1,549 results match your criteria Bmc Biology[Journal]


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

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

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

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

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

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

Protein assembly systems in natural and synthetic biology.

BMC Biol 2020 03 26;18(1):35. Epub 2020 Mar 26.

Biological Design Center, Boston University, Boston, MA, 02215, USA.

The traditional view of protein aggregation as being strictly disease-related has been challenged by many examples of cellular aggregates that regulate beneficial biological functions. When coupled with the emerging view that many regulatory proteins undergo phase separation to form dynamic cellular compartments, it has become clear that supramolecular assembly plays wide-ranging and critical roles in cellular regulation. This presents opportunities to develop new tools to probe and illuminate this biology, and to harness the unique properties of these self-assembling systems for synthetic biology for the purposeful manipulation of biological function. Read More

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http://dx.doi.org/10.1186/s12915-020-0751-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099826PMC

Identification of berberine as a novel drug for the treatment of multiple myeloma via targeting UHRF1.

BMC Biol 2020 03 25;18(1):33. Epub 2020 Mar 25.

Department of Biochemistry and Molecular Biology, Medical College of Jinan University, 601 Western Huangpu Avenue, Guangzhou, 510632, China.

Background: Current therapies for multiple myeloma (MM) are associated with toxicity and resistance, highlighting the need for novel effective therapeutics. Berberine (BBR), a botanical alkaloid derived from several Berberis medicinal plants, has exhibited anti-tumor effects, including against multiple myeloma (MM); however, the molecular mechanism underlying the anti-MM effect has not been previously described. This study aimed to identify the target of berberine and related mechanisms involved in its therapeutic activity against MM. Read More

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http://dx.doi.org/10.1186/s12915-020-00766-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7098108PMC

DDX39B interacts with the pattern recognition receptor pathway to inhibit NF-κB and sensitize to alkylating chemotherapy.

BMC Biol 2020 03 24;18(1):32. Epub 2020 Mar 24.

Department of Surgery, Section of Neurosurgery, The University of Chicago, Chicago, IL, 60637, USA.

Background: Nuclear factor-κB (NF-κB) plays a prominent role in promoting inflammation and resistance to DNA damaging therapy. We searched for proteins that modulate the NF-κB response as a prerequisite to identifying novel factors that affect sensitivity to DNA damaging chemotherapy.

Results: Using streptavidin-agarose pull-down, we identified the DExD/H-box RNA helicase, DDX39B, as a factor that differentially interacts with κB DNA probes. Read More

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http://dx.doi.org/10.1186/s12915-020-0764-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7093963PMC

A metabolic switch regulates the transition between growth and diapause in C. elegans.

BMC Biol 2020 03 18;18(1):31. Epub 2020 Mar 18.

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.

Background: Metabolic activity alternates between high and low states during different stages of an organism's life cycle. During the transition from growth to quiescence, a major metabolic shift often occurs from oxidative phosphorylation to glycolysis and gluconeogenesis. We use the entry of Caenorhabditis elegans into the dauer larval stage, a developmentally arrested stage formed in response to harsh environmental conditions, as a model to study the global metabolic changes and underlying molecular mechanisms associated with growth to quiescence transition. Read More

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http://dx.doi.org/10.1186/s12915-020-0760-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081555PMC

Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans.

BMC Biol 2020 03 19;18(1):30. Epub 2020 Mar 19.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.

Background: Annotation of cell identity is an essential process in neuroscience that allows comparison of cells, including that of neural activities across different animals. In Caenorhabditis elegans, although unique identities have been assigned to all neurons, the number of annotatable neurons in an intact animal has been limited due to the lack of quantitative information on the location and identity of neurons.

Results: Here, we present a dataset that facilitates the annotation of neuronal identities, and demonstrate its application in a comprehensive analysis of whole-brain imaging. Read More

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http://dx.doi.org/10.1186/s12915-020-0745-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081613PMC

The role of T cell trafficking in CTLA-4 blockade-induced gut immunopathology.

BMC Biol 2020 03 17;18(1):29. Epub 2020 Mar 17.

Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Background: Immune checkpoint inhibitor (ICPI) can augment the anti-tumour response by blocking negative immunoregulators with monoclonal antibodies. The anti-cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) antibody is the first ICPI which has shown remarkable benefits in the clinical treatment of cancers. However, the increased activity of the immune system also causes some side effects called immune-related adverse events (irAEs). Read More

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http://dx.doi.org/10.1186/s12915-020-00765-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079427PMC

A heat-sensitive Osh protein controls PI4P polarity.

BMC Biol 2020 03 13;18(1):28. Epub 2020 Mar 13.

MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, United Kingdom.

