1,296 results match your criteria BMC Biology [Journal]


Determinants of the cytosolic turnover of mitochondrial intermembrane space proteins.

BMC Biol 2018 Jun 22;16(1):66. Epub 2018 Jun 22.

Centre of New Technologies, University of Warsaw, Warsaw, Poland.

Background: The proteome of mitochondria comprises mostly proteins that originate as precursors in the cytosol. Before import into the organelle, such proteins are exposed to cytosolic quality control mechanisms. Multiple lines of evidence indicate a significant contribution of the major cytosolic protein degradation machinery, the ubiquitin-proteasome system, to the quality control of mitochondrial proteins. Read More

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Proteasomal degradation competes with Mia40-mediated import into mitochondria.

BMC Biol 2018 Jun 22;16(1):63. Epub 2018 Jun 22.

Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany.

Tandem fluorescent protein timers are elegant tools to determine proteolytic stabilities of cytosolic proteins with high spatial and temporal resolution. In a new study published in BMC Biology, Kowalski et al. fused timers to precursors of proteins of the mitochondrial intermembrane space and found that they are under surveillance of the ubiquitin-proteasome system. Read More

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Application of long single-stranded DNA donors in genome editing: generation and validation of mouse mutants.

BMC Biol 2018 Jun 21;16(1):70. Epub 2018 Jun 21.

The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon, OX11 0RD, UK.

Background: Recent advances in clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing have led to the use of long single-stranded DNA (lssDNA) molecules for generating conditional mutations. However, there is still limited available data on the efficiency and reliability of this method.

Results: We generated conditional mouse alleles using lssDNA donor templates and performed extensive characterization of the resulting mutations. Read More

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June 2018
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Comparative analysis of single-stranded DNA donors to generate conditional null mouse alleles.

BMC Biol 2018 Jun 21;16(1):69. Epub 2018 Jun 21.

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX, 77030, USA.

Background: The International Mouse Phenotyping Consortium is generating null allele mice for every protein-coding gene in the genome and characterizing these mice to identify gene-phenotype associations. While CRISPR/Cas9-mediated null allele production in mice is highly efficient, generation of conditional alleles has proven to be more difficult. To test the feasibility of using CRISPR/Cas9 gene editing to generate conditional knockout mice for this large-scale resource, we employed Cas9-initiated homology-driven repair (HDR) with short and long single stranded oligodeoxynucleotides (ssODNs and lssDNAs). Read More

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Ultrastructural analysis of mitotic Drosophila S2 cells identifies distinctive microtubule and intracellular membrane behaviors.

BMC Biol 2018 Jun 15;16(1):68. Epub 2018 Jun 15.

Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia.

Background: S2 cells are one of the most widely used Drosophila melanogaster cell lines. A series of studies has shown that they are particularly suitable for RNAi-based screens aimed at the dissection of cellular pathways, including those controlling cell shape and motility, cell metabolism, and host-pathogen interactions. In addition, RNAi in S2 cells has been successfully used to identify many new mitotic genes that are conserved in the higher eukaryotes, and for the analysis of several aspects of the mitotic process. Read More

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June 2018
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A bacterial route for folic acid supplementation.

BMC Biol 2018 Jun 15;16(1):67. Epub 2018 Jun 15.

Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK.

Background: To prevent folate deficiencies, many countries supplement various foodstuffs with folic acid. This compound is a synthetic oxidised folate that differs from naturally occurring reduced folates in its metabolism and uptake. Notably, safety reviews of folic acid supplementation have not considered interactions with gut bacteria. Read More

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June 2018
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Glucocorticoid-dependent REDD1 expression reduces muscle metabolism to enable adaptation under energetic stress.

BMC Biol 2018 Jun 12;16(1):65. Epub 2018 Jun 12.

DMEM, Univ. Montpellier, INRA, Montpellier, France.

