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    1186 results match your criteria BMC Biology [Journal]

    1 OF 24

    Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination.
    BMC Biol 2017 Sep 19;15(1):86. Epub 2017 Sep 19.
    Iwate Biotechnology Research Center, Kitakami, Japan.
    Background: Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected "orphan" crop that would benefit from crop improvement efforts. Read More

    Q&A: Morphological insights into evolution.
    BMC Biol 2017 Sep 15;15(1):83. Epub 2017 Sep 15.
    Department of Craniofacial Development and Stem Cell Biology, King's College London, Floor 27 Guy's Tower, Guy's Hospital, London Bridge, London, SE1 9RT, UK.
    In this question and answer article we discuss how evolution shapes morphology (the shape and pattern of our bodies) but also how learning about morphology, and specifically how that morphology arises during development, can shed light on mechanisms that might allow change during evolution. For this we concentrate on recent findings from our lab on how the middle ear has formed in mammals. Read More

    Blind free-living kiwi offer a unique window into the ecology and evolution of vertebrate vision.
    BMC Biol 2017 Sep 15;15(1):85. Epub 2017 Sep 15.
    From the Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA.
    The first report of multiple, blind, wild birds in good health suggests vision is not necessary for the survival of kiwi. Read More

    Antibiotic resistance: it's bad, but why isn't it worse?
    BMC Biol 2017 Sep 15;15(1):84. Epub 2017 Sep 15.
    Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 4K1, Canada.
    Antibiotic natural products are ancient and so is resistance. Consequently, environmental bacteria harbor numerous and varied antibiotic resistance elements. Nevertheless, despite long histories of antibiotic production and exposure, environmental bacteria are not resistant to all known antibiotics. Read More

    Q&A: The brain under a mesoscope: the forest and the trees.
    BMC Biol 2017 Sep 14;15(1):82. Epub 2017 Sep 14.
    Janelia Research Campus, Ashburn, VA, 20147, USA.
    Neurons relevant to a particular behavior are often widely dispersed across the brain. To record activity in groups of individual neurons that might be distributed across large distances, neuroscientists and optical engineers have been developing a new type of microscope called a mesoscope. Mesoscopes have high spatial resolution and a large field of view. Read More

    How driving endonuclease genes can be used to combat pests and disease vectors.
    BMC Biol 2017 Sep 11;15(1):81. Epub 2017 Sep 11.
    Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, SL5 7PY, UK.
    Driving endonuclease genes (DEGs) spread through a population by a non-Mendelian mechanism. In a heterozygote, the protein encoded by a DEG causes a double-strand break in the homologous chromosome opposite to where its gene is inserted and when the break is repaired using the homologue as a template the DEG heterozygote is converted to a homozygote. Some DEGs occur naturally while several classes of endonucleases can be engineered to spread in this way, with CRISPR-Cas9 based systems being particularly flexible. Read More

    SKIP controls flowering time via the alternative splicing of SEF pre-mRNA in Arabidopsis.
    BMC Biol 2017 Sep 11;15(1):80. Epub 2017 Sep 11.
    Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China.
    Background: Similar to other eukaryotes, splicing is emerging as an important process affecting development and stress tolerance in plants. Ski-interacting protein (SKIP), a splicing factor, is essential for circadian clock function and abiotic stress tolerance; however, the mechanisms whereby it regulates flowering time are unknown.

    Results: In this study, we found that SKIP is required for the splicing of serrated leaves and early flowering (SEF) pre-messenger RNA (mRNA), which encodes a component of the ATP-dependent SWR1 chromatin remodeling complex (SWR1-C). Read More

    Thioester-containing proteins regulate the Toll pathway and play a role in Drosophila defence against microbial pathogens and parasitoid wasps.
    BMC Biol 2017 Sep 5;15(1):79. Epub 2017 Sep 5.
    Global Health Institute, School of Life Sciences, École Polytechnique Fédérale Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
    Background: Members of the thioester-containing protein (TEP) family contribute to host defence in both insects and mammals. However, their role in the immune response of Drosophila is elusive. In this study, we address the role of TEPs in Drosophila immunity by generating a mutant fly line, referred to as TEPq (Δ) , lacking the four immune-inducible TEPs, TEP1, 2, 3 and 4. Read More

