@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 {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},
mesh = {*Aneuploidy ; Cell Cycle Checkpoints/genetics ; Cell Proliferation/genetics ; Cell Transformation, Neoplastic/genetics/metabolism ; Cellular Senescence/*genetics ; Chromosomal Instability/genetics ; Chromosome Segregation/genetics ; Epithelial Cells/*metabolism ; Gene Knockdown Techniques ; HEK293 Cells ; Humans ; Karyotype ; Retinal Pigment Epithelium/*cytology ; Tumor Suppressor Protein p53/genetics/*metabolism ; },
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.},
}

*Aneuploidy
Cell Cycle Checkpoints/genetics
Cell Proliferation/genetics
Cell Transformation, Neoplastic/genetics/metabolism
Cellular Senescence/*genetics
Chromosomal Instability/genetics
Chromosome Segregation/genetics
Epithelial Cells/*metabolism
Gene Knockdown Techniques
HEK293 Cells
Humans
Karyotype
Retinal Pigment Epithelium/*cytology
Tumor Suppressor Protein p53/genetics/*metabolism

@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},
mesh = {Humans ; In Vitro Techniques ; *Induced Pluripotent Stem Cells ; *Toxicity Tests ; United States ; },
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.},
}

Humans
In Vitro Techniques
*Induced Pluripotent Stem Cells
*Toxicity Tests
United States

@article {pmid33355212,
year = {2021},
author = {Stresser, DM and Sun, J and Wilson, SS},
title = {Evaluation of Tissue Stem Cell-Derived Human Intestinal Organoids, a Physiologically Relevant Model to Evaluate Cytochrome P450 Induction in Gut.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {49},
number = {3},
pages = {245-253},
doi = {10.1124/dmd.120.000281},
pmid = {33355212},
issn = {1521-009X},
mesh = {Cell Line ; Cytochrome P-450 Enzyme Inducers/*pharmacology ; Cytochrome P-450 Enzyme System/*biosynthesis ; Dose-Response Relationship, Drug ; Enzyme Induction/drug effects/physiology ; Humans ; Intestines/cytology/drug effects/*enzymology ; Organoids/drug effects/*enzymology ; Rifampin/pharmacology ; Stem Cells/drug effects/*enzymology ; },
abstract = {Induction of cytochrome P450 can cause drug-drug interactions and efficacy failure. Induction risk in liver and gut is typically inferred from experiments with plated hepatocytes. Organoids are physiologically relevant, multicellular structures originating from stem cells. Intestinal stem cell-derived organoids retain traits of normal gut physiology, such as an epithelial barrier and cellular diversity. Matched human enteroid and colonoid lines, generated from ileal and colon biopsies from two donors, were cultured in extracellular matrix for 3 days, followed by a single 48-hour treatment with rifampin, omeprazole, CITCO, and phenytoin at concentrations that induce target genes in hepatocytes. After treatment, mRNA was analyzed for induction of target genes. Rifampin induced CYP3A4; estimated EC50 and maximal fold induction were 3.75 µM and 8.96-fold, respectively, for ileal organoids and 1.40 µM and 11.3-fold, respectively, for colon organoids. Ileal, but not colon, organoids exhibited nifedipine oxidase activity, which was induced by rifampin up to 14-fold. The test compounds did not increase mRNA expression of CYP1A2, CYP2B6, multidrug resistance transporter 1 (P-glycoprotein), breast cancer resistance protein, and UDP-glucuronosyltransferase 1A1 in ileal organoids. Whereas omeprazole induced CYP3A4 (up to 5.3-fold, geometric mean, n = 4 experiments), constitutive androstane receptor activators phenytoin and CITCO did not. Omeprazole failed to induce CYP1A2 mRNA but did induce CYP1A1 mRNA (up to 7.7-fold and 15-fold in ileal and colon organoids, respectively, n = 4 experiments). Despite relatively high intra- and interexperimental variability, data suggest that the model yields induction responses that are distinct from hepatocytes and holds promise to enable evaluation of CYP1A1 and CYP3A4 induction in gut. SIGNIFICANCE STATEMENT: An adult intestinal stem cell-derived organoid model to test P450 induction in gut was evaluated. Testing several prototypical inducers for mRNA induction of P450 isoforms, UDP-glucuronosyltransferase 1A1, P-glycoprotein, and breast cancer resistance protein with both human colon and ileal organoids resulted in a range of responses, often distinct from those found in hepatocytes, indicating the potential for further development of this model as a physiologically relevant gut induction test system.},
}

Cell Line
Cytochrome P-450 Enzyme Inducers/*pharmacology
Cytochrome P-450 Enzyme System/*biosynthesis
Dose-Response Relationship, Drug
Enzyme Induction/drug effects/physiology
Humans
Intestines/cytology/drug effects/*enzymology
Organoids/drug effects/*enzymology
Rifampin/pharmacology
Stem Cells/drug effects/*enzymology

@article {pmid33373044,
year = {2021},
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 = {44},
number = {3},
pages = {544-553},
pmid = {33373044},
issn = {1573-2665},
mesh = {ATP Binding Cassette Transporter, Subfamily D, Member 1/*genetics ; Adrenoleukodystrophy/epidemiology/*genetics ; Adult ; Animals ; Biological Evolution ; Fatty Acids/metabolism ; Female ; Humans ; Male ; *Models, Animal ; *Models, Biological ; Mutation ; Sex Factors ; Spinal Cord Diseases/epidemiology ; },
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.},
}

ATP Binding Cassette Transporter, Subfamily D, Member 1/*genetics
Adrenoleukodystrophy/epidemiology/*genetics
Adult
Animals
Biological Evolution
Fatty Acids/metabolism
Female
Humans
Male
*Models, Animal
*Models, Biological
Mutation
Sex Factors
Spinal Cord Diseases/epidemiology

@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 = {107},
number = {4-5},
pages = {337-353},
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/ ; },
mesh = {Amino Acid Sequence ; Anthocerotophyta/*genetics ; Computer Simulation ; Evolution, Molecular ; *Genetic Variation ; Genome, Plant/*genetics ; Genomics/methods ; Phylogeny ; Plant Proteins/chemistry/classification/*genetics ; Protein Domains ; Protein Kinases/chemistry/classification/*genetics ; Sequence Homology, Amino Acid ; Signal Transduction/genetics ; Sphagnopsida/*genetics ; },
abstract = {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.},
}

Amino Acid Sequence
Anthocerotophyta/*genetics
Computer Simulation
Evolution, Molecular
*Genetic Variation
Genome, Plant/*genetics
Genomics/methods
Phylogeny
Plant Proteins/chemistry/classification/*genetics
Protein Domains
Protein Kinases/chemistry/classification/*genetics
Sequence Homology, Amino Acid
Signal Transduction/genetics
Sphagnopsida/*genetics

@article {pmid33397407,
year = {2021},
author = {Bourdareau, S and Tirichine, L and Lombard, B and Loew, D and Scornet, D and Wu, Y and Coelho, SM and Cock, JM},
title = {Histone modifications during the life cycle of the brown alga Ectocarpus.},
journal = {Genome biology},
volume = {22},
number = {1},
pages = {12},
pmid = {33397407},
issn = {1474-760X},
mesh = {Chromatin/metabolism ; Epigenesis, Genetic ; Genome ; Germ Cells, Plant ; *Histone Code ; *Histones ; *Life Cycle Stages ; Phaeophyceae/*genetics/physiology ; Phylogeny ; Plants/genetics ; *Protein Processing, Post-Translational ; },
abstract = {BACKGROUND: Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here, we focus on mechanisms of epigenetic regulation involving post-translational modifications of histone proteins.

RESULTS: A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression.

CONCLUSIONS: The overview of histone post-translational modifications in the brown alga presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.},
}

Chromatin/metabolism
Epigenesis, Genetic
Genome
Germ Cells, Plant
*Histone Code
*Histones
*Life Cycle Stages
Phaeophyceae/*genetics/physiology
Phylogeny
Plants/genetics
*Protein Processing, Post-Translational

@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},
mesh = {Female ; Humans ; Male ; *Pharmacology ; *Toxicology ; },
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.},
}

Female
Humans
Male
*Pharmacology
*Toxicology

@article {pmid33412387,
year = {2021},
author = {Liu, Q and Piao, H and Wang, Y and Zheng, D and Wang, W},
title = {Circulating exosomes in cardiovascular disease: Novel carriers of biological information.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {135},
number = {},
pages = {111148},
doi = {10.1016/j.biopha.2020.111148},
pmid = {33412387},
issn = {1950-6007},
mesh = {Animals ; Biomarkers/metabolism ; Cardiovascular Diseases/blood/genetics/*metabolism/therapy ; Cardiovascular System/*metabolism ; *Cell Communication ; Drug Carriers ; Exosomes/genetics/*metabolism/transplantation ; Gene Transfer Techniques ; Genetic Therapy ; Humans ; Signal Transduction ; },
abstract = {Exosomes are a group of nanosized extracellular vesicles that include various bioactive nucleic acids, lipids, and proteins. They originate from membrane invagination and are released by exocytosis, which can transmit signals to target cells to achieve cell-to-cell communication and maintain homeostasis. The heart is a complex multicellular organ that contains resident cell types such as fibroblasts, endothelial cells, and smooth muscle cells. Communication between different cell types and immune systems is essential for the dynamic equilibrium of the cardiac internal environment. Intercellular communication is a universal phenomenon mediated by exosomes and their contents during several pathological processes in cardiovascular diseases, such as cardiomyocyte hypertrophy, apoptosis, and angiogenesis. Therefore, exosomes can be used as novel invasive diagnostic biomarkers in multiple diseases, including atherosclerosis, myocardial ischemia, cardiac fibrosis, and ischemia-reperfusion injury. In addition, the biocompatible nature and low immunogenicity of exosomes make them high-quality nanoparticle drug carriers with potential applications in translational medicine and therapeutic strategies. Here, we focus on the biogenesis, isolation, biological functions, and future application prospects of exosomes in cardiovascular disease.},
}

Animals
Biomarkers/metabolism
Cardiovascular Diseases/blood/genetics/*metabolism/therapy
Cardiovascular System/*metabolism
*Cell Communication
Drug Carriers
Exosomes/genetics/*metabolism/transplantation
Gene Transfer Techniques
Genetic Therapy
Humans
Signal Transduction

@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 {pmid33421998,
year = {2021},
author = {Mondal, M and Peter, J and Scarbrough, O and Flynt, A},
title = {Environmental RNAi pathways in the two-spotted spider mite.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {42},
pmid = {33421998},
issn = {1471-2164},
support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; 1616725//Directorate for Biological Sciences/ ; P204M103476//Mississippi IDeA Network of Biomedical Research Excellence (US)/ ; },
mesh = {Animals ; Gene Expression ; Plants ; RNA Interference ; *Tetranychidae/genetics ; },
abstract = {BACKGROUND: RNA interference (RNAi) regulates gene expression in most multicellular organisms through binding of small RNA effectors to target transcripts. Exploiting this process is a popular strategy for genetic manipulation and has applications that includes arthropod pest control. RNAi technologies are dependent on delivery method with the most convenient likely being feeding, which is effective in some animals while others are insensitive. The two-spotted spider mite, Tetranychus urticae, is prime candidate for developing RNAi approaches due to frequent occurrence of conventional pesticide resistance. Using a sequencing-based approach, the fate of ingested RNAs was explored to identify features and conditions that affect small RNA biogenesis from external sources to better inform RNAi design.

RESULTS: Biochemical and sequencing approaches in conjunction with extensive computational assessment were used to evaluate metabolism of ingested RNAs in T. urticae. This chelicerae arthropod shows only modest response to oral RNAi and has biogenesis pathways distinct from model organisms. Processing of synthetic and plant host RNAs ingested during feeding were evaluated to identify active substrates for spider mite RNAi pathways. Through cataloging characteristics of biochemically purified RNA from these sources, trans-acting small RNAs could be distinguished from degradation fragments and their origins documented.

