@article {pmid33972551,
year = {2021},
author = {Tsutsui, K and Machida, H and Nakagawa, A and Ahn, K and Morita, R and Sekiguchi, K and Miner, JH and Fujiwara, H},
title = {Mapping the molecular and structural specialization of the skin basement membrane for inter-tissue interactions.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2577},
pmid = {33972551},
issn = {2041-1723},
support = {25122720//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 26670533//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20H03706//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMJCR1926//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; },
abstract = {Inter-tissue interaction is fundamental to multicellularity. Although the basement membrane (BM) is located at tissue interfaces, its mode of action in inter-tissue interactions remains poorly understood, mainly because the molecular and structural details of the BM at distinct inter-tissue interfaces remain unclear. By combining quantitative transcriptomics and immunohistochemistry, we systematically identify the cellular origin, molecular identity and tissue distribution of extracellular matrix molecules in mouse hair follicles, and reveal that BM composition and architecture are exquisitely specialized for distinct inter-tissue interactions, including epithelial-fibroblast, epithelial-muscle and epithelial-nerve interactions. The epithelial-fibroblast interface, namely, hair germ-dermal papilla interface, makes asymmetrically organized side-specific heterogeneity in the BM, defined by the newly characterized interface, hook and mesh BMs. One component of these BMs, laminin α5, is required for hair cycle regulation and hair germ-dermal papilla anchoring. Our study highlights the significance of BM heterogeneity in distinct inter-tissue interactions.},
}

@article {pmid33961843,
year = {2021},
author = {Levin, M},
title = {Bioelectrical approaches to cancer as a problem of the scaling of the cellular self.},
journal = {Progress in biophysics and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pbiomolbio.2021.04.007},
pmid = {33961843},
issn = {1873-1732},
abstract = {One lens with which to understand the complex phenomenon of cancer is that of developmental biology. Cancer is the inevitable consequence of a breakdown of the communication that enables individual cells to join into computational networks that work towards large-scale, morphogenetic goals instead of more primitive, unicellular objectives. This perspective suggests that cancer may be a physiological disorder, not necessarily due to problems with the genetically-specified protein hardware. One aspect of morphogenetic coordination is bioelectric signaling, and indeed an abnormal bioelectric signature non-invasively reveals the site of incipient tumors in amphibian models. Functionally, a disruption of resting potential states triggers metastatic melanoma phenotypes in embryos with no genetic defects or carcinogen exposure. Conversely, optogenetic or molecular-biological modulation of bioelectric states can over-ride powerful oncogenic mutations and prevent or normalize tumors. The bioelectrically-mediated information flows that harness cells toward body-level anatomical outcomes represent a very attractive and tractable endogenous control system, which is being targeted by emerging approaches to cancer.},
}

@article {pmid33952585,
year = {2021},
author = {Russo, M and Sogari, A and Bardelli, A},
title = {Adaptive Evolution: How Bacteria and Cancer Cells Survive Stressful Conditions and Drug Treatment.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-20-1588},
pmid = {33952585},
issn = {2159-8290},
abstract = {Cancer is characterized by loss of the regulatory mechanisms that preserve homeostasis in multicellular organisms, such as controlled proliferation, cell-cell adhesion, and tissue differentiation. The breakdown of multicellularity rules is accompanied by activation of "selfish," unicellular-like life features, which are linked to the increased adaptability to environmental changes displayed by cancer cells. Mechanisms of stress response, resembling those observed in unicellular organisms, are actively exploited by mammalian cancer cells to boost genetic diversity and increase chances of survival under unfavorable conditions, such as lack of oxygen/nutrients or exposure to drugs. Unicellular organisms under stressful conditions (e.g., antibiotic treatment) stop replicating or slowly divide and transiently increase their mutation rates to foster diversity, a process known as adaptive mutability. Analogously, tumor cells exposed to drugs enter a persister phenotype and can reduce DNA replication fidelity, which in turn fosters genetic diversity. The implications of adaptive evolution are of relevance to understand resistance to anticancer therapies.},
}

@article {pmid33950183,
year = {2021},
author = {Li, X and Hou, Z and Xu, C and Shi, X and Yang, L and Lewis, LA and Zhong, B},
title = {Large phylogenomic datasets reveal deep relationships and trait evolution in chlorophyte green algae.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evab101},
pmid = {33950183},
issn = {1759-6653},
abstract = {The chlorophyte green algae (Chlorophyta) are species-rich ancient groups ubiquitous in various habitats with high cytological diversity, ranging from microscopic to macroscopic organisms. However, the deep phylogeny within core Chlorophyta remains unresolved, in part due to the relatively sparse taxon and gene sampling in previous studies. Here we contribute new transcriptomic data and reconstruct phylogenetic relationships of core Chlorophyta based on four large datasets up to 2698 genes of 70 species, representing 80% of extant orders. The impacts of outgroup choice, missing data, bootstrap-support cutoffs, and model misspecification in phylogenetic inference of core Chlorophyta are examined. The species tree topologies of core Chlorophyta from different analyses are highly congruent, with strong supports at many relationships (e.g., the Bryopsidales and the Scotinosphaerales-Dasycladales clade). The monophyly of Chlorophyceae and of Trebouxiophyceae as well as the uncertain placement of Chlorodendrophyceae and Pedinophyceae corroborate results from previous studies. The reconstruction of ancestral scenarios illustrates the evolution of the freshwater-sea and microscopic-macroscopic transition in the Ulvophyceae, and the transformation of unicellular→colonial→multicellular in the chlorophyte green algae. In addition, we provided new evidence that serine is encoded by both canonical codons and non-canonical TAG code in Scotinosphaerales, and stop-to-sense codon reassignment in the Ulvophyceae has originated independently at least three times. Our robust phylogenetic framework of core Chlorophyta unveils the evolutionary history of phycoplast, cyto-morphology and non-canonical genetic codes in chlorophyte green algae.},
}

@article {pmid33947812,
year = {2021},
author = {Hartl, B and Hübl, M and Kahl, G and Zöttl, A},
title = {Microswimmers learning chemotaxis with genetic algorithms.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {19},
pages = {},
doi = {10.1073/pnas.2019683118},
pmid = {33947812},
issn = {1091-6490},
abstract = {Various microorganisms and some mammalian cells are able to swim in viscous fluids by performing nonreciprocal body deformations, such as rotating attached flagella or by distorting their entire body. In order to perform chemotaxis (i.e., to move toward and to stay at high concentrations of nutrients), they adapt their swimming gaits in a nontrivial manner. Here, we propose a computational model, which features autonomous shape adaptation of microswimmers moving in one dimension toward high field concentrations. As an internal decision-making machinery, we use artificial neural networks, which control the motion of the microswimmer. We present two methods to measure chemical gradients, spatial and temporal sensing, as known for swimming mammalian cells and bacteria, respectively. Using the genetic algorithm NeuroEvolution of Augmenting Topologies, surprisingly simple neural networks evolve. These networks control the shape deformations of the microswimmers and allow them to navigate in static and complex time-dependent chemical environments. By introducing noisy signal transmission in the neural network, the well-known biased run-and-tumble motion emerges. Our work demonstrates that the evolution of a simple and interpretable internal decision-making machinery coupled to the environment allows navigation in diverse chemical landscapes. These findings are of relevance for intracellular biochemical sensing mechanisms of single cells or for the simple nervous system of small multicellular organisms such as Caenorhabditis elegans.},
}

@article {pmid33947439,
year = {2021},
author = {Wang, SY and Pollina, EA and Wang, IH and Pino, LK and Bushnell, HL and Takashima, K and Fritsche, C and Sabin, G and Garcia, BA and Greer, PL and Greer, EL},
title = {Role of epigenetics in unicellular to multicellular transition in Dictyostelium.},
journal = {Genome biology},
volume = {22},
number = {1},
pages = {134},
pmid = {33947439},
issn = {1474-760X},
support = {Simon Yuan Wang//Croucher Foundation/ ; Yuan Wang//Charles A. King Trust (US)/ ; Elizabeth Pollina//Life Sciences Research Foundation/ ; K99AG064042/AG/NIA NIH HHS/United States ; DP2AG067490/AG/NIA NIH HHS/United States ; R00AG043550/AG/NIA NIH HHS/United States ; DP2AG055947/AG/NIA NIH HHS/United States ; T32CA009140/NH/NIH HHS/United States ; Ken Takashima//Japan Society for the Promotion of Science/ ; R01GM110174/GM/NIGMS NIH HHS/United States ; Paul Greer//Searle Scholars Program/ ; Paul Greer//Rita Allen Foundation/ ; },
abstract = {BACKGROUND: The evolution of multicellularity is a critical event that remains incompletely understood. We use the social amoeba, Dictyostelium discoideum, one of the rare organisms that readily transits back and forth between both unicellular and multicellular stages, to examine the role of epigenetics in regulating multicellularity.

RESULTS: While transitioning to multicellular states, patterns of H3K4 methylation and H3K27 acetylation significantly change. By combining transcriptomics, epigenomics, chromatin accessibility, and orthologous gene analyses with other unicellular and multicellular organisms, we identify 52 conserved genes, which are specifically accessible and expressed during multicellular states. We validated that four of these genes, including the H3K27 deacetylase hdaD, are necessary and that an SMC-like gene, smcl1, is sufficient for multicellularity in Dictyostelium.

CONCLUSIONS: These results highlight the importance of epigenetics in reorganizing chromatin architecture to facilitate multicellularity in Dictyostelium discoideum and raise exciting possibilities about the role of epigenetics in the evolution of multicellularity more broadly.},
}

@article {pmid33947322,
year = {2021},
author = {Orban, A and Weber, A and Herzog, R and Hennicke, F and Rühl, M},
title = {Transcriptome of different fruiting stages in the cultivated mushroom Cyclocybe aegerita suggests a complex regulation of fruiting and reveals enzymes putatively involved in fungal oxylipin biosynthesis.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {324},
pmid = {33947322},
issn = {1471-2164},
abstract = {BACKGROUND: Cyclocybe aegerita (syn. Agrocybe aegerita) is a commercially cultivated mushroom. Its archetypal agaric morphology and its ability to undergo its whole life cycle under laboratory conditions makes this fungus a well-suited model for studying fruiting body (basidiome, basidiocarp) development. To elucidate the so far barely understood biosynthesis of fungal volatiles, alterations in the transcriptome during different developmental stages of C. aegerita were analyzed and combined with changes in the volatile profile during its different fruiting stages.

RESULTS: A transcriptomic study at seven points in time during fruiting body development of C. aegerita with seven mycelial and five fruiting body stages was conducted. Differential gene expression was observed for genes involved in fungal fruiting body formation showing interesting transcriptional patterns and correlations of these fruiting-related genes with the developmental stages. Combining transcriptome and volatilome data, enzymes putatively involved in the biosynthesis of C8 oxylipins in C. aegerita including lipoxygenases (LOXs), dioxygenases (DOXs), hydroperoxide lyases (HPLs), alcohol dehydrogenases (ADHs) and ene-reductases could be identified. Furthermore, we were able to localize the mycelium as the main source for sesquiterpenes predominant during sporulation in the headspace of C. aegerita cultures. In contrast, changes in the C8 profile detected in late stages of development are probably due to the activity of enzymes located in the fruiting bodies.

CONCLUSIONS: In this study, the combination of volatilome and transcriptome data of C. aegerita revealed interesting candidates both for functional genetics-based analysis of fruiting-related genes and for prospective enzyme characterization studies to further elucidate the so far barely understood biosynthesis of fungal C8 oxylipins.},
}

@article {pmid33924996,
year = {2021},
author = {Isaksson, H and Conlin, PL and Kerr, B and Ratcliff, WC and Libby, E},
title = {The Consequences of Budding versus Binary Fission on Adaptation and Aging in Primitive Multicellularity.},
journal = {Genes},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/genes12050661},
pmid = {33924996},
issn = {2073-4425},
support = {IOS-1656849//National Science Foundation/ ; IOS-1656549//National Science Foundation/ ; },
abstract = {Early multicellular organisms must gain adaptations to outcompete their unicellular ancestors, as well as other multicellular lineages. The tempo and mode of multicellular adaptation is influenced by many factors including the traits of individual cells. We consider how a fundamental aspect of cells, whether they reproduce via binary fission or budding, can affect the rate of adaptation in primitive multicellularity. We use mathematical models to study the spread of beneficial, growth rate mutations in unicellular populations and populations of multicellular filaments reproducing via binary fission or budding. Comparing populations once they reach carrying capacity, we find that the spread of mutations in multicellular budding populations is qualitatively distinct from the other populations and in general slower. Since budding and binary fission distribute age-accumulated damage differently, we consider the effects of cellular senescence. When growth rate decreases with cell age, we find that beneficial mutations can spread significantly faster in a multicellular budding population than its corresponding unicellular population or a population reproducing via binary fission. Our results demonstrate that basic aspects of the cell cycle can give rise to different rates of adaptation in multicellular organisms.},
}

@article {pmid33923657,
year = {2021},
author = {Romanova, MA and Maksimova, AI and Pawlowski, K and Voitsekhovskaja, OV},
title = {YABBY Genes in the Development and Evolution of Land Plants.},
journal = {International journal of molecular sciences},
volume = {22},
number = {8},
pages = {},
doi = {10.3390/ijms22084139},
pmid = {33923657},
issn = {1422-0067},
support = {#13-04-02000, #14-04-01397, #17-04-00837//Russian Foundation for Basic Research/ ; #075-15-2020-933//the Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Mounting evidence from genomic and transcriptomic studies suggests that most genetic networks regulating the morphogenesis of land plant sporophytes were co-opted and modified from those already present in streptophyte algae and gametophytes of bryophytes sensu lato. However, thus far, no candidate genes have been identified that could be responsible for "planation", a conversion from a three-dimensional to a two-dimensional growth pattern. According to the telome theory, "planation" was required for the genesis of the leaf blade in the course of leaf evolution. The key transcription factors responsible for leaf blade development in angiosperms are YABBY proteins, which until recently were thought to be unique for seed plants. Yet, identification of a YABBY homologue in a green alga and the recent findings of YABBY homologues in lycophytes and hornworts suggest that YABBY proteins were already present in the last common ancestor of land plants. Thus, these transcriptional factors could have been involved in "planation", which fosters our understanding of the origin of leaves. Here, we summarise the current data on functions of YABBY proteins in the vegetative and reproductive development of diverse angiosperms and gymnosperms as well as in the development of lycophytes. Furthermore, we discuss a putative role of YABBY proteins in the genesis of multicellular shoot apical meristems and in the evolution of leaves in early divergent terrestrial plants.},
}

@article {pmid33911080,
year = {2021},
author = {Moreira, D and Zivanovic, Y and López-Archilla, AI and Iniesto, M and López-García, P},
title = {Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2454},
pmid = {33911080},
issn = {2041-1723},
abstract = {The Candidate Phyla Radiation (CPR) constitutes a large group of mostly uncultured bacterial lineages with small cell sizes and limited biosynthetic capabilities. They are thought to be symbionts of other organisms, but the nature of this symbiosis has been ascertained only for cultured Saccharibacteria, which are epibiotic parasites of other bacteria. Here, we study the biology and the genome of Vampirococcus lugosii, which becomes the first described species of Vampirococcus, a genus of epibiotic bacteria morphologically identified decades ago. Vampirococcus belongs to the CPR phylum Absconditabacteria. It feeds on anoxygenic photosynthetic gammaproteobacteria, fully absorbing their cytoplasmic content. The cells divide epibiotically, forming multicellular stalks whose apical cells can reach new hosts. The genome is small (1.3 Mbp) and highly reduced in biosynthetic metabolism genes, but is enriched in genes possibly related to a fibrous cell surface likely involved in interactions with the host. Gene loss has been continuous during the evolution of Absconditabacteria, and generally most CPR bacteria, but this has been compensated by gene acquisition by horizontal gene transfer and de novo evolution. Our findings support parasitism as a widespread lifestyle of CPR bacteria, which probably contribute to the control of bacterial populations in diverse ecosystems.},
}

@article {pmid33449147,
year = {2021},
author = {Kruger, AN and Mueller, JL},
title = {Mechanisms of meiotic drive in symmetric and asymmetric meiosis.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {78},
number = {7},
pages = {3205-3218},
pmid = {33449147},
issn = {1420-9071},
support = {HD094736//National Institute of Child Health and Human Development/ ; R01 HD094736/HD/NICHD NIH HHS/United States ; 1256260//National Science Foundation/ ; T32 GM007544/GM/NIGMS NIH HHS/United States ; T32GM007544/GM/NIGMS NIH HHS/United States ; T32GM007544/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Biological Evolution ; *Chromosome Segregation ; Humans ; *Meiosis ; Spindle Apparatus/*physiology ; },
abstract = {Meiotic drive, the non-Mendelian transmission of chromosomes to the next generation, functions in asymmetric or symmetric meiosis across unicellular and multicellular organisms. In asymmetric meiosis, meiotic drivers act to alter a chromosome's spatial position in a single egg. In symmetric meiosis, meiotic drivers cause phenotypic differences between gametes with and without the driver. Here we discuss existing models of meiotic drive, highlighting the underlying mechanisms and regulation governing systems for which the most is known. We focus on outstanding questions surrounding these examples and speculate on how new meiotic drive systems evolve and how to detect them.},
}

Animals
*Biological Evolution
*Chromosome Segregation
Humans
*Meiosis
Spindle Apparatus/*physiology

@article {pmid33897656,
year = {2021},
author = {Garg, R and Maldener, I},
title = {The Dual Role of the Glycolipid Envelope in Different Cell Types of the Multicellular Cyanobacterium Anabaena variabilis ATCC 29413.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {645028},
doi = {10.3389/fmicb.2021.645028},
pmid = {33897656},
issn = {1664-302X},
abstract = {Anabaena variabilis is a filamentous cyanobacterium that is capable to differentiate specialized cells, the heterocysts and akinetes, to survive under different stress conditions. Under nitrogen limited condition, heterocysts provide the filament with nitrogen by fixing N2. Akinetes are spore-like dormant cells that allow survival during adverse environmental conditions. Both cell types are characterized by the presence of a thick multilayered envelope, including a glycolipid layer. While in the heterocyst this glycolipid layer is required for the maintenance of a microoxic environment and nitrogen fixation, its function in akinetes is completely unknown. Therefore, we constructed a mutant deficient in glycolipid synthesis and investigated the performance of heterocysts and akinetes in that mutant strain. We chose to delete the gene Ava_2595, which is homolog to the known hglB gene, encoding a putative polyketide synthase previously shown to be involved in heterocyst glycolipid synthesis in Anabaena sp. PCC 7120, a species which does not form akinetes. Under the respective conditions, the Ava_2595 null mutant strain formed aberrant heterocysts and akinete-like cells, in which the specific glycolipid layers were absent. This confirmed firstly that both cell types use a glycolipid of identical chemical composition in their special envelopes and, secondly, that HglB is essential for glycolipid synthesis in both types of differentiated cells. As a consequence, the mutant was not able to fix N2 and to grow under diazotrophic conditions. Furthermore, the akinetes lacking the glycolipids showed a severely reduced tolerance to stress conditions, but could germinate normally under standard conditions. This demonstrates the importance of the glycolipid layer for the ability of akinetes as spore-like dormant cells to withstand freezing, desiccation, oxidative stress and attack by lytic enzymes. Our study established the dual role of the glycolipid layer in fulfilling different functions in the evolutionary-related specialized cells of cyanobacteria. It also indicates the existence of a common pathway involving HglB for the synthesis of glycolipids in heterocysts and akinetes.},
}