    Dosage-sensitive genes in evolution and disease.
    BMC Biol 2017 Sep 1;15(1):78. Epub 2017 Sep 1.
    Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland.
    For a subset of genes in our genome a change in gene dosage, by duplication or deletion, causes a phenotypic effect. These dosage-sensitive genes may confer an advantage upon copy number change, but more typically they are associated with disease, including heart disease, cancers and neuropsychiatric disorders. This gene copy number sensitivity creates characteristic evolutionary constraints that can serve as a diagnostic to identify dosage-sensitive genes. Read More

    Blob-ology and biology of cryo-EM: an interview with Helen Saibil.
    BMC Biol 2017 Aug 31;15(1):77. Epub 2017 Aug 31.
    Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, UK.
    Helen Saibil is Bernal Professor of Structural Biology at Birkbeck, University of London. After undergraduate work at McGill University, Canada, Helen moved to London for her PhD at Kings College. After stints at CEA Grenoble and the University of Oxford, she moved to Birkbeck where her lab studies the operation of macromolecular machinery-including molecular chaperones, protein folding/misfolding, and host cell interactions with pathogens. Read More

    Q&A: Where did the Neanderthals go?
    BMC Biol 2017 Sep 1;15(1):73. Epub 2017 Sep 1.
    Department of Integrative Biology, University of California, Berkeley, California, USA.
    Genomic evidence has demonstrated that humans and Neanderthals interbred. Today, the genomes of most individuals outside Africa contain 2-3% Neanderthal DNA. However, it is still hotly debated why the Neanderthals went extinct and if humans contributed to the Neanderthal extinction. Read More

    Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution.
    BMC Biol 2017 Aug 31;15(1):74. Epub 2017 Aug 31.
    Department of Plant & Wildlife Sciences, Brigham Young University, 5144 LSB, Provo, UT, 84602, USA.
    Background: Amaranth (Amaranthus hypochondriacus) was a food staple among the ancient civilizations of Central and South America that has recently received increased attention due to the high nutritional value of the seeds, with the potential to help alleviate malnutrition and food security concerns, particularly in arid and semiarid regions of the developing world. Here, we present a reference-quality assembly of the amaranth genome which will assist the agronomic development of the species.

    Results: Utilizing single-molecule, real-time sequencing (Pacific Biosciences) and chromatin interaction mapping (Hi-C) to close assembly gaps and scaffold contigs, respectively, we improved our previously reported Illumina-based assembly to produce a chromosome-scale assembly with a scaffold N50 of 24. Read More

    Ribosome signatures aid bacterial translation initiation site identification.
    BMC Biol 2017 Aug 30;15(1):76. Epub 2017 Aug 30.
    Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, 5020, Norway.
    Background: While methods for annotation of genes are increasingly reliable, the exact identification of translation initiation sites remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information, developing a robust method for start site identification is crucial. Ribosome profiling reads show distinct patterns of read length distributions around translation initiation sites. Read More

    A widespread family of polymorphic toxins encoded by temperate phages.
    BMC Biol 2017 Aug 29;15(1):75. Epub 2017 Aug 29.
    Microbial Evolutionary Genomics, Institut Pasteur, Paris, 75015, France.
    Background: Polymorphic toxins (PTs) are multi-domain bacterial exotoxins belonging to distinct families that share common features in terms of domain organization. PTs are found in all major bacterial clades, including many toxic effectors of type V and type VI secretion systems. PTs modulate the dynamics of microbial communities by killing or inhibiting the growth of bacterial competitors lacking protective immunity proteins. Read More

    Distinct unfolded protein responses mitigate or mediate effects of nonlethal deprivation of C. elegans sleep in different tissues.
    BMC Biol 2017 Aug 28;15(1):67. Epub 2017 Aug 28.
    Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.
    Background: Disrupting sleep during development leads to lasting deficits in chordates and arthropods. To address lasting impacts of sleep deprivation in Caenorhabditis elegans, we established a nonlethal deprivation protocol.

    Results: Deprivation triggered protective insulin-like signaling and two unfolded protein responses (UPRs): the mitochondrial (UPR(mt)) and the endoplasmic reticulum (UPR(ER)) responses. Read More

    Erratum to: Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule".
    BMC Biol 2017 Aug 18;15(1):72. Epub 2017 Aug 18.
    Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore.

