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  1. Article: Genetic variation at the O-antigen biosynthetic locus in Pseudomonas aeruginosa.

    Raymond, Christopher K / Sims, Elizabeth H / Kas, Arnold / Spencer, David H / Kutyavin, Tanya V / Ivey, Richard G / Zhou, Yang / Kaul, Rajinder / Clendenning, James B / Olson, Maynard V

    Journal of bacteriology

    2001  Volume 184, Issue 13, Page(s) 3614–3622

    Abstract: The outer carbohydrate layer, or O antigen, of Pseudomonas aeruginosa varies markedly in different isolates of these bacteria, and at least 20 distinct O-antigen serotypes have been described. Previous studies have indicated that the major enzymes ... ...

    Abstract The outer carbohydrate layer, or O antigen, of Pseudomonas aeruginosa varies markedly in different isolates of these bacteria, and at least 20 distinct O-antigen serotypes have been described. Previous studies have indicated that the major enzymes responsible for O-antigen synthesis are encoded in a cluster of genes that occupy a common genetic locus. We used targeted yeast recombinational cloning to isolate this locus from the 20 internationally recognized serotype strains. DNA sequencing of these isolated segments revealed that at least 11 highly divergent gene clusters occupy this region. Homology searches of the encoded protein products indicated that these gene clusters are likely to direct O-antigen biosynthesis. The O15 serotype strains lack functional gene clusters in the region analyzed, suggesting that O-antigen biosynthesis genes for this serotype are harbored in a different portion of the genome. The overall pattern underscores the plasticity of the P. aeruginosa genome, in which a specific site in a well-conserved genomic region can be occupied by any of numerous islands of functionally related DNA with diverse sequences.
    MeSH term(s) Amino Acid Sequence ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Base Sequence ; Cloning, Molecular ; Conserved Sequence ; Genetic Variation ; Molecular Sequence Data ; O Antigens/biosynthesis ; O Antigens/genetics ; Pseudomonas aeruginosa/genetics ; Pseudomonas aeruginosa/metabolism ; Yeasts/genetics
    Chemical Substances Bacterial Proteins ; O Antigens ; O antigen, Pseudomonas
    Language English
    Publishing date 2001-10-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.184.13.3614-3622.2002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The DNA sequence, annotation and analysis of human chromosome 3.

    Muzny, Donna M / Scherer, Steven E / Kaul, Rajinder / Wang, Jing / Yu, Jun / Sudbrak, Ralf / Buhay, Christian J / Chen, Rui / Cree, Andrew / Ding, Yan / Dugan-Rocha, Shannon / Gill, Rachel / Gunaratne, Preethi / Harris, R Alan / Hawes, Alicia C / Hernandez, Judith / Hodgson, Anne V / Hume, Jennifer / Jackson, Andrew /
    Khan, Ziad Mohid / Kovar-Smith, Christie / Lewis, Lora R / Lozado, Ryan J / Metzker, Michael L / Milosavljevic, Aleksandar / Miner, George R / Morgan, Margaret B / Nazareth, Lynne V / Scott, Graham / Sodergren, Erica / Song, Xing-Zhi / Steffen, David / Wei, Sharon / Wheeler, David A / Wright, Mathew W / Worley, Kim C / Yuan, Ye / Zhang, Zhengdong / Adams, Charles Q / Ansari-Lari, M Ali / Ayele, Mulu / Brown, Mary J / Chen, Guan / Chen, Zhijian / Clendenning, James / Clerc-Blankenburg, Kerstin P / Chen, Runsheng / Chen, Zhu / Davis, Clay / Delgado, Oliver / Dinh, Huyen H / Dong, Wei / Draper, Heather / Ernst, Stephen / Fu, Gang / Gonzalez-Garay, Manuel L / Garcia, Dawn K / Gillett, Will / Gu, Jun / Hao, Bailin / Haugen, Eric / Havlak, Paul / He, Xin / Hennig, Steffen / Hu, Songnian / Huang, Wei / Jackson, Laronda R / Jacob, Leni S / Kelly, Susan H / Kube, Michael / Levy, Ruth / Li, Zhangwan / Liu, Bin / Liu, Jing / Liu, Wen / Lu, Jing / Maheshwari, Manjula / Nguyen, Bao-Viet / Okwuonu, Geoffrey O / Palmeiri, Anthony / Pasternak, Shiran / Perez, Lesette M / Phelps, Karen A / Plopper, Farah J H / Qiang, Boqin / Raymond, Christopher / Rodriguez, Ruben / Saenphimmachak, Channakhone / Santibanez, Jireh / Shen, Hua / Shen, Yan / Subramanian, Sandhya / Tabor, Paul E / Verduzco, Daniel / Waldron, Lenee / Wang, Jian / Wang, Jun / Wang, Qiaoyan / Williams, Gabrielle A / Wong, Gane K-S / Yao, Zhijian / Zhang, JingKun / Zhang, Xiuqing / Zhao, Guoping / Zhou, Jianling / Zhou, Yang / Nelson, David / Lehrach, Hans / Reinhardt, Richard / Naylor, Susan L / Yang, Huanming / Olson, Maynard / Weinstock, George / Gibbs, Richard A

    Nature

    2006  Volume 440, Issue 7088, Page(s) 1194–1198

    Abstract: After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human ...