@article {pmid32101166,
year = {2020},
author = {Kaur, G and Burroughs, AM and Iyer, LM and Aravind, L},
title = {Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
pmid = {32101166},
issn = {2050-084X},
mesh = {ATPases Associated with Diverse Cellular Activities/metabolism ; Archaea/*cytology/genetics/metabolism ; Bacteria/*cytology/genetics/metabolism ; Biological Evolution ; CRISPR-Cas Systems ; Nucleotides/*metabolism ; Prokaryotic Cells ; },
abstract = {Social cellular aggregation or multicellular organization pose increased risk of transmission of infections through the system upon infection of a single cell. The generality of the evolutionary responses to this outside of Metazoa remains unclear. We report the discovery of several thematically unified, remarkable biological conflict systems preponderantly present in multicellular prokaryotes. These combine thresholding mechanisms utilizing NTPase chaperones (the MoxR-vWA couple), GTPases and proteolytic cascades with hypervariable effectors, which vary either by using a reverse transcriptase-dependent diversity-generating system or through a system of acquisition of diverse protein modules, typically in inactive form, from various cellular subsystems. Conciliant lines of evidence indicate their deployment against invasive entities, like viruses, to limit their spread in multicellular/social contexts via physical containment, dominant-negative interactions or apoptosis. These findings argue for both a similar operational 'grammar' and shared protein domains in the sensing and limiting of infections during the multiple emergences of multicellularity.},
}

ATPases Associated with Diverse Cellular Activities/metabolism
Archaea/*cytology/genetics/metabolism
Bacteria/*cytology/genetics/metabolism
Biological Evolution
CRISPR-Cas Systems
Nucleotides/*metabolism
Prokaryotic Cells

@article {pmid33802617,
year = {2021},
author = {Baluška, F and Miller, WB and Reber, AS},
title = {Biomolecular Basis of Cellular Consciousness via Subcellular Nanobrains.},
journal = {International journal of molecular sciences},
volume = {22},
number = {5},
pages = {},
pmid = {33802617},
issn = {1422-0067},
mesh = {Animals ; Biological Evolution ; Cell Biology ; Cell Membrane/*physiology ; Consciousness/*physiology ; },
abstract = {Cells emerged at the very beginning of life on Earth and, in fact, are coterminous with life. They are enclosed within an excitable plasma membrane, which defines the outside and inside domains via their specific biophysical properties. Unicellular organisms, such as diverse protists and algae, still live a cellular life. However, fungi, plants, and animals evolved a multicellular existence. Recently, we have developed the cellular basis of consciousness (CBC) model, which proposes that all biological awareness, sentience and consciousness are grounded in general cell biology. Here we discuss the biomolecular structures and processes that allow for and maintain this cellular consciousness from an evolutionary perspective.},
}

Animals
Biological Evolution
Cell Biology
Cell Membrane/*physiology
Consciousness/*physiology

@article {pmid33880702,
year = {2021},
author = {Wang, Z and Sun, X and Zhang, X and Dong, B and Yu, H},
title = {Development of a miRNA Sensor by an Inducible CRISPR-Cas9 Construct in Ciona Embryogenesis.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {33880702},
issn = {1559-0305},
support = {2019YFE0190900//The National Key Research and Development Program of China/ ; 2018YFD0900705//The National Key Research and Development Program of China/ ; 201961017//The Fundamental Research Funds for the Central Universities/ ; },
abstract = {MicroRNAs (miRNAs) regulate multicellular processes and diverse signaling pathways in organisms. The detection of the spatiotemporal expression of miRNA in vivo is crucial for uncovering the function of miRNA. However, most of the current detecting techniques cannot reflect the dynamics of miRNA sensitively in vivo. Here, we constructed a miRNA-induced CRISPR-Cas9 platform (MICR) used in marine chordate Ciona. The key component of MICR is a pre-single guide RNA (sgRNA) flanked by miRNA-binding sites that can be released by RNA-induced silencing complex (RISC) cleavage to form functional sgRNA in the presence of complementary miRNA. By using the miRNA-inducible CRISPR-on system (MICR-ON), we successfully detected the dynamic expression of a miRNA csa-miR-4018a during development of Ciona embryo. The detected patterns were validated to be consistent with the results by in situ hybridization. It is worth noting that the expression of csa-miR-4018a was examined by MICR-ON to be present in additional tissues, where no obvious signaling was detected by in situ hybridization, suggesting that the MICR-ON might be a more sensitive approach to detect miRNA signal in living animal. Thus, MICR-ON was demonstrated to be a sensitive and highly efficient approach for monitoring the dynamics of expression of miRNA in vivo and will facilitate the exploration of miRNA functions in biological systems.},
}

@article {pmid33060828,
year = {2021},
author = {Metcalfe, KS and Murali, R and Mullin, SW and Connon, SA and Orphan, VJ},
title = {Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy.},
journal = {The ISME journal},
volume = {15},
number = {2},
pages = {377-396},
pmid = {33060828},
issn = {1751-7370},
mesh = {Anaerobiosis ; Archaea/genetics ; Costa Rica ; Geologic Sediments ; In Situ Hybridization, Fluorescence ; *Methane ; *Nitrogen Fixation ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Archaeal anaerobic methanotrophs ("ANME") and sulfate-reducing Deltaproteobacteria ("SRB") form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence in situ hybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a complete nifHDK operon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g within ANME-2b-SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain reaction (HCR-) FISH targeting nifH transcripts and diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b-SEEP-SRB1g consortia incubated with a headspace containing CH4 and 15N2 revealed differences in cellular 15N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in 15N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph.},
}

Anaerobiosis
Archaea/genetics
Costa Rica
Geologic Sediments
In Situ Hybridization, Fluorescence
*Methane
*Nitrogen Fixation
Oxidation-Reduction
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid33875673,
year = {2021},
author = {Thongsripong, P and Chandler, JA and Kittayapong, P and Wilcox, BA and Kapan, DD and Bennett, SN},
title = {Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {8448},
pmid = {33875673},
issn = {2045-2322},
support = {0549514//NSF Integrative Graduate Education and Research Traineeship/ ; 0549514//NSF Integrative Graduate Education and Research Traineeship/ ; 0549514//NSF Integrative Graduate Education and Research Traineeship/ ; U54AI065359//NIH/NIAID Pacific Southwest Regional Center of Excellence/ ; P20RR018727//NIH/NCRR COBRE University of Hawai'i/ ; },
abstract = {High-throughput nucleic acid sequencing has greatly accelerated the discovery of viruses in the environment. Mosquitoes, because of their public health importance, are among those organisms whose viromes are being intensively characterized. Despite the deluge of sequence information, our understanding of the major drivers influencing the ecology of mosquito viromes remains limited. Using methods to increase the relative proportion of microbial RNA coupled with RNA-seq we characterize RNA viruses and other symbionts of three mosquito species collected along a rural to urban habitat gradient in Thailand. The full factorial study design allows us to explicitly investigate the relative importance of host species and habitat in structuring viral communities. We found that the pattern of virus presence was defined primarily by host species rather than by geographic locations or habitats. Our result suggests that insect-associated viruses display relatively narrow host ranges but are capable of spreading through a mosquito population at the geographical scale of our study. We also detected various single-celled and multicellular microorganisms such as bacteria, alveolates, fungi, and nematodes. Our study emphasizes the importance of including ecological information in viromic studies in order to gain further insights into viral ecology in systems where host specificity is driving both viral ecology and evolution.},
}

@article {pmid33874589,
year = {1993},
author = {Lucas, WJ and Ding, B and VAN DER Schoot, C},
title = {Plasmodesmata and the supracellular nature of plants.},
journal = {The New phytologist},
volume = {125},
number = {3},
pages = {435-476},
doi = {10.1111/j.1469-8137.1993.tb03897.x},
pmid = {33874589},
issn = {1469-8137},
abstract = {In the classical formulation of Münch (1930), plasmodesmata are considered to form simple cytoplasmic bridges between neighbouring plant cells to create the symplasm. This concept has dominated, if not monopolized, the thinking of plant biologists and in particular plant physiologists over the last few decades. Recent advances in ultrastructural, physiological and molecular studies on plasmodesmata indicate that this simple view is in need of revision. Structurally, the higher plant plasmodesma has been revealed to be a supramolecular complex consisting of membranes and proteins. Functionally, evidence is at hand that this complex structure appears to have evolved not only to control the size exclusion limit for intercellular diffusion of metabolites and small molecules, but also to potentiate and regulate intercellular trafficking of macromolecules, including proteins and nucleic acids. In this regard, plasmodesmal transport may share parallel regulatory mechanisms with nucleocytoplasmic transport. Based on these findings, we advance the hypothesis that plants function as supracellular, rather than multicellular, organisms. As such, the dynamics of the plant body, including cell differentiation, tissue formation, organogenesis and specialized physiological function(s), is subject to plasmodesmal regulation. Plasmodesmata presumably accomplish such regulatory roles by trafficking informational molecules which orchestrate both metabolic activity and gene expression. Current and future studies on the evolutionary origin(s) of plasmodesmata are likely to provide valuable information in terms of the genetic and molecular basis for the supracellular nature of plants. Contents Summary 435 I. Introduction 436 II. Plasmodesmal formation, structure and biochemistry 436 III. Evolution of plasmodesmata 445 IV. Symplasmic dynamics 452 V. Plasniodesmal trafficking of macromolecules: parallels with nucleocytoplasmic transport 457 VI. Role of plasmodesmata in plant development 464 VII. Concluding remarks 469 Acknowledgements 470 References 470.},
}

@article {pmid33861755,
year = {2021},
author = {Menichelli, C and Guitard, V and Martins, RM and Lèbre, S and Lopez-Rubio, JJ and Lecellier, CH and Bréhélin, L},
title = {Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes.},
journal = {PLoS computational biology},
volume = {17},
number = {4},
pages = {e1008909},
doi = {10.1371/journal.pcbi.1008909},
pmid = {33861755},
issn = {1553-7358},
abstract = {Long regulatory elements (LREs), such as CpG islands, polydA:dT tracts or AU-rich elements, are thought to play key roles in gene regulation but, as opposed to conventional binding sites of transcription factors, few methods have been proposed to formally and automatically characterize them. We present here a computational approach named DExTER (Domain Exploration To Explain gene Regulation) dedicated to the identification of candidate LREs (cLREs) and apply it to the analysis of the genomes of P. falciparum and other eukaryotes. Our analyses show that all tested genomes contain several cLREs that are somewhat conserved along evolution, and that gene expression can be predicted with surprising accuracy on the basis of these long regions only. Regulation by cLREs exhibits very different behaviours depending on species and conditions. In P. falciparum and other Apicomplexan organisms as well as in Dictyostelium discoideum, the process appears highly dynamic, with different cLREs involved at different phases of the life cycle. For multicellular organisms, the same cLREs are involved in all tissues, but a dynamic behavior is observed along embryonic development stages. In P. falciparum, whose genome is known to be strongly depleted of transcription factors, cLREs are predictive of expression with an accuracy above 70%, and our analyses show that they are associated with both transcriptional and post-transcriptional regulation signals. Moreover, we assessed the biological relevance of one LRE discovered by DExTER in P. falciparum using an in vivo reporter assay. The source code (python) of DExTER is available at https://gite.lirmm.fr/menichelli/DExTER.},
}

@article {pmid33852871,
year = {2021},
author = {Strother, PK and Brasier, MD and Wacey, D and Timpe, L and Saunders, M and Wellman, CH},
title = {A possible billion-year-old holozoan with differentiated multicellularity.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2021.03.051},
pmid = {33852871},
issn = {1879-0445},
abstract = {Sediments of the Torridonian sequence of the Northwest Scottish Highlands contain a wide array of microfossils, documenting life in a non-marine setting a billion years ago (1 Ga).1-4 Phosphate nodules from the Diabaig Formation at Loch Torridon preserve microorganisms with cellular-level fidelity,5,6 allowing for partial reconstruction of the developmental stages of a new organism, Bicellum brasieri gen. et sp. nov. The mature form of Bicellum consists of a solid, spherical ball of tightly packed cells (a stereoblast) of isodiametric cells enclosed in a monolayer of elongated, sausage-shaped cells. However, two populations of naked stereoblasts show mixed cell shapes, which we infer to indicate incipient development of elongated cells that were migrating to the periphery of the cell mass. These simple morphogenetic movements could be explained by differential cell-cell adhesion.7,8 In fact, the basic morphology of Bicellum is topologically similar to that of experimentally produced cell masses that were shown to spontaneously segregate into two distinct domains based on differential cadherin-based cell adhesion.9 The lack of rigid cell walls in the stereoblast renders an algal affinity for Bicellum unlikely: its overall morphology is more consistent with a holozoan origin. Unicellular holozoans are known today to form multicellular stages within complex life cycles,10-13 so the occurrence of such simple levels of transient multicellularity seen here is consistent with a holozoan affinity. Regardless of precise phylogenetic placement, these fossils demonstrate simple cell differentiation and morphogenic processes that are similar to those seen in some metazoans today.},
}

@article {pmid33850152,
year = {2021},
author = {Brosnan, CA and Palmer, AJ and Zuryn, S},
title = {Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2194},
pmid = {33850152},
issn = {2041-1723},
support = {P40 OD010440/OD/NIH HHS/United States ; },
abstract = {Multicellularity has coincided with the evolution of microRNAs (miRNAs), small regulatory RNAs that are integrated into cellular differentiation and homeostatic gene-regulatory networks. However, the regulatory mechanisms underpinning miRNA activity have remained largely obscured because of the precise, and thus difficult to access, cellular contexts under which they operate. To resolve these, we have generated a genome-wide map of active miRNAs in Caenorhabditis elegans by revealing cell-type-specific patterns of miRNAs loaded into Argonaute (AGO) silencing complexes. Epitope-labelled AGO proteins were selectively expressed and immunoprecipitated from three distinct tissue types and associated miRNAs sequenced. In addition to providing information on biological function, we define adaptable miRNA:AGO interactions with single-cell-type and AGO-specific resolution. We demonstrate spatial and temporal dynamicism, flexibility of miRNA loading, and suggest miRNA regulatory mechanisms via AGO selectivity in different tissues and during ageing. Additionally, we resolve widespread changes in AGO-regulated gene expression by analysing translatomes specifically in neurons.},
}

@article {pmid33834782,
year = {2021},
author = {Kwon, HY and Kumar Das, R and Jung, GT and Lee, HG and Lee, SH and Berry, SN and Tan, JKS and Park, S and Yang, JS and Park, S and Baek, K and Park, KM and Lee, JW and Choi, YK and Kim, KH and Kim, S and Kim, KP and Kang, NY and Kim, K and Chang, YT},
title = {Lipid-Oriented Live-Cell Distinction of B and T Lymphocytes.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.1c00944},
pmid = {33834782},
issn = {1520-5126},
abstract = {The identification of each cell type is essential for understanding multicellular communities. Antibodies set as biomarkers have been the main toolbox for cell-type recognition, and chemical probes are emerging surrogates. Herein we report the first small-molecule probe, CDgB, to discriminate B lymphocytes from T lymphocytes, which was previously impossible without the help of antibodies. Through the study of the origin of cell specificity, we discovered an unexpected novel mechanism of membrane-oriented live-cell distinction. B cells maintain higher flexibility in their cell membrane than T cells and accumulate the lipid-like probe CDgB more preferably. Because B and T cells share common ancestors, we tracked the cell membrane changes of the progenitor cells and disclosed the dynamic reorganization of the membrane properties over the lymphocyte differentiation progress. This study casts an orthogonal strategy for the small-molecule cell identifier and enriches the toolbox for live-cell distinction from complex cell communities.},
}

@article {pmid33816460,
year = {2021},
author = {Vassalli, QA and Colantuono, C and Nittoli, V and Ferraioli, A and Fasano, G and Berruto, F and Chiusano, ML and Kelsh, RN and Sordino, P and Locascio, A},
title = {Onecut Regulates Core Components of the Molecular Machinery for Neurotransmission in Photoreceptor Differentiation.},
journal = {Frontiers in cell and developmental biology},
volume = {9},
number = {},
pages = {602450},
pmid = {33816460},
issn = {2296-634X},
abstract = {Photoreceptor cells (PRC) are neurons highly specialized for sensing light stimuli and have considerably diversified during evolution. The genetic mechanisms that underlie photoreceptor differentiation and accompanied the progressive increase in complexity and diversification of this sensory cell type are a matter of great interest in the field. A role of the homeodomain transcription factor Onecut (Oc) in photoreceptor cell formation is proposed throughout multicellular organisms. However, knowledge of the identity of the Oc downstream-acting factors that mediate specific tasks in the differentiation of the PRC remains limited. Here, we used transgenic perturbation of the Ciona robusta Oc protein to show its requirement for ciliary PRC differentiation. Then, transcriptome profiling between the trans-activation and trans-repression Oc phenotypes identified differentially expressed genes that are enriched in exocytosis, calcium homeostasis, and neurotransmission. Finally, comparison of RNA-Seq datasets in Ciona and mouse identifies a set of Oc downstream genes conserved between tunicates and vertebrates. The transcription factor Oc emerges as a key regulator of neurotransmission in retinal cell types.},
}

@article {pmid33801615,
year = {2021},
author = {Kin, K and Schaap, P},
title = {Evolution of Multicellular Complexity in The Dictyostelid Social Amoebas.},
journal = {Genes},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/genes12040487},
pmid = {33801615},
issn = {2073-4425},
support = {742288/ERC_/European Research Council/International ; 100293/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; ALTF 295-2015//European Molecular Biology Organization/ ; H28-1002//Japanese Organisation for the Promotion of Science/ ; },
abstract = {Multicellularity evolved repeatedly in the history of life, but how it unfolded varies greatly between different lineages. Dictyostelid social amoebas offer a good system to study the evolution of multicellular complexity, with a well-resolved phylogeny and molecular genetic tools being available. We compare the life cycles of the Dictyostelids with closely related amoebozoans to show that complex life cycles were already present in the unicellular common ancestor of Dictyostelids. We propose frost resistance as an early driver of multicellular evolution in Dictyostelids and show that the cell signalling pathways for differentiating spore and stalk cells evolved from that for encystation. The stalk cell differentiation program was further modified, possibly through gene duplication, to evolve a new cell type, cup cells, in Group 4 Dictyostelids. Studies in various multicellular organisms, including Dictyostelids, volvocine algae, and metazoans, suggest as a common principle in the evolution of multicellular complexity that unicellular regulatory programs for adapting to environmental change serve as "proto-cell types" for subsequent evolution of multicellular organisms. Later, new cell types could further evolve by duplicating and diversifying the "proto-cell type" gene regulatory networks.},
}

@article {pmid33800339,
year = {2021},
author = {Patthy, L},
title = {Exon Shuffling Played a Decisive Role in the Evolution of the Genetic Toolkit for the Multicellular Body Plan of Metazoa.},
journal = {Genes},
volume = {12},
number = {3},
pages = {},
pmid = {33800339},
issn = {2073-4425},
support = {GINOP-2.3.2-15-2016-00001//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; },
abstract = {Division of labor and establishment of the spatial pattern of different cell types of multicellular organisms require cell type-specific transcription factor modules that control cellular phenotypes and proteins that mediate the interactions of cells with other cells. Recent studies indicate that, although constituent protein domains of numerous components of the genetic toolkit of the multicellular body plan of Metazoa were present in the unicellular ancestor of animals, the repertoire of multidomain proteins that are indispensable for the arrangement of distinct body parts in a reproducible manner evolved only in Metazoa. We have shown that the majority of the multidomain proteins involved in cell-cell and cell-matrix interactions of Metazoa have been assembled by exon shuffling, but there is no evidence for a similar role of exon shuffling in the evolution of proteins of metazoan transcription factor modules. A possible explanation for this difference in the intracellular and intercellular toolkits is that evolution of the transcription factor modules preceded the burst of exon shuffling that led to the creation of the proteins controlling spatial patterning in Metazoa. This explanation is in harmony with the temporal-to-spatial transition hypothesis of multicellularity that proposes that cell differentiation may have predated spatial segregation of cell types in animal ancestors.},
}

@article {pmid33795155,
year = {2021},
author = {Vos, M},
title = {Myxococcus xanthus.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2021.03.006},
pmid = {33795155},
issn = {1878-4380},
}

