@article {pmid31302471,
year = {2019},
author = {Newman, SA},
title = {Inherency and homomorphy in the evolution of development.},
journal = {Current opinion in genetics & development},
volume = {57},
number = {},
pages = {1-8},
doi = {10.1016/j.gde.2019.05.006},
pmid = {31302471},
issn = {1879-0380},
abstract = {Organismal development occurs when expression of certain genes leads to the mobilization of physical forces and effects that shape and pattern multicellular clusters. All materials exhibit preferred forms, but the inherent morphological motifs of some, such as liquids and crystalline solids are well-characterized. Recent work has shown that the origin of the animals (Metazoa) was accompanied by the acquisition by their developing tissues of liquid-like and liquid-crystalline properties. This and the novel capacity to produce stiff internal substrata (basal laminae) set these organisms apart from their closest relatives by the propensity (predictable from their material nature) to form complex bodies and organs. Once functional forms became established, however, they were susceptible to further genetic change as well as partial or full supplanting of original physical determinants by different ones. This results in the increasingly recognized phenomenon of homomorphy, the presence of the same structure in descendent organisms, brought about by transformed developmental mechanisms.},
}

@article {pmid31295970,
year = {2019},
author = {Joukov, V and De Nicolo, A},
title = {The Centrosome and the Primary Cilium: The Yin and Yang of a Hybrid Organelle.},
journal = {Cells},
volume = {8},
number = {7},
pages = {},
doi = {10.3390/cells8070701},
pmid = {31295970},
issn = {2073-4409},
abstract = {Centrosomes and primary cilia are usually considered as distinct organelles, although both are assembled with the same evolutionary conserved, microtubule-based templates, the centrioles. Centrosomes serve as major microtubule- and actin cytoskeleton-organizing centers and are involved in a variety of intracellular processes, whereas primary cilia receive and transduce environmental signals to elicit cellular and organismal responses. Understanding the functional relationship between centrosomes and primary cilia is important because defects in both structures have been implicated in various diseases, including cancer. Here, we discuss evidence that the animal centrosome evolved, with the transition to complex multicellularity, as a hybrid organelle comprised of the two distinct, but intertwined, structural-functional modules: the centriole/primary cilium module and the pericentriolar material/centrosome module. The evolution of the former module may have been caused by the expanding cellular diversification and intercommunication, whereas that of the latter module may have been driven by the increasing complexity of mitosis and the requirement for maintaining cell polarity, individuation, and adhesion. Through its unique ability to serve both as a plasma membrane-associated primary cilium organizer and a juxtanuclear microtubule-organizing center, the animal centrosome has become an ideal integrator of extracellular and intracellular signals with the cytoskeleton and a switch between the non-cell autonomous and the cell-autonomous signaling modes. In light of this hypothesis, we discuss centrosome dynamics during cell proliferation, migration, and differentiation and propose a model of centrosome-driven microtubule assembly in mitotic and interphase cells. In addition, we outline the evolutionary benefits of the animal centrosome and highlight the hierarchy and modularity of the centrosome biogenesis networks.},
}

@article {pmid31291955,
year = {2019},
author = {Yang, YJ and Singh, RP and Lan, X and Zhang, CS and Sheng, DH and Li, YQ},
title = {Whole transcriptome analysis and gene deletion to understand the chloramphenicol resistance mechanism and develop a screening method for homologous recombination in Myxococcus xanthus.},
journal = {Microbial cell factories},
volume = {18},
number = {1},
pages = {123},
doi = {10.1186/s12934-019-1172-3},
pmid = {31291955},
issn = {1475-2859},
support = {ASTIP-TRIC07//Agricultural Science and Technology Innovation Program of China/ ; },
abstract = {BACKGROUND: Myxococcus xanthus DK1622 is a model system for studying multicellular development, predation, cellular differentiation, and evolution. Furthermore, it is a rich source of novel secondary metabolites and is widely used as heterologous expression host of exogenous biosynthetic gene clusters. For decades, genetic modification of M. xanthus DK1622 has mainly relied on kanamycin and tetracycline selection systems.

RESULTS: Here, we introduce an alternative selection system based on chloramphenicol (Cm) to broaden the spectrum of available molecular tools. A chloramphenicol-resistant growth phase and a chloramphenicol-susceptible growth phase before and after chloramphenicol-induction were prepared, and later sequenced to identify specific genes related to chloramphenicol-repercussion and drug-resistance. A total of 481 differentially expressed genes were revealed in chloramphenicol-resistant Cm5_36h and 1920 differentially expressed genes in chloramphenicol-dormant Cm_8h. Moreover, the gene expression profile in the chloramphenicol-dormant strain Cm_8h was quite different from that of Cm5_36 which had completely adapted to Cm, and 1513 differentially expression genes were identified between these two phenotypes. Besides upregulated acetyltransferases, several transporter encoding genes, including ABC transporters, major facilitator superfamily transporters (MFS), resistance-nodulation-cell division (RND) super family transporters and multidrug and toxic compound extrusion family transporters (MATE) were found to be involved in Cm resistance. After the knockout of the most highly upregulated MXAN_2566 MFS family gene, mutant strain DK-2566 was proved to be sensitive to Cm by measuring the growth curve in the Cm-added condition. A plasmid with a Cm resistance marker was constructed and integrated into chromosomes via homologous recombination and Cm screening. The integration efficiency was about 20% at different concentrations of Cm.

CONCLUSIONS: This study provides a new antibiotic-based selection system, and will help to understand antibiotic resistance mechanisms in M. xanthus DK1622.},
}

@article {pmid31286803,
year = {2019},
author = {Rezaei-Lotfi, S and Hunter, N and Farahani, RM},
title = {Coupled cycling programs multicellular self-organization of neural progenitors.},
journal = {Cell cycle (Georgetown, Tex.)},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/15384101.2019.1638692},
pmid = {31286803},
issn = {1551-4005},
abstract = {Self-organization is central to the morphogenesis of multicellular organisms. However, the molecular platform that coordinates the robust emergence of complex morphological patterns from local interactions between cells remains unresolved. Here we demonstrate that neural self- organization is driven by coupled cycling of progenitor cells. In a coupled cycling mode, intercellular contacts relay extrinsic cues to override the intrinsic cycling rhythm of an individual cell and synchronize the population. The stringency of coupling and hence the synchronicity of the population is programmed by recruitment of a key coupler, β-catenin, into junctional complexes. As such, multicellular self-organization is driven by the same basic mathematical principle that governs synchronized behavior of macro-scale biological systems as diverse as the synchronized chirping of crickets, flashing of fireflies and schooling of fish; that is synchronization by coupling. It is proposed that coupled cycling foreshadows a fundamental adaptive change that facilitated evolution and diversification of multicellular life forms.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1038/s41559-019-0940-0},
pmid = {31285576},
issn = {2397-334X},
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.},
}

@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 = {},
number = {},
pages = {1-16},
doi = {10.1080/1040841X.2019.1630359},
pmid = {31267819},
issn = {1549-7828},
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.},
}

@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},
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.},
}

@article {pmid31246972,
year = {2019},
author = {Aufrecht, JA and Fowlkes, JD and Bible, AN and Morrell-Falvey, J and Doktycz, MJ and Retterer, ST},
title = {Pore-scale hydrodynamics influence the spatial evolution of bacterial biofilms in a microfluidic porous network.},
journal = {PloS one},
volume = {14},
number = {6},
pages = {e0218316},
doi = {10.1371/journal.pone.0218316},
pmid = {31246972},
issn = {1932-6203},
abstract = {Bacteria occupy heterogeneous environments, attaching and growing within pores in materials, living hosts, and matrices like soil. Systems that permit high-resolution visualization of dynamic bacterial processes within the physical confines of a realistic and tractable porous media environment are rare. Here we use microfluidics to replicate the grain shape and packing density of natural sands in a 2D platform to study the flow-induced spatial evolution of bacterial biofilms underground. We discover that initial bacterial dispersal and grain attachment is influenced by bacterial transport across pore space velocity gradients, a phenomenon otherwise known as rheotaxis. We find that gravity-driven flow conditions activate different bacterial cell-clustering phenotypes depending on the strain's ability to product extracellular polymeric substances (EPS). A wildtype, biofilm-producing bacteria formed compact, multicellular patches while an EPS-defective mutant displayed a linked-cell phenotype in the presence of flow. These phenotypes subsequently influenced the overall spatial distribution of cells across the porous media network as colonies grew and altered the fluid dynamics of their microenvironment.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1038/s41559-019-0907-1},
pmid = {31239554},
issn = {2397-334X},
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.},
}

@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},
doi = {10.1155/2019/7853586},
pmid = {31236128},
issn = {1748-6718},
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.},
}

@article {pmid31227860,
year = {2019},
author = {Tian, L and Zhang, B and Zhang, J and Zhang, T and Cai, Y and Qin, H and Metzner, W and Pan, Y},
title = {A magnetic compass guides the direction of foraging in a bat.},
journal = {Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00359-019-01353-1},
pmid = {31227860},
issn = {1432-1351},
support = {41674071//National Natural Science Foundation of China/ ; 41621004//National Natural Science Foundation of China/ ; QYZDJ-SSW-DQC024//the Chinese Academy of Sciences project/ ; },
abstract = {Previously, two studies have provided evidence that bats can use magnetic field cues for homing or roosting. For insectivorous bats, it is well established that foraging represents one of the most fundamental behaviors in animals relies on their ability to echolocate. Whether echolocating bats can also use magnetic cues during foraging remains unknown, however. Here, we tested the orientation behavior of Chinese noctules (Nyctalus plancyi) during foraging in a plus-shaped, 4-channel apparatus under different magnetic field conditions. To minimize the effects of spatial memory on orientation from repeated experiments, naïve bats were tested only once in each experimental condition. As expected, under geomagnetic field and a food resource offered conditions, the bats significantly preferred to enter the channel containing food, indicating that they primarily relied on direct sensory signals unrelated to magnetic cues. In contrast, when we offered food simultaneously in all four channels and minimized any differences in all other sensory signals available, the bats exhibited a clear directional preference to forage along the magnetic field direction under either geomagnetic field or a magnetic field in which the horizontal component was rotated by 90°. Our study offers a novel evidence for the importance of a geomagnetic field during foraging.},
}

@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},
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.},
}

@article {pmid31209997,
year = {2019},
author = {Bonner, JT},
title = {The evolution of evolution.},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.b.22859},
pmid = {31209997},
issn = {1552-5015},
abstract = {In the past, most biologists, myself included, did not think of evolution as changing over time. The wonders of natural selection were always at hand and went into operation once there was life. However, with a little reflection it becomes obvious that evolution has changed-there has been an evolution of evolution. Evolution can be separated into four phases, or eras, that may or may not overlap. The first era starts with the evolution of life on earth, which led to single cells that multiply asexually. The second era takes advantage of the invention of sexual reproduction as evolution could now gallop forward because of a richer fare of diverse offspring for natural selection. The third era begins with the introduction of multicellularity. In the fourth era there is a radical innovation: the nervous system that arises animals by standard Darwinian selection. This has allowed major rapid changes to proceed, such as language that led to all the rapid progress we call civilization; a true revolution, and one that does not depend on the slow genetic changes of all other standard gene-controlled evolutionary steps.},
}

@article {pmid30668717,
year = {2019},
author = {Belato, FA and Schrago, CG and Coates, CJ and Halanych, KM and Costa-Paiva, EM},
title = {Newly Discovered Occurrences and Gene Tree of the Extracellular Globins and Linker Chains from the Giant Hexagonal Bilayer Hemoglobin in Metazoans.},
journal = {Genome biology and evolution},
volume = {11},
number = {3},
pages = {597-612},
doi = {10.1093/gbe/evz012},
pmid = {30668717},
issn = {1759-6653},
mesh = {Animals ; Globins/*genetics ; Invertebrates/*genetics ; *Phylogeny ; },
abstract = {Multicellular organisms depend on oxygen-carrying proteins to transport oxygen throughout the body; therefore, proteins such as hemoglobins (Hbs), hemocyanins, and hemerythrins are essential for maintenance of tissues and cellular respiration. Vertebrate Hbs are among the most extensively studied proteins; however, much less is known about invertebrate Hbs. Recent studies of hemocyanins and hemerythrins have demonstrated that they have much wider distributions than previously thought, suggesting that oxygen-binding protein diversity is underestimated across metazoans. Hexagonal bilayer hemoglobin (HBL-Hb), a blood pigment found exclusively in annelids, is a polymer comprised up to 144 extracellular globins and 36 linker chains. To further understand the evolutionary history of this protein complex, we explored the diversity of linkers and extracellular globins from HBL-Hbs using in silico approaches on 319 metazoan and one choanoflagellate transcriptomes. We found 559 extracellular globin and 414 linker genes transcribed in 171 species from ten animal phyla with new records in Echinodermata, Hemichordata, Brachiopoda, Mollusca, Nemertea, Bryozoa, Phoronida, Platyhelminthes, and Priapulida. Contrary to previous suggestions that linkers and extracellular globins emerged in the annelid ancestor, our findings indicate that they have putatively emerged before the protostome-deuterostome split. For the first time, we unveiled the comprehensive evolutionary history of metazoan HBL-Hb components, which consists of multiple episodes of gene gains and losses. Moreover, because our study design surveyed linkers and extracellular globins independently, we were able to cross-validate our results, significantly reducing the rate of false positives. We confirmed that the distribution of HBL-Hb components has until now been underestimated among animals.},
}

Animals
Globins/*genetics
Invertebrates/*genetics
*Phylogeny

@article {pmid31196608,
year = {2019},
author = {Pirkmajer, S and Chibalin, AV},
title = {Hormonal regulation of Na+-K+-ATPase from the evolutionary perspective.},
journal = {Current topics in membranes},
volume = {83},
number = {},
pages = {315-351},
doi = {10.1016/bs.ctm.2019.01.009},
pmid = {31196608},
issn = {1063-5823},
abstract = {Na+-K+-ATPase, an α/β heterodimer, is an ancient enzyme that maintains Na+ and K+ gradients, thus preserving cellular ion homeostasis. In multicellular organisms, this basic housekeeping function is integrated to fulfill the needs of specialized organs and preserve whole-body homeostasis. In vertebrates, Na+-K+-ATPase is essential for many fundamental physiological processes, such as nerve conduction, muscle contraction, nutrient absorption, and urine excretion. During vertebrate evolution, three key developments contributed to diversification and integration of Na+-K+-ATPase functions. Generation of novel α- and β-subunits led to formation of multiple Na+-K+-ATPase isoenyzmes with distinct functional characteristics. Development of a complex endocrine system enabled efficient coordination of diverse Na+-K+-ATPase functions. Emergence of FXYDs, small transmembrane proteins that regulate Na+-K+-ATPase, opened new ways to modulate its function. FXYDs are a vertebrate innovation and an important site of hormonal action, suggesting they played an especially prominent role in evolving interaction between Na+-K+-ATPase and the endocrine system in vertebrates.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1038/s41586-019-1290-4},
pmid = {31189954},
issn = {1476-4687},
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.},
}