    Abstract After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.
    MeSH term(s) Animals ; Base Sequence ; Chromosome Breakage/genetics ; Chromosome Inversion/genetics ; Chromosomes, Human, Pair 3/genetics ; Contig Mapping ; CpG Islands/genetics ; DNA, Complementary/genetics ; Evolution, Molecular ; Expressed Sequence Tags ; Human Genome Project ; Humans ; Macaca mulatta/genetics ; Molecular Sequence Data ; Pan troglodytes/genetics ; Sequence Analysis, DNA ; Synteny/genetics
    Chemical Substances DNA, Complementary
    Language English
    Publishing date 2006-04-12
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/nature04728
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The DNA sequence of human chromosome 7.

    Hillier, Ladeana W / Fulton, Robert S / Fulton, Lucinda A / Graves, Tina A / Pepin, Kymberlie H / Wagner-McPherson, Caryn / Layman, Dan / Maas, Jason / Jaeger, Sara / Walker, Rebecca / Wylie, Kristine / Sekhon, Mandeep / Becker, Michael C / O'Laughlin, Michelle D / Schaller, Mark E / Fewell, Ginger A / Delehaunty, Kimberly D / Miner, Tracie L / Nash, William E /
    Cordes, Matt / Du, Hui / Sun, Hui / Edwards, Jennifer / Bradshaw-Cordum, Holland / Ali, Johar / Andrews, Stephanie / Isak, Amber / Vanbrunt, Andrew / Nguyen, Christine / Du, Feiyu / Lamar, Betty / Courtney, Laura / Kalicki, Joelle / Ozersky, Philip / Bielicki, Lauren / Scott, Kelsi / Holmes, Andrea / Harkins, Richard / Harris, Anthony / Strong, Cynthia Madsen / Hou, Shunfang / Tomlinson, Chad / Dauphin-Kohlberg, Sara / Kozlowicz-Reilly, Amy / Leonard, Shawn / Rohlfing, Theresa / Rock, Susan M / Tin-Wollam, Aye-Mon / Abbott, Amanda / Minx, Patrick / Maupin, Rachel / Strowmatt, Catrina / Latreille, Phil / Miller, Nancy / Johnson, Doug / Murray, Jennifer / Woessner, Jeffrey P / Wendl, Michael C / Yang, Shiaw-Pyng / Schultz, Brian R / Wallis, John W / Spieth, John / Bieri, Tamberlyn A / Nelson, Joanne O / Berkowicz, Nicolas / Wohldmann, Patricia E / Cook, Lisa L / Hickenbotham, Matthew T / Eldred, James / Williams, Donald / Bedell, Joseph A / Mardis, Elaine R / Clifton, Sandra W / Chissoe, Stephanie L / Marra, Marco A / Raymond, Christopher / Haugen, Eric / Gillett, Will / Zhou, Yang / James, Rose / Phelps, Karen / Iadanoto, Shawn / Bubb, Kerry / Simms, Elizabeth / Levy, Ruth / Clendenning, James / Kaul, Rajinder / Kent, W James / Furey, Terrence S / Baertsch, Robert A / Brent, Michael R / Keibler, Evan / Flicek, Paul / Bork, Peer / Suyama, Mikita / Bailey, Jeffrey A / Portnoy, Matthew E / Torrents, David / Chinwalla, Asif T / Gish, Warren R / Eddy, Sean R / McPherson, John D / Olson, Maynard V / Eichler, Evan E / Green, Eric D / Waterston, Robert H / Wilson, Richard K

    Nature

    2003  Volume 424, Issue 6945, Page(s) 157–164

    Abstract: Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present ... ...

    Abstract Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame.
    MeSH term(s) Animals ; Base Sequence ; Chromosomes, Human, Pair 7 ; Gene Duplication ; Humans ; Mice ; Molecular Sequence Data ; Physical Chromosome Mapping ; Proteins/genetics ; Pseudogenes ; RNA, Untranslated ; Sequence Analysis, DNA ; Species Specificity ; Williams Syndrome/genetics
    Chemical Substances Proteins ; RNA, Untranslated
    Language English
    Publishing date 2003-07-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/nature01782
    Database MEDical Literature Analysis and Retrieval System OnLINE

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