interpret the system. Here, we present the first systematic survey of Euplotes endosymbionts, adopting a classical as well as a metagenomic approach, and review the state of knowledge. The emerging picture is indeed quite complex, with some Euplotes harbouring rich, stable prokaryotic communities not unlike those of multicellular animals. We provide insights into the distribution, evolution and diversity of these symbionts (including the establishment of six novel bacterial taxa), and outline differences and similarities with the most well-understood group of eukaryotic hosts: insects.},
}

@article {pmid31285576,
year = {2019},
author = {Staps, M and van Gestel, J and Tarnita, CE},
title = {Emergence of diverse life cycles and life histories at the origin of multicellularity.},
journal = {Nature ecology & evolution},
volume = {3},
number = {8},
pages = {1197-1205},
doi = {10.1038/s41559-019-0940-0},
pmid = {31285576},
issn = {2397-334X},
mesh = {Animals ; *Biological Evolution ; },
abstract = {The evolution of multicellularity has given rise to a remarkable diversity of multicellular life cycles and life histories. Whereas some multicellular organisms are long-lived, grow through cell division, and repeatedly release single-celled propagules (for example, animals), others are short-lived, form by aggregation, and propagate only once, by generating large numbers of solitary cells (for example, cellular slime moulds). There are no systematic studies that explore how diverse multicellular life cycles can come about. Here, we focus on the origin of multicellularity and develop a mechanistic model to examine the primitive life cycles that emerge from a unicellular ancestor when an ancestral gene is co-opted for cell adhesion. Diverse life cycles readily emerge, depending on ecological conditions, group-forming mechanism, and ancestral constraints. Among these life cycles, we recapitulate both extremes of long-lived groups that propagate continuously and short-lived groups that propagate only once, with the latter type of life cycle being particularly favoured when groups can form by aggregation. Our results show how diverse life cycles and life histories can easily emerge at the origin of multicellularity, shaped by ancestral constraints and ecological conditions. Beyond multicellularity, this finding has similar implications for other major transitions, such as the evolution of sociality.},
}

Animals
*Biological Evolution

@article {pmid31254720,
year = {2019},
author = {Falz, AL and Müller-Schüssele, SJ},
title = {Physcomitrella as a model system for plant cell biology and organelle-organelle communication.},
journal = {Current opinion in plant biology},
volume = {52},
number = {},
pages = {7-13},
doi = {10.1016/j.pbi.2019.05.007},
pmid = {31254720},
issn = {1879-0356},
mesh = {*Bryopsida ; Genomics ; Models, Biological ; Organelles ; Plant Cells ; },
abstract = {In multicellular eukaryotic cells, metabolism and growth are sustained by the cooperative functioning of organelles in combination with cell-to-cell communication at the organism level. In land plants, multiple strategies have evolved to adapt to life outside water. As basal land plant, the moss Physcomitrella patens is used for comparative genomics, allowing to study lineage-specific features, as well as to track the evolution of fundamental parameters of plant cell organisation and physiology. P. patens is a versatile model for cell biology research, especially to investigate adaptive growth, stress biology as well as organelle dynamics and interactions. Recent advances include the use of genetically encoded biosensors for in vivo imaging of physiological parameters.},
}

*Bryopsida
Genomics
Models, Biological
Organelles
Plant Cells

@article {pmid31239554,
year = {2019},
author = {Ågren, JA and Davies, NG and Foster, KR},
title = {Enforcement is central to the evolution of cooperation.},
journal = {Nature ecology & evolution},
volume = {3},
number = {7},
pages = {1018-1029},
doi = {10.1038/s41559-019-0907-1},
pmid = {31239554},
issn = {2397-334X},
support = {209397/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Biological Evolution ; *Cooperative Behavior ; Humans ; Symbiosis ; },
abstract = {Cooperation occurs at all levels of life, from genomes, complex cells and multicellular organisms to societies and mutualisms between species. A major question for evolutionary biology is what these diverse systems have in common. Here, we review the full breadth of cooperative systems and find that they frequently rely on enforcement mechanisms that suppress selfish behaviour. We discuss many examples, including the suppression of transposable elements, uniparental inheritance of mitochondria and plastids, anti-cancer mechanisms, reciprocation and punishment in humans and other vertebrates, policing in eusocial insects and partner choice in mutualisms between species. To address a lack of accompanying theory, we develop a series of evolutionary models that show that the enforcement of cooperation is widely predicted. We argue that enforcement is an underappreciated, and often critical, ingredient for cooperation across all scales of biological organization.},
}

Animals
*Biological Evolution
*Cooperative Behavior
Humans
Symbiosis

@article {pmid31236128,
year = {2019},
author = {Robu, A and Mironov, V and Neagu, A},
title = {Using Sacrificial Cell Spheroids for the Bioprinting of Perfusable 3D Tissue and Organ Constructs: A Computational Study.},
journal = {Computational and mathematical methods in medicine},
volume = {2019},
number = {},
pages = {7853586},
pmid = {31236128},
issn = {1748-6718},
mesh = {3T3 Cells ; Algorithms ; Animals ; Bioprinting/*methods ; Carcinoma, Lewis Lung/metabolism ; Computer Simulation ; Humans ; Hydrogels/*chemistry ; Metal Nanoparticles/chemistry ; Mice ; Monte Carlo Method ; Perfusion ; *Printing, Three-Dimensional ; Silicon/chemistry ; Spheroids, Cellular/*cytology ; Tissue Engineering/*methods ; Tissue Scaffolds ; },
abstract = {A long-standing problem in tissue engineering is the biofabrication of perfusable tissue constructs that can be readily connected to the patient's vasculature. It was partially solved by three-dimensional (3D) printing of sacrificial material (e.g., hydrogel) strands: upon incorporation in another cell-laden hydrogel, the strands were removed, leaving behind perfusable channels. Their complexity, however, did not match that of the native vasculature. Here, we propose to use multicellular spheroids as a sacrificial material and investigate their potential benefits in the context of 3D bioprinting of cell aggregates and/or cell-laden hydrogels. Our study is based on computer simulations of postprinting cellular rearrangements. The computational model of the biological system is built on a cubic lattice, whereas its evolution is simulated using the Metropolis Monte Carlo algorithm. The simulations describe structural changes in three types of tissue constructs: a tube made of a single cell type, a tube made of two cell types, and a cell-laden hydrogel slab that incorporates a branching tube. In all three constructs, the lumen is obtained after the elimination of the sacrificial cell population. Our study suggests that sacrificial cell spheroids (sacrospheres) enable one to print tissue constructs outfitted with a finer and more complex network of channels than the ones obtained so far. Moreover, cellular interactions might give rise to a tissue microarchitecture that lies beyond the bioprinter's resolution. Although more expensive than inert materials, sacrificial cells have the potential to bring further progress towards the biofabrication of fully vascularized tissue substitutes.},
}

