1,573 results match your criteria BMC Biol.[Journal]


The roles of hybridization and habitat fragmentation in the evolution of Brazil's enigmatic longwing butterflies, Heliconius nattereri and H. hermathena.

BMC Biol 2020 Jul 3;18(1):84. Epub 2020 Jul 3.

Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA.

Background: Heliconius butterflies are widely distributed across the Neotropics and have evolved a stunning array of wing color patterns that mediate Müllerian mimicry and mating behavior. Their rapid radiation has been strongly influenced by hybridization, which has created new species and allowed sharing of color patterning alleles between mimetic species pairs. While these processes have frequently been observed in widespread species with contiguous distributions, many Heliconius species inhabit patchy or rare habitats that may strongly influence the origin and spread of species and color patterns. Read More

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http://dx.doi.org/10.1186/s12915-020-00797-1DOI Listing

Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human.

BMC Biol 2020 Jul 3;18(1):80. Epub 2020 Jul 3.

Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, BARC-East, Beltsville, MD, 20705, USA.

Background: Lack of comprehensive functional annotations across a wide range of tissues and cell types severely hinders the biological interpretations of phenotypic variation, adaptive evolution, and domestication in livestock. Here we used a combination of comparative epigenomics, genome-wide association study (GWAS), and selection signature analysis, to shed light on potential adaptive evolution in cattle.

Results: We cross-mapped 8 histone marks of 1300 samples from human to cattle, covering 178 unique tissues/cell types. Read More

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http://dx.doi.org/10.1186/s12915-020-00792-6DOI Listing

TDP-43 prevents retrotransposon activation in the Drosophila motor system through regulation of Dicer-2 activity.

BMC Biol 2020 Jul 3;18(1):82. Epub 2020 Jul 3.

International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy.

Background: Mutations in the small RNA-binding protein TDP-43 lead to the formation of insoluble cytoplasmic aggregates that have been associated with the onset and progression of amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder affecting homeostasis of the motor system which is also characterized by aberrant expression of retrotransposable elements (RTEs). Although the TDP-43 function was shown to be required in the neurons and glia to maintain the organization of neuromuscular synapses and prevent denervation of the skeletal muscles, the molecular mechanisms involved in physiological dysregulation remain elusive. Here, we address this issue using a null mutation of the TDP-43 Drosophila homolog, TBPH. Read More

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http://dx.doi.org/10.1186/s12915-020-00816-1DOI Listing

Real-time tracking of stem cell viability, proliferation, and differentiation with autonomous bioluminescence imaging.

BMC Biol 2020 Jul 3;18(1):79. Epub 2020 Jul 3.

490 BioTech, Knoxville, TN, 37996, USA.

Background: Luminescent reporter proteins are vital tools for visualizing cells and cellular activity. Among the current toolbox of bioluminescent systems, only bacterial luciferase has genetically defined luciferase and luciferin synthesis pathways that are functional at the mammalian cell temperature optimum of 37 °C and have the potential for in vivo applications. However, this system is not functional in all cell types, including stem cells, where the ability to monitor continuously and in real-time cellular processes such as differentiation and proliferation would be particularly advantageous. Read More

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http://dx.doi.org/10.1186/s12915-020-00815-2DOI Listing

Temporospatial shifts within commercial laboratory mouse gut microbiota impact experimental reproducibility.

BMC Biol 2020 Jul 3;18(1):83. Epub 2020 Jul 3.

Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, USA.

Background: Experimental reproducibility in mouse models is impacted by both genetics and environment. The generation of reproducible data is critical for the biomedical enterprise and has become a major concern for the scientific community and funding agencies alike. Among the factors that impact reproducibility in experimental mouse models is the variable composition of the microbiota in mice supplied by different commercial vendors. Read More

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http://dx.doi.org/10.1186/s12915-020-00810-7DOI Listing
July 2020
7.984 Impact Factor

AIMTOR, a BRET biosensor for live imaging, reveals subcellular mTOR signaling and dysfunctions.

BMC Biol 2020 Jul 3;18(1):81. Epub 2020 Jul 3.

DMEM, University of Montpellier, INRAE, Montpellier, France.