Background: Skeletal muscle atrophy is a common feature of numerous chronic pathologies and is correlated with patient mortality. The REDD1 protein is currently recognized as a negative regulator of muscle mass through inhibition of the Akt/mTORC1 signaling pathway. REDD1 expression is notably induced following glucocorticoid secretion, which is a component of energy stress responses. Read More

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Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types.

BMC Biol 2018 Jun 5;16(1):62. Epub 2018 Jun 5.

Division of Engineering in Medicine, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA.

Background: Single-cell genomic methods now provide unprecedented resolution for characterizing the component cell types and states of tissues such as the epithelial subsets of the gastrointestinal tract. Nevertheless, functional studies of these subsets at scale require faithful in vitro models of identified in vivo biology. While intestinal organoids have been invaluable in providing mechanistic insights in vitro, the extent to which organoid-derived cell types recapitulate their in vivo counterparts remains formally untested, with no systematic approach for improving model fidelity. Read More

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Using in vivo oxidation status of one- and two-component redox relays to determine HO levels linked to signaling and toxicity.

BMC Biol 2018 Jun 1;16(1):61. Epub 2018 Jun 1.

Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/ Dr. Aiguader 88, 08003, Barcelona, Spain.

Background: Hydrogen peroxide (HO) is generated as a by-product of metabolic reactions during oxygen use by aerobic organisms, and can be toxic or participate in signaling processes. Cells, therefore, need to be able to sense and respond to HO in an appropriate manner. This is often accomplished through thiol switches: Cysteine residues in proteins that can act as sensors, and which are both scarce and finely tuned. Read More

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Dehydration triggers ecdysone-mediated recognition-protein priming and elevated anti-bacterial immune responses in Drosophila Malpighian tubule renal cells.

BMC Biol 2018 May 31;16(1):60. Epub 2018 May 31.

Division of Biology and Medicine, Brown University, Providence, RI, USA.

Background: Drosophila is a powerful model for the study of factors modulating innate immunity. This study examines the effect of water-loss dehydration on innate immune responsiveness in the Drosophila renal system (Malpighian tubules; MTs), and how this leads to elevated host defense and contributes to immunosenescence.

Results: A short period of desiccation-elevated peptidoglycan recognition protein-LC (PGRP-LC) expression in MTs, increased antimicrobial peptide (AMP) gene induction, and protected animals from bacterial infection. Read More

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Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography.

BMC Biol 2018 May 31;16(1):59. Epub 2018 May 31.

Physics Department, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA.

Background: Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases.

Results: Here, we demonstrate a general method for capturing enzyme catalysis "in action" by mix-and-inject serial crystallography (MISC). Read More

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Entering an era of dynamic structural biology….

Authors:
Allen M Orville

BMC Biol 2018 May 31;16(1):55. Epub 2018 May 31.

Diamond Light Source, Research Complex at Harwell, and University of Oxford, Oxfordshire, OX11 0DE, UK.

A recent paper in BMC Biology presents a general method for mix-and-inject serial crystallography, to facilitate the visualization of enzyme intermediates via time-resolved serial femtosecond crystallography (tr-SFX). They apply their method to resolve in near atomic detail the cleavage and inactivation of the antibiotic ceftriaxone by a β-lactamase enzyme from Mycobacterium tuberculosis. Their work demonstrates the general applicability of time-resolved crystallography, from which dynamic structures, at atomic resolution, can be obtained. Read More

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Light sheet theta microscopy for rapid high-resolution imaging of large biological samples.

BMC Biol 2018 May 29;16(1):57. Epub 2018 May 29.

Department of Biological Sciences, Columbia University, New York, NY, USA.

Background: Advances in tissue clearing and molecular labeling methods are enabling unprecedented optical access to large intact biological systems. These developments fuel the need for high-speed microscopy approaches to image large samples quantitatively and at high resolution. While light sheet microscopy (LSM), with its high planar imaging speed and low photo-bleaching, can be effective, scaling up to larger imaging volumes has been hindered by the use of orthogonal light sheet illumination. Read More

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Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory.