@article {pmid33779495,
year = {2021},
author = {Porfírio-Sousa, AL and Tice, AK and Brown, MW and J G Lahr, D},
title = {Phylogenetic reconstruction and evolution of the Rab GTPase gene family in Amoebozoa.},
journal = {Small GTPases},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/21541248.2021.1903794},
pmid = {33779495},
issn = {2154-1256},
abstract = {Rab GTPase is a paralog-rich gene family that controls the maintenance of the eukaryotic cell compartmentalization system. Diverse eukaryotes have varying numbers of Rab paralogs. Currently, little is known about the evolutionary pattern of Rab GTPase in most major eukaryotic 'supergroups'. Here, we present a comprehensive phylogenetic reconstruction of the Rab GTPase gene family in the eukaryotic 'supergroup' Amoebozoa, a diverse lineage represented by unicellular and multicellular organisms. We demonstrate that Amoebozoa conserved 20 of the 23 ancestral Rab GTPases predicted to be present in the last eukaryotic common ancestor and massively expanded several 'novel' in-paralogs. Due to these 'novel' in-paralogs, the Rab family composition dramatically varies between the members of Amoebozoa; as a consequence, 'supergroup'-based studies may significantly change our current understanding of the evolution and diversity of this gene family. The high diversity of the Rab GTPase gene family in Amoebozoa makes this 'supergroup' a key lineage to study and advance our knowledge of the evolution of Rab in Eukaryotes.},
}

@article {pmid33767367,
year = {2021},
author = {Wang, S and Liang, H and Xu, Y and Li, L and Wang, H and Sahu, DN and Petersen, M and Melkonian, M and Sahu, SK and Liu, H},
title = {Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {412},
pmid = {33767367},
issn = {2399-3642},
abstract = {Small RNAs play a major role in the post-transcriptional regulation of gene expression in eukaryotes. Despite the evolutionary importance of streptophyte algae, knowledge on small RNAs in this group of green algae is almost non-existent. We used genome and transcriptome data of 34 algal and plant species, and performed genome-wide analyses of small RNA (miRNA & siRNA) biosynthetic and degradation pathways. The results suggest that Viridiplantae started to evolve plant-like miRNA biogenesis and degradation after the divergence of the Mesostigmatophyceae in the streptophyte algae. We identified two major evolutionary transitions in small RNA metabolism in streptophyte algae; during the first transition, the origin of DCL-New, DCL1, AGO1/5/10 and AGO4/6/9 in the last common ancestor of Klebsormidiophyceae and all other streptophytes could be linked to abiotic stress responses and evolution of multicellularity in streptophytes. During the second transition, the evolution of DCL 2,3,4, and AGO 2,3,7 as well as DRB1 in the last common ancestor of Zygnematophyceae and embryophytes, suggests their possible contribution to pathogen defense and antibacterial immunity. Overall, the origin and diversification of DICER and AGO along with several other small RNA pathway-related genes among streptophyte algae suggested progressive adaptations of streptophyte algae during evolution to a subaerial environment.},
}

@article {pmid33763054,
year = {2020},
author = {Roudaire, T and Héloir, MC and Wendehenne, D and Zadoroznyj, A and Dubrez, L and Poinssot, B},
title = {Cross Kingdom Immunity: The Role of Immune Receptors and Downstream Signaling in Animal and Plant Cell Death.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {612452},
pmid = {33763054},
issn = {1664-3224},
abstract = {Both plants and animals are endowed with sophisticated innate immune systems to combat microbial attack. In these multicellular eukaryotes, innate immunity implies the presence of cell surface receptors and intracellular receptors able to detect danger signal referred as damage-associated molecular patterns (DAMPs) and pathogen-associated molecular patterns (PAMPs). Membrane-associated pattern recognition receptors (PRRs), such as Toll-like receptors (TLRs), C-type lectin receptors (CLRs), receptor-like kinases (RLKs), and receptor-like proteins (RLPs) are employed by these organisms for sensing different invasion patterns before triggering antimicrobial defenses that can be associated with a form of regulated cell death. Intracellularly, animals nucleotide-binding and oligomerization domain (NOD)-like receptors or plants nucleotide-binding domain (NBD)-containing leucine rich repeats (NLRs) immune receptors likely detect effectors injected into the host cell by the pathogen to hijack the immune signaling cascade. Interestingly, during the co-evolution between the hosts and their invaders, key cross-kingdom cell death-signaling macromolecular NLR-complexes have been selected, such as the inflammasome in mammals and the recently discovered resistosome in plants. In both cases, a regulated cell death located at the site of infection constitutes a very effective mean for blocking the pathogen spread and protecting the whole organism from invasion. This review aims to describe the immune mechanisms in animals and plants, mainly focusing on cell death signaling pathways, in order to highlight recent advances that could be used on one side or the other to identify the missing signaling elements between the perception of the invasion pattern by immune receptors, the induction of defenses or the transmission of danger signals to other cells. Although knowledge of plant immunity is less advanced, these organisms have certain advantages allowing easier identification of signaling events, regulators and executors of cell death, which could then be exploited directly for crop protection purposes or by analogy for medical research.},
}

@article {pmid33760661,
year = {2021},
author = {Barnett, AM and Mullaney, JA and Hendriks, C and Le Borgne, L and McNabb, WC and Roy, N},
title = {Porcine colonoids and enteroids keep the memory of their origin during regeneration.},
journal = {American journal of physiology. Cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpcell.00420.2020},
pmid = {33760661},
issn = {1522-1563},
support = {//New Zealand Tertiary Education Commission/ ; MAUX1803//New Zealand Ministry of Business, Innovation and Employment/ ; },
abstract = {The development of alternative in vitro culture methods has increased in the last decade as three-dimensional organoids of various tissues, including those of the small and large intestines. Due to their multicellular composition, organoids offer advantages over traditionally used immortalized or primary cell lines. However, organoids must be accurate models of their tissues of origin. This study compared gene expression profiles with respect to markers of specific cell-types (stem-cells, enterocytes, goblet and enteroendocrine cells) and barrier maturation (tight junctions) of colonoid and enteroid cultures with their tissues of origin, and colonoids with enteroids. Colonoids derived from three healthy pigs formed multi-lobed structures with a monolayer of cells similar to the crypt structures in colonic tissue. Colonoid and enteroid gene expression signatures were more similar to those found for the tissues of their origin than to each other. However, relative to their derived tissues, organoids had increased gene expression levels of stem-cell markers Sox9 and Lgr5 encoding Sex determining region Y-box 9 and leucine-rich repeat-containing G-protein coupled rector 5, respectively. In contrast, expression levels of Occl and Zo1 encoding occludin and zonula occludens 1 respectively, were decreased. Expression levels of the cell lineage markers Atoh1, Cga and Muc2 encoding atonal homolog 1, chromogranin A and mucin 2 respectively, were decreased in colonoids, while Sglt1 and Apn encoding sodium-glucose transporter 1 and aminopeptidase A respectively, were decreased in enteroids. These results indicate colonoid and enteroid cultures were predominantly comprised of undifferentiated cell-types with decreased barrier maturation relative to their tissues of origin.},
}

@article {pmid33748102,
year = {2021},
author = {Dhakshinamoorthy, R and Singh, SP},
title = {Evolution of Reproductive Division of Labor - Lessons Learned From the Social Amoeba Dictyostelium discoideum During Its Multicellular Development.},
journal = {Frontiers in cell and developmental biology},
volume = {9},
number = {},
pages = {599525},
pmid = {33748102},
issn = {2296-634X},
abstract = {The origin of multicellular life from unicellular beings is an epochal step in the evolution of eukaryotes. There are several factors influencing cell fate choices during differentiation and morphogenesis of an organism. Genetic make-up of two cells that unite and fertilize is the key factor to signal the formation of various cell-types in due course of development. Although ploidy of the cell-types determines the genetics of an individual, the role of ploidy in cell fate decisions remains unclear. Dictyostelium serves as a versatile model to study the emergence of multicellular life from unicellular life forms. In this work, we investigate the role played by ploidy status of a cell on cell fate commitments during Dictyostelium development. To answer this question, we created Dictyostelium cells of different ploidy: haploid parents and derived isogenic diploids, allowing them to undergo development. The diploid strains used in this study were generated using parasexual genetics. The ploidy status of the haploids and diploids were confirmed by microscopy, flow cytometry, and karyotyping. Prior to reconstitution, we labeled the cells by two methods. First, intragenic expression of red fluorescent protein (RFP) and second, staining the amoebae with a vital, fluorescent dye carboxyfluorescein succinimidyl ester (CFSE). RFP labeled haploid cells allowed us to track the haploids in the chimeric aggregates, slugs, and fruiting bodies. The CFSE labeling method allowed us to track both the haploids and the diploids in the chimeric developmental structures. Our findings illustrate that the haploids demonstrate sturdy cell fate commitment starting from the aggregation stage. The haploids remain crowded at the aggregation centers of the haploid-diploid chimeric aggregates. At the slug stage haploids are predominantly occupying the slug posterior, and are visible in the spore population in the fruiting bodies. Our findings show that cell fate decisions during D. discoideum development are highly influenced by the ploidy status of a cell, adding a new aspect to already known factors Here, we report that ploidy status of a cell could also play a crucial role in regulating the cell fate commitments.},
}

@article {pmid33741994,
year = {2021},
author = {Redmond, AK and McLysaght, A},
title = {Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {1783},
pmid = {33741994},
issn = {2041-1723},
mesh = {Animals ; Biological Evolution ; Ctenophora/classification/*genetics ; Genome/*genetics ; Genomics/*methods ; Models, Genetic ; *Phylogeny ; Porifera/classification/*genetics ; Species Specificity ; },
abstract = {Resolving the relationships between the major lineages in the animal tree of life is necessary to understand the origin and evolution of key animal traits. Sponges, characterized by their simple body plan, were traditionally considered the sister group of all other animal lineages, implying a gradual increase in animal complexity from unicellularity to complex multicellularity. However, the availability of genomic data has sparked tremendous controversy as some phylogenomic studies support comb jellies taking this position, requiring secondary loss or independent origins of complex traits. Here we show that incorporating site-heterogeneous mixture models and recoding into partitioned phylogenomics alleviates systematic errors that hamper commonly-applied phylogenetic models. Testing on real datasets, we show a great improvement in model-fit that attenuates branching artefacts induced by systematic error. We reanalyse key datasets and show that partitioned phylogenomics does not support comb jellies as sister to other animals at either the supermatrix or partition-specific level.},
}

Animals
Biological Evolution
Ctenophora/classification/*genetics
Genome/*genetics
Genomics/*methods
Models, Genetic
*Phylogeny
Porifera/classification/*genetics
Species Specificity

@article {pmid33727612,
year = {2021},
author = {Matriano, DM and Alegado, RA and Conaco, C},
title = {Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {5993},
pmid = {33727612},
issn = {2045-2322},
abstract = {Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome-evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.},
}

@article {pmid33717121,
year = {2021},
author = {Ramos-Martínez, E and Hernández-González, L and Ramos-Martínez, I and Pérez-Campos Mayoral, L and López-Cortés, GI and Pérez-Campos, E and Mayoral Andrade, G and Hernández-Huerta, MT and José, MV},
title = {Multiple Origins of Extracellular DNA Traps.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {621311},
pmid = {33717121},
issn = {1664-3224},
abstract = {Extracellular DNA traps (ETs) are evolutionarily conserved antimicrobial mechanisms present in protozoa, plants, and animals. In this review, we compare their similarities in species of different taxa, and put forward the hypothesis that ETs have multiple origins. Our results are consistent with a process of evolutionary convergence in multicellular organisms through the application of a congruency test. Furthermore, we discuss why multicellularity is related to the presence of a mechanism initiating the formation of ETs.},
}

@article {pmid33711511,
year = {2021},
author = {Vijg, J},
title = {From DNA damage to mutations: All roads lead to aging.},
journal = {Ageing research reviews},
volume = {68},
number = {},
pages = {101316},
doi = {10.1016/j.arr.2021.101316},
pmid = {33711511},
issn = {1872-9649},
abstract = {Damage to the repository of genetic information in cells has plagued life since its very beginning 3-4 billion years ago. Initially, in the absence of an ozone layer, especially damage from solar UV radiation must have been frequent, with other sources, most notably endogenous sources related to cell metabolism, gaining in importance over time. To cope with this high frequency of damage to the increasingly long DNA molecules that came to encode the growing complexity of cellular functions in cells, DNA repair evolved as one of the earliest genetic traits. Then as now, errors during the repair of DNA damage generated mutations, which provide the substrate for evolution by natural selection. With the emergence of multicellular organisms also the soma became a target of DNA damage and mutations. In somatic cells selection against the adverse effects of DNA damage is greatly diminished, especially in postmitotic cells after the age of first reproduction. Based on an abundance of evidence, DNA damage is now considered as the single most important driver of the degenerative processes that collectively cause aging. Here I will first briefly review the evidence for DNA damage as a cause of aging since the beginning of life. Then, after discussing the possible direct adverse effects of DNA damage and its cellular responses, I will provide an overview of the considerable progress that has recently been made in analyzing a major consequence of DNA damage in humans and other complex organisms: somatic mutations and the resulting genome mosaicism. Recent advances in studying somatic mutagenesis and genome mosaicism in different human and animal tissues will be discussed with a focus on the possible mechanisms through which loss of DNA sequence integrity could cause age-related functional decline and disease.},
}

@article {pmid33690952,
year = {2021},
author = {Darveau, RP and Curtis, MA},
title = {Oral biofilms revisited: A novel host tissue of bacteriological origin.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12374},
pmid = {33690952},
issn = {1600-0757},
abstract = {The central theme of this volume of Periodontology 2000 is that the microbial dental plaque biofilm, specifically the subgingival dental plaque biofilm, mimics a human tissue in both structure and function. As a basis for this assertion we use the definition of a tissue as an aggregate of similar cells and cell products forming a defined structure with a specific function, in a multicellular organism. Accordingly, we propose that the dental plaque biofilm represents an acquired human tissue largely of bacterial origin that maintains the health of gingival tissue. Furthermore, we acknowledge that disease can be defined as a deviation from the normal structure or an interruption to the function of any body part, organ, or system, and that is manifested by a characteristic set of symptoms and signs whose etiology, pathology, and prognosis may be known or unknown. Therefore, in this volume we present the concept that periodontitis is a disruption of the normal function of the healthy subgingival plaque biofilm with concomitant disruption to its functional properties in relation to innate defense surveillance and tissue maintenance, leading to excessive, deregulated inflammation and tissue destruction.},
}

@article {pmid33683515,
year = {2021},
author = {Ben-David, Y and Weihs, D},
title = {Modeling force application configurations and morphologies required for cancer cell invasion.},
journal = {Biomechanics and modeling in mechanobiology},
volume = {},
number = {},
pages = {},
pmid = {33683515},
issn = {1617-7940},
support = {3-17427//Ministry of Science and Technology, Israel (IL)/ ; Polak Fund for Applied Research//Technion-Israel Institute of Technology/ ; },
abstract = {We show that cell-applied, normal mechanical stresses are required for cells to penetrate into soft substrates, matching experimental observations in invasive cancer cells, while in-plane traction forces alone reproduce observations in non-cancer/noninvasive cells. Mechanobiological interactions of cells with their microenvironment drive migration and cancer invasion. We have previously shown that invasive cancer cells forcefully and rapidly push into impenetrable, physiological stiffness gels and indent them to cell-scale depths (up to 10 μm); normal, noninvasive cells indent at most to 0.7 μm. Significantly indenting cells signpost increased cancer invasiveness and higher metastatic risk in vitro and in vivo, as verified experimentally in different cancer types, yet the underlying cell-applied, force magnitudes and configurations required to produce the cell-scale gel indentations have yet to be evaluated. Hence, we have developed finite element models of forces applied onto soft, impenetrable gels using experimental cell/gel morphologies, gel mechanics, and force magnitudes. We show that in-plane traction forces can only induce small-scale indentations in soft gels (< 0.7 μm), matching experiments with various single, normal cells. Addition of a normal force (on the scale of experimental traction forces) produced cell-scale indentations that matched observations in invasive cancer cells. We note that normal stresses (force and area) determine the indentation depth, while contact area size and morphology have a minor effect, explaining the origin of experimentally observed cell morphologies. We have thus revealed controlling features facilitating invasive indentations by single cancer cells, which will allow application of our model to complex problems, such as multicellular systems.},
}

@article {pmid33678014,
year = {2021},
author = {Pen, I and Flatt, T},
title = {Asymmetry, division of labour and the evolution of ageing in multicellular organisms.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1823},
pages = {20190729},
doi = {10.1098/rstb.2019.0729},
pmid = {33678014},
issn = {1471-2970},
abstract = {Between the 1930s and 1960s, evolutionary geneticists worked out the basic principles of why organisms age. Despite much progress in the evolutionary biology of ageing since that time, however, many puzzles remain. The perhaps most fundamental of these is the question of which organisms should exhibit senescence and which should not (or which should age rapidly and which should not). The evolutionary origin of ageing from a non-senescent state has been conceptually framed, for example, in terms of the separation between germ-line and soma, the distinction between parents and their offspring, and-in unicellular organisms-the unequal distribution of cellular damage at cell division. These ideas seem to be closely related to the concept of 'division of labour' between reproduction and somatic maintenance. Here, we review these concepts and develop a toy model to explore the importance of such asymmetries for the evolution of senescence. We apply our model to the simplest case of a multicellular system: an organism consisting of two totipotent cells. Notably, we find that in organisms which reproduce symmetrically and partition damage equally, senescence is still able to evolve, contrary to previous claims. Our results might have some bearing on understanding the origin of the germ-line-soma separation and the evolution of senescence in multicellular organisms and in colonial species consisting of multiple types of individuals, such as, for example, eusocial insects with their different castes. This article is part of the theme issue 'Ageing and sociality: why, when and how does sociality change ageing patterns?'},
}

@article {pmid33677158,
year = {2021},
author = {Li, B and Tian, Y and Wen, H and Qi, X and Wang, L and Zhang, J and Li, J and Dong, X and Zhang, K and Li, Y},
title = {Systematic identification and expression analysis of the Sox gene family in spotted sea bass (Lateolabrax maculatus).},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {38},
number = {},
pages = {100817},
doi = {10.1016/j.cbd.2021.100817},
pmid = {33677158},
issn = {1878-0407},
abstract = {The Sox gene family encodes a set of transcription factors characterized by a conserved Sry-related high mobility group (HMG)-box domain, which performs a series of essential biological functions in diverse tissues and developmental processes. In this study, the Sox gene family was systematically characterized in spotted sea bass (Lateolabrax maculatus). A total of 26 Sox genes were identified and classified into eight subfamilies, namely, SoxB1, SoxB2, SoxC, SoxD, SoxE, SoxF, SoxH and SoxK. The phylogenetic relationship, exon-intron and domain structure analyses supported their annotation and classification. Comparison of gene copy numbers and chromosome locations among different species indicated that except tandem duplicated paralogs of Sox17/Sox32, duplicated Sox genes in spotted sea bass were generated from teleost-specific whole genome duplication during evolution. In addition, qRT-PCR was performed to detect the expression profiles of Sox genes during development and adulthood. The results showed that the expression of 16 out of 26 Sox genes was induced dramatically at different starting points after the multicellular stage, which is consistent with embryogenesis. At the early stage of sex differentiation, 9 Sox genes exhibited sexually dimorphic expression patterns, among which Sox3, Sox19 and Sox6b showed the most significant ovary-biased expression. Moreover, the distinct expression pattern of Sox genes was observed in different adult tissues. Our results provide a fundamental resource for further investigating the functions of Sox genes in embryonic processes, sex determination and differentiation as well as controlling the homeostasis of adult tissues in spotted sea bass.},
}

