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bioRxiv (pronounced "bio-archive") is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals.



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biorxiv
by Robert J Williamson; Emily B Josephs; Adrian E Platts; Khaled M Hazzouri; Annabelle Haudry; Mathieu Blanchette; Stephen I Wright
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The extent that both positive and negative selection vary across different portions of plant genomes remains poorly understood. Here, we sequence whole genomes of 13 Capsella grandiflora individuals and quantify the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we show that selection is strong in coding regions, but weak in most noncoding regions, with the exception of 5 and 3 untranslated regions (UTRs). However, estimates of selection in...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/06/09/002428
biorxiv
by John G Cleary; Ross Braithwaite; Kurt Gaastra; Brian S Hilbush; Stuart Inglis; Sean A Irvine; Alan Jackson; Richard Littin; Sahar Nohzadeh-Malakshah; Minita Shah; Mehul Rathod; David Ware; Len Trigg; Francisco M De La Vega
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The analysis of whole-genome or exome sequencing data from trios and pedigrees has being successfully applied to the identification of disease-causing mutations. However, most methods used to identify and genotype genetic variants from next-generation sequencing data ignore the relationships between samples, resulting in significant Mendelian errors, false positives and negatives. Here we present a Bayesian network framework that jointly analyses data from all members of a pedigree...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/01/24/001958
biorxiv
by Mathieu Larocque; Thierry Chénard; Rafael Najmanovich
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Clostridium difficile is the leading cause of hospital-borne infections occurring when the natural intestinal flora is depleted following antibiotic treatment. We present i MLTC804cdf, an extensively curated reconstructed metabolic network for the C. difficile pathogenic strain 630. i MLTC804cdf contains 804 genes, 705 metabolites and 766 metabolic, 145 exchange and 118 transport reactions. i MLTC804cdf is the most complete and accurate metabolic reconstruction of a gram-positive anaerobic...
Topic: Systems Biology
Source: http://biorxiv.org/content/early/2014/07/25/006932
biorxiv
by Nicholas E Banovich; Xun Lan; Graham McVicker; Bryce Van de Geijn; Jacob F Degner; John D. Blischak; Julien Roux; Jonathan K. Pritchard; Yoav Gilad
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DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ~300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. We identified (at...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/08/12/006171
biorxiv
by Anna-Sophie Fiston-Lavier; Maite G. Barrón; Dmitri A. Petrov; Josefa González
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Transposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analysis of TEs still represents a challenge due to the repetitive nature of these genomic entities. In this work, we present a broadly applicable and flexible tool: T-lex2. T-lex2 is the only available software that allows routine,...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/09/16/002964
biorxiv
by Lucas Dennis; Andrew McDavid; Patrick Danaher; Greg Finak; Michael Krouse; Alice Wang; Philippa Webster; Joseph Beechem; Raphael Gottardo
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Advances in high-throughput, single cell gene expression are allowing interrogation of cell heterogeneity. However, there is concern that the cell cycle phase of a cell might bias characterizations of gene expression at the single-cell level. We assess the effect of cell cycle phase on gene expression in single cells by measuring 333 genes in 930 cells across three phases and three cell lines. We determine each cell's phase non-invasively without chemical arrest and use it as a covariate in...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/07/10/002295
biorxiv
by Iosif Lazaridis; Nick Patterson; Alissa Mittnik; Gabriel Renaud; Swapan Mallick; Karola Kirsanow; Peter H. Sudmant; Joshua G. Schraiber; Sergi Castellano; Mark Lipson; Bonnie Berger; Tatijana Zemunik; Alan Cooper; Cristian Capelli; Mark G. Thomas; Andres Ruiz-Linares; Sarah A. Tishkoff; Lalji Singh; Kumarasamy Thangaraj; Richard Villems; David Comas; Christos Economou; Rem Sukernik; Mait Metspalu; Matthias Meyer; Evan E. Eichler; Joachim Burger; Montgomery Slatkin; Svante Pååbo; Janet Kelso;...
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We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 year old hunter-gatherer from Luxembourg, and seven ~8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/04/05/001552
biorxiv
by Sebastian Gil Anthony Konietzny; Phillip Byron Pope; Aaron Weimann; Alice Carolyn McHardy
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Background: Efficient industrial processes for converting plant lignocellulosic materials into biofuels are a key challenge in global efforts to use alternative energy sources to fossil fuels. Novel cellulolytic enzymes have been discovered from microbial genomes and metagenomes of microbial communities. However, the identification of relevant genes without known homologs, and elucidation of the lignocellulolytic pathways and protein complexes for different microorganisms remain a challenge....