Background: Phosphoinositide lipids provide spatial landmarks during polarized cell growth and migration. Yet how phosphoinositide gradients are oriented in response to extracellular cues and environmental conditions is not well understood. Here, we elucidate an unexpected mode of phosphatidylinositol 4-phosphate (PI4P) regulation in the control of polarized secretion. Read More

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http://dx.doi.org/10.1186/s12915-020-0758-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7071650PMC

Linked-read sequencing identifies abundant microinversions and introgression in the arboviral vector Aedes aegypti.

BMC Biol 2020 03 12;18(1):26. Epub 2020 Mar 12.

Harvard TH Chan School of Public Health, Boston, MA, USA.

Background: Aedes aegypti is the principal mosquito vector of Zika, dengue, and yellow fever viruses. Two subspecies of Ae. aegypti exhibit phenotypic divergence with regard to habitat, host preference, and vectorial capacity. Read More

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http://dx.doi.org/10.1186/s12915-020-0757-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7068900PMC

Performance analysis of novel toxin-antidote CRISPR gene drive systems.

BMC Biol 2020 03 12;18(1):27. Epub 2020 Mar 12.

Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA.

Background: CRISPR gene drive systems allow the rapid spread of a genetic construct throughout a population. Such systems promise novel strategies for the management of vector-borne diseases and invasive species by suppressing a target population or modifying it with a desired trait. However, current homing-type drives have two potential shortcomings. Read More

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http://dx.doi.org/10.1186/s12915-020-0761-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7068947PMC

Introducing our series: research synthesis and meta-research in biology.

BMC Biol 2020 03 5;18(1):20. Epub 2020 Mar 5.

Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Faculty of Health, Medicine, and Life Sciences, Maastricht University, 6200 MD, Maastricht, The Netherlands.

Research synthesis is the process of bringing together findings and attributes from different publications, for example, to give a more complete description of phenomena than is usually possible in a single work. We bring the Research Synthesis Series to BMC Biology to promote meta-analyses, other research syntheses including meta-research studies, and research synthesis methodologies in biology, facilitating their dissemination to broader communities. Read More

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http://dx.doi.org/10.1186/s12915-020-0755-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7057525PMC

Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells.

BMC Biol 2020 03 4;18(1):25. Epub 2020 Mar 4.

MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, Scotland.

Background: Thousands of mammalian promoters are defined by co-enrichment of the histone tail modifications H3K27me3 (repressive) and H3K4me3 (activating) and are thus termed bivalent. It was previously observed that bivalent genes in human ES cells (hESC) are frequent targets for hypermethylation in human cancers, and depletion of DNA methylation in mouse embryonic stem cells has a marked impact on H3K27me3 distribution at bivalent promoters. However, only a fraction of bivalent genes in stem cells are targets of hypermethylation in cancer, and it is currently unclear whether all bivalent promoters are equally sensitive to DNA hypomethylation and whether H3K4me3 levels play a role in the interplay between DNA methylation and H3K27me3. Read More

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http://dx.doi.org/10.1186/s12915-020-0752-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7057567PMC

The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome.

BMC Biol 2020 03 2;18(1):22. Epub 2020 Mar 2.

Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada.

Background: Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. Read More

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http://dx.doi.org/10.1186/s12915-020-0741-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7050145PMC

Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability.

BMC Biol 2020 03 2;18(1):24. Epub 2020 Mar 2.

Institute of Biomedicine of Valencia, IBV-CSIC, St. Jaume Roig 11, 46010, Valencia, Spain.

Background: Contaminant DNA is a well-known confounding factor in molecular biology and in genomic repositories. Strikingly, analysis workflows for whole-genome sequencing (WGS) data commonly do not account for errors potentially introduced by contamination, which could lead to the wrong assessment of allele frequency both in basic and clinical research.

Results: We used a taxonomic filter to remove contaminant reads from more than 4000 bacterial samples from 20 different studies and performed a comprehensive evaluation of the extent and impact of contaminant DNA in WGS. Read More

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http://dx.doi.org/10.1186/s12915-020-0748-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7053099PMC

Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids.

BMC Biol 2020 03 2;18(1):23. Epub 2020 Mar 2.

Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.

Background: The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifestyles, and particularly the transition from free-living to parasitic, likely require different metabolic capabilities. Read More

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http://dx.doi.org/10.1186/s12915-020-0754-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052976PMC

X-ray computed tomography in life sciences.

BMC Biol 2020 02 27;18(1):21. Epub 2020 Feb 27.

The Henry Royce Institute and School of Materials, The University of Manchester, Manchester, M13 9PL, UK.

Recent developments within micro-computed tomography (μCT) imaging have combined to extend our capacity to image tissue in three (3D) and four (4D) dimensions at micron and sub-micron spatial resolutions, opening the way for virtual histology, live cell imaging, subcellular imaging and correlative microscopy. Pivotal to this has been the development of methods to extend the contrast achievable for soft tissue. Herein, we review the new capabilities within the field of life sciences imaging, and consider how future developments in this field could further benefit the life sciences community. Read More

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http://dx.doi.org/10.1186/s12915-020-0753-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7045626PMC
February 2020

Ca mobilization-dependent reduction of the endoplasmic reticulum lumen is due to influx of cytosolic glutathione.