@article {pmid33672596,
year = {2021},
author = {Ye, M and Wilhelm, M and Gentschev, I and Szalay, A},
title = {A Modified Limiting Dilution Method for Monoclonal Stable Cell Line Selection Using a Real-Time Fluorescence Imaging System: A Practical Workflow and Advanced Applications.},
journal = {Methods and protocols},
volume = {4},
number = {1},
pages = {},
pmid = {33672596},
issn = {2409-9279},
support = {82-5495702//Hope Realized Medical Foundation/ ; },
abstract = {Stable cell lines are widely used in laboratory research and pharmaceutical industry. They are mainly applied in recombinant protein and antibody productions, gene function studies, drug screens, toxicity assessments, and for cancer therapy investigation. There are two types of cell lines, polyclonal and monoclonal origin, that differ regarding their homogeneity and heterogeneity. Generating a high-quality stable cell line, which can grow continuously and carry a stable genetic modification without alteration is very important for most studies, because polyclonal cell lines of multicellular origin can be highly variable and unstable and lead to inconclusive experimental results. The most commonly used technologies of single cell originate monoclonal stable cell isolation in laboratory are fluorescence-activated cell sorting (FACS) sorting and limiting dilution cloning. Here, we describe a modified limiting dilution method of monoclonal stable cell line selection using the real-time fluorescence imaging system IncuCyte®S3.},
}

@article {pmid33671243,
year = {2021},
author = {Rathor, P and Borza, T and Stone, S and Tonon, T and Yurgel, S and Potin, P and Prithiviraj, B},
title = {A Novel Protein from Ectocarpus sp. Improves Salinity and High Temperature Stress Tolerance in Arabidopsis thaliana.},
journal = {International journal of molecular sciences},
volume = {22},
number = {4},
pages = {},
pmid = {33671243},
issn = {1422-0067},
support = {1177546//Natural Sciences and Engineering Research Council of Canada/ ; ANR-10-BTBR-04//Agence Nationale de la Recherche/ ; },
mesh = {*Adaptation, Physiological/genetics ; Algal Proteins/chemistry/genetics/*metabolism ; Arabidopsis/*genetics/growth & development/*physiology ; Electrolytes/metabolism ; Escherichia coli/metabolism ; Gene Expression Regulation, Plant ; *Hot Temperature ; Phaeophyta/*metabolism ; Phylogeny ; Plants, Genetically Modified ; Promoter Regions, Genetic/genetics ; *Salinity ; Seedlings/genetics ; *Stress, Physiological/genetics ; Tobacco/metabolism ; },
abstract = {Brown alga Ectocarpus sp. belongs to Phaeophyceae, a class of macroalgae that evolved complex multicellularity. Ectocarpus sp. is a dominant seaweed in temperate regions, abundant mostly in the intertidal zones, an environment with high levels of abiotic stresses. Previous transcriptomic analysis of Ectocarpus sp. revealed several genes consistently induced by various abiotic stresses; one of these genes is Esi0017_0056, which encodes a protein with unknown function. Bioinformatics analyses indicated that the protein encoded by Esi0017_0056 is soluble and monomeric. The protein was successfully expressed in Escherichia coli,Arabidopsis thaliana and Nicotiana benthamiana. In A. thaliana the gene was expressed under constitutive and stress inducible promoters which led to improved tolerance to high salinity and temperature stresses. The expression of several key abiotic stress-related genes was studied in transgenic and wild type A. thaliana by qPCR. Expression analysis revealed that genes involved in ABA-induced abiotic stress tolerance, K+ homeostasis, and chaperon activities were significantly up-regulated in the transgenic line. This study is the first report in which an unknown function Ectocarpus sp. gene, highly responsive to abiotic stresses, was successfully expressed in A. thaliana, leading to improved tolerance to salt and temperature stress.},
}

*Adaptation, Physiological/genetics
Algal Proteins/chemistry/genetics/*metabolism
Arabidopsis/*genetics/growth & development/*physiology
Electrolytes/metabolism
Escherichia coli/metabolism
Gene Expression Regulation, Plant
*Hot Temperature
Phaeophyta/*metabolism
Phylogeny
Plants, Genetically Modified
Promoter Regions, Genetic/genetics
*Salinity
Seedlings/genetics
*Stress, Physiological/genetics
Tobacco/metabolism

@article {pmid33657376,
year = {2021},
author = {Wang, J and Sun, H and Jiang, M and Li, J and Zhang, P and Chen, H and Mei, Y and Fei, L and Lai, S and Han, X and Song, X and Xu, S and Chen, M and Ouyang, H and Zhang, D and Yuan, GC and Guo, G},
title = {Tracing cell-type evolution by cross-species comparison of cell atlases.},
journal = {Cell reports},
volume = {34},
number = {9},
pages = {108803},
doi = {10.1016/j.celrep.2021.108803},
pmid = {33657376},
issn = {2211-1247},
abstract = {Cell types are the basic building units of multicellular life, with extensive diversities. The evolution of cell types is a crucial layer of comparative cell biology but is thus far not comprehensively studied. We define a compendium of cell atlases using single-cell RNA-seq (scRNA-seq) data from seven animal species and construct a cross-species cell-type evolutionary hierarchy. We present a roadmap for the origin and diversity of major cell categories and find that muscle and neuron cells are conserved cell types. Furthermore, we identify a cross-species transcription factor (TF) repertoire that specifies major cell categories. Overall, our study reveals conservation and divergence of cell types during animal evolution, which will further expand the landscape of comparative genomics.},
}

@article {pmid33656551,
year = {2021},
author = {Yang, H and Shi, X and Chen, C and Hou, J and Ji, T and Cheng, J and Birchler, JA},
title = {Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maize.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koab029},
pmid = {33656551},
issn = {1532-298X},
abstract = {The phenotypic consequences of the addition or subtraction of part of a chromosome is more severe than changing the dosage of the whole genome. By crossing diploid trisomies to a haploid inducer, we identified 17 distal segmental haploid disomies that cover ∼80% of the maize genome. Disomic haploids provide a level of genomic imbalance that is not ordinarily achievable in multicellular eukaryotes, allowing the impact to be stronger and more easily studied. Transcriptome size estimates revealed that a few disomies inversely modulate most of the transcriptome. Based on RNA sequencing, the expression levels of genes located on the varied chromosome arms (cis) in disomies ranged from being proportional to chromosomal dosage (dosage effect) to showing dosage compensation with no expression change with dosage. For genes not located on the varied chromosome arm (trans), an obvious trans-acting effect can be observed, with the majority showing a decreased modulation (inverse effect). The extent of dosage compensation of varied cis genes correlates with the extent of trans inverse effects across the 17 genomic regions studied. The results also have implications for the role of stoichiometry in gene expression, the control of quantitative traits, and the evolution of dosage-sensitive genes.},
}

@article {pmid33624753,
year = {2021},
author = {Junqueira Alves, C and Silva Ladeira, J and Hannah, T and Pedroso Dias, RJ and Zabala Capriles, PV and Yotoko, K and Zou, H and Friedel, RH},
title = {Evolution and Diversity of Semaphorins and Plexins in Choanoflagellates.},
journal = {Genome biology and evolution},
volume = {13},
number = {3},
pages = {},
pmid = {33624753},
issn = {1759-6653},
support = {R01 NS092735/NS/NINDS NIH HHS/United States ; },
abstract = {Semaphorins and plexins are cell surface ligand/receptor proteins that affect cytoskeletal dynamics in metazoan cells. Interestingly, they are also present in Choanoflagellata, a class of unicellular heterotrophic flagellates that forms the phylogenetic sister group to Metazoa. Several members of choanoflagellates are capable of forming transient colonies, whereas others reside solitary inside exoskeletons; their molecular diversity is only beginning to emerge. Here, we surveyed genomics data from 22 choanoflagellate species and detected semaphorin/plexin pairs in 16 species. Choanoflagellate semaphorins (Sema-FN1) contain several domain features distinct from metazoan semaphorins, including an N-terminal Reeler domain that may facilitate dimer stabilization, an array of fibronectin type III domains, a variable serine/threonine-rich domain that is a potential site for O-linked glycosylation, and a SEA domain that can undergo autoproteolysis. In contrast, choanoflagellate plexins (Plexin-1) harbor a domain arrangement that is largely identical to metazoan plexins. Both Sema-FN1 and Plexin-1 also contain a short homologous motif near the C-terminus, likely associated with a shared function. Three-dimensional molecular models revealed a highly conserved structural architecture of choanoflagellate Plexin-1 as compared to metazoan plexins, including similar predicted conformational changes in a segment that is involved in the activation of the intracellular Ras-GAP domain. The absence of semaphorins and plexins in several choanoflagellate species did not appear to correlate with unicellular versus colonial lifestyle or ecological factors such as fresh versus salt water environment. Together, our findings support a conserved mechanism of semaphorin/plexin proteins in regulating cytoskeletal dynamics in unicellular and multicellular organisms.},
}

@article {pmid33622124,
year = {2021},
author = {Evans, SD and Droser, ML and Erwin, DH},
title = {Developmental processes in Ediacara macrofossils.},
journal = {Proceedings. Biological sciences},
volume = {288},
number = {1945},
pages = {20203055},
pmid = {33622124},
issn = {1471-2954},
abstract = {The Ediacara Biota preserves the oldest fossil evidence of abundant, complex metazoans. Despite their significance, assigning individual taxa to specific phylogenetic groups has proved problematic. To better understand these forms, we identify developmentally controlled characters in representative taxa from the Ediacaran White Sea assemblage and compare them with the regulatory tools underlying similar traits in modern organisms. This analysis demonstrates that the genetic pathways for multicellularity, axial polarity, musculature, and a nervous system were likely present in some of these early animals. Equally meaningful is the absence of evidence for major differentiation of macroscopic body units, including distinct organs, localized sensory machinery or appendages. Together these traits help to better constrain the phylogenetic position of several key Ediacara taxa and inform our views of early metazoan evolution. An apparent lack of heads with concentrated sensory machinery or ventral nerve cords in such taxa supports the hypothesis that these evolved independently in disparate bilaterian clades.},
}

@article {pmid33622103,
year = {2021},
author = {Ros-Rocher, N and Pérez-Posada, A and Leger, MM and Ruiz-Trillo, I},
title = {The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition.},
journal = {Open biology},
volume = {11},
number = {2},
pages = {200359},
doi = {10.1098/rsob.200359},
pmid = {33622103},
issn = {2046-2441},
abstract = {How animals evolved from a single-celled ancestor, transitioning from a unicellular lifestyle to a coordinated multicellular entity, remains a fascinating question. Key events in this transition involved the emergence of processes related to cell adhesion, cell-cell communication and gene regulation. To understand how these capacities evolved, we need to reconstruct the features of both the last common multicellular ancestor of animals and the last unicellular ancestor of animals. In this review, we summarize recent advances in the characterization of these ancestors, inferred by comparative genomic analyses between the earliest branching animals and those radiating later, and between animals and their closest unicellular relatives. We also provide an updated hypothesis regarding the transition to animal multicellularity, which was likely gradual and involved the use of gene regulatory mechanisms in the emergence of early developmental and morphogenetic plans. Finally, we discuss some new avenues of research that will complement these studies in the coming years.},
}

@article {pmid33603764,
year = {2021},
author = {Castañeda, V and González, EM and Wienkoop, S},
title = {Phloem Sap Proteins Are Part of a Core Stress Responsive Proteome Involved in Drought Stress Adjustment.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {625224},
pmid = {33603764},
issn = {1664-462X},
abstract = {During moderate drought stress, plants can adjust by changes in the protein profiles of the different organs. Plants transport and modulate extracellular stimuli local and systemically through commonly induced inter- and intracellular reactions. However, most proteins are frequently considered, cell and organelle specific. Hence, while signaling molecules and peptides can travel systemically throughout the whole plant, it is not clear, whether protein isoforms may exist ubiquitously across organs, and what function those may have during drought regulation. By applying shotgun proteomics, we extracted a core proteome of 92 identical protein isoforms, shared ubiquitously amongst several Medicago truncatula tissues, including roots, phloem sap, petioles, and leaves. We investigated their relative distribution across the different tissues and their response to moderate drought stress. In addition, we functionally compared this plant core stress responsive proteome with the organ-specific proteomes. Our study revealed plant ubiquitous protein isoforms, mainly related to redox homeostasis and signaling and involved in protein interaction networks across the whole plant. Furthermore, about 90% of these identified core protein isoforms were significantly involved in drought stress response, indicating a crucial role of the core stress responsive proteome (CSRP) in the plant organ cross-communication, important for a long-distance stress-responsive network. Besides, the data allowed for a comprehensive characterization of the phloem proteome, revealing new insights into its function. For instance, CSRP protein levels involved in stress and redox are relatively more abundant in the phloem compared to the other tissues already under control conditions. This suggests a major role of the phloem in stress protection and antioxidant activity enabling the plants metabolic maintenance and rapid response upon moderate stress. We anticipate our study to be a starting point for future investigations of the role of the core plant proteome. Under an evolutionary perspective, CSRP would enable communication of different cells with each other and the environment being crucial for coordinated stress response of multicellular organisms.},
}

@article {pmid33602485,
year = {2021},
author = {McKenna, KZ and Wagner, GP and Cooper, KL},
title = {A developmental perspective of homology and evolutionary novelty.},
journal = {Current topics in developmental biology},
volume = {141},
number = {},
pages = {1-38},
doi = {10.1016/bs.ctdb.2020.12.001},
pmid = {33602485},
issn = {1557-8933},
abstract = {The development and evolution of multicellular body plans is complex. Many distinct organs and body parts must be reproduced at each generation, and those that are traceable over long time scales are considered homologous. Among the most pressing and least understood phenomena in evolutionary biology is the mode by which new homologs, or "novelties" are introduced to the body plan and whether the developmental changes associated with such evolution deserve special treatment. In this chapter, we address the concepts of homology and evolutionary novelty through the lens of development. We present a series of case studies, within insects and vertebrates, from which we propose a developmental model of multicellular organ identity. With this model in hand, we make predictions regarding the developmental evolution of body plans and highlight the need for more integrative analysis of developing systems.},
}

@article {pmid33593190,
year = {2021},
author = {He, S and Sieksmeyer, T and Che, Y and Mora, MAE and Stiblik, P and Banasiak, R and Harrison, MC and Šobotník, J and Wang, Z and Johnston, PR and McMahon, DP},
title = {Evidence for reduced immune gene diversity and activity during the evolution of termites.},
journal = {Proceedings. Biological sciences},
volume = {288},
number = {1945},
pages = {20203168},
pmid = {33593190},
issn = {1471-2954},
abstract = {The evolution of biological complexity is associated with the emergence of bespoke immune systems that maintain and protect organism integrity. Unlike the well-studied immune systems of cells and individuals, little is known about the origins of immunity during the transition to eusociality, a major evolutionary transition comparable to the evolution of multicellular organisms from single-celled ancestors. We aimed to tackle this by characterizing the immune gene repertoire of 18 cockroach and termite species, spanning the spectrum of solitary, subsocial and eusocial lifestyles. We find that key transitions in termite sociality are correlated with immune gene family contractions. In cross-species comparisons of immune gene expression, we find evidence for a caste-specific social defence system in termites, which appears to operate at the expense of individual immune protection. Our study indicates that a major transition in organismal complexity may have entailed a fundamental reshaping of the immune system optimized for group over individual defence.},
}

@article {pmid33575354,
year = {2021},
author = {Pourhasanzade, F and Sabzpoushan, SH},
title = {A New Mathematical Model for Controlling Tumor Growth Based on Microenvironment Acidity and Oxygen Concentration.},
journal = {BioMed research international},
volume = {2021},
number = {},
pages = {8886050},
pmid = {33575354},
issn = {2314-6141},
abstract = {Hypoxia and the pH level of the tumor microenvironment have a great impact on the treatment of tumors. Here, the tumor growth is controlled by regulating the oxygen concentration and the acidity of the tumor microenvironment by introducing a two-dimensional multiscale cellular automata model of avascular tumor growth. The spatiotemporal evolution of tumor growth and metabolic variations is modeled based on biological assumptions, physical structure, states of cells, and transition rules. Each cell is allocated to one of the following states: proliferating cancer, nonproliferating cancer, necrotic, and normal cells. According to the response of the microenvironmental conditions, each cell consumes/produces metabolic factors and updates its state based on some stochastic rules. The input parameters are compatible with cancer biology using experimental data. The effect of neighborhoods during mitosis and simulating spatial heterogeneity is studied by considering multicellular layer structure of tumor. A simple Darwinist mutation is considered by introducing a critical parameter (Nmm) that affects division probability of the proliferative tumor cells based on the microenvironmental conditions and cancer hallmarks. The results show that Nmm regulation has a significant influence on the dynamics of tumor growth, the growth fraction, necrotic fraction, and the concentration levels of the metabolic factors. The model not only is able to simulate the in vivo tumor growth quantitatively and qualitatively but also can simulate the concentration of metabolic factors, oxygen, and acidity graphically. The results show the spatial heterogeneity effects on the proliferation of cancer cells and the rest of the system. By increasing Nmm, tumor shrinkage and significant increasing in the oxygen concentration and the pH value of the tumor microenvironment are observed. The results demonstrate the model's ability, providing an essential tool for simulating different tumor evolution scenarios of a patient and reliable prediction of spatiotemporal progression of tumors for utilizing in personalized therapy.},
}

@article {pmid33561386,
year = {2021},
author = {Prostak, SM and Robinson, KA and Titus, MA and Fritz-Laylin, LK},
title = {The actin networks of chytrid fungi reveal evolutionary loss of cytoskeletal complexity in the fungal kingdom.},
journal = {Current biology : CB},
volume = {31},
number = {6},
pages = {1192-1205.e6},
doi = {10.1016/j.cub.2021.01.001},
pmid = {33561386},
issn = {1879-0445},
support = {R01 GM122917/GM/NIGMS NIH HHS/United States ; },
abstract = {Cells from across the eukaryotic tree use actin polymer networks for a wide variety of functions, including endocytosis, cytokinesis, and cell migration. Despite this functional conservation, the actin cytoskeleton has undergone significant diversification, highlighted by the differences in the actin networks of mammalian cells and yeast. Chytrid fungi diverged before the emergence of the Dikarya (multicellular fungi and yeast) and therefore provide a unique opportunity to study actin cytoskeletal evolution. Chytrids have two life stages: zoospore cells that can swim with a flagellum and sessile sporangial cells that, like multicellular fungi, are encased in a chitinous cell wall. Here, we show that zoospores of the amphibian-killing chytrid Batrachochytrium dendrobatidis (Bd) build dynamic actin structures resembling those of animal cells, including an actin cortex, pseudopods, and filopodia-like spikes. In contrast, Bd sporangia assemble perinuclear actin shells and actin patches similar to those of yeast. The use of specific small-molecule inhibitors indicate that nearly all of Bd's actin structures are dynamic and use distinct nucleators: although pseudopods and actin patches are Arp2/3 dependent, the actin cortex appears formin dependent and actin spikes require both nucleators. Our analysis of multiple chytrid genomes reveals actin regulators and myosin motors found in animals, but not dikaryotic fungi, as well as fungal-specific components. The presence of animal- and yeast-like actin cytoskeletal components in the genome combined with the intermediate actin phenotypes in Bd suggests that the simplicity of the yeast cytoskeleton may be due to evolutionary loss.},
}

@article {pmid33550954,
year = {2021},
author = {Jékely, G and Godfrey-Smith, P and Keijzer, F},
title = {Reafference and the origin of the self in early nervous system evolution.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1821},
pages = {20190764},
pmid = {33550954},
issn = {1471-2970},
abstract = {Discussions of the function of early nervous systems usually focus on a causal flow from sensors to effectors, by which an animal coordinates its actions with exogenous changes in its environment. We propose, instead, that much early sensing was reafferent; it was responsive to the consequences of the animal's own actions. We distinguish two general categories of reafference-translocational and deformational-and use these to survey the distribution of several often-neglected forms of sensing, including gravity sensing, flow sensing and proprioception. We discuss sensing of these kinds in sponges, ctenophores, placozoans, cnidarians and bilaterians. Reafference is ubiquitous, as ongoing action, especially whole-body motility, will almost inevitably influence the senses. Corollary discharge-a pathway or circuit by which an animal tracks its own actions and their reafferent consequences-is not a necessary feature of reafferent sensing but a later-evolving mechanism. We also argue for the importance of reafferent sensing to the evolution of the body-self, a form of organization that enables an animal to sense and act as a single unit. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.},
}