CONCLUSIONS: Using a strategy that delineates small RNA processing, we found many transcripts have the potential to enter spider mite RNAi pathways, however, trans-acting RNAs appear very unstable and rare. This suggests potential RNAi pathway substrates from ingested materials are mostly degraded and infrequently converted into regulators of gene expression. Spider mites infest a variety of plants, and it would be maladaptive to generate diverse gene regulators from dietary RNAs. This study provides a framework for assessing RNAi technology in organisms where genetic and biochemical tools are absent and benefit rationale design of RNAi triggers for T.urticae.},
}

Animals
Gene Expression
Plants
RNA Interference
*Tetranychidae/genetics

@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 {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 {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 {pmid33455859,
year = {2021},
author = {Jana, SC},
title = {Centrosome structure and biogenesis: Variations on a theme?.},
journal = {Seminars in cell & developmental biology},
volume = {110},
number = {},
pages = {123-138},
doi = {10.1016/j.semcdb.2020.10.014},
pmid = {33455859},
issn = {1096-3634},
mesh = {Actins/genetics/metabolism ; Animals ; Biodiversity ; Biological Evolution ; Cell Cycle/genetics ; Centrioles/metabolism/*ultrastructure ; Chlorophyta/genetics/metabolism/ultrastructure ; Cilia/metabolism/*ultrastructure ; Eukaryotic Cells/metabolism/ultrastructure ; Gene Expression Regulation ; Humans ; Microtubule-Associated Proteins/classification/*genetics/metabolism ; Microtubules/metabolism/*ultrastructure ; *Organelle Biogenesis ; Species Specificity ; Tubulin/genetics/metabolism ; },
abstract = {Centrosomes are composed of two orthogonally arranged centrioles surrounded by an electron-dense matrix called the pericentriolar material (PCM). Centrioles are cylinders with diameters of ~250 nm, are several hundred nanometres in length and consist of 9-fold symmetrically arranged microtubules (MT). In dividing animal cells, centrosomes act as the principal MT-organising centres and they also organise actin, which tunes cytoplasmic MT nucleation. In some specialised cells, the centrosome acquires additional critical structures and converts into the base of a cilium with diverse functions including signalling and motility. These structures are found in most eukaryotes and are essential for development and homoeostasis at both cellular and organism levels. The ultrastructure of centrosomes and their derived organelles have been known for more than half a century. However, recent advances in a number of techniques have revealed the high-resolution structures (at Å-to-nm scale resolution) of centrioles and have begun to uncover the molecular principles underlying their properties, including: protein components; structural elements; and biogenesis in various model organisms. This review covers advances in our understanding of the features and processes that are critical for the biogenesis of the evolutionarily conserved structures of the centrosomes. Furthermore, it discusses how variations of these aspects can generate diversity in centrosome structure and function among different species and even between cell types within a multicellular organism.},
}

Actins/genetics/metabolism
Animals
Biodiversity
Biological Evolution
Cell Cycle/genetics
Centrioles/metabolism/*ultrastructure
Chlorophyta/genetics/metabolism/ultrastructure
Cilia/metabolism/*ultrastructure
Eukaryotic Cells/metabolism/ultrastructure
Gene Expression Regulation
Humans
Microtubule-Associated Proteins/classification/*genetics/metabolism
Microtubules/metabolism/*ultrastructure
*Organelle Biogenesis
Species Specificity
Tubulin/genetics/metabolism

@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},
pmid = {33460641},
issn = {1095-564X},
support = {F32 ES029843/ES/NIEHS NIH HHS/United States ; R01 ES027921/ES/NIEHS NIH HHS/United States ; R01 ES030318/ES/NIEHS NIH HHS/United States ; },
mesh = {ATP-Binding Cassette Transporters/genetics/*metabolism ; Animals ; Biological Transport ; Endoderm/*metabolism ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; In Situ Hybridization ; Intestinal Mucosa/metabolism ; Intestines/embryology ; Mesoderm/*metabolism ; Sea Urchins/*embryology/genetics/metabolism ; Signal Transduction ; },
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.},
}

ATP-Binding Cassette Transporters/genetics/*metabolism
Animals
Biological Transport
Endoderm/*metabolism
Female
Gene Expression Profiling
Gene Expression Regulation, Developmental
In Situ Hybridization
Intestinal Mucosa/metabolism
Intestines/embryology
Mesoderm/*metabolism
Sea Urchins/*embryology/genetics/metabolism
Signal Transduction

@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},
mesh = {*Biological Evolution ; Cell Aggregation/*physiology ; Cell Movement/*physiology ; Computational Biology ; Dictyostelium/cytology/physiology ; *Models, Biological ; },
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.},
}

*Biological Evolution
Cell Aggregation/*physiology
Cell Movement/*physiology
Computational Biology
Dictyostelium/cytology/physiology
*Models, Biological

@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},
support = {BB/D013453/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G020426/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Dictyostelium/classification/*cytology/*genetics ; *Evolution, Molecular ; *Phylogeny ; RNA, Untranslated/*genetics ; },
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.},
}

Dictyostelium/classification/*cytology/*genetics
*Evolution, Molecular
*Phylogeny
RNA, Untranslated/*genetics

@article {pmid33479850,
year = {2021},
author = {Tourigny, DS},
title = {Cooperative metabolic resource allocation in spatially-structured systems.},
journal = {Journal of mathematical biology},
volume = {82},
number = {1-2},
pages = {5},
pmid = {33479850},
issn = {1432-1416},
mesh = {Biological Evolution ; Entropy ; Humans ; Models, Biological ; Quorum Sensing ; Resource Allocation ; *Selection, Genetic ; *Social Behavior ; },
abstract = {Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic metabolic resource allocation based on the maximum entropy principle to spatiotemporal models of metabolism with cooperation. Much like the maximum entropy principle encapsulates 'bet-hedging' behaviour displayed by organisms dealing with future uncertainty in a fluctuating environment, its cooperative extension describes how individuals adapt their metabolic resource allocation strategy to further accommodate limited knowledge about the welfare of others within a community. The resulting theory explains why local regulation of metabolic cross-feeding can fulfil a community-wide metabolic objective if individuals take into consideration an ensemble measure of total population performance as the only form of global information. The latter is likely supplied by quorum sensing in microbial systems or signalling molecules such as hormones in multi-cellular eukaryotic organisms.},
}

Biological Evolution
Entropy
Humans
Models, Biological
Quorum Sensing
Resource Allocation
*Selection, Genetic
*Social Behavior

@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},
mesh = {*Biological Evolution ; *Cognition ; Dictyosteliida/*physiology ; *Quorum Sensing ; *Signal Transduction ; },
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'.},
}

*Biological Evolution
*Cognition
Dictyosteliida/*physiology
*Quorum Sensing
*Signal Transduction

@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 = {236},
number = {9},
pages = {6154-6167},
doi = {10.1002/jcp.30300},
pmid = {33507545},
issn = {1097-4652},
mesh = {Animals ; Atherosclerosis/*pathology ; Cell Communication ; Cholesterol/metabolism ; Esterification ; Foam Cells/metabolism/*pathology ; Humans ; Metabolome ; },
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.},
}

Animals
Atherosclerosis/*pathology
Cell Communication
Cholesterol/metabolism
Esterification
Foam Cells/metabolism/*pathology
Humans
Metabolome

@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 {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},
mesh = {*Adaptation, Physiological ; Animals ; *Climate Change ; Coleoptera/*genetics ; DNA Mutational Analysis ; Mutation ; *Selection, Genetic ; *Temperature ; },
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.},
}

*Adaptation, Physiological
Animals
*Climate Change
Coleoptera/*genetics
DNA Mutational Analysis
Mutation
*Selection, Genetic
*Temperature

@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},
mesh = {Animals ; Female ; Insecta ; Male ; Sexual Selection/*physiology ; },
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.},
}

Animals
Female
Insecta
Male
Sexual Selection/*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 {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 {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},
mesh = {Animals ; Behavior, Animal/*physiology ; *Biological Evolution ; *Body Size ; Cilia/*physiology ; Nerve Net/*physiology ; },
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'.},
}

Animals
Behavior, Animal/*physiology
*Biological Evolution
*Body Size
Cilia/*physiology
Nerve Net/*physiology

@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},
support = {R01 NS114491/NS/NINDS NIH HHS/United States ; },
mesh = {Animals ; Cell Communication/*physiology ; *Evolution, Molecular ; Neurotransmitter Agents/*chemistry ; Placozoa/physiology ; *Signal Transduction ; },
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'.},
}

Animals
Cell Communication/*physiology
*Evolution, Molecular
Neurotransmitter Agents/*chemistry
Placozoa/physiology
*Signal Transduction

@article {pmid33550950,
year = {2021},
author = {Levin, M and Keijzer, F and Lyon, P and Arendt, D},
title = {Uncovering cognitive similarities and differences, conservation and innovation.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1821},
pages = {20200458},
pmid = {33550950},
issn = {1471-2970},
mesh = {Animals ; *Biological Evolution ; Cognition/*physiology ; *Nervous System Physiological Phenomena ; },
abstract = {This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.},
}

Animals
*Biological Evolution
Cognition/*physiology
*Nervous System Physiological Phenomena

@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},
mesh = {*Biological Evolution ; Choanoflagellata/*physiology ; R-SNARE Proteins/*metabolism ; Synaptic Vesicles/*physiology ; },
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'.},
}

*Biological Evolution
Choanoflagellata/*physiology
R-SNARE Proteins/*metabolism
Synaptic Vesicles/*physiology

@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},
mesh = {Animals ; *Cell Communication ; *Cognition ; Cognitive Science ; Electrophysiological Phenomena/physiology ; Models, Neurological ; Planarians/*physiology ; *Regeneration ; },
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'.},
}

Animals
*Cell Communication
*Cognition
Cognitive Science
Electrophysiological Phenomena/physiology
Models, Neurological
Planarians/*physiology
*Regeneration

@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},
mesh = {Animals ; Cnidaria/physiology ; Ctenophora/physiology ; Efferent Pathways/*physiology ; Nervous System/chemistry ; *Nervous System Physiological Phenomena ; Placozoa/physiology ; Porifera/physiology ; *Proprioception ; },
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'.},
}

Animals
Cnidaria/physiology
Ctenophora/physiology
Efferent Pathways/*physiology
Nervous System/chemistry
*Nervous System Physiological Phenomena
Placozoa/physiology
Porifera/physiology
*Proprioception

@article {pmid33550955,
year = {2021},
author = {Ginsburg, S and Jablonka, E},
title = {Evolutionary transitions in learning and cognition.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1821},
pages = {20190766},
pmid = {33550955},
issn = {1471-2970},
mesh = {Animals ; *Biological Evolution ; Cognition/*physiology ; Learning/*physiology ; Phylogeny ; },
abstract = {We define a cognitive system as a system that can learn, and adopt an evolutionary-transition-oriented framework for analysing different types of neural cognition. This enables us to classify types of cognition and point to the continuities and discontinuities among them. The framework we use for studying evolutionary transitions in learning capacities focuses on qualitative changes in the integration, storage and use of neurally processed information. Although there are always grey areas around evolutionary transitions, we recognize five major neural transitions, the first two of which involve animals at the base of the phylogenetic tree: (i) the evolutionary transition from learning in non-neural animals to learning in the first neural animals; (ii) the transition to animals showing limited, elemental associative learning, entailing neural centralization and primary brain differentiation; (iii) the transition to animals capable of unlimited associative learning, which, on our account, constitutes sentience and entails hierarchical brain organization and dedicated memory and value networks; (iv) the transition to imaginative animals that can plan and learn through selection among virtual events; and (v) the transition to human symbol-based cognition and cultural learning. The focus on learning provides a unifying framework for experimental and theoretical studies of cognition in the living world. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.},
}

Animals
*Biological Evolution
Cognition/*physiology
Learning/*physiology
Phylogeny

@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},
pmid = {33561386},
issn = {1879-0445},
support = {R01 GM122917/GM/NIGMS NIH HHS/United States ; },
mesh = {Actin Cytoskeleton/*metabolism ; Actins/*metabolism ; Amphibians/microbiology ; Animals ; Chytridiomycota/*classification/*metabolism ; *Evolution, Molecular ; },
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.},
}

Actin Cytoskeleton/*metabolism
Actins/*metabolism
Amphibians/microbiology
Animals
Chytridiomycota/*classification/*metabolism
*Evolution, Molecular

@article {pmid33565083,
year = {2021},
author = {Bustamante, DE and Yeon Won, B and Wynne, MJ and Cho, TO},
title = {Molecular and morphological analyses reveal new taxa additions to the tribe Streblocladieae (Rhodomelaceae, Rhodophyta).},
journal = {Journal of phycology},
volume = {57},
number = {3},
pages = {817-830},
doi = {10.1111/jpy.13144},
pmid = {33565083},
issn = {1529-8817},
mesh = {Evolution, Molecular ; Phylogeny ; *Rhodophyta ; },
abstract = {The recent segregation of 12 genera in the tribe Streblocladieae suggests that the taxonomy of some species belonging to Polysiphonia sensu lato is updated with the transfer and the proposal of new combinations. Accordingly, six new additions to the tribe Streblocladieae on the basis of morphological and molecular analyses are presented as a consequence of this new segregation. These additions include the description of the new species Carradoriella platensis sp. nov., the proposal of the following new combinations Eutrichosiphonia paniculata comb. nov., E. tapinocarpa comb. nov., and the reinstatement of Vertebrata curta, V. decipiens, and V. patersonis. Additionally, our morphological observations identified additional diagnostic features for two genera of the Streblocladieae. Carradoriella has branches with sexual reproductive structures arranged adaxially on branchlets, and the recently described Eutrichosiphonia has rhizoids with multicellular digitate haptera. Our study gives insights in regards to the distribution, the diagnostic features for delimiting genera morphologically, and the molecular evolutionary relationships in the Streblocladieae.},
}