@article {pmid31187926,
year = {2019},
author = {Qian, XX and Santini, CL and Kosta, A and Menguy, N and Le Guenno, H and Zhang, W and Li, J and Chen, YR and Liu, J and Alberto, F and Espinosa, L and Xiao, T and Wu, LF},
title = {Juxtaposed membranes underpin cellular adhesion and display unilateral cell division of multicellular magnetotactic prokaryotes.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14710},
pmid = {31187926},
issn = {1462-2920},
abstract = {Multicellular magnetotactic prokaryotes (MMPs) exhibit peculiar coordination of swimming along geomagnetic field lines. Approximate 40-80 cells assemble, with a helical geometry or axisymmetry, into spherical or ellipsoidal MMPs, respectively. To contribute to a comprehensive understanding of bacterial multicellularity here we took multiple microscopic approaches to study the diversity, assembly, reproduction and motility of ellipsoidal MMPs. Using correlative fluorescence in situ hybridization and scanning electron microscopy analysis, we found an unexpected diversity in populations of ellipsoidal MMPs in the Mediterranean Sea. The high-pressure freezing/freeze substitution fixation technique allowed us to show, for the first time, that cells adhere via juxtaposed membranes and are held together by a rimming lattice. Fluorescence confocal microscopy and ultra-thin section images revealed not only the one-layer hollow three-dimensional architecture, but also periphery-core unilateral constriction of constituent cells and unidirectional binary fission of the ellipsoidal MMPs. This finding suggests the evolution toward MMPs multicellularity via the mechanism of incomplete separation of offspring. Remarkably, thousands of flagellar at the periphery surface of cells underpin the coordinated swimming of MMPs in response to mechanical, chemical, magnetic and optical stimuli, including a magnetotactic photokinesis behavior. Together these results unveil the unique structure and function property of ellipsoidal MMPs. This article is protected by copyright. All rights reserved.},
}

@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},
doi = {10.1186/s12862-019-1452-x},
pmid = {31185890},
issn = {1471-2148},
support = {17J03439//Japan Society for the Promotion of Science/ ; 16H02518//Japan Society for the Promotion of Science/ ; },
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).},
}

@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},
doi = {10.1371/journal.pcbi.1007053},
pmid = {31185009},
issn = {1553-7358},
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.},
}

@article {pmid31183520,
year = {2019},
author = {Chaplain, MAJ and Lorenzi, T and Macfarlane, FR},
title = {Bridging the gap between individual-based and continuum models of growing cell populations.},
journal = {Journal of mathematical biology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00285-019-01391-y},
pmid = {31183520},
issn = {1432-1416},
support = {EP/N014642/1//Engineering and Physical Sciences Research Council/ ; },
abstract = {Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations that describe the evolution of cellular densities in response to pressure gradients generated by population growth. Little prior work has explored the relation between such continuum models and related single-cell-based models. We present here a simple stochastic individual-based model for the spatial dynamics of multicellular systems whereby cells undergo pressure-driven movement and pressure-dependent proliferation. We show that nonlinear partial differential equations commonly used to model the spatial dynamics of growing cell populations can be formally derived from the branching random walk that underlies our discrete model. Moreover, we carry out a systematic comparison between the individual-based model and its continuum counterparts, both in the case of one single cell population and in the case of multiple cell populations with different biophysical properties. The outcomes of our comparative study demonstrate that the results of computational simulations of the individual-based model faithfully mirror the qualitative and quantitative properties of the solutions to the corresponding nonlinear partial differential equations. Ultimately, these results illustrate how the simple rules governing the dynamics of single cells in our individual-based model can lead to the emergence of complex spatial patterns of population growth observed in continuum models.},
}

@article {pmid31175188,
year = {2019},
author = {Kees, ED and Pendleton, AR and Paquete, CM and Arriola, MB and Kane, AL and Kotloski, NJ and Intile, PJ and Gralnick, JA},
title = {On the Cost and Role of Secreted Flavin Cofactors for Anaerobic Respiration of Fumarate and Urocanate by Shewanella oneidensis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.00852-19},
pmid = {31175188},
issn = {1098-5336},
abstract = {Shewanella oneidensis strain MR-1, a facultative anaerobe and model organism for dissimilatory metal reduction, uses a periplasmic flavocytochrome, FccA, as both a terminal fumarate reductase and as a periplasmic electron transfer hub for extracellular respiration of a variety of substrates. It is currently unclear how maturation of FccA and other periplasmic flavoproteins is achieved, specifically in the context of flavin cofactor loading nor has the fitness cost of flavin secretion been quantified. We demonstrate that deletion of the inner membrane flavin adenine dinucleotide (FAD) exporter Bfe results in a 23% slower growth rate than wild-type during fumarate respiration, and an 80-90% loss in fumarate reductase activity. Exogenous flavin supplementation does not restore FccA activity in a Δbfe mutant unless the gene encoding the periplasmic FAD hydrolase UshA is also deleted. We demonstrate that the small Bfe-independent pool of FccA is sufficient for anaerobic growth with fumarate. Strains lacking Bfe were unable to grow using urocanate as the sole electron acceptor, which relies on the periplasmic flavoprotein UrdA. We show that periplasmic flavoprotein maturation occurs in careful balance with periplasmic FAD hydrolysis, and that the current model for periplasmic flavin cofactor loading must account for a Bfe-independent mechanism for flavin transport. Finally, we determine that the metabolic burden of flavin secretion is not significant during growth with flavin-independent anaerobic electron acceptors. Our work helps frame the physiological motivations that drove evolution of flavin secretion by ShewanellaImportanceShewanella species are prevalent in marine and aquatic environments, throughout stratified water columns, mineral rich sediments and in association with multicellular marine and aquatic organisms. The diversity of niches Shewanellae can occupy are due largely to their respiratory versatility. Shewanella oneidensis is a model organism for dissimilatory metal reduction and can respire a diverse array of organic and inorganic compounds including dissolved and solid metal oxides. The fumarate reductase FccA is a highly abundant multifunctional periplasmic protein that acts to bridge the periplasm and temporarily store electrons in a variety of respiratory nodes including metal, nitrate and dimethyl sulfoxide respiration. However, maturation of this central protein, particularly flavin cofactor acquisition, is poorly understood. Here we quantify the fitness cost of flavin secretion and describe how free flavins are acquired by FccA and a homologous periplasmic flavoprotein UrdA.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1093/intbio/zyz012},
pmid = {31172192},
issn = {1757-9708},
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.},
}

@article {pmid31171786,
year = {2019},
author = {Rossy, T and Nadell, CD and Persat, A},
title = {Cellular advective-diffusion drives the emergence of bacterial surface colonization patterns and heterogeneity.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {2471},
doi = {10.1038/s41467-019-10469-6},
pmid = {31171786},
issn = {2041-1723},
support = {31003A_169377//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/International ; 31003A_169377//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/International ; MCB 1817342//National Science Foundation (NSF)/International ; STANTO15RO//Cystic Fibrosis Foundation (CF Foundation)/International ; P20-GM113132//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/International ; },
abstract = {Microorganisms navigate and divide on surfaces to form multicellular structures called biofilms, the most widespread survival strategy found in the bacterial world. One common assumption is that cellular components guide the spatial architecture and arrangement of multiple species in a biofilm. However, bacteria must contend with mechanical forces generated through contact with surfaces and under fluid flow, whose contributions to colonization patterns are poorly understood. Here, we show how the balance between motility and flow promotes the emergence of morphological patterns in Caulobacter crescentus biofilms. By modeling transport of single cells by flow and Brownian-like swimming, we show that the emergence of these patterns is guided by an effective Péclet number. By analogy with transport phenomena we show that, counter-intuitively, fluid flow represses mixing of distinct clonal lineages, thereby affecting the interaction landscapes between biofilm-dwelling bacteria. This demonstrates that hydrodynamics influence species interaction and evolution within surface-associated communities.},
}

@article {pmid31170405,
year = {2019},
author = {Edgar, JA},
title = {L-Ascorbic Acid and the Evolution of Multicellular Eukaryotes.},
journal = {Journal of theoretical biology},
volume = {},
number = {},
pages = {},
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},
doi = {10.1371/journal.pbio.3000275},
pmid = {31170137},
issn = {1545-7885},
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.},
}

@article {pmid31169232,
year = {2019},
author = {Siddiqui, S and Singh, A and Faizi, N and Khalid, A},
title = {Cell cannibalism in oral cancer: A sign of aggressiveness, de-evolution, and retroversion of multicellularity.},
journal = {Journal of cancer research and therapeutics},
volume = {15},
number = {3},
pages = {631-637},
doi = {10.4103/jcrt.JCRT_504_17},
pmid = {31169232},
issn = {1998-4138},
abstract = {Background: According to Darwin's theory of evolution, complex creatures evolve from more simplistic ancestors. Dollo's law of irreversibility states that evolution is irreversible. However, cancer cells tend to follow anti-Dollo's law. Unfavorable conditions such as hypoxia, acidic pH and low nutrients cause the cancer cells to switch their lifestyle atavistically in order to survive. They start behaving like a unicellular organism. There is a switch from normal metabolism to Warburg effect and finally cannibalism. Cannibalism is a cell eating cell phenomenon. It is defined as a large cell enclosing a smaller one within its cytoplasm and is known by odd names such as "bird's eye cells" or "signet ring cells." Smaller tumor cells are found in the cytoplasm of larger tumor cells with crescent-shaped nucleus. Cannibalistic cells (CCs) are a feature of aggressive tumors. These cell types are vulnerable to metastasis.

Aim: The aim of this study is to identify CCs in various histological grades of oral squamous cell carcinoma (OSCC) and to relate them with the pattern of invasion, lymphocytic response (LR), and mitotic figures (Mfs). The purpose of the article is to establish it as a marker of aggressiveness and metastasis and as an evidence of de-evolution and retroversion of multicellularity.

Materials and Methods: Sixty-five histologically confirmed cases of OSCC were studied. Pattern of invasion, LR, number of CCs, and Mfs were recorded on 5 μ hematoxylin and eosin-stained tissue sections. ANOVA and t-test were applied; P < 0.05 was considered statistically significant.

Results: CCs were more in sections with patchy LR, increased Mfs, and grade IV pattern of invasion.

Conclusion: With increase in dedifferentiation, tumor cells start behaving like unicellular organisms with cell eating cell characteristics.},
}

@article {pmid31163162,
year = {2019},
author = {Ostrowski, EA},
title = {Enforcing Cooperation in the Social Amoebae.},
journal = {Current biology : CB},
volume = {29},
number = {11},
pages = {R474-R484},
doi = {10.1016/j.cub.2019.04.022},
pmid = {31163162},
issn = {1879-0445},
abstract = {Cooperation has been essential to the evolution of biological complexity, but many societies struggle to overcome internal conflicts and divisions. Dictyostelium discoideum, or the social amoeba, has been a useful model system for exploring these conflicts and how they can be resolved. When starved, these cells communicate, gather into groups, and build themselves into a multicellular fruiting body. Some cells altruistically die to form the rigid stalk, while the remainder sit atop the stalk, become spores, and disperse. Evolutionary theory predicts that conflict will arise over which cells die to form the stalk and which cells become spores and survive. The power of the social amoeba lies in the ability to explore how cooperation and conflict work across multiple levels, ranging from proximate mechanisms (how does it work?) to ultimate evolutionary answers (why does it work?). Recent studies point to solutions to the problem of ensuring fairness, such as the ability to suppress selfishness and to recognize and avoid unrelated individuals. This work confirms a central role for kin selection, but also suggests new explanations for how social amoebae might enforce cooperation. New approaches based on genomics are also enabling researchers to decipher for the first time the evolutionary history of cooperation and conflict and to determine its role in shaping the biology of multicellular organisms.},
}

@article {pmid31163154,
year = {2019},
author = {Smith, P and Schuster, M},
title = {Public goods and cheating in microbes.},
journal = {Current biology : CB},
volume = {29},
number = {11},
pages = {R442-R447},
doi = {10.1016/j.cub.2019.03.001},
pmid = {31163154},
issn = {1879-0445},
abstract = {Communication and cooperation are not restricted to complex, higher organisms. Microbes, too, perform a variety of collective, multicellular behaviors, including biofilm formation, quorum sensing, nutrient acquisition, and dispersal. The products of these microbial cooperative behaviors are generally referred to as public goods. Here we describe the nature of microbial public goods, the associated problem of cheating, and ways in which microbes maintain public goods in the face of cheating. We highlight work in a growing field at the interface of microbiology, evolution, and ecology that combines multiple approaches in experimental evolution, genetics, and mathematical modeling.},
}

@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 {pmid31150287,
year = {2019},
author = {Moreno, MA and Ofria, C},
title = {Toward Open-Ended Fraternal Transitions in Individuality.},
journal = {Artificial life},
volume = {25},
number = {2},
pages = {117-133},
doi = {10.1162/artl_a_00284},
pmid = {31150287},
issn = {1530-9185},
abstract = {The emergence of new replicating entities from the union of simpler entities characterizes some of the most profound events in natural evolutionary history. Such transitions in individuality are essential to the evolution of the most complex forms of life. Thus, understanding these transitions is critical to building artificial systems capable of open-ended evolution. Alas, these transitions are challenging to induce or detect, even with computational organisms. Here, we introduce the DISHTINY (Distributed Hierarchical Transitions in Individuality) platform, which provides simple cell-like organisms with the ability and incentive to unite into new individuals in a manner that can continue to scale to subsequent transitions. The system is designed to encourage these transitions so that they can be studied: Organisms that coordinate spatiotemporally can maximize the rate of resource harvest, which is closely linked to their reproductive ability. We demonstrate the hierarchical emergence of multiple levels of individuality among simple cell-like organisms that evolve parameters for manually designed strategies. During evolution, we observe reproductive division of labor and close cooperation among cells, including resource-sharing, aggregation of resource endowments for propagules, and emergence of an apoptosis response to somatic mutation. Many replicate populations evolved to direct their resources toward low-level groups (behaving like multicellular individuals), and many others evolved to direct their resources toward high-level groups (acting as larger-scale multicellular individuals).},
}