@article {pmid33550952,
year = {2021},
author = {Pezzulo, G and LaPalme, J and Durant, F and Levin, M},
title = {Bistability of somatic pattern memories: stochastic outcomes in bioelectric circuits underlying regeneration.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1821},
pages = {20190765},
pmid = {33550952},
issn = {1471-2970},
abstract = {Nervous systems' computational abilities are an evolutionary innovation, specializing and speed-optimizing ancient biophysical dynamics. Bioelectric signalling originated in cells' communication with the outside world and with each other, enabling cooperation towards adaptive construction and repair of multicellular bodies. Here, we review the emerging field of developmental bioelectricity, which links the field of basal cognition to state-of-the-art questions in regenerative medicine, synthetic bioengineering and even artificial intelligence. One of the predictions of this view is that regeneration and regulative development can restore correct large-scale anatomies from diverse starting states because, like the brain, they exploit bioelectric encoding of distributed goal states-in this case, pattern memories. We propose a new interpretation of recent stochastic regenerative phenotypes in planaria, by appealing to computational models of memory representation and processing in the brain. Moreover, we discuss novel findings showing that bioelectric changes induced in planaria can be stored in tissue for over a week, thus revealing that somatic bioelectric circuits in vivo can implement a long-term, re-writable memory medium. A consideration of the mechanisms, evolution and functionality of basal cognition makes novel predictions and provides an integrative perspective on the evolution, physiology and biomedicine of information processing in vivo. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.},
}

@article {pmid33550951,
year = {2021},
author = {Göhde, R and Naumann, B and Laundon, D and Imig, C and McDonald, K and Cooper, BH and Varoqueaux, F and Fasshauer, D and Burkhardt, P},
title = {Choanoflagellates and the ancestry of neurosecretory vesicles.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1821},
pages = {20190759},
pmid = {33550951},
issn = {1471-2970},
abstract = {Neurosecretory vesicles are highly specialized trafficking organelles that store neurotransmitters that are released at presynaptic nerve endings and are, therefore, important for animal cell-cell signalling. Despite considerable anatomical and functional diversity of neurons in animals, the protein composition of neurosecretory vesicles in bilaterians appears to be similar. This similarity points towards a common evolutionary origin. Moreover, many putative homologues of key neurosecretory vesicle proteins predate the origin of the first neurons, and some even the origin of the first animals. However, little is known about the molecular toolkit of these vesicles in non-bilaterian animals and their closest unicellular relatives, making inferences about the evolutionary origin of neurosecretory vesicles extremely difficult. By comparing 28 proteins of the core neurosecretory vesicle proteome in 13 different species, we demonstrate that most of the proteins are present in unicellular organisms. Surprisingly, we find that the vesicular membrane-associated soluble N-ethylmaleimide-sensitive factor attachment protein receptor protein synaptobrevin is localized to the vesicle-rich apical and basal pole in the choanoflagellate Salpingoeca rosetta. Our 3D vesicle reconstructions reveal that the choanoflagellates S. rosetta and Monosiga brevicollis exhibit a polarized and diverse vesicular landscape reminiscent of the polarized organization of chemical synapses that secrete the content of neurosecretory vesicles into the synaptic cleft. This study sheds light on the ancestral molecular machinery of neurosecretory vesicles and provides a framework to understand the origin and evolution of secretory cells, synapses and neurons. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.},
}

@article {pmid33550949,
year = {2021},
author = {Moroz, LL and Romanova, DY and Kohn, AB},
title = {Neural versus alternative integrative systems: molecular insights into origins of neurotransmitters.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1821},
pages = {20190762},
pmid = {33550949},
issn = {1471-2970},
abstract = {Transmitter signalling is the universal chemical language of any nervous system, but little is known about its early evolution. Here, we summarize data about the distribution and functions of neurotransmitter systems in basal metazoans as well as outline hypotheses of their origins. We explore the scenario that neurons arose from genetically different populations of secretory cells capable of volume chemical transmission and integration of behaviours without canonical synapses. The closest representation of this primordial organization is currently found in Placozoa, disk-like animals with the simplest known cell composition but complex behaviours. We propose that injury-related signalling was the evolutionary predecessor for integrative functions of early transmitters such as nitric oxide, ATP, protons, glutamate and small peptides. By contrast, acetylcholine, dopamine, noradrenaline, octopamine, serotonin and histamine were recruited as canonical neurotransmitters relatively later in animal evolution, only in bilaterians. Ligand-gated ion channels often preceded the establishment of novel neurotransmitter systems. Moreover, lineage-specific diversification of neurotransmitter receptors occurred in parallel within Cnidaria and several bilaterian lineages, including acoels. In summary, ancestral diversification of secretory signal molecules provides unique chemical microenvironments for behaviour-driven innovations that pave the way to complex brain functions and elementary cognition. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.},
}

@article {pmid33550948,
year = {2021},
author = {Arendt, D},
title = {Elementary nervous systems.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1821},
pages = {20200347},
pmid = {33550948},
issn = {1471-2970},
abstract = {The evolutionary origin of the nervous system has been a matter of long-standing debate. This is due to the different perspectives taken. Earlier studies addressed nervous system origins at the cellular level. They focused on the selective advantage of the first neuron in its local context, and considered vertical sensory-motor reflex arcs the first nervous system. Later studies emphasized the value of the nervous system at the tissue level. Rather than acting locally, early neurons were seen as part of an elementary nerve net that enabled the horizontal coordination of tissue movements. Opinions have also differed on the nature of effector cells. While most authors have favoured contractile systems, others see the key output of the incipient nervous system in the coordination of motile cilia, or the secretion of antimicrobial peptides. I will discuss these divergent views and explore how they can be validated by molecular and single-cell data. From this survey, possible consensus emerges: (i) the first manifestation of the nervous system likely was a nerve net, whereas specialized local circuits evolved later; (ii) different nerve nets may have evolved for the coordination of contractile or cilia-driven movements; (iii) all evolving nerve nets facilitated new forms of animal behaviour with increasing body size. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.},
}

@article {pmid33550946,
year = {2021},
author = {Jékely, G},
title = {The chemical brain hypothesis for the origin of nervous systems.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1821},
pages = {20190761},
pmid = {33550946},
issn = {1471-2970},
abstract = {In nervous systems, there are two main modes of transmission for the propagation of activity between cells. Synaptic transmission relies on close contact at chemical or electrical synapses while volume transmission is mediated by diffusible chemical signals and does not require direct contact. It is possible to wire complex neuronal networks by both chemical and synaptic transmission. Both types of networks are ubiquitous in nervous systems, leading to the question which of the two appeared first in evolution. This paper explores a scenario where chemically organized cellular networks appeared before synapses in evolution, a possibility supported by the presence of complex peptidergic signalling in all animals except sponges. Small peptides are ideally suited to link up cells into chemical networks. They have unlimited diversity, high diffusivity and high copy numbers derived from repetitive precursors. But chemical signalling is diffusion limited and becomes inefficient in larger bodies. To overcome this, peptidergic cells may have developed projections and formed synaptically connected networks tiling body surfaces and displaying synchronized activity with pulsatile peptide release. The advent of circulatory systems and neurohemal organs further reduced the constraint imposed on chemical signalling by diffusion. This could have contributed to the explosive radiation of peptidergic signalling systems in stem bilaterians. Neurosecretory centres in extant nervous systems are still predominantly chemically wired and coexist with the synaptic brain. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.},
}

@article {pmid33542245,
year = {2021},
author = {Grum-Grzhimaylo, AA and Bastiaans, E and van den Heuvel, J and Berenguer Millanes, C and Debets, AJM and Aanen, DK},
title = {Somatic deficiency causes reproductive parasitism in a fungus.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {783},
pmid = {33542245},
issn = {2041-1723},
mesh = {Cell Fusion ; DNA Mutational Analysis ; *Evolution, Molecular ; Fungal Proteins/*genetics/metabolism ; Gene Knockout Techniques ; Genes, Fungal/genetics ; Hyphae/*physiology ; Mutation ; Neurospora crassa/*physiology ; },
abstract = {Some multicellular organisms can fuse because mergers potentially provide mutual benefits. However, experimental evolution in the fungus Neurospora crassa has demonstrated that free fusion of mycelia favours cheater lineages, but the mechanism and evolutionary dynamics of this exploitation are unknown. Here we show, paradoxically, that all convergently evolved cheater lineages have similar fusion deficiencies. These mutants are unable to initiate fusion but retain access to wild-type mycelia that fuse with them. This asymmetry reduces cheater-mutant contributions to somatic substrate-bound hyphal networks, but increases representation of their nuclei in the aerial reproductive hyphae. Cheaters only benefit when relatively rare and likely impose genetic load reminiscent of germline senescence. We show that the consequences of somatic fusion can be unequally distributed among fusion partners, with the passive non-fusing partner profiting more. We discuss how our findings may relate to the extensive variation in fusion frequency of fungi found in nature.},
}

Cell Fusion
DNA Mutational Analysis
*Evolution, Molecular
Fungal Proteins/*genetics/metabolism
Gene Knockout Techniques
Genes, Fungal/genetics
Hyphae/*physiology
Mutation
Neurospora crassa/*physiology

@article {pmid33539025,
year = {2021},
author = {Gostner, JM and Fuchs, D and Kurz, K},
title = {Metabolic Stress and Immunity: Nutrient-Sensing Kinases and Tryptophan Metabolism.},
journal = {Advances in experimental medicine and biology},
volume = {1275},
number = {},
pages = {395-405},
pmid = {33539025},
issn = {0065-2598},
mesh = {Indoleamine-Pyrrole 2,3,-Dioxygenase/genetics ; Kynurenine ; Nutrients ; *Protein-Serine-Threonine Kinases ; Stress, Physiological ; *Tryptophan ; },
abstract = {The tryptophan catabolizing enzyme indoleamine 2,3-dioxygenase (IDO-1) has gained major attention due the immunoregulatory nature of this pathway. Both depletion of tryptophan concentrations as well as the accumulation of downstream metabolites are relevant for the mediation of the manifold consequences of increased tryptophan metabolism. Increased tryptophan catabolism is indicative for several chronic inflammatory disorders such as infections, autoimmune diseases or cancer. Low tryptophan availability is likely to be involved in the manifestation of a variety of comorbidities such as anemia, cachexia, depression and neurocognitive disturbances.Several nutrient sensing kinases are implicated in the downstream effects of dysregulated tryptophan metabolism. These include mechanisms that were conserved during evolution but have gained special features in multicellular eukaryotes, such as pathways regulated by eukaryotic translation initiation factor 2 (eIF-2)-alpha kinase (GCN2, also named general control nonderepressible 2 kinase), 5'-adenosine monophosphate (AMP)-activated protein kinase (AMPK) and target of rapamycin (TOR).The interplay between IDO-1 and above-mentioned pathway seems to be highly context dependent. A better understanding of the crosstalk is necessary to support the search for druggable targets for the treatment of inflammatory and autoimmune disorders.},
}

Indoleamine-Pyrrole 2,3,-Dioxygenase/genetics
Kynurenine
Nutrients
*Protein-Serine-Threonine Kinases
Stress, Physiological
*Tryptophan

@article {pmid33535472,
year = {2021},
author = {Bonmati-Carrion, MA and Tomas-Loba, A},
title = {Melatonin and Cancer: A Polyhedral Network Where the Source Matters.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {10},
number = {2},
pages = {},
pmid = {33535472},
issn = {2076-3921},
support = {20401/SF/17//Fundación Séneca/ ; 19899/GERM/15//Fundación Séneca/ ; RYC2018-025622-I//Ministerio de Ciencia, Innovación y Universidades/ ; BFERO2020.01//Fundación Fero/ ; LeonardoFellowship//Fundación BBVA/ ; RTI2018-093528-B-I00//Ministerio de Ciencia, Innovación y Universidades/ ; CB16/10/00239//Ministerio de Economía y Competitividad/ ; },
abstract = {Melatonin is one of the most phylogenetically conserved signals in biology. Although its original function was probably related to its antioxidant capacity, this indoleamine has been "adopted" by multicellular organisms as the "darkness signal" when secreted in a circadian manner and is acutely suppressed by light at night by the pineal gland. However, melatonin is also produced by other tissues, which constitute its extrapineal sources. Apart from its undisputed chronobiotic function, melatonin exerts antioxidant, immunomodulatory, pro-apoptotic, antiproliferative, and anti-angiogenic effects, with all these properties making it a powerful antitumor agent. Indeed, this activity has been demonstrated to be mediated by interfering with various cancer hallmarks, and different epidemiological studies have also linked light at night (melatonin suppression) with a higher incidence of different types of cancer. In 2007, the World Health Organization classified night shift work as a probable carcinogen due to circadian disruption, where melatonin plays a central role. Our aim is to review, from a global perspective, the role of melatonin both from pineal and extrapineal origin, as well as their possible interplay, as an intrinsic factor in the incidence, development, and progression of cancer. Particular emphasis will be placed not only on those mechanisms related to melatonin's antioxidant nature but also on the recently described novel roles of melatonin in microbiota and epigenetic regulation.},
}

@article {pmid33535413,
year = {2021},
author = {Parker, GA},
title = {How Soon Hath Time… A History of Two "Seminal" Publications.},
journal = {Cells},
volume = {10},
number = {2},
pages = {},
pmid = {33535413},
issn = {2073-4409},
abstract = {This review documents the history of the two papers written half a century ago that relate to this special issue of Cells. The first, "Sperm competition and its evolutionary consequences in the insects" (Biological Reviews, 1970), stressed that sexual selection continues after ejaculation, resulting in many adaptations (e.g., postcopulatory guarding phases, copulatory plugs, seminal fluid components that modify female reproduction, and optimal ejaculation strategies), an aspect not considered by Darwin in his classic treatise of 1871. Sperm competition has subsequently been studied in many taxa, and post-copulatory sexual selection is now considered an important sequel to Darwinian pre-copulatory sexual selection. The second, "The origin and evolution of gamete dimorphism and the male-female phenomenon" (Journal of Theoretical Biology, 1972) showed how selection, based on gamete competition between individuals, can give rise to anisogamy in an isogamous broadcast spawning ancestor. This theory, which has subsequently been developed in various ways, is argued to form the most powerful explanation of why there are two sexes in most multicellular organisms. Together, the two papers have influenced our general understanding of the evolutionary differentiation of the two forms of gametic cells, and the divergence of sexual strategies between males and females under sexual selection.},
}

@article {pmid33529558,
year = {2021},
author = {Berger, D and Stångberg, J and Baur, J and Walters, RJ},
title = {Elevated temperature increases genome-wide selection on de novo mutations.},
journal = {Proceedings. Biological sciences},
volume = {288},
number = {1944},
pages = {20203094},
pmid = {33529558},
issn = {1471-2954},
abstract = {Adaptation in new environments depends on the amount of genetic variation available for evolution, and the efficacy by which natural selection discriminates among this variation. However, whether some ecological factors reveal more genetic variation, or impose stronger selection pressures than others, is typically not known. Here, we apply the enzyme kinetic theory to show that rising global temperatures are predicted to intensify natural selection throughout the genome by increasing the effects of DNA sequence variation on protein stability. We test this prediction by (i) estimating temperature-dependent fitness effects of induced mutations in seed beetles adapted to ancestral or elevated temperature, and (ii) calculate 100 paired selection estimates on mutations in benign versus stressful environments from unicellular and multicellular organisms. Environmental stress per se did not increase mean selection on de novo mutation, suggesting that the cost of adaptation does not generally increase in new ecological settings to which the organism is maladapted. However, elevated temperature increased the mean strength of selection on genome-wide polymorphism, signified by increases in both mutation load and mutational variance in fitness. These results have important implications for genetic diversity gradients and the rate and repeatability of evolution under climate change.},
}

@article {pmid33520185,
year = {2021},
author = {Naimark, E and Kirpotin, D and Boeva, N and Gmoshinskiy, V and Kalinina, M and Lyupina, Y and Markov, A and Nikitin, M and Shokurov, A and Volkov, D},
title = {Taphonomic experiments imply a possible link between the evolution of multicellularity and the fossilization potential of soft-bodied organisms.},
journal = {Ecology and evolution},
volume = {11},
number = {2},
pages = {1037-1056},
pmid = {33520185},
issn = {2045-7758},
abstract = {The reliability of evolutionary reconstructions based on the fossil record critically depends on our knowledge of the factors affecting the fossilization of soft-bodied organisms. Despite considerable research effort, these factors are still poorly understood. In order to elucidate the main prerequisites for the preservation of soft-bodied organisms, we conducted long-term (1-5 years) taphonomic experiments with the model crustacean Artemia salina buried in five different sediments. The subsequent analysis of the carcasses and sediments revealed that, in our experimental settings, better preservation was associated with the fast deposition of aluminum and silicon on organic tissues. Other elements such as calcium, magnesium, and iron, which can also accumulate quickly on the carcasses, appear to be much less efficient in preventing decay. Next, we asked if the carcasses of uni- and multicellular organisms differ in their ability to accumulate aluminum ions on their surface. The experiments with the flagellate Euglena gracilis and the sponge Spongilla lacustris showed that aluminum ions are more readily deposited onto a multicellular body. This was further confirmed by the experiments with uni- and multicellular stages of the social ameba Dictyostelium discoideum. The results lead us to speculate that the evolution of cell adhesion molecules, which provide efficient cell-cell and cell-substrate binding, probably can explain the rich fossil record of soft-bodied animals, the comparatively poor fossil record of nonskeletal unicellular eukaryotes, and the explosive emergence of the Cambrian diversity of soft-bodied fossils.},
}

@article {pmid33507545,
year = {2021},
author = {Li, J and Meng, Q and Fu, Y and Yu, X and Ji, T and Chao, Y and Chen, Q and Li, Y and Bian, H},
title = {Novel insights: Dynamic foam cells derived from the macrophage in atherosclerosis.},
journal = {Journal of cellular physiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jcp.30300},
pmid = {33507545},
issn = {1097-4652},
support = {81774029//National Natural Science Foundation of China/ ; },
abstract = {Atherosclerosis can be regarded as a chronic disease derived from the interaction between disordered lipoproteins and an unsuitable immune response. The evolution of foam cells is not only a significant pathological change in the early stage of atherosclerosis but also a key stage in the occurrence and development of atherosclerosis. The formation of foam cells is mainly caused by the imbalance among lipids uptake, lipids treatment, and reverse cholesterol transport. Although a large number of studies have summarized the source of foam cells and the mechanism of foam cells formation, we propose a new idea about foam cells in atherosclerosis. Rather than an isolated microenvironment, the macrophage multiple lipid uptake pathways, lipid internalization, lysosome, mitochondria, endoplasmic reticulum, neutral cholesterol ester hydrolase (NCEH), acyl-coenzyme A-cholesterol acyltransferase (ACAT), and reverse cholesterol transport are mutually influential, and form a dynamic process under multi-factor regulation. The macrophage takes on different uptake lipid statuses depending on multiple uptake pathways and intracellular lipids, lipid metabolites versus pro-inflammatory factors. Except for NCEH and ACAT, the lipid internalization of macrophages also depends on multicellular organelles including the lysosome, mitochondria, and endoplasmic reticulum, which are associated with each other. A dynamic balance between esterification and hydrolysis of cholesterol for macrophages is essential for physiology and pathology. Therefore, we propose that the foam cell in the process of atherosclerosis may be dynamic under multi-factor regulation, and collate this study to provide a holistic and dynamic idea of the foam cell.},
}