Evolution, Molecular
Phylogeny
*Rhodophyta

@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},
mesh = {Animals ; Humans ; Male ; Mice ; Mice, Nude ; Neoplasms/*metabolism ; Oxygen/*metabolism ; *Tumor Microenvironment/drug effects/physiology ; },
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.},
}

Animals
Humans
Male
Mice
Mice, Nude
Neoplasms/*metabolism
Oxygen/*metabolism
*Tumor Microenvironment/drug effects/physiology

@article {pmid33588307,
year = {2021},
author = {Crawford, MA and Schmidt, WF and Broadhurst, CL and Wang, Y},
title = {Lipids in the origin of intracellular detail and speciation in the Cambrian epoch and the significance of the last double bond of docosahexaenoic acid in cell signaling.},
journal = {Prostaglandins, leukotrienes, and essential fatty acids},
volume = {166},
number = {},
pages = {102230},
doi = {10.1016/j.plefa.2020.102230},
pmid = {33588307},
issn = {1532-2823},
mesh = {Animals ; Brain/metabolism ; Carbon/metabolism ; Cell Membrane/metabolism ; Docosahexaenoic Acids/chemistry/*history/*metabolism ; *Electrons ; Fatty Acids, Unsaturated/chemistry/*history/*metabolism ; History, Ancient ; Humans ; Hydrogen/metabolism ; Intracellular Space/*metabolism ; Neurons/metabolism ; Retina/metabolism ; *Signal Transduction ; },
abstract = {One of the great unanswered biological questions is the absolute necessity of the polyunsaturated lipid docosahexaenoic acid (DHA; 22:6n-3) in retinal and neural tissues. Everything from the simple eye spot of dinoflagellates to cephalopods to every class of vertebrates uses DHA, yet it is abundant only in cold water marine food chains. Docosapentaenoic acids (DPAs; 22:5n-6 and especially 22:5n-3) are fairly plentiful in food chains yet cannot substitute for DHA. About 600 million years ago, multi-cellular, air breathing systems evolved rapidly and 32 phyla came into existence in a short geological time span; the "Cambrian Explosion". Eukaryotic intracellular detail requires cell membranes, which are constructed of complex lipids, and proteins. Proteins and nucleic acids would have been abundant during the first 2.5-5 billion years of anaerobic life but lipids, especially unsaturated fatty acids, would not. We hypothesize lipid biology was a key driver of the Cambrian Explosion, because it alone provides for compartmentalization and specialization within cells DHA has six methylene interrupted double bonds providing controlled electron flow at precise energy levels; this is essential for visual acuity and truthful execution of the neural pathways which make up our recollections, information processing and consciousness. The last double bond is critical for the evolution and function of the photoreceptor and neuronal and synaptic signaling systems. It completes a quantum mechanical device for the regulation of current flow with absolute signal precision based on electron tunneling (ET). DHA's methylene interruption distance is < 6 Å, making ET transfer between the π-orbitals feasible throughout the molecule. The possibility fails if one double bond is removed and replaced by a saturated bond as in the DPAs. The molecular biophysical foundation of neural signaling can also include the discrete pattern of paired spin states that arise in the DHA double bond and methylene regions. The complexity depends upon the number of C13 and H1 molecular sites in which spin states are coupled. Electron wave harmonics with entanglement and cohesion provide a mechanism for learning and memory, and power cognition and complex human brain functions.},
}

Animals
Brain/metabolism
Carbon/metabolism
Cell Membrane/metabolism
Docosahexaenoic Acids/chemistry/*history/*metabolism
*Electrons
Fatty Acids, Unsaturated/chemistry/*history/*metabolism
History, Ancient
Humans
Hydrogen/metabolism
Intracellular Space/*metabolism
Neurons/metabolism
Retina/metabolism
*Signal Transduction

@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},
mesh = {Animals ; Biological Evolution ; *Cockroaches ; *Isoptera/genetics ; Phylogeny ; Social Behavior ; },
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.},
}

Animals
Biological Evolution
*Cockroaches
*Isoptera/genetics
Phylogeny
Social Behavior

@article {pmid33600401,
year = {2021},
author = {Goldberg, Y and Friedman, J},
title = {Positive interactions within and between populations decrease the likelihood of evolutionary rescue.},
journal = {PLoS computational biology},
volume = {17},
number = {2},
pages = {e1008732},
pmid = {33600401},
issn = {1553-7358},
mesh = {*Adaptation, Physiological ; Animals ; *Biological Evolution ; Computational Biology ; Computer Simulation ; *Ecosystem ; Extinction, Biological ; Humans ; *Models, Biological ; Phenotype ; Probability ; Selection, Genetic ; Stress, Physiological ; *Symbiosis ; },
abstract = {Positive interactions, including intraspecies cooperation and interspecies mutualisms, play crucial roles in shaping the structure and function of many ecosystems, ranging from plant communities to the human microbiome. While the evolutionary forces that form and maintain positive interactions have been investigated extensively, the influence of positive interactions on the ability of species to adapt to new environments is still poorly understood. Here, we use numerical simulations and theoretical analyses to study how positive interactions impact the likelihood that populations survive after an environment deteriorates, such that survival in the new environment requires quick adaptation via the rise of new mutants-a scenario known as evolutionary rescue. We find that the probability of evolutionary rescue in populations engaged in positive interactions is reduced significantly. In cooperating populations, this reduction is largely due to the fact that survival may require at least a minimal number of individuals, meaning that adapted mutants must arise and spread before the population declines below this threshold. In mutualistic populations, the rescue probability is decreased further due to two additional effects-the need for both mutualistic partners to adapt to the new environment, and competition between the two species. Finally, we show that the presence of cheaters reduces the likelihood of evolutionary rescue even further, making it extremely unlikely. These results indicate that while positive interactions may be beneficial in stable environments, they can hinder adaptation to changing environments and thereby elevate the risk of population collapse. Furthermore, these results may hint at the selective pressures that drove co-dependent unicellular species to form more adaptable organisms able to differentiate into multiple phenotypes, including multicellular life.},
}

*Adaptation, Physiological
Animals
*Biological Evolution
Computational Biology
Computer Simulation
*Ecosystem
Extinction, Biological
Humans
*Models, Biological
Phenotype
Probability
Selection, Genetic
Stress, Physiological
*Symbiosis

@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},
mesh = {Animals ; *Biological Evolution ; Crustacea/anatomy & histology ; Developmental Biology ; *Gene Regulatory Networks ; Genes, Homeobox ; Genitalia, Male/physiology ; Homeodomain Proteins/genetics ; Insecta ; Male ; Pelvis ; Phylogeny ; Transcription Factors/genetics ; Vertebrates/*anatomy & histology ; *Wings, Animal/anatomy & histology ; },
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.},
}

Animals
*Biological Evolution
Crustacea/anatomy & histology
Developmental Biology
*Gene Regulatory Networks
Genes, Homeobox
Genitalia, Male/physiology
Homeodomain Proteins/genetics
Insecta
Male
Pelvis
Phylogeny
Transcription Factors/genetics
Vertebrates/*anatomy & histology
*Wings, Animal/anatomy & histology

@article {pmid33617837,
year = {2021},
author = {Debets, VE and Janssen, LMC and Storm, C},
title = {Enhanced persistence and collective migration in cooperatively aligning cell clusters.},
journal = {Biophysical journal},
volume = {120},
number = {8},
pages = {1483-1497},
pmid = {33617837},
issn = {1542-0086},
mesh = {Attention ; Biophysics ; Cell Movement ; Humans ; *Neoplasms ; },
abstract = {Most cells possess the capacity to locomote. Alone or collectively, this allows them to adapt, to rearrange, and to explore their surroundings. The biophysical characterization of such motile processes, in health and in disease, has so far focused mostly on two limiting cases: single-cell motility on the one hand and the dynamics of confluent tissues such as the epithelium on the other. The in-between regime of clusters, composed of relatively few cells moving as a coherent unit, has received less attention. Such small clusters are, however, deeply relevant in development but also in cancer metastasis. In this work, we use cellular Potts models and analytical active matter theory to understand how the motility of small cell clusters changes with N, the number of cells in the cluster. Modeling and theory reveal our two main findings: cluster persistence time increases with N, whereas the intrinsic diffusivity decreases with N. We discuss a number of settings in which the motile properties of more complex clusters can be analytically understood, revealing that the focusing effects of small-scale cooperation and cell-cell alignment can overcome the increased bulkiness and internal disorder of multicellular clusters to enhance overall migrational efficacy. We demonstrate this enhancement for small-cluster collective durotaxis, which is shown to proceed more effectively than for single cells. Our results may provide some novel, to our knowledge, insights into the connection between single-cell and large-scale collective motion and may point the way to the biophysical origins of the enhanced metastatic potential of small tumor cell clusters.},
}

Attention
Biophysics
Cell Movement
Humans
*Neoplasms

@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},
pmid = {33622103},
issn = {2046-2441},
mesh = {Alveolata/cytology/genetics ; Animals ; *Evolution, Molecular ; Phylogeny ; },
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.},
}

Alveolata/cytology/genetics
Animals
*Evolution, Molecular
Phylogeny

@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},
mesh = {Animals ; *Biological Evolution ; Biota ; *Fossils ; Nervous System ; Phylogeny ; },
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.},
}

Animals
*Biological Evolution
Biota
*Fossils
Nervous System
Phylogeny

@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 ; },
mesh = {Animals ; Axon Guidance ; Biodiversity ; Biological Evolution ; Cell Adhesion Molecules/chemistry/*genetics/metabolism ; Choanoflagellata/classification/*genetics/*metabolism ; Ligands ; Models, Molecular ; Nerve Tissue Proteins/chemistry/*genetics/metabolism ; Phylogeny ; Protein Conformation ; Protein Domains ; Receptors, Cell Surface/genetics ; Semaphorins/*genetics/*metabolism ; },
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.},
}

Animals
Axon Guidance
Biodiversity
Biological Evolution
Cell Adhesion Molecules/chemistry/*genetics/metabolism
Choanoflagellata/classification/*genetics/*metabolism
Ligands
Models, Molecular
Nerve Tissue Proteins/chemistry/*genetics/metabolism
Phylogeny
Protein Conformation
Protein Domains
Receptors, Cell Surface/genetics
Semaphorins/*genetics/*metabolism

@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 = {33},
number = {4},
pages = {901-916},
pmid = {33656551},
issn = {1532-298X},
mesh = {Chromosomes, Plant ; Dosage Compensation, Genetic ; *Gene Expression Regulation, Plant ; Genes, Plant ; Genome, Plant ; *Haploidy ; Sequence Analysis, RNA ; Zea mays/*genetics ; },
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.},
}

Chromosomes, Plant
Dosage Compensation, Genetic
*Gene Expression Regulation, Plant
Genes, Plant
Genome, Plant
*Haploidy
Sequence Analysis, RNA
Zea mays/*genetics

@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},
mesh = {Animals ; Caenorhabditis elegans/genetics/metabolism ; Caenorhabditis elegans Proteins/genetics/metabolism ; *Cell Lineage ; Ciona intestinalis/genetics/metabolism ; Databases, Genetic ; *Evolution, Molecular ; *Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Genomics ; Humans ; Mice ; Muscle Cells/classification/*metabolism ; Neurons/classification/*metabolism ; *Single-Cell Analysis ; Species Specificity ; Transcription Factors/*genetics/metabolism ; *Transcriptome ; Zebrafish/genetics/metabolism ; Zebrafish Proteins/genetics/metabolism ; },
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.},
}

Animals
Caenorhabditis elegans/genetics/metabolism
Caenorhabditis elegans Proteins/genetics/metabolism
*Cell Lineage
Ciona intestinalis/genetics/metabolism
Databases, Genetic
*Evolution, Molecular
*Gene Expression Profiling
Gene Expression Regulation, Developmental
Genomics
Humans
Mice
Muscle Cells/classification/*metabolism
Neurons/classification/*metabolism
*Single-Cell Analysis
Species Specificity
Transcription Factors/*genetics/metabolism
*Transcriptome
Zebrafish/genetics/metabolism
Zebrafish Proteins/genetics/metabolism

@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 ; Phaeophyceae/*metabolism ; Phylogeny ; Plants, Genetically Modified ; Promoter Regions, Genetic/genetics ; *Salinity ; Seedlings/genetics ; *Stress, Physiological/genetics ; Nicotiana/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
Phaeophyceae/*metabolism
Phylogeny
Plants, Genetically Modified
Promoter Regions, Genetic/genetics
*Salinity
Seedlings/genetics
*Stress, Physiological/genetics
Nicotiana/metabolism