BMC Biol 2018 May 29;16(1):56. Epub 2018 May 29.

Institut d'Histoire et de Philosophie des Sciences et des Techniques (CNRS / Paris I Sorbonne), F-75006, Paris, France.

The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology. Read More

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Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum.

BMC Biol 2018 May 18;16(1):54. Epub 2018 May 18.

Department of Biology, University of Rochester, Rochester, New York, 14627, USA.

Background: Trichogrammatids are minute parasitoid wasps that develop within other insect eggs. They are less than half a millimeter long, smaller than some protozoans. The Trichogrammatidae are one of the earliest branching families of Chalcidoidea: a diverse superfamily of approximately half a million species of parasitoid wasps, proposed to have evolved from a miniaturized ancestor. Read More

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May 2018
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Caring for parents: an evolutionary rationale.

BMC Biol 2018 May 15;16(1):53. Epub 2018 May 15.

Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049, Pullach/Munich, Germany.

Background: The evolutionary roots of human moral behavior are a key precondition to understanding human nature. Investigations usually start with a social dilemma and end up with a norm that can provide some insight into the origin of morality. We take the opposite direction by investigating whether the cultural norm that promotes helping parents and which is respected in different variants across cultures and is codified in several religions can spread through Darwinian competition. Read More

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Small RNA profiling of low biomass samples: identification and removal of contaminants.

BMC Biol 2018 May 14;16(1):52. Epub 2018 May 14.

Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg.

Background: Sequencing-based analyses of low-biomass samples are known to be prone to misinterpretation due to the potential presence of contaminating molecules derived from laboratory reagents and environments. DNA contamination has been previously reported, yet contamination with RNA is usually considered to be very unlikely due to its inherent instability. Small RNAs (sRNAs) identified in tissues and bodily fluids, such as blood plasma, have implications for physiology and pathology, and therefore the potential to act as disease biomarkers. Read More

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Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3.

BMC Biol 2018 May 7;16(1):47. Epub 2018 May 7.

Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital and Science for Life Laboratory, 17176, Stockholm, Sweden.

Background: Regulatory T cells (Tregs) expressing the transcription factor FOXP3 are crucial mediators of self-tolerance, preventing autoimmune diseases but possibly hampering tumor rejection. Clinical manipulation of Tregs is of great interest, and first-in-man trials of Treg transfer have achieved promising outcomes. Yet, the mechanisms governing induced Treg (iTreg) differentiation and the regulation of FOXP3 are incompletely understood. Read More

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Early life diet conditions the molecular response to post-weaning protein restriction in the mouse.

BMC Biol 2018 May 2;16(1):51. Epub 2018 May 2.

The Blizard Institute, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.

Background: Environmental influences fluctuate throughout the life course of an organism. It is therefore important to understand how the timing of exposure impacts molecular responses. Herein, we examine the responses of two key molecular markers of dietary stress, namely variant-specific methylation at ribosomal DNA (rDNA) and small RNA distribution, including tRNA fragments, in a mouse model of protein restriction (PR) with exposure at pre- and/or post-weaning. Read More

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Green monomeric photosensitizing fluorescent protein for photo-inducible protein inactivation and cell ablation.

BMC Biol 2018 Apr 30;16(1):50. Epub 2018 Apr 30.

Graduate School of Engineering, Osaka University, 1-3 Yamadaoka Suita, Osaka, 565-0871, Japan.

Background: Photosensitizing fluorescent proteins, which generate reactive oxygen species (ROS) upon light irradiation, are useful for spatiotemporal protein inactivation and cell ablation. They give us clues about protein function, intracellular signaling pathways and intercellular interactions. Since ROS generation of a photosensitizer is specifically controlled by certain excitation wavelengths, utilizing colour variants of photosensitizing protein would allow multi-spatiotemporal control of inactivation. Read More

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Position-specific intron retention is mediated by the histone methyltransferase SDG725.