3T3 Cells
Algorithms
Animals
Bioprinting/*methods
Carcinoma, Lewis Lung/metabolism
Computer Simulation
Humans
Hydrogels/*chemistry
Metal Nanoparticles/chemistry
Mice
Monte Carlo Method
Perfusion
*Printing, Three-Dimensional
Silicon/chemistry
Spheroids, Cellular/*cytology
Tissue Engineering/*methods
Tissue Scaffolds

@article {pmid31214991,
year = {2019},
author = {Muras, V and Toulouse, C and Fritz, G and Steuber, J},
title = {Respiratory Membrane Protein Complexes Convert Chemical Energy.},
journal = {Sub-cellular biochemistry},
volume = {92},
number = {},
pages = {301-335},
doi = {10.1007/978-3-030-18768-2_10},
pmid = {31214991},
issn = {0306-0225},
mesh = {Archaea/cytology/enzymology/*metabolism ; Bacteria/cytology/enzymology/*metabolism ; Cell Membrane/*metabolism ; *Electron Transport ; *Energy Metabolism ; Membrane Proteins/*chemistry/*metabolism ; },
abstract = {The invention of a biological membrane which is used as energy storage system to drive the metabolism of a primordial, unicellular organism represents a key event in the evolution of life. The innovative, underlying principle of this key event is respiration. In respiration, a lipid bilayer with insulating properties is chosen as the site for catalysis of an exergonic redox reaction converting substrates offered from the environment, using the liberated Gibbs free energy (ΔG) for the build-up of an electrochemical H+ (proton motive force, PMF) or Na+ gradient (sodium motive force, SMF) across the lipid bilayer. Very frequently , several redox reactions are performed in a consecutive manner, with the first reaction delivering a product which is used as substrate for the second redox reaction, resulting in a respiratory chain. From today's perspective, the (mostly) unicellular bacteria and archaea seem to be much simpler and less evolved when compared to multicellular eukaryotes. However, they are overwhelmingly complex with regard to the various respiratory chains which permit survival in very different habitats of our planet, utilizing a plethora of substances to drive metabolism. This includes nitrogen, sulfur and carbon compounds which are oxidized or reduced by specialized, respiratory enzymes of bacteria and archaea which lie at the heart of the geochemical N, S and C-cycles. This chapter gives an overview of general principles of microbial respiration considering thermodynamic aspects, chemical reactions and kinetic restraints. The respiratory chains of Escherichia coli and Vibrio cholerae are discussed as models for PMF- versus SMF-generating processes, respectively. We introduce main redox cofactors of microbial respiratory enzymes, and the concept of intra-and interelectron transfer. Since oxygen is an electron acceptor used by many respiratory chains, the formation and removal of toxic oxygen radicals is described. Promising directions of future research are respiratory enzymes as novel bacterial targets, and biotechnological applications relying on respiratory complexes.},
}

Archaea/cytology/enzymology/*metabolism
Bacteria/cytology/enzymology/*metabolism
Cell Membrane/*metabolism
*Electron Transport
*Energy Metabolism
Membrane Proteins/*chemistry/*metabolism

@article {pmid31189954,
year = {2019},
author = {Sogabe, S and Hatleberg, WL and Kocot, KM and Say, TE and Stoupin, D and Roper, KE and Fernandez-Valverde, SL and Degnan, SM and Degnan, BM},
title = {Pluripotency and the origin of animal multicellularity.},
journal = {Nature},
volume = {570},
number = {7762},
pages = {519-522},
doi = {10.1038/s41586-019-1290-4},
pmid = {31189954},
issn = {1476-4687},
mesh = {Animals ; Cell Proliferation ; *Cell Transdifferentiation ; Epithelial Cells/cytology/metabolism ; Evolution, Molecular ; *Models, Biological ; *Phylogeny ; Pluripotent Stem Cells/*cytology/metabolism ; Porifera/*cytology/metabolism ; Reproducibility of Results ; Transcriptome ; },
abstract = {A widely held-but rarely tested-hypothesis for the origin of animals is that they evolved from a unicellular ancestor, with an apical cilium surrounded by a microvillar collar, that structurally resembled modern sponge choanocytes and choanoflagellates1-4. Here we test this view of animal origins by comparing the transcriptomes, fates and behaviours of the three primary sponge cell types-choanocytes, pluripotent mesenchymal archaeocytes and epithelial pinacocytes-with choanoflagellates and other unicellular holozoans. Unexpectedly, we find that the transcriptome of sponge choanocytes is the least similar to the transcriptomes of choanoflagellates and is significantly enriched in genes unique to either animals or sponges alone. By contrast, pluripotent archaeocytes upregulate genes that control cell proliferation and gene expression, as in other metazoan stem cells and in the proliferating stages of two unicellular holozoans, including a colonial choanoflagellate. Choanocytes in the sponge Amphimedon queenslandica exist in a transient metastable state and readily transdifferentiate into archaeocytes, which can differentiate into a range of other cell types. These sponge cell-type conversions are similar to the temporal cell-state changes that occur in unicellular holozoans5. Together, these analyses argue against homology of sponge choanocytes and choanoflagellates, and the view that the first multicellular animals were simple balls of cells with limited capacity to differentiate. Instead, our results are consistent with the first animal cell being able to transition between multiple states in a manner similar to modern transdifferentiating and stem cells.},
}

Animals
Cell Proliferation
*Cell Transdifferentiation
Epithelial Cells/cytology/metabolism
Evolution, Molecular
*Models, Biological
*Phylogeny
Pluripotent Stem Cells/*cytology/metabolism
Porifera/*cytology/metabolism
Reproducibility of Results
Transcriptome

@article {pmid31185890,
year = {2019},
author = {Yamashita, S and Nozaki, H},
title = {Embryogenesis of flattened colonies implies the innovation required for the evolution of spheroidal colonies in volvocine green algae.},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {120},
pmid = {31185890},
issn = {1471-2148},
mesh = {Basal Bodies/metabolism ; *Biological Evolution ; Cell Division ; Cell Nucleus/metabolism ; Chlorophyta/classification/cytology/*embryology ; Microtubules/metabolism ; Phylogeny ; Time-Lapse Imaging ; },
abstract = {BACKGROUND: Volvocine algae provide a suitable model for investigation of the evolution of multicellular organisms. Within this group, evolution of the body plan from flattened to spheroidal colonies is thought to have occurred independently in two different lineages, Volvocaceae and Astrephomene. Volvocacean species undergo inversion to form a spheroidal cell layer following successive cell divisions during embryogenesis. During inversion, the daughter protoplasts change their shape and develop acute chloroplast ends (opposite to basal bodies). By contrast, Astrephomene does not undergo inversion; rather, its daughter protoplasts rotate during successive cell divisions to form a spheroidal colony. However, the evolutionary pathways of these cellular events involved in the two tactics for formation of spheroidal colony are unclear, since the embryogenesis of extant volvocine genera with ancestral flattened colonies, such as Gonium and Tetrabaena, has not previously been investigated in detail.