@article {pmid33675395,
year = {2021},
author = {Jong, LW and Fujiwara, T and Hirooka, S and Miyagishima, SY},
title = {Cell size for commitment to cell division and number of successive cell divisions in cyanidialean red algae.},
journal = {Protoplasma},
volume = {258},
number = {5},
pages = {1103-1118},
pmid = {33675395},
issn = {1615-6102},
support = {17H01446, 20H00477//Japan Society for the Promotion of Science (JP)/ ; 19J13366//Japan Society for the Promotion of Science/ ; },
mesh = {Biological Evolution ; Cell Division ; Cell Size ; *Chlorophyta ; *Rhodophyta ; },
abstract = {Several eukaryotic cell lineages proliferate by multiple fission cell cycles, during which cells grow to manyfold of their original size, then undergo several rounds of cell division without intervening growth. A previous study on volvocine green algae, including both unicellular and multicellular (colonial) species, showed a correlation between the minimum number of successive cell divisions without intervening cellular growth, and the threshold cell size for commitment to the first round of successive cell divisions: two times the average newly born daughter cell volume for unicellular Chlamydomonas reinhardtii, four times for four-celled Tetrabaena socialis, in which each cell in the colony produces a daughter colony by two successive cell divisions, and eight times for the eight-celled Gonium pectorale, in which each cell produces a daughter colony by three successive cell divisions. To assess whether this phenomenon is also applicable to other lineages, we have characterized cyanidialean red algae, namely, Cyanidioschyzon merolae, which proliferates by binary fission, as well as Cyanidium caldarium and Galdieria sulphuraria, which form up to four and 32 daughter cells (autospores), respectively, in a mother cell before hatching out. The result shows that there is also a correlation between the number of successive cell divisions and the threshold cell size for cell division or the first round of the successive cell divisions. In both C. merolae and C. caldarium, the cell size checkpoint for cell division(s) exists in the G1-phase, as previously shown in volvocine green algae. When C. merolae cells were arrested in the G1-phase and abnormally enlarged by conditional depletion of CDKA, the cells underwent two or more successive cell divisions without intervening cellular growth after recovery of CDKA, similarly to C. caldarium and G. sulphuraria. These results suggest that the threshold size for cell division is a major factor in determining the number of successive cell divisions and that evolutionary changes in the mechanism of cell size monitoring resulted in a variation of multiple fission cell cycle in eukaryotic algae.},
}

Biological Evolution
Cell Division
Cell Size
*Chlorophyta
*Rhodophyta

@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},
mesh = {Animals ; Bass/*genetics ; Fish Proteins/*genetics ; Multigene Family ; Phylogeny ; SOX Transcription Factors/*genetics ; Transcriptome ; },
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.},
}

Animals
Bass/*genetics
Fish Proteins/*genetics
Multigene Family
Phylogeny
SOX Transcription Factors/*genetics
Transcriptome

@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},
pmid = {33678014},
issn = {1471-2970},
mesh = {*Aging ; Animals ; *Biological Evolution ; *Cell Differentiation ; *Cell Division ; Germ Cells/physiology ; Insecta/*physiology ; Models, Biological ; },
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?'},
}

*Aging
Animals
*Biological Evolution
*Cell Differentiation
*Cell Division
Germ Cells/physiology
Insecta/*physiology
Models, Biological

@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 = {20},
number = {3},
pages = {1187-1194},
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/ ; },
mesh = {Biomechanical Phenomena/physiology ; Computer Simulation ; Elastic Modulus ; Finite Element Analysis ; Humans ; *Models, Biological ; Neoplasm Invasiveness ; Neoplasms/*pathology ; },
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.},
}

Biomechanical Phenomena/physiology
Computer Simulation
Elastic Modulus
Finite Element Analysis
Humans
*Models, Biological
Neoplasm Invasiveness
Neoplasms/*pathology

@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 = {86},
number = {1},
pages = {8-13},
doi = {10.1111/prd.12374},
pmid = {33690952},
issn = {1600-0757},
support = {MR/J011118/1/MRC_/Medical Research Council/United Kingdom ; MR/P012175/2/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Biofilms ; *Dental Plaque ; Gingiva ; Humans ; *Periodontitis ; },
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.},
}

Biofilms
*Dental Plaque
Gingiva
Humans
*Periodontitis

@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},
pmid = {33711511},
issn = {1872-9649},
support = {U01 HL145560/HL/NHLBI NIH HHS/United States ; P01 AG047200/AG/NIA NIH HHS/United States ; P30 AG013319/AG/NIA NIH HHS/United States ; U01 ES029519/ES/NIEHS NIH HHS/United States ; U19 AG056278/AG/NIA NIH HHS/United States ; P30 AG038072/AG/NIA NIH HHS/United States ; P01 AG017242/AG/NIA NIH HHS/United States ; },
mesh = {Aging/genetics ; Animals ; *DNA Damage ; *DNA Repair/genetics ; Humans ; Mutagenesis ; Mutation ; },
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.},
}

Aging/genetics
Animals
*DNA Damage
*DNA Repair/genetics
Humans
Mutagenesis
Mutation

@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},
mesh = {Animals ; Biological Evolution ; Extracellular Traps/*metabolism ; Humans ; Immunity, Innate ; Neutrophils/*immunology ; Phylogeny ; },
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.},
}

Animals
Biological Evolution
Extracellular Traps/*metabolism
Humans
Immunity, Innate
Neutrophils/*immunology
Phylogeny

@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},
mesh = {Choanoflagellata/classification/*genetics ; Computational Biology/methods ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Genomics/methods ; Molecular Sequence Annotation ; Phylogeny ; },
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.},
}

Choanoflagellata/classification/*genetics
Computational Biology/methods
Evolution, Molecular
*Gene Transfer, Horizontal
*Genome
Genomics/methods
Molecular Sequence Annotation
Phylogeny

@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 {pmid33745906,
year = {2021},
author = {Johnson, JD and White, NL and Kangabire, A and Abrams, DM},
title = {A dynamical model for the origin of anisogamy.},
journal = {Journal of theoretical biology},
volume = {521},
number = {},
pages = {110669},
doi = {10.1016/j.jtbi.2021.110669},
pmid = {33745906},
issn = {1095-8541},
mesh = {*Biological Evolution ; Computer Simulation ; Female ; Germ Cells ; Humans ; Male ; *Models, Biological ; Reproduction ; },
abstract = {The vast majority of multi-cellular organisms are anisogamous, meaning that male and female sex cells differ in size. It remains an open question how this asymmetric state evolved, presumably from the symmetric isogamous state where all gametes are roughly the same size (drawn from the same distribution). Here, we use tools from the study of nonlinear dynamical systems to develop a simple mathematical model for this phenomenon. Unlike some prior work, we do not assume the existence of mating types. We also model frequency dependent selection via "mean-field coupling," whereby the likelihood that a gamete survives is an increasing function of its size relative to the population's mean gamete size. Using theoretical analysis and numerical simulation, we demonstrate that this mean-referenced competition will almost inevitably result in a stable anisogamous equilibrium, and thus isogamy may naturally lead to anisogamy.},
}

*Biological Evolution
Computer Simulation
Female
Germ Cells
Humans
Male
*Models, Biological
Reproduction

@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 {pmid33760661,
year = {2021},
author = {Barnett, AM and Mullaney, JA and Hendriks, C and Le Borgne, L and McNabb, WC and Roy, NC},
title = {Porcine colonoids and enteroids keep the memory of their origin during regeneration.},
journal = {American journal of physiology. Cell physiology},
volume = {320},
number = {5},
pages = {C794-C805},
doi = {10.1152/ajpcell.00420.2020},
pmid = {33760661},
issn = {1522-1563},
mesh = {Animals ; Biomarkers/metabolism ; *Cell Differentiation ; *Cell Lineage ; Cell Proliferation ; Colon/cytology/metabolism/*physiology ; Gene Expression Regulation ; Ileum/cytology/metabolism/*physiology ; Intestinal Mucosa/cytology/metabolism/*physiology ; Male ; Organoids/cytology/metabolism/*physiology ; Phenotype ; Signal Transduction ; Sus scrofa ; Time Factors ; Tissue Culture Techniques ; Transcriptome ; },
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 multilobed 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, whereas 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.},
}

Animals
Biomarkers/metabolism
*Cell Differentiation
*Cell Lineage
Cell Proliferation
Colon/cytology/metabolism/*physiology
Gene Expression Regulation
Ileum/cytology/metabolism/*physiology
Intestinal Mucosa/cytology/metabolism/*physiology
Male
Organoids/cytology/metabolism/*physiology
Phenotype
Signal Transduction
Sus scrofa
Time Factors
Tissue Culture Techniques
Transcriptome

@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},
mesh = {Animals ; Cell Death/*immunology ; Humans ; Immunity, Innate/immunology ; Inflammasomes/immunology ; Plant Cells/*immunology ; Plant Immunity/*immunology ; Plants/*immunology ; Receptors, Immunologic/*immunology ; Receptors, Pattern Recognition/immunology ; Signal Transduction/*immunology ; },
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.},
}

Animals
Cell Death/*immunology
Humans
Immunity, Innate/immunology
Inflammasomes/immunology
Plant Cells/*immunology
Plant Immunity/*immunology
Plants/*immunology
Receptors, Immunologic/*immunology
Receptors, Pattern Recognition/immunology
Signal Transduction/*immunology

@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},
mesh = {*Evolution, Molecular ; Genes, Plant ; *Genome, Plant ; Phylogeny ; RNA, Small Untranslated/*genetics ; Viridiplantae/*genetics ; },
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.},
}

*Evolution, Molecular
Genes, Plant
*Genome, Plant
Phylogeny
RNA, Small Untranslated/*genetics
Viridiplantae/*genetics

@article {pmid33779495,
year = {2022},
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 = {13},
number = {1},
pages = {100-113},
pmid = {33779495},
issn = {2154-1256},
mesh = {Phylogeny ; *rab GTP-Binding Proteins/genetics/metabolism ; Evolution, Molecular ; *Amoebozoa/genetics/metabolism ; Eukaryota/metabolism ; },
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.},
}

Phylogeny
*rab GTP-Binding Proteins/genetics/metabolism
Evolution, Molecular
*Amoebozoa/genetics/metabolism
Eukaryota/metabolism

@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},
mesh = {Animals ; *Cell Differentiation ; *Evolution, Molecular ; *Exons ; *Models, Genetic ; Transcription Factors/*genetics ; },
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.},
}

Animals
*Cell Differentiation
*Evolution, Molecular
*Exons
*Models, Genetic
Transcription Factors/*genetics

@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 = {},
pmid = {33801615},
issn = {2073-4425},
support = {742288/ERC_/European Research Council/International ; 100293/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Amoeba/*physiology ; Biological Evolution ; Cold Temperature ; Dictyostelium/*physiology ; Evolution, Molecular ; Life Cycle Stages ; Phylogeny ; Signal Transduction ; *Stress, Physiological ; },
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.},
}

Amoeba/*physiology
Biological Evolution
Cold Temperature
Dictyostelium/*physiology
Evolution, Molecular
Life Cycle Stages
Phylogeny
Signal Transduction
*Stress, Physiological

@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 {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 = {143},
number = {15},
pages = {5836-5844},
doi = {10.1021/jacs.1c00944},
pmid = {33834782},
issn = {1520-5126},
mesh = {Animals ; B-Lymphocytes/chemistry/*cytology/immunology ; Bone Marrow Cells/cytology/metabolism ; Cell Differentiation ; Cell Membrane/chemistry/*metabolism ; Flow Cytometry ; Fluorescent Dyes/*chemistry ; Lipidomics ; Mice ; T-Lymphocytes/chemistry/*cytology/immunology ; },
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.},
}

Animals
B-Lymphocytes/chemistry/*cytology/immunology
Bone Marrow Cells/cytology/metabolism
Cell Differentiation
Cell Membrane/chemistry/*metabolism
Flow Cytometry
Fluorescent Dyes/*chemistry
Lipidomics
Mice
T-Lymphocytes/chemistry/*cytology/immunology

@article {pmid33837641,
year = {2021},
author = {Abe-Fukasawa, N and Watanabe, R and Gen, Y and Nishino, T and Itasaki, N},
title = {A liquid culture cancer spheroid model reveals low PI3K/Akt pathway activity and low adhesiveness to the extracellular matrix.},
journal = {The FEBS journal},
volume = {288},
number = {19},
pages = {5650-5667},
doi = {10.1111/febs.15867},
pmid = {33837641},
issn = {1742-4658},
mesh = {Animals ; Cell Adhesion/*genetics ; *Cell Culture Techniques ; Cell Line, Tumor ; Cell Polarity/genetics ; Extracellular Matrix/genetics ; Humans ; Mice ; Neoplasm Metastasis ; Neoplasms/*genetics/pathology ; Oncogene Protein v-akt/genetics ; Phosphatidylinositol 3-Kinases/genetics ; Signal Transduction/genetics ; Spheroids, Cellular/metabolism/*pathology ; Transplantation, Heterologous ; },
abstract = {Three-dimensional (3D) cultures of cancer cells in liquid without extracellular matrix (ECM) offer in vitro models for metastasising conditions such as those in vessels and effusion. However, liquid culturing is often hindered by cell adhesiveness, which causes large cell clumps. We previously described a liquid culture material, LA717, which prevents nonclonal cell adhesion and subsequent clumping, thus allowing clonal growth of spheroids in an anchorage-independent manner. Here, we examined such liquid culture cancer spheroids for the acquisition of apical-basal polarity, sensitivity to an Akt inhibitor (anticancer drug MK-2206) and interaction with ECM. The spheroids present apical plasma membrane on the surface, which originated from the failure of polarisation at the single-cell stage and subsequent defects in phosphorylated ezrin accumulation at the cell boundary during the first cleavage, failing internal lumen formation. At the multicellular stage, liquid culture spheroids presented bleb-like protrusion on the surface, which was enhanced by the activation of the PI3K/Akt pathway and reduced by PI3K/Akt inhibitors. Liquid culture spheroids exhibited slow proliferation speed and low endogenous pAkt levels compared with gel-cultured spheroids and 2D-cultured cells, explaining the susceptibility to the Akt-inhibiting anticancer drug. Subcutaneous xenografting and in vitro analysis demonstrated low viability and adhesive property of liquid culture spheroids to ECM, while migratory and invasive capacities were comparable with gel-cultured spheroids. These features agree with the low efficacy of circulating tumour spheroids in the settling step of metastasis. This study demonstrates the feature of anchorage-independent spheroids and validates liquid cultures as a useful method in cancer spheroid research.},
}