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/05/21/005355
biorxiv
by Irene Gallego Romero; Bryan J Pavlovic; Irene Hernando-Herraez; Nicholas E Banovich; Courtney L Kagan; Jonathan E Burnett; Constance H Huang; Amy Mitrano; Claudia I Chavarria; Inbar F Ben-Nun; Yingchun Li; Karen Sabatini; Trevor R Leonardo; Mana Parast; Tomas Marques-Bonet; Louise C Laurent; Jeanne F Loring; Yoav Gilad
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Comparative genomics studies in primates are extremely restricted because we only have access to a few types of cell lines from non-human apes and to a limited collection of frozen tissues. In order to gain better insight into regulatory processes that underlie variation in complex phenotypes, we must have access to faithful model systems for a wide range of tissues and cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee (Pan troglodytes) induced...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/09/06/008862.1
biorxiv
by Fillip Port; Hui-Min Chen; Tzumin Lee; Simon L Bullock
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The type II CRISPR/Cas system has recently emerged as a powerful method to manipulate the genomes of various organisms. Here, we report a novel toolbox for high efficiency genome engineering of Drosophila melanogaster consisting of transgenic Cas9 lines and versatile guide RNA (gRNA) expression plasmids. Systematic evaluation reveals Cas9 lines with ubiquitous or germline restricted patterns of activity. We also demonstrate differential activity of the same gRNA expressed from different U6...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/03/26/003541
biorxiv
by Alexander Kubisch; Anna-Marie Winter; Emanuel A. Fronhofer
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In times of severe environmental changes and resulting shifts in the geographical distribution of animal and plant species it is crucial to unravel the mechanisms responsible for the dynamics of species’ ranges. Without such a mechanistic understanding reliable projections of future species distributions are difficult to derive. Species ranges may be highly dynamic and subject to ‘elastic’ behavior, i.e. a range contraction following a period of range expansion as a consequence of...
Topic: Ecology
Source: http://biorxiv.org/content/early/2014/08/26/008458
biorxiv
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The debate over the ethnogenesis of Ashkenazi Jewry is longstanding, and has been hampered by a lack of Jewish historiographical work between the Biblical and the early Modern eras. Most historians, as well as geneticists, situate them as the descendants of Israelite tribes whose presence in Europe is owed to deportations during the Roman conquest of Palestine, as well as migration from Babylonia, and eventual settlement along the Rhine. By contrast, a few historians and other writers, most...
Topic: Genetics
Source: http://biorxiv.org/content/early/2013/12/12/001354
biorxiv
by Àlex Bravo; Janet Piñero; Núria Queralt; Michael Rautschka; Laura I. Furlong
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Background Current biomedical research needs to leverage and exploit the large amount of information reported in publications. Automated text mining approaches, in particular those aimed at finding relationships between entities, are key for identification of actionable knowledge from free text repositories. We present the BeFree system aimed at identifying relationships between biomedical entities with a special focus on genes and their associated diseases. Results By exploiting...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/07/24/007443
biorxiv
by Roni H. G. Wright; Francois LeDily; Daniel Soronellas; Andy Pohl; Jaume Bonet; A. Silvina Nacht; Guillermo P Vicent; Michael Wierer; Baldo Oliva; Miguel Beato
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Key nuclear processes in eukaryotes including DNA replication or repair and gene regulation require extensive chromatin remodeling catalyzed by energy consuming enzymes. How the energetic demands of such processes are ensured in response to rapid stimuli remains unclear. We have analyzed this question in the context of the massive gene regulation changes induced by progestins in breast cancer cells and found that ATP is generated in the cell nucleus via the hydrolysis of poly-ADP-ribose to...
Topic: Molecular Biology
Source: http://biorxiv.org/content/early/2014/06/25/006593
biorxiv
by Thomas F. Willems; Melissa Gymrek; Gareth Highnam; - The 1000 Genomes Project; David Mittelman; Yaniv Erlich
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Short Tandem Repeats are among the most polymorphic loci in the human genome. These loci play a role in the etiology of a range of genetic diseases and have been frequently utilized in forensics, population genetics, and genetic genealogy. Despite this plethora of applications, little is known about the variation of most STRs in the human population. Here, we report the largest-scale analysis of human STR variation to date. We collected information for nearly 700,000 STR loci across over 1,000...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/07/10/004671
biorxiv
by Aleksandra Pekowska; Bernd Klaus; Felix Alexander Klein; Simon Anders; Malgorzata Oles; Lars Michael Steinmetz; Paul Bertone; Wolfgang Huber
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Regulation of gene expression underlies cell identity. Chromatin structure and gene activity are linked at multiple levels, via positioning of genomic loci to transcriptionally permissive or repressive environments and by connecting cis-regulatory elements such as promoters and enhancers. However, the genome-wide dynamics of these processes during cell differentiation has not been characterized. Using tethered chromatin conformation capture (TCC) sequencing we determined global...
Topic: Molecular Biology
Source: http://biorxiv.org/content/early/2014/04/11/004168
biorxiv
by Emilia S. Gracia; Charissa de Bekker; Jim Russell; Kezia Manlove; Ephraim Hanks; David P. Hughes
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Every level of biological organization from cells to societies require that composing units come together to form parts of a bigger unit (1). Our knowledge of how behavioral manipulating parasites change social interactions between social hosts is limited. Here we use an endoparasite to observe changes in social interactions between infected and healthy ants, using trophallaxis (liquid food exchange) and spatial data as proxies for food sharing and social segregation. We found no change in...
Topic: Ecology
Source: http://biorxiv.org/content/early/2014/02/12/002501
biorxiv
movies

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We recently demonstrated that dynein and kinesin motors drive multiple aspects of endosomal function in mammalian cells. These functions include driving motility, maintaining morphology (notably through providing longitudinal tension to support vesicle fission), and driving cargo sorting. Microtubule motors drive bidirectional motility during traffic between the endoplasmic reticulum (ER) and Golgi. Here, we have examined the role of microtubule motors in transport carrier motility, morphology,...