@article {pmid33487114,
year = {2021},
author = {Dinet, C and Michelot, A and Herrou, J and Mignot, T},
title = {Linking single-cell decisions to collective behaviours in social bacteria.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1820},
pages = {20190755},
pmid = {33487114},
issn = {1471-2970},
abstract = {Social bacteria display complex behaviours whereby thousands of cells collectively and dramatically change their form and function in response to nutrient availability and changing environmental conditions. In this review, we focus on Myxococcus xanthus motility, which supports spectacular transitions based on prey availability across its life cycle. A large body of work suggests that these behaviours require sensory capacity implemented at the single-cell level. Focusing on recent genetic work on a core cellular pathway required for single-cell directional decisions, we argue that signal integration, multi-modal sensing and memory are at the root of decision making leading to multicellular behaviours. Hence, Myxococcus may be a powerful biological system to elucidate how cellular building blocks cooperate to form sensory multicellular assemblages, a possible origin of cognitive mechanisms in biological systems. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.},
}

@article {pmid33487113,
year = {2021},
author = {Schaap, P},
title = {From environmental sensing to developmental control: cognitive evolution in dictyostelid social amoebas.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1820},
pages = {20190756},
pmid = {33487113},
issn = {1471-2970},
abstract = {Dictyostelid social amoebas respond to starvation by self-organizing into multicellular slugs that migrate towards light to construct spore-bearing structures. These behaviours depend on excitable networks that enable amoebas to produce propagating waves of the chemoattractant cAMP, and to respond by directional movement. cAMP additionally regulates cell differentiation throughout development, with differentiation and cell movement being coordinated by interaction of the stalk inducer c-di-GMP with the adenylate cyclase that generates cAMP oscillations. Evolutionary studies indicate how the manifold roles of cAMP in multicellular development evolved from a role as intermediate for starvation-induced encystation in the unicellular ancestor. A merger of this stress response with the chemotaxis excitable networks yielded the developmental complexity and cognitive capabilities of extant Dictyostelia. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.},
}

@article {pmid33479022,
year = {2021},
author = {Kjellin, J and Avesson, L and Reimegård, J and Liao, Z and Eichinger, L and Noegel, A and Glöckner, G and Schaap, P and Söderbom, F},
title = {Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas.},
journal = {Genome research},
volume = {31},
number = {3},
pages = {436-447},
pmid = {33479022},
issn = {1549-5469},
abstract = {Aggregative multicellularity has evolved multiple times in diverse groups of eukaryotes, exemplified by the well-studied development of dictyostelid social amoebas, for example, Dictyostelium discoideum However, it is still poorly understood why multicellularity emerged in these amoebas while the majority of other members of Amoebozoa are unicellular. Previously, a novel type of noncoding RNA, Class I RNAs, was identified in D. discoideum and shown to be important for normal multicellular development. Here, we investigated Class I RNA evolution and its connection to multicellular development. We identified a large number of new Class I RNA genes by constructing a covariance model combined with a scoring system based on conserved upstream sequences. Multiple genes were predicted in representatives of each major group of Dictyostelia and expression analysis confirmed that our search approach identifies expressed Class I RNA genes with high accuracy and sensitivity and that the RNAs are developmentally regulated. Further studies showed that Class I RNAs are ubiquitous in Dictyostelia and share highly conserved structure and sequence motifs. In addition, Class I RNA genes appear to be unique to dictyostelid social amoebas because they could not be identified in outgroup genomes, including their closest known relatives. Our results show that Class I RNA is an ancient class of ncRNAs, likely to have been present in the last common ancestor of Dictyostelia dating back at least 600 million years. Based on previous functional analyses and the presented evolutionary investigation, we hypothesize that Class I RNAs were involved in evolution of multicellularity in Dictyostelia.},
}

@article {pmid33471791,
year = {2021},
author = {Miele, L and De Monte, S},
title = {Aggregative cycles evolve as a solution to conflicts in social investment.},
journal = {PLoS computational biology},
volume = {17},
number = {1},
pages = {e1008617},
pmid = {33471791},
issn = {1553-7358},
abstract = {Multicellular organization is particularly vulnerable to conflicts between different cell types when the body forms from initially isolated cells, as in aggregative multicellular microbes. Like other functions of the multicellular phase, coordinated collective movement can be undermined by conflicts between cells that spend energy in fuelling motion and 'cheaters' that get carried along. The evolutionary stability of collective behaviours against such conflicts is typically addressed in populations that undergo extrinsically imposed phases of aggregation and dispersal. Here, via a shift in perspective, we propose that aggregative multicellular cycles may have emerged as a way to temporally compartmentalize social conflicts. Through an eco-evolutionary mathematical model that accounts for individual and collective strategies of resource acquisition, we address regimes where different motility types coexist. Particularly interesting is the oscillatory regime that, similarly to life cycles of aggregative multicellular organisms, alternates on the timescale of several cell generations phases of prevalent solitary living and starvation-triggered aggregation. Crucially, such self-organized oscillations emerge as a result of evolution of cell traits associated to conflict escalation within multicellular aggregates.},
}

@article {pmid33468253,
year = {2021},
author = {Xu, L and Zhang, M and Shi, L and Yang, X and Chen, L and Cao, N and Lei, A and Cao, Y},
title = {Neural stemness contributes to cell tumorigenicity.},
journal = {Cell & bioscience},
volume = {11},
number = {1},
pages = {21},
pmid = {33468253},
issn = {2045-3701},
support = {31671499//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Previous studies demonstrated the dependence of cancer on nerve. Recently, a growing number of studies reveal that cancer cells share the property and regulatory network with neural stem/progenitor cells. However, relationship between the property of neural stemness and cell tumorigenicity is unknown.

RESULTS: We show that neural stem/progenitor cells, but not non-neural embryonic or somatic stem/progenitor cell types, exhibit tumorigenicity and the potential for differentiation into tissue types of all germ layers when they are placed in non-native environment by transplantation into immunodeficient nude mice. Likewise, cancer cells capable of tumor initiation have the property of neural stemness because of their abilities in neurosphere formation in neural stem cell-specific serum-free medium and in differentiation potential, in addition to their neuronal differentiation potential that was characterized previously. Moreover, loss of a pro-differentiation factor in myoblasts, which have no tumorigenicity, lead to the loss of myoblast identity, and gain of the property of neural stemness, tumorigenicity and potential for re-differentiation. By contrast, loss of neural stemness via differentiation results in the loss of tumorigenicity. These suggest that the property of neural stemness contributes to cell tumorigenicity, and tumor phenotypic heterogeneity might be an effect of differentiation potential of neural stemness. Bioinformatic analysis reveals that neural genes in general are correlated with embryonic development and cancer, in addition to their role in neural development; whereas non-neural genes are not. Most of neural specific genes emerged in typical species representing transition from unicellularity to multicellularity during evolution. Genes in Monosiga brevicollis, a unicellular species that is a closest known relative of metazoans, are biased toward neural cells.

CONCLUSIONS: We suggest that the property of neural stemness is the source of cell tumorigenicity. This is due to that neural biased unicellular state is the ground state for multicellularity and hence cell type diversification or differentiation during evolution, and tumorigenesis is a process of restoration of neural ground state in somatic cells along a default route that is pre-determined by an evolutionary advantage of neural state.},
}

@article {pmid33460641,
year = {2021},
author = {Schrankel, CS and Hamdoun, A},
title = {Early patterning of ABCB, ABCC, and ABCG transporters establishes unique territories of small molecule transport in embryonic mesoderm and endoderm.},
journal = {Developmental biology},
volume = {472},
number = {},
pages = {115-124},
doi = {10.1016/j.ydbio.2020.12.021},
pmid = {33460641},
issn = {1095-564X},
abstract = {Directed intercellular movement of diverse small molecules, including metabolites, signal molecules and xenobiotics, is a key feature of multicellularity. Networks of small molecule transporters (SMTs), including several ATP Binding Cassette (ABC) transporters, are central to this process. While small molecule transporters are well described in differentiated organs, little is known about their patterns of expression in early embryogenesis. Here we report the pattern of ABC-type SMT expression and activity during the early development of sea urchins. Of the six major ABCs in this embryo (ABCB1, -B4, -C1, -C4, -C5 and -G2), three expression patterns were observed: 1) ABCB1 and ABCC1 are first expressed ubiquitously, and then become enriched in endoderm and ectoderm-derived structures. 2) ABCC4 and ABCC5 are restricted to a ring of mesoderm in the blastula and ABCC4 is later expressed in the coelomic pouches, the embryonic niche of the primordial germ cells. 3) ABCB4 and ABCG2 are expressed exclusively in endoderm-fated cells. Assays with fluorescent substrates and inhibitors of transporters revealed a ring of ABCC4 efflux activity emanating from ABCC4+ mesodermal cells. Similarly, ABCB1 and ABCB4 efflux activity was observed in the developing gut, prior to the onset of feeding. This study reveals the early establishment of unique territories of small molecule transport during embryogenesis. A pattern of ABCC4/C5 expression is consistent with signaling functions during gut invagination and germ line development, while a later pattern of ABCB1/B4 and ABCG2 is consistent with roles in the embryonic gut. This work provides a conceptual framework with which to examine the function and evolution of SMT networks and to define the specific developmental pathways that drive the expression of these genes.},
}

@article {pmid33449631,
year = {2021},
author = {Duran-Nebreda, S and Pla, J and Vidiella, B and Piñero, J and Conde-Pueyo, N and Solé, R},
title = {Synthetic Lateral Inhibition in Periodic Pattern Forming Microbial Colonies.},
journal = {ACS synthetic biology},
volume = {10},
number = {2},
pages = {277-285},
doi = {10.1021/acssynbio.0c00318},
pmid = {33449631},
issn = {2161-5063},
abstract = {Multicellular entities are characterized by intricate spatial patterns, intimately related to the functions they perform. These patterns are often created from isotropic embryonic structures, without external information cues guiding the symmetry breaking process. Mature biological structures also display characteristic scales with repeating distributions of signals or chemical species across space. Many candidate patterning modules have been used to explain processes during development and typically include a set of interacting and diffusing chemicals or agents known as morphogens. Great effort has been put forward to better understand the conditions in which pattern-forming processes can occur in the biological domain. However, evidence and practical knowledge allowing us to engineer symmetry-breaking is still lacking. Here we follow a different approach by designing a synthetic gene circuit in E. coli that implements a local activation long-range inhibition mechanism. The synthetic gene network implements an artificial differentiation process that changes the physicochemical properties of the agents. Using both experimental results and modeling, we show that the proposed system is capable of symmetry-breaking leading to regular spatial patterns during colony growth. Studying how these patterns emerge is fundamental to further our understanding of the evolution of biocomplexity and the role played by self-organization. The artificial system studied here and the engineering perspective on embryogenic processes can help validate developmental theories and identify universal properties underpinning biological pattern formation, with special interest for the area of synthetic developmental biology.},
}

@article {pmid33446527,
year = {2021},
author = {Stadler, T and Pybus, OG and Stumpf, MPH},
title = {Phylodynamics for cell biologists.},
journal = {Science (New York, N.Y.)},
volume = {371},
number = {6526},
pages = {},
doi = {10.1126/science.aah6266},
pmid = {33446527},
issn = {1095-9203},
mesh = {Animals ; Caenorhabditis elegans/cytology/growth & development ; Cell Biology/trends ; *Cell Lineage ; Humans ; *Phylogeny ; *Single-Cell Analysis ; Stem Cells/cytology/physiology ; },
abstract = {Multicellular organisms are composed of cells connected by ancestry and descent from progenitor cells. The dynamics of cell birth, death, and inheritance within an organism give rise to the fundamental processes of development, differentiation, and cancer. Technical advances in molecular biology now allow us to study cellular composition, ancestry, and evolution at the resolution of individual cells within an organism or tissue. Here, we take a phylogenetic and phylodynamic approach to single-cell biology. We explain how "tree thinking" is important to the interpretation of the growing body of cell-level data and how ecological null models can benefit statistical hypothesis testing. Experimental progress in cell biology should be accompanied by theoretical developments if we are to exploit fully the dynamical information in single-cell data.},
}

Animals
Caenorhabditis elegans/cytology/growth & development
Cell Biology/trends
*Cell Lineage
Humans
*Phylogeny
*Single-Cell Analysis
Stem Cells/cytology/physiology

@article {pmid33440882,
year = {2021},
author = {Takahashi, T},
title = {Multiple Roles for Cholinergic Signaling from the Perspective of Stem Cell Function.},
journal = {International journal of molecular sciences},
volume = {22},
number = {2},
pages = {},
pmid = {33440882},
issn = {1422-0067},
support = {JP17K07495 and JP20K06751//Japan Society for the Promotion of Science/ ; },
mesh = {Acetylcholine/*metabolism ; Age Factors ; Animals ; Biomarkers ; Brain/cytology/metabolism ; Cell Differentiation/genetics ; Homeostasis ; Humans ; Organ Specificity ; Receptors, Cholinergic/*metabolism ; *Signal Transduction ; Stem Cells/cytology/*metabolism ; },
abstract = {Stem cells have extensive proliferative potential and the ability to differentiate into one or more mature cell types. The mechanisms by which stem cells accomplish self-renewal provide fundamental insight into the origin and design of multicellular organisms. These pathways allow the repair of damage and extend organismal life beyond that of component cells, and they probably preceded the evolution of complex metazoans. Understanding the true nature of stem cells can only come from discovering how they are regulated. The concept that stem cells are controlled by particular microenvironments, also known as niches, has been widely accepted. Technical advances now allow characterization of the zones that maintain and control stem cell activity in several organs, including the brain, skin, and gut. Cholinergic neurons release acetylcholine (ACh) that mediates chemical transmission via ACh receptors such as nicotinic and muscarinic receptors. Although the cholinergic system is composed of organized nerve cells, the system is also involved in mammalian non-neuronal cells, including stem cells, embryonic stem cells, epithelial cells, and endothelial cells. Thus, cholinergic signaling plays a pivotal role in controlling their behaviors. Studies regarding this signal are beginning to unify our understanding of stem cell regulation at the cellular and molecular levels, and they are expected to advance efforts to control stem cells therapeutically. The present article reviews recent findings about cholinergic signaling that is essential to control stem cell function in a cholinergic niche.},
}

Acetylcholine/*metabolism
Age Factors
Animals
Biomarkers
Brain/cytology/metabolism
Cell Differentiation/genetics
Homeostasis
Humans
Organ Specificity
Receptors, Cholinergic/*metabolism
*Signal Transduction
Stem Cells/cytology/*metabolism

@article {pmid33440837,
year = {2021},
author = {Bredon, M and Depuydt, E and Brisson, L and Moulin, L and Charles, C and Haenn, S and Moumen, B and Bouchon, D},
title = {Effects of Dysbiosis and Dietary Manipulation on the Digestive Microbiota of a Detritivorous Arthropod.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
pmid = {33440837},
issn = {2076-2607},
support = {BiodivUP//State-Region Planning Contracts (CPER), European Regional Development Fund (FEDER)/ ; },
abstract = {The crucial role of microbes in the evolution, development, health, and ecological interactions of multicellular organisms is now widely recognized in the holobiont concept. However, the structure and stability of microbiota are highly dependent on abiotic and biotic factors, especially in the gut, which can be colonized by transient bacteria depending on the host's diet. We studied these impacts by manipulating the digestive microbiota of the detritivore Armadillidium vulgare and analyzing the consequences on its structure and function. Hosts were exposed to initial starvation and then were fed diets that varied the different components of lignocellulose. A total of 72 digestive microbiota were analyzed according to the type of the diet (standard or enriched in cellulose, lignin, or hemicellulose) and the period following dysbiosis. The results showed that microbiota from the hepatopancreas were very stable and resilient, while the most diverse and labile over time were found in the hindgut. Dysbiosis and selective diets may have affected the host fitness by altering the structure of the microbiota and its predicted functions. Overall, these modifications can therefore have effects not only on the holobiont, but also on the "eco-holobiont" conceptualization of macroorganisms.},
}

@article {pmid33436625,
year = {2021},
author = {Chaikeeratisak, V and Birkholz, EA and Prichard, AM and Egan, ME and Mylvara, A and Nonejuie, P and Nguyen, KT and Sugie, J and Meyer, JR and Pogliano, J},
title = {Viral speciation through subcellular genetic isolation and virogenesis incompatibility.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {342},
pmid = {33436625},
issn = {2041-1723},
support = {R01 GM104556/GM/NIGMS NIH HHS/United States ; R01 GM129245/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteriophages/*genetics ; Cell Nucleus/metabolism ; *Genetic Speciation ; Green Fluorescent Proteins/metabolism ; Pseudomonas aeruginosa/virology ; Species Specificity ; Subcellular Fractions ; },
abstract = {Understanding how biological species arise is critical for understanding the evolution of life on Earth. Bioinformatic analyses have recently revealed that viruses, like multicellular life, form reproductively isolated biological species. Viruses are known to share high rates of genetic exchange, so how do they evolve genetic isolation? Here, we evaluate two related bacteriophages and describe three factors that limit genetic exchange between them: 1) A nucleus-like compartment that physically separates replicating phage genomes, thereby limiting inter-phage recombination during co-infection; 2) A tubulin-based spindle that orchestrates phage replication and forms nonfunctional hybrid polymers; and 3) A nuclear incompatibility factor that reduces phage fitness. Together, these traits maintain species differences through Subcellular Genetic Isolation where viral genomes are physically separated during co-infection, and Virogenesis Incompatibility in which the interaction of cross-species components interferes with viral production.},
}

Bacteriophages/*genetics
Cell Nucleus/metabolism
*Genetic Speciation
Green Fluorescent Proteins/metabolism
Pseudomonas aeruginosa/virology
Species Specificity
Subcellular Fractions

@article {pmid33418487,
year = {2021},
author = {Sagova-Mareckova, M and Boenigk, J and Bouchez, A and Cermakova, K and Chonova, T and Cordier, T and Eisendle, U and Elersek, T and Fazi, S and Fleituch, T and Frühe, L and Gajdosova, M and Graupner, N and Haegerbaeumer, A and Kelly, AM and Kopecky, J and Leese, F and Nõges, P and Orlic, S and Panksep, K and Pawlowski, J and Petrusek, A and Piggott, JJ and Rusch, JC and Salis, R and Schenk, J and Simek, K and Stovicek, A and Strand, DA and Vasquez, MI and Vrålstad, T and Zlatkovic, S and Zupancic, M and Stoeck, T},
title = {Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring.},
journal = {Water research},
volume = {191},
number = {},
pages = {116767},
doi = {10.1016/j.watres.2020.116767},
pmid = {33418487},
issn = {1879-2448},
mesh = {Archaea/genetics ; *Biological Monitoring ; *Ecosystem ; Environmental Biomarkers ; Environmental Monitoring ; Fresh Water ; },
abstract = {Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.},
}

Archaea/genetics
*Biological Monitoring
*Ecosystem
Environmental Biomarkers
Environmental Monitoring
Fresh Water

@article {pmid33411582,
year = {2021},
author = {Costa, M and Blaschke, TF and Amara, SG and Meyer, UA and Insel, PA},
title = {Introduction to the Theme "Old and New Toxicology: Interfaces with Pharmacology".},
journal = {Annual review of pharmacology and toxicology},
volume = {61},
number = {},
pages = {1-7},
doi = {10.1146/annurev-pharmtox-092220-033032},
pmid = {33411582},
issn = {1545-4304},
abstract = {The theme of Volume 61 is "Old and New Toxicology: Interfaces with Pharmacology." Old toxicology is exemplified by the authors of the autobiographical articles: B.M. Olivera's work on toxins and venoms from cone snails and P. Taylor's studies of acetylcholinesterase and the nicotinic cholinergic receptor, which serve as sites of action for numerous pesticides and venoms. Other articles in this volume focus on new understanding and new types of toxicology, including (a) arsenic toxicity, which is an ancient poison that, through evolution, has caused most multicellular organisms to express an active arsenic methyltransferase to methylate arsenite, which accelerates the excretion of arsenic from the body; (b) small molecules that react with lipid dicarbonyls, which are now considered the most toxic oxidative stress end products; (c) immune checkpoint inhibitors (ICIs), which have revolutionized cancer therapy but have numerous immune-related adverse events, including cardiovascular complications; (d) autoimmunity caused by the environment; (e) idiosyncratic drug-induced liver disease, which together with the toxicity of ICIs represents new toxicology interfacing with pharmacology; and (f) sex differences in the development of cardiovascular disease, with men more susceptible than women to vascular inflammation that initiates and perpetuates disease. These articles and others in Volume 61 reflect the interface and close integration of pharmacology and toxicology that began long ago but continues today.},
}