Animals
Cell Adhesion/*genetics
*Cell Culture Techniques
Cell Line, Tumor
Cell Polarity/genetics
Extracellular Matrix/genetics
Humans
Mice
Neoplasm Metastasis
Neoplasms/*genetics/pathology
Oncogene Protein v-akt/genetics
Phosphatidylinositol 3-Kinases/genetics
Signal Transduction/genetics
Spheroids, Cellular/metabolism/*pathology
Transplantation, Heterologous

@article {pmid33839924,
year = {2021},
author = {Genau, AC and Li, Z and Renzaglia, KS and Fernandez Pozo, N and Nogué, F and Haas, FB and Wilhelmsson, PKI and Ullrich, KK and Schreiber, M and Meyberg, R and Grosche, C and Rensing, SA},
title = {HAG1 and SWI3A/B control of male germ line development in P. patens suggests conservation of epigenetic reproductive control across land plants.},
journal = {Plant reproduction},
volume = {34},
number = {2},
pages = {149-173},
pmid = {33839924},
issn = {2194-7961},
support = {5R25GM107760-07/NH/NIH HHS/United States ; R25 GM107760/GM/NIGMS NIH HHS/United States ; },
mesh = {Biological Evolution ; *Embryophyta ; Epigenesis, Genetic ; *Germ Cells, Plant ; Reproduction/genetics ; },
abstract = {Bryophytes as models to study the male germ line: loss-of-function mutants of epigenetic regulators HAG1 and SWI3a/b demonstrate conserved function in sexual reproduction. With the water-to-land transition, land plants evolved a peculiar haplodiplontic life cycle in which both the haploid gametophyte and the diploid sporophyte are multicellular. The switch between these phases was coined alternation of generations. Several key regulators that control the bauplan of either generation are already known. Analyses of such regulators in flowering plants are difficult due to the highly reduced gametophytic generation, and the fact that loss of function of such genes often is embryo lethal in homozygous plants. Here we set out to determine gene function and conservation via studies in bryophytes. Bryophytes are sister to vascular plants and hence allow evolutionary inferences. Moreover, embryo lethal mutants can be grown and vegetatively propagated due to the dominance of the bryophyte gametophytic generation. We determined candidates by selecting single copy orthologs that are involved in transcriptional control, and of which flowering plant mutants show defects during sexual reproduction, with a focus on the under-studied male germ line. We selected two orthologs, SWI3a/b and HAG1, and analyzed loss-of-function mutants in the moss P. patens. In both mutants, due to lack of fertile spermatozoids, fertilization and hence the switch to the diploid generation do not occur. Pphag1 additionally shows arrested male and impaired female gametangia development. We analyzed HAG1 in the dioecious liverwort M. polymorpha and found that in Mphag1 the development of gametangiophores is impaired. Taken together, we find that involvement of both regulators in sexual reproduction is conserved since the earliest divergence of land plants.},
}

Biological Evolution
*Embryophyta
Epigenesis, Genetic
*Germ Cells, Plant
Reproduction/genetics

@article {pmid33846299,
year = {2021},
author = {Shemesh, N and Jubran, J and Dror, S and Simonovsky, E and Basha, O and Argov, C and Hekselman, I and Abu-Qarn, M and Vinogradov, E and Mauer, O and Tiago, T and Carra, S and Ben-Zvi, A and Yeger-Lotem, E},
title = {The landscape of molecular chaperones across human tissues reveals a layered architecture of core and variable chaperones.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2180},
pmid = {33846299},
issn = {2041-1723},
mesh = {Aging/metabolism ; Animals ; Caenorhabditis elegans/metabolism ; Cell Line ; Conserved Sequence ; Evolution, Molecular ; Gene Expression Regulation ; Humans ; Mice ; Molecular Chaperones/genetics/*metabolism ; Open Reading Frames/genetics ; *Organ Specificity/genetics ; },
abstract = {The sensitivity of the protein-folding environment to chaperone disruption can be highly tissue-specific. Yet, the organization of the chaperone system across physiological human tissues has received little attention. Through computational analyses of large-scale tissue transcriptomes, we unveil that the chaperone system is composed of core elements that are uniformly expressed across tissues, and variable elements that are differentially expressed to fit with tissue-specific requirements. We demonstrate via a proteomic analysis that the muscle-specific signature is functional and conserved. Core chaperones are significantly more abundant across tissues and more important for cell survival than variable chaperones. Together with variable chaperones, they form tissue-specific functional networks. Analysis of human organ development and aging brain transcriptomes reveals that these functional networks are established in development and decline with age. In this work, we expand the known functional organization of de novo versus stress-inducible eukaryotic chaperones into a layered core-variable architecture in multi-cellular organisms.},
}

Aging/metabolism
Animals
Caenorhabditis elegans/metabolism
Cell Line
Conserved Sequence
Evolution, Molecular
Gene Expression Regulation
Humans
Mice
Molecular Chaperones/genetics/*metabolism
Open Reading Frames/genetics
*Organ Specificity/genetics

@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 ; },
mesh = {Animals ; Animals, Genetically Modified ; Argonaute Proteins/*genetics/*metabolism ; Caenorhabditis elegans/*genetics ; Caenorhabditis elegans Proteins/genetics/metabolism ; Gene Expression Regulation ; MicroRNAs/*genetics/*metabolism ; Nervous System ; Protein Isoforms ; },
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.},
}

Animals
Animals, Genetically Modified
Argonaute Proteins/*genetics/*metabolism
Caenorhabditis elegans/*genetics
Caenorhabditis elegans Proteins/genetics/metabolism
Gene Expression Regulation
MicroRNAs/*genetics/*metabolism
Nervous System
Protein Isoforms

@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},
pmid = {33861755},
issn = {1553-7358},
mesh = {Eukaryota/genetics ; Gene Expression Regulation ; Gene Ontology ; Genes, Reporter ; *Genome, Protozoan ; Histones/metabolism ; Plasmodium falciparum/*genetics ; RNA Processing, Post-Transcriptional ; RNA, Antisense/genetics ; RNA, Messenger/genetics ; *Regulatory Sequences, Nucleic Acid ; Transcription, Genetic ; },
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.},
}

Eukaryota/genetics
Gene Expression Regulation
Gene Ontology
Genes, Reporter
*Genome, Protozoan
Histones/metabolism
Plasmodium falciparum/*genetics
RNA Processing, Post-Transcriptional
RNA, Antisense/genetics
RNA, Messenger/genetics
*Regulatory Sequences, Nucleic Acid
Transcription, Genetic

@article {pmid33865238,
year = {2021},
author = {Xu, X and Smaczniak, C and Muino, JM and Kaufmann, K},
title = {Cell identity specification in plants: lessons from flower development.},
journal = {Journal of experimental botany},
volume = {72},
number = {12},
pages = {4202-4217},
pmid = {33865238},
issn = {1460-2431},
mesh = {Cell Differentiation ; Flowers/metabolism ; Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; *Plants/genetics/metabolism ; Transcription Factors/genetics/metabolism ; },
abstract = {Multicellular organisms display a fascinating complexity of cellular identities and patterns of diversification. The concept of 'cell type' aims to describe and categorize this complexity. In this review, we discuss the traditional concept of cell types and highlight the impact of single-cell technologies and spatial omics on the understanding of cellular differentiation in plants. We summarize and compare position-based and lineage-based mechanisms of cell identity specification using flower development as a model system. More than understanding ontogenetic origins of differentiated cells, an important question in plant science is to understand their position- and developmental stage-specific heterogeneity. Combinatorial action and crosstalk of external and internal signals is the key to cellular heterogeneity, often converging on transcription factors that orchestrate gene expression programs.},
}

Cell Differentiation
Flowers/metabolism
Gene Expression Regulation, Developmental
*Gene Expression Regulation, Plant
*Plants/genetics/metabolism
Transcription Factors/genetics/metabolism

@article {pmid33865960,
year = {2021},
author = {Hage, H and Rosso, MN and Tarrago, L},
title = {Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes.},
journal = {Free radical biology & medicine},
volume = {169},
number = {},
pages = {187-215},
doi = {10.1016/j.freeradbiomed.2021.04.013},
pmid = {33865960},
issn = {1873-4596},
mesh = {*Eukaryota/metabolism ; Fungi/genetics ; Methionine/metabolism ; *Methionine Sulfoxide Reductases/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.},
}

*Eukaryota/metabolism
Fungi/genetics
Methionine/metabolism
*Methionine Sulfoxide Reductases/genetics/metabolism
Oxidation-Reduction
Phylogeny

@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 = {P01 AI106695/AI/NIAID NIH HHS/United States ; P20 RR018727/RR/NCRR NIH HHS/United States ; U01 AI151788/AI/NIAID NIH HHS/United States ; U54 AI065359/AI/NIAID NIH HHS/United States ; },
mesh = {Aedes/*virology ; Animals ; Culex/*virology ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Host Specificity ; *Metagenome ; Mosquito Vectors/*virology ; Phylogeny ; RNA Viruses/*physiology ; RNA-Seq ; Thailand ; *Virome ; },
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.},
}

Aedes/*virology
Animals
Culex/*virology
*Genome, Viral
High-Throughput Nucleotide Sequencing
Host Specificity
*Metagenome
Mosquito Vectors/*virology
Phylogeny
RNA Viruses/*physiology
RNA-Seq
Thailand
*Virome

@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 = {63},
number = {7},
pages = {613-620},
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/ ; },
mesh = {Animals ; CRISPR-Cas Systems ; Ciona/*embryology/genetics ; Gene Editing/*methods ; Gene Silencing ; MicroRNAs/*genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; },
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.},
}

Animals
CRISPR-Cas Systems
Ciona/*embryology/genetics
Gene Editing/*methods
Gene Silencing
MicroRNAs/*genetics
RNA, Guide, CRISPR-Cas Systems/genetics

@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 = {},
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/ ; },
mesh = {*Evolution, Molecular ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Magnoliopsida/*genetics/growth & development/metabolism ; Plant Proteins/chemistry/*genetics/metabolism ; Transcription Factors/chemistry/*genetics/metabolism ; },
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.},
}

*Evolution, Molecular
Gene Expression Regulation, Developmental
Gene Expression Regulation, Plant
Magnoliopsida/*genetics/growth & development/metabolism
Plant Proteins/chemistry/*genetics/metabolism
Transcription Factors/chemistry/*genetics/metabolism

@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 = {},
pmid = {33924996},
issn = {2073-4425},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; },
mesh = {*Adaptation, Physiological ; Aging/*genetics ; Animals ; *Cell Division ; Cellular Senescence ; *Models, Theoretical ; Mutation ; },
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.},
}

*Adaptation, Physiological
Aging/*genetics
Animals
*Cell Division
Cellular Senescence
*Models, Theoretical
Mutation

@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},
mesh = {*Agaricales/genetics ; Agrocybe ; Fruiting Bodies, Fungal/genetics ; Fungal Proteins/genetics/metabolism ; Gene Expression Regulation, Fungal ; Oxylipins ; Prospective Studies ; *Transcriptome ; },
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.},
}

*Agaricales/genetics
Agrocybe
Fruiting Bodies, Fungal/genetics
Fungal Proteins/genetics/metabolism
Gene Expression Regulation, Fungal
Oxylipins
Prospective Studies
*Transcriptome

@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 = {DP2 AG067490/AG/NIA NIH HHS/United States ; R00 AG043550/AG/NIA NIH HHS/United States ; T32 CA009140/CA/NCI NIH HHS/United States ; K99 AG064042/AG/NIA NIH HHS/United States ; R01 GM110174/GM/NIGMS NIH HHS/United States ; DP2 AG055947/AG/NIA NIH HHS/United States ; },
mesh = {Acetylation ; Animals ; Caenorhabditis elegans/cytology ; Chromatin/metabolism ; Dictyostelium/*cytology/*genetics ; *Epigenesis, Genetic ; Gene Expression Profiling ; Histones/metabolism ; Methylation ; Schizosaccharomyces/cytology ; Transcription Factors/metabolism ; },
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.},
}