Topic: Cell Biology
Source: http://biorxiv.org/content/early/2014/01/10/001743
biorxiv
by Alex Graudenzi; Giulio Caravagna; Giovanni De Matteis; Marco Antoniotti
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Colorectal tumors originate and develop within intestinal crypts. Even though some of the essential phenomena that characterize crypt structure and dynamics have been effectively described in the past, the relation between the differentiation process and the overall crypt homeostasis is still partially understood. We here investigate this relation and other important biological phenomena by introducing a novel multiscale model that combines a morphological description of the crypt with a gene...
Topic: Systems Biology
Source: http://biorxiv.org/content/early/2013/11/25/000927
biorxiv
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The t(1,11) chromosome translocation co-segregates with major psychiatric disorders in a large Scottish family. The translocation disrupts the DISC1and Boymaw (DISC1FP1) genes on chromosomes 1 and 11, respectively. After translocation, two fusion genes are generated. Our recent studies found that the DISC1-Boymaw fusion protein is localized in mitochondria and inhibits oxidoreductase activity, rRNA expression, and protein translation. Mice carrying the DISC1-Boymaw fusion genes display...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/05/31/005728
biorxiv
by Rodrick Wallace
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We generalize the recently-uncovered Data Rate Theorem in the context of cognitive systems having a 'dual' information source, including those of the living state that is particularly characterized by cognition at every scale and level of organization. The unification of information theory and control theory via the Data Rate Theorem is not additive, but synergistic, generating new statistical tools that greatly constrain the possible dynamics of that state. Thus, in addition to providing novel...
Topic: Biophysics
Source: http://biorxiv.org/content/early/2014/03/04/003186
biorxiv
by Russell B. Corbett-Detig; Daniel L. Hartl; Timothy B. Sackton
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The range of genetic diversity observed within natural populations is much more narrow than expected based on models of neutral molecular evolution. Although the increased efficacy of natural selection in larger populations has been invoked to explain this paradox, to date no tests of this hypothesis have been conducted. Here, we present an analysis of whole-genome polymorphism data and genetic maps from 39 species to estimate for each species the reduction in genetic variation attributable to...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/06/09/006122
biorxiv
by Irene Gallego Romero; Athma A. Pai; Jenny Tung; Yoav Gilad
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The use of low quality RNA samples in whole-genome gene expression profiling remains controversial. It is unclear if transcript degradation in low quality RNA samples occurs uniformly, in which case the effects of degradation can be normalized, or whether different transcripts are degraded at different rates, potentially biasing measurements of expression levels. This concern has rendered the use of low quality RNA samples in whole-genome expression profiling problematic. Yet, low quality...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/01/30/002261
biorxiv
by Angus Chadwick; Mark C. W. van Rossum; Matthew F. Nolan
movies

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Populations of hippocampal place cells encode an animal's past, current and future location through sequences of action potentials generated within each cycle of the network theta rhythm. These sequential representations have been suggested to result from temporally coordinated synaptic interactions within and between cell assemblies. In contrast, we show that a model based on rate and phase coding in independent neurons is sufficient to explain the organization of CA1 population activity...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/05/12/005066
biorxiv
by Juhan Aru; Jaan Aru; Viola Priesemann; Michael Wibral; Luiz Lana; Gordon Pipa; Wolf Singer; Raul Vicente
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Cross-frequency coupling (CFC) has been proposed to coordinate neural dynamics across spatial and temporal scales. Despite its potential relevance for understanding healthy and pathological brain function, the standard CFC analysis and physiological interpretation come with fundamental problems. For example, apparent CFC can appear because of spectral correlations due to common non-stationarities that may arise in the total absence of interactions between neural frequency components. To provide...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/08/25/005926
biorxiv
by Ting Liu; Rui-Ping Wan; Ling-Jia Tang; Shu-Jing Liu; Hai-Jun Li; Qi-Hua Zhao; Wei-Ping Liao; Xiao-Fang Sun; Yong-Hong Yi; Yue-Sheng Long
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Fragile X syndrome (FXS), a common form of inherited mental retardation, is caused by a loss of expression of the fragile X mental retardation protein (FMRP). FMRP is involved in brain functions by interacting with mRNAs and microRNAs (miRNAs) that selectively control gene expression at translational level. However, little is known about the role of FMRP in regulating miRNA expression. Here, we found a development-dependant dynamic expression of Fmr1 mRNA (encoding FMRP) in mouse hippocampus...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/01/26/002071
biorxiv
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The systematic classification of Osmundaceae has long remained controversial. Recent molecular data indicate that Osmunda is paraphyletic, and needs to be separated into Osmundastrum and Osmunda s. str. Here we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network...