@article {pmid31142622,
year = {2019},
author = {Sweeney, EG and Nishida, A and Weston, A and Bañuelos, MS and Potter, K and Conery, J and Guillemin, K},
title = {Agent-Based Modeling Demonstrates How Local Chemotactic Behavior Can Shape Biofilm Architecture.},
journal = {mSphere},
volume = {4},
number = {3},
pages = {},
doi = {10.1128/mSphere.00285-19},
pmid = {31142622},
issn = {2379-5042},
abstract = {Bacteria are often found living in aggregated multicellular communities known as biofilms. Biofilms are three-dimensional structures that confer distinct physical and biological properties to the collective of cells living within them. We used agent-based modeling to explore whether local cellular interactions were sufficient to give rise to global structural features of biofilms. Specifically, we asked whether chemorepulsion from a self-produced quorum-sensing molecule, autoinducer-2 (AI-2), was sufficient to recapitulate biofilm growth and cellular organization observed for biofilms of Helicobacter pylori, a common bacterial resident of human stomachs. To carry out this modeling, we modified an existing platform, Individual-based Dynamics of Microbial Communities Simulator (iDynoMiCS), to incorporate three-dimensional chemotaxis, planktonic cells that could join or leave the biofilm structure, and cellular production of AI-2. We simulated biofilm growth of previously characterized H. pylori strains with various AI-2 production and sensing capacities. Using biologically plausible parameters, we were able to recapitulate both the variation in biofilm mass and cellular distributions observed with these strains. Specifically, the strains that were competent to chemotax away from AI-2 produced smaller and more heterogeneously spaced biofilms, whereas the AI-2 chemotaxis-defective strains produced larger and more homogeneously spaced biofilms. The model also provided new insights into the cellular demographics contributing to the biofilm patterning of each strain. Our analysis supports the idea that cellular interactions at small spatial and temporal scales are sufficient to give rise to larger-scale emergent properties of biofilms.IMPORTANCE Most bacteria exist in aggregated, three-dimensional structures called biofilms. Although biofilms play important ecological roles in natural and engineered settings, they can also pose societal problems, for example, when they grow in plumbing systems or on medical implants. Understanding the processes that promote the growth and disassembly of biofilms could lead to better strategies to manage these structures. We had previously shown that Helicobacter pylori bacteria are repulsed by high concentrations of a self-produced molecule, AI-2, and that H. pylori mutants deficient in AI-2 sensing form larger and more homogeneously spaced biofilms. Here, we used computer simulations of biofilm formation to show that local H. pylori behavior of repulsion from high AI-2 could explain the overall architecture of H. pylori biofilms. Our findings demonstrate that it is possible to change global biofilm organization by manipulating local cell behaviors, which suggests that simple strategies targeting cells at local scales could be useful for controlling biofilms in industrial and medical settings.},
}

@article {pmid31118944,
year = {2019},
author = {Liu, T and Wang, X and Wang, G and Jia, S and Liu, G and Shan, G and Chi, S and Zhang, J and Yu, Y and Xue, T and Yu, J},
title = {Evolution of Complex Thallus Alga: Genome Sequencing of Saccharina japonica.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {378},
doi = {10.3389/fgene.2019.00378},
pmid = {31118944},
issn = {1664-8021},
abstract = {Saccharina, as one of the most important brown algae (Phaeophyceae) with multicellular thallus, has a very remarkable evolutionary history, and globally accounts for most of the economic marine aquaculture production worldwide. Here, we present the 580.5 million base pairs of genome sequence of Saccharina japonica, whose current assembly contains 35,725 protein-coding genes. In a comparative analysis with Ectocarpus siliculosus, the integrated virus sequence suggested the genome evolutionary footprints, which derived from their co-ancestry and experienced genomic arrangements. Furthermore, the gene expansion was found to be an important strategy for functional evolution, especially with regard to extracelluar components, stress-related genes, and vanadium-dependent haloperoxidases, and we proposed a hypothesis that gene duplication events were the main driving force for the evolution history from multicellular filamentous algae to thallus algae. The sequenced Saccharina genome paves the way for further molecular studies and is useful for genome-assisted breeding of S. japonica and other related algae species.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1038/s41586-019-1217-0},
pmid = {31118507},
issn = {1476-4687},
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.},
}

@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},
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.},
}

@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},
doi = {10.1371/journal.pone.0215946},
pmid = {31095603},
issn = {1932-6203},
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.},
}

@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},
doi = {10.1098/rsif.2019.0054},
pmid = {31088261},
issn = {1742-5662},
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.},
}

@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},
doi = {10.1371/journal.pcbi.1006987},
pmid = {31086369},
issn = {1553-7358},
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.},
}

@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},
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.},
}

@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},
doi = {10.1038/s42003-019-0417-3},
pmid = {31069269},
issn = {2399-3642},
abstract = {The multiplicity of cell types comprising multicellular organisms begs the question as to how cell type identities evolve over time. Cell type phylogenetics informs this question by comparing gene expression of homologous cell types in distantly related taxa. We employ this approach to inform the identity of larval skeletogenic cells of echinoderms, a clade for which there are phylogenetically diverse datasets of spatial gene expression patterns. We determined ancestral spatial expression patterns of alx1, ets1, tbr, erg, and vegfr, key components of the skeletogenic gene regulatory network driving identity of the larval skeletogenic cell. Here we show ancestral state reconstructions of spatial gene expression of extant eleutherozoan echinoderms support homology and common ancestry of echinoderm larval skeletogenic cells. We propose larval skeletogenic cells arose in the stem lineage of eleutherozoans during a cell type duplication event that heterochronically activated adult skeletogenic cells in a topographically distinct tissue in early development.},
}

@article {pmid31069245,
year = {2018},
author = {Wang, P and Liang, J and Shi, LZ and Wang, Y and Zhang, P and Ouyang, M and Preece, D and Peng, Q and Shao, L and Fan, J and Sun, J and Li, SS and Berns, MW and Zhao, H and Wang, Y},
title = {Visualizing Spatiotemporal Dynamics of Intercellular Mechanotransmission upon Wounding.},
journal = {ACS photonics},
volume = {5},
number = {9},
pages = {3565-3574},
doi = {10.1021/acsphotonics.8b00383},
pmid = {31069245},
issn = {2330-4022},
support = {R01 GM126016/GM/NIGMS NIH HHS/United States ; R01 GM125379/GM/NIGMS NIH HHS/United States ; R33 CA204704/CA/NCI NIH HHS/United States ; R01 HL121365/HL/NHLBI NIH HHS/United States ; R21 CA209629/CA/NCI NIH HHS/United States ; },
abstract = {During cell-to-cell communications, the interplay between physical and biochemical cues is essential for informational exchange and functional coordination, especially in multicellular organisms. However, it remains a challenge to visualize intercellular signaling dynamics in single live cells. Here, we report a photonic approach, based on laser microscissors and Förster resonance energy transfer (FRET) microscopy, to study intercellular signaling transmission. First, using our high-throughput screening platform, we developed a highly sensitive FRET-based biosensor (SCAGE) for Src kinase, a key regulator of intercellular interactions and signaling cascades. Notably, SCAGE showed a more than 40-fold sensitivity enhancement than the original biosensor in live mammalian cells. Next, upon local severance of physical intercellular connections by femtosecond laser pulses, SCAGE enabled the visualization of a transient Src activation across neighboring cells. Lastly, we found that this observed transient Src activation following the loss of cell-cell contacts depends on the passive structural support of cytoskeleton but not on the active actomyosin contractility. Hence, by precisely introducing local physical perturbations and directly visualizing spatiotemporal transmission of ensuing signaling events, our integrated approach could be broadly applied to mimic and investigate the wounding process at single-cell resolutions. This integrated approach with highly sensitive FRET-based biosensors provides a unique system to advance our in-depth understanding of molecular mechanisms underlying the physical-biochemical basis of intercellular coupling and wounding processes.},
}

@article {pmid31062469,
year = {2019},
author = {Turan, ZG and Parvizi, P and Dönertaş, HM and Tung, J and Khaitovich, P and Somel, M},
title = {Molecular footprint of Medawar's mutation accumulation process in mammalian aging.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e12965},
doi = {10.1111/acel.12965},
pmid = {31062469},
issn = {1474-9726},
support = {//Science Academy/ ; 114C040//Scientific and Technological Research Council of Turkey/ ; 215Z495//Scientific and Technological Research Council of Turkey/ ; //Middle East Technical University (METU)/ ; },
abstract = {Medawar's mutation accumulation hypothesis explains aging by the declining force of natural selection with age: Slightly deleterious germline mutations expressed in old age can drift to fixation and thereby lead to aging-related phenotypes. Although widely cited, empirical evidence for this hypothesis has remained limited. Here, we test one of its predictions that genes relatively highly expressed in old adults should be under weaker purifying selection than genes relatively highly expressed in young adults. Combining 66 transcriptome datasets (including 16 tissues from five mammalian species) with sequence conservation estimates across mammals, here we report that the overall conservation level of expressed genes is lower at old age compared to young adulthood. This age-related decrease in transcriptome conservation (ADICT) is systematically observed in diverse mammalian tissues, including the brain, liver, lung, and artery, but not in others, most notably in the muscle and heart. Where observed, ADICT is driven partly by poorly conserved genes being up-regulated during aging. In general, the more often a gene is found up-regulated with age among tissues and species, the lower its evolutionary conservation. Poorly conserved and up-regulated genes have overlapping functional properties that include responses to age-associated tissue damage, such as apoptosis and inflammation. Meanwhile, these genes do not appear to be under positive selection. Hence, genes contributing to old age phenotypes are found to harbor an excess of slightly deleterious alleles, at least in certain tissues. This supports the notion that genetic drift shapes aging in multicellular organisms, consistent with Medawar's mutation accumulation hypothesis.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1111/mec.15117},
pmid = {31055860},
issn = {1365-294X},
abstract = {Recent studies show that soil eukaryotic diversity is immense and dominated by microorganisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to microorganisms. 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 phylogeographic 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 habitat. 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 habitat. 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 microorganisms, propagule dispersal is slow enough that historical processes may contribute to their diversification and phylogeographic patterns and may partly explain their very high overall diversity. This article is protected by copyright. All rights reserved.},
}

@article {pmid31053584,
year = {2019},
author = {Li, J and Zhang, H and Liu, P and Menguy, N and Roberts, AP and Chen, H and Wang, Y and Pan, Y},
title = {Phylogenetic and structural identification of a novel magnetotactic Deltaproteobacterium strain WYHR-1 from a freshwater lake.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.00731-19},
pmid = {31053584},
issn = {1098-5336},
abstract = {Magnetotactic bacteria (MTB) are phylogenetically diverse prokaryotes that are able to biomineralize intracellular, magnetic chains of magnetite or greigite nanocrystals called magnetosomes. Simultaneous characterization of MTB phylogeny and biomineralization is crucial but challenging because most MTB are extremely difficult to culture. We identify a large rod, bean-like MTB (tentatively named WYHR-1) from freshwater sediments of Weiyang Lake, Xi'an, China, using a coupled fluorescence and scanning electron microscopy approach at the single-cell scale. Phylogenetic analysis of 16S rRNA gene sequences indicates that WYHR-1 is a novel genus from the Deltaproteobacteria class. Transmission electron microscope observations reveal that WYHR-1 cells contain tens of magnetite magnetosomes that are organized into a single chain bundle along the cell long axis. Mature WYHR-1 magnetosomes are bullet-shaped, straight and elongated along the (001) direction, with a large flat end terminated by a {100}
face at the base and a conical top. This crystal morphology is distinctively different from bullet-shaped magnetosomes produced by other MTB in the Deltaproteobacteria class and the Nitrospirae phylum. This indicates that WYHR-1 may have a different crystal growth process and mechanism from other species, which results from species-specific magnetosome biomineralization in MTB.IMPORTANCE Magnetotactic bacteria (MTB) are a model system for understanding biomineralization, and are also studied intensively in biogeomagnetic and paleomagnetic research. However, many uncultured MTB strains have not been identified phylogenetically or investigated structurally at the single-cell level, which limits comprehensive understanding of MTB diversity and their role in biomineralization. We have identified a novel MTB strain WYHR-1 from a freshwater lake using a coupled fluorescence and scanning electron microscopy approach at the single-cell scale. Our analyses further indicate that strain WYHR-1 represents a novel genus from the Deltaproteobacteria class. In contrast to bullet-shaped magnetosomes produced by other MTB in the Deltaproteobacteria class and the Nitrospirae phylum, WYHR-1 magnetosomes are bullet-shaped, straight, and highly elongated along the (001) direction, and are terminated by a large {100}
face at their base and have a conical top. Our findings imply that, consistent with phylogenetic diversity of MTB, bullet-shaped magnetosomes have diverse crystal habits and growth patterns.},
}

@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 = {},
number = {},
pages = {},
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 {pmid31040327,
year = {2019},
author = {Salvi, M and Morbiducci, U and Amadeo, F and Santoro, R and Angelini, F and Chimenti, I and Massai, D and Messina, E and Giacomello, A and Pesce, M and Molinari, F},
title = {Automated Segmentation of Fluorescence Microscopy Images for 3D Cell Detection in human-derived Cardiospheres.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {6644},
doi = {10.1038/s41598-019-43137-2},
pmid = {31040327},
issn = {2045-2322},
abstract = {The 'cardiosphere' is a 3D cluster of cardiac progenitor cells recapitulating a stem cell niche-like microenvironment with a potential for disease and regeneration modelling of the failing human myocardium. In this multicellular 3D context, it is extremely important to decrypt the spatial distribution of cell markers for dissecting the evolution of cellular phenotypes by direct quantification of fluorescent signals in confocal microscopy. In this study, we present a fully automated method, named CARE ('CARdiosphere Evaluation'), for the segmentation of membranes and cell nuclei in human-derived cardiospheres. The proposed method is tested on twenty 3D-stacks of cardiospheres, for a total of 1160 images. Automatic results are compared with manual annotations and two open-source software designed for fluorescence microscopy. CARE performance was excellent in cardiospheres membrane segmentation and, in cell nuclei detection, the algorithm achieved the same performance as two expert operators. To the best of our knowledge, CARE is the first fully automated algorithm for segmentation inside in vitro 3D cell spheroids, including cardiospheres. The proposed approach will provide, in the future, automated quantitative analysis of markers distribution within the cardiac niche-like environment, enabling predictive associations between cell mechanical stresses and dynamic phenotypic changes.},
}