RESULTS: We conducted time-lapse imaging by light microscopy and indirect immunofluorescence microscopy with staining of basal bodies, nuclei, and microtubules to observe embryogenesis in G. pectorale and T. socialis, which form 16-celled or 4-celled flattened colonies, respectively. In G. pectorale, a cup-shaped cell layer of the 16-celled embryo underwent gradual expansion after successive cell divisions, with the apical ends (position of basal bodies) of the square embryo's peripheral protoplasts separated from each other. In T. socialis, on the other hand, there was no apparent expansion of the daughter protoplasts in 4-celled embryos after successive cell divisions, however the two pairs of diagonally opposed daughter protoplasts shifted slightly and flattened after hatching. Neither of these two species exhibited rotation of daughter protoplasts during successive cell divisions as in Astrephomene or the formation of acute chloroplast ends of daughter protoplasts as in volvocacean inversion.

CONCLUSIONS: The present results indicate that the ancestor of Astrephomene might have newly acquired the rotation of daughter protoplasts after it diverged from the ancestor of Gonium, while the ancestor of Volvocaceae might have newly acquired the formation of acute chloroplast ends to complete inversion after divergence from the ancestor of Goniaceae (Gonium and Astrephomene).},
}

Basal Bodies/metabolism
*Biological Evolution
Cell Division
Cell Nucleus/metabolism
Chlorophyta/classification/cytology/*embryology
Microtubules/metabolism
Phylogeny
Time-Lapse Imaging

@article {pmid31185009,
year = {2019},
author = {Roy, M and Finley, SD},
title = {Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model.},
journal = {PLoS computational biology},
volume = {15},
number = {6},
pages = {e1007053},
pmid = {31185009},
issn = {1553-7358},
mesh = {Cell Line, Tumor ; Cell Proliferation/physiology ; Computational Biology/*methods ; Humans ; Kinetics ; *Models, Biological ; Neoplasms/*metabolism ; Spheroids, Cellular/*metabolism ; },
abstract = {Mathematical modeling provides the predictive ability to understand the metabolic reprogramming and complex pathways that mediate cancer cells' proliferation. We present a mathematical model using a multiscale, multicellular approach to simulate avascular tumor growth, applied to pancreatic cancer. The model spans three distinct spatial and temporal scales. At the extracellular level, reaction diffusion equations describe nutrient concentrations over a span of seconds. At the cellular level, a lattice-based energy driven stochastic approach describes cellular phenomena including adhesion, proliferation, viability and cell state transitions, occurring on the timescale of hours. At the sub-cellular level, we incorporate a detailed kinetic model of intracellular metabolite dynamics on the timescale of minutes, which enables the cells to uptake and excrete metabolites and use the metabolites to generate energy and building blocks for cell growth. This is a particularly novel aspect of the model. Certain defined criteria for the concentrations of intracellular metabolites lead to cancer cell growth, proliferation or death. Overall, we model the evolution of the tumor in both time and space. Starting with a cluster of tumor cells, the model produces an avascular tumor that quantitatively and qualitatively mimics experimental measurements of multicellular tumor spheroids. Through our model simulations, we can investigate the response of individual intracellular species under a metabolic perturbation and investigate how that response contributes to the response of the tumor as a whole. The predicted response of intracellular metabolites under various targeted strategies are difficult to resolve with experimental techniques. Thus, the model can give novel predictions as to the response of the tumor as a whole, identifies potential therapies to impede tumor growth, and predicts the effects of those therapeutic strategies. In particular, the model provides quantitative insight into the dynamic reprogramming of tumor cells at the intracellular level in response to specific metabolic perturbations. Overall, the model is a useful framework to study targeted metabolic strategies for inhibiting tumor growth.},
}

Cell Line, Tumor
Cell Proliferation/physiology
Computational Biology/*methods
Humans
Kinetics
*Models, Biological
Neoplasms/*metabolism
Spheroids, Cellular/*metabolism

@article {pmid31172192,
year = {2019},
author = {St-Georges-Robillard, A and Cahuzac, M and Péant, B and Fleury, H and Lateef, MA and Ricard, A and Sauriol, A and Leblond, F and Mes-Masson, AM and Gervais, T},
title = {Long-term fluorescence hyperspectral imaging of on-chip treated co-culture tumour spheroids to follow clonal evolution.},
journal = {Integrative biology : quantitative biosciences from nano to macro},
volume = {11},
number = {4},
pages = {130-141},
doi = {10.1093/intbio/zyz012},
pmid = {31172192},
issn = {1757-9708},
mesh = {*Cell Culture Techniques ; Cell Line, Tumor ; Cell Proliferation/drug effects ; *Clonal Evolution ; *Coculture Techniques ; Drug Screening Assays, Antitumor ; Female ; Humans ; *Lab-On-A-Chip Devices ; Microfluidics ; Microscopy, Fluorescence/*methods ; Ovarian Neoplasms/drug therapy/pathology ; Spheroids, Cellular/*drug effects ; },
abstract = {Multicellular tumour spheroids are an ideal in vitro tumour model to study clonal heterogeneity and drug resistance in cancer research because different cell types can be mixed at will. However, measuring the individual response of each cell population over time is challenging: current methods are either destructive, such as flow cytometry, or cannot image throughout a spheroid, such as confocal microscopy. Our group previously developed a wide-field fluorescence hyperspectral imaging system to study spheroids formed and cultured in microfluidic chips. In the present study, two subclones of a single parental ovarian cancer cell line transfected to express different fluorophores were produced and co-culture spheroids were formed on-chip using ratios forming highly asymmetric subpopulations. We performed a 3D proliferation assay on each cell population forming the spheroids that matched the 2D growth behaviour. Response assays to PARP inhibitors and platinum-based drugs were also performed to follow the clonal evolution of mixed populations. Our experiments show that hyperspectral imaging can detect spheroid response before observing a decrease in spheroid diameter. Hyperspectral imaging and microfluidic-based spheroid assays provide a versatile solution to study clonal heterogeneity, able to measure response in subpopulations presenting as little as 10% of the initial spheroid.},
}

*Cell Culture Techniques
Cell Line, Tumor
Cell Proliferation/drug effects
*Clonal Evolution
*Coculture Techniques
Drug Screening Assays, Antitumor
Female
Humans
*Lab-On-A-Chip Devices
Microfluidics
Microscopy, Fluorescence/*methods
Ovarian Neoplasms/drug therapy/pathology
Spheroids, Cellular/*drug effects

