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  • Articles  (274)
  • Protein Structure, Tertiary  (148)
  • Signal Transduction  (137)
  • Meteorology and Climatology
  • 2005-2009  (274)
  • 1950-1954
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  • 1
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    The genome of the sea urchin Strongylocentrotus purpuratus (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-11
    Description: We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sea Urchin Genome Sequencing Consortium -- Sodergren, Erica -- Weinstock, George M -- Davidson, Eric H -- Cameron, R Andrew -- Gibbs, Richard A -- Angerer, Robert C -- Angerer, Lynne M -- Arnone, Maria Ina -- Burgess, David R -- Burke, Robert D -- Coffman, James A -- Dean, Michael -- Elphick, Maurice R -- Ettensohn, Charles A -- Foltz, Kathy R -- Hamdoun, Amro -- Hynes, Richard O -- Klein, William H -- Marzluff, William -- McClay, David R -- Morris, Robert L -- Mushegian, Arcady -- Rast, Jonathan P -- Smith, L Courtney -- Thorndyke, Michael C -- Vacquier, Victor D -- Wessel, Gary M -- Wray, Greg -- Zhang, Lan -- Elsik, Christine G -- Ermolaeva, Olga -- Hlavina, Wratko -- Hofmann, Gretchen -- Kitts, Paul -- Landrum, Melissa J -- Mackey, Aaron J -- Maglott, Donna -- Panopoulou, Georgia -- Poustka, Albert J -- Pruitt, Kim -- Sapojnikov, Victor -- Song, Xingzhi -- Souvorov, Alexandre -- Solovyev, Victor -- Wei, Zheng -- Whittaker, Charles A -- Worley, Kim -- Durbin, K James -- Shen, Yufeng -- Fedrigo, Olivier -- Garfield, David -- Haygood, Ralph -- Primus, Alexander -- Satija, Rahul -- Severson, Tonya -- Gonzalez-Garay, Manuel L -- Jackson, Andrew R -- Milosavljevic, Aleksandar -- Tong, Mark -- Killian, Christopher E -- Livingston, Brian T -- Wilt, Fred H -- Adams, Nikki -- Belle, Robert -- Carbonneau, Seth -- Cheung, Rocky -- Cormier, Patrick -- Cosson, Bertrand -- Croce, Jenifer -- Fernandez-Guerra, Antonio -- Geneviere, Anne-Marie -- Goel, Manisha -- Kelkar, Hemant -- Morales, Julia -- Mulner-Lorillon, Odile -- Robertson, Anthony J -- Goldstone, Jared V -- Cole, Bryan -- Epel, David -- Gold, Bert -- Hahn, Mark E -- Howard-Ashby, Meredith -- Scally, Mark -- Stegeman, John J -- Allgood, Erin L -- Cool, Jonah -- Judkins, Kyle M -- McCafferty, Shawn S -- Musante, Ashlan M -- Obar, Robert A -- Rawson, Amanda P -- Rossetti, Blair J -- Gibbons, Ian R -- Hoffman, Matthew P -- Leone, Andrew -- Istrail, Sorin -- Materna, Stefan C -- Samanta, Manoj P -- Stolc, Viktor -- Tongprasit, Waraporn -- Tu, Qiang -- Bergeron, Karl-Frederik -- Brandhorst, Bruce P -- Whittle, James -- Berney, Kevin -- Bottjer, David J -- Calestani, Cristina -- Peterson, Kevin -- Chow, Elly -- Yuan, Qiu Autumn -- Elhaik, Eran -- Graur, Dan -- Reese, Justin T -- Bosdet, Ian -- Heesun, Shin -- Marra, Marco A -- Schein, Jacqueline -- Anderson, Michele K -- Brockton, Virginia -- Buckley, Katherine M -- Cohen, Avis H -- Fugmann, Sebastian D -- Hibino, Taku -- Loza-Coll, Mariano -- Majeske, Audrey J -- Messier, Cynthia -- Nair, Sham V -- Pancer, Zeev -- Terwilliger, David P -- Agca, Cavit -- Arboleda, Enrique -- Chen, Nansheng -- Churcher, Allison M -- Hallbook, F -- Humphrey, Glen W -- Idris, Mohammed M -- Kiyama, Takae -- Liang, Shuguang -- Mellott, Dan -- Mu, Xiuqian -- Murray, Greg -- Olinski, Robert P -- Raible, Florian -- Rowe, Matthew -- Taylor, John S -- Tessmar-Raible, Kristin -- Wang, D -- Wilson, Karen H -- Yaguchi, Shunsuke -- Gaasterland, Terry -- Galindo, Blanca E -- Gunaratne, Herath J -- Juliano, Celina -- Kinukawa, Masashi -- Moy, Gary W -- Neill, Anna T -- Nomura, Mamoru -- Raisch, Michael -- Reade, Anna -- Roux, Michelle M -- Song, Jia L -- Su, Yi-Hsien -- Townley, Ian K -- Voronina, Ekaterina -- Wong, Julian L -- Amore, Gabriele -- Branno, Margherita -- Brown, Euan R -- Cavalieri, Vincenzo -- Duboc, Veronique -- Duloquin, Louise -- Flytzanis, Constantin -- Gache, Christian -- Lapraz, Francois -- Lepage, Thierry -- Locascio, Annamaria -- Martinez, Pedro -- Matassi, Giorgio -- Matranga, Valeria -- Range, Ryan -- Rizzo, Francesca -- Rottinger, Eric -- Beane, Wendy -- Bradham, Cynthia -- Byrum, Christine -- Glenn, Tom -- Hussain, Sofia -- Manning, Gerard -- Miranda, Esther -- Thomason, Rebecca -- Walton, Katherine -- Wikramanayke, Athula -- Wu, Shu-Yu -- Xu, Ronghui -- Brown, C Titus -- Chen, Lili -- Gray, Rachel F -- Lee, Pei Yun -- Nam, Jongmin -- Oliveri, Paola -- Smith, Joel -- Muzny, Donna -- Bell, Stephanie -- Chacko, Joseph -- Cree, Andrew -- Curry, Stacey -- Davis, Clay -- Dinh, Huyen -- Dugan-Rocha, Shannon -- Fowler, Jerry -- Gill, Rachel -- Hamilton, Cerrissa -- Hernandez, Judith -- Hines, Sandra -- Hume, Jennifer -- Jackson, Laronda -- Jolivet, Angela -- Kovar, Christie -- Lee, Sandra -- Lewis, Lora -- Miner, George -- Morgan, Margaret -- Nazareth, Lynne V -- Okwuonu, Geoffrey -- Parker, David -- Pu, Ling-Ling -- Thorn, Rachel -- Wright, Rita -- 2P42 ESO7381/PHS HHS/ -- 5 U54 HG003273/HG/NHGRI NIH HHS/ -- EY11930/EY/NEI NIH HHS/ -- F32 ESO12794/PHS HHS/ -- F32 HD047136/HD/NICHD NIH HHS/ -- F32 HD047136-02/HD/NICHD NIH HHS/ -- F32 HD047136-03/HD/NICHD NIH HHS/ -- F32-HD47136/HD/NICHD NIH HHS/ -- GM058231/GM/NIGMS NIH HHS/ -- GM070840/GM/NIGMS NIH HHS/ -- GM61005/GM/NIGMS NIH HHS/ -- GM61464/GM/NIGMS NIH HHS/ -- HD-37105/HD/NICHD NIH HHS/ -- HD039948/HD/NICHD NIH HHS/ -- HD14483/HD/NICHD NIH HHS/ -- HD66219/HD/NICHD NIH HHS/ -- P30-CA14051/CA/NCI NIH HHS/ -- R01 ES006272/ES/NIEHS NIH HHS/ -- R01 ES006272-13/ES/NIEHS NIH HHS/ -- R01 GM070840/GM/NIGMS NIH HHS/ -- R01 HD028152/HD/NICHD NIH HHS/ -- R01ES006272/ES/NIEHS NIH HHS/ -- R37-HD12896/HD/NICHD NIH HHS/ -- RR-15044/RR/NCRR NIH HHS/ -- S19916/Biotechnology and Biological Sciences Research Council/United Kingdom -- T32 GM007601/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):941-52.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095691" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcification, Physiologic ; Cell Adhesion Molecules/genetics/physiology ; Complement Activation/genetics ; Computational Biology ; Embryonic Development/genetics ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Genes ; *Genome ; Immunity, Innate/genetics ; Immunologic Factors/genetics/physiology ; Male ; Nervous System Physiological Phenomena ; Proteins/genetics/physiology ; *Sequence Analysis, DNA ; Signal Transduction ; Strongylocentrotus purpuratus/embryology/*genetics/immunology/physiology ; Transcription Factors/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-16