@article {pmid31036299,
year = {2019},
author = {Borisenko, I and Podgornaya, OI and Ereskovsky, AV},
title = {From traveler to homebody: Which signaling mechanisms sponge larvae use to become adult sponges?.},
journal = {Advances in protein chemistry and structural biology},
volume = {116},
number = {},
pages = {421-449},
doi = {10.1016/bs.apcsb.2019.02.002},
pmid = {31036299},
issn = {1876-1631},
abstract = {Cell-to-cell signaling is responsible for regulation of many developmental processes such as proliferation, cell migration, survival, cell fate specification and axis patterning. In this article we discussed the role of signaling in the metamorphosis of sponges with a focus on epithelial-mesenchymal transition (EMT) accompanying this event. Sponges (Porifera) are an ancient lineage of morphologically simple animals occupying a basal position on the tree of life. The study of these animals is necessary for understanding the origin of multicellularity and the evolution of developmental processes. Development of sponges is quite diverse. It finishes with the metamorphosis of a free-swimming larva into a young settled sponge. The outer surface of sponge larvae consists of a ciliated epithelial sheath, which ensures locomotion, while their internal structure varies from genus to genus. The fate of larval ciliated cells is the most intriguing aspect of metamorphosis. In this review we discuss the fate of larval ciliated cells, the processes going on in cells during metamorphosis at the molecular level and the regulation of this process. The review is based on information about several sponge species with a focus on Halisarca dujardini, Sycon ciliatum and Amphimedon queenslandica. In our model sponge, H. dujardini, ciliated cells leave the larval epithelium during metamorphosis and migrate to the internal cell mass as amoeboid cells to be differentiated into choanocytes of the juvenile sponge. Ciliated cells undergo EMT and internalize within minutes. As EMT involves the disappearance of adherens junctions and as cadherin, the main adherens junction protein, was identified in the transcriptome of several sponges, we suppose that EMT is regulated through cadherin-containing adherens junctions between ciliated cells. We failed to identify the master genes of EMT in the H. dujardini transcriptome, possibly because transcription was absent in the sequenced stages. They may be revealed by a search in the genome. The master genes themselves are controlled by various signaling pathways. Sponges have all the six signaling pathways conserved in Metazoa: Wnt, TGF-beta, Hedgehog, Notch, FGF and NO-dependent pathways. Summarizing the new data about intercellular communication in sponges, we can put forward two main questions regarding metamorphosis: (1) Which of the signaling pathways and in what hierarchical order are involved in metamorphosis? (2) How is the organization of a young sponge related to that of the larva or, in other words, is there a heredity of axes between the larva and the adult sponge?},
}

@article {pmid31032028,
year = {2019},
author = {Rivera-Yoshida, N and Arzola, AV and Arias Del Angel, JA and Franci, A and Travisano, M and Escalante, AE and Benítez, M},
title = {Plastic multicellular development of Myxococcus xanthus: genotype-environment interactions in a physical gradient.},
journal = {Royal Society open science},
volume = {6},
number = {3},
pages = {181730},
doi = {10.1098/rsos.181730},
pmid = {31032028},
issn = {2054-5703},
abstract = {In order to investigate the contribution of the physical environment to variation in multicellular development of Myxococcus xanthus, phenotypes developed by different genotypes in a gradient of substrate stiffness conditions were quantitatively characterized. Statistical analysis showed that plastic phenotypes result from the genotype, the substrate conditions and the interaction between them. Also, phenotypes were expressed in two distinguishable scales, the individual and the population levels, and the interaction with the environment showed scale and trait specificity. Overall, our results highlight the constructive role of the physical context in the development of microbial multicellularity, with both ecological and evolutionary implications.},
}

@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},
doi = {10.3389/fpls.2019.00454},
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 {pmid31023220,
year = {2019},
author = {Krishnan, A and Degnan, BM and Degnan, SM},
title = {The first identification of complete Eph-ephrin signalling in ctenophores and sponges reveals a role for neofunctionalization in the emergence of signalling domains.},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {96},
doi = {10.1186/s12862-019-1418-z},
pmid = {31023220},
issn = {1471-2148},
abstract = {BACKGROUND: Animals have a greater diversity of signalling pathways than their unicellular relatives, consistent with the evolution and expansion of these pathways occurring in parallel with the origin of animal multicellularity. However, the genomes of sponges and ctenophores - non-bilaterian basal animals - typically encode no, or far fewer, recognisable signalling ligands compared to bilaterians and cnidarians. For instance, the largest subclass of receptor tyrosine kinases (RTKs) in bilaterians, the Eph receptors (Ephs), are present in sponges and ctenophores, but their cognate ligands, the ephrins, have not yet been detected.

RESULTS: Here, we use an iterative HMM analysis to identify for the first time membrane-bound ephrins in sponges and ctenophores. We also expand the number of Eph-receptor subtypes identified in these animals and in cnidarians. Both sequence and structural analyses are consistent with the Eph ligand binding domain (LBD) and the ephrin receptor binding domain (RBD) having evolved via the co-option of ancient galactose-binding (discoidin-domain)-like and monodomain cupredoxin domains, respectively. Although we did not detect a complete Eph-ephrin signalling pathway in closely-related unicellular holozoans or in other non-metazoan eukaryotes, truncated proteins with Eph receptor LBDs and ephrin RBDs are present in some choanoflagellates. Together, these results indicate that Eph-ephrin signalling was present in the last common ancestor of extant metazoans, and perhaps even in the last common ancestor of animals and choanoflagellates. Either scenario pushes the origin of Eph-ephrin signalling back much earlier than previously reported.

CONCLUSIONS: We propose that the Eph-LBD and ephrin-RBD, which were ancestrally localised in the cytosol, became linked to the extracellular parts of two cell surface proteins before the divergence of sponges and ctenophores from the rest of the animal kingdom. The ephrin-RBD lost the ancestral capacity to bind copper, and the Eph-LBD became linked to an ancient RTK. The identification of divergent ephrin ligands in sponges and ctenophores suggests that these ligands evolve faster than their cognate receptors. As this may be a general phenomena, we propose that the sequence-structure approach used in this study may be usefully applied to other signalling systems where no, or a small number of, ligands have been identified.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1002/cncr.32053},
pmid = {31012964},
issn = {1097-0142},
support = {1 S10 RR 15768-01//U.S. Public Health Service/ ; RP110355//Cancer Prevention and Research Institute of Texas/ ; RP120124//Cancer Prevention and Research Institute of Texas/ ; RP150094//Cancer Prevention and Research Institute of Texas/ ; DBI-1254185//National Science Foundation/ ; HU0001//National Foundation for Cancer Research/ ; 1R01 CA218025-01//National Cancer Institute/ ; 1R01CA160394-01A1//National Cancer Institute/ ; 2P30-CA-51008//National Cancer Institute/ ; 5R01CA132012-02//National Cancer Institute/ ; 5T32CA009686-19//National Institutes of Health/ ; C06RR14567//National Institutes of Health/ ; R00DK094981//National Institutes of Health/ ; },
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.},
}

@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},
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.},
}

@article {pmid31002575,
year = {2019},
author = {Lehtonen, J and Parker, GA},
title = {Evolution of the Two Sexes under Internal Fertilization and Alternative Evolutionary Pathways.},
journal = {The American naturalist},
volume = {193},
number = {5},
pages = {702-716},
doi = {10.1086/702588},
pmid = {31002575},
issn = {1537-5323},
abstract = {Transition from isogamy to anisogamy, hence males and females, leads to sexual selection, sexual conflict, sexual dimorphism, and sex roles. Gamete dynamics theory links biophysics of gamete limitation, gamete competition, and resource requirements for zygote survival and assumes broadcast spawning. It makes testable predictions, but most comparative tests use volvocine algae, which feature internal fertilization. We broaden this theory by comparing broadcast-spawning predictions with two plausible internal-fertilization scenarios: gamete casting/brooding (one mating type retains gametes internally, the other broadcasts them) and packet casting/brooding (one type retains gametes internally, the other broadcasts packets containing gametes, which are released for fertilization). Models show that predictions are remarkably robust to these radical changes, yielding (1) isogamy under low gamete limitation, low gamete competition, and similar required resources for gametes and zygotes, (2) anisogamy when gamete competition and/or limitation are higher and when zygotes require more resources than gametes, as is likely as multicellularity develops, (3) a positive correlation between multicellular complexity and anisogamy ratio, and (4) under gamete competition, only brooders becoming female. Thus, gamete dynamics theory represents a potent rationale for isogamy/anisogamy and makes similar testable predictions for broadcast spawners and internal fertilizers, regardless of whether anisogamy or internal fertilization evolved first.},
}

@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 {pmid30989357,
year = {2019},
author = {Pérez, P and Soto, T and Gómez-Gil, E and Cansado, J},
title = {Functional interaction between Cdc42 and the stress MAPK signaling pathway during the regulation of fission yeast polarized growth.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10123-019-00072-6},
pmid = {30989357},
issn = {1618-1905},
support = {BIO2015-69958-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; BFU2017-82423-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; CSI068P17//Consejería de Educación, Junta de Castilla y León/ ; CLU-2017-03//Consejería de Educación, Junta de Castilla y León/ ; },
abstract = {Cell polarization can be defined as the generation and maintenance of directional cellular organization. The spatial distribution and protein or lipid composition of the cell are not symmetric but organized in specialized domains which allow cells to grow and acquire a certain shape that is closely linked to their physiological function. The establishment and maintenance of polarized growth requires the coordination of diverse processes including cytoskeletal dynamics, membrane trafficking, and signaling cascade regulation. Some of the major players involved in the selection and maintenance of sites for polarized growth are Rho GTPases, which recognize the polarization site and transmit the signal to regulatory proteins of the cytoskeleton. Additionally, cytoskeletal organization, polarized secretion, and endocytosis are controlled by signaling pathways including those mediated by mitogen-activated protein kinases (MAPKs). Rho GTPases and the MAPK signaling pathways are strongly conserved from yeast to mammals, suggesting that the basic mechanisms of polarized growth have been maintained throughout evolution. For this reason, the study of how polarized growth is established and regulated in simple organisms such as the fission yeast Schizosaccharomyces pombe has contributed to broaden our knowledge about these processes in multicellular organisms. We review here the function of the Cdc42 GTPase and the stress activated MAPK (SAPK) signaling pathways during fission yeast polarized growth, and discuss the relevance of the crosstalk between both pathways.},
}

@article {pmid30980502,
year = {2019},
author = {Qian, XX and Liu, J and Menguy, N and Li, J and Alberto, F and Teng, Z and Xiao, T and Zhang, W and Wu, LF},
title = {Identification of novel species of marine magnetotactic bacteria affiliated with Nitrospirae phylum.},
journal = {Environmental microbiology reports},
volume = {11},
number = {3},
pages = {330-337},
doi = {10.1111/1758-2229.12755},
pmid = {30980502},
issn = {1758-2229},
support = {//CNRS/ ; 41522402//NSFC/ ; U1706208//NSFC/ ; 41776131//NSFC/ ; },
abstract = {Magnetotactic bacteria (MTB) are a group of Gram-negative bacteria characterized by synthesizing magnetosomes and swimming along geomagnetic field lines. Phylogenetically, they belong to different taxonomic lineages including Proteobacteria, Nitrospirae, Omnitrophica, Latescibacteria and Planctomycetes phyla on the phylogenetic tree. To date, six Nitrospirae MTB phylotypes have been identified from freshwater or low-salinity environments and described in the literature. Here, we report the identification of two Nitrospirae MTB phylotypes collected, for the first time, from the marine environment. Both have a spherical morphology with a cell size of ~ 5 μM and similar motility but are different colours (black-brown and ivory-white) under the optic microscope. They synthesized bullet-shaped iron-oxide magnetosomes that were arranged in multiple bundles of chains. Moreover, the cytoplasm of the black-brown Nitrospirae MTB contained sulphur inclusions that conferred on cells a rough, granular appearance. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that they are two novel species and cluster with the previously reported MTB affiliated with the phylum Nitrospirae, thus extending the distribution of Nitrospirae MTB from freshwater to the marine environment.},
}

@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},
doi = {10.1371/journal.pbio.3000226},
pmid = {30978201},
issn = {1545-7885},
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.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1111/mec.15085},
pmid = {30963641},
issn = {1365-294X},
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.},
}

@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},
doi = {10.1098/rsif.2018.0736},
pmid = {30958167},
issn = {1742-5662},
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.},
}

@article {pmid30952878,
year = {2019},
author = {Baade, T and Paone, C and Baldrich, A and Hauck, CR},
title = {Clustering of integrin β cytoplasmic domains triggers nascent adhesion formation and reveals a protozoan origin of the integrin-talin interaction.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {5728},
doi = {10.1038/s41598-019-42002-6},
pmid = {30952878},
issn = {2045-2322},
support = {CRC969 B06//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Integrins and integrin-dependent cell-matrix adhesions are essential for a number of physiological processes. Integrin function is tightly regulated via binding of cytoplasmic proteins to integrin intracellular domains. Yet, the complexity of cell-matrix adhesions in mammals, with more than 150 core adhesome proteins, complicates the analysis of integrin-associated protein complexes. Interestingly, the evolutionary origin of integrins dates back before the transition from unicellular life to complex multicellular animals. Though unicellular relatives of metazoa have a less complex adhesome, nothing is known about the initial steps of integrin activation and adhesion complex assembly in protozoa. Therefore, we developed a minimal, microscope-based system using chimeric integrins to investigate receptor-proximal events during focal adhesion assembly. Clustering of the human integrin β1 tail led to recruitment of talin, kindlin, and paxillin and mutation of the known talin binding site abolished recruitment of this protein. Proteins indirectly linked to integrins, such as vinculin, migfilin, p130CAS, or zyxin were not enriched around the integrin β1 tail. With the exception of integrin β4 and integrin β8, the cytoplasmic domains of all human integrin β subunits supported talin binding. Likewise, the cytoplasmic domains of integrin β subunits expressed by the protozoan Capsaspora owczarzaki readily recruited talin and this interaction was based on an evolutionary conserved NPXY/F amino acid motif. The results we present here validate the use of our novel microscopic assay to uncover details of integrin-based protein-protein interactions in a cellular context and suggest that talin binding to integrin β cytoplasmic tails is an ancient feature of integrin regulation.},
}

