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    1 OF 25

    Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus).
    BMC Biol 2017 Nov 16;15(1):110. Epub 2017 Nov 16.
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
    Background: The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications. Here, we present an iterative approach to hybrid de novo genome assembly that incorporates datasets stemming from multiple genomic technologies and methods. We used this approach to improve the gray mouse lemur (Microcebus murinus) genome from early draft status to a near chromosome-scale assembly. Read More

    Targeting protein quality control pathways in breast cancer.
    BMC Biol 2017 Nov 16;15(1):109. Epub 2017 Nov 16.
    Department of Biological Sciences, University of Pittsburgh, A320 Langley Hall, 4249 Fifth Ave, Pittsburgh, PA, 15260, USA.
    The efficient production, folding, and secretion of proteins is critical for cancer cell survival. However, cancer cells thrive under stress conditions that damage proteins, so many cancer cells overexpress molecular chaperones that facilitate protein folding and target misfolded proteins for degradation via the ubiquitin-proteasome or autophagy pathway. Stress response pathway induction is also important for cancer cell survival. Read More

    A yeast two-hybrid system for the screening and characterization of small-molecule inhibitors of protein-protein interactions identifies a novel putative Mdm2-binding site in p53.
    BMC Biol 2017 Nov 9;15(1):108. Epub 2017 Nov 9.
    Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore.
    Background: Protein-protein interactions (PPIs) are fundamental to the growth and survival of cells and serve as excellent targets to develop inhibitors of biological processes such as host-pathogen interactions and cancer cell proliferation. However, isolation of PPI inhibitors is extremely challenging. While several in vitro assays to screen for PPI inhibitors are available, they are often expensive, cumbersome, and require large amounts of purified protein. Read More

    Divide and conquer? Size adjustment with allometry and intermediate outcomes.
    BMC Biol 2017 Nov 9;15(1):107. Epub 2017 Nov 9.
    Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
    Many trait measurements are size-dependent, and while we often divide these traits by size before fitting statistical models to control for the effect of size, this approach does not account for allometry and the intermediate outcome problem. We describe these problems and outline potential solutions. Read More

    RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination.
    BMC Biol 2017 Nov 8;15(1):105. Epub 2017 Nov 8.
    Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK.
    Background: TRIM25 is a novel RNA-binding protein and a member of the Tripartite Motif (TRIM) family of E3 ubiquitin ligases, which plays a pivotal role in the innate immune response. However, there is scarce knowledge about its RNA-related roles in cell biology. Furthermore, its RNA-binding domain has not been characterized. Read More

    Erv1 of Arabidopsis thaliana can directly oxidize mitochondrial intermembrane space proteins in the absence of redox-active Mia40.
    BMC Biol 2017 Nov 8;15(1):106. Epub 2017 Nov 8.
    Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany.
    Background: Many proteins of the mitochondrial intermembrane space (IMS) contain structural disulfide bonds formed by the mitochondrial disulfide relay. In fungi and animals, the sulfhydryl oxidase Erv1 'generates' disulfide bonds that are passed on to the oxidoreductase Mia40, which oxidizes substrate proteins. A different structural organization of plant Erv1 proteins compared to that of animal and fungal orthologs was proposed to explain its inability to complement the corresponding yeast mutant. Read More

    Characterization of a thalamic nucleus mediating habenula responses to changes in ambient illumination.
    BMC Biol 2017 Oct 31;15(1):104. Epub 2017 Oct 31.
    Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore.
    Background: Neural activity in the vertebrate habenula is affected by ambient illumination. The nucleus that links photoreceptor activity with the habenula is not well characterized. Here, we describe the location, inputs and potential function of this nucleus in larval zebrafish. Read More

    Optical inhibition of larval zebrafish behaviour with anion channelrhodopsins.
    BMC Biol 2017 Nov 3;15(1):103. Epub 2017 Nov 3.
    Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
    Background: Optical silencing of activity provides a way to test the necessity of neurons in behaviour. Two light-gated anion channels, GtACR1 and GtACR2, have recently been shown to potently inhibit activity in cultured mammalian neurons and in Drosophila. Here, we test the usefulness of these channels in larval zebrafish, using spontaneous coiling behaviour as the assay. Read More