Acetylation
Animals
Caenorhabditis elegans/cytology
Chromatin/metabolism
Dictyostelium/*cytology/*genetics
*Epigenesis, Genetic
Gene Expression Profiling
Histones/metabolism
Methylation
Schizosaccharomyces/cytology
Transcription Factors/metabolism

@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 = {},
pmid = {33947812},
issn = {1091-6490},
mesh = {Algorithms ; Animals ; Caenorhabditis elegans/physiology ; Chemotaxis/*genetics/*physiology ; Computer Simulation ; Flagella/physiology ; Learning/*physiology ; Machine Learning ; Models, Biological ; Motion ; Neural Networks, Computer ; Swimming/*physiology ; },
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.},
}

Algorithms
Animals
Caenorhabditis elegans/physiology
Chemotaxis/*genetics/*physiology
Computer Simulation
Flagella/physiology
Learning/*physiology
Machine Learning
Models, Biological
Motion
Neural Networks, Computer
Swimming/*physiology

@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 Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae.},
journal = {Genome biology and evolution},
volume = {13},
number = {7},
pages = {},
pmid = {33950183},
issn = {1759-6653},
mesh = {*Chlorophyta/genetics ; Evolution, Molecular ; Genetic Code ; Phylogeny ; },
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 data sets up to 2,698 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 noncanonical 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 noncanonical genetic codes in chlorophyte green algae.},
}

*Chlorophyta/genetics
Evolution, Molecular
Genetic Code
Phylogeny

@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 = {11},
number = {8},
pages = {1886-1895},
doi = {10.1158/2159-8290.CD-20-1588},
pmid = {33952585},
issn = {2159-8290},
mesh = {*Bacteria ; *Biological Evolution ; *Homeostasis ; Humans ; *Neoplasms ; },
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.},
}

*Bacteria
*Biological Evolution
*Homeostasis
Humans
*Neoplasms

@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 = {165},
number = {},
pages = {102-113},
doi = {10.1016/j.pbiomolbio.2021.04.007},
pmid = {33961843},
issn = {1873-1732},
mesh = {Electrophysiological Phenomena ; Humans ; Membrane Potentials ; Morphogenesis ; *Neoplasms ; *Signal Transduction ; },
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 override 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.},
}

Electrophysiological Phenomena
Humans
Membrane Potentials
Morphogenesis
*Neoplasms
*Signal Transduction

@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 = {R01 DK078314/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Basement Membrane/*cytology/metabolism/ultrastructure ; Epithelial Cells/metabolism ; Extracellular Matrix/genetics/*metabolism ; Female ; Fibroblasts/metabolism ; Hair Follicle/*metabolism ; Immunohistochemistry ; Laminin/*metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Microscopy, Electron, Transmission ; Multigene Family ; Muscle Cells/metabolism ; Neurons/metabolism ; Single-Cell Analysis ; Transcriptome/*genetics ; },
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.},
}

Animals
Basement Membrane/*cytology/metabolism/ultrastructure
Epithelial Cells/metabolism
Extracellular Matrix/genetics/*metabolism
Female
Fibroblasts/metabolism
Hair Follicle/*metabolism
Immunohistochemistry
Laminin/*metabolism
Mice
Mice, Inbred C57BL
Mice, Knockout
Microscopy, Electron, Transmission
Multigene Family
Muscle Cells/metabolism
Neurons/metabolism
Single-Cell Analysis
Transcriptome/*genetics

@article {pmid33979602,
year = {2021},
author = {Joy, DA and Libby, ARG and McDevitt, TC},
title = {Deep neural net tracking of human pluripotent stem cells reveals intrinsic behaviors directing morphogenesis.},
journal = {Stem cell reports},
volume = {16},
number = {5},
pages = {1317-1330},
pmid = {33979602},
issn = {2213-6711},
support = {T32 HD007470/HD/NICHD NIH HHS/United States ; },
mesh = {Bone Morphogenetic Protein 4/pharmacology ; Cell Count ; Cell Differentiation/drug effects ; Cell Lineage/drug effects ; Cell Movement/drug effects ; Cell Tracking ; Cells, Cultured ; Humans ; Image Processing, Computer-Assisted ; Induced Pluripotent Stem Cells/*cytology/drug effects ; *Morphogenesis/drug effects ; *Neural Networks, Computer ; Smad Proteins/metabolism ; },
abstract = {Lineage tracing is a powerful tool in developmental biology to interrogate the evolution of tissue formation, but the dense, three-dimensional nature of tissue limits the assembly of individual cell trajectories into complete reconstructions of development. Human induced pluripotent stem cells (hiPSCs) can recapitulate aspects of developmental processes, providing an in vitro platform to assess the dynamic collective behaviors directing tissue morphogenesis. Here, we trained an ensemble of neural networks to track individual hiPSCs in time-lapse microscopy, generating longitudinal measures of cell and cellular neighborhood properties on timescales from minutes to days. Our analysis reveals that, while individual cell parameters are not strongly affected by pluripotency maintenance conditions or morphogenic cues, regional changes in cell behavior predict cell fate and colony organization. By generating complete multicellular reconstructions of hiPSC behavior, our tracking pipeline enables fine-grained understanding of morphogenesis by elucidating the role of regional behavior in early tissue formation.},
}

Bone Morphogenetic Protein 4/pharmacology
Cell Count
Cell Differentiation/drug effects
Cell Lineage/drug effects
Cell Movement/drug effects
Cell Tracking
Cells, Cultured
Humans
Image Processing, Computer-Assisted
Induced Pluripotent Stem Cells/*cytology/drug effects
*Morphogenesis/drug effects
*Neural Networks, Computer
Smad Proteins/metabolism

@article {pmid33983920,
year = {2021},
author = {van Gestel, J and Wagner, A},
title = {Cryptic surface-associated multicellularity emerges through cell adhesion and its regulation.},
journal = {PLoS biology},
volume = {19},
number = {5},
pages = {e3001250},
pmid = {33983920},
issn = {1545-7885},
mesh = {Animals ; Bacteria/metabolism ; Bacterial Adhesion/*physiology ; Biological Evolution ; Cell Adhesion/*physiology ; Cell Communication/physiology ; Cell Polarity/physiology ; Evolution, Molecular ; Fungi/metabolism ; Humans ; },
abstract = {The repeated evolution of multicellularity led to a wide diversity of organisms, many of which are sessile, including land plants, many fungi, and colonial animals. Sessile organisms adhere to a surface for most of their lives, where they grow and compete for space. Despite the prevalence of surface-associated multicellularity, little is known about its evolutionary origin. Here, we introduce a novel theoretical approach, based on spatial lineage tracking of cells, to study this origin. We show that multicellularity can rapidly evolve from two widespread cellular properties: cell adhesion and the regulatory control of adhesion. By evolving adhesion, cells attach to a surface, where they spontaneously give rise to primitive cell collectives that differ in size, life span, and mode of propagation. Selection in favor of large collectives increases the fraction of adhesive cells until a surface becomes fully occupied. Through kin recognition, collectives then evolve a central-peripheral polarity in cell adhesion that supports a division of labor between cells and profoundly impacts growth. Despite this spatial organization, nascent collectives remain cryptic, lack well-defined boundaries, and would require experimental lineage tracking technologies for their identification. Our results suggest that cryptic multicellularity could readily evolve and originate well before multicellular individuals become morphologically evident.},
}

Animals
Bacteria/metabolism
Bacterial Adhesion/*physiology
Biological Evolution
Cell Adhesion/*physiology
Cell Communication/physiology
Cell Polarity/physiology
Evolution, Molecular
Fungi/metabolism
Humans

@article {pmid33984158,
year = {2021},
author = {Lineweaver, CH and Bussey, KJ and Blackburn, AC and Davies, PCW},
title = {Cancer progression as a sequence of atavistic reversions.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {43},
number = {7},
pages = {e2000305},
pmid = {33984158},
issn = {1521-1878},
support = {U54 CA217376/CA/NCI NIH HHS/United States ; U54-CA143682/CA/NCI NIH HHS/United States ; },
mesh = {*Biological Evolution ; Eukaryota ; Eukaryotic Cells ; Humans ; *Neoplasms/genetics ; Phenotype ; },
abstract = {It has long been recognized that cancer onset and progression represent a type of reversion to an ancestral quasi-unicellular phenotype. This general concept has been refined into the atavistic model of cancer that attempts to provide a quantitative analysis and testable predictions based on genomic data. Over the past decade, support for the multicellular-to-unicellular reversion predicted by the atavism model has come from phylostratigraphy. Here, we propose that cancer onset and progression involve more than a one-off multicellular-to-unicellular reversion, and are better described as a series of reversionary transitions. We make new predictions based on the chronology of the unicellular-eukaryote-to-multicellular-eukaryote transition. We also make new predictions based on three other evolutionary transitions that occurred in our lineage: eukaryogenesis, oxidative phosphorylation and the transition to adaptive immunity. We propose several modifications to current phylostratigraphy to improve age resolution to test these predictions. Also see the video abstract here: https://youtu.be/3unEu5JYJrQ.},
}

*Biological Evolution
Eukaryota
Eukaryotic Cells
Humans
*Neoplasms/genetics
Phenotype

@article {pmid33988501,
year = {2021},
author = {Lu, YX and Regan, JC and Eßer, J and Drews, LF and Weinseis, T and Stinn, J and Hahn, O and Miller, RA and Grönke, S and Partridge, L},
title = {A TORC1-histone axis regulates chromatin organisation and non-canonical induction of autophagy to ameliorate ageing.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {33988501},
issn = {2050-084X},
support = {U19 AG023122/AG/NIA NIH HHS/United States ; UH3 AG064706/AG/NIA NIH HHS/United States ; U01 AG022303/AG/NIA NIH HHS/United States ; P40 OD018537/OD/NIH HHS/United States ; P30 AG024824/AG/NIA NIH HHS/United States ; },
mesh = {Aging/*drug effects/metabolism ; Animals ; *Autophagy ; Chromatin/metabolism ; Drosophila melanogaster ; Eukaryotic Initiation Factor-3/metabolism ; Female ; Gene Expression Regulation ; Histones/genetics/*metabolism ; Intestines ; Mechanistic Target of Rapamycin Complex 1/genetics/*metabolism ; Mice ; Sirolimus/pharmacology ; },
abstract = {Age-related changes to histone levels are seen in many species. However, it is unclear whether changes to histone expression could be exploited to ameliorate the effects of ageing in multicellular organisms. Here we show that inhibition of mTORC1 by the lifespan-extending drug rapamycin increases expression of histones H3 and H4 post-transcriptionally through eIF3-mediated translation. Elevated expression of H3/H4 in intestinal enterocytes in Drosophila alters chromatin organisation, induces intestinal autophagy through transcriptional regulation, and prevents age-related decline in the intestine. Importantly, it also mediates rapamycin-induced longevity and intestinal health. Histones H3/H4 regulate expression of an autophagy cargo adaptor Bchs (WDFY3 in mammals), increased expression of which in enterocytes mediates increased H3/H4-dependent healthy longevity. In mice, rapamycin treatment increases expression of histone proteins and Wdfy3 transcription, and alters chromatin organisation in the small intestine, suggesting that the mTORC1-histone axis is at least partially conserved in mammals and may offer new targets for anti-ageing interventions.},
}

Aging/*drug effects/metabolism
Animals
*Autophagy
Chromatin/metabolism
Drosophila melanogaster
Eukaryotic Initiation Factor-3/metabolism
Female
Gene Expression Regulation
Histones/genetics/*metabolism
Intestines
Mechanistic Target of Rapamycin Complex 1/genetics/*metabolism
Mice
Sirolimus/pharmacology

@article {pmid33990594,
year = {2021},
author = {Bozdag, GO and Libby, E and Pineau, R and Reinhard, CT and Ratcliff, WC},
title = {Oxygen suppression of macroscopic multicellularity.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2838},
pmid = {33990594},
issn = {2041-1723},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; },
mesh = {Aerobiosis ; Anaerobiosis ; *Biological Evolution ; Biophysical Phenomena ; DNA-Binding Proteins/genetics ; Directed Molecular Evolution ; Eukaryotic Cells/*cytology/*metabolism ; Gene Deletion ; Genetic Engineering ; *Models, Biological ; Oxygen/*metabolism ; Saccharomyces cerevisiae/*cytology/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Selection, Genetic ; Synthetic Biology ; Transcription Factors/genetics ; },
abstract = {Atmospheric oxygen is thought to have played a vital role in the evolution of large, complex multicellular organisms. Challenging the prevailing theory, we show that the transition from an anaerobic to an aerobic world can strongly suppress the evolution of macroscopic multicellularity. Here we select for increased size in multicellular 'snowflake' yeast across a range of metabolically-available O2 levels. While yeast under anaerobic and high-O2 conditions evolved to be considerably larger, intermediate O2 constrained the evolution of large size. Through sequencing and synthetic strain construction, we confirm that this is due to O2-mediated divergent selection acting on organism size. We show via mathematical modeling that our results stem from nearly universal evolutionary and biophysical trade-offs, and thus should apply broadly. These results highlight the fact that oxygen is a double-edged sword: while it provides significant metabolic advantages, selection for efficient use of this resource may paradoxically suppress the evolution of macroscopic multicellular organisms.},
}