Background: mTOR signaling is an essential nutrient and energetic sensing pathway. Here we describe AIMTOR, a sensitive genetically encoded BRET (Bioluminescent Resonance Energy Transfer) biosensor to study mTOR activity in living cells.

Results: As a proof of principle, we show in both cell lines and primary cell cultures that AIMTOR BRET intensities are modified by mTOR activity changes induced by specific inhibitors and activators of mTORC1 including amino acids and insulin. Read More

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http://dx.doi.org/10.1186/s12915-020-00790-8DOI Listing

Relationship between oxygen consumption and neuronal activity in a defined neural circuit.

BMC Biol 2020 Jul 3;18(1):76. Epub 2020 Jul 3.

Department Biology II, Ludwig-Maximilians-University Munich, Großhaderner Str. 2, 82152, Planegg, Germany.

Background: Neuronal computations related to sensory and motor activity along with the maintenance of spike discharge, synaptic transmission, and associated housekeeping are energetically demanding. The most efficient metabolic process to provide large amounts of energy equivalents is oxidative phosphorylation and thus dependent on O consumption. Therefore, O levels in the brain are a critical parameter that influences neuronal function. Read More

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http://dx.doi.org/10.1186/s12915-020-00811-6DOI Listing

The evolution of the Puf superfamily of proteins across the tree of eukaryotes.

BMC Biol 2020 Jun 30;18(1):77. Epub 2020 Jun 30.

Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic.

Background: Eukaryotic gene expression is controlled by a number of RNA-binding proteins (RBP), such as the proteins from the Puf (Pumilio and FBF) superfamily (PufSF). These proteins bind to RNA via multiple Puf repeat domains, each of which specifically recognizes a single RNA base. Recently, three diversified PufSF proteins have been described in model organisms, each of which is responsible for the maturation of ribosomal RNA or the translational regulation of mRNAs; however, less is known about the role of these proteins across eukaryotic diversity. Read More

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http://dx.doi.org/10.1186/s12915-020-00814-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325665PMC

Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion.

BMC Biol 2020 Jun 30;18(1):78. Epub 2020 Jun 30.

Department of Genetics, Evolution & Environment, University College London, London, UK.

Background: Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. Read More

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http://dx.doi.org/10.1186/s12915-020-00808-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329446PMC

The evolutionarily conserved ESRE stress response network is activated by ROS and mitochondrial damage.

BMC Biol 2020 Jun 29;18(1):74. Epub 2020 Jun 29.

Department of BioSciences, Rice University, 6100 Main St, MS140, Houston, TX, 77005, USA.

Background: Mitochondrial dysfunction causes or contributes to a wide variety of pathologies, including neurodegenerative diseases, cancer, metabolic diseases, and aging. Cells actively surveil a number of mitochondrial readouts to ensure that cellular homeostasis is maintained.

Results: In this article, we characterize the role of the ethanol and stress response element (ESRE) pathway in mitochondrial surveillance and show that it is robustly activated when the concentration of reactive oxygen species (ROS) in the cell increases. Read More

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http://dx.doi.org/10.1186/s12915-020-00812-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7322875PMC

Phosphatidic acid-dependent localization and basal de-phosphorylation of RA-GEFs regulate lymphocyte trafficking.

BMC Biol 2020 Jun 29;18(1):75. Epub 2020 Jun 29.

Department of Biosciences, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku, Sagamihara, Kanagawa, 252-0344, Japan.

Background: Lymphocytes circulate between peripheral lymphoid tissues via blood and lymphatic systems, and chemokine-induced migration is important in trafficking lymphocytes to distant sites. The small GTPase Rap1 is important in mediating lymphocyte motility, and Rap1-GEFs are involved in chemokine-mediated Rap1 activation. Here, we describe the roles and mechanisms of Rap1-GEFs in lymphocyte trafficking. Read More

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http://dx.doi.org/10.1186/s12915-020-00809-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325102PMC

A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice.

BMC Biol 2020 Jun 26;18(1):73. Epub 2020 Jun 26.

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture; Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.

Background: Copy number variations (CNVs) are an important type of structural variations in the genome that usually affect gene expression levels by gene dosage effect. Understanding CNVs as part of genome evolution may provide insights into the genetic basis of important agricultural traits and contribute to the crop breeding in the future. While available methods to detect CNVs utilizing next-generation sequencing technology have helped shed light on prevalence and effects of CNVs, the complexity of crop genomes poses a major challenge and requires development of additional tools. Read More

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http://dx.doi.org/10.1186/s12915-020-00798-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318451PMC

The merger that made us.