@article {pmid31170405,
year = {2019},
author = {Edgar, JA},
title = {L-ascorbic acid and the evolution of multicellular eukaryotes.},
journal = {Journal of theoretical biology},
volume = {476},
number = {},
pages = {62-73},
doi = {10.1016/j.jtbi.2019.06.001},
pmid = {31170405},
issn = {1095-8541},
abstract = {The lifeless earth was formed around 4.5 billion years ago and the first anaerobic unicellular "organisms" may have appeared half a billion years later. Despite subsequent prokaryotes (bacteria and archaea) evolving quite complex biochemistry and some eukaryote characteristics, the transition from unicellular prokaryotes to multicellular, aerobic eukaryotes took a further 2.5 billion years to begin. The key factor or factors that eventually caused this long-delayed transition is a question that has been a focus of considerable research and a topic of discussion over many years. On the basis of the extensive literature available and consideration of some of the characteristics that distinguish multicellular eukaryotes from prokaryotes, it is proposed that, as well as the development of oxygenic photosynthesis producing high levels of environmental oxygen and the formation of vital organelles such as aerobic adenosine triphosphate-generating mitochondria, the concurrent evolution of the L-ascorbic acid redox system should be considered as a key factor that led to the evolution of multicellular eukaryotes and it remains vitally involved in the maintenance of multicellularity and many other eukaryote characteristics.},
}

@article {pmid31170137,
year = {2019},
author = {Thomas, F and Madsen, T and Giraudeau, M and Misse, D and Hamede, R and Vincze, O and Renaud, F and Roche, B and Ujvari, B},
title = {Transmissible cancer and the evolution of sex.},
journal = {PLoS biology},
volume = {17},
number = {6},
pages = {e3000275},
pmid = {31170137},
issn = {1545-7885},
mesh = {Animals ; Biological Evolution ; Cell Transformation, Neoplastic/genetics ; Eukaryota ; Genotype ; Humans ; Recombination, Genetic/genetics/*physiology ; Reproduction/*genetics/*physiology ; Selection, Genetic/genetics ; Sexual Behavior/physiology ; },
abstract = {The origin and subsequent maintenance of sex and recombination are among the most elusive and controversial problems in evolutionary biology. Here, we propose a novel hypothesis, suggesting that sexual reproduction not only evolved to reduce the negative effects of the accumulation of deleterious mutations and processes associated with pathogen and/or parasite resistance but also to prevent invasion by transmissible selfish neoplastic cheater cells, henceforth referred to as transmissible cancer cells. Sexual reproduction permits systematic change of the multicellular organism's genotype and hence an enhanced detection of transmissible cancer cells by immune system. Given the omnipresence of oncogenic processes in multicellular organisms, together with the fact that transmissible cancer cells can have dramatic effects on their host fitness, our scenario suggests that the benefits of sex and concomitant recombination will be large and permanent, explaining why sexual reproduction is, despite its costs, the dominant mode of reproduction among eukaryotes.},
}

Animals
Biological Evolution
Cell Transformation, Neoplastic/genetics
Eukaryota
Genotype
Humans
Recombination, Genetic/genetics/*physiology
Reproduction/*genetics/*physiology
Selection, Genetic/genetics
Sexual Behavior/physiology

@article {pmid31155362,
year = {2019},
author = {Russell, SL and Chappell, L and Sullivan, W},
title = {A symbiont's guide to the germline.},
journal = {Current topics in developmental biology},
volume = {135},
number = {},
pages = {315-351},
doi = {10.1016/bs.ctdb.2019.04.007},
pmid = {31155362},
issn = {1557-8933},
abstract = {Microbial symbioses exhibit astounding adaptations, yet all symbionts face the problem of how to reliably associate with host offspring every generation. A common strategy is vertical transmission, in which symbionts are directly transmitted from the female to her offspring. The diversity of symbionts and vertical transmission mechanisms is as expansive as the diversity of eukaryotic host taxa that house them. However, there are several common themes among these mechanisms based on the degree to which symbionts associate with the host germline during transmission. In this review, we detail three distinct vertical transmission strategies, starting with associations that are transmitted from host somatic cells to offspring somatic cells, either due to lacking a germline or avoiding it. A second strategy involves somatically-localized symbionts that migrate into the germline during host development. The third strategy we discuss is one in which the symbiont maintains continuous association with the germline throughout development. Unexpectedly, the vast majority of documented vertically inherited symbionts rely on the second strategy: soma-to-germline migration. Given that not all eukaryotes contain a sequestered germline and instead produce offspring from somatic stem cell lineages, this soma-to-germline migration is discussed in the context of multicellular evolution. Lastly, as recent genomics data have revealed an abundance of horizontal gene transfer events from symbiotic and non-symbiotic bacteria to host genomes, we discuss their impact on eukaryotic host evolution.},
}

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

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

@article {pmid31118507,
year = {2019},
author = {Loron, CC and François, C and Rainbird, RH and Turner, EC and Borensztajn, S and Javaux, EJ},
title = {Early fungi from the Proterozoic era in Arctic Canada.},
journal = {Nature},
volume = {570},
number = {7760},
pages = {232-235},
doi = {10.1038/s41586-019-1217-0},
pmid = {31118507},
issn = {1476-4687},
mesh = {Arctic Regions ; Canada ; *Fossils ; Fungi/*classification/*isolation & purification/ultrastructure ; History, Ancient ; Phylogeny ; Spectroscopy, Fourier Transform Infrared ; Time Factors ; },
abstract = {Fungi are crucial components of modern ecosystems. They may have had an important role in the colonization of land by eukaryotes, and in the appearance and success of land plants and metazoans1-3. Nevertheless, fossils that can unambiguously be identified as fungi are absent from the fossil record until the middle of the Palaeozoic era4,5. Here we show, using morphological, ultrastructural and spectroscopic analyses, that multicellular organic-walled microfossils preserved in shale of the Grassy Bay Formation (Shaler Supergroup, Arctic Canada), which dates to approximately 1,010-890 million years ago, have a fungal affinity. These microfossils are more than half a billion years older than previously reported unambiguous occurrences of fungi, a date which is consistent with data from molecular clocks for the emergence of this clade6,7. In extending the fossil record of the fungi, this finding also pushes back the minimum date for the appearance of eukaryotic crown group Opisthokonta, which comprises metazoans, fungi and their protist relatives8,9.},
}

Arctic Regions
Canada
*Fossils
Fungi/*classification/*isolation & purification/ultrastructure
History, Ancient
Phylogeny
Spectroscopy, Fourier Transform Infrared
Time Factors