Topic: Paleontology
Source: http://biorxiv.org/content/early/2014/06/04/005777
biorxiv
by Esther R. Berko; Masako Suzuki; Faygel Beren; Christophe Lemetre; Christine M. Alaimo; R. Brent Calder; Karen Ballaban-Gil; Batya Gounder; Kaylee Kampf; Jill Kirschen; Shahina B. Maqbool; Zeineen Momin; David M. Reynolds; Natalie Russo; Lisa Shulman; Edyta Stasiek; Jessica Tozour; Maria Valicenti-McDermott; Shenglong Wang; Brett S. Abrahams; Joseph Hargitai; Dov Inbar; Zhengdong Zhang; Joseph D. Buxbaum; Sophie Molholm; John J. Foxe; Robert W. Marion; Adam Auton; John Greally
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DNA mutational events are increasingly being identified in autism spectrum disorder (ASD), but the potential additional role of dysregulation of the epigenome in the pathogenesis of the condition remains unclear. The epigenome is of interest as a possible mediator of environmental effects during development, encoding a cellular memory reflected by altered function of progeny cells. Advanced maternal age (AMA) is associated with an increased risk of having a child with ASD for reasons that are...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/05/06/004853
biorxiv
by Roberto Toro; Jean-Baptiste Poline; Guillaume Huguet; Eva Loth; Vincent Frouin; Tobias Banaschewski; Gareth J Barker; Arun Bokde; Christian Büchel; Fabiana Carvalho; Patricia Conrod; Mira Fauth-Bühler; Herta Flor; Jürgen Gallinat; Hugh Garavan; Penny Gowloan; Andreas Heinz; Bernd Ittermann; Claire Lawrence; Hervé Lemaître; Karl Mann; Frauke Nees; TomᚠPaus; Zdenka Pausova; Marcella Rietschel; Trevor Robbins; Michael Smolka; Andreas Ströhle; Gunter Schumann; Thomas Bourgeron
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Human brain anatomy is strikingly diverse and highly inheritable: genetic factors may explain up to 80% of its variability. Prior studies have tried to detect genetic variants with a large effect on neuroanatomical diversity, but those currently identified account for
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2013/12/05/001198
biorxiv
by Qiyun Zhu; Michael Kosoy; Kevin J Olival; Katharina Dittmar
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Bartonellae are mammalian pathogens vectored by blood-feeding arthropods. Although of increasing medical importance, little is known about their ecological past, and host associations are underexplored. Previous studies suggest an influence of horizontal gene transfers in ecological niche colonization by acquisition of host pathogenicity genes. We here expand these analyses to metabolic pathways of 28 Bartonella genomes, and experimentally explore the distribution of bartonellae in 21 species...
Topic: Microbiology
Source: http://biorxiv.org/content/early/2014/03/17/003350
biorxiv
by Jonathan Rodenfels; Oksana Lavrynenko; Sophie Ayciriex; Julio L Sampaio; Andrej Shevchenko; Suzanne Eaton
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In Drosophila larvae, growth and developmental timing are regulated by nutrition in a tightly coordinated fashion. The networks that couple these processes are far from understood. Here, we show that the intestine responds to nutrient availability by regulating production of a circulating lipoprotein-associated form of the signaling protein Hedgehog (Hh). Levels of circulating Hh tune the rates of growth and developmental timing in a coordinated fashion. Circulating Hh signals to the fat body...
Topic: Developmental Biology
Source: http://biorxiv.org/content/early/2014/07/29/002626
biorxiv
by Thaddeus R Cybulski; Joshua I Glaser; Adam H Marblestone; Bradley M Zamft; Edward S Boyden; George M Church; Konrad P Kording
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A central issue in neural recording is that of distinguishing the activities of many neurons. Here, we develop a framework, based on Fisher information, to quantify how separable a neuron's activity is from the activities of nearby neurons. We (1) apply this framework to model information flow and spatial distinguishability for several electrical and optical neural recording methods, (2) provide analytic expressions for information content, and (3) demonstrate potential applications of the...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/02/21/002923
biorxiv
by Nicholas Loman; Aaron Quinlan
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Motivation: Nanopore sequencing may be the next disruptive technology in genomics. Nanopore sequencing has many attractive properties including the ability to detect single DNA molecules without prior amplification, the lack of reliance on expensive optical components, and the ability to sequence very long fragments. The MinION from Oxford Nanopore Technologies (ONT) is the first nanopore sequencer to be commercialised and made available to early-access users. The MinION(TM) is a USB-connected,...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/07/23/007401
biorxiv
by Andrew M. Oster; Philippe Faure; Boris S. Gutkin
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Midbrain ventral segmental area (VTA) dopaminergic neurons send numerous projections to cortical and sub-cortical areas, and diffusely release dopamine (DA) to their targets. DA neurons display a range of activity modes that vary in frequency and degree of burst ring. Importantly, DA neuronal bursting is associated with a significantly greater degree of DA release than an equivalent tonic activity pattern. Here, we introduce a single compartmental, conductance-based computational model for DA...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/09/09/008920
biorxiv
by Fabien Delahaye; Neil Ari Wijetunga; Hye J Heo; Jessica N Tozour; Yong Mei Zhao; John M Greally; Francine H Einstein
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Extreme fetal growth is associated with increased susceptibility to a range of adult diseases through an unknown mechanism of cellular memory. We tested whether heritable epigenetic processes in long-lived CD34+ hematopoietic stem/progenitor cells (HSPCs) showed evidence for re-programming associated with the extremes of fetal growth. Here we show that both fetal growth restriction and over-growth are associated with global shifts towards DNA hypermethylation, targeting cis-regulatory elements...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/08/27/008482
biorxiv
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In a recent article entitled On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE , Graur et al. dismantle ENCODEs evidence and conclusion that 80% of the human genome is functional. However, the article by Graur et al. contains assumptions and statements that are questionable. Primarily, the authors limit their evaluation of DNAs biological functions to informational roles, sidestepping putative non-informational...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2013/11/18/000588
biorxiv
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Understanding the mapping of genotypes into phenotypes is a central challenge of current biological research. Such mapping, conceptually represents a developmental mechanism through which phenotypic variation can be generated. Given the nongenetic character of developmental dynamics, phenotypic variation to a great extent has been neglected in the study of evolution. What is the relevance of considering this generative process in the study of evolution? How can we study its evolutionary...