BMC Biol 2020 Jun 24;18(1):72. Epub 2020 Jun 24.

University of Wisconsin - Madison, 430 Lincoln Drive, Madison, WI, 53726, USA.

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http://dx.doi.org/10.1186/s12915-020-00806-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315558PMC

New targeted approaches for epigenetic age predictions.

BMC Biol 2020 Jun 24;18(1):71. Epub 2020 Jun 24.

Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.

Background: Age-associated DNA methylation changes provide a promising biomarker for the aging process. While genome-wide DNA methylation profiles enable robust age-predictors by integration of many age-associated CG dinucleotides (CpGs), there are various alternative approaches for targeted measurements at specific CpGs that better support standardized and cost-effective high-throughput analysis.

Results: In this study, we utilized 4647 Illumina BeadChip profiles of blood to select CpG sites that facilitate reliable age-predictions based on pyrosequencing. Read More

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http://dx.doi.org/10.1186/s12915-020-00807-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315536PMC

A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity.

BMC Biol 2020 Jun 19;18(1):70. Epub 2020 Jun 19.

Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.

Background: Fleas (Insecta: Siphonaptera) are small flightless parasites of birds and mammals; their blood-feeding can transmit many serious pathogens (i.e., the etiological agents of bubonic plague, endemic and murine typhus). Read More

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http://dx.doi.org/10.1186/s12915-020-00802-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7305587PMC

The rise of diversity in metabolic platforms across the Candidate Phyla Radiation.

BMC Biol 2020 Jun 19;18(1):69. Epub 2020 Jun 19.

Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.

Background: A unifying feature of the bacterial Candidate Phyla Radiation (CPR) is a limited and highly variable repertoire of biosynthetic capabilities. However, the distribution of metabolic traits across the CPR and the evolutionary processes underlying them are incompletely resolved.

Results: Here, we selected ~ 1000 genomes of CPR bacteria from diverse environments to construct a robust internal phylogeny that was consistent across two unlinked marker sets. Read More

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http://dx.doi.org/10.1186/s12915-020-00804-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304191PMC

Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants.

BMC Biol 2020 Jun 18;18(1):63. Epub 2020 Jun 18.

Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.

Background: Plants have evolved a panoply of specialized metabolites that increase their environmental fitness. Two examples are caffeine, a purine psychotropic alkaloid, and crocins, a group of glycosylated apocarotenoid pigments. Both classes of compounds are found in a handful of distantly related plant genera (Coffea, Camellia, Paullinia, and Ilex for caffeine; Crocus, Buddleja, and Gardenia for crocins) wherein they presumably evolved through convergent evolution. Read More

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http://dx.doi.org/10.1186/s12915-020-00795-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7302004PMC

Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii.

BMC Biol 2020 Jun 16;18(1):67. Epub 2020 Jun 16.

Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland.

Background: Acetyl-CoA is a key molecule in all organisms, implicated in several metabolic pathways as well as in transcriptional regulation and post-translational modification. The human pathogen Toxoplasma gondii possesses at least four enzymes which generate acetyl-CoA in the nucleo-cytosol (acetyl-CoA synthetase (ACS); ATP citrate lyase (ACL)), mitochondrion (branched-chain α-keto acid dehydrogenase-complex (BCKDH)) and apicoplast (pyruvate dehydrogenase complex (PDH)). Given the diverse functions of acetyl-CoA, we know very little about the role of sub-cellular acetyl-CoA pools in parasite physiology. Read More

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http://dx.doi.org/10.1186/s12915-020-00791-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7296777PMC

Mutation of amphioxus Pdx and Cdx demonstrates conserved roles for ParaHox genes in gut, anus and tail patterning.

BMC Biol 2020 Jun 16;18(1):68. Epub 2020 Jun 16.

Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK.