BMC Biol 2018 Apr 30;16(1):44. Epub 2018 Apr 30.

State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.

Background: Intron retention (IR), the most prevalent alternative splicing form in plants, plays a critical role in gene expression during plant development and stress response. However, the molecular mechanisms underlying IR regulation remain largely unknown.

Results: Knockdown of SDG725, a histone H3 lysine 36 (H3K36)-specific methyltransferase in rice, leads to alterations of IR in more than 4700 genes. Read More

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InsPR-SEC5 interaction on phagosomes modulates innate immunity to Candida albicans by promoting cytosolic Ca elevation and TBK1 activity.

BMC Biol 2018 Apr 27;16(1):46. Epub 2018 Apr 27.

NHFPC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, 2140 Xie Tu Road, Shanghai, 200032, China.

Background: Candida albicans (C. albicans) invasion triggers antifungal innate immunity, and the elevation of cytoplasmic Ca levels via the inositol 1,4,5-trisphosphate receptor (InsPR) plays a critical role in this process. However, the molecular pathways linking the InsPR-mediated increase in Ca and immune responses remain elusive. Read More

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Individual odour signatures that mice learn are shaped by involatile major urinary proteins (MUPs).

BMC Biol 2018 Apr 27;16(1):48. Epub 2018 Apr 27.

Mammalian Behaviour & Evolution Group, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK.

Background: Reliable recognition of individuals requires phenotypic identity signatures that are both individually distinctive and appropriately stable over time. Individual-specific vocalisations or visual patterning are well documented among birds and some mammals, whilst odours play a key role in social recognition across many vertebrates and invertebrates. Less well understood, though, is whether individuals are recognised through variation in cues that arise incidentally from a wide variety of genetic and non-genetic differences between individuals, or whether animals evolve distinctive polymorphic signals to advertise identity reliably. Read More

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April 2018
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Phylogenomics resolves the evolutionary chronicle of our squirting closest relatives.

Authors:
Gonzalo Giribet

BMC Biol 2018 Apr 27;16(1):49. Epub 2018 Apr 27.

Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.

A recent paper in BMC Biology has resolved the family relationships of sea squirts, one of our closest invertebrate relatives, by using a large phylogenomic data set derived from available genomes and newly generated transcriptomes. The work confirms previous ideas that ascidians (the sea squirts) are not monophyletic, as they include some pelagic jelly-like relatives, and proposes a chronogram for a group that has been difficult to resolve due to their accelerated genome evolution.See research article: https://bmcbiol. Read More

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Identification of a neuronal population in the telencephalon essential for fear conditioning in zebrafish.

BMC Biol 2018 Apr 25;16(1):45. Epub 2018 Apr 25.

Division of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.

Background: Fear conditioning is a form of learning essential for animal survival and used as a behavioral paradigm to study the mechanisms of learning and memory. In mammals, the amygdala plays a crucial role in fear conditioning. In teleost, the medial zone of the dorsal telencephalon (Dm) has been postulated to be a homolog of the mammalian amygdala by anatomical and ablation studies, showing a role in conditioned avoidance response. Read More

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Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation.

BMC Biol 2018 Apr 18;16(1):43. Epub 2018 Apr 18.

Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France.

Background: Oomycetes are a group of filamentous eukaryotic microorganisms that have colonized all terrestrial and oceanic ecosystems, and they include prominent plant pathogens. The Aphanomyces genus is unique in its ability to infect both plant and animal species, and as such exemplifies oomycete versatility in adapting to different hosts and environments. Dissecting the underpinnings of oomycete diversity provides insights into their specificity and pathogenic mechanisms. Read More

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April 2018
4 Reads

A G-type opsin mediates the shadow reflex in the annelid Platynereis dumerilii.