@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},
doi = {10.1016/j.csbj.2019.03.001},
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 {pmid30941746,
year = {2019},
author = {Gulli, JG and Herron, MD and Ratcliff, WC},
title = {Evolution of altruistic cooperation among nascent multicellular organisms.},
journal = {Evolution; international journal of organic evolution},
volume = {73},
number = {5},
pages = {1012-1024},
doi = {10.1111/evo.13727},
pmid = {30941746},
issn = {1558-5646},
support = {NNA17BB05A//National Aeronautics and Space Administration/ ; DGE-1148903//Division of Graduate Education/ ; DEB-1723293//National Science Foundation/ ; },
abstract = {Cooperation is a classic solution to hostile environments that limit individual survival. In extreme cases this may lead to the evolution of new types of biological individuals (e.g., eusocial super-organisms). We examined the potential for interindividual cooperation to evolve via experimental evolution, challenging nascent multicellular "snowflake yeast" with an environment in which solitary multicellular clusters experienced low survival. In response, snowflake yeast evolved to form cooperative groups composed of thousands of multicellular clusters that typically survive selection. Group formation occurred through the creation of protein aggregates, only arising in strains with high (>2%) rates of cell death. Nonetheless, it was adaptive and repeatable, although ultimately evolutionarily unstable. Extracellular protein aggregates act as a common good, as they can be exploited by cheats that do not contribute to aggregate production. These results highlight the importance of group formation as a mechanism for surviving environmental stress, and underscore the remarkable ease with which even simple multicellular entities may evolve-and lose-novel social traits.},
}

@article {pmid30923125,
year = {2019},
author = {Pedchenko, V and Bauer, R and Pokidysheva, EN and Al-Shaer, A and Forde, NR and Fidler, AL and Hudson, BG and Boudko, SP},
title = {A chloride ring is an ancient evolutionary innovation mediating the assembly of the collagen IV scaffold of basement membranes.},
journal = {The Journal of biological chemistry},
volume = {294},
number = {20},
pages = {7968-7981},
doi = {10.1074/jbc.RA119.007426},
pmid = {30923125},
issn = {1083-351X},
support = {R01 DK018381/DK/NIDDK NIH HHS/United States ; T32 DK007569/DK/NIDDK NIH HHS/United States ; },
abstract = {Collagen IV scaffold is a principal component of the basement membrane (BM), a specialized extracellular matrix that is essential for animal multicellularity and tissue evolution. Scaffold assembly begins with the trimerization of α-chains into protomers inside the cell, which then are secreted and undergo oligomerization outside the cell. For the ubiquitous scaffold composed of α1- and α2-chains, both intracellular and extracellular stages are mediated by the noncollagenous domain (NC1). The association of protomers is chloride-dependent, whereby chloride ions induce interactions of the protomers' trimeric NC1 domains leading to NC1 hexamer formation. Here, we investigated the mechanisms, kinetics, and functionality of the chloride ion-mediated protomer assembly by using a single-chain technology to produce a stable NC1 trimer comprising α1, α2, and α1 NC1 monomers. We observed that in the presence of chloride, the single-chain NC1-trimer self-assembles into a hexamer, for which the crystal structure was determined. We discovered that a chloride ring, comprising 12 ions, induces the assembly of and stabilizes the NC1 hexamer. Furthermore, we found that the chloride ring is evolutionarily conserved across all animals, first appearing in cnidarians. These findings reveal a fundamental role for the chloride ring in the assembly of collagen IV scaffolds of BMs, a critical event enabling tissue evolution and development. Moreover, the single-chain technology is foundational for generating trimeric NC1 domains of other α-chain compositions to investigate the α121, α345, and α565 collagen IV scaffolds and to develop therapies for managing Alport syndrome, Goodpasture's disease, and cancerous tumor growth.},
}

@article {pmid30919568,
year = {2019},
author = {Zhu, SQ and Zhang, YJ and Abbas, MN and Hao, XW and Zhao, YZ and Liang, HH and Cui, HJ and Yang, LQ},
title = {Hedgehog promotes cell proliferation in the midgut of silkworm, Bombyx mori.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.12672},
pmid = {30919568},
issn = {1744-7917},
support = {No. XDJK2015C129//Fundamental Research Funds for the Central Universities/ ; No. 2362015XK09//Fundamental Research Funds for the Central Universities/ ; No. XDJK2013B020//Fundamental Research Funds for the Central Universities/ ; No. 20120524//Fundamental Research Funds for the Central Universities/ ; CXTDX201601010//Chongqing University Innovation Team Building Program funded projects/ ; 2017ZBX10//Scientific Research Foundation of the Chongqing University of Arts and Sciences/ ; No. 31672496//National Natural Science Foundation of China/ ; cstc2016jcyjA0425//Natural Science Foundation of Chongqing/ ; },
abstract = {The Hedgehog (Hh) signaling pathway is one of the major regulators of embryonic development and tissue homeostasis in multicellular organisms. However, the role of this pathway in the silkworm, especially in the silkworm midgut, remains poorly understood. Here, we report that Bombyx mori Hedgehog (BmHh) is expressed in most tissues of silkworm larvae and that its functions are well-conserved throughout evolution. We further demonstrate that the messenger RNA of four Hh signaling components, BmHh ligand, BmPtch receptor, signal transducer BmSmo and transcription factor BmCi, are all upregulated following Escherichia coli or Bacillus thuringiensis infection, indicating the activation of the Hh pathway. Simultaneously, midgut cell proliferation is strongly promoted. Conversely, the repression of Hh signal transduction with double-stranded RNA or cyclopamine inhibits the expression of BmHh and BmCi and reduces cell proliferation. Overall, these findings provide new insights into the Hh signaling pathway in the silkworm, B. mori.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsz002},
pmid = {30918953},
issn = {1756-1663},
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.},
}

@article {pmid30918448,
year = {2019},
author = {Stucky, BJ and Balhoff, JP and Barve, N and Barve, V and Brenskelle, L and Brush, MH and Dahlem, GA and Gilbert, JDJ and Kawahara, AY and Keller, O and Lucky, A and Mayhew, PJ and Plotkin, D and Seltmann, KC and Talamas, E and Vaidya, G and Walls, R and Yoder, M and Zhang, G and Guralnick, R},
title = {Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions.},
journal = {Biodiversity data journal},
volume = {7},
number = {},
pages = {e33303},
doi = {10.3897/BDJ.7.e33303},
pmid = {30918448},
issn = {1314-2828},
abstract = {Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1007/s00248-019-01358-y},
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/ ; },
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.},
}

@article {pmid30911363,
year = {2019},
author = {Bielska, E and Birch, PRJ and Buck, AH and Abreu-Goodger, C and Innes, RW and Jin, H and Pfaffl, MW and Robatzek, S and Regev-Rudzki, N and Tisserant, C and Wang, S and Weiberg, A},
title = {Highlights of the mini-symposium on extracellular vesicles in inter-organismal communication, held in Munich, Germany, August 2018.},
journal = {Journal of extracellular vesicles},
volume = {8},
number = {1},
pages = {1590116},
doi = {10.1080/20013078.2019.1590116},
pmid = {30911363},
issn = {2001-3078},
abstract = {All living organisms secrete molecules for intercellular communication. Recent research has revealed that extracellular vesicles (EVs) play an important role in inter-organismal cell-to-cell communication by transporting diverse messenger molecules, including RNA, DNA, lipids and proteins. These discoveries have raised fundamental questions regarding EV biology. How are EVs biosynthesized and loaded with messenger/cargo molecules? How are EVs secreted into the extracellular matrix? What are the EV uptake mechanisms of recipient cells? As EVs are produced by all kind of organisms, from unicellular bacteria and protists, filamentous fungi and oomycetes, to complex multicellular life forms such as plants and animals, basic research in diverse model systems is urgently needed to shed light on the multifaceted biology of EVs and their role in inter-organismal communications. To help catalyse progress in this emerging field, a mini-symposium was held in Munich, Germany in August 2018. This report highlights recent progress and major questions being pursued across a very diverse group of model systems, all united by the question of how EVs contribute to inter-organismal communication.},
}

@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 = {},
doi = {10.3390/ijms20061466},
pmid = {30909510},
issn = {1422-0067},
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.},
}

@article {pmid30902897,
year = {2019},
author = {Krizsán, K and Almási, É and Merényi, Z and Sahu, N and Virágh, M and Kószó, T and Mondo, S and Kiss, B and Bálint, B and Kües, U and Barry, K and Cseklye, J and Hegedüs, B and Henrissat, B and Johnson, J and Lipzen, A and Ohm, RA and Nagy, I and Pangilinan, J and Yan, J and Xiong, Y and Grigoriev, IV and Hibbett, DS and Nagy, LG},
title = {Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {15},
pages = {7409-7418},
doi = {10.1073/pnas.1817822116},
pmid = {30902897},
issn = {1091-6490},
mesh = {*Agaricales/genetics/growth & development ; *Databases, Nucleic Acid ; *Fruiting Bodies, Fungal/genetics/growth & development ; *Fungal Proteins/biosynthesis/genetics ; Gene Expression Regulation, Fungal/physiology ; *Genes, Fungal ; Transcriptome/*physiology ; },
abstract = {The evolution of complex multicellularity has been one of the major transitions in the history of life. In contrast to simple multicellular aggregates of cells, it has evolved only in a handful of lineages, including animals, embryophytes, red and brown algae, and fungi. Despite being a key step toward the evolution of complex organisms, the evolutionary origins and the genetic underpinnings of complex multicellularity are incompletely known. The development of fungal fruiting bodies from a hyphal thallus represents a transition from simple to complex multicellularity that is inducible under laboratory conditions. We constructed a reference atlas of mushroom formation based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes). Nearly 300 conserved gene families and >70 functional groups contained developmentally regulated genes from five to six species, covering functions related to fungal cell wall remodeling, targeted protein degradation, signal transduction, adhesion, and small secreted proteins (including effector-like orphan genes). Several of these families, including F-box proteins, expansin-like proteins, protein kinases, and transcription factors, showed expansions in Agaricomycetes, many of which convergently expanded in multicellular plants and/or animals too, reflecting convergent solutions to genetic hurdles imposed by complex multicellularity among independently evolved lineages. This study provides an entry point to studying mushroom development and complex multicellularity in one of the largest clades of complex eukaryotic organisms.},
}

*Agaricales/genetics/growth & development
*Databases, Nucleic Acid
*Fruiting Bodies, Fungal/genetics/growth & development
*Fungal Proteins/biosynthesis/genetics
Gene Expression Regulation, Fungal/physiology
*Genes, Fungal
Transcriptome/*physiology

@article {pmid30898932,
year = {2019},
author = {Wielgoss, S and Wolfensberger, R and Sun, L and Fiegna, F and Velicer, GJ},
title = {Social genes are selection hotspots in kin groups of a soil microbe.},
journal = {Science (New York, N.Y.)},
volume = {363},
number = {6433},
pages = {1342-1345},
doi = {10.1126/science.aar4416},
pmid = {30898932},
issn = {1095-9203},
abstract = {The composition of cooperative systems, including animal societies, organismal bodies, and microbial groups, reflects their past and shapes their future evolution. However, genomic diversity within many multiunit systems remains uncharacterized, limiting our ability to understand and compare their evolutionary character. We have analyzed genomic and social-phenotype variation among 120 natural isolates of the cooperative bacterium Myxococcus xanthus derived from six multicellular fruiting bodies. Each fruiting body was composed of multiple lineages radiating from a unique recent ancestor. Genomic evolution was concentrated in selection hotspots associated with evolutionary change in social phenotypes. Synonymous mutations indicated that kin lineages within the same fruiting body often first diverged from a common ancestor more than 100 generations ago. Thus, selection appears to promote endemic diversification of kin lineages that remain together over long histories of local interaction, thereby potentiating social coevolution.},
}

@article {pmid30886348,
year = {2019},
author = {Talbert, PB and Meers, MP and Henikoff, S},
title = {Old cogs, new tricks: the evolution of gene expression in a chromatin context.},
journal = {Nature reviews. Genetics},
volume = {20},
number = {5},
pages = {283-297},
doi = {10.1038/s41576-019-0105-7},
pmid = {30886348},
issn = {1471-0064},
abstract = {Sophisticated gene-regulatory mechanisms probably evolved in prokaryotes billions of years before the emergence of modern eukaryotes, which inherited the same basic enzymatic machineries. However, the epigenomic landscapes of eukaryotes are dominated by nucleosomes, which have acquired roles in genome packaging, mitotic condensation and silencing parasitic genomic elements. Although the molecular mechanisms by which nucleosomes are displaced and modified have been described, just how transcription factors, histone variants and modifications and chromatin regulators act on nucleosomes to regulate transcription is the subject of considerable ongoing study. We explore the extent to which these transcriptional regulatory components function in the context of the evolutionarily ancient role of chromatin as a barrier to processes acting on DNA and how chromatin proteins have diversified to carry out evolutionarily recent functions that accompanied the emergence of differentiation and development in multicellular eukaryotes.},
}

@article {pmid30886148,
year = {2019},
author = {Xu, S and Stapley, J and Gablenz, S and Boyer, J and Appenroth, KJ and Sree, KS and Gershenzon, J and Widmer, A and Huber, M},
title = {Low genetic variation is associated with low mutation rate in the giant duckweed.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1243},
doi = {10.1038/s41467-019-09235-5},
pmid = {30886148},
issn = {2041-1723},
mesh = {Africa ; Americas ; Araceae/classification/*genetics ; Asia ; DNA Mutational Analysis ; Europe ; *Genetic Variation ; *Genome, Plant ; *Mutation Rate ; Phylogeography ; Plant Dispersal/*genetics ; },
abstract = {Mutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. Here we investigate genetic diversity, spontaneous mutation rate and Ne in the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals reveals extremely low intraspecific genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereas Ne is large. These results demonstrate that low genetic diversity can be associated with large-Ne species, where selection can reduce mutation rates to very low levels. This study also highlights that accurate estimates of mutation rate can help to explain seemingly unexpected patterns of genome-wide variation.},
}

Africa
Americas
Araceae/classification/*genetics
Asia
DNA Mutational Analysis
Europe
*Genetic Variation
*Genome, Plant
*Mutation Rate
Phylogeography
Plant Dispersal/*genetics