Background: The homeobox genes Pdx and Cdx are widespread across the animal kingdom and part of the small ParaHox gene cluster. Gene expression patterns suggest ancient roles for Pdx and Cdx in patterning the through-gut of bilaterian animals although functional data are available for few lineages. To examine evolutionary conservation of Pdx and Cdx gene functions, we focus on amphioxus, small marine animals that occupy a pivotal position in chordate evolution and in which ParaHox gene clustering was first reported. Read More

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http://dx.doi.org/10.1186/s12915-020-00796-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7296684PMC

DNA interference is controlled by R-loop length in a type I-F1 CRISPR-Cas system.

BMC Biol 2020 Jun 15;18(1):65. Epub 2020 Jun 15.

Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania.

Background: CRISPR-Cas systems, which provide adaptive immunity against foreign nucleic acids in prokaryotes, can serve as useful molecular tools for multiple applications in genome engineering. Diverse CRISPR-Cas systems originating from distinct prokaryotes function through a common mechanism involving the assembly of small crRNA molecules and Cas proteins into a ribonucleoprotein (RNP) effector complex, and formation of an R-loop structure upon binding to the target DNA. Extensive research on the I-E subtype established the prototypical mechanism of DNA interference in type I systems, where the coordinated action of a ribonucleoprotein Cascade complex and Cas3 protein destroys foreign DNA. Read More

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http://dx.doi.org/10.1186/s12915-020-00799-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7296934PMC

Stimulus-specific behavioral responses of zebrafish to a large range of odors exhibit individual variability.

BMC Biol 2020 Jun 15;18(1):66. Epub 2020 Jun 15.

Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7030, Trondheim, Norway.

Background: Odor-driven behaviors such as feeding, mating, and predator avoidance are crucial for animal survival. The neural pathways processing these behaviors have been well characterized in a number of species, and involve the activity of diverse brain regions following stimulation of the olfactory bulb by specific odors. However, while the zebrafish olfactory circuitry is well understood, a comprehensive characterization linking odor-driven behaviors to specific odors is needed to better relate olfactory computations to animal responses. Read More

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http://dx.doi.org/10.1186/s12915-020-00801-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7296676PMC

A mutation that blocks integrin αβ activation prevents adaptive immune-mediated colitis without increasing susceptibility to innate colitis.

BMC Biol 2020 Jun 10;18(1):64. Epub 2020 Jun 10.

State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 YueYang Road, Shanghai, 200031, China.

Background: β integrins are responsible for the efficient recruitment of lymphocytes from the blood and their retention in gut-associated lymphoid tissues. Integrin αβ binds MAdCAM-1, mediating rolling adhesion of lymphocytes on blood vessel walls when inactive and firm adhesion when activated, thereby controlling two critical steps of lymphocyte homing to the gut. By contrast, integrin αβ mediates the adhesion of lymphocytes to gut epithelial cells by interacting with E-cadherin. Read More

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http://dx.doi.org/10.1186/s12915-020-00784-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7288534PMC

Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions.

BMC Biol 2020 Jun 9;18(1):62. Epub 2020 Jun 9.

Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg.

Background: Parkinson's disease (PD) is a systemic disease clinically defined by the degeneration of dopaminergic neurons in the brain. While alterations in the gut microbiome composition have been reported in PD, their functional consequences remain unclear. Herein, we addressed this question by an analysis of stool samples from the Luxembourg Parkinson's Study (n = 147 typical PD cases, n = 162 controls). Read More

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http://dx.doi.org/10.1186/s12915-020-00775-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285525PMC

The replication machinery of LUCA: common origin of DNA replication and transcription.

BMC Biol 2020 Jun 9;18(1):61. Epub 2020 Jun 9.

Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan.

Origin of DNA replication is an enigma because the replicative DNA polymerases (DNAPs) are not homologous among the three domains of life, Bacteria, Archaea, and Eukarya. The homology between the archaeal replicative DNAP (PolD) and the large subunits of the universal RNA polymerase (RNAP) responsible for transcription suggests a parsimonious evolutionary scenario. Under this model, RNAPs and replicative DNAPs evolved from a common ancestor that functioned as an RNA-dependent RNA polymerase in the RNA-protein world that predated the advent of DNA replication. Read More

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http://dx.doi.org/10.1186/s12915-020-00800-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281927PMC

A tissue level atlas of the healthy human virome.

BMC Biol 2020 Jun 4;18(1):55. Epub 2020 Jun 4.

Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan.