@article {pmid31113629,
year = {2019},
author = {Ballinger, MJ and Perlman, SJ},
title = {The defensive Spiroplasma.},
journal = {Current opinion in insect science},
volume = {32},
number = {},
pages = {36-41},
doi = {10.1016/j.cois.2018.10.004},
pmid = {31113629},
issn = {2214-5753},
mesh = {Animals ; Arthropods/*microbiology/*parasitology ; Fungi ; Nematoda ; Saporins ; Spiroplasma/*physiology ; Symbiosis ; Wasps ; },
abstract = {Defensive microbes are of great interest for their roles in arthropod health, disease transmission, and biocontrol efforts. Obligate bacterial passengers of arthropods, such as Spiroplasma, confer protection against the natural enemies of their hosts to improve their own fitness. Although known for less than a decade, Spiroplasma's defensive reach extends to diverse parasites, both microbial and multicellular. We provide an overview of known defensive phenotypes against nematodes, parasitoid wasps, and fungi, and highlight recent studies supporting the role of Spiroplasma-encoded ribosome-inactivating proteins in protection. With cellular features well-suited for life in the hemolymph, broad distribution among invertebrate hosts, and the capacity to repeatedly evolve vertical transmission, Spiroplasma may be uniquely equipped to form intimate, defensive associations to combat extracellular parasites. Along with insights into defensive mechanisms, recent significant advances have been made in male-killing - a phenotype with interesting evolutionary ties to defense. Finally, we look forward to an exciting decade using the genetic tools of Drosophila, and the rapidly-advancing tractability of Spiroplasma itself, to better understand mechanisms and evolution in defensive symbiosis.},
}

Animals
Arthropods/*microbiology/*parasitology
Fungi
Nematoda
Saporins
Spiroplasma/*physiology
Symbiosis
Wasps

@article {pmid31095603,
year = {2019},
author = {Khan, MAW and Stephens, WZ and Mohammed, AD and Round, JL and Kubinak, JL},
title = {Does MHC heterozygosity influence microbiota form and function?.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0215946},
pmid = {31095603},
issn = {1932-6203},
support = {T32 AI055434/AI/NIAID NIH HHS/United States ; K22 AI095375/AI/NIAID NIH HHS/United States ; DP2 AT008746/AT/NCCIH NIH HHS/United States ; K22 AI123481/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Feces/microbiology ; Female ; Genetic Variation ; Genotype ; *Heterozygote ; Homozygote ; Major Histocompatibility Complex/*genetics ; Mice ; Microbiota/*genetics ; },
abstract = {MHC molecules are essential for the adaptive immune response, and they are the most polymorphic genetic loci in vertebrates. Extreme genetic variation at these loci is paradoxical given their central importance to host health. Classic models of MHC gene evolution center on antagonistic host-pathogen interactions to promote gene diversification and allelic diversity in host populations. However, all multicellular organisms are persistently colonized by their microbiota that perform essential metabolic functions for their host and protect from infection. Here, we provide data to support the hypothesis that MHC heterozygote advantage (a main force of selection thought to drive MHC gene evolution), may operate by enhancing fitness advantages conferred by the host's microbiome. We utilized fecal 16S rRNA gene sequences and their predicted metagenome datasets collected from multiple MHC congenic homozygote and heterozygote mouse strains to describe the influence of MHC heterozygosity on microbiome form and function. We find that in contrast to homozygosity at MHC loci, MHC heterozygosity promotes functional diversification of the microbiome, enhances microbial network connectivity, and results in enrichment for a variety of microbial functions that are positively associated with host fitness. We demonstrate that taxonomic and functional diversity of the microbiome is positively correlated in MHC heterozygote but not homozygote animals, suggesting that heterozygote microbiomes are more functionally adaptive under similar environmental conditions than homozygote microbiomes. Our data complement previous observations on the role of MHC polymorphism in sculpting microbiota composition, but also provide functional insights into how MHC heterozygosity may enhance host health by modulating microbiome form and function. We also provide evidence to support that MHC heterozygosity limits functional redundancy among commensal microbes and may enhance the metabolic versatility of their microbiome. Results from our analyses yield multiple testable predictions regarding the role of MHC heterozygosity on the microbiome that will help guide future research in the area of MHC-microbiome interactions.},
}

Animals
Feces/microbiology
Female
Genetic Variation
Genotype
*Heterozygote
Homozygote
Major Histocompatibility Complex/*genetics
Mice
Microbiota/*genetics

@article {pmid31086369,
year = {2019},
author = {Gao, Y and Traulsen, A and Pichugin, Y},
title = {Interacting cells driving the evolution of multicellular life cycles.},
journal = {PLoS computational biology},
volume = {15},
number = {5},
pages = {e1006987},
pmid = {31086369},
issn = {1553-7358},
mesh = {Animals ; Biological Evolution ; Cell Communication/*physiology ; Cell Division ; Computer Simulation ; Game Theory ; Humans ; Life Cycle Stages/genetics/*physiology ; Models, Biological ; Phenotype ; Reproduction ; },
abstract = {Evolution of complex multicellular life began from the emergence of a life cycle involving the formation of cell clusters. The opportunity for cells to interact within clusters provided them with an advantage over unicellular life forms. However, what kind of interactions may lead to the evolution of multicellular life cycles? Here, we combine evolutionary game theory with a model for the emergence of multicellular groups to investigate how cell interactions can influence reproduction modes during the early stages of the evolution of multicellularity. In our model, the presence of both cell types is maintained by stochastic phenotype switching during cell division. We identify evolutionary optimal life cycles as those which maximize the population growth rate. Among all interactions captured by two-player games, the vast majority promotes two classes of life cycles: (i) splitting into unicellular propagules or (ii) fragmentation into two offspring clusters of equal (or almost equal) size. Our findings indicate that the three most important characteristics, determining whether multicellular life cycles will evolve, are the average performance of homogeneous groups, heterogeneous groups, and solitary cells.},
}

Animals
Biological Evolution
Cell Communication/*physiology
Cell Division
Computer Simulation
Game Theory
Humans
Life Cycle Stages/genetics/*physiology
Models, Biological
Phenotype
Reproduction

@article {pmid31046194,
year = {2019},
author = {Biscotti, MA and Barucca, M and Carducci, F and Forconi, M and Canapa, A},
title = {The p53 gene family in vertebrates: Evolutionary considerations.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {332},
number = {6},
pages = {171-178},
doi = {10.1002/jez.b.22856},
pmid = {31046194},
issn = {1552-5015},
support = {467-2014//Ministero della Ricerca e dell'Istruzione/ ; },
abstract = {The origin of the p53 gene family predates multicellular life since TP53 members of this gene family have been found in unicellular eukaryotes. In invertebrates one or two genes attributable to a TP53-like or TP63/73-like gene are present. The radiation into three genes, TP53, TP63, and TP73, has been reported as a vertebrate invention. TP53 is considered the "guardian of the genome" given its role in protecting cells against the DNA damage and cellular stressors. TP63 and TP73 play a role in epithelial development and neurogenesis, respectively. The evolution of the p53 gene family has been the subject of considerable analyses even if several questions remain still open. In this study we addressed the evolutionary history of the p53 gene family in vertebrates performing an extended microsyntenic investigation coupled with a phylogenetic analysis, together with protein domain organization and structure assessment. On the basis of our results we discussed a possible evolutionary scenario according to which a TP53/63/73 ancestor form gave rise to the current TP53 and a TP63/73 form, which in turn independently duplicated into two genes in agnathe and gnathostome lineages.},
}