Topic: Systems Biology
Source: http://biorxiv.org/content/early/2014/04/14/004218
biorxiv
by Haijun Liu; Xiaqing Wang; Marilyn Warburton; Weiwei Wen; Minliang Jin; Min Deng; Jie Liu; Hao Tong; Qingchun Pan; Xiaohong Yang; Jianbing Yan
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The temperate-tropical division of early maize germplasm to different agricultural environments was arguably the greatest adaptation process associated with the success and near ubiquitous importance of global maize production. Deciphering this history is challenging, but new insight has been gained from the genomic, transcriptomic and phenotypic variation collected from 368 diverse temperate and tropical maize inbred lines in this study. This is the first attempt to systematically explore the...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/06/03/005751
biorxiv
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Correlations in neuronal spike times are thought to be key to processing in many neural systems. Many measures have been proposed to summarise these correlations and of these the correlation index is widely used and is the standard in studies of spontaneous retinal activity. We show that this measure has two undesirable properties: it is unbounded above and confounded by firing rate. We list properties needed for a measure to fairly quantify and compare correlations and we propose a novel...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/09/09/006635
biorxiv
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Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/09/18/009373
biorxiv
by David N Olivieri; Bernardo von Haeften; Christian Sánchez-Espinel; Francisco Gambón-Deza
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From recent whole genome shotgun data of 48 mammalian species, we have used our software VgenExtractor to obtain the functional V-gene sequence repertoire in order to conduct comparative phylogenetic studies. These studies reveal a large variation in the number of V-genes across mammalian species, ranging from a mere 36 V-genes in dolphins to nearly 600 V-genes in rats. Monotremes and marsupials are the only mammals possessing an additional locus, the TRMV, apart from the seven common loci...
Topic: Immunology
Source: http://biorxiv.org/content/early/2014/02/13/002667
biorxiv
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The Data Rate Theorem carries deep implications for theories of embodied cognition, extensions providing a spectrum of necessary conditions dynamic statistical models useful in empirical studies. A large deviations argument, however, implies that the regulation and stabilization of such systems is itself an interpenetrating phenomenon necessarily convoluted with embodied cognition. For humans, the central regulatory role of culture has long been known. Although a ground-state collapse analogous...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/01/13/001586
biorxiv
by Gonçalo Lopes; Niccolò Bonacchi; João Frazão; Joana Neto; Bassam Atallah; Sofia Soares; Luís Moreira; Sara Matias; Pavel M. Itskov; Patrícia Correia; Roberto Medina; Elena Dreosti; Joseph J. Paton; Adam R. Kampff
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The design of modern scientific experiments requires the control and monitoring of many parallel data streams. However, the serial execution of programming instructions in a computer makes it a challenge to develop software that can deal with the asynchronous, parallel nature of scientific data. Here we present Bonsai, a modular, high-performance, open-source visual programming framework for processing data streams. We will describe Bonsai's core principles and architecture while specifically...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/07/02/006791
biorxiv
by Neil R Smalheiser; Giovanni Lugli
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Synaptosomes are a popular type of isolated synaptic fraction intensively used in neuroscience and cell biology. They are prepared by layering on density gradients and thought to consist largely of axonal endings with attached postsynaptic structures (Morgan, 1976), in contrast to synaptoneurosomes (Hollingsworth et al, 1985) which are prepared by filtration and are thought to consist largely of pinched-off dendritic spines with attached presynaptic structures. Although most studies of...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/06/24/006510
biorxiv
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The development of CRISPR/Cas9 technologies promises a quantum leap in genome-engineering of model organisms. However, CRISPR-mediated gene targeting reports in Drosophila are still restricted to a few genes, use variable experimental conditions and vary in efficiency, questioning the universal applicability of the method. Here, we developed an efficient, two-step strategy to flexibly engineer the fly genome by combining CRISPR with recombinase-mediated cassette exchange (RMCE). In the first...
Topic: Developmental Biology
Source: http://biorxiv.org/content/early/2014/08/11/007864
Accurately making a decision in the face of incongruent options increases the efficiency of making similar congruency decisions in the future. This adaptive process is modulated by reward, suggesting that ventral corticostriatal circuits may contribute to the process of conflict adaptation. To evaluate this possibility, a group of healthy adults (N=30) were tested using functional MRI (fMRI) while they performed a color-word Stroop task. In a conflict-related region of the medial orbitofrontal...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/02/03/002311
biorxiv
by Krzysztof M Kozak; Niklas Wahlberg; Andrew Neild; Kanchon K Dasmahapatra; James Mallet; Chris D Jiggins
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Müllerian mimicry among Neotropical Heliconiini butterflies is an excellent example of natural selection, and is associated with the diversification of a large continental-scale radiation. Some of the processes driving the evolution of mimicry rings are likely to generate incongruent phylogenetic signals across the assemblage, and thus pose a challenge for systematics. We use a dataset of 22 mitochondrial and nuclear markers from 92% of species in the tribe to re-examine the phylogeny of...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/04/02/003749
biorxiv
by Manuel Corpas; Mike Cariaso; Alain Coletta; David Weiss; Andrew P Harrison; Federico Moran; Huanming Yang
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BACKGROUND: The availability of open access genomic data is essential for the personal genomics field. Public genomic data allow comparative analyses, testing of new tools and genotype-phenotype association studies. Personal genomics data of unrelated individuals are available in the public domain, notably the Personal Genome Project; however, to date genomics family data and metadata are severely lacking, mainly due to cost, privacy concerns or restricted access to Next Generation Sequencing...