Background: Human-resident microbes can influence both health and disease. Investigating the microbiome using next-generation sequencing technology has revealed examples of mutualism and conflict between microbes and humans. Comparing to bacteria, the viral component of the microbiome (i. Read More

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http://dx.doi.org/10.1186/s12915-020-00785-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7269688PMC

Intramembrane proteolysis of an extracellular serine protease, epithin/PRSS14, enables its intracellular nuclear function.

BMC Biol 2020 Jun 3;18(1):60. Epub 2020 Jun 3.

Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea.

Background: Epithin/PRSS14, a type II transmembrane serine protease, is an emerging target of cancer therapy because of its critical roles in tumor progression and metastasis. In many circumstances, the protease, through its ectodomain shedding, exists as a soluble form and performs its proteolytic functions in extracellular environments increasing cellular invasiveness. The seemingly functional integrity of the soluble form raises the question of why the protease is initially made as a membrane-associated protein. Read More

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http://dx.doi.org/10.1186/s12915-020-00787-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271384PMC
June 2020
7.984 Impact Factor

Unraveling the molecular interactions involved in phase separation of glucocorticoid receptor.

BMC Biol 2020 Jun 2;18(1):59. Epub 2020 Jun 2.

Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA, Buenos Aires, Argentina.

Background: Functional compartmentalization has emerged as an important factor modulating the kinetics and specificity of biochemical reactions in the nucleus, including those involved in transcriptional regulation. The glucocorticoid receptor (GR) is a ligand-activated transcription factor that translocates to the nucleus upon hormone stimulation and distributes between the nucleoplasm and membraneless compartments named nuclear foci. While a liquid-liquid phase separation process has been recently proposed to drive the formation of many nuclear compartments, the mechanisms governing the heterogeneous organization of GR in the nucleus and the functional relevance of foci formation remain elusive. Read More

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http://dx.doi.org/10.1186/s12915-020-00788-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7268505PMC

Deficits in coordinated neuronal activity and network topology are striatal hallmarks in Huntington's disease.

BMC Biol 2020 May 28;18(1):58. Epub 2020 May 28.

Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.

Background: Network alterations underlying neurodegenerative diseases often precede symptoms and functional deficits. Thus, their early identification is central for improved prognosis. In Huntington's disease (HD), the cortico-striatal networks, involved in motor function processing, are the most compromised neural substrate. Read More

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http://dx.doi.org/10.1186/s12915-020-00794-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7254676PMC

Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution.

BMC Biol 2020 May 27;18(1):57. Epub 2020 May 27.

Origins Center, Nijenborgh 7, 9747AG, Groningen, The Netherlands.

Background: Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals. Read More

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http://dx.doi.org/10.1186/s12915-020-00789-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7251882PMC

Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions.

BMC Biol 2020 May 24;18(1):56. Epub 2020 May 24.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.

Background: Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Read More

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http://dx.doi.org/10.1186/s12915-020-00782-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245778PMC

Genomic history of the Italian population recapitulates key evolutionary dynamics of both Continental and Southern Europeans.

BMC Biol 2020 May 22;18(1):51. Epub 2020 May 22.

Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy.

Background: The cline of human genetic diversity observable across Europe is recapitulated at a micro-geographic scale by variation within the Italian population. Besides resulting from extensive gene flow, this might be ascribable also to local adaptations to diverse ecological contexts evolved by people who anciently spread along the Italian Peninsula. Dissecting the evolutionary history of the ancestors of present-day Italians may thus improve the understanding of demographic and biological processes that contributed to shape the gene pool of European populations. Read More

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http://dx.doi.org/10.1186/s12915-020-00778-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7243322PMC

NetConfer: a web application for comparative analysis of multiple biological networks.

BMC Biol 2020 May 19;18(1):53. Epub 2020 May 19.

Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India.

Background: Most biological experiments are inherently designed to compare changes or transitions of state between conditions of interest. The advancements in data intensive research have in particular elevated the need for resources and tools enabling comparative analysis of biological data. The complexity of biological systems and the interactions of their various components, such as genes, proteins, taxa, and metabolites, have been inferred, represented, and visualized via graph theory-based networks. Read More

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http://dx.doi.org/10.1186/s12915-020-00781-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236966PMC

Using a chimeric respiratory chain and EPR spectroscopy to determine the origin of semiquinone species previously assigned to mitochondrial complex I.