BMC Biol 2020 02 26;18(1):19. Epub 2020 Feb 26.

Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary.

Background: The lumen of the endoplasmic reticulum (ER) acts as a cellular Ca store and a site for oxidative protein folding, which is controlled by the reduced glutathione (GSH) and glutathione-disulfide (GSSG) redox pair. Although depletion of luminal Ca from the ER provokes a rapid and reversible shift towards a more reducing poise in the ER, the underlying molecular basis remains unclear.

Results: We found that Ca mobilization-dependent ER luminal reduction was sensitive to inhibition of GSH synthesis or dilution of cytosolic GSH by selective permeabilization of the plasma membrane. Read More

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http://dx.doi.org/10.1186/s12915-020-0749-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7043043PMC
February 2020

Unexpected cell type-dependent effects of autophagy on polyglutamine aggregation revealed by natural genetic variation in C. elegans.

BMC Biol 2020 02 24;18(1):18. Epub 2020 Feb 24.

Biology Department, Drexel University, Philadelphia, PA, 19104, USA.

Background: Monogenic protein aggregation diseases, in addition to cell selectivity, exhibit clinical variation in the age of onset and progression, driven in part by inter-individual genetic variation. While natural genetic variants may pinpoint plastic networks amenable to intervention, the mechanisms by which they impact individual susceptibility to proteotoxicity are still largely unknown.

Results: We have previously shown that natural variation modifies polyglutamine (polyQ) aggregation phenotypes in C. Read More

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http://dx.doi.org/10.1186/s12915-020-0750-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038566PMC
February 2020

Patterns of African and Asian admixture in the Afrikaner population of South Africa.

BMC Biol 2020 02 24;18(1):16. Epub 2020 Feb 24.

Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden.

Background: The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. Read More

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http://dx.doi.org/10.1186/s12915-020-0746-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038537PMC
February 2020

The tanning hormone, bursicon, does not act directly on the epidermis to tan the Drosophila exoskeleton.

BMC Biol 2020 02 19;18(1):17. Epub 2020 Feb 19.

Instituto de Neurociencia, Universidad de Valparaíso, Valparaiso, Chile.

Background: In insects, continuous growth requires the periodic replacement of the exoskeleton. Once the remains of the exoskeleton from the previous stage have been shed during ecdysis, the new one is rapidly sclerotized (hardened) and melanized (pigmented), a process collectively known as tanning. The rapid tanning that occurs after ecdysis is critical for insect survival, as it reduces desiccation, and gives the exoskeleton the rigidity needed to support the internal organs and to provide a solid anchor for the muscles. Read More

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http://dx.doi.org/10.1186/s12915-020-0742-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7029472PMC
February 2020

Membrane and synaptic defects leading to neurodegeneration in Adar mutant Drosophila are rescued by increased autophagy.

BMC Biol 2020 02 14;18(1):15. Epub 2020 Feb 14.

CEITEC Masaryk University, Kamenice 735/5, A35, CZ 62 500, Brno, Czech Republic.

Background: In fly brains, the Drosophila Adar (adenosine deaminase acting on RNA) enzyme edits hundreds of transcripts to generate edited isoforms of encoded proteins. Nearly all editing events are absent or less efficient in larvae but increase at metamorphosis; the larger number and higher levels of editing suggest editing is most required when the brain is most complex. This idea is consistent with the fact that Adar mutations affect the adult brain most dramatically. Read More

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http://dx.doi.org/10.1186/s12915-020-0747-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7020516PMC
February 2020

The quail genome: insights into social behaviour, seasonal biology and infectious disease response.

BMC Biol 2020 02 12;18(1):14. Epub 2020 Feb 12.

The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.

Background: The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research.

Results: We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. Read More

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http://dx.doi.org/10.1186/s12915-020-0743-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017630PMC
February 2020

The wild species genome ancestry of domestic chickens.

BMC Biol 2020 02 12;18(1):13. Epub 2020 Feb 12.

Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.

Background: Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. Read More

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http://dx.doi.org/10.1186/s12915-020-0738-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7014787PMC
February 2020

A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici.

BMC Biol 2020 02 11;18(1):12. Epub 2020 Feb 11.

Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.

Background: The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. Read More

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http://dx.doi.org/10.1186/s12915-020-0744-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7014611PMC
February 2020

The round goby genome provides insights into mechanisms that may facilitate biological invasions.

BMC Biol 2020 01 28;18(1):11. Epub 2020 Jan 28.

Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.

Background: The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. Read More

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http://dx.doi.org/10.1186/s12915-019-0731-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988351PMC
January 2020