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Journal ArticleDOI

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

24 Apr 2009-Science (American Association for the Advancement of Science)-Vol. 324, Iss: 5926, pp 522-528
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.

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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

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

Journal ArticleDOI
John K. Colbourne1, Michael E. Pfrender2, Michael E. Pfrender3, Donald L. Gilbert1, W. Kelley Thomas4, Abraham E. Tucker4, Abraham E. Tucker1, Todd H. Oakley5, Shin-ichi Tokishita6, Andrea Aerts7, Georg J. Arnold8, Malay Kumar Basu9, Malay Kumar Basu10, Darren J Bauer4, Carla E. Cáceres11, Liran Carmel12, Liran Carmel9, Claudio Casola1, Jeong Hyeon Choi1, John C. Detter7, Qunfeng Dong1, Qunfeng Dong13, Serge Dusheyko7, Brian D. Eads1, Thomas Fröhlich8, Kerry Geiler-Samerotte14, Kerry Geiler-Samerotte5, Daniel Gerlach15, Daniel Gerlach16, Phil Hatcher4, Sanjuro Jogdeo4, Sanjuro Jogdeo17, Jeroen Krijgsveld18, Evgenia V. Kriventseva15, Dietmar Kültz19, Christian Laforsch8, Erika Lindquist7, Jacqueline Lopez1, J. Robert Manak20, J. Robert Manak21, Jean Muller22, Jasmyn Pangilinan7, Rupali P Patwardhan1, Rupali P Patwardhan23, Samuel Pitluck7, Ellen J. Pritham24, Andreas Rechtsteiner25, Andreas Rechtsteiner1, Mina Rho1, Igor B. Rogozin9, Onur Sakarya26, Onur Sakarya5, Asaf Salamov7, Sarah Schaack1, Sarah Schaack24, Harris Shapiro7, Yasuhiro Shiga6, Courtney Skalitzky20, Zachary Smith1, Alexander Souvorov9, Way Sung4, Zuojian Tang27, Zuojian Tang1, Dai Tsuchiya1, Hank Tu7, Hank Tu26, Harmjan R. Vos18, Mei Wang7, Yuri I. Wolf9, Hideo Yamagata6, Takuji Yamada, Yuzhen Ye1, Joseph R. Shaw1, Justen Andrews1, Teresa J. Crease28, Haixu Tang1, Susan Lucas7, Hugh M. Robertson11, Peer Bork, Eugene V. Koonin9, Evgeny M. Zdobnov15, Evgeny M. Zdobnov29, Igor V. Grigoriev7, Michael Lynch1, Jeffrey L. Boore30, Jeffrey L. Boore7 
04 Feb 2011-Science
TL;DR: The Daphnia genome reveals a multitude of genes and shows adaptation through gene family expansions, and the coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random.
Abstract: We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.

1,204 citations

Journal ArticleDOI
Martien A. M. Groenen1, Alan Archibald2, Hirohide Uenishi, Christopher K. Tuggle3, Yasuhiro Takeuchi4, Max F. Rothschild3, Claire Rogel-Gaillard5, Chankyu Park6, Denis Milan7, Hendrik-Jan Megens1, Shengting Li8, Denis M. Larkin9, Heebal Kim10, Laurent A. F. Frantz1, Mario Caccamo11, Hyeonju Ahn10, Bronwen Aken12, Anna Anselmo13, Christian Anthon14, Loretta Auvil15, Bouabid Badaoui13, Craig W. Beattie16, Christian Bendixen8, Daniel Berman17, Frank Blecha18, Jonas Blomberg19, Lars Bolund8, Mirte Bosse1, Sara Botti13, Zhan Bujie8, Megan Bystrom3, Boris Capitanu15, Denise Carvalho-Silva20, Patrick Chardon5, Celine Chen21, Ryan Cheng3, Sang-Haeng Choi, William Chow12, Richard Clark12, C M Clee12, Richard P. M. A. Crooijmans1, Harry D. Dawson21, Patrice Dehais7, Fioravante De Sapio2, Bert Dibbits1, Nizar Drou11, Zhi-Qiang Du3, Kellye Eversole, João Fadista22, João Fadista8, Susan Fairley12, Thomas Faraut7, Geoffrey J. Faulkner2, Geoffrey J. Faulkner22, Katie E. Fowler23, Merete Fredholm14, Eric Fritz3, James G. R. Gilbert12, Elisabetta Giuffra5, Elisabetta Giuffra13, Jan Gorodkin14, Darren K. Griffin23, Jennifer Harrow12, Alexander Hayward24, Kerstin Howe12, Zhi-Liang Hu3, Sean Humphray12, Sean Humphray22, Toby Hunt12, Henrik Hornshøj8, Jin-Tae Jeon25, Patric Jern24, Matthew Jones12, Jerzy Jurka26, Hiroyuki Kanamori, Ronan Kapetanovic2, Jaebum Kim6, Jaebum Kim15, Jae-Hwan Kim, Kyu-Won Kim, Tae-Hun Kim, Greger Larson27, Kyooyeol Lee6, Kyung-Tai Lee, Richard M. Leggett11, Harris A. Lewin28, Yingrui Li, Wan Sheng Liu29, Jane E. Loveland12, Yao Lu, Joan K. Lunney17, Jian Ma15, Ole Madsen1, Katherine M. Mann17, Katherine M. Mann22, Lucy Matthews12, Stuart McLaren12, Takeya Morozumi, Michael P. Murtaugh30, Jitendra Narayan9, Dinh Truong Nguyen6, Peixiang Ni, Song-Jung Oh31, Suneel Kumar Onteru3, Frank Panitz8, Eung-Woo Park, Hong-Seog Park, Géraldine Pascal32, Yogesh Paudel1, Miguel Pérez-Enciso, Ricardo H. Ramirez-Gonzalez11, James M. Reecy3, Sandra L. Rodriguez-Zas15, Gary A. Rohrer17, Lauretta A. Rund15, Yongming Sang18, Kyle M. Schachtschneider15, Joshua G. Schraiber33, John C. Schwartz30, Linda Scobie34, Carol Scott12, Stephen M. J. Searle12, Bertrand Servin7, Bruce R. Southey15, Göran O. Sperber19, Peter F. Stadler35, Jonathan V. Sweedler15, Hakim Tafer35, Bo Thomsen8, Rashmi Wali34, Jian Wang, Jun Wang14, Simon D. M. White12, Xun Xu, Martine Yerle7, Guojie Zhang, Jianguo Zhang, Jie Zhang36, Shuhong Zhao36, Jane Rogers11, Carol Churcher12, Lawrence B. Schook15 
15 Nov 2012-Nature
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