@article {pmid30883720,
year = {2019},
author = {Kapsetaki, SE and West, SA},
title = {The costs and benefits of multicellular group formation in algae.},
journal = {Evolution; international journal of organic evolution},
volume = {73},
number = {6},
pages = {1296-1308},
doi = {10.1111/evo.13712},
pmid = {30883720},
issn = {1558-5646},
support = {//Alexander S. Onassis Public Benefit Foundation/ ; //European Research Council/ ; //A.G. Leventis Foundation/ ; },
abstract = {The first step in the evolution of complex multicellular organisms involves single cells forming a cooperative group. Consequently, to understand multicellularity, we need to understand the costs and benefits associated with multicellular group formation. We found that in the facultatively multicellular algae Chlorella sorokiniana: (1) the presence of the flagellate Ochromonas danica or the crustacean Daphnia magna leads to the formation of multicellular groups; (2) the formation of multicellular groups reduces predation by O. danica, but not by the larger predator D. magna; (3) under conditions of relatively low light intensity, where competition for light is greater, multicellular groups grow slower than single cells; (4) in the absence of live predators, the proportion of cells in multicellular groups decreases at a rate that does not vary with light intensity. These results can explain why, in cases such as this algae species, multicellular group formation is facultative, in response to the presence of predators.},
}

@article {pmid30875767,
year = {2019},
author = {Goh, GH and Maloney, SK and Mark, PJ and Blache, D},
title = {Episodic Ultradian Events-Ultradian Rhythms.},
journal = {Biology},
volume = {8},
number = {1},
pages = {},
doi = {10.3390/biology8010015},
pmid = {30875767},
issn = {2079-7737},
abstract = {In the fast lane of chronobiology, ultradian events are short-term rhythms that have been observed since the beginning of modern biology and were quantified about a century ago. They are ubiquitous in all biological systems and found in all organisms, from unicellular organisms to mammals, and from single cells to complex biological functions in multicellular animals. Since these events are aperiodic and last for a few minutes to a few hours, they are better classified as episodic ultradian events (EUEs). Their origin is unclear. However, they could have a molecular basis and could be controlled by hormonal inputs-in vertebrates, they originate from the activity of the central nervous system. EUEs are receiving increasing attention but their aperiodic nature requires specific sampling and analytic tools. While longer scale rhythms are adaptations to predictable changes in the environment, in theory, EUEs could contribute to adaptation by preparing organisms and biological functions for unpredictability.},
}

@article {pmid30863851,
year = {2019},
author = {Shoemark, DK and Ziegler, B and Watanabe, H and Strompen, J and Tucker, RP and Özbek, S and Adams, JC},
title = {Emergence of a Thrombospondin Superfamily at the Origin of Metazoans.},
journal = {Molecular biology and evolution},
volume = {36},
number = {6},
pages = {1220-1238},
doi = {10.1093/molbev/msz060},
pmid = {30863851},
issn = {1537-1719},
abstract = {Extracellular matrix (ECM) is considered central to the evolution of metazoan multicellularity; however, the repertoire of ECM proteins in nonbilaterians remains unclear. Thrombospondins (TSPs) are known to be well conserved from cnidarians to vertebrates, yet to date have been considered a unique family, principally studied for matricellular functions in vertebrates. Through searches utilizing the highly conserved C-terminal region of TSPs, we identify undisclosed new families of TSP-related proteins in metazoans, designated mega-TSP, sushi-TSP, and poriferan-TSP, each with a distinctive phylogenetic distribution. These proteins share the TSP C-terminal region domain architecture, as determined by domain composition and analysis of molecular models against known structures. Mega-TSPs, the only form identified in ctenophores, are typically >2,700 aa and are also characterized by N-terminal leucine-rich repeats and central cadherin/immunoglobulin domains. In cnidarians, which have a well-defined ECM, Mega-TSP was expressed throughout embryogenesis in Nematostella vectensis, with dynamic endodermal expression in larvae and primary polyps and widespread ectodermal expression in adult Nematostella vectensis and Hydra magnipapillata polyps. Hydra Mega-TSP was also expressed during regeneration and siRNA-silencing of Mega-TSP in Hydra caused specific blockade of head regeneration. Molecular phylogenetic analyses based on the conserved TSP C-terminal region identified each of the TSP-related groups to form clades distinct from the canonical TSPs. We discuss models for the evolution of the newly defined TSP superfamily by gene duplications, radiation, and gene losses from a debut in the last metazoan common ancestor. Together, the data provide new insight into the evolution of ECM and tissue organization in metazoans.},
}

@article {pmid30862622,
year = {2019},
author = {Lenhart, BA and Meeks, B and Murphy, HA},
title = {Variation in Filamentous Growth and Response to Quorum-Sensing Compounds in Environmental Isolates of Saccharomyces cerevisiae.},
journal = {G3 (Bethesda, Md.)},
volume = {9},
number = {5},
pages = {1533-1544},
doi = {10.1534/g3.119.400080},
pmid = {30862622},
issn = {2160-1836},
support = {R15 GM122032/GM/NIGMS NIH HHS/United States ; },
abstract = {In fungi, filamentous growth is a major developmental transition that occurs in response to environmental cues. In diploid Saccharomyces cerevisiae, it is known as pseudohyphal growth and presumed to be a foraging mechanism. Rather than unicellular growth, multicellular filaments composed of elongated, attached cells spread over and into surfaces. This morphogenetic switch can be induced through quorum sensing with the aromatic alcohols phenylethanol and tryptophol. Most research investigating pseudohyphal growth has been conducted in a single lab background, Σ1278b. To investigate the natural variation in this phenotype and its induction, we assayed the diverse 100-genomes collection of environmental isolates. Using computational image analysis, we quantified the production of pseudohyphae and observed a large amount of variation. Population origin was significantly associated with pseudohyphal growth, with the West African population having the most. Surprisingly, most strains showed little or no response to exogenous phenylethanol or tryptophol. We also investigated the amount of natural genetic variation in pseudohyphal growth using a mapping population derived from a highly-heterozygous clinical isolate that contained as much phenotypic variation as the environmental panel. A bulk-segregant analysis uncovered five major peaks with candidate loci that have been implicated in the Σ1278b background. Our results indicate that the filamentous growth response is a generalized, highly variable phenotype in natural populations, while response to quorum sensing molecules is surprisingly rare. These findings highlight the importance of coupling studies in tractable lab strains with natural isolates in order to understand the relevance and distribution of well-studied traits.},
}

@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 = {},
doi = {10.7554/eLife.43599},
pmid = {30857590},
issn = {2050-084X},
support = {ANR-14-CE02-0014//Agence Nationale de la Recherche/ ; },
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.},
}

@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},
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.},
}

@article {pmid30826447,
year = {2019},
author = {Fillinger, RJ and Anderson, MZ},
title = {Seasons of change: Mechanisms of genome evolution in human fungal pathogens.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {70},
number = {},
pages = {165-174},
doi = {10.1016/j.meegid.2019.02.031},
pmid = {30826447},
issn = {1567-7257},
abstract = {Fungi are a diverse kingdom of organisms capable of thriving in various niches across the world including those in close association with multicellular eukaryotes. Fungal pathogens that contribute to human disease reside both within the host as commensal organisms of the microbiota and the environment. Their niche of origin dictates how infection initiates but also places specific selective pressures on the fungal pathogen that contributes to its genome organization and genetic repertoire. Recent efforts to catalogue genomic variation among major human fungal pathogens have unveiled evolutionary themes that shape the fungal genome. Mechanisms ranging from large scale changes such as aneuploidy and ploidy cycling as well as more targeted mutations like base substitutions and gene copy number variations contribute to the evolution of these species, which are often under multiple competing selective pressures with their host, environment, and other microbes. Here, we provide an overview of the major selective pressures and mechanisms acting to evolve the genome of clinically important fungal pathogens of humans.},
}

@article {pmid30824779,
year = {2019},
author = {Kabir, M and Wenlock, S and Doig, AJ and Hentges, KE},
title = {The Essentiality Status of Mouse Duplicate Gene Pairs Correlates with Developmental Co-Expression Patterns.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {3224},
doi = {10.1038/s41598-019-39894-9},
pmid = {30824779},
issn = {2045-2322},
support = {BB/L018276/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/L018276/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
abstract = {During the evolution of multicellular eukaryotes, gene duplication occurs frequently to generate new genes and/or functions. A duplicated gene may have a similar function to its ancestral gene. Therefore, it may be expected that duplicated genes are less likely to be critical for the survival of an organism, since there are multiple copies of the gene rendering each individual copy redundant. In this study, we explored the developmental expression patterns of duplicate gene pairs and the relationship between development co-expression and phenotypes resulting from the knockout of duplicate genes in the mouse. We define genes that generate lethal phenotypes in single gene knockout experiments as essential genes. We found that duplicate gene pairs comprised of two essential genes tend to be expressed at different stages of development, compared to duplicate gene pairs with at least one non-essential member, showing that the timing of developmental expression affects the ability of one paralogue to compensate for the loss of the other. Gene essentiality, developmental expression and gene duplication are thus closely linked.},
}

@article {pmid30824706,
year = {2019},
author = {Lurgi, M and Thomas, T and Wemheuer, B and Webster, NS and Montoya, JM},
title = {Modularity and predicted functions of the global sponge-microbiome network.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {992},
doi = {10.1038/s41467-019-08925-4},
pmid = {30824706},
issn = {2041-1723},
mesh = {Animals ; Bacteria/classification/genetics ; Biodiversity ; Biological Evolution ; Ecology ; Host Microbial Interactions/*physiology ; Microbiota/genetics/*physiology ; Phylogeny ; Porifera/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Symbiosis ; },
abstract = {Defining the organisation of species interaction networks and unveiling the processes behind their assembly is fundamental to understanding patterns of biodiversity, community stability and ecosystem functioning. Marine sponges host complex communities of microorganisms that contribute to their health and survival, yet the mechanisms behind microbiome assembly are largely unknown. We present the global marine sponge-microbiome network and reveal a modular organisation in both community structure and function. Modules are linked by a few sponge species that share microbes with other species around the world. Further, we provide evidence that abiotic factors influence the structuring of the sponge microbiome when considering all microbes present, but biotic interactions drive the assembly of more intimately associated 'core' microorganisms. These findings suggest that both ecological and evolutionary processes are at play in host-microbe network assembly. We expect mechanisms behind microbiome assembly to be consistent across multicellular hosts throughout the tree of life.},
}

Animals
Bacteria/classification/genetics
Biodiversity
Biological Evolution
Ecology
Host Microbial Interactions/*physiology
Microbiota/genetics/*physiology
Phylogeny
Porifera/classification/*microbiology
RNA, Ribosomal, 16S/genetics
Species Specificity
Symbiosis

@article {pmid30808737,
year = {2019},
author = {El Albani, A and Mangano, MG and Buatois, LA and Bengtson, S and Riboulleau, A and Bekker, A and Konhauser, K and Lyons, T and Rollion-Bard, C and Bankole, O and Lekele Baghekema, SG and Meunier, A and Trentesaux, A and Mazurier, A and Aubineau, J and Laforest, C and Fontaine, C and Recourt, P and Chi Fru, E and Macchiarelli, R and Reynaud, JY and Gauthier-Lafaye, F and Canfield, DE},
title = {Organism motility in an oxygenated shallow-marine environment 2.1 billion years ago.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {9},
pages = {3431-3436},
doi = {10.1073/pnas.1815721116},
pmid = {30808737},
issn = {1091-6490},
mesh = {Atmosphere ; *Biological Evolution ; Biota/physiology ; *Fossils ; Gabon ; Geologic Sediments/*chemistry ; Oxidation-Reduction ; Oxygen/*chemistry ; },
abstract = {Evidence for macroscopic life in the Paleoproterozoic Era comes from 1.8 billion-year-old (Ga) compression fossils [Han TM, Runnegar B (1992) Science 257:232-235; Knoll et al. (2006) Philos Trans R Soc Lond B 361:1023-1038], Stirling biota [Bengtson S et al. (2007) Paleobiology 33:351-381], and large colonial organisms exhibiting signs of coordinated growth from the 2.1-Ga Francevillian series, Gabon. Here we report on pyritized string-shaped structures from the Francevillian Basin. Combined microscopic, microtomographic, geochemical, and sedimentologic analyses provide evidence for biogenicity, and syngenicity and suggest that the structures underwent fossilization during early diagenesis close to the sediment-water interface. The string-shaped structures are up to 6 mm across and extend up to 170 mm through the strata. Morphological and 3D tomographic reconstructions suggest that the producer may have been a multicellular or syncytial organism able to migrate laterally and vertically to reach food resources. A possible modern analog is the aggregation of amoeboid cells into a migratory slug phase in cellular slime molds at times of starvation. This unique ecologic window established in an oxygenated, shallow-marine environment represents an exceptional record of the biosphere following the crucial changes that occurred in the atmosphere and ocean in the aftermath of the great oxidation event (GOE).},
}

Atmosphere
*Biological Evolution
Biota/physiology
*Fossils
Gabon
Geologic Sediments/*chemistry
Oxidation-Reduction
Oxygen/*chemistry

@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 = {},
doi = {10.7554/eLife.40947},
pmid = {30803482},
issn = {2050-084X},
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.},
}

@article {pmid30799483,
year = {2019},
author = {Xie, P and Gao, M and Wang, C and Zhang, J and Noel, P and Yang, C and Von Hoff, D and Han, H and Zhang, MQ and Lin, W},
title = {SuperCT: a supervised-learning framework for enhanced characterization of single-cell transcriptomic profiles.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkz116},
pmid = {30799483},
issn = {1362-4962},
abstract = {Characterization of individual cell types is fundamental to the study of multicellular samples. Single-cell RNAseq techniques, which allow high-throughput expression profiling of individual cells, have significantly advanced our ability of this task. Currently, most of the scRNA-seq data analyses are commenced with unsupervised clustering. Clusters are often assigned to different cell types based on the enriched canonical markers. However, this process is inefficient and arbitrary. In this study, we present a technical framework of training the expandable supervised-classifier in order to reveal the single-cell identities as soon as the single-cell expression profile is input. Using multiple scRNA-seq datasets we demonstrate the superior accuracy, robustness, compatibility and expandability of this new solution compared to the traditional methods. We use two examples of the model upgrade to demonstrate how the projected evolution of the cell-type classifier is realized.},
}