Topic: Genomics
Source: http://biorxiv.org/content/early/2013/11/11/000216
biorxiv
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Abstract: Discovery of novel natural products is an accepted method for the elucidation of pharmacologically active molecules and drug leads. Best known sources for such discovery have been terrestrial plants and microbes, accounting for about 85% of the approved natural products in pharmaceutical use (1), and about 60% of approved pharmaceuticals and new drug applications annually (2). Discovery in the marine environment has lagged due to the difficulty of exploration in this ecological niche....
Topic: Pharmacology
Source: http://biorxiv.org/content/early/2014/05/24/005454
biorxiv
by Krzysztof Jacek Gorgolewski; Natacha Mendes; Domenica Wilfling; Elisabeth Wladimirow; Claudine Gauthier; Tyler Bonnen; Florence J. M. Ruby; Robert Trampel; Pierre-Louis Bazin; Roberto Cozatl; Jonathan Smallwood; Daniel Margulies
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Here we present a test-retest dataset of functional magnetic resonance imaging (fMRI) data acquired at rest. 22 participants were scanned during two sessions spaced one week apart. Each session includes two 1.5 mm isotropic whole-brain scans and one 0.75 mm isotropic scan of the prefrontal cortex, giving a total of six timepoints. Additionally, the dataset includes measures of mood, sustained attention, blood pressure, respiration, pulse, and the content of self-generated thoughts (mind...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/09/03/008706
biorxiv
by Josef C Uyeda; Daniel S. Caetano; Matthew W Pennell
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Quantitative geneticists long ago recognized the value of studying evolution in a multivariate framework (Pearson, 1903). Due to linkage, pleiotropy, coordinated selection and mutational covariance, the evolutionary response in any phenotypic trait can only be properly understood in the context of other traits (Lande, 1979; Lynch and Walsh, 1998). This is of course also well?appreciated by comparative biologists. However, unlike in quantitative genetics, most of the statistical and conceptual...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/07/22/007369
biorxiv
by Takafumi Katsumura; Shoji Oda; Shigeki Nakagome; Tsunehiko Hanihara; Hiroshi Kataoka; Hiroshi Mitani; Shoji Kawamura; Hiroki Oota
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Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection [1, 2]. Interestingly, sexually selected traits show geographic variations within species despite strong directional selective pressures [3, 4]. However, genetic factors that regulate varied sexual differences remain unknown. In this study, we show that polymorphisms in cytochrome P450 ( CYP ) 1B1 , which encodes a xenobiotic-metabolising enzyme, are associated with local differences...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2013/11/25/000661
In the recent paper by Kim et al. (Genome biology, 2013. 14(4): p. R36) the accuracy of TopHat2 was compared to other RNA-seq aligners. In this comment we re-examine most important analyses from this paper and identify several deficiencies that significantly diminished performance of some of the aligners, including incorrect choice of mapping parameters, unfair comparison metrics, and unrealistic simulated data. Using STAR (Dobin et al., Bioinformatics, 2013. 29(1): p. 15-21) as an exemplar, we...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2013/11/22/000851
biorxiv
by Biranchi Patra; Yoshiko Kon; Gitanjali Yadav; Anthony Sevold; Jesse P Frumkin; Ravishankar R Vallabhajosyula; Arend Hintze; Bjørn Østman; Jory Schossau; Ashish Bhan; Bruz Marzolf; Jenna K Tamashiro; Amardeep Kaur; Nitin S Baliga; Elizabeth J Grayhack; Christoph Adami; David J Galas; Alpan Raval; Eric M Phizicky; Animesh Ray
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Mutational robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of mutational robustness in the budding yeast by genome wide dosage suppressor analysis of 53 conditional lethal mutations in cell division cycle and RNA synthesis related genes, revealing 660 suppressor interactions of which 642 are novel. This collection has several distinctive features, including high co-occurrence of mutant-suppressor pairs within...
Topic: Genomics
Source: http://biorxiv.org/content/early/2013/11/11/000265
biorxiv
by Adam Kimbrough; Yuying Wu; Yi Zhou; Thomas A. Houpt
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Protein 14-3-3 isoforms are key to many cellular processes and are ubiquitous throughout the brain. 14-3-3 is a regulator of ser/thr phospho-signaling by binding and sequestering phosphorylated substrates including kinases, histone deactylases, and transcription factors. The role of protein 14-3-3 in conditioned taste aversion learning (CTA) has not previously been examined. We parameterized CTA learning in difopein- YFP transgenic mice, which have widespread by expression of the artificial...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/04/30/004663
biorxiv
by Taylor Jensen; Sung K Kim; Zhanyang Zhu; Christine Chin; Claudia Gebhard; Tim Lu; Cosmin Deciu; Dirk van den Boom; Mathias Ehrich
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Background Circulating cell free fetal DNA has enabled non-invasive prenatal fetal aneuploidy testing without direct discrimination of the genetically distinct maternal and fetal DNA. Current testing may be improved by specifically enriching the sample material for fetal DNA. DNA methylation may allow for such a separation of DNA and thus support additional clinical opportunities; however, this depends on knowledge of the methylomes of ccf DNA and its cellular contributors. Results Whole genome...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/04/11/004101
biorxiv
by Liya Wang; Doreen Ware; Carol Lushbough; Nirav Merchant; Lincoln Stein
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We demonstrated a flexible Genome-Wide Association Study (GWAS) platform built upon the iPlant Collaborative Cyber-infrastructure. The platform supports big data management, sharing, and large scale study of both genotype and phenotype data on clusters. End users can add their own analysis tools, and create customized analysis workflows through the graphical user interfaces in both iPlant Discovery Environment and BioExtract server.