    Membrane dynamics and organelle biogenesis-lipid pipelines and vesicular carriers.
    BMC Biol 2017 Oct 31;15(1):102. Epub 2017 Oct 31.
    Montreal Neurological Institute, McGill University, 3801 University Avenue, Montreal, Quebec, H3A 2B4, Canada.
    Discoveries spanning several decades have pointed to vital membrane lipid trafficking pathways involving both vesicular and non-vesicular carriers. But the relative contributions for distinct membrane delivery pathways in cell growth and organelle biogenesis continue to be a puzzle. This is because lipids flow from many sources and across many paths via transport vesicles, non-vesicular transfer proteins, and dynamic interactions between organelles at membrane contact sites. Read More

    MultiBac: from protein complex structures to synthetic viral nanosystems.
    BMC Biol 2017 Oct 30;15(1):99. Epub 2017 Oct 30.
    The School of Biochemistry and Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, Tankard's Close, Bristol, BS8 1TD, UK.
    The MultiBac baculovirus/insect cell expression vector system was conceived as a user-friendly, modular tool-kit for producing multiprotein complexes for structural biology applications. MultiBac has allowed the structure and function of many molecular machines to be elucidated, including previously inaccessible high-value drug targets. More recently, MultiBac developments have shifted to customized baculoviral genomes that are tailored for a range of applications, including synthesizing artificial proteins by genetic code expansion. Read More

    Digital tissue and what it may reveal about the brain.
    BMC Biol 2017 Oct 30;15(1):101. Epub 2017 Oct 30.
    Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA.
    Imaging as a means of scientific data storage has evolved rapidly over the past century from hand drawings, to photography, to digital images. Only recently can sufficiently large datasets be acquired, stored, and processed such that tissue digitization can actually reveal more than direct observation of tissue. One field where this transformation is occurring is connectomics: the mapping of neural connections in large volumes of digitized brain tissue. Read More

    Sequence-based prediction of permissive stretches for internal protein tagging and knockdown.
    BMC Biol 2017 Oct 30;15(1):100. Epub 2017 Oct 30.
    Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
    Background: Internal tagging of proteins by inserting small functional peptides into surface accessible permissive sites has proven to be an indispensable tool for basic and applied science. Permissive sites are typically identified by transposon mutagenesis on a case-by-case basis, limiting scalability and their exploitation as a system-wide protein engineering tool.

    Methods: We developed an apporach for predicting permissive stretches (PSs) in proteins based on the identification of length-variable regions (regions containing indels) in homologous proteins. Read More

    Detecting positive selection in the genome.
    BMC Biol 2017 Oct 30;15(1):98. Epub 2017 Oct 30.
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK.
    Population geneticists have long sought to understand the contribution of natural selection to molecular evolution. A variety of approaches have been proposed that use population genetics theory to quantify the rate and strength of positive selection acting in a species' genome. In this review we discuss methods that use patterns of between-species nucleotide divergence and within-species diversity to estimate positive selection parameters from population genomic data. Read More

    An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook.
    BMC Biol 2017 Oct 27;15(1):97. Epub 2017 Oct 27.
    Trans-membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, Okinawa, 904-0495, Japan.
    Background: In a macro-molecular complex, any minor change may prove detrimental. For a supra-molecular nano-machine like the bacterial flagellum, which consists of several distinct parts with specific characteristics, stability is important. During the rotation of the bacterial flagellar motor, which is located in the membrane, the flagella rotate at speeds between 200 and 2000 rpm, depending on the bacterial species. Read More

    Sexual conflict explains the extraordinary diversity of mechanisms regulating mitochondrial inheritance.
    BMC Biol 2017 Oct 26;15(1):94. Epub 2017 Oct 26.
    Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, Gower Street, London, WC1E 6BT, UK.
    Background: Mitochondria are predominantly inherited from the maternal gamete, even in unicellular organisms. Yet an extraordinary array of mechanisms enforce uniparental inheritance, which implies shifting selection pressures and multiple origins.

    Results: We consider how this high turnover in mechanisms controlling uniparental inheritance arises using a novel evolutionary model in which control of mitochondrial transmission occurs either during spermatogenesis (by paternal nuclear genes) or at/after fertilization (by maternal nuclear genes). Read More

    Lipid metabolism fattens up hedgehog signaling.
    BMC Biol 2017 Oct 26;15(1):95. Epub 2017 Oct 26.
    Nuffield Department of Clinical Neurosciences (NDCN), Level 6, West Wing, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK.
    Signaling pathways direct organogenesis, often through concentration-dependent effects on cells. The hedgehog pathway enables cells to sense and respond to hedgehog ligands, of which the best studied is sonic hedgehog. Hedgehog signaling is essential for development, proliferation, and stem cell maintenance, and it is a driver of certain cancers. Read More