Aerobiosis
Anaerobiosis
*Biological Evolution
Biophysical Phenomena
DNA-Binding Proteins/genetics
Directed Molecular Evolution
Eukaryotic Cells/*cytology/*metabolism
Gene Deletion
Genetic Engineering
*Models, Biological
Oxygen/*metabolism
Saccharomyces cerevisiae/*cytology/genetics/*metabolism
Saccharomyces cerevisiae Proteins/genetics
Selection, Genetic
Synthetic Biology
Transcription Factors/genetics

@article {pmid34007033,
year = {2021},
author = {Maier, BA and Kiefer, P and Field, CM and Hemmerle, L and Bortfeld-Miller, M and Emmenegger, B and Schäfer, M and Pfeilmeier, S and Sunagawa, S and Vogel, CM and Vorholt, JA},
title = {A general non-self response as part of plant immunity.},
journal = {Nature plants},
volume = {7},
number = {5},
pages = {696-705},
pmid = {34007033},
issn = {2055-0278},
support = {668991/ERC_/European Research Council/International ; },
mesh = {Arabidopsis/*immunology/microbiology/physiology ; Bacteria/genetics/immunology ; Gene Expression Regulation, Plant ; Genes, Plant/immunology/physiology ; Metabolome ; Phylogeny ; Plant Diseases/immunology/microbiology ; Plant Immunity/genetics/physiology ; Secondary Metabolism ; Tryptophan/metabolism ; },
abstract = {Plants, like other multicellular lifeforms, are colonized by microorganisms. How plants respond to their microbiota is currently not well understood. We used a phylogenetically diverse set of 39 endogenous bacterial strains from Arabidopsis thaliana leaves to assess host transcriptional and metabolic adaptations to bacterial encounters. We identified a molecular response, which we termed the general non-self response (GNSR) that involves the expression of a core set of 24 genes. The GNSR genes are not only consistently induced by the presence of most strains, they also comprise the most differentially regulated genes across treatments and are predictive of a hierarchical transcriptional reprogramming beyond the GNSR. Using a complementary untargeted metabolomics approach we link the GNSR to the tryptophan-derived secondary metabolism, highlighting the importance of small molecules in plant-microbe interactions. We demonstrate that several of the GNSR genes are required for resistance against the bacterial pathogen Pseudomonas syringae. Our results suggest that the GNSR constitutes a defence adaptation strategy that is consistently elicited by diverse strains from various phyla, contributes to host protection and involves secondary metabolism.},
}

Arabidopsis/*immunology/microbiology/physiology
Bacteria/genetics/immunology
Gene Expression Regulation, Plant
Genes, Plant/immunology/physiology
Metabolome
Phylogeny
Plant Diseases/immunology/microbiology
Plant Immunity/genetics/physiology
Secondary Metabolism
Tryptophan/metabolism

@article {pmid34020820,
year = {2021},
author = {Tanay, A and Sebé-Pedrós, A},
title = {Evolutionary cell type mapping with single-cell genomics.},
journal = {Trends in genetics : TIG},
volume = {37},
number = {10},
pages = {919-932},
doi = {10.1016/j.tig.2021.04.008},
pmid = {34020820},
issn = {0168-9525},
mesh = {Animals ; Cells/*classification/*metabolism ; *Evolution, Molecular ; Genome/*genetics ; *Genomics ; Humans ; Organ Specificity ; *Single-Cell Analysis ; },
abstract = {A fundamental characteristic of animal multicellularity is the spatial coexistence of functionally specialized cell types that are all encoded by a single genome sequence. Cell type transcriptional programs are deployed and maintained by regulatory mechanisms that control the asymmetric, differential access to genomic information in each cell. This genome regulation ultimately results in specific cellular phenotypes. However, the emergence, diversity, and evolutionary dynamics of animal cell types remain almost completely unexplored beyond a few species. Single-cell genomics is emerging as a powerful tool to build comprehensive catalogs of cell types and their associated gene regulatory programs in non-traditional model species. We review the current state of sampling efforts across the animal tree of life and challenges ahead for the comparative study of cell type programs. We also discuss how the phylogenetic integration of cell atlases can lead to the development of models of cell type evolution and a phylogenetic taxonomy of cells.},
}

Animals
Cells/*classification/*metabolism
*Evolution, Molecular
Genome/*genetics
*Genomics
Humans
Organ Specificity
*Single-Cell Analysis

@article {pmid34023299,
year = {2021},
author = {Schneider, P and Reece, SE},
title = {The private life of malaria parasites: Strategies for sexual reproduction.},
journal = {Molecular and biochemical parasitology},
volume = {244},
number = {},
pages = {111375},
pmid = {34023299},
issn = {1872-9428},
support = {202769/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Biological Coevolution ; Culicidae/parasitology ; Erythrocytes/parasitology ; Female ; *Gametogenesis ; Host-Parasite Interactions/genetics ; Humans ; Insect Vectors/parasitology ; Life Cycle Stages/*genetics ; Liver/parasitology ; Malaria/*parasitology/transmission ; Male ; Plasmodium berghei/genetics/*growth & development/metabolism ; Plasmodium chabaudi/genetics/*growth & development/metabolism ; Plasmodium falciparum/genetics/*growth & development/metabolism ; Plasmodium knowlesi/genetics/*growth & development/metabolism ; Reproduction, Asexual ; Sex Ratio ; },
abstract = {Malaria parasites exhibit a complex lifecycle, requiring extensive asexual replication in the liver and blood of the vertebrate host, and in the haemocoel of the insect vector. Yet, they must also undergo a single round of sexual reproduction, which occurs in the vector's midgut upon uptake of a blood meal. Sexual reproduction is obligate for infection of the vector and thus, is essential for onwards transmission to new hosts. Sex in malaria parasites involves several bottlenecks in parasite number, making the stages involved attractive targets for blocking disease transmission. Malaria parasites have evolved a suite of adaptations ("strategies") to maximise the success of sexual reproduction and transmission, which could undermine transmission-blocking interventions. Yet, understanding parasite strategies may also reveal novel opportunities for such interventions. Here, we outline how evolutionary and ecological theories, developed to explain reproductive strategies in multicellular taxa, can be applied to explain two reproductive strategies (conversion rate and sex ratio) expressed by malaria parasites within the vertebrate host.},
}

Animals
Biological Coevolution
Culicidae/parasitology
Erythrocytes/parasitology
Female
*Gametogenesis
Host-Parasite Interactions/genetics
Humans
Insect Vectors/parasitology
Life Cycle Stages/*genetics
Liver/parasitology
Malaria/*parasitology/transmission
Male
Plasmodium berghei/genetics/*growth & development/metabolism
Plasmodium chabaudi/genetics/*growth & development/metabolism
Plasmodium falciparum/genetics/*growth & development/metabolism
Plasmodium knowlesi/genetics/*growth & development/metabolism
Reproduction, Asexual
Sex Ratio

@article {pmid34026448,
year = {2021},
author = {Jiang, S and Li, H and Zeng, Q and Xiao, Z and Zhang, X and Xu, M and He, Y and Wei, Y and Deng, X},
title = {The Dynamic Counterbalance of RAC1-YAP/OB-Cadherin Coordinates Tissue Spreading with Stem Cell Fate Patterning.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {8},
number = {10},
pages = {2004000},
pmid = {34026448},
issn = {2198-3844},
mesh = {Animals ; Cadherins/*metabolism ; Cell Adhesion/physiology ; Cell Differentiation/physiology ; Cell Lineage ; Cell Movement/physiology ; Cells, Cultured ; Mesenchymal Stem Cells/cytology/*metabolism ; Mice ; Models, Animal ; Morphogenesis ; Signal Transduction ; YAP-Signaling Proteins/*metabolism ; rac1 GTP-Binding Protein/*metabolism ; },
abstract = {Tissue spreading represents a key morphogenetic feature of embryonic development and regenerative medicine. However, how molecular signaling orchestrates the spreading dynamics and cell fate commitment of multicellular tissue remains poorly understood. Here, it is demonstrated that the dynamic counterbalance between RAC1-YAP and OB-cadherin plays a key role in coordinating heterogeneous spreading dynamics with distinct cell fate patterning during collective spreading. The spatiotemporal evolution of individual stem cells in spheroids during collective spreading is mapped. Time-lapse cell migratory trajectory analysis combined with in situ cellular biomechanics detection reveal heterogeneous patterns of collective spreading characteristics, where the cells at the periphery are faster, stiffer, and directional compared to those in the center of the spheroid. Single-cell sequencing shows that the divergent spreading result in distinct cell fate patterning, where differentiation, proliferation, and metabolism are enhanced in peripheral cells. Molecular analysis demonstrates that the increased expression of RAC1-YAP rather than OB-cadherin facilitated cell spreading and induced differentiation, and vice versa. The in vivo wound healing experiment confirms the functional role of RAC1-YAP signaling in tissue spreading. These findings shed light on the mechanism of tissue morphogenesis in the progression of development and provide a practical strategy for desirable regenerative therapies.},
}

Animals
Cadherins/*metabolism
Cell Adhesion/physiology
Cell Differentiation/physiology
Cell Lineage
Cell Movement/physiology
Cells, Cultured
Mesenchymal Stem Cells/cytology/*metabolism
Mice
Models, Animal
Morphogenesis
Signal Transduction
YAP-Signaling Proteins/*metabolism
rac1 GTP-Binding Protein/*metabolism

@article {pmid34031540,
year = {2021},
author = {Kumari, P and Dahiya, P and Livanos, P and Zergiebel, L and Kölling, M and Poeschl, Y and Stamm, G and Hermann, A and Abel, S and Müller, S and Bürstenbinder, K},
title = {IQ67 DOMAIN proteins facilitate preprophase band formation and division-plane orientation.},
journal = {Nature plants},
volume = {7},
number = {6},
pages = {739-747},
pmid = {34031540},
issn = {2055-0278},
mesh = {Arabidopsis/*cytology/genetics ; Arabidopsis Proteins/genetics/*metabolism ; Dinitrobenzenes ; Gene Expression Regulation, Plant ; Green Fluorescent Proteins/genetics/metabolism ; Microtubules/drug effects/metabolism ; Mutation ; Phylogeny ; Plant Cells/drug effects/metabolism ; Plants, Genetically Modified ; Prophase ; Protein Domains ; Sulfanilamides ; Nicotiana/genetics ; Vesicular Transport Proteins/metabolism ; },
abstract = {Spatiotemporal control of cell division is essential for the growth and development of multicellular organisms. In plant cells, proper cell plate insertion during cytokinesis relies on the premitotic establishment of the division plane at the cell cortex. Two plant-specific cytoskeleton arrays, the preprophase band (PPB) and the phragmoplast, play important roles in division-plane orientation and cell plate formation, respectively[1]. Microtubule organization and dynamics and their communication with membranes at the cortex and cell plate are coordinated by multiple, mostly distinct microtubule-associated proteins[2]. How division-plane selection and establishment are linked, however, is still unknown. Here, we report members of the Arabidopsis IQ67 DOMAIN (IQD) family[3] as microtubule-targeted proteins that localize to the PPB and phragmoplast and additionally reside at the cell plate and a polarized cortical region including the cortical division zone (CDZ). IQDs physically interact with PHRAGMOPLAST ORIENTING KINESIN (POK) proteins[4,5] and PLECKSTRIN HOMOLOGY GTPase ACTIVATING (PHGAP) proteins[6], which are core components of the CDZ[1]. The loss of IQD function impairs PPB formation and affects CDZ recruitment of POKs and PHGAPs, resulting in division-plane positioning defects. We propose that IQDs act as cellular scaffolds that facilitate PPB formation and CDZ set-up during symmetric cell division.},
}

Arabidopsis/*cytology/genetics
Arabidopsis Proteins/genetics/*metabolism
Dinitrobenzenes
Gene Expression Regulation, Plant
Green Fluorescent Proteins/genetics/metabolism
Microtubules/drug effects/metabolism
Mutation
Phylogeny
Plant Cells/drug effects/metabolism
Plants, Genetically Modified
Prophase
Protein Domains
Sulfanilamides
Nicotiana/genetics
Vesicular Transport Proteins/metabolism