@article {pmid31031789,
year = {2019},
author = {Hajheidari, M and Koncz, C and Bucher, M},
title = {Chromatin Evolution-Key Innovations Underpinning Morphological Complexity.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {454},
pmid = {31031789},
issn = {1664-462X},
abstract = {The history of life consists of a series of major evolutionary transitions, including emergence and radiation of complex multicellular eukaryotes from unicellular ancestors. The cells of multicellular organisms, with few exceptions, contain the same genome, however, their organs are composed of a variety of cell types that differ in both structure and function. This variation is largely due to the transcriptional activity of different sets of genes in different cell types. This indicates that complex transcriptional regulation played a key role in the evolution of complexity in eukaryotes. In this review, we summarize how gene duplication and subsequent evolutionary innovations, including the structural evolution of nucleosomes and chromatin-related factors, contributed to the complexity of the transcriptional system and provided a basis for morphological diversity.},
}

@article {pmid31002570,
year = {2019},
author = {Olito, C and Connallon, T},
title = {Sexually Antagonistic Variation and the Evolution of Dimorphic Sexual Systems.},
journal = {The American naturalist},
volume = {193},
number = {5},
pages = {688-701},
doi = {10.1086/702847},
pmid = {31002570},
issn = {1537-5323},
abstract = {Multicellular Eukaryotes use a broad spectrum of sexual reproduction strategies, ranging from simultaneous hermaphroditism to complete dioecy (separate sexes). The evolutionary pathway from hermaphroditism to dioecy involves the spread of sterility alleles that eliminate female or male reproductive functions, producing unisexual individuals. Classical theory predicts that evolutionary transitions to dioecy are feasible when female and male sex functions genetically trade off with one another (allocation to sex functions is sexually antagonistic) and rates of self-fertilization and inbreeding depression are high within the ancestral hermaphrodite population. We show that genetic linkage between sterility alleles and loci under sexually antagonistic selection significantly alters these classical predictions. We identify three specific consequences of linkage for the evolution of dimorphic sexual systems. First, linkage broadens conditions for the invasion of unisexual sterility alleles, facilitating transitions to sexual systems that are intermediate between hermaphroditism and dioecy (androdioecy and gynodioecy). Second, linkage elevates the equilibrium frequencies of unisexual individuals within androdioecious and gynodioecious populations, which promotes subsequent transitions to full dioecy. Third, linkage dampens the role of inbreeding during transitions to androdioecy and gynodioecy, making these transitions feasible in outbred populations. We discuss implications of these results for the evolution of dimorphic reproductive systems and sex chromosomes.},
}

@article {pmid30978201,
year = {2019},
author = {Laundon, D and Larson, BT and McDonald, K and King, N and Burkhardt, P},
title = {The architecture of cell differentiation in choanoflagellates and sponge choanocytes.},
journal = {PLoS biology},
volume = {17},
number = {4},
pages = {e3000226},
pmid = {30978201},
issn = {1545-7885},
mesh = {Animals ; Cell Differentiation/genetics ; Choanoflagellata/genetics/metabolism/*physiology ; Microscopy, Electron, Transmission ; Morphogenesis/*physiology ; Phylogeny ; Porifera/genetics/*physiology ; },
abstract = {Although collar cells are conserved across animals and their closest relatives, the choanoflagellates, little is known about their ancestry, their subcellular architecture, or how they differentiate. The choanoflagellate Salpingoeca rosetta expresses genes necessary for animal development and can alternate between unicellular and multicellular states, making it a powerful model for investigating the origin of animal multicellularity and mechanisms underlying cell differentiation. To compare the subcellular architecture of solitary collar cells in S. rosetta with that of multicellular 'rosette' colonies and collar cells in sponges, we reconstructed entire cells in 3D through transmission electron microscopy on serial ultrathin sections. Structural analysis of our 3D reconstructions revealed important differences between single and colonial choanoflagellate cells, with colonial cells exhibiting a more amoeboid morphology consistent with higher levels of macropinocytotic activity. Comparison of multiple reconstructed rosette colonies highlighted the variable nature of cell sizes, cell-cell contact networks, and colony arrangement. Importantly, we uncovered the presence of elongated cells in some rosette colonies that likely represent a distinct and differentiated cell type, pointing toward spatial cell differentiation. Intercellular bridges within choanoflagellate colonies displayed a variety of morphologies and connected some but not all neighbouring cells. Reconstruction of sponge choanocytes revealed ultrastructural commonalities but also differences in major organelle composition in comparison to choanoflagellates. Together, our comparative reconstructions uncover the architecture of cell differentiation in choanoflagellates and sponge choanocytes and constitute an important step in reconstructing the cell biology of the last common ancestor of animals.},
}

Animals
Cell Differentiation/genetics
Choanoflagellata/genetics/metabolism/*physiology
Microscopy, Electron, Transmission
Morphogenesis/*physiology
Phylogeny
Porifera/genetics/*physiology

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

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

@article {pmid30963641,
year = {2019},
author = {Rêgo, A and Messina, FJ and Gompert, Z},
title = {Dynamics of genomic change during evolutionary rescue in the seed beetle Callosobruchus maculatus.},
journal = {Molecular ecology},
volume = {28},
number = {9},
pages = {2136-2154},
doi = {10.1111/mec.15085},
pmid = {30963641},
issn = {1365-294X},
mesh = {Adaptation, Physiological/genetics ; Animals ; Bayes Theorem ; Biological Evolution ; Coleoptera/*genetics ; Gene Frequency ; Genetic Drift ; Genetic Fitness ; Lens Plant ; Linkage Disequilibrium ; Models, Genetic ; Polymorphism, Single Nucleotide ; Seeds ; *Selection, Genetic ; },
abstract = {Rapid adaptation can prevent extinction when populations are exposed to extremely marginal or stressful environments. Factors that affect the likelihood of evolutionary rescue from extinction have been identified, but much less is known about the evolutionary dynamics (e.g., rates and patterns of allele frequency change) and genomic basis of successful rescue, particularly in multicellular organisms. We conducted an evolve-and-resequence experiment to investigate the dynamics of evolutionary rescue at the genetic level in the cowpea seed beetle, Callosobruchus maculatus, when it is experimentally shifted to a stressful host plant, lentil. Low survival (~1%) at the onset of the experiment caused population decline. But adaptive evolution quickly rescued the population, with survival rates climbing to 69% by the F5 generation and 90% by the F10 generation. Population genomic data showed that rescue likely was caused by rapid evolutionary change at multiple loci, with many alleles fixing or nearly fixing within five generations of selection on lentil. Selection on these loci was only moderately consistent in time, but parallel evolutionary changes were evident in sublines formed after the lentil line had passed through a bottleneck. By comparing estimates of selection and genomic change on lentil across five independent C. maculatus lines (the new lentil-adapted line, three long-established lines and one case of failed evolutionary rescue), we found that adaptation on lentil occurred via somewhat idiosyncratic evolutionary changes. Overall, our results suggest that evolutionary rescue in this system can be caused by very strong selection on multiple loci driving rapid and pronounced genomic change.},
}