@article {pmid30796309,
year = {2019},
author = {Zhang, L and Tan, Y and Fan, S and Zhang, X and Zhang, Z},
title = {Phylostratigraphic analysis of gene co-expression network reveals the evolution of functional modules for ovarian cancer.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {2623},
doi = {10.1038/s41598-019-40023-9},
pmid = {30796309},
issn = {2045-2322},
support = {31800185//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31800185//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Ovarian cancer (OV) is an extremely lethal disease. However, the evolutionary machineries of OV are still largely unknown. Here, we used a method that combines phylostratigraphy information with gene co-expression networks to extensively study the evolutionary compositions of OV. The present co-expression network construction yielded 18,549 nodes and 114,985 edges based on 307 OV expression samples obtained from the Genome Data Analysis Centers database. A total of 20 modules were identified as OV related clusters. The human genome sequences were divided into 19 phylostrata (PS), the majority (67.45%) of OV genes was already present in the eukaryotic ancestor. There were two strong peaks of the emergence of OV genes screened by hypergeometric test: the evolution of the multicellular metazoan organisms (PS5 and PS6, P value = 0.002) and the emergence of bony fish (PS11 and PS12, P value = 0.009). Hence, the origin of OV is far earlier than its emergence. The integrated analysis of the topology of OV modules and the phylogenetic data revealed an evolutionary pattern of OV in human, namely, OV modules have arisen step by step during the evolution of the respective lineages. New genes have evolved and become locked into a pathway, where more and more biological pathways are fixed into OV modules by recruiting new genes during human evolution.},
}

@article {pmid30787483,
year = {2019},
author = {Herron, MD and Borin, JM and Boswell, JC and Walker, J and Chen, IK and Knox, CA and Boyd, M and Rosenzweig, F and Ratcliff, WC},
title = {De novo origins of multicellularity in response to predation.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {2328},
doi = {10.1038/s41598-019-39558-8},
pmid = {30787483},
issn = {2045-2322},
support = {DEB-1457701//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-1456652//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-1457701//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-1456652//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-1456652//NSF | BIO | Division of Environmental Biology (DEB)/ ; NNA17BB05A//National Aeronautics and Space Administration (NASA)/ ; NNA17BB05A//National Aeronautics and Space Administration (NASA)/ ; 43285//John Templeton Foundation (JTF)/ ; Packard Foundation Fellowship//David and Lucile Packard Foundation (David & Lucile Packard Foundation)/ ; },
abstract = {The transition from unicellular to multicellular life was one of a few major events in the history of life that created new opportunities for more complex biological systems to evolve. Predation is hypothesized as one selective pressure that may have driven the evolution of multicellularity. Here we show that de novo origins of simple multicellularity can evolve in response to predation. We subjected outcrossed populations of the unicellular green alga Chlamydomonas reinhardtii to selection by the filter-feeding predator Paramecium tetraurelia. Two of five experimental populations evolved multicellular structures not observed in unselected control populations within ~750 asexual generations. Considerable variation exists in the evolved multicellular life cycles, with both cell number and propagule size varying among isolates. Survival assays show that evolved multicellular traits provide effective protection against predation. These results support the hypothesis that selection imposed by predators may have played a role in some origins of multicellularity.},
}

@article {pmid30787193,
year = {2019},
author = {Dunning, LT and Olofsson, JK and Parisod, C and Choudhury, RR and Moreno-Villena, JJ and Yang, Y and Dionora, J and Quick, WP and Park, M and Bennetzen, JL and Besnard, G and Nosil, P and Osborne, CP and Christin, PA},
title = {Lateral transfers of large DNA fragments spread functional genes among grasses.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1810031116},
pmid = {30787193},
issn = {1091-6490},
support = {638333//European Research Council/International ; },
abstract = {A fundamental tenet of multicellular eukaryotic evolution is that vertical inheritance is paramount, with natural selection acting on genetic variants transferred from parents to offspring. This lineal process means that an organism's adaptive potential can be restricted by its evolutionary history, the amount of standing genetic variation, and its mutation rate. Lateral gene transfer (LGT) theoretically provides a mechanism to bypass many of these limitations, but the evolutionary importance and frequency of this process in multicellular eukaryotes, such as plants, remains debated. We address this issue by assembling a chromosome-level genome for the grass Alloteropsis semialata, a species surmised to exhibit two LGTs, and screen it for other grass-to-grass LGTs using genomic data from 146 other grass species. Through stringent phylogenomic analyses, we discovered 57 additional LGTs in the A. semialata nuclear genome, involving at least nine different donor species. The LGTs are clustered in 23 laterally acquired genomic fragments that are up to 170 kb long and have accumulated during the diversification of Alloteropsis. The majority of the 59 LGTs in A. semialata are expressed, and we show that they have added functions to the recipient genome. Functional LGTs were further detected in the genomes of five other grass species, demonstrating that this process is likely widespread in this globally important group of plants. LGT therefore appears to represent a potent evolutionary force capable of spreading functional genes among distantly related grass species.},
}

@article {pmid30775966,
year = {2019},
author = {Nakahara, N and Nobu, MK and Takaki, Y and Miyazaki, M and Tasumi, E and Sakai, S and Ogawara, M and Yoshida, N and Tamaki, H and Yamanaka, Y and Katayama, A and Yamaguchi, T and Takai, K and Imachi, H},
title = {Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {69},
number = {4},
pages = {1185-1194},
doi = {10.1099/ijsem.0.003291},
pmid = {30775966},
issn = {1466-5034},
mesh = {Bacterial Typing Techniques ; Base Composition ; Bioreactors/*microbiology ; Chloroflexi/*classification/isolation & purification ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Geologic Sediments/*microbiology ; Japan ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; },
abstract = {A novel slow-growing, facultatively anaerobic, filamentous bacterium, strain MO-CFX2T, was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediment collected off the Shimokita Peninsula of Japan. Cells were multicellular filamentous, non-motile and Gram-stain-negative. The filaments were generally more than 20 µm (up to approximately 200 µm) long and 0.5-0.6 µm wide. Cells possessed pili-like structures on the cell surface and a multilayer structure in the cytoplasm. Growth of the strain was observed at 20-37 °C (optimum, 30 °C), pH 5.5-8.0 (pH 6.5-7.0), and 0-30 g l-1 NaCl (5 g l-1 NaCl). Under optimum growth conditions, doubling time and maximum cell density were estimated to be approximately 19 days and ~105 cells ml-1, respectively. Strain MO-CFX2T grew chemoorganotrophically on a limited range of organic substrates in anaerobic conditions. The major cellular fatty acids were saturated C16 : 0 (47.9 %) and C18 : 0 (36.9 %), and unsaturated C18 : 1ω9c (6.0 %) and C16 : 1ω7 (5.1 %). The G+C content of genomic DNA was 63.2 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-CFX2T shares a notably low sequence identity with its closest relatives, which were Thermanaerothrix daxensis GNS-1T and Thermomarinilinea lacunifontana SW7T (both 85.8 % sequence identity). Based on these phenotypic and genomic properties, we propose the name Aggregatilinea lenta gen. nov., sp. nov. for strain MO-CFX2T (=KCTC 15625T, =JCM 32065T). In addition, we also propose the associated family and order as Aggregatilineaceae fam. nov. and Aggregatilineales ord. nov., respectively.},
}

Bacterial Typing Techniques
Base Composition
Bioreactors/*microbiology
Chloroflexi/*classification/isolation & purification
DNA, Bacterial/genetics
Fatty Acids/chemistry
Geologic Sediments/*microbiology
Japan
*Phylogeny
RNA, Ribosomal, 16S/genetics
Seawater/*microbiology
Sequence Analysis, DNA

@article {pmid30764885,
year = {2019},
author = {Lipinska, AP and Serrano-Serrano, ML and Cormier, A and Peters, AF and Kogame, K and Cock, JM and Coelho, SM},
title = {Rapid turnover of life-cycle-related genes in the brown algae.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {35},
doi = {10.1186/s13059-019-1630-6},
pmid = {30764885},
issn = {1474-760X},
support = {638240//European Research Council/International ; },
mesh = {*Evolution, Molecular ; Gene Duplication ; *Gene Expression ; Germ Cells, Plant ; Life Cycle Stages/*genetics ; Phaeophyta/*genetics/growth & development/metabolism ; Phenotype ; *Selection, Genetic ; },
abstract = {BACKGROUND: Sexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, many plants and algae alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. In many algae, gametophytes and sporophytes are independent and free-living and may present dramatic phenotypic differences. The same shared genome can therefore be subject to different, even conflicting, selection pressures during each of the life cycle generations. Here, we analyze the nature and extent of genome-wide, generation-biased gene expression in four species of brown algae with contrasting levels of dimorphism between life cycle generations.

RESULTS: We show that the proportion of the transcriptome that is generation-specific is broadly associated with the level of phenotypic dimorphism between the life cycle stages. Importantly, our data reveals a remarkably high turnover rate for life-cycle-related gene sets across the brown algae and highlights the importance not only of co-option of regulatory programs from one generation to the other but also of a role for newly emerged, lineage-specific gene expression patterns in the evolution of the gametophyte and sporophyte developmental programs in this major eukaryotic group. Moreover, we show that generation-biased genes display distinct evolutionary modes, with gametophyte-biased genes evolving rapidly at the coding sequence level whereas sporophyte-biased genes tend to exhibit changes in their patterns of expression.

CONCLUSION: Our analysis uncovers the characteristics, expression patterns, and evolution of generation-biased genes and underlines the selective forces that shape this previously underappreciated source of phenotypic diversity.},
}

*Evolution, Molecular
Gene Duplication
*Gene Expression
Germ Cells, Plant
Life Cycle Stages/*genetics
Phaeophyta/*genetics/growth & development/metabolism
Phenotype
*Selection, Genetic

@article {pmid30763317,
year = {2019},
author = {Raza, Q and Choi, JY and Li, Y and O'Dowd, RM and Watkins, SC and Chikina, M and Hong, Y and Clark, NL and Kwiatkowski, AV},
title = {Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila.},
journal = {PLoS genetics},
volume = {15},
number = {2},
pages = {e1007720},
doi = {10.1371/journal.pgen.1007720},
pmid = {30763317},
issn = {1553-7404},
support = {R01 HG009299/HG/NHGRI NIH HHS/United States ; R01 HL127711/HL/NHLBI NIH HHS/United States ; R01 GM086423/GM/NIGMS NIH HHS/United States ; },
mesh = {Actin Cytoskeleton/metabolism ; Actins/*metabolism ; Adherens Junctions/metabolism ; Animals ; Cadherins/*metabolism ; Cell Adhesion/*physiology ; Cell Membrane/metabolism ; Cell Movement/physiology ; Circadian Rhythm Signaling Peptides and Proteins/*metabolism ; Drosophila/*metabolism ; Drosophila Proteins/*metabolism ; Signal Transduction/physiology ; },
abstract = {The adherens junction couples the actin cytoskeletons of neighboring cells to provide the foundation for multicellular organization. The core of the adherens junction is the cadherin-catenin complex that arose early in the evolution of multicellularity to link actin to intercellular adhesions. Over time, evolutionary pressures have shaped the signaling and mechanical functions of the adherens junction to meet specific developmental and physiological demands. Evolutionary rate covariation (ERC) identifies proteins with correlated fluctuations in evolutionary rate that can reflect shared selective pressures and functions. Here we use ERC to identify proteins with evolutionary histories similar to the Drosophila E-cadherin (DE-cad) ortholog. Core adherens junction components α-catenin and p120-catenin displayed positive ERC correlations with DE-cad, indicating that they evolved under similar selective pressures during evolution between Drosophila species. Further analysis of the DE-cad ERC profile revealed a collection of proteins not previously associated with DE-cad function or cadherin-mediated adhesion. We then analyzed the function of a subset of ERC-identified candidates by RNAi during border cell (BC) migration and identified novel genes that function to regulate DE-cad. Among these, we found that the gene CG42684, which encodes a putative GTPase activating protein (GAP), regulates BC migration and adhesion. We named CG42684 raskol ("to split" in Russian) and show that it regulates DE-cad levels and actin protrusions in BCs. We propose that Raskol functions with DE-cad to restrict Ras/Rho signaling and help guide BC migration. Our results demonstrate that a coordinated selective pressure has shaped the adherens junction and this can be leveraged to identify novel components of the complexes and signaling pathways that regulate cadherin-mediated adhesion.},
}

Actin Cytoskeleton/metabolism
Actins/*metabolism
Adherens Junctions/metabolism
Animals
Cadherins/*metabolism
Cell Adhesion/*physiology
Cell Membrane/metabolism
Cell Movement/physiology
Circadian Rhythm Signaling Peptides and Proteins/*metabolism
Drosophila/*metabolism
Drosophila Proteins/*metabolism
Signal Transduction/physiology

@article {pmid30762281,
year = {2019},
author = {Chen, IK and Satinsky, BM and Velicer, GJ and Yu, YN},
title = {sRNA-pathway genes regulating myxobacterial development exhibit clade-specific evolution.},
journal = {Evolution & development},
volume = {21},
number = {2},
pages = {82-95},
doi = {10.1111/ede.12281},
pmid = {30762281},
issn = {1525-142X},
support = {GM079690/NH/NIH HHS/United States ; },
mesh = {*Evolution, Molecular ; Genome, Bacterial ; Mutagenesis, Insertional ; Myxococcus xanthus/*genetics/growth & development ; Phenotype ; Phylogeny ; RNA, Small Untranslated/*genetics ; },
abstract = {Small non-coding RNAs (sRNAs) control bacterial gene expression involved in a wide range of important cellular processes. In the highly social bacterium Myxococcus xanthus, the sRNA Pxr prevents multicellular fruiting-body development when nutrients are abundant. Pxr was discovered from the evolution of a developmentally defective strain (OC) into a developmentally proficient strain (PX). In OC, Pxr is constitutively expressed and blocks development even during starvation. In PX, one mutation deactivates Pxr allowing development to proceed. We screened for transposon mutants that suppress the OC defect and thus potentially reveal new Pxr-pathway components. Insertions significantly restoring development were found in four genes-rnd, rnhA, stkA and Mxan_5793-not previously associated with an sRNA activity. Phylogenetic analysis suggests that the Pxr pathway was constructed within the Cystobacterineae suborder both by co-option of genes predating the Myxococcales order and incorporation of a novel gene (Mxan_5793). Further, the sequence similarity of rnd, rnhA and stkA homologs relative to M. xanthus alleles was found to decrease greatly among species beyond the Cystobacterineae suborder compared to the housekeeping genes examined. Finally, ecological context differentially affected the developmental phenotypes of distinct mutants, with implications for the evolution of development in variable environments.},
}

*Evolution, Molecular
Genome, Bacterial
Mutagenesis, Insertional
Myxococcus xanthus/*genetics/growth & development
Phenotype
Phylogeny
RNA, Small Untranslated/*genetics