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/02/20/002881
biorxiv
by Andre M Bastos; Julien Vezoli; Conrado A Bosman; Jan-Mathijs Schoffelen; Robert Oostenveld; Jarrod R Dowdall; Peter De Weerd; Henry Kennedy; Pascal Fries
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Visual cortical areas are thought to form a hierarchy and to subserve cognitive functions by interacting in both feedforward and feedback directions. While feedforward influences convey sensory signals, feedback influences modulate brain responses to a given sensory stimulus according to the current behavioural context. Many studies have demonstrated effects of feedback influences on feedforward driven responses and on behaviour. Also, anatomical projections in both directions have been...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/05/06/004804
biorxiv
by Alvaro H. Crevenna; Marcelino Arciniega; Aurelie Dupont; Kaja Kowalska; Oliver Lange; Roland Wedlich-Soldner; Don C. Lamb
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Actin filament dynamics govern many key physiological processes from cell motility to tissue morphogenesis. A central feature of actin dynamics is the capacity of the filament to polymerize and depolymerize at its ends in response to cellular conditions. It is currently thought that filament kinetics can be described by a single rate constant for each end. Here, using direct visualization of single actin filament elongation, we show that actin polymerization kinetics at both filament ends are...
Topic: Biophysics
Source: http://biorxiv.org/content/early/2014/08/18/008128
biorxiv
by Zahra Aghajan; Lavanya Acharya; Jesse Cushman; Cliff Vuong; Jason Moore; Mayank Mehta
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Dorsal Hippocampal neurons provide an allocentric map of space, characterized by three key properties. First, their firing is spatially selective, termed a rate code. Second, as animals traverse through place fields, neurons sustain elevated firing rates for long periods, however this has received little attention. Third the theta-phase of spikes within this sustained activity varies with animal's location, termed phase-precession or a temporal code. The precise relationship between these...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2013/12/31/001636
biorxiv
by Shinya Oki; Kazumitsu Maehara; Yasuyuki Ohkawa; Chikara Meno
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Raw high-throughput sequence data are deposited in public databases as SRAs (Sequence Read Archives) and are publically available to every researcher. However, in order to graphically visualize the sequence data of interest, the corresponding SRAs must be downloaded and converted into BigWig format through complicated command-line processing. This task requires users to possess skill with script languages and sequence data processing, a requirement that prevents a wide range of biologists from...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/05/16/005231
As a direct result of intense heat and aridity, deserts are thought to be among the most harsh of environments, particularly for their mammalian inhabitants. Given that osmoregulation can be challenging for these animals, with failure resulting in death, strong selection should be observed on genes related to the maintenance of water and solute balance. One such animal, Peromyscus eremicus , is native to the desert regions of the southwest United States and may live its entire life without oral...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/09/15/009134
biorxiv
by Imran S Haque; Kyle A Beauchamp; Vijay S Pande
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The bottleneck for the rapid calculation of the root-mean-square deviation in atomic coordinates (RMSD) between pairs of protein structures for large numbers of conformations is the evaluation of a (3xN) x (Nx3) matrix product over conformation pairs. Here we describe two matrix multiply routines specialized for the 3xN case that are able to significantly outperform (by up to 3X) off- the-shelf high-performance linear algebra libraries for this computation, reaching machine limits on...
Topic: Biophysics
Source: http://biorxiv.org/content/early/2014/09/02/008631
biorxiv
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The constant removal of deleterious mutations by natural selection causes a reduction in neutral diversity and efficacy of selection at genetically linked sites (a process called Background Selection, BGS). Population genetic studies, however, often ignore BGS effects when investigating demographic events or the presence of other types of selection. To obtain a more realistic evolutionary expectation that incorporates the unavoidable consequences of deleterious mutations, we generated...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/05/09/005017
biorxiv
by Jennifer Lachowiec; Xia Shen; Christine Queitsch; Örjan Carlborg
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Efforts to identify loci underlying complex traits generally assume that most genetic variance is additive. This is despite the fact that non-additive genetic effects, such as epistatic interactions and developmental noise, are also likely to make important contributions to the phenotypic variability. Analyses beyond additivity require additional care in the design and collection of data, and introduce significant analytical and computational challenges in the statistical analyses. Here, we...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/09/04/008789
biorxiv
by Amy L. Williams; Giulio Geneovese; Thomas Dyer; Katherine Truax; Goo Jun; Nick Patterson; Joanne E. Curran; Ravi Duggirala; John Blangero; David Reich; Molly Przeworski; the T2D-GENES Consortium
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Although the past decade has seen tremendous progress in our understanding of fine-scale recombination, little is known about non-crossover (or "gene conversion") resolutions. We report the first genome-wide study of non-crossover gene conversion events in humans. Using SNP array data from 94 meioses, we identified 107 sites affected by non-crossover events, of which 51/53 were confirmed in sequence data. Our results suggest that a site is involved in a non-crossover event at a rate...