    Biological function in the twilight zone of sequence conservation.
    BMC Biol 2017 Aug 16;15(1):71. Epub 2017 Aug 16.
    MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
    Strong DNA conservation among divergent species is an indicator of enduring functionality. With weaker sequence conservation we enter a vast 'twilight zone' in which sequence subject to transient or lower constraint cannot be distinguished easily from neutrally evolving, non-functional sequence. Twilight zone functional sequence is illuminated instead by principles of selective constraint and positive selection using genomic data acquired from within a species' population. Read More

    Multiple essential functions of Plasmodium falciparum actin-1 during malaria blood-stage development.
    BMC Biol 2017 Aug 15;15(1):70. Epub 2017 Aug 15.
    Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow, G12 8TA, UK.
    Background: The phylum Apicomplexa includes intracellular parasites causing immense global disease burden, the deadliest of them being the human malaria parasite Plasmodium falciparum, which invades and replicates within erythrocytes. The cytoskeletal protein actin is well conserved within apicomplexans but divergent from mammalian actins, and was primarily reported to function during host cell invasion. However, novel invasion mechanisms have been described for several apicomplexans, and specific functions of the acto-myosin system are being reinvestigated. Read More

    Examining non-LTR retrotransposons in the context of the evolving primate brain.
    BMC Biol 2017 Aug 11;15(1):68. Epub 2017 Aug 11.
    Salk Institute for Biological Studies, La Jolla, CA, 92037-1002, USA.
    Researchers have long sought to understand the genetic basis of the cognitive differences between primates, with particular focus on the human brain. Although all mutational types have worked in concert with evolutionary forces to generate the current human brain, in this review we will explore the impact of mobile elements, specifically non-LTR retrotransposons. Non-LTR retrotransposons have contributed coding and regulatory sequences to the genome throughout evolution. Read More

    The house spider genome reveals an ancient whole-genome duplication during arachnid evolution.
    BMC Biol 2017 Jul 31;15(1):62. Epub 2017 Jul 31.
    Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
    Background: The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. Read More

    Silicanin-1 is a conserved diatom membrane protein involved in silica biomineralization.
    BMC Biol 2017 Jul 24;15(1):65. Epub 2017 Jul 24.
    B CUBE Center for Molecular Bioengineering, CMCB, TU Dresden, Arnoldstrasse 18, 01307, Dresden, Germany.
    Background: Biological mineral formation (biomineralization) proceeds in specialized compartments often bounded by a lipid bilayer membrane. Currently, the role of membranes in biomineralization is hardly understood.

    Results: Investigating biomineralization of SiO2 (silica) in diatoms we identified Silicanin-1 (Sin1) as a conserved diatom membrane protein present in silica deposition vesicles (SDVs) of Thalassiosira pseudonana. Read More

    Q&A: What is human language, when did it evolve and why should we care?
    BMC Biol 2017 Jul 24;15(1):64. Epub 2017 Jul 24.
    School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK.
    Human language is unique among all forms of animal communication. It is unlikely that any other species, including our close genetic cousins the Neanderthals, ever had language, and so-called sign 'language' in Great Apes is nothing like human language. Language evolution shares many features with biological evolution, and this has made it useful for tracing recent human history and for studying how culture evolves among groups of people with related languages. Read More

    Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule".
    BMC Biol 2017 Jul 24;15(1):66. Epub 2017 Jul 24.
    Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Singapore.
    Background: Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane's hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein's biological functions.

