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BMC Biology

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https://www.readbyqxmd.com/read/29145861/hybrid-de-novo-genome-assembly-and-centromere-characterization-of-the-gray-mouse-lemur-microcebus-murinus
#1
Peter A Larsen, R Alan Harris, Yue Liu, Shwetha C Murali, C Ryan Campbell, Adam D Brown, Beth A Sullivan, Jennifer Shelton, Susan J Brown, Muthuswamy Raveendran, Olga Dudchenko, Ido Machol, Neva C Durand, Muhammad S Shamim, Erez Lieberman Aiden, Donna M Muzny, Richard A Gibbs, Anne D Yoder, Jeffrey Rogers, Kim C Worley
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...
November 16, 2017: BMC Biology
https://www.readbyqxmd.com/read/29145850/targeting-protein-quality-control-pathways-in-breast-cancer
#2
REVIEW
Sara Sannino, Jeffrey L Brodsky
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. Indeed, validated targets for anti-cancer treatments include molecular chaperones, components of the unfolded protein response, the ubiquitin-proteasome system, and autophagy...
November 16, 2017: BMC Biology
https://www.readbyqxmd.com/read/29121928/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
#3
Jin Huei Wong, Mohammad Alfatah, Mei Fang Sin, Hong May Sim, Chandra S Verma, David P Lane, Prakash Arumugam
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. In contrast, limited in vivo assays are available to screen for small-molecule inhibitors of PPI...
November 9, 2017: BMC Biology
https://www.readbyqxmd.com/read/29121927/divide-and-conquer-size-adjustment-with-allometry-and-intermediate-outcomes
#4
Shinichi Nakagawa, Fonti Kar, Rose E O'Dea, Joel L Pick, Malgorzata Lagisz
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.
November 9, 2017: BMC Biology
https://www.readbyqxmd.com/read/29117863/rna-binding-activity-of-trim25-is-mediated-by-its-pry-spry-domain-and-is-required-for-ubiquitination
#5
Nila Roy Choudhury, Gregory Heikel, Maryia Trubitsyna, Peter Kubik, Jakub Stanislaw Nowak, Shaun Webb, Sander Granneman, Christos Spanos, Juri Rappsilber, Alfredo Castello, Gracjan Michlewski
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. RESULTS: Here, we reveal that the RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain, which we postulate to be a novel RNA-binding domain...
November 8, 2017: BMC Biology
https://www.readbyqxmd.com/read/29117860/erv1-of-arabidopsis-thaliana-can-directly-oxidize-mitochondrial-intermembrane-space-proteins-in-the-absence-of-redox-active-mia40
#6
Valentina Peleh, Flavien Zannini, Sandra Backes, Nicolas Rouhier, Johannes M Herrmann
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...
November 8, 2017: BMC Biology
https://www.readbyqxmd.com/read/29100505/optical-inhibition-of-larval-zebrafish-behaviour-with-anion-channelrhodopsins
#7
Gadisti Aisha Mohamed, Ruey-Kuang Cheng, Joses Ho, Seetha Krishnan, Farhan Mohammad, Adam Claridge-Chang, Suresh Jesuthasan
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. RESULTS: When the GtACRs were expressed in spinal neurons of embryonic zebrafish and actuated with blue or green light, spontaneous movement was inhibited...
November 3, 2017: BMC Biology
https://www.readbyqxmd.com/read/29100543/characterization-of-a-thalamic-nucleus-mediating-habenula-responses-to-changes-in-ambient-illumination
#8
Ruey-Kuang Cheng, Seetha Krishnan, Qian Lin, Caroline Kibat, Suresh Jesuthasan
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. RESULTS: High-speed calcium imaging shows that light ON and OFF both evoke a rapid response in the dorsal left neuropil of the habenula, indicating preferential targeting of this neuropil by afferents conveying information about ambient illumination...
October 31, 2017: BMC Biology
https://www.readbyqxmd.com/read/29089042/membrane-dynamics-and-organelle-biogenesis-lipid-pipelines-and-vesicular-carriers
#9
EDITORIAL
Christopher J Stefan, William S Trimble, Sergio Grinstein, Guillaume Drin, Karin Reinisch, Pietro De Camilli, Sarah Cohen, Alex M Valm, Jennifer Lippincott-Schwartz, Tim P Levine, David B Iaea, Frederick R Maxfield, Clare E Futter, Emily R Eden, Delphine Judith, Alexander R van Vliet, Patrizia Agostinis, Sharon A Tooze, Ayumu Sugiura, Heidi M McBride
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. This forum presents our latest understanding, appreciation, and queries regarding the lipid transport mechanisms necessary to drive membrane expansion during organelle biogenesis and cell growth...