@article {pmid34047647,
year = {2021},
author = {Sheng, Y and Pan, B and Wei, F and Wang, Y and Gao, S},
title = {Case Study of the Response of N[6]-Methyladenine DNA Modification to Environmental Stressors in the Unicellular Eukaryote Tetrahymena thermophila.},
journal = {mSphere},
volume = {6},
number = {3},
pages = {e0120820},
pmid = {34047647},
issn = {2379-5042},
mesh = {Adenine/*analogs & derivatives/pharmacology ; Epigenesis, Genetic ; Genome, Protozoan ; Methylation ; Protein Processing, Post-Translational ; Stress, Physiological/*drug effects/genetics ; Tetrahymena thermophila/*drug effects/*genetics/metabolism ; },
abstract = {Rediscovered as a potential epigenetic mark, N[6]-methyladenine DNA modification (6mA) was recently reported to be sensitive to environmental stressors in several multicellular eukaryotes. As 6mA distribution and function differ significantly in multicellular and unicellular organisms, whether and how 6mA in unicellular eukaryotes responds to environmental stress remains elusive. Here, we characterized the dynamic changes of 6mA under starvation in the unicellular model organism Tetrahymena thermophila. Single-molecule, real-time (SMRT) sequencing reveals that DNA 6mA levels in starved cells are significantly reduced, especially symmetric 6mA, compared to those in vegetatively growing cells. Despite a global 6mA reduction, the fraction of asymmetric 6mA with a high methylation level was increased, which might be the driving force for stronger nucleosome positioning in starved cells. Starvation affects expression of many metabolism-related genes, the expression level change of which is associated with the amount of 6mA change, thereby linking 6mA with global transcription and starvation adaptation. The reduction of symmetric 6mA and the increase of asymmetric 6mA coincide with the downregulation of AMT1 and upregulation of AMT2 and AMT5, which are supposedly the MT-A70 methyltransferases required for symmetric and asymmetric 6mA, respectively. These results demonstrated that a regulated 6mA response to environmental cues is evolutionarily conserved in eukaryotes. IMPORTANCE Increasing evidence indicated that 6mA could respond to environmental stressors in multicellular eukaryotes. As 6mA distribution and function differ significantly in multicellular and unicellular organisms, whether and how 6mA in unicellular eukaryotes responds to environmental stress remains elusive. In the present work, we characterized the dynamic changes of 6mA under starvation in the unicellular model organism Tetrahymena thermophila. Our results provide insights into how Tetrahymena fine-tunes its 6mA level and composition upon starvation, suggesting that a regulated 6mA response to environmental cues is evolutionarily conserved in eukaryotes.},
}

Adenine/*analogs & derivatives/pharmacology
Epigenesis, Genetic
Genome, Protozoan
Methylation
Protein Processing, Post-Translational
Stress, Physiological/*drug effects/genetics
Tetrahymena thermophila/*drug effects/*genetics/metabolism

@article {pmid34050941,
year = {2021},
author = {Grandhi, TSP and To, J and Romero, A and Luna, F and Barnes, W and Walker, J and Moran, R and Newlin, R and Miraglia, L and Orth, AP and Horman, SR},
title = {High-throughput CRISPR-mediated 3D enrichment platform for functional interrogation of chemotherapeutic resistance.},
journal = {Biotechnology and bioengineering},
volume = {118},
number = {8},
pages = {3187-3199},
doi = {10.1002/bit.27844},
pmid = {34050941},
issn = {1097-0290},
mesh = {Antineoplastic Agents/*pharmacology ; *Breast Neoplasms/drug therapy/genetics/metabolism ; *CRISPR-Cas Systems ; *Cell Culture Techniques ; Cell Line, Tumor ; *Drug Resistance, Neoplasm ; Drug Screening Assays, Antitumor ; Female ; Humans ; Spheroids, Cellular/*metabolism ; *Tumor Microenvironment ; },
abstract = {Cancer is a disease of somatic mutations. These cellular mutations compete to dominate their microenvironment and dictate the disease outcome. While a therapeutic approach to target-specific oncogenic driver mutations helps to manage the disease, subsequent molecular evolution of tumor cells threatens to overtake therapeutic progress. There is a need for rapid, high-throughput, unbiased in vitro discovery screening platforms that capture the native complexities of the tumor and rapidly identify mutations that confer chemotherapeutic drug resistance. Taking the example of the CDK4/6 inhibitor (CDK4/6i) class of drugs, we show that the pooled in vitro CRISPR screening platform enables rapid discovery of drug resistance mutations in a three-dimensional (3D) setting. Gene-edited cancer cell clones assembled into an organotypic multicellular tumor spheroid (MCTS), exposed to CDK4/6i caused selection and enrichment of the most drug-resistant phenotypes, detectable by next-gen sequencing after a span of 28 days. The platform was sufficiently sensitive to enrich for even a single drug-resistant cell within a large, drug-responsive complex 3D tumor spheroid. The genome-wide 3D CRISPR-mediated knockout screen (>18,000 genes) identified several genes whose disruptions conferred resistance to CDK4/6i. Furthermore, multiple novel candidate genes were identified as top hits only in the microphysiological 3D enrichment assay platform and not the conventional 2D assays. Taken together, these findings suggest that including phenotypic 3D resistance profiling in decision trees could improve discovery and reconfirmation of drug resistance mechanisms and afford a platform for exploring noncell autonomous interactions, selection pressures, and clonal competition.},
}

Antineoplastic Agents/*pharmacology
*Breast Neoplasms/drug therapy/genetics/metabolism
*CRISPR-Cas Systems
*Cell Culture Techniques
Cell Line, Tumor
*Drug Resistance, Neoplasm
Drug Screening Assays, Antitumor
Female
Humans
Spheroids, Cellular/*metabolism
*Tumor Microenvironment

@article {pmid34052880,
year = {2022},
author = {Fernández, LD and Seppey, CVW and Singer, D and Fournier, B and Tatti, D and Mitchell, EAD and Lara, E},
title = {Niche Conservatism Drives the Elevational Diversity Gradient in Major Groups of Free-Living Soil Unicellular Eukaryotes.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {459-469},
pmid = {34052880},
issn = {1432-184X},
mesh = {Biodiversity ; *Ciliophora/genetics ; Ecosystem ; Phylogeny ; *Soil ; },
abstract = {Ancestral adaptations to tropical-like climates drive most multicellular biogeography and macroecology. Observational studies suggest that this niche conservatism could also be shaping unicellular biogeography and macroecology, although evidence is limited to Acidobacteria and testate amoebae. We tracked the phylogenetic signal of this niche conservatism in far related and functionally contrasted groups of common soil protists (Bacillariophyta, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida) along a humid but increasingly cold elevational gradient in Switzerland. Protist diversity decreased, and the size of the geographic ranges of taxa increased with elevation and associated decreasing temperature (climate), which is consistent with a macroecological pattern known as the Rapoport effect. Bacillariophyta exhibited phylogenetically overdispersed communities assembled by competitive exclusion of closely related taxa with shared (conserved) niches. By contrast, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida exhibited phylogenetically clustered communities assembled by habitat filtering, revealing the coexistence of closely related taxa with shared (conserved) adaptations to cope with the humid but temperate to cold climate of the study site. Phylobetadiversity revealed that soil protists exhibit a strong phylogenetic turnover among elevational sites, suggesting that most taxa have evolutionary constraints that prevent them from colonizing the colder and higher sites of the elevation gradient. Our results suggest that evolutionary constraints determine how soil protists colonize climates departing from warm and humid conditions. We posit that these evolutionary constraints are linked to an ancestral adaptation to tropical-like climates, which limits their survival in exceedingly cold sites. This niche conservatism possibly drives their biogeography and macroecology along latitudinal and altitudinal climatic gradients.},
}

Biodiversity
*Ciliophora/genetics
Ecosystem
Phylogeny
*Soil

@article {pmid34061031,
year = {2021},
author = {Kaur, G and Iyer, LM and Burroughs, AM and Aravind, L},
title = {Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34061031},
issn = {2050-084X},
support = {F38 LM000084/LM/NLM NIH HHS/United States ; Z01 LM000084/ImNIH/Intramural NIH HHS/United States ; },
mesh = {*Apoptosis ; Bacteria/genetics/immunology/*metabolism ; Bacterial Proteins/genetics/immunology/*metabolism ; *Death Domain Superfamily ; Evolution, Molecular ; Genomics ; Host-Pathogen Interactions ; Microbial Viability ; Phylogeny ; Prokaryotic Cells/immunology/*metabolism ; Signal Transduction ; Symbiosis ; TNF Receptor-Associated Death Domain Protein/genetics/immunology/*metabolism ; },
abstract = {Several homologous domains are shared by eukaryotic immunity and programmed cell-death systems and poorly understood bacterial proteins. Recent studies show these to be components of a network of highly regulated systems connecting apoptotic processes to counter-invader immunity, in prokaryotes with a multicellular habit. However, the provenance of key adaptor domains, namely those of the Death-like and TRADD-N superfamilies, a quintessential feature of metazoan apoptotic systems, remained murky. Here, we use sensitive sequence analysis and comparative genomics methods to identify unambiguous bacterial homologs of the Death-like and TRADD-N superfamilies. We show the former to have arisen as part of a radiation of effector-associated α-helical adaptor domains that likely mediate homotypic interactions bringing together diverse effector and signaling domains in predicted bacterial apoptosis- and counter-invader systems. Similarly, we show that the TRADD-N domain defines a key, widespread signaling bridge that links effector deployment to invader-sensing in multicellular bacterial and metazoan counter-invader systems. TRADD-N domains are expanded in aggregating marine invertebrates and point to distinctive diversifying immune strategies probably directed both at RNA and retroviruses and cellular pathogens that might infect such communities. These TRADD-N and Death-like domains helped identify several new bacterial and metazoan counter-invader systems featuring underappreciated, common functional principles: the use of intracellular invader-sensing lectin-like (NPCBM and FGS), transcription elongation GreA/B-C, glycosyltransferase-4 family, inactive NTPase (serving as nucleic acid receptors), and invader-sensing GTPase switch domains. Finally, these findings point to the possibility of multicellular bacteria-stem metazoan symbiosis in the emergence of the immune/apoptotic systems of the latter.},
}

*Apoptosis
Bacteria/genetics/immunology/*metabolism
Bacterial Proteins/genetics/immunology/*metabolism
*Death Domain Superfamily
Evolution, Molecular
Genomics
Host-Pathogen Interactions
Microbial Viability
Phylogeny
Prokaryotic Cells/immunology/*metabolism
Signal Transduction
Symbiosis
TNF Receptor-Associated Death Domain Protein/genetics/immunology/*metabolism

@article {pmid34063320,
year = {2021},
author = {Mahajan, D and Kancharla, S and Kolli, P and Sharma, AK and Singh, S and Kumar, S and Mohanty, AK and Jena, MK},
title = {Role of Fibulins in Embryonic Stage Development and Their Involvement in Various Diseases.},
journal = {Biomolecules},
volume = {11},
number = {5},
pages = {},
pmid = {34063320},
issn = {2218-273X},
mesh = {Animals ; Calcium-Binding Proteins/genetics/*metabolism ; *Embryonic Development ; Extracellular Matrix/metabolism ; Gene Expression Regulation, Developmental ; Humans ; Neoplasms/*genetics/metabolism ; Protein Isoforms/metabolism ; },
abstract = {The extracellular matrix (ECM) plays an important role in the evolution of early metazoans, as it provides structural and biochemical support to the surrounding cells through the cell-cell and cell-matrix interactions. In multi-cellular organisms, ECM plays a pivotal role in the differentiation of tissues and in the development of organs. Fibulins are ECM glycoproteins, found in a variety of tissues associated with basement membranes, elastic fibers, proteoglycan aggregates, and fibronectin microfibrils. The expression profile of fibulins reveals their role in various developmental processes such as elastogenesis, development of organs during the embryonic stage, tissue remodeling, maintenance of the structural integrity of basement membrane, and elastic fibers, as well as other cellular processes. Apart from this, fibulins are also involved in the progression of human diseases such as cancer, cardiac diseases, congenital disorders, and chronic fibrotic disorders. Different isoforms of fibulins show a dual role of tumor-suppressive and tumor-promoting activities, depending on the cell type and cellular microenvironment in the body. Knockout animal models have provided deep insight into their role in development and diseases. The present review covers details of the structural and expression patterns, along with the role of fibulins in embryonic development and disease progression, with more emphasis on their involvement in the modulation of cancer diseases.},
}

Animals
Calcium-Binding Proteins/genetics/*metabolism
*Embryonic Development
Extracellular Matrix/metabolism
Gene Expression Regulation, Developmental
Humans
Neoplasms/*genetics/metabolism
Protein Isoforms/metabolism

@article {pmid34066959,
year = {2021},
author = {Miller, WB and Enguita, FJ and Leitão, AL},
title = {Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution.},
journal = {Cells},
volume = {10},
number = {5},
pages = {},
pmid = {34066959},
issn = {2073-4409},
mesh = {Animals ; *Biological Evolution ; *Cell Engineering ; Cognition/*physiology ; *Gene Editing ; *Homeostasis ; Humans ; *Selection, Genetic ; },
abstract = {Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alternative approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a 'harnessing of stochasticity'. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.},
}

Animals
*Biological Evolution
*Cell Engineering
Cognition/*physiology
*Gene Editing
*Homeostasis
Humans
*Selection, Genetic