    Results: With statistics derived from a large body of protein sequences, we demonstrate that, in addition to the positive charge preference at the cytoplasmic inside (positive-inside rule), negatively charged residues preferentially occur or are even enriched at the non-cytoplasmic flank or, at least, they are suppressed at the cytoplasmic flank (negative-not-inside/negative-outside (NNI/NO) rule). Read More

    C. elegans SUP-46, an HNRNPM family RNA-binding protein that prevents paternally-mediated epigenetic sterility.
    BMC Biol 2017 Jul 17;15(1):61. Epub 2017 Jul 17.
    Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
    Background: In addition to DNA, gametes contribute epigenetic information in the form of histones and non-coding RNA. Epigenetic programs often respond to stressful environmental conditions and provide a heritable history of ancestral stress that allows for adaptation and propagation of the species. In the nematode C. Read More

    Peto's Paradox: how has evolution solved the problem of cancer prevention?
    BMC Biol 2017 Jul 13;15(1):60. Epub 2017 Jul 13.
    Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 727 E. Tyler St., Tempe, AZ, 85287-5001, USA.
    The risk of developing cancer should theoretically increase with both the number of cells and the lifespan of an organism. However, gigantic animals do not get more cancer than humans, suggesting that super-human cancer suppression has evolved numerous times across the tree of life. This is the essence and promise of Peto's Paradox. Read More

    Life behind the wall: sensing mechanical cues in plants.
    BMC Biol 2017 Jul 11;15(1):59. Epub 2017 Jul 11.
    Department of Biology, Washington University in Saint Louis, Mailbox 1137, Saint Louis, MO, 63130, USA.
    There is increasing evidence that all cells sense mechanical forces in order to perform their functions. In animals, mechanotransduction has been studied during the establishment of cell polarity, fate, and division in single cells, and increasingly is studied in the context of a multicellular tissue. What about plant systems? Our goal in this review is to summarize what is known about the perception of mechanical cues in plants, and to provide a brief comparison with animals. Read More

    Q&A: using Patch-seq to profile single cells.
    BMC Biol 2017 Jul 6;15(1):58. Epub 2017 Jul 6.
    Department of Neuroscience, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA.
    Individual neurons vary widely in terms of their gene expression, morphology, and electrophysiological properties. While many techniques exist to study single-cell variability along one or two of these dimensions, very few techniques can assess all three features for a single cell. We recently developed Patch-seq, which combines whole-cell patch clamp recording with single-cell RNA-sequencing and immunohistochemistry to comprehensively profile the transcriptomic, morphologic, and physiologic features of individual neurons. Read More

    Nanobodies raised against monomeric ɑ-synuclein inhibit fibril formation and destabilize toxic oligomeric species.
    BMC Biol 2017 Jul 3;15(1):57. Epub 2017 Jul 3.
    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
    Background: The aggregation of the protein ɑ-synuclein (ɑS) underlies a range of increasingly common neurodegenerative disorders including Parkinson's disease. One widely explored therapeutic strategy for these conditions is the use of antibodies to target aggregated ɑS, although a detailed molecular-level mechanism of the action of such species remains elusive. Here, we characterize ɑS aggregation in vitro in the presence of two ɑS-specific single-domain antibodies (nanobodies), NbSyn2 and NbSyn87, which bind to the highly accessible C-terminal region of ɑS. Read More

    Olfactory coding from the periphery to higher brain centers in the Drosophila brain.
    BMC Biol 2017 Jun 30;15(1):56. Epub 2017 Jun 30.
    Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany.
    Background: Odor information is processed through multiple receptor-glomerular channels in the first order olfactory center, the antennal lobe (AL), then reformatted into higher brain centers and eventually perceived by the fly. To reveal the logic of olfaction, it is fundamental to map odor representations from the glomerular channels into higher brain centers.

    Results: We characterize odor response profiles of AL projection neurons (PNs) originating from 31 glomeruli using whole cell patch-clamp recordings in Drosophila melanogaster. Read More

    Mov10 suppresses retroelements and regulates neuronal development and function in the developing brain.
    BMC Biol 2017 Jun 29;15(1):54. Epub 2017 Jun 29.
    Neuroscience Program, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA.
    Background: Moloney leukemia virus 10 (Mov10) is an RNA helicase that mediates access of the RNA-induced silencing complex to messenger RNAs (mRNAs). Until now, its role as an RNA helicase and as a regulator of retrotransposons has been characterized exclusively in cell lines. We investigated the role of Mov10 in the mouse brain by examining its expression over development and attempting to create a Mov10 knockout mouse. Read More

    Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues.
    BMC Biol 2017 Jun 29;15(1):52. Epub 2017 Jun 29.
    School of Biology, University of Leeds, Leeds, LS2 9JT, UK.
    Background: Strigolactones (SLs) are a class of plant hormones that control many aspects of plant growth. The SL signalling mechanism is homologous to that of karrikins (KARs), smoke-derived compounds that stimulate seed germination. In angiosperms, the SL receptor is an α/β-hydrolase known as DWARF14 (D14); its close homologue, KARRIKIN INSENSITIVE2 (KAI2), functions as a KAR receptor and likely recognizes an uncharacterized, endogenous signal ('KL'). Read More

    Tissue macrophages: heterogeneity and functions.
    BMC Biol 2017 Jun 29;15(1):53. Epub 2017 Jun 29.
    Nuffield Department of Primary Care Health Sciences, University of Oxford, Woodstock Road, Oxford, OX2 6GG, UK.
    Macrophages are present in all vertebrate tissues, from mid-gestation throughout life, constituting a widely dispersed organ system. They promote homeostasis by responding to internal and external changes within the body, not only as phagocytes in defence against microbes and in clearance of dead and senescent cells, but also through trophic, regulatory and repair functions. In this review, we describe macrophage phenotypic heterogeneity in different tissue environments, drawing particular attention to organ-specific functions. Read More

    Non-model model organisms.
    BMC Biol 2017 Jun 29;15(1):55. Epub 2017 Jun 29.
    Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
    Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future. Read More

    Organelle acidification: an ancient cellular leak detector.
    BMC Biol 2017 Jun 26;15(1):51. Epub 2017 Jun 26.
    Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India.
    Intracellular membrane-bounded organelles of eukaryotic cells transiently contact the extracellular environment during endocytosis and secretion. Such contacts must be precisely timed to prevent leakage of cargo. I argue that early eukaryotes evolved organelle acidification as a way to detect and prevent leakage. Read More

    Q&A: Expansion microscopy.
    BMC Biol 2017 Jun 19;15(1):50. Epub 2017 Jun 19.
    Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.
    Expansion microscopy (ExM) is a recently invented technology that uses swellable charged polymers, synthesized densely and with appropriate topology throughout a preserved biological specimen, to physically magnify the specimen 100-fold in volume, or more, in an isotropic fashion. ExM enables nanoscale resolution imaging of preserved samples on inexpensive, fast, conventional microscopes. How does ExM work? How good is its performance? How do you get going on using it? In this Q&A, we provide the answers to these and other questions about this new and rapidly spreading toolbox. Read More

    Dynamics of transcriptional (re)-programming of syncytial nuclei in developing muscles.
    BMC Biol 2017 Jun 9;15(1):48. Epub 2017 Jun 9.
    Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France.
    Background: A stereotyped array of body wall muscles enables precision and stereotypy of animal movements. In Drosophila, each syncytial muscle forms via fusion of one founder cell (FC) with multiple fusion competent myoblasts (FCMs). The specific morphology of each muscle, i. Read More

    Open questions: completing the parts list and finding the integrating signals.
    BMC Biol 2017 Jun 8;15(1):47. Epub 2017 Jun 8.
    Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
    One of the great revelations of post-genomic biology has been the extent to which essential functions and mechanisms are conserved across vast phylogenetic distances. Because of this, we can look to the fruit fly for answers to pressing open questions on the unknown functions of genes and the mechanisms of their physiological integration. Read More

    Matriptase zymogen supports epithelial development, homeostasis and regeneration.
    BMC Biol 2017 Jun 1;15(1):46. Epub 2017 Jun 1.
    Proteases and Tissue Remodeling Section, Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, Room 320, Bethesda, MD, 20892, USA.
    Background: Matriptase is a membrane serine protease essential for epithelial development, homeostasis, and regeneration, as well as a central orchestrator of pathogenic pericellular signaling in the context of inflammatory and proliferative diseases. Matriptase is an unusual protease in that its zymogen displays measurable enzymatic activity.