BMC Biol 2020 May 20;18(1):54. Epub 2020 May 20.

School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.

Background: For decades, semiquinone intermediates have been suggested to play an essential role in catalysis by one of the most enigmatic proton-pumping enzymes, respiratory complex I, and different mechanisms have been proposed on their basis. However, the difficulty in investigating complex I semiquinones, due to the many different enzymes embedded in the inner mitochondrial membrane, has resulted in an ambiguous picture and no consensus.

Results: In this paper, we re-examine the highly debated origin of semiquinone species in mitochondrial membranes using a novel approach. Read More

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http://dx.doi.org/10.1186/s12915-020-00768-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7238650PMC

Tropomyosin 1 genetically constrains in vitro hematopoiesis.

BMC Biol 2020 May 14;18(1):52. Epub 2020 May 14.

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

Background: Identifying causal variants and genes from human genetic studies of hematopoietic traits is important to enumerate basic regulatory mechanisms underlying these traits, and could ultimately augment translational efforts to generate platelets and/or red blood cells in vitro. To identify putative causal genes from these data, we performed computational modeling using available genome-wide association datasets for platelet and red blood cell traits.

Results: Our model identified a joint collection of genomic features enriched at established trait associations and plausible candidate variants. Read More

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http://dx.doi.org/10.1186/s12915-020-00783-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7227211PMC

Modeling confinement and reversibility of threshold-dependent gene drive systems in spatially-explicit Aedes aegypti populations.

BMC Biol 2020 May 12;18(1):50. Epub 2020 May 12.

Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA.

Background: The discovery of CRISPR-based gene editing and its application to homing-based gene drive systems has been greeted with excitement, for its potential to control mosquito-borne diseases on a wide scale, and concern, for the invasiveness and potential irreversibility of a release. Gene drive systems that display threshold-dependent behavior could potentially be used during the trial phase of this technology, or when localized control is otherwise desired, as simple models predict them to spread into partially isolated populations in a confineable manner, and to be reversible through releases of wild-type organisms. Here, we model hypothetical releases of two recently engineered threshold-dependent gene drive systems-reciprocal chromosomal translocations and a form of toxin-antidote-based underdominance known as UD-to explore their ability to be confined and remediated. Read More

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http://dx.doi.org/10.1186/s12915-020-0759-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7218562PMC

Discordant evolution of mitochondrial and nuclear yeast genomes at population level.

BMC Biol 2020 May 11;18(1):49. Epub 2020 May 11.

Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.

Background: Mitochondria are essential organelles partially regulated by their own genomes. The mitochondrial genome maintenance and inheritance differ from the nuclear genome, potentially uncoupling their evolutionary trajectories. Here, we analysed mitochondrial sequences obtained from the 1011 Saccharomyces cerevisiae strain collection and identified pronounced differences with their nuclear genome counterparts. Read More

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http://dx.doi.org/10.1186/s12915-020-00786-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216626PMC

Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans.

BMC Biol 2020 May 6;18(1):48. Epub 2020 May 6.

Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.

Background: Opportunistic yeast pathogens of the genus Candida are an important medical problem. Candida albicans, the most prevalent Candida species, is a natural commensal of humans that can adopt a pathogenic behavior. This species is highly heterozygous and cannot undergo meiosis, adopting instead a parasexual cycle that increases genetic variability and potentially leads to advantages under stress conditions. Read More

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http://dx.doi.org/10.1186/s12915-020-00776-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7204223PMC

Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31.

BMC Biol 2020 May 4;18(1):47. Epub 2020 May 4.

Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.

Background: Genome-wide association studies (GWAS) have uncovered many genetic risk loci for psoriasis, yet many remain uncharacterised in terms of the causal gene and their biological mechanism in disease. This is largely a result of the findings that over 90% of GWAS variants map outside of protein-coding DNA and instead are enriched in cell type- and stimulation-specific gene regulatory regions.

Results: Here, we use a disease-focused Capture Hi-C (CHi-C) experiment to link psoriasis-associated variants with their target genes in psoriasis-relevant cell lines (HaCaT keratinocytes and My-La CD8+ T cells). Read More

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http://dx.doi.org/10.1186/s12915-020-00779-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7199343PMC

An automated aquatic rack system for rearing marine invertebrates.