@article {pmid33389562,
year = {2021},
author = {Furumizu, C and Sawa, S},
title = {Insight into early diversification of leucine-rich repeat receptor-like kinases provided by the sequenced moss and hornwort genomes.},
journal = {Plant molecular biology},
volume = {},
number = {},
pages = {},
pmid = {33389562},
issn = {1573-5028},
support = {17H03967//Japan Society for the Promotion of Science/ ; 18H04841//Japan Society for the Promotion of Science/ ; 18H04625//Japan Society for the Promotion of Science/ ; 18H05487//Japan Society for the Promotion of Science/ ; 20H00422//Japan Society for the Promotion of Science/ ; 20K06770//Japan Society for the Promotion of Science/ ; },
abstract = {KEY MESSAGE: Identification of the subfamily X leucine-rich repeat receptor-like kinases in the recently sequenced moss and hornwort genomes points to their diversification into distinct groups during early evolution of land plants. Signal transduction mediated through receptor-ligand interactions plays key roles in controlling developmental and physiological processes of multicellular organisms, and plants employ diverse receptors in signaling. Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent one of the largest receptor classes in plants and are structurally classified into subfamilies. LRR-RLKs of the subfamily X are unique in the variety of their signaling roles; they include receptors for steroid or peptide hormones as well as negative regulators of signaling through binding to other LRR-RLKs, raising a question as to how they diversified. However, our understanding of diversification processes of LRR-RLKs has been hindered by the paucity of genomic data in non-seed plants and limited taxa sampling in previous phylogenetic analyses. Here we analyzed the phylogeny of LRR-RLK X sequences collected from all major land plant lineages and show that this subfamily diversified into six major clades before the divergence between bryophytes and vascular plants. Notably, we have identified homologues of the brassinosteroid receptor, BRASSINOSTEROID INSENSITIVE 1 (BRI1), in the genomes of Sphagnum mosses, hornworts, and ferns, contrary to earlier reports that postulate the origin of BRI1-like LRR-RLKs in the seed plant lineage. The phylogenetic distribution of major clades illustrates that the current receptor repertoire was shaped through lineage-specific gene family expansion and independent gene losses, highlighting dynamic changes in the evolution of LRR-RLKs.},
}

@article {pmid33373044,
year = {2020},
author = {Montoro, R and Heine, VM and Kemp, S and Engelen, M},
title = {Evolution of adrenoleukodystrophy model systems.},
journal = {Journal of inherited metabolic disease},
volume = {},
number = {},
pages = {},
doi = {10.1002/jimd.12357},
pmid = {33373044},
issn = {1573-2665},
support = {2019-020C2//Association Européenne contre les Leucodystrophies/ ; 016.196.310//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {X-linked adrenoleukodystrophy (ALD) is a neurometabolic disorder affecting the adrenal glands, testes, spinal cord and brain. The disease is caused by mutations in the ABCD1 gene resulting in a defect in peroxisomal degradation of very long-chain fatty acids and their accumulation in plasma and tissues. Males with ALD have a near 100% life-time risk to develop myelopathy. The life-time prevalence to develop progressive cerebral white matter lesions (known as cerebral ALD) is about 60%. Adrenal insufficiency occurs in about 80% of male patients. In adulthood, 80% of women with ALD also develop myelopathy, but adrenal insufficiency or cerebral ALD are very rare. The complex clinical presentation and the absence of a genotype-phenotype correlation are complicating our understanding of the disease. In an attempt to understand the pathophysiology of ALD various model systems have been developed. While these model systems share the basic genetics and biochemistry of ALD they fail to fully recapitulate the complex neurodegenerative etiology of ALD. Each model system recapitulates certain aspects of the disorder. This exposes the complexity of ALD and therefore the challenge to create a comprehensive model system to fully understand ALD. In this review, we provide an overview of the different ALD modeling strategies from single-celled to multicellular organisms and from in vitro to in vivo approaches, and introduce how emerging iPSC-derived technologies could improve the understanding of this highly complex disorder.},
}

@article {pmid33354870,
year = {2021},
author = {Fritsche, E and Haarmann-Stemmann, T and Kapr, J and Galanjuk, S and Hartmann, J and Mertens, PR and Kämpfer, AAM and Schins, RPF and Tigges, J and Koch, K},
title = {Stem Cells for Next Level Toxicity Testing in the 21st Century.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {17},
number = {15},
pages = {e2006252},
doi = {10.1002/smll.202006252},
pmid = {33354870},
issn = {1613-6829},
support = {233-1.08.03.03-121972/131//State of North-Rhine Westphalia, Germany/ ; 1.08.03.03//State of North-Rhine Westphalia, Germany/ ; 121972//State of North-Rhine Westphalia, Germany/ ; 825759//Grant Agreement/ ; 97850925//German Research Foundation/ ; SFB 854//German Research Foundation/ ; GRK 2408//German Research Foundation/ ; ME-1365/7-2//German Research Foundation/ ; ME-1365/9-2//German Research Foundation/ ; 825759//Horizon 2020/ ; 825759//European Union's Horizon 2020 Research and Innovation Program/ ; },
abstract = {The call for a paradigm change in toxicology from the United States National Research Council in 2007 initiates awareness for the invention and use of human-relevant alternative methods for toxicological hazard assessment. Simple 2D in vitro systems may serve as first screening tools, however, recent developments infer the need for more complex, multicellular organotypic models, which are superior in mimicking the complexity of human organs. In this review article most critical organs for toxicity assessment, i.e., skin, brain, thyroid system, lung, heart, liver, kidney, and intestine are discussed with regards to their functions in health and disease. Embracing the manifold modes-of-action how xenobiotic compounds can interfere with physiological organ functions and cause toxicity, the need for translation of such multifaceted organ features into the dish seems obvious. Currently used in vitro methods for toxicological applications and ongoing developments not yet arrived in toxicity testing are discussed, especially highlighting the potential of models based on embryonic stem cells and induced pluripotent stem cells of human origin. Finally, the application of innovative technologies like organs-on-a-chip and genome editing point toward a toxicological paradigm change moves into action.},
}

@article {pmid33329717,
year = {2020},
author = {Clairambault, J},
title = {Stepping From Modeling Cancer Plasticity to the Philosophy of Cancer.},
journal = {Frontiers in genetics},
volume = {11},
number = {},
pages = {579738},
pmid = {33329717},
issn = {1664-8021},
}

@article {pmid33329624,
year = {2020},
author = {Lal, A and Vo, TTB and Sanjaya, IGNPW and Ho, PT and Kim, JK and Kil, EJ and Lee, S},
title = {Nanovirus Disease Complexes: An Emerging Threat in the Modern Era.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {558403},
pmid = {33329624},
issn = {1664-462X},
abstract = {Multipartite viruses package their genomic segments independently and mainly infect plants; few target animals. Nanoviridae is a family of multipartite single-stranded DNA plant viruses that individually encapsidate single-stranded DNAs of approximately 1 kb and transmit them through aphids without replication in the aphid vectors, thereby causing important diseases of leguminous crops and banana. Significant findings regarding nanoviruses have recently been made on important features, such as their multicellular way of life, the transmission of distinct encapsidated genome segments through the vector body, evolutionary ambiguities, mode of infection, host range and geographical distribution. This review deals with all the above-mentioned features in view of recent advances with special emphasis on the emergence of new species and recognition of new host range of nanoviruses and aims to shed light on the evolutionary linkages, the potentially devastating impact on the world economy, and the future challenges imposed by nanoviruses.},
}

@article {pmid33305692,
year = {2020},
author = {Giam, M and Wong, CK and Low, JS and Sinelli, M and Dreesen, O and Rancati, G},
title = {P53 induces senescence in the unstable progeny of aneuploid cells.},
journal = {Cell cycle (Georgetown, Tex.)},
volume = {19},
number = {24},
pages = {3508-3520},
pmid = {33305692},
issn = {1551-4005},
abstract = {Aneuploidy is the condition of having an imbalanced karyotype, which is associated with tumor initiation, evolution, and acquisition of drug-resistant features, possibly by generating heterogeneous populations of cells with distinct genotypes and phenotypes. Multicellular eukaryotes have therefore evolved a range of extrinsic and cell-autonomous mechanisms for restraining proliferation of aneuploid cells, including activation of the tumor suppressor protein p53. However, accumulating evidence indicates that a subset of aneuploid cells can escape p53-mediated growth restriction and continue proliferating in vitro. Here we show that such aneuploid cell lines display a robust modal karyotype and low frequency of chromosomal aberrations despite ongoing chromosome instability. Indeed, while these aneuploid cells are able to survive for extended periods in vitro, their chromosomally unstable progeny remain subject to p53-induced senescence and growth restriction, leading to subsequent elimination from the aneuploid pool. This mechanism helps maintain low levels of heterogeneity in aneuploid populations and may prevent detrimental evolutionary processes such as cancer progression and development of drug resistance.},
}

@article {pmid33292459,
year = {2020},
author = {Zhang, J and Gu, C and Song, Q and Zhu, M and Xu, Y and Xiao, M and Zheng, W},
title = {Identifying cancer-associated fibroblasts as emerging targets for hepatocellular carcinoma.},
journal = {Cell & bioscience},
volume = {10},
number = {1},
pages = {127},
pmid = {33292459},
issn = {2045-3701},
support = {81702419//National Natural Science Foundation of China/ ; BE2019692//Key Research and Development Program of Jiangxi Province/ ; MS12019013//Nantong Science and Technology Bureau/ ; MS22018006//Nantong Science and Technology Bureau/ ; },
abstract = {The tumor microenvironment (TME) is a complex multicellular functional compartment that includes fibroblasts, myofibroblasts, endothelial cells, immune cells, and extracellular matrix (ECM) elements. The microenvironment provides an optimum condition for the initiation, growth, and dissemination of hepatocellular carcinoma (HCC). As one of the critical and abundant components in tumor microenvironment, cancer-associated fibroblasts (CAFs) have been implicated in the progression of HCC. Through secreting various growth factors and cytokines, CAFs contribute to the ECM remodeling, stem features, angiogenesis, immunosuppression, and vasculogenic mimicry (VM), which reinforce the initiation and development of HCC. In order to restrain the CAFs-initiated HCC progression, current strategies include targeting specific markers, engineering CAFs with tumor-suppressive phenotype, depleting CAFs' precursors, and repressing the secretions or downstream signaling. In this review, we update the emerging understanding of CAFs in HCC, with particular emphasis on cellular origin, phenotypes, biological functions and targeted strategies. It provides insights into the targeting CAFs for HCC treatment.},
}

@article {pmid33272929,
year = {2020},
author = {Ruiz-Trillo, I and de Mendoza, A},
title = {Towards understanding the origin of animal development.},
journal = {Development (Cambridge, England)},
volume = {147},
number = {23},
pages = {},
doi = {10.1242/dev.192575},
pmid = {33272929},
issn = {1477-9129},
mesh = {Animals ; *Biological Evolution ; Choanoflagellata/genetics/*growth & development ; Embryonic Development/*genetics ; Gene Expression Regulation, Developmental/genetics ; Mammals/genetics ; Morphogenesis/*genetics ; Phylogeny ; Zygote/growth & development ; },
abstract = {Almost all animals undergo embryonic development, going from a single-celled zygote to a complex multicellular adult. We know that the patterning and morphogenetic processes involved in development are deeply conserved within the animal kingdom. However, the origins of these developmental processes are just beginning to be unveiled. Here, we focus on how the protist lineages sister to animals are reshaping our view of animal development. Most intriguingly, many of these protistan lineages display transient multicellular structures, which are governed by similar morphogenetic and gene regulatory processes as animal development. We discuss here two potential alternative scenarios to explain the origin of animal embryonic development: either it originated concomitantly at the onset of animals or it evolved from morphogenetic processes already present in their unicellular ancestors. We propose that an integrative study of several unicellular taxa closely related to animals will allow a more refined picture of how the last common ancestor of animals underwent embryonic development.},
}

Animals
*Biological Evolution
Choanoflagellata/genetics/*growth & development
Embryonic Development/*genetics
Gene Expression Regulation, Developmental/genetics
Mammals/genetics
Morphogenesis/*genetics
Phylogeny
Zygote/growth & development

@article {pmid33266251,
year = {2020},
author = {Lyall, R and Nikoloski, Z and Gechev, T},
title = {Comparative Analysis of ROS Network Genes in Extremophile Eukaryotes.},
journal = {International journal of molecular sciences},
volume = {21},
number = {23},
pages = {},
pmid = {33266251},
issn = {1422-0067},
support = {SGA-CSA No. 739582//Project PlantaSYST, European Union's Horizon 2020 Research & Innovation Programme/ ; GA No. 823746//Project RESIST, European Union's Horizon 2020 Research & Innovation Programme/ ; BG05M2OP001-1.003-001-C01//European Regional Development Fund/ ; },
mesh = {Biomarkers ; Eukaryota/*genetics/*metabolism ; Extremophiles/*genetics/*metabolism ; Gene Expression Regulation ; Gene Expression Regulation, Enzymologic ; *Gene Regulatory Networks ; Oxidative Stress ; Plants/genetics/metabolism ; Reactive Oxygen Species/*metabolism ; },
abstract = {The reactive oxygen species (ROS) gene network, consisting of both ROS-generating and detoxifying enzymes, adjusts ROS levels in response to various stimuli. We performed a cross-kingdom comparison of ROS gene networks to investigate how they have evolved across all Eukaryotes, including protists, fungi, plants and animals. We included the genomes of 16 extremotolerant Eukaryotes to gain insight into ROS gene evolution in organisms that experience extreme stress conditions. Our analysis focused on ROS genes found in all Eukaryotes (such as catalases, superoxide dismutases, glutathione reductases, peroxidases and glutathione peroxidase/peroxiredoxins) as well as those specific to certain groups, such as ascorbate peroxidases, dehydroascorbate/monodehydroascorbate reductases in plants and other photosynthetic organisms. ROS-producing NADPH oxidases (NOX) were found in most multicellular organisms, although several NOX-like genes were identified in unicellular or filamentous species. However, despite the extreme conditions experienced by extremophile species, we found no evidence for expansion of ROS-related gene families in these species compared to other Eukaryotes. Tardigrades and rotifers do show ROS gene expansions that could be related to their extreme lifestyles, although a high rate of lineage-specific horizontal gene transfer events, coupled with recent tetraploidy in rotifers, could explain this observation. This suggests that the basal Eukaryotic ROS scavenging systems are sufficient to maintain ROS homeostasis even under the most extreme conditions.},
}

Biomarkers
Eukaryota/*genetics/*metabolism
Extremophiles/*genetics/*metabolism
Gene Expression Regulation
Gene Expression Regulation, Enzymologic
*Gene Regulatory Networks
Oxidative Stress
Plants/genetics/metabolism
Reactive Oxygen Species/*metabolism

@article {pmid33263876,
year = {2020},
author = {Kaczanowski, S},
title = {Symbiotic Origin of Apoptosis.},
journal = {Results and problems in cell differentiation},
volume = {69},
number = {},
pages = {253-280},
doi = {10.1007/978-3-030-51849-3_10},
pmid = {33263876},
issn = {0080-1844},
mesh = {Animals ; *Apoptosis ; *Biological Evolution ; *Eukaryota ; Mitochondria/*microbiology ; Phylogeny ; *Symbiosis ; },
abstract = {The progress of evolutionary biology has revealed that symbiosis played a basic role in the evolution of complex eukaryotic organisms, including humans. Mitochondria are actually simplified endosymbiotic bacteria currently playing the role of cellular organelles. Mitochondrial domestication occurred at the very beginning of eukaryotic evolution. Mitochondria have two different basic functions: they produce energy using oxidative respiration, and they initiate different forms of apoptotic programmed/regulated cell death. Apoptotic programmed cell death may have different cytological forms. Mechanisms of apoptotic programmed cell death exist even in the unicellular organisms, and they play a basic role in the development of complex multicellular organisms, such as fungi, green plants, and animals. Multicellularity was independently established many times among eukaryotes. There are indications that apoptotic programmed cell death is a trait required for the establishment of multicellularity. Regulated cell death is initiated by many different parallel biochemical pathways. It is generally accepted that apoptosis evolved during mitochondrial domestication. However, there are different hypothetical models of the origin of apoptosis. The phylogenetic studies of my group indicate that apoptosis probably evolved during an evolutionary arms race between host ancestral eukaryotic predators and ancestral prey mitochondria (named protomitochondria). Protomitochondrial prey produced many different toxins as a defense against predators. From these toxins evolved extant apoptotic factors. There are indications that aerobic respiration and apoptosis co-evolved and are functionally linked in extant organisms. Perturbations of apoptosis and oxidative respiration are frequently observed during neoplastic transition. Our group showed that perturbations of apoptosis in yeasts also cause perturbations of oxidative respiration.},
}

Animals
*Apoptosis
*Biological Evolution
*Eukaryota
Mitochondria/*microbiology
Phylogeny
*Symbiosis

@article {pmid33262337,
year = {2020},
author = {McEvoy, E and Han, YL and Guo, M and Shenoy, VB},
title = {Gap junctions amplify spatial variations in cell volume in proliferating tumor spheroids.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {6148},
pmid = {33262337},
issn = {2041-1723},
mesh = {Breast Neoplasms/chemistry/pathology/*physiopathology ; Cell Line, Tumor ; *Cell Proliferation ; Cell Size ; Disease Progression ; Female ; Gap Junctions/*chemistry ; Humans ; Osmotic Pressure ; Spheroids, Cellular/chemistry/*cytology ; },
abstract = {Sustained proliferation is a significant driver of cancer progression. Cell-cycle advancement is coupled with cell size, but it remains unclear how multiple cells interact to control their volume in 3D clusters. In this study, we propose a mechano-osmotic model to investigate the evolution of volume dynamics within multicellular systems. Volume control depends on an interplay between multiple cellular constituents, including gap junctions, mechanosensitive ion channels, energy-consuming ion pumps, and the actomyosin cortex, that coordinate to manipulate cellular osmolarity. In connected cells, we show that mechanical loading leads to the emergence of osmotic pressure gradients between cells with consequent increases in cellular ion concentrations driving swelling. We identify how gap junctions can amplify spatial variations in cell volume within multicellular spheroids and, further, describe how the process depends on proliferation-induced solid stress. Our model may provide new insight into the role of gap junctions in breast cancer progression.},
}

Breast Neoplasms/chemistry/pathology/*physiopathology
Cell Line, Tumor
*Cell Proliferation
Cell Size
Disease Progression
Female
Gap Junctions/*chemistry
Humans
Osmotic Pressure
Spheroids, Cellular/chemistry/*cytology