Journal ArticleDOI
10 Feb 2011-Nature
TL;DR: The decade since the Human Genome Project ended has witnessed a remarkable sequencing technology explosion that has permitted a multitude of questions to be asked and answered, at unprecedented speed and resolution.
Abstract: The decade since the Human Genome Project ended has witnessed a remarkable sequencing technology explosion that has permitted a multitude of questions about the genome to be asked and answered, at unprecedented speed and resolution. Here I present examples of how the resulting information has both enhanced our knowledge and expanded the impact of the genome on biomedical research. New sequencing technologies have also introduced exciting new areas of biological endeavour. The continuing upward trajectory of sequencing technology development is enabling clinical applications that are aimed at improving medical diagnosis and treatment.

865 citations

References
More filters
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

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

Journal ArticleDOI
TL;DR: The neonatal Fc receptor for IgG (FcRn) has been well characterized in the transfer of passive humoral immunity from a mother to her fetus and throughout life, FcRm protects IgG from degradation, thereby explaining the long half-life of this class of antibody in the serum.
Abstract: The neonatal Fc receptor for IgG (FcRn) has been well characterized in the transfer of passive humoral immunity from a mother to her fetus. In addition, throughout life, FcRn protects IgG from degradation, thereby explaining the long half-life of this class of antibody in the serum. In recent years, it has become clear that FcRn is expressed in various sites in adults, where its potential function is now beginning to emerge. In addition, recent studies have examined the interaction between FcRn and the Fc portion of IgG with the aim of either improving the serum half-life of therapeutic monoclonal antibodies or reducing the half-life of pathogenic antibodies. This Review summarizes these two areas of FcRn biology.

1,998 citations

Journal ArticleDOI
09 Aug 2002-Science
TL;DR: A method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun sequence has the ability to detect duplications larger than 15 kilobases irrespective of copy number, location, or high sequence similarity.
Abstract: Primate-specific segmental duplications are considered important in human disease and evolution. The inability to distinguish between allelic and duplication sequence overlap has hampered their characterization as well as assembly and annotation of our genome. We developed a method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun sequence. This test has the ability to detect duplications larger than 15 kilobases irrespective of copy number, location, or high sequence similarity. We mapped 169 large regions flanked by highly similar duplications. Twenty-four of these hot spots of genomic instability have been associated with genetic disease. Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity.

1,320 citations

Journal ArticleDOI
TL;DR: The interplay between the IFN system and four medically important and challenging viruses — influenza, hepatitis C, herpes simplex and vaccinia — is discussed to highlight the diversity of viral strategies.
Abstract: The action of interferons (IFNs) on virus-infected cells and surrounding tissues elicits an antiviral state that is characterized by the expression and antiviral activity of IFN-stimulated genes. In turn, viruses encode mechanisms to counteract the host response and support efficient viral replication, thereby minimizing the therapeutic antiviral power of IFNs. In this review, we discuss the interplay between the IFN system and four medically important and challenging viruses -- influenza, hepatitis C, herpes simplex and vaccinia -- to highlight the diversity of viral strategies. Understanding the complex network of cellular antiviral processes and virus-host interactions should aid in identifying new and common targets for the therapeutic intervention of virus infection. This effort must take advantage of the recent developments in functional genomics, bioinformatics and other emerging technologies.

1,256 citations