BMC Biol 2020 May 4;18(1):46. Epub 2020 May 4.

Department of Cell & Developmental Biology, University of Illinois, 601 South Goodwin Ave., Urbana, IL, 61801, USA.

Background: One hundred years ago, marine organisms were the dominant systems for the study of developmental biology. The challenges in rearing these organisms outside of a marine setting ultimately contributed to a shift towards work on a smaller number of so-called model systems. Those animals are typically non-marine organisms with advantages afforded by short life cycles, high fecundity, and relative ease in laboratory culture. Read More

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http://dx.doi.org/10.1186/s12915-020-00772-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7199361PMC

Microtubule self-organisation during seed germination in Arabidopsis.

BMC Biol 2020 Apr 30;18(1):44. Epub 2020 Apr 30.

Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, F-75005, Paris, France.

Background: Upon water uptake and release of seed dormancy, embryonic plant cells expand, while being mechanically constrained by the seed coat. Cortical microtubules (CMTs) are key players of cell elongation in plants: their anisotropic orientation channels the axis of cell elongation through the guidance of oriented deposition of load-bearing cellulose microfibrils in the cell wall. Interestingly, CMTs align with tensile stress, and consistently, they reorient upon compressive stress in growing hypocotyls. Read More

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http://dx.doi.org/10.1186/s12915-020-00774-8DOI Listing

Direct evidence for transport of RNA from the mouse brain to the germline and offspring.

BMC Biol 2020 Apr 30;18(1):45. Epub 2020 Apr 30.

QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia.

Background: The traditional concept that heritability occurs exclusively from the transfer of germline-restricted genetics is being challenged by the increasing accumulation of evidence confirming the existence of experience-dependent transgenerational inheritance. However, questions remain unanswered as to how heritable information can be passed from somatic cells. Previous studies have implicated the critical involvement of RNA in heritable transgenerational effects, and the high degree of mobility and genomic impact of RNAs in all organisms is an attractive model for the efficient transfer of genetic information. Read More

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http://dx.doi.org/10.1186/s12915-020-00780-wDOI Listing

Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae.

BMC Biol 2020 Apr 29;18(1):43. Epub 2020 Apr 29.

Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France.

Background: In fast-growing bacteria, the genomic location of ribosomal protein (RP) genes is biased towards the replication origin (oriC). This trait allows optimizing their expression during exponential phase since oriC neighboring regions are in higher dose due to multifork replication. Relocation of s10-spc-α locus (S10), which codes for most of the RP, to ectopic genomic positions shows that its relative distance to the oriC correlates to a reduction on its dosage, its expression, and bacterial growth rate. Read More

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http://dx.doi.org/10.1186/s12915-020-00777-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7191768PMC

Nucleus size and DNA accessibility are linked to the regulation of paraspeckle formation in cellular differentiation.

BMC Biol 2020 Apr 22;18(1):42. Epub 2020 Apr 22.

Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany.

Background: Many long noncoding RNAs (lncRNAs) have been implicated in general and cell type-specific molecular regulation. Here, we asked what underlies the fundamental basis for the seemingly random appearance of nuclear lncRNA condensates in cells, and we sought compounds that can promote the disintegration of lncRNA condensates in vivo.

Results: As a basis for comparing lncRNAs and cellular properties among different cell types, we screened lncRNAs in human pluripotent stem cells (hPSCs) that were differentiated to an atlas of cell lineages. Read More

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http://dx.doi.org/10.1186/s12915-020-00770-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178590PMC

Integrating evolutionarily novel horns within the deeply conserved insect head.

BMC Biol 2020 Apr 20;18(1):41. Epub 2020 Apr 20.

Department of Biology, Indiana University, Bloomington, IN, 47405, USA.

Background: How novel traits integrate within ancient trait complexes without compromising ancestral functions is a foundational challenge in evo-devo. The insect head represents an ancient body region patterned by a deeply conserved developmental genetic network, yet at the same time constitutes a hot spot for morphological innovation. However, the mechanisms that facilitate the repeated emergence, integration, and diversification of morphological novelties within this body region are virtually unknown. Read More

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http://dx.doi.org/10.1186/s12915-020-00773-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171871PMC

Multiple links between 5-methylcytosine content of mRNA and translation.