Adaptation, Physiological/genetics
Animals
Bayes Theorem
Biological Evolution
Coleoptera/*genetics
Gene Frequency
Genetic Drift
Genetic Fitness
Lens Plant
Linkage Disequilibrium
Models, Genetic
Polymorphism, Single Nucleotide
Seeds
*Selection, Genetic

@article {pmid30958167,
year = {2019},
author = {Nguyen, H and Koehl, MAR and Oakes, C and Bustamante, G and Fauci, L},
title = {Effects of cell morphology and attachment to a surface on the hydrodynamic performance of unicellular choanoflagellates.},
journal = {Journal of the Royal Society, Interface},
volume = {16},
number = {150},
pages = {20180736},
pmid = {30958167},
issn = {1742-5662},
mesh = {Cell Adhesion/*physiology ; Choanoflagellata/cytology/*physiology ; *Hydrodynamics ; *Models, Biological ; Surface Properties ; Swimming/*physiology ; },
abstract = {Choanoflagellates, eukaryotes that are important predators on bacteria in aquatic ecosystems, are closely related to animals and are used as a model system to study the evolution of animals from protozoan ancestors. The choanoflagellate Salpingoeca rosetta has a complex life cycle with different morphotypes, some unicellular and some multicellular. Here we use computational fluid dynamics to study the hydrodynamics of swimming and feeding by different unicellular stages of S. rosetta: a swimming cell with a collar of prey-capturing microvilli surrounding a single flagellum, a thecate cell attached to a surface and a dispersal-stage cell with a slender body, long flagellum and short collar. We show that a longer flagellum increases swimming speed, longer microvilli reduce speed and cell shape only affects speed when the collar is very short. The flux of prey-carrying water into the collar capture zone is greater for swimming than sessile cells, but this advantage decreases with collar size. Stalk length has little effect on flux for sessile cells. We show that ignoring the collar, as earlier models have done, overestimates flux and greatly overestimates the benefit to feeding performance of swimming versus being attached, and of a longer stalk for attached cells.},
}

Cell Adhesion/*physiology
Choanoflagellata/cytology/*physiology
*Hydrodynamics
*Models, Biological
Surface Properties
Swimming/*physiology

@article {pmid30949307,
year = {2019},
author = {Bohlin, J and Pettersson, JH},
title = {Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals.},
journal = {Computational and structural biotechnology journal},
volume = {17},
number = {},
pages = {362-370},
pmid = {30949307},
issn = {2001-0370},
abstract = {Whole genome sequencing (WGS) of thousands of microbial genomes has provided considerable insight into evolutionary mechanisms in the microbial world. While substantially fewer eukaryotic genomes are available for analyses the number is rapidly increasing. This mini-review summarizes broadly evolutionary dynamics of base composition in the different domains of life from the perspective of prokaryotes. Common and different evolutionary mechanisms influencing genomic base composition in eukaryotes and prokaryotes are discussed. The conclusion from the data currently available suggests that while there are similarities there are also striking differences in how genomic base composition has evolved within prokaryotes and eukaryotes. For instance, homologous recombination appears to increase GC content locally in eukaryotes due to a non-selective process termed GC-biased gene conversion (gBGC). For prokaryotes on the other hand, increase in genomic GC content seems to be driven by the environment and selection. We find that similar phenomena observed for some organisms in each respective domain may be caused by very different mechanisms: while gBGC and recombination rates appear to explain the negative correlation between GC3 (GC content based on the third codon nucleotides) and genome size in some eukaryotes uptake of AT rich DNA sequences is the main reason for a similar negative correlation observed in prokaryotes. We provide further examples that indicate that base composition in prokaryotes and eukaryotes have evolved under very different constraints.},
}

@article {pmid30918953,
year = {2019},
author = {Arimoto, A and Nishitsuji, K and Higa, Y and Arakaki, N and Hisata, K and Shinzato, C and Satoh, N and Shoguchi, E},
title = {A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {26},
number = {2},
pages = {183-192},
pmid = {30918953},
issn = {1756-1663},
mesh = {Caulerpa/*genetics ; Chlorophyta/genetics ; Embryophyta/genetics ; *Evolution, Molecular ; Gene Expression Profiling ; Genes, Homeobox/*genetics ; *Genome, Plant ; Genomics ; *Phylogeny ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; },
abstract = {Genome evolution and development of unicellular, multinucleate macroalgae (siphonous algae) are poorly known, although various multicellular organisms have been studied extensively. To understand macroalgal developmental evolution, we assembled the ∼26 Mb genome of a siphonous green alga, Caulerpa lentillifera, with high contiguity, containing 9,311 protein-coding genes. Molecular phylogeny using 107 nuclear genes indicates that the diversification of the class Ulvophyceae, including C. lentillifera, occurred before the split of the Chlorophyceae and Trebouxiophyceae. Compared with other green algae, the TALE superclass of homeobox genes, which expanded in land plants, shows a series of lineage-specific duplications in this siphonous macroalga. Plant hormone signalling components were also expanded in a lineage-specific manner. Expanded transport regulators, which show spatially different expression, suggest that the structural patterning strategy of a multinucleate cell depends on diversification of nuclear pore proteins. These results not only imply functional convergence of duplicated genes among green plants, but also provide insight into evolutionary roots of green plants. Based on the present results, we propose cellular and molecular mechanisms involved in the structural differentiation in the siphonous alga.},
}

Caulerpa/*genetics
Chlorophyta/genetics
Embryophyta/genetics
*Evolution, Molecular
Gene Expression Profiling
Genes, Homeobox/*genetics
*Genome, Plant
Genomics
*Phylogeny
Sequence Analysis, DNA
Sequence Analysis, RNA