BMC Biol 2018 Apr 18;16(1):41. Epub 2018 Apr 18.

Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria.

Background: The presence of photoreceptive molecules outside the eye is widespread among animals, yet their functions in the periphery are less well understood. Marine organisms, such as annelid worms, exhibit a 'shadow reflex', a defensive withdrawal behaviour triggered by a decrease in illumination. Herein, we examine the cellular and molecular underpinnings of this response, identifying a role for a photoreceptor molecule of the G-opsin class in the shadow response of the marine bristle worm Platynereis dumerilii. Read More

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April 2018
2 Reads

Developing accurate prediction systems for the terrestrial environment.

BMC Biol 2018 Apr 18;16(1):42. Epub 2018 Apr 18.

Fenner School of Environment and Society, The Australian National University, Canberra, ACT 2601, Australia.

In recent decades, meteorologists have made remarkable progress in predicting the weather, thereby saving lives and considerable sums of money. However, we are way behind when it comes to predicting the effects of environmental change on ecosystems, even when we are ourselves the agent of such change. Given the substantial environmental problems facing our living planet, and the need to tackle these in an ecologically responsible and cost-effective way, we should aspire to develop terrestrial environmental prediction systems that reach the levels of accuracy and precision which characterize weather prediction systems. Read More

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April 2018
1 Read

Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes.

BMC Biol 2018 Apr 16;16(1):40. Epub 2018 Apr 16.

Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Hyogo, 650-0047, Japan.

Background: Conventionally, comparison among amniotes - birds, mammals, and reptiles - has often been approached through analyses of mammals and, for comparison, birds. However, birds are morphologically and physiologically derived and, moreover, some parts of their genomes are recognized as difficult to sequence and/or assemble and are thus missing in genome assemblies. Therefore, sequencing the genomes of reptiles would aid comparative studies on amniotes by providing more comprehensive coverage to help understand the molecular mechanisms underpinning evolutionary changes. Read More

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April 2018
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A phylogenomic framework and timescale for comparative studies of tunicates.

BMC Biol 2018 Apr 13;16(1):39. Epub 2018 Apr 13.

ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.

Background: Tunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood, and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolutionary relationships and provide a first estimate of their divergence times, we used a transcriptomic approach to build a phylogenomic dataset including all major tunicate lineages, consisting of 258 evolutionarily conserved orthologous genes from representative species. Read More

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April 2018
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Q&A: How do gene regulatory networks control environmental responses in plants?

BMC Biol 2018 Apr 11;16(1):38. Epub 2018 Apr 11.

Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA.

A gene regulatory network (GRN) describes the hierarchical relationship between transcription factors, associated proteins, and their target genes. Studying GRNs allows us to understand how a plant's genotype and environment are integrated to regulate downstream physiological responses. Current efforts in plants have focused on defining the GRNs that regulate functions such as development and stress response and have been performed primarily in genetically tractable model plant species such as Arabidopsis thaliana. Read More

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April 2018
1 Read

From top to bottom: Cell polarity in Hedgehog and Wnt trafficking.

BMC Biol 2018 Apr 10;16(1):37. Epub 2018 Apr 10.

Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.

Spatial organization of membrane domains within cells and cells within tissues is key to the development of organisms and the maintenance of adult tissue. Cell polarization is crucial for correct cell-cell signalling, which, in turn, promotes cell differentiation and tissue patterning. However, the mechanisms linking internal cell polarity to intercellular signalling are just beginning to be unravelled. Read More

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April 2018
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The integrated stress response regulates BMP signalling through effects on translation.

BMC Biol 2018 Apr 3;16(1):34. Epub 2018 Apr 3.

Cambridge Institute for Medical Research (CIMR), University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.