@article {pmid33259762,
year = {2020},
author = {König, SG and Nedelcu, AM},
title = {The genetic basis for the evolution of soma: mechanistic evidence for the co-option of a stress-induced gene into a developmental master regulator.},
journal = {Proceedings. Biological sciences},
volume = {287},
number = {1940},
pages = {20201414},
pmid = {33259762},
issn = {1471-2954},
mesh = {*Biological Evolution ; Chlorophyta/*genetics ; Clonal Evolution/*genetics ; Stress, Physiological/*genetics ; },
abstract = {In multicellular organisms with specialized cells, the most significant distinction among cell types is between reproductive (germ) cells and non-reproductive/somatic cells (soma). Although soma contributed to the marked increase in complexity of many multicellular lineages, little is known about its evolutionary origins. We have previously suggested that the evolution of genes responsible for the differentiation of somatic cells involved the co-option of life history trade-off genes that in unicellular organisms enhanced survival at a cost to immediate reproduction. In the multicellular green alga, Volvox carteri, cell fate is established early in development by the differential expression of a master regulatory gene known as regA. A closely related RegA-Like Sequence (RLS1) is present in its single-celled relative, Chlamydomonas reinhardtii. RLS1 is expressed in response to stress, and we proposed that an environmentally induced RLS1-like gene was co-opted into a developmental pathway in the lineage leading to V. carteri. However, the exact evolutionary scenario responsible for the postulated co-option event remains to be determined. Here, we show that in addition to being developmentally regulated, regA can also be induced by environmental cues, indicating that regA has maintained its ancestral regulation. We also found that the absence of a functional RegA protein confers increased sensitivity to stress, consistent with RegA having a direct or indirect role in stress responses. Overall, this study (i) provides mechanistic evidence for the co-option of an environmentally induced gene into a major developmental regulator, (ii) supports the view that major morphological innovations can evolve via regulatory changes and (iii) argues for the role of stress in the evolution of multicellular complexity.},
}

*Biological Evolution
Chlorophyta/*genetics
Clonal Evolution/*genetics
Stress, Physiological/*genetics

@article {pmid33254563,
year = {2020},
author = {Retzinger, AC and Retzinger, GS},
title = {Mites, ticks, anaphylaxis and allergy: The Acari hypothesis.},
journal = {Medical hypotheses},
volume = {144},
number = {},
pages = {110257},
doi = {10.1016/j.mehy.2020.110257},
pmid = {33254563},
issn = {1532-2777},
abstract = {Anaphylaxis is a poorly understood immune process in which a Th2-/IgE-mediated adaptive response commandeers cellular machinery, typically reserved for defense against multicellular ectoparasites, to activate against otherwise benign molecules. Its clinical manifestations consist of rapid pathophysiological reflexes that target epithelial surfaces. The galactose-α-1,3-galactose hypersensitivity response is a compelling model of anaphylaxis for which causation has been demonstrated. At the core of the model, a tick bite sensitizes a recipient to a tick foodstuff. As proposed herein, the model likely informs on the origin of all allergic inflammation; namely, allergy is not intended to protect against seemingly harmless and irrelevant materials, but is, instead, intended to rid epithelial surfaces of pathogen-bearing Acari, i.e., mites and ticks. The demonstrated adjuvant activity of acarian gastrointestinal secretions, when paired with the polyphagous diet of mites, renders acarians eminently suited to accounting, mechanistically, for many, if not all, human allergies.},
}

@article {pmid33248278,
year = {2020},
author = {Chi, S and Wang, G and Liu, T and Wang, X and Liu, C and Jin, Y and Yin, H and Xu, X and Yu, J},
title = {Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in Saccharina japonica.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.gpb.2018.12.012},
pmid = {33248278},
issn = {2210-3244},
abstract = {As a carbon-storage compound and osmoprotectant in brown algae, mannitol is synthesized and then accumulated at high levels in Saccharina japonica (Sja); however, the underlying control mechanisms have not been studied. Our analysis of genomic and transcriptomic data from Sja shows that mannitol metabolism is a cyclic pathway composed of four distinct steps. A mannitol-1-phosphate dehydrogenase (M1PDH2) and two mannitol-1-phosphatases (M1Pase1 and MIPase2) work together or in combination to exhibit full enzymatic properties. Based on comprehensive transcriptomic data from different tissues, generations, and sexes as well as under different stress conditions, coupled with droplet digital PCR (ddPCR) and proteomic confirmation, we suggest that SjaM1Pase1 plays a major role in mannitol biosynthesis and that the basic mannitol anabolism and the carbohydrate pool dynamics are responsible for carbon storage and anti-stress mechanism. Our proteomic data indicate that mannitol metabolism remains constant during diurnal cycle in Sja. In addition, we discover that mannitol-metabolism-associated (MMA) genes show differential expression between the multicellular filamentous (gametophyte) and large parenchymal thallus (sporophyte) generations and respond differentially to environmental stresses, such as hyposaline and hyperthermia conditions. Our results indicate that the ecophysiological significance of such differentially expressed genes may be attributable to the evolution of heteromorphic generations (filamentous and thallus) and environmental adaptation of Laminariales.},
}

@article {pmid33241195,
year = {2020},
author = {Boutry, J and Dujon, AM and Gerard, AL and Tissot, S and Macdonald, N and Schultz, A and Biro, PA and Beckmann, C and Hamede, R and Hamilton, DG and Giraudeau, M and Ujvari, B and Thomas, F},
title = {Ecological and Evolutionary Consequences of Anticancer Adaptations.},
journal = {iScience},
volume = {23},
number = {11},
pages = {101716},
pmid = {33241195},
issn = {2589-0042},
abstract = {Cellular cheating leading to cancers exists in all branches of multicellular life, favoring the evolution of adaptations to avoid or suppress malignant progression, and/or to alleviate its fitness consequences. Ecologists have until recently largely neglected the importance of cancer cells for animal ecology, presumably because they did not consider either the potential ecological or evolutionary consequences of anticancer adaptations. Here, we review the diverse ways in which the evolution of anticancer adaptations has significantly constrained several aspects of the evolutionary ecology of multicellular organisms at the cell, individual, population, species, and ecosystem levels and suggest some avenues for future research.},
}

@article {pmid33239636,
year = {2020},
author = {Xu, Z and Wang, S and Zhao, C and Li, S and Liu, X and Wang, L and Li, M and Huang, X and Mann, S},
title = {Photosynthetic hydrogen production by droplet-based microbial micro-reactors under aerobic conditions.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5985},
pmid = {33239636},
issn = {2041-1723},
mesh = {Aerobiosis/physiology ; Bioreactors/*microbiology ; Cell Hypoxia/physiology ; Chlorella/metabolism ; Escherichia coli/metabolism ; Hydrogen/*metabolism ; Industrial Microbiology/*methods ; Microbiota/*physiology ; Oxygen/*metabolism ; Photosynthesis/physiology ; Renewable Energy ; },
abstract = {The spontaneous self-assembly of multicellular ensembles into living materials with synergistic structure and function remains a considerable challenge in biotechnology and synthetic biology. Here, we exploit the aqueous two-phase separation of dextran-in-PEG emulsion micro-droplets for the capture, spatial organization and immobilization of algal cells or algal/bacterial cell communities to produce discrete multicellular spheroids capable of both aerobic (oxygen producing) and hypoxic (hydrogen producing) photosynthesis in daylight under air. We show that localized oxygen depletion results in hydrogen production from the core of the algal microscale reactor, and demonstrate that enhanced levels of hydrogen evolution can be achieved synergistically by spontaneously enclosing the photosynthetic cells within a shell of bacterial cells undergoing aerobic respiration. Our results highlight a promising droplet-based environmentally benign approach to dispersible photosynthetic microbial micro-reactors comprising segregated cellular micro-niches with dual functionality, and provide a step towards photobiological hydrogen production under aerobic conditions.},
}

Aerobiosis/physiology
Bioreactors/*microbiology
Cell Hypoxia/physiology
Chlorella/metabolism
Escherichia coli/metabolism
Hydrogen/*metabolism
Industrial Microbiology/*methods
Microbiota/*physiology
Oxygen/*metabolism
Photosynthesis/physiology
Renewable Energy

@article {pmid33231627,
year = {2021},
author = {Hammerschmidt, K and Landan, G and Domingues Kümmel Tria, F and Alcorta, J and Dagan, T},
title = {The Order of Trait Emergence in the Evolution of Cyanobacterial Multicellularity.},
journal = {Genome biology and evolution},
volume = {13},
number = {2},
pages = {},
pmid = {33231627},
issn = {1759-6653},
abstract = {The transition from unicellular to multicellular organisms is one of the most significant events in the history of life. Key to this process is the emergence of Darwinian individuality at the higher level: Groups must become single entities capable of reproduction for selection to shape their evolution. Evolutionary transitions in individuality are characterized by cooperation between the lower level entities and by division of labor. Theory suggests that division of labor may drive the transition to multicellularity by eliminating the trade off between two incompatible processes that cannot be performed simultaneously in one cell. Here, we examine the evolution of the most ancient multicellular transition known today, that of cyanobacteria, where we reconstruct the sequence of ecological and phenotypic trait evolution. Our results show that the prime driver of multicellularity in cyanobacteria was the expansion in metabolic capacity offered by nitrogen fixation, which was accompanied by the emergence of the filamentous morphology and succeeded by a reproductive life cycle. This was followed by the progression of multicellularity into higher complexity in the form of differentiated cells and patterned multicellularity.},
}

@article {pmid33228413,
year = {2020},
author = {Coelho, SM and Cock, JM},
title = {Brown Algal Model Organisms.},
journal = {Annual review of genetics},
volume = {54},
number = {},
pages = {71-92},
doi = {10.1146/annurev-genet-030620-093031},
pmid = {33228413},
issn = {1545-2948},
abstract = {Model organisms are extensively used in research as accessible and convenient systems for studying a particular area or question in biology. Traditionally, only a limited number of organisms have been studied in detail, but modern genomic tools are enabling researchers to extend beyond the set of classical model organisms to include novel species from less-studied phylogenetic groups. This review focuses on model species for an important group of multicellular organisms, the brown algae. The development of genetic and genomic tools for the filamentous brown alga Ectocarpus has led to it emerging as a general model system for this group, but additional models, such as Fucus or Dictyota dichotoma, remain of interest for specific biological questions. In addition, Saccharina japonica has emerged as a model system to directly address applied questions related to algal aquaculture. We discuss the past, present, and future of brown algal model organisms in relation to the opportunities and challenges in brown algal research.},
}

@article {pmid33228223,
year = {2020},
author = {Anatskaya, OV and Vinogradov, AE and Vainshelbaum, NM and Giuliani, A and Erenpreisa, J},
title = {Phylostratic Shift of Whole-Genome Duplications in Normal Mammalian Tissues towards Unicellularity Is Driven by Developmental Bivalent Genes and Reveals a Link to Cancer.},
journal = {International journal of molecular sciences},
volume = {21},
number = {22},
pages = {},
pmid = {33228223},
issn = {1422-0067},
support = {1.1.1.1/18/A/099//European Regional Development Fund (ERDF)/ ; 12//Institute of Cytology Director's Fund/ ; XX//Natural Sciences PhD Student Scholarship from the University of Latvia Foundation/ ; },
mesh = {Animals ; Antineoplastic Agents/therapeutic use ; Carcinogenesis/*genetics/metabolism/pathology ; Circadian Rhythm Signaling Peptides and Proteins/genetics/metabolism ; Drug Resistance, Neoplasm/genetics ; Epigenesis, Genetic ; Gene Duplication ; *Gene Expression Regulation, Neoplastic ; *Genome ; Humans ; Metabolic Networks and Pathways/genetics ; Mice ; Neoplasm Proteins/*genetics/metabolism ; Neoplasms/drug therapy/*genetics/metabolism/pathology ; Oncogenes ; *Ploidies ; Protein Interaction Mapping ; Proto-Oncogene Proteins c-myc/genetics/metabolism ; },
abstract = {Tumours were recently revealed to undergo a phylostratic and phenotypic shift to unicellularity. As well, aggressive tumours are characterized by an increased proportion of polyploid cells. In order to investigate a possible shared causation of these two features, we performed a comparative phylostratigraphic analysis of ploidy-related genes, obtained from transcriptomic data for polyploid and diploid human and mouse tissues using pairwise cross-species transcriptome comparison and principal component analysis. Our results indicate that polyploidy shifts the evolutionary age balance of the expressed genes from the late metazoan phylostrata towards the upregulation of unicellular and early metazoan phylostrata. The up-regulation of unicellular metabolic and drug-resistance pathways and the downregulation of pathways related to circadian clock were identified. This evolutionary shift was associated with the enrichment of ploidy with bivalent genes (p < 10-16). The protein interactome of activated bivalent genes revealed the increase of the connectivity of unicellulars and (early) multicellulars, while circadian regulators were depressed. The mutual polyploidy-c-MYC-bivalent genes-associated protein network was organized by gene-hubs engaged in both embryonic development and metastatic cancer including driver (proto)-oncogenes of viral origin. Our data suggest that, in cancer, the atavistic shift goes hand-in-hand with polyploidy and is driven by epigenetic mechanisms impinging on development-related bivalent genes.},
}

Animals
Antineoplastic Agents/therapeutic use
Carcinogenesis/*genetics/metabolism/pathology
Circadian Rhythm Signaling Peptides and Proteins/genetics/metabolism
Drug Resistance, Neoplasm/genetics
Epigenesis, Genetic
Gene Duplication
*Gene Expression Regulation, Neoplastic
*Genome
Humans
Metabolic Networks and Pathways/genetics
Mice
Neoplasm Proteins/*genetics/metabolism
Neoplasms/drug therapy/*genetics/metabolism/pathology
Oncogenes
*Ploidies
Protein Interaction Mapping
Proto-Oncogene Proteins c-myc/genetics/metabolism

@article {pmid33216655,
year = {2021},
author = {Snyder-Beattie, AE and Sandberg, A and Drexler, KE and Bonsall, MB},
title = {The Timing of Evolutionary Transitions Suggests Intelligent Life is Rare.},
journal = {Astrobiology},
volume = {21},
number = {3},
pages = {265-278},
pmid = {33216655},
issn = {1557-8070},
abstract = {It is unknown how abundant extraterrestrial life is, or whether such life might be complex or intelligent. On Earth, the emergence of complex intelligent life required a preceding series of evolutionary transitions such as abiogenesis, eukaryogenesis, and the evolution of sexual reproduction, multicellularity, and intelligence itself. Some of these transitions could have been extraordinarily improbable, even in conducive environments. The emergence of intelligent life late in Earth's lifetime is thought to be evidence for a handful of rare evolutionary transitions, but the timing of other evolutionary transitions in the fossil record is yet to be analyzed in a similar framework. Using a simplified Bayesian model that combines uninformative priors and the timing of evolutionary transitions, we demonstrate that expected evolutionary transition times likely exceed the lifetime of Earth, perhaps by many orders of magnitude. Our results corroborate the original argument suggested by Brandon Carter that intelligent life in the Universe is exceptionally rare, assuming that intelligent life elsewhere requires analogous evolutionary transitions. Arriving at the opposite conclusion would require exceptionally conservative priors, evidence for much earlier transitions, multiple instances of transitions, or an alternative model that can explain why evolutionary transitions took hundreds of millions of years without appealing to rare chance events. Although the model is simple, it provides an initial basis for evaluating how varying biological assumptions and fossil record data impact the probability of evolving intelligent life, and also provides a number of testable predictions, such as that some biological paradoxes will remain unresolved and that planets orbiting M dwarf stars are uninhabitable.},
}

@article {pmid33211685,
year = {2020},
author = {Pichugin, Y and Traulsen, A},
title = {Evolution of multicellular life cycles under costly fragmentation.},
journal = {PLoS computational biology},
volume = {16},
number = {11},
pages = {e1008406},
pmid = {33211685},
issn = {1553-7358},
mesh = {*Biological Evolution ; Clostridiales/cytology/growth & development/physiology ; Computational Biology ; Cyanobacteria/cytology/growth & development/physiology ; Environment ; *Life Cycle Stages/physiology ; *Models, Biological ; Reproduction/physiology ; },
abstract = {A fascinating wealth of life cycles is observed in biology, from unicellularity to the concerted fragmentation of multicellular units. However, the understanding of factors driving their evolution is still limited. We show that costs of fragmentation have a major impact on the evolution of life cycles due to their influence on the growth rates of the associated populations. We model a group structured population of undifferentiated cells, where cell clusters reproduce by fragmentation. Fragmentation events are associated with a cost expressed by either a fragmentation delay, an additional risk, or a cell loss. The introduction of such fragmentation costs vastly increases the set of possible life cycles. Based on these findings, we suggest that the evolution of life cycles involving splitting into multiple offspring can be directly associated with the fragmentation cost. Moreover, the impact of this cost alone is strong enough to drive the emergence of multicellular units that eventually split into many single cells, even under scenarios that strongly disfavour collectives compared to solitary individuals.},
}

*Biological Evolution
Clostridiales/cytology/growth & development/physiology
Computational Biology
Cyanobacteria/cytology/growth & development/physiology
Environment
*Life Cycle Stages/physiology
*Models, Biological
Reproduction/physiology

@article {pmid33211684,
year = {2020},
author = {Aubier, TG and Galipaud, M and Erten, EY and Kokko, H},
title = {Transmissible cancers and the evolution of sex under the Red Queen hypothesis.},
journal = {PLoS biology},
volume = {18},
number = {11},
pages = {e3000916},
pmid = {33211684},
issn = {1545-7885},
support = {U54 CA217376/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Biological Evolution ; Genetics, Population/methods ; Host-Parasite Interactions/genetics ; Humans ; Models, Biological ; Models, Genetic ; Neoplasms/etiology/genetics ; Parasites ; Reproduction/*genetics/physiology ; Selection, Genetic/genetics/*physiology ; Sex ; },
abstract = {The predominance of sexual reproduction in eukaryotes remains paradoxical in evolutionary theory. Of the hypotheses proposed to resolve this paradox, the 'Red Queen hypothesis' emphasises the potential of antagonistic interactions to cause fluctuating selection, which favours the evolution and maintenance of sex. Whereas empirical and theoretical developments have focused on host-parasite interactions, the premises of the Red Queen theory apply equally well to any type of antagonistic interactions. Recently, it has been suggested that early multicellular organisms with basic anticancer defences were presumably plagued by antagonistic interactions with transmissible cancers and that this could have played a pivotal role in the evolution of sex. Here, we dissect this argument using a population genetic model. One fundamental aspect distinguishing transmissible cancers from other parasites is the continual production of cancerous cell lines from hosts' own tissues. We show that this influx dampens fluctuating selection and therefore makes the evolution of sex more difficult than in standard Red Queen models. Although coevolutionary cycling can remain sufficient to select for sex under some parameter regions of our model, we show that the size of those regions shrinks once we account for epidemiological constraints. Altogether, our results suggest that horizontal transmission of cancerous cells is unlikely to cause fluctuating selection favouring sexual reproduction. Nonetheless, we confirm that vertical transmission of cancerous cells can promote the evolution of sex through a separate mechanism, known as similarity selection, that does not depend on coevolutionary fluctuations.},
}

Animals
Biological Evolution
Genetics, Population/methods
Host-Parasite Interactions/genetics
Humans
Models, Biological
Models, Genetic
Neoplasms/etiology/genetics
Parasites
Reproduction/*genetics/physiology
Selection, Genetic/genetics/*physiology
Sex

@article {pmid33193544,
year = {2020},
author = {Li, HJ and Yang, WC},
title = {Central Cell in Flowering Plants: Specification, Signaling, and Evolution.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {590307},
pmid = {33193544},
issn = {1664-462X},
abstract = {During the reproduction of animals and lower plants, one sperm cell usually outcompetes the rivals to fertilize a single egg cell. But in flowering plants, two sperm cells fertilize the two adjacent dimorphic female gametes, the egg and central cell, respectively, to initiate the embryo and endosperm within a seed. The endosperm nourishes the embryo development and is also the major source of nutrition in cereals for humankind. Central cell as one of the key innovations of flowering plants is the biggest cell in the multicellular haploid female gametophyte (embryo sac). The embryo sac differentiates from the meiotic products through successive events of nuclear divisions, cellularization, and cell specification. Nowadays, accumulating lines of evidence are raveling multiple roles of the central cell rather than only the endosperm precursor. In this review, we summarize the current understanding on its cell fate specification, intercellular communication, and evolution. We also highlight some key unsolved questions for the further studies in this field.},
}