Topic: Genetics
Source: http://biorxiv.org/content/early/2014/09/18/009175
Modification of spatial attention via reinforcement learning (Lee & Shomstein, 2013) requires the integration of reward, attention, and executive processes. Corticostriatal pathways are an ideal neural substrate for this integration because these projections exhibit a globally parallel (Alexander, De Long, and Strick, 1985), but locally overlapping (Haber, 2003), topographical organization. Here, we explored whether there are unique striatal regions that exhibit convergent anatomical...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/06/25/006619
biorxiv
by Gurinder Singh Atwal
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The stochastic dynamics of multistable perception poses an enduring challenge to our understanding of neural signal processing in the brain. We show that the emergence of perception switching and stability can be understood using principles of probabilistic Bayesian inference where the prior temporal expectations are matched to a scale-free power spectrum, characteristic of fluctuations in the natural environment. The optimal percept dynamics are inferred by an exact mapping of the statistical...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/08/19/008177
biorxiv
by Gabriel Rosser; Ruth E. Baker; Judith P. Armitage; Alexander George Fletcher
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Most free-swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. A key open question concerns varying mechanisms by which reorientation occurs. We combine mathematical modelling with analysis of a large tracking dataset to study the poorly-understood reorientation mechanism in the monoflagellate species Rhodobacter sphaeroides . The flagellum on this species rotates counterclockwise to propel the bacterium, periodically ceasing rotation to enable...
Topic: Microbiology
Source: http://biorxiv.org/content/early/2014/01/19/001917
biorxiv
by Julia Fueller; Mikhail Egorov; Kirstin A. Walther; Ola Sabet; Jana Mallah; Markus Grabenbauer; Ali Kinkhabwala
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The canonical protein tyrosine phosphatase PTP1B has traditionally been considered to exclusively reside on the endoplasmic reticulum (ER). Using confocal microscopy, we show that endogenous PTP1B actually exhibits a higher local concentration at the mitochondria in all mammalian cell lines that we tested. Fluorescently labeled chimeras containing full-length PTP1B or only its 35 amino acid tail anchor localized identically, demonstrating the complete dependence of PTP1Bs subcellular...
Topic: Cell Biology
Source: http://biorxiv.org/content/early/2013/11/22/000836
biorxiv
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Activity in the theta frequency band (4-8 Hz) over medial prefrontal regions has been consistently implicated in top-down cognitive control processes, including recognizing and resolving response conflict. It remains an unanswered question whether these theta-band dynamics are a neural mechanism of cognitive control, or instead are epiphenomenal to the neural computational machinery but are useful indices of brain function. Here we addressed this question by attempting to boost conflict...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/05/05/004747
biorxiv
by Liang Chen; Feng Zhu; Chenglong Xiong; Zhijie Zhang; Lufang Jiang; Rui Li; Genming Zhao; Yue Chen; Qingwu Jiang
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In 2013, two new avian influenza viruses (AIVs) H7N9 and H10N8 emerged in China caused worldwide concerns. Previous studies have studied their originations independently; this study is the first time to investigate their co-originating characteristics. Gene segments of assorted subtype influenza A viruses, as well as H10N8 and H7N9, were collected from public database. With the help of series software, small and large-scale phylogenetic trees, mean evolutionary rates, and divergence years were...
Topic: Pathology
Source: http://biorxiv.org/content/early/2014/04/21/004390
biorxiv
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A standard methodology in systems neuroscience is to establish correlations between the brain and the world. These correlations have been robustly observed when probing the activity of single neurons. For example, there are cells that activate vigorously when subjects are presented with images of certain celebrities (e.g. the "Jennifer Aniston" neuron, Quiroga et al., 2005). While single neuron measurements provide remarkable insights into the functional specificity of different brain...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/08/29/008557
biorxiv
by Ying-Wooi Wan; Claire Mach; Genevera I. Allen; Matthew Anderson; Zhandong Liu
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Dysregulated microRNA (miRNA) expression is a well-established feature of human cancer. However, the role of specific miRNAs in determining cancer outcomes remains unclear. Using Level 3 expression data from the Cancer Genome Atlas (TCGA), we identified 61 miRNAs that are associated with overall survival in 469 ovarian cancers profiled by microarray (p
Topic: Genomics
Source: http://biorxiv.org/content/early/2013/11/13/000315
biorxiv
by Matthew Maurano; Hao Wang; Sam John; Anthony Shafer; Theresa Canfield; Kristen Lee; John A Stamatoyannopoulos
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The nuclear genome of every cell harbors millions of unoccupied transcription factor (TF) recognition sequences that harbor methylated cytosines. Although DNA methylation is commonly invoked as a repressive mechanism, the extent to which it actively silences specific TF occupancy sites is unknown. To define the role of DNA methylation in modulating TF binding, we quantified the effect of DNA methyltransferase abrogation on the occupancy patterns of a ubiquitous TF capable of autonomous binding...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/02/27/003061