Background: Developmental pathways must be responsive to the environment. Phosphorylation of eIF2α enables a family of stress-sensing kinases to trigger the integrated stress response (ISR), which has pro-survival and developmental consequences. Bone morphogenetic proteins (BMPs) regulate multiple developmental processes in organisms from insects to mammals. Read More

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April 2018
1 Read

Combined flow cytometry and high-throughput image analysis for the study of essential genes in Caenorhabditis elegans.

BMC Biol 2018 Mar 29;16(1):36. Epub 2018 Mar 29.

Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville, Spain.

Background: Advances in automated image-based microscopy platforms coupled with high-throughput liquid workflows have facilitated the design of large-scale screens utilising multicellular model organisms such as Caenorhabditis elegans to identify genetic interactions, therapeutic drugs or disease modifiers. However, the analysis of essential genes has lagged behind because lethal or sterile mutations pose a bottleneck for high-throughput approaches, and a systematic way to analyse genetic interactions of essential genes in multicellular organisms has been lacking.

Results: In C. Read More

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March 2018
1 Read

Correction to: A sophisticated, differentiated Golgi in the ancestor of eukaryotes.

BMC Biol 2018 Mar 28;16(1):35. Epub 2018 Mar 28.

Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 5-31 Medical Sciences Building, Edmonton, Alberta, T6G 2H7, Canada.

Upon publication of the original article, Barlow et al. [1], the authors noticed that Fig. 4b contained an inaccuracy when additional data is taken into account. Read More

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March 2018
1 Read

Downregulation of the NLRP3 inflammasome by adiponectin rescues Duchenne muscular dystrophy.

BMC Biol 2018 Mar 20;16(1):33. Epub 2018 Mar 20.

Endocrinology, Diabetes and Nutrition Unit, Institute of Experimental and Clinical Research, Medical Sector, Catholic University of Louvain, 1200, Brussels, Belgium.

Background: The hormone adiponectin (ApN) exerts powerful anti-inflammatory effects on skeletal muscle and can reverse devastating myopathies, like Duchenne muscular dystrophy (DMD), where inflammation exacerbates disease progression. The NLRP3 inflammasome plays a key role in the inflammation process, and its aberrant activation leads to several inflammatory or immune diseases. Here we investigated the expression of the NLRP inflammasome in skeletal muscle and its contribution to DMD. Read More

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March 2018
1 Read

Structural insights into the inactivation of CRISPR-Cas systems by diverse anti-CRISPR proteins.

BMC Biol 2018 Mar 19;16(1):32. Epub 2018 Mar 19.

HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.

A molecular arms race is progressively being unveiled between prokaryotes and viruses. Prokaryotes utilize CRISPR-mediated adaptive immune systems to kill the invading phages and mobile genetic elements, and in turn, the viruses evolve diverse anti-CRISPR proteins to fight back. The structures of several anti-CRISPR proteins have now been reported, and here we discuss their structural features, with a particular emphasis on topology, to discover their similarities and differences. Read More

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March 2018
1 Read

How structural elements evolving from bacterial to human SLC6 transporters enabled new functional properties.

BMC Biol 2018 Mar 14;16(1):31. Epub 2018 Mar 14.

Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA.

Background: Much of the structure-based mechanistic understandings of the function of SLC6A neurotransmitter transporters emerged from the study of their bacterial LeuT-fold homologs. It has become evident, however, that structural differences such as the long N- and C-termini of the eukaryotic neurotransmitter transporters are involved in an expanded set of functional properties to the eukaryotic transporters. These functional properties are not shared by the bacterial homologs, which lack the structural elements that appeared later in evolution. Read More

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March 2018
6 Reads

Formation of chimeric genes with essential functions at the origin of eukaryotes.

BMC Biol 2018 Mar 13;16(1):30. Epub 2018 Mar 13.

Sorbonne Universités, UPMC Univ Paris 06, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005, Paris, France.