October 31, 2017: BMC Biology
https://www.readbyqxmd.com/read/29084535/multibac-from-protein-complex-structures-to-synthetic-viral-nanosystems
#10
REVIEW
Martin Pelosse, Hannah Crocker, Barbara Gorda, Paul Lemaire, Jens Rauch, Imre Berger
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...
October 30, 2017: BMC Biology
https://www.readbyqxmd.com/read/29084528/digital-tissue-and-what-it-may-reveal-about-the-brain
#11
REVIEW
Josh L Morgan, Jeff W Lichtman
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.
October 30, 2017: BMC Biology
https://www.readbyqxmd.com/read/29084520/sequence-based-prediction-of-permissive-stretches-for-internal-protein-tagging-and-knockdown
#12
Sabine Oesterle, Tania Michelle Roberts, Lukas Andreas Widmer, Harun Mustafa, Sven Panke, Sonja Billerbeck
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...
October 30, 2017: BMC Biology
https://www.readbyqxmd.com/read/29084517/detecting-positive-selection-in-the-genome
#13
REVIEW
Tom R Booker, Benjamin C Jackson, Peter D Keightley
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. We also discuss recently proposed methods to detect positive selection from a population's haplotype structure...
October 30, 2017: BMC Biology
https://www.readbyqxmd.com/read/29078764/an-intrinsically-disordered-linker-controlling-the-formation-and-the-stability-of-the-bacterial-flagellar-hook
#14
Clive S Barker, Irina V Meshcheryakova, Alla S Kostyukova, Peter L Freddolino, Fadel A Samatey
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. The hook substructure of the bacterial flagellum acts as a universal joint connecting the motor to the flagellar filament...
October 27, 2017: BMC Biology
https://www.readbyqxmd.com/read/29073898/sexual-conflict-explains-the-extraordinary-diversity-of-mechanisms-regulating-mitochondrial-inheritance
#15
Arunas L Radzvilavicius, Nick Lane, Andrew Pomiankowski
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)...
October 26, 2017: BMC Biology
https://www.readbyqxmd.com/read/29073896/lipid-metabolism-fattens-up-hedgehog-signaling
#16
REVIEW
Robert Blassberg, John Jacob
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. Lipid metabolism has a profound influence on both hedgehog signal transduction and the properties of the ligands themselves, leading to changes in the strength of hedgehog signaling and cellular functions...
October 26, 2017: BMC Biology
https://www.readbyqxmd.com/read/29073895/spatial-phylogenetics-of-the-native-california-flora
#17
Andrew H Thornhill, Bruce G Baldwin, William A Freyman, Sonia Nosratinia, Matthew M Kling, Naia Morueta-Holme, Thomas P Madsen, David D Ackerly, Brent D Mishler
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 1.39 million herbarium specimens, a phylogeny of 1083 operational taxonomic units (OTUs) and 9 genes, and a spatial randomization test to identify regions of significant phylogenetic diversity, relative phylogenetic diversity, and phylogenetic endemism (PE), as well as to conduct a categorical analysis of neo- and paleo-endemism (CANAPE)...
October 26, 2017: BMC Biology
https://www.readbyqxmd.com/read/29070024/plant-hormone-transporters-what-we-know-and-what-we-would-like-to-know
#18
REVIEW
Jiyoung Park, Youngsook Lee, Enrico Martinoia, Markus Geisler
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)...
October 25, 2017: BMC Biology
https://www.readbyqxmd.com/read/29065871/q-a-cellular-near-death-experiences-what-is-anastasis
#19
Gongping Sun, Denise J Montell
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. This process is called anastasis. In this Q&A, we answer common questions that arise regarding anastasis, including how it is defined, the origin of the name, the potential physiological consequences, molecular mechanisms, and open questions for this new field of study...
October 24, 2017: BMC Biology
https://www.readbyqxmd.com/read/29052511/q-a-what-are-pathogens-and-what-have-they-done-to-and-for-us
#20
Francois Balloux, Lucy van Dorp
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. Others, however, are either obligate or facultative pathogens exerting a spectrum of deleterious effects on their hosts. Infectious diseases have historically represented the most common cause of death in humans until recently, exceeding by far the toll taken by wars or famines...
October 19, 2017: BMC Biology
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