    Spatial phylogenetics of the native California flora.
    BMC Biol 2017 Oct 26;15(1):96. Epub 2017 Oct 26.
    University and Jepson Herbaria and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, CA, 94720, USA.
    Background: California is a world floristic biodiversity hotspot where the terms neo- and paleo-endemism were first applied. Using spatial phylogenetics, it is now possible to evaluate biodiversity from an evolutionary standpoint, including discovering significant areas of neo- and paleo-endemism, by combining spatial information from museum collections and DNA-based phylogenies. Here we used a distributional dataset of 1. Read More

    Plant hormone transporters: what we know and what we would like to know.
    BMC Biol 2017 Oct 25;15(1):93. Epub 2017 Oct 25.
    Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland.
    Hormone transporters are crucial for plant hormone action, which is underlined by severe developmental and physiological impacts caused by their loss-of-function mutations. Here, we summarize recent knowledge on the individual roles of plant hormone transporters in local and long-distance transport. Our inventory reveals that many hormones are transported by members of distinct transporter classes, with an apparent dominance of the ATP-binding cassette (ABC) family and of the Nitrate transport1/Peptide transporter family (NPF). Read More

    Q&A: Cellular near death experiences-what is anastasis?
    BMC Biol 2017 Oct 24;15(1):92. Epub 2017 Oct 24.
    Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, USA.
    Apoptosis is a form of programmed cell death that is carried out by proteolytic enzymes called caspases. Executioner caspase activity causes cells to shrink, bleb, and disintegrate into apoptotic bodies and has been considered a point of no return for apoptotic cells. However, relatively recent work has shown that cells can survive transient apoptotic stimuli, even after executioner caspase activation. Read More

    Q&A: What are pathogens, and what have they done to and for us?
    BMC Biol 2017 Oct 19;15(1):91. Epub 2017 Oct 19.
    UCL Genetics Institute (UGI), Darwin Building, Gower Street, London, WC1E 6BT, UK.
    Microbes are found on us, within us and around us. They inhabit virtually every environment on the planet and the bacteria carried by an average human, mostly in their gut, outnumber human cells. The vast majority of microbes are harmless to us, and many play essential roles in plant, animal and human health. Read More

    Role of PCNA and RFC in promoting Mus81-complex activity.
    BMC Biol 2017 Oct 2;15(1):90. Epub 2017 Oct 2.
    Department of Biology, Masaryk University, Kamenice 5/A7, CZ-62500, Brno, Czech Republic.
    Background: Proper DNA replication is essential for faithful transmission of the genome. However, replication stress has serious impact on the integrity of the cell, leading to stalling or collapse of replication forks, and has been determined as a driving force of carcinogenesis. Mus81-Mms4 complex is a structure-specific endonuclease previously shown to be involved in processing of aberrant replication intermediates and promotes POLD3-dependent DNA synthesis via break-induced replication. Read More

    Human evolution: the non-coding revolution.
    BMC Biol 2017 Oct 2;15(1):89. Epub 2017 Oct 2.
    Gladstone Institutes, San Francisco, CA, 94158, USA.
    What made us human? Gene expression changes clearly played a significant part in human evolution, but pinpointing the causal regulatory mutations is hard. Comparative genomics enabled the identification of human accelerated regions (HARs) and other human-specific genome sequences. The major challenge in the past decade has been to link diverged sequences to uniquely human biology. Read More

    A Drosophila female pheromone elicits species-specific long-range attraction via an olfactory channel with dual specificity for sex and food.
    BMC Biol 2017 Sep 29;15(1):88. Epub 2017 Sep 29.
    Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, 23053, Alnarp, Sweden.
    Background: Mate finding and recognition in animals evolves during niche adaptation and involves social signals and habitat cues. Drosophila melanogaster and related species are known to be attracted to fermenting fruit for feeding and egg-laying, which poses the question of whether species-specific fly odours contribute to long-range premating communication.

    Results: We have discovered an olfactory channel in D. Read More

    Q&A: How can advances in tissue clearing and optogenetics contribute to our understanding of normal and diseased biology?
    BMC Biol 2017 Sep 25;15(1):87. Epub 2017 Sep 25.
    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
    Mammalian organs comprise a variety of cells that interact with each other and have distinct biological roles. Access to evaluate and perturb intact biological systems at the cellular and molecular levels is essential to fully understand their functioning in normal and diseased conditions, yet technical limitations have constrained most research to small pieces of tissue. Tissue clearing and optogenetics can help overcome this hurdle: tissue clearing affords optical interrogation of whole organs at the molecular level, and optogenetics enables the scalable control and measurement of cellular activity with light. Read More

    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

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