Background: Eukaryotes evolved from the symbiotic association of at least two prokaryotic partners, and a good deal is known about the timings, mechanisms, and dynamics of these evolutionary steps. Recently, it was shown that a new class of nuclear genes, symbiogenetic genes (S-genes), was formed concomitant with endosymbiosis and the subsequent evolution of eukaryotic photosynthetic lineages. Understanding their origins and contributions to eukaryogenesis would provide insights into the ways in which cellular complexity has evolved. Read More

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March 2018
2 Reads

A sophisticated, differentiated Golgi in the ancestor of eukaryotes.

BMC Biol 2018 Mar 7;16(1):27. Epub 2018 Mar 7.

Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 5-31 Medical Sciences Building, Edmonton, Alberta, T6G 2H7, Canada.

Background: The Golgi apparatus is a central meeting point for the endocytic and exocytic systems in eukaryotic cells, and the organelle's dysfunction results in human disease. Its characteristic morphology of multiple differentiated compartments organized into stacked flattened cisternae is one of the most recognizable features of modern eukaryotic cells, and yet how this is maintained is not well understood. The Golgi is also an ancient aspect of eukaryotes, but the extent and nature of its complexity in the ancestor of eukaryotes is unclear. Read More

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March 2018
1 Read

An RNAi screen of Rho signalling networks identifies RhoH as a regulator of Rac1 in prostate cancer cell migration.

BMC Biol 2018 Mar 6;16(1):29. Epub 2018 Mar 6.

Randall Centre of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK.

Background: Cell migration is essential for development and tissue repair, but it also contributes to disease. Rho GTPases regulate cell migration, but a comprehensive analysis of how each Rho signalling component affects migration has not been carried out.

Results: Through an RNA interference screen, and using a prostate cancer cell line, we find that approximately 25% of Rho network components alter migration. Read More

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March 2018
1 Read

A software tool 'CroCo' detects pervasive cross-species contamination in next generation sequencing data.

BMC Biol 2018 Mar 5;16(1):28. Epub 2018 Mar 5.

Centre for Life's Origins and Evolution, Department of Genetics Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.

Background: Multiple RNA samples are frequently processed together and often mixed before multiplex sequencing in the same sequencing run. While different samples can be separated post sequencing using sample barcodes, the possibility of cross contamination between biological samples from different species that have been processed or sequenced in parallel has the potential to be extremely deleterious for downstream analyses.

Results: We present CroCo, a software package for identifying and removing such cross contaminants from assembled transcriptomes. Read More

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March 2018
1 Read

Factors driving metabolic diversity in the budding yeast subphylum.

BMC Biol 2018 Mar 2;16(1):26. Epub 2018 Mar 2.

Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA.

Background: Associations between traits are prevalent in nature, occurring across a diverse range of taxa and traits. Individual traits may co-evolve with one other, and these correlations can be driven by factors intrinsic or extrinsic to an organism. However, few studies, especially in microbes, have simultaneously investigated both across a broad taxonomic range. Read More

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March 2018
1 Read

Cross-communication between G and G in a G-protein-coupled receptor heterotetramer guided by a receptor C-terminal domain.

BMC Biol 2018 Feb 28;16(1):24. Epub 2018 Feb 28.

Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.

Background: G-protein-coupled receptor (GPCR) heteromeric complexes have distinct properties from homomeric GPCRs, giving rise to new receptor functionalities. Adenosine receptors (AR or AR) can form AR-AR heteromers (A-AHet), and their activation leads to canonical G-protein-dependent (adenylate cyclase mediated) and -independent (β-arrestin mediated) signaling. Adenosine has different affinities for AR and AR, allowing the heteromeric receptor to detect its concentration by integrating the downstream G- and G-dependent signals. Read More

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February 2018
4 Reads

An adaptable chromosome preparation methodology for use in invertebrate research organisms.

BMC Biol 2018 Feb 26;16(1):25. Epub 2018 Feb 26.

Stowers Institute for Medical Research, Kansas City, MO, USA.