@article {pmid30761165,
year = {2019},
author = {Dipp-Álvarez, M and Cruz-Ramírez, A},
title = {A Phylogenetic Study of the ANT Family Points to a preANT Gene as the Ancestor of Basal and euANT Transcription Factors in Land Plants.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {17},
doi = {10.3389/fpls.2019.00017},
pmid = {30761165},
issn = {1664-462X},
abstract = {Comparative genomics has revealed that members of early divergent lineages of land plants share a set of highly conserved transcription factors (TFs) with flowering plants. While gene copy numbers have expanded through time, it has been predicted that diversification, co-option, and reassembly of gene regulatory networks implicated in development are directly related to morphological innovations that led to more complex land plant bodies. Examples of key networks have been deeply studied in Arabidopsis thaliana, such as those involving the AINTEGUMENTA (ANT) gene family that encodes AP2-type TFs. These TFs play significant roles in plant development such as the maintenance of stem cell niches, the correct development of the embryo and the formation of lateral organs, as well as fatty acid metabolism. Previously, it has been hypothesized that the common ancestor of mosses and vascular plants encoded two ANT genes that later diversified in seed plants. However, algae and bryophyte sequences have been underrepresented from such phylogenetic analyses. To understand the evolution of ANT in a complete manner, we performed phylogenetic analyses of ANT protein sequences of representative species from across the Streptophyta clade, including algae, liverworts, and hornworts, previously unrepresented. Moreover, protein domain architecture, selection analyses, and regulatory cis elements prediction, allowed us to propose a scenario of how the evolution of ANT genes occurred. In this study we show that a duplication of a preANT-like gene in the ancestor of embryophytes may have given rise to the land plant-exclusive basalANT and euANT lineages. We hypothesize that the absence of euANT-type and basalANT-type sequences in algae, and its presence in extant land plant species, suggests that the divergence of pre-ANT into basal and eu-ANT clades in embryophytes may have influenced the conquest of land by plants, as ANT TFs play important roles in tolerance to desiccation and the establishment, maintenance, and development of complex multicellular structures which either became more complex or appeared in land plants.},
}

@article {pmid30760850,
year = {2019},
author = {Junqueira Alves, C and Yotoko, K and Zou, H and Friedel, RH},
title = {Origin and evolution of plexins, semaphorins, and Met receptor tyrosine kinases.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {1970},
doi = {10.1038/s41598-019-38512-y},
pmid = {30760850},
issn = {2045-2322},
support = {R01 NS092735/NS/NINDS NIH HHS/United States ; R01 NS092735/NS/NINDS NIH HHS/United States ; },
abstract = {The transition from unicellular to multicellular organisms poses the question as to when genes that regulate cell-cell interactions emerged during evolution. The receptor and ligand pairing of plexins and semaphorins regulates cellular interactions in a wide range of developmental and physiological contexts. We surveyed here genomes of unicellular eukaryotes and of non-bilaterian and bilaterian Metazoa and performed phylogenetic analyses to gain insight into the evolution of plexin and semaphorin families. Remarkably, we detected plexins and semaphorins in unicellular choanoflagellates, indicating their evolutionary origin in a common ancestor of Choanoflagellida and Metazoa. The plexin domain structure is conserved throughout all clades; in contrast, semaphorins are structurally diverse. Choanoflagellate semaphorins are transmembrane proteins with multiple fibronectin type III domains following the N-terminal Sema domain (termed Sema-FN). Other previously not yet described semaphorin classes include semaphorins of Ctenophora with tandem immunoglobulin domains (Sema-IG) and secreted semaphorins of Echinoderamata (Sema-SP, Sema-SI). Our study also identified Met receptor tyrosine kinases (RTKs), which carry a truncated plexin extracellular domain, in several bilaterian clades, indicating evolutionary origin in a common ancestor of Bilateria. In addition, a novel type of Met-like RTK with a complete plexin extracellular domain was detected in Lophotrochozoa and Echinodermata (termed Met-LP RTK). Our findings are consistent with an ancient function of plexins and semaphorins in regulating cytoskeletal dynamics and cell adhesion that predates their role as axon guidance molecules.},
}

@article {pmid30760717,
year = {2019},
author = {Ferrari, C and Proost, S and Janowski, M and Becker, J and Nikoloski, Z and Bhattacharya, D and Price, D and Tohge, T and Bar-Even, A and Fernie, A and Stitt, M and Mutwil, M},
title = {Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {737},
doi = {10.1038/s41467-019-08703-2},
pmid = {30760717},
issn = {2041-1723},
mesh = {Chlorophyta/genetics ; *Circadian Rhythm ; Embryophyta/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; Gene Expression Profiling/*methods ; Photosynthesis/genetics ; Phylogeny ; Rhodophyta/genetics ; Transcriptome/*genetics ; },
abstract = {Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.},
}

Chlorophyta/genetics
*Circadian Rhythm
Embryophyta/genetics
Eukaryota/classification/*genetics
*Evolution, Molecular
Gene Expression Profiling/*methods
Photosynthesis/genetics
Phylogeny
Rhodophyta/genetics
Transcriptome/*genetics

@article {pmid30740458,
year = {2019},
author = {Oborník, M},
title = {In the beginning was the word: How terminology drives our understanding of endosymbiotic organelles.},
journal = {Microbial cell (Graz, Austria)},
volume = {6},
number = {2},
pages = {134-141},
doi = {10.15698/mic2019.02.669},
pmid = {30740458},
issn = {2311-2638},
abstract = {The names we give objects of research, to some extent, predispose our ways of thinking about them. Misclassifications of Oomycota, Microsporidia, Myxosporidia, and Helicosporidia have obviously affected not only their formal taxonomic names, but also the methods and approaches with which they have been investigated. Therefore, it is important to name biological entities with accurate terms in order to avoid discrepancies in researching them. The endosymbiotic origin of mitochondria and plastids is now the most accepted scenario for their evolution. Since it is apparent that there is no natural definitive border between bacteria and semiautonomous organelles, I propose that mitochondria and plastids should be called bacteria and classified accordingly, in the bacterial classification system. I discuss some consequences of this approach, including: i) the resulting "changes" in the abundances of bacteria, ii) the definitions of terms like microbiome or multicellularity, and iii) the concept of endosymbiotic domestication.},
}

@article {pmid30729842,
year = {2019},
author = {Tan, J and He, Q and Pentz, JT and Peng, C and Yang, X and Tsai, MH and Chen, Y and Ratcliff, WC and Jiang, L},
title = {Copper oxide nanoparticles promote the evolution of multicellularity in yeast.},
journal = {Nanotoxicology},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/17435390.2018.1553253},
pmid = {30729842},
issn = {1743-5404},
abstract = {Engineered nanomaterials are rapidly becoming an essential component of modern technology. Thousands of tons of nanomaterials are manufactured, used, and subsequently released into the environment annually. While the presence of these engineered nanomaterials in the environment has profound effects on various biological systems in the short term, little work has been done to understand their consequences over long, evolutionary timescales. The evolution of multicellularity is a critical step in the origin of complex life on Earth and a unique strategy for microorganisms to alleviate adverse environmental impacts, yet the selective pressures that favor the evolution of multicellular groups remain poorly understood. Here, we show that engineered nanomaterials, specifically copper oxide nanoparticles (CuO NPs), promote the evolution of undifferentiated multicellularity in Baker's yeast (Saccharomyces cerevisiae strain Y55). Transcriptomic analysis suggests that multicellularity mitigates the negative effects of CuO NPs in yeast cells and shifts their metabolism from alcoholic fermentation towards aerobic respiration, potentially increasing resource efficiency and providing a fitness benefit during CuO NP exposure. Competition assays also confirm that the multicellular yeast possesses a fitness advantage when exposed to CuO NPs. Our results, therefore, demonstrate that nanoparticles can have profound and unexpected evolutionary consequences, underscoring the need for a more comprehensive understanding of the long-term biological impacts of nanomaterial pollution.},
}

@article {pmid30728304,
year = {2019},
author = {Peyraud, R and Mbengue, M and Barbacci, A and Raffaele, S},
title = {Intercellular cooperation in a fungal plant pathogen facilitates host colonization.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {8},
pages = {3193-3201},
doi = {10.1073/pnas.1811267116},
pmid = {30728304},
issn = {1091-6490},
support = {336808//European Research Council/International ; },
mesh = {Arabidopsis/genetics/growth & development/*microbiology ; Ascomycota/genetics/*pathogenicity ; Genome, Plant/genetics ; Host-Pathogen Interactions/*genetics ; Hyphae/genetics/pathogenicity ; Plant Diseases/*genetics/microbiology ; },
abstract = {Cooperation is associated with major transitions in evolution such as the emergence of multicellularity. It is central to the evolution of many complex traits in nature, including growth and virulence in pathogenic bacteria. Whether cells of multicellular parasites function cooperatively during infection remains, however, largely unknown. Here, we show that hyphal cells of the fungal pathogen Sclerotinia sclerotiorum reprogram toward division of labor to facilitate the colonization of host plants. Using global transcriptome sequencing, we reveal that gene expression patterns diverge markedly in cells at the center and apex of hyphae during Arabidopsis thaliana colonization compared with in vitro growth. We reconstructed a genome-scale metabolic model for S. sclerotiorum and used flux balance analysis to demonstrate metabolic heterogeneity supporting division of labor between hyphal cells. Accordingly, continuity between the central and apical compartments of invasive hyphae was required for optimal growth in planta Using a multicell model of fungal hyphae, we show that this cooperative functioning enhances fungal growth predominantly during host colonization. Our work identifies cooperation in fungal hyphae as a mechanism emerging at the multicellular level to support host colonization and virulence.},
}

Arabidopsis/genetics/growth & development/*microbiology
Ascomycota/genetics/*pathogenicity
Genome, Plant/genetics
Host-Pathogen Interactions/*genetics
Hyphae/genetics/pathogenicity
Plant Diseases/*genetics/microbiology

@article {pmid30718271,
year = {2019},
author = {Fischer, MS and Jonkers, W and Glass, NL},
title = {Integration of Self and Non-self Recognition Modulates Asexual Cell-to-Cell Communication in Neurospora crassa.},
journal = {Genetics},
volume = {211},
number = {4},
pages = {1255-1267},
doi = {10.1534/genetics.118.301780},
pmid = {30718271},
issn = {1943-2631},
support = {P01 GM068087/GM/NIGMS NIH HHS/United States ; S10 OD021828/OD/NIH HHS/United States ; T32 GM007127/GM/NIGMS NIH HHS/United States ; },
mesh = {*Chemotaxis ; Fungal Proteins/genetics/metabolism ; MAP Kinase Signaling System ; Neurospora crassa/genetics/*physiology ; *Quorum Sensing ; },
abstract = {Cells rarely exist alone, which drives the evolution of diverse mechanisms for identifying and responding appropriately to the presence of other nearby cells. Filamentous fungi depend on somatic cell-to-cell communication and fusion for the development and maintenance of a multicellular, interconnected colony that is characteristic of this group of organisms. The filamentous fungus Neurospora crassa is a model for investigating the mechanisms of somatic cell-to-cell communication and fusion. N. crassa cells chemotropically grow toward genetically similar cells, which ultimately make physical contact and undergo cell fusion. Here, we describe the development of a Pprm1-luciferase reporter system that differentiates whether genes function upstream or downstream of a conserved MAP kinase (MAPK) signaling complex, by using a set of mutants required for communication and cell fusion. The vast majority of these mutants are deficient for self-fusion and for fusion when paired with wild-type cells. However, the Δham-11 mutant is unique in that it fails to undergo self-fusion, but chemotropic interactions and cell fusion are restored in Δham-11 + wild-type interactions. In genetically dissimilar cells, chemotropic interactions are regulated by genetic differences at doc-1 and doc-2, which regulate prefusion non-self recognition; cells with dissimilar doc-1 and doc-2 alleles show greatly reduced cell-fusion frequencies. Here, we show that HAM-11 functions in parallel with the DOC-1 and DOC-2 proteins to regulate the activity of the MAPK signaling complex. Together, our data support a model of integrated self and non-self recognition processes that modulate somatic cell-to-cell communication in N. crassa.},
}

*Chemotaxis
Fungal Proteins/genetics/metabolism
MAP Kinase Signaling System
Neurospora crassa/genetics/*physiology
*Quorum Sensing

@article {pmid30717103,
year = {2019},
author = {Gonçalves, DS and Ferreira, MDS and Guimarães, AJ},
title = {Extracellular Vesicles from the Protozoa Acanthamoeba castellanii: Their Role in Pathogenesis, Environmental Adaptation and Potential Applications.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {6},
number = {1},
pages = {},
doi = {10.3390/bioengineering6010013},
pmid = {30717103},
issn = {2306-5354},
support = {JCNE 2018//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro - FAPERJ./ ; },
abstract = {Extracellular vesicles (EVs) are membranous compartments of distinct cellular origin and biogenesis, displaying different sizes and include exosomes, microvesicles, and apoptotic bodies. The EVs have been described in almost every living organism, from simple unicellular to higher evolutionary scale multicellular organisms, such as mammals. Several functions have been attributed to these structures, including roles in energy acquisition, cell-to-cell communication, gene expression modulation and pathogenesis. In this review, we described several aspects of the recently characterized EVs of the protozoa Acanthamoeba castellanii, a free-living amoeba (FLA) of emerging epidemiological importance, and compare their features to other parasites' EVs. These A. castellanii EVs are comprised of small microvesicles and exosomes and carry a wide range of molecules involved in many biological processes like cell signaling, carbohydrate metabolism and proteolytic activity, such as kinases, glucanases, and proteases, respectively. Several biomedical applications of these EVs have been proposed lately, including their use in vaccination, biofuel production, and the pharmaceutical industry, such as platforms for drug delivery.},
}

@article {pmid30714631,
year = {2019},
author = {Baluška, F and Reber, A},
title = {Sentience and Consciousness in Single Cells: How the First Minds Emerged in Unicellular Species.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {41},
number = {3},
pages = {e1800229},
doi = {10.1002/bies.201800229},
pmid = {30714631},
issn = {1521-1878},
abstract = {A reductionistic, bottom-up, cellular-based concept of the origins of sentience and consciousness has been put forward. Because all life is based on cells, any evolutionary theory of the emergence of sentience and consciousness must be grounded in mechanisms that take place in prokaryotes, the simplest unicellular species. It has been posited that subjective awareness is a fundamental property of cellular life. It emerges as an inherent feature of, and contemporaneously with, the very first life-forms. All other varieties of mentation are the result of evolutionary mechanisms based on this singular event. Therefore, all forms of sentience and consciousness evolve from this original instantiation in prokaryotes. It has also been identified that three cellular structures and mechanisms that likely play critical roles here are excitable membranes, oscillating cytoskeletal polymers, and structurally flexible proteins. Finally, basic biophysical principles are proposed to guide those processes that underly the emergence of supracellular sentience from cellular sentience in multicellular organisms.},
}