@article {pmid30915518,
year = {2019},
author = {Kolasa, M and Ścibior, R and Mazur, MA and Kubisz, D and Dudek, K and Kajtoch, Ł},
title = {How Hosts Taxonomy, Trophy, and Endosymbionts Shape Microbiome Diversity in Beetles.},
journal = {Microbial ecology},
volume = {78},
number = {4},
pages = {995-1013},
pmid = {30915518},
issn = {1432-184X},
support = {DEC-2013/11/D/NZ8/00583//National Science Centre, Poland/ ; small grants for young researchers//Polish Ministry of Science and Higher Education/ ; },
mesh = {Animals ; Bacteria/*classification ; Bacterial Physiological Phenomena ; Coleoptera/classification/*microbiology/*physiology ; Feeding Behavior ; Microbiota/*physiology ; Phylogeny ; *Symbiosis ; },
abstract = {Bacterial communities play a crucial role in the biology, ecology, and evolution of multicellular organisms. In this research, the microbiome of 24 selected beetle species representing five families (Carabidae, Staphylinidae, Curculionidae, Chrysomelidae, Scarabaeidae) and three trophic guilds (carnivorous, herbivorous, detrivorous) was examined using 16S rDNA sequencing on the Illumina platform. The aim of the study was to compare diversity within and among species on various levels of organization, including evaluation of the impact of endosymbiotic bacteria. Collected data showed that beetles possess various bacterial communities and that microbiota of individuals of particular species hosts are intermixed. The most diverse microbiota were found in Carabidae and Scarabaeidae; the least diverse, in Staphylinidae. On higher organization levels, the diversity of bacteria was more dissimilar between families, while the most distinct with respect to their microbiomes were trophic guilds. Moreover, eight taxa of endosymbiotic bacteria were detected including common genera such as Wolbachia, Rickettsia, and Spiroplasma, as well as the rarely detected Cardinium, Arsenophonus, Buchnera, Sulcia, Regiella, and Serratia. There were no correlations among the abundance of the most common Wolbachia and Rickettsia; a finding that does not support the hypothesis that these bacteria occur interchangeably. The abundance of endosymbionts only weakly and negatively correlates with diversity of the whole microbiome in beetles. Overall, microbiome diversity was found to be more dependent on host phylogeny than on the abundance of endosymbionts. This is the first study in which bacteria diversity is compared between numerous species of beetles in a standardized manner.},
}

Animals
Bacteria/*classification
Bacterial Physiological Phenomena
Coleoptera/classification/*microbiology/*physiology
Feeding Behavior
Microbiota/*physiology
Phylogeny
*Symbiosis

@article {pmid30912879,
year = {2019},
author = {Aripovsky, AV and Titov, VN},
title = {[Biologocally active peptides in metabolism regulation. Peptons, peptides, amino acids, fatty acids, lipoproteins, lipids, and the effect of nutriceuticals.].},
journal = {Klinicheskaia laboratornaia diagnostika},
volume = {64},
number = {1},
pages = {14-23},
doi = {10.18821/0869-2084-2019-64-1-14-23},
pmid = {30912879},
issn = {0869-2084},
mesh = {Amino Acids ; Animals ; Dietary Proteins/metabolism ; *Dietary Supplements ; Fatty Acids ; Humans ; Lipids ; Lipoproteins ; Lysosomes ; Peptides/*metabolism ; Phylogeny ; Proteolysis ; },
abstract = {According to phylogenetic theory of general pathology, formation of multicellular organisms started when each cell (a unicellular organism) reached the first level of relative biological perfection. By that time the stimuli for perfection of the unicellular exhausted, and formation of the multicellular became a biological necessity. All cells, being associated, formed the second level of relative biological perfection within the principle of biological succession. The association included highly organized unicellular organisms with their specific autocrine biological functions and reactions. At the second level of relative biological perfection all humoral mediators in paracrine regulated cell communities (PC) and organs were predominantly hydrophilic and short living. They had a small molecular weight and were probably biologically active peptides (BAP). We believe that functional difference of PC and later of organs is based on differentiation of lysosomal function and production of various enzymes involved in proteolysis of dietary proteins. This allowed various PC and organs to form chemically and functionally different BAP pools from one protein upon proteolysis. Individual peptide pools in PC created the basis for morphologically and functionally different cells and organs. Cell that produces peptides can modify their concentration, chemical parameters and ratios by varying the selectivity of its proteases. In vivo regulation of metabolism by BAP has a common root in bacteria, plants and vertebrates, including Homo sapiens. The third level of relative biological perfection in the organism has formed in close association with cognitive biological function.},
}

Amino Acids
Animals
Dietary Proteins/metabolism
*Dietary Supplements
Fatty Acids
Humans
Lipids
Lipoproteins
Lysosomes
Peptides/*metabolism
Phylogeny
Proteolysis

@article {pmid30909510,
year = {2019},
author = {Moffitt, L and Karimnia, N and Stephens, A and Bilandzic, M},
title = {Therapeutic Targeting of Collective Invasion in Ovarian Cancer.},
journal = {International journal of molecular sciences},
volume = {20},
number = {6},
pages = {},
pmid = {30909510},
issn = {1422-0067},
mesh = {Animals ; Antineoplastic Agents/pharmacology/therapeutic use ; *Biomarkers, Tumor ; Clinical Studies as Topic ; Disease Management ; Drug Evaluation, Preclinical ; Female ; Humans ; *Molecular Targeted Therapy/methods ; Neoplasm Invasiveness ; Neoplasm Metastasis ; Neoplasm Staging ; Neoplastic Stem Cells/drug effects/metabolism/pathology ; Ovarian Neoplasms/*etiology/pathology/*therapy ; Standard of Care ; Treatment Outcome ; },
abstract = {Ovarian cancer is the seventh most commonly diagnosed cancer amongst women and has the highest mortality rate of all gynaecological malignancies. It is a heterogeneous disease attributed to one of three cell types found within the reproductive milieu: epithelial, stromal, and germ cell. Each histotype differs in etiology, pathogenesis, molecular biology, risk factors, and prognosis. Furthermore, the origin of ovarian cancer remains unclear, with ovarian involvement secondary to the contribution of other gynaecological tissues. Despite these complexities, the disease is often treated as a single entity, resulting in minimal improvement to survival rates since the introduction of platinum-based chemotherapy over 30 years ago. Despite concerted research efforts, ovarian cancer remains one of the most difficult cancers to detect and treat, which is in part due to the unique mode of its dissemination. Ovarian cancers tend to invade locally to neighbouring tissues by direct extension from the primary tumour, and passively to pelvic and distal organs within the peritoneal fluid or ascites as multicellular spheroids. Once at their target tissue, ovarian cancers, like most epithelial cancers including colorectal, melanoma, and breast, tend to invade as a cohesive unit in a process termed collective invasion, driven by specialized cells termed "leader cells". Emerging evidence implicates leader cells as essential drivers of collective invasion and metastasis, identifying collective invasion and leader cells as a viable target for the management of metastatic disease. However, the development of targeted therapies specifically against this process and this subset of cells is lacking. Here, we review our understanding of metastasis, collective invasion, and the role of leader cells in ovarian cancer. We will discuss emerging research into the development of novel therapies targeting collective invasion and the leader cell population.},
}

Animals
Antineoplastic Agents/pharmacology/therapeutic use
*Biomarkers, Tumor
Clinical Studies as Topic
Disease Management
Drug Evaluation, Preclinical
Female
Humans
*Molecular Targeted Therapy/methods
Neoplasm Invasiveness
Neoplasm Metastasis
Neoplasm Staging
Neoplastic Stem Cells/drug effects/metabolism/pathology
Ovarian Neoplasms/*etiology/pathology/*therapy
Standard of Care
Treatment Outcome