Background: The ability to efficiently visualize and manipulate chromosomes is fundamental to understanding the genome architecture of organisms. Conventional chromosome preparation protocols developed for mammalian cells and those relying on species-specific conditions are not suitable for many invertebrates. Hence, a simple and inexpensive chromosome preparation protocol, adaptable to multiple invertebrate species, is needed. Read More

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February 2018
1 Read

Measuring behavior across scales.

Authors:
Gordon J Berman

BMC Biol 2018 Feb 23;16(1):23. Epub 2018 Feb 23.

Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, 30322, GA, USA.

The need for high-throughput, precise, and meaningful methods for measuring behavior has been amplified by our recent successes in measuring and manipulating neural circuitry. The largest challenges associated with moving in this direction, however, are not technical but are instead conceptual: what numbers should one put on the movements an animal is performing (or not performing)? In this review, I will describe how theoretical and data analytical ideas are interfacing with recently-developed computational and experimental methodologies to answer these questions across a variety of contexts, length scales, and time scales. I will attempt to highlight commonalities between approaches and areas where further advances are necessary to place behavior on the same quantitative footing as other scientific fields. Read More

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February 2018
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Nothing in cancer makes sense except….

Authors:
Mel Greaves

BMC Biol 2018 Feb 21;16(1):22. Epub 2018 Feb 21.

Centre for Evolution and Cancer, The Institute of Cancer Research, Brookes Lawley Building, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK.

Paraphrasing Dobzhansky's famous dictum, I discuss how interrogating cancer through the lens of evolution has transformed our understanding of its development, causality and treatment resistance. The emerging picture of cancer captures its extensive diversity and therapeutic resilience, highlighting the need for more innovative approaches to control. Read More

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February 2018
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Hormonal and environmental signals guiding stomatal development.

BMC Biol 2018 Feb 20;16(1):21. Epub 2018 Feb 20.

Howard Hughes Medical Institute and Department of Biology, University of Washington, Seattle, WA, 98195, USA.

Stomata are pores on plant epidermis that facilitate gas exchange and water evaporation between plants and the environment. Given the central role of stomata in photosynthesis and water-use efficiency, two vital events for plant growth, stomatal development is tightly controlled by a diverse range of signals. A family of peptide hormones regulates stomatal patterning and differentiation. Read More

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February 2018
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A phosphoinositide map at the shoot apical meristem in Arabidopsis thaliana.

BMC Biol 2018 Feb 7;16(1):20. Epub 2018 Feb 7.

Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRA, CNRS, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France.

Background: In plants, the shoot apical meristem (SAM) has two main functions, involving the production of all aerial organs on the one hand and self-maintenance on the other, allowing the production of organs during the entire post-embryonic life of the plant. Transcription factors, microRNA, hormones, peptides and forces have been involved in meristem function. Whereas phosphatidylinositol phosphates (PIPs) have been involved in almost all biological functions, including stem cell maintenance and organogenesis in animals, the processes in meristem biology to which PIPs contribute still need to be delineated. Read More

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February 2018
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Marked differences in tight junction composition and macromolecular permeability among different intestinal cell types.

BMC Biol 2018 Feb 1;16(1):19. Epub 2018 Feb 1.

Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.

Background: Mammalian small intestinal tight junctions (TJ) link epithelial cells to one another and function as a permselective barrier, strictly modulating the passage of ions and macromolecules through the pore and leak pathways, respectively, thereby preventing the absorption of harmful compounds and microbes while allowing regulated transport of nutrients and electrolytes. Small intestinal epithelial permeability is ascribed primarily to the properties of TJs between adjoining enterocytes (ENTs), because there is almost no information on TJ composition and the paracellular permeability of nonenterocyte cell types that constitute a small but significant fraction of the intestinal epithelia.

Results: Here we directed murine intestinal crypts to form specialized organoids highly enriched in intestinal stem cells (ISCs), absorptive ENTs, secretory goblet cells, or Paneth cells. Read More

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February 2018
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