Author
Bruce R. Southey
Bio: Bruce R. Southey is an academic researcher from University of Illinois at Urbana–Champaign. The author has contributed to research in topics: Prohormone & Transcriptome. The author has an hindex of 30, co-authored 94 publications receiving 5438 citations.
Topics: Prohormone, Transcriptome, Medicine, Offspring, Honey bee
Papers published on a yearly basis
Papers
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Wageningen University and Research Centre1, University of Edinburgh2, Iowa State University3, University College London4, Agro ParisTech5, Konkuk University6, Institut national de la recherche agronomique7, Aarhus University8, Aberystwyth University9, Seoul National University10, Norwich Research Park11, Wellcome Trust Sanger Institute12, Parco Tecnologico Padano13, University of Copenhagen14, University of Illinois at Urbana–Champaign15, University of Illinois at Chicago16, Agricultural Research Service17, Kansas State University18, Uppsala University19, European Bioinformatics Institute20, United States Department of Agriculture21, Washington University in St. Louis22, University of Kent23, Science for Life Laboratory24, Gyeongsang National University25, Genetic Information Research Institute26, Durham University27, University of California, Davis28, Pennsylvania State University29, University of Minnesota30, Jeju National University31, François Rabelais University32, University of California, Berkeley33, Glasgow Caledonian University34, Leipzig University35, Huazhong Agricultural University36
TL;DR: The assembly and analysis of the genome sequence of a female domestic Duroc pig and a comparison with the genomes of wild and domestic pigs from Europe and Asia reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago.
Abstract: For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
1,189 citations
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Christine G. Elsik1, Christine G. Elsik2, Christine G. Elsik3, Ross L. Tellam3 +325 more•Institutions (65)
TL;DR: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage and provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
Abstract: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
1,144 citations
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Washington University in St. Louis1, University of Illinois at Urbana–Champaign2, Uppsala University3, University of California, Los Angeles4, Wellcome Trust Sanger Institute5, University of Oxford6, Duke University7, University of Houston8, University of Kent9, University of Oviedo10, Weizmann Institute of Science11, Institute for Systems Biology12, Louisiana State University13, University of Colorado Denver14, University of Washington15, University of Sheffield16, University of Edinburgh17, Max Planck Society18, Free University of Berlin19, Harvard University20, Monsanto21
TL;DR: This work shows that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets and shows evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience.
Abstract: The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.
837 citations
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University of Illinois at Urbana–Champaign1, Utah State University2, University of Copenhagen3, Johns Hopkins University School of Medicine4, Johns Hopkins University5, University of Chicago6, Hobart and William Smith Colleges7, University of Utah8, United States Department of Agriculture9, Autonomous University of Barcelona10, Swiss Institute of Bioinformatics11, University of Geneva12, Queen Mary University of London13, Martin Luther University of Halle-Wittenberg14, Georgia Institute of Technology15, University of Georgia16, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto17, Sao Paulo State University18, Federal University of São Carlos19, University of São Paulo20, Agricultural Research Service21, East Carolina University22, Ohio Agricultural Research and Development Center23, University of Michigan24, University of Hohenheim25, York University26, Janelia Farm Research Campus27, Texas A&M University28, Harvard University29
TL;DR: There is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings and these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements.
Abstract: The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks
325 citations
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TL;DR: It is shown that aggression-related genes with inherited patterns of brain expression are also environmentally regulated, and it appears that one element in the evolution of different degrees of aggressive behavior in honey bees involved changes in regulation of genes that mediate the response to alarm pheromone.
Abstract: A prominent theory states that animal phenotypes arise by evolutionary changes in gene regulation, but the extent to which this theory holds true for behavioral evolution is not known. Because "nature and nurture" are now understood to involve hereditary and environmental influences on gene expression, we studied whether environmental influences on a behavioral phenotype, i.e., aggression, could have evolved into inherited differences via changes in gene expression. Here, with microarray analysis of honey bees, we show that aggression-related genes with inherited patterns of brain expression are also environmentally regulated. There were expression differences in the brain for hundreds of genes between the highly aggressive Africanized honey bee compared with European honey bee (EHB) subspecies. Similar results were obtained for EHB in response to exposure to alarm pheromone (which provokes aggression) and when comparing old and young bees (aggressive tendencies increase with age). There was significant overlap of the gene lists generated from these three microarray experiments. Moreover, there was statistical enrichment of several of the same cis regulatory motifs in promoters of genes on all three gene lists. Aggression shows a remarkably robust brain molecular signature regardless of whether it occurs because of inherited, age-related, or environmental (social) factors. It appears that one element in the evolution of different degrees of aggressive behavior in honey bees involved changes in regulation of genes that mediate the response to alarm pheromone.
253 citations
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28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。
18,940 citations
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TL;DR: The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or her own research.
Abstract: I have developed "tennis elbow" from lugging this book around the past four weeks, but it is worth the pain, the effort, and the aspirin. It is also worth the (relatively speaking) bargain price. Including appendixes, this book contains 894 pages of text. The entire panorama of the neural sciences is surveyed and examined, and it is comprehensive in its scope, from genomes to social behaviors. The editors explicitly state that the book is designed as "an introductory text for students of biology, behavior, and medicine," but it is hard to imagine any audience, interested in any fragment of neuroscience at any level of sophistication, that would not enjoy this book. The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or
7,563 citations
01 Jan 2000
3,536 citations
01 Jan 2010
TL;DR: In this paper, the authors describe a scenario where a group of people are attempting to find a solution to the problem of "finding the needle in a haystack" in the environment.
Abstract: 中枢神経系疾患の治療は正常細胞(ニューロン)の機能維持を目的とするが,脳血管障害のように機能障害の原因が細胞の死滅に基づくことは多い.一方,脳腫瘍の治療においては薬物療法や放射線療法といった腫瘍細胞の死滅を目標とするものが大きな位置を占める.いずれの場合にも,細胞死の機序を理解することは各種病態や治療法の理解のうえで重要である.現在のところ最も研究の進んでいる細胞死の型はアポトーシスである.そのなかで重要な位置を占めるミトコンドリアにおける反応および抗アポトーシス因子について概要を紹介する.
2,716 citations
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Duke University1, University of Texas at Austin2, Heidelberg Institute for Theoretical Studies3, American Museum of Natural History4, Xi'an Jiaotong University5, Beijing Genomics Institute6, New Mexico State University7, University of Sydney8, University of California9, Uppsala University10, University of Copenhagen11, Okinawa Institute of Science and Technology12, University of Georgia13, Griffith University14, Catalan Institution for Research and Advanced Studies15, Oak Ridge National Laboratory16, Joint Institute for Nuclear Research17, Aarhus University18, Washington University in St. Louis19, University of California, Santa Cruz20, Cardiff University21, Kunming Institute of Zoology22, China Agricultural University23, Tulane University24, Louisiana State University25, Copenhagen Zoo26, Federal University of Pará27, Oregon Health & Science University28, Technical University of Denmark29, Canterbury Museum30, Curtin University31, Novosibirsk State University32, Smithsonian Institution33, National University of Singapore34, National Museum of Natural History35, Nova Southeastern University36, Occidental College37, University of Edinburgh38, Harvard University39, University of California, San Francisco40, University of Florida41, University of Illinois at Urbana–Champaign42
TL;DR: A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
1,624 citations