    Results: Here, we used gain and loss of function genetics to investigate the possible biological functions of zymogen matriptase. Read More

    Differential DARC/ACKR1 expression distinguishes venular from non-venular endothelial cells in murine tissues.
    BMC Biol 2017 May 19;15(1):45. Epub 2017 May 19.
    Department of Microbiology and Immunobiology & HMS Center for Immune Imaging, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
    Background: Intravascular leukocyte recruitment in most vertebrate tissues is restricted to postcapillary and collecting venules, whereas capillaries and arterioles usually support little or no leukocyte adhesion. This segmental restriction is thought to be mediated by endothelial, rather than hemodynamic, differences. The underlying mechanisms are largely unknown, in part because effective tools to distinguish, isolate, and analyze venular endothelial cells (V-ECs) and non-venular endothelial cells (NV-ECs) have been unavailable. Read More

    Cell fixation and preservation for droplet-based single-cell transcriptomics.
    BMC Biol 2017 May 19;15(1):44. Epub 2017 May 19.
    Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
    Background: Recent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not altered by stress or ageing. Other challenges are rare cells that need to be collected over several days or samples prepared at different times or locations. Read More

    Open Questions: We don't really know anything, do we? Open questions in sensory biology.
    BMC Biol 2017 May 17;15(1):43. Epub 2017 May 17.
    Biology Department, Duke University, Durham, NC, USA.
    Senses connect organisms to both the world and to each other, yet there is much we don't know about them. Using examples drawn primarily from the author's subfield of vision research, this article discusses five major open questions. Read More

    OptiMouse: a comprehensive open source program for reliable detection and analysis of mouse body and nose positions.
    BMC Biol 2017 May 15;15(1):41. Epub 2017 May 15.
    Department of Medical Neurobiology, The Hebrew University, Faculty of Medicine, Jerusalem, Israel.
    Background: Accurate determination of mouse positions from video data is crucial for various types of behavioral analyses. While detection of body positions is straightforward, the correct identification of nose positions, usually more informative, is far more challenging. The difficulty is largely due to variability in mouse postures across frames. Read More

    Knowing where the nose is.
    BMC Biol 2017 May 15;15(1):42. Epub 2017 May 15.
    Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA.
    Improvements in imaging technology and the development of powerful machine learning algorithms are revolutionizing the study of animal behavior in the laboratory. These innovations promise to reveal both global and local features of action relevant to understanding how the brain functions. A study in BMC Biology describes one such tool called OptiMouse, which is an open source platform that uses video to capture key features of mouse behavior, including information relevant to olfactory investigation. Read More

    Optogenetic interrogation reveals separable G-protein-dependent and -independent signalling linking G-protein-coupled receptors to the circadian oscillator.
    BMC Biol 2017 May 15;15(1):40. Epub 2017 May 15.
    Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.
    Background: Endogenous circadian oscillators distributed across the mammalian body are synchronised among themselves and with external time via a variety of signalling molecules, some of which interact with G-protein-coupled receptors (GPCRs). GPCRs can regulate cell physiology via pathways originating with heterotrimeric G-proteins or β-arrestins. We applied an optogenetic approach to determine the contribution of these two signalling modes on circadian phase. Read More

    Heterosis as a consequence of regulatory incompatibility.
    BMC Biol 2017 May 11;15(1):38. Epub 2017 May 11.
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
    Background: The merging of genomes in inter-specific hybrids can result in novel phenotypes, including increased growth rate and biomass yield, a phenomenon known as heterosis. Heterosis is typically viewed as the opposite of hybrid incompatibility. In this view, the superior performance of the hybrid is attributed to heterozygote combinations that compensate for deleterious mutations accumulating in each individual genome, or lead to new, over-dominating interactions with improved performance. Read More

    Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors.
    BMC Biol 2017 May 11;15(1):39. Epub 2017 May 11.
    Sainsbury Laboratory Cambridge University (SLCU), Cambridge, UK.
    Background: Plant-pathogenic oomycetes are responsible for economically important losses in crops worldwide. Phytophthora palmivora, a tropical relative of the potato late blight pathogen, causes rotting diseases in many tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus. Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. Read More

    Can a biologist fix a smartphone?-Just hack it!
    BMC Biol 2017 May 8;15(1):37. Epub 2017 May 8.
    The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
    Biological systems integrate multiscale processes and networks and are, therefore, viewed as difficult to dissect. However, because of the clear-cut separation between the software code (the information encoded in the genome sequence) and hardware (organism), genome editors can operate as software engineers to hack biological systems without any particularly deep understanding of the complexity of the systems. Read More

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