BMC Biol 2020 Apr 15;18(1):40. Epub 2020 Apr 15.

EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia.

Background: 5-Methylcytosine (mC) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pursuit of potential links of mC with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise. Read More

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http://dx.doi.org/10.1186/s12915-020-00769-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158060PMC
April 2020
7.984 Impact Factor

Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner.

BMC Biol 2020 Apr 13;18(1):38. Epub 2020 Apr 13.

Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.

Background: The advent of next generation sequencing (NGS) has allowed the discovery of short and long non-coding RNAs (ncRNAs) in an unbiased manner using reverse genetics approaches, enabling the discovery of multiple categories of ncRNAs and characterization of the way their expression is regulated. We previously showed that the identities and abundances of microRNA isoforms (isomiRs) and transfer RNA-derived fragments (tRFs) are tightly regulated, and that they depend on a person's sex and population origin, as well as on tissue type, tissue state, and disease type. Here, we characterize the regulation and distribution of fragments derived from ribosomal RNAs (rRNAs). Read More

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http://dx.doi.org/10.1186/s12915-020-0763-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153239PMC

Insights into the origin of metazoan multicellularity from predatory unicellular relatives of animals.

BMC Biol 2020 Apr 9;18(1):39. Epub 2020 Apr 9.

Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.

Background: The origin of animals from their unicellular ancestor was one of the most important events in evolutionary history, but the nature and the order of events leading up to the emergence of multicellular animals are still highly uncertain. The diversity and biology of unicellular relatives of animals have strongly informed our understanding of the transition from single-celled organisms to the multicellular Metazoa. Here, we analyze the cellular structures and complex life cycles of the novel unicellular holozoans Pigoraptor and Syssomonas (Opisthokonta), and their implications for the origin of animals. Read More

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http://dx.doi.org/10.1186/s12915-020-0762-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147346PMC

Improving the usability and comprehensiveness of microbial databases.

BMC Biol 2020 Apr 7;18(1):37. Epub 2020 Apr 7.

Department of Clinical Pharmacy, University of Southern California School of Pharmacy, 1985 Zonal Ave, Los Angeles, CA, 90089, USA.

Metagenomics studies leverage genomic reference databases to generate discoveries in basic science and translational research. However, current microbial studies use disparate reference databases that lack consistent standards of specimen inclusion, data preparation, taxon labelling and accessibility, hindering their quality and comprehensiveness, and calling for the establishment of recommendations for reference genome database assembly. Here, we analyze existing fungal and bacterial databases and discuss guidelines for the development of a master reference database that promises to improve the quality and quantity of omics research. Read More

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http://dx.doi.org/10.1186/s12915-020-0756-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140547PMC

Persistent DNA damage triggers activation of the integrated stress response to promote cell survival under nutrient restriction.

BMC Biol 2020 03 30;18(1):36. Epub 2020 Mar 30.

Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, 8057, Zürich, Switzerland.

Background: Base-excision repair (BER) is a central DNA repair mechanism responsible for the maintenance of genome integrity. Accordingly, BER defects have been implicated in cancer, presumably by precipitating cellular transformation through an increase in the occurrence of mutations. Hence, tight adaptation of BER capacity is essential for DNA stability. Read More

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http://dx.doi.org/10.1186/s12915-020-00771-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106853PMC

TDP-43 promotes the formation of neuromuscular synapses through the regulation of Disc-large expression in Drosophila skeletal muscles.

BMC Biol 2020 03 26;18(1):34. Epub 2020 Mar 26.

International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy.

Background: The ribonuclear protein TDP-43 has been implicated in the pathophysiology of amyotrophic lateral sclerosis (ALS), with genetic mutations being linked to the neurological symptoms of the disease. Though alterations in the intracellular distribution of TDP-43 have been observed in skeletal muscles of patients suffering from ALS, it is not clear whether such modifications play an active role in the disease or merely represent an expression of muscle homeostatic mechanisms. Also, the molecular and metabolic pathways regulated by TDP-43 in the skeletal muscle remain largely unknown. Read More

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http://dx.doi.org/10.1186/s12915-020-00767-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099817PMC