    Description: Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (〉1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉El-Sayed, Najib M -- Myler, Peter J -- Bartholomeu, Daniella C -- Nilsson, Daniel -- Aggarwal, Gautam -- Tran, Anh-Nhi -- Ghedin, Elodie -- Worthey, Elizabeth A -- Delcher, Arthur L -- Blandin, Gaelle -- Westenberger, Scott J -- Caler, Elisabet -- Cerqueira, Gustavo C -- Branche, Carole -- Haas, Brian -- Anupama, Atashi -- Arner, Erik -- Aslund, Lena -- Attipoe, Philip -- Bontempi, Esteban -- Bringaud, Frederic -- Burton, Peter -- Cadag, Eithon -- Campbell, David A -- Carrington, Mark -- Crabtree, Jonathan -- Darban, Hamid -- da Silveira, Jose Franco -- de Jong, Pieter -- Edwards, Kimberly -- Englund, Paul T -- Fazelina, Gholam -- Feldblyum, Tamara -- Ferella, Marcela -- Frasch, Alberto Carlos -- Gull, Keith -- Horn, David -- Hou, Lihua -- Huang, Yiting -- Kindlund, Ellen -- Klingbeil, Michele -- Kluge, Sindy -- Koo, Hean -- Lacerda, Daniela -- Levin, Mariano J -- Lorenzi, Hernan -- Louie, Tin -- Machado, Carlos Renato -- McCulloch, Richard -- McKenna, Alan -- Mizuno, Yumi -- Mottram, Jeremy C -- Nelson, Siri -- Ochaya, Stephen -- Osoegawa, Kazutoyo -- Pai, Grace -- Parsons, Marilyn -- Pentony, Martin -- Pettersson, Ulf -- Pop, Mihai -- Ramirez, Jose Luis -- Rinta, Joel -- Robertson, Laura -- Salzberg, Steven L -- Sanchez, Daniel O -- Seyler, Amber -- Sharma, Reuben -- Shetty, Jyoti -- Simpson, Anjana J -- Sisk, Ellen -- Tammi, Martti T -- Tarleton, Rick -- Teixeira, Santuza -- Van Aken, Susan -- Vogt, Christy -- Ward, Pauline N -- Wickstead, Bill -- Wortman, Jennifer -- White, Owen -- Fraser, Claire M -- Stuart, Kenneth D -- Andersson, Bjorn -- AI045039/AI/NIAID NIH HHS/ -- AI45038/AI/NIAID NIH HHS/ -- AI45061/AI/NIAID NIH HHS/ -- R01 AI031077/AI/NIAID NIH HHS/ -- R01 AI031077-11/AI/NIAID NIH HHS/ -- U01 AI045038/AI/NIAID NIH HHS/ -- U01 AI045039/AI/NIAID NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2005 Jul 15;309(5733):409-15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Parasite Genomics, Institute for Genomic Research, Rockville, MD 20850, USA. nelsayed@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16020725" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chagas Disease/drug therapy/parasitology ; DNA Repair ; DNA Replication ; DNA, Mitochondrial/genetics ; DNA, Protozoan/genetics ; Genes, Protozoan ; *Genome, Protozoan ; Humans ; Meiosis ; Membrane Proteins/chemistry/genetics/physiology ; Multigene Family ; Protozoan Proteins/chemistry/*genetics/physiology ; Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; Retroelements ; *Sequence Analysis, DNA ; Signal Transduction ; Telomere/genetics ; Trypanocidal Agents/pharmacology/therapeutic use ; Trypanosoma cruzi/chemistry/*genetics/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-16
    Description: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tuskan, G A -- Difazio, S -- Jansson, S -- Bohlmann, J -- Grigoriev, I -- Hellsten, U -- Putnam, N -- Ralph, S -- Rombauts, S -- Salamov, A -- Schein, J -- Sterck, L -- Aerts, A -- Bhalerao, R R -- Bhalerao, R P -- Blaudez, D -- Boerjan, W -- Brun, A -- Brunner, A -- Busov, V -- Campbell, M -- Carlson, J -- Chalot, M -- Chapman, J -- Chen, G-L -- Cooper, D -- Coutinho, P M -- Couturier, J -- Covert, S -- Cronk, Q -- Cunningham, R -- Davis, J -- Degroeve, S -- Dejardin, A -- Depamphilis, C -- Detter, J -- Dirks, B -- Dubchak, I -- Duplessis, S -- Ehlting, J -- Ellis, B -- Gendler, K -- Goodstein, D -- Gribskov, M -- Grimwood, J -- Groover, A -- Gunter, L -- Hamberger, B -- Heinze, B -- Helariutta, Y -- Henrissat, B -- Holligan, D -- Holt, R -- Huang, W -- Islam-Faridi, N -- Jones, S -- Jones-Rhoades, M -- Jorgensen, R -- Joshi, C -- Kangasjarvi, J -- Karlsson, J -- Kelleher, C -- Kirkpatrick, R -- Kirst, M -- Kohler, A -- Kalluri, U -- Larimer, F -- Leebens-Mack, J -- Leple, J-C -- Locascio, P -- Lou, Y -- Lucas, S -- Martin, F -- Montanini, B -- Napoli, C -- Nelson, D R -- Nelson, C -- Nieminen, K -- Nilsson, O -- Pereda, V -- Peter, G -- Philippe, R -- Pilate, G -- Poliakov, A -- Razumovskaya, J -- Richardson, P -- Rinaldi, C -- Ritland, K -- Rouze, P -- Ryaboy, D -- Schmutz, J -- Schrader, J -- Segerman, B -- Shin, H -- Siddiqui, A -- Sterky, F -- Terry, A -- Tsai, C-J -- Uberbacher, E -- Unneberg, P -- Vahala, J -- Wall, K -- Wessler, S -- Yang, G -- Yin, T -- Douglas, C -- Marra, M -- Sandberg, G -- Van de Peer, Y -- Rokhsar, D -- New York, N.Y. -- Science. 2006 Sep 15;313(5793):1596-604.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. gtk@ornl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16973872" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics ; Chromosome Mapping ; Computational Biology ; Evolution, Molecular ; Expressed Sequence Tags ; *Gene Duplication ; Gene Expression ; Genes, Plant ; *Genome, Plant ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Plant Proteins/chemistry/genetics ; Polymorphism, Single Nucleotide ; Populus/*genetics/growth & development/metabolism ; Protein Structure, Tertiary ; RNA, Plant/analysis ; RNA, Untranslated/analysis ; *Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    The genome of the simian and human malaria parasite Plasmodium knowlesi (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-10-10
    Description: Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the 'kra' monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia. Plasmodium knowlesi was the first malaria parasite species in which antigenic variation was demonstrated, and it has a close phylogenetic relationship to Plasmodium vivax, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood cell preference, absence of a dormant liver stage or 'hypnozoite' in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone) nuclear genome sequence. This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome and other sequenced Plasmodium genomes. In contrast to other Plasmodium genomes, putative variant antigen families are dispersed throughout the genome and are associated with intrachromosomal telomere repeats. One of these families, the KIRs, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656934/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656934/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pain, A -- Bohme, U -- Berry, A E -- Mungall, K -- Finn, R D -- Jackson, A P -- Mourier, T -- Mistry, J -- Pasini, E M -- Aslett, M A -- Balasubrammaniam, S -- Borgwardt, K -- Brooks, K -- Carret, C -- Carver, T J -- Cherevach, I -- Chillingworth, T -- Clark, T G -- Galinski, M R -- Hall, N -- Harper, D -- Harris, D -- Hauser, H -- Ivens, A -- Janssen, C S -- Keane, T -- Larke, N -- Lapp, S -- Marti, M -- Moule, S -- Meyer, I M -- Ormond, D -- Peters, N -- Sanders, M -- Sanders, S -- Sargeant, T J -- Simmonds, M -- Smith, F -- Squares, R -- Thurston, S -- Tivey, A R -- Walker, D -- White, B -- Zuiderwijk, E -- Churcher, C -- Quail, M A -- Cowman, A F -- Turner, C M R -- Rajandream, M A -- Kocken, C H M -- Thomas, A W -- Newbold, C I -- Barrell, B G -- Berriman, M -- 085775/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2008 Oct 9;455(7214):799-803. doi: 10.1038/nature07306.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. ap2@sanger.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18843368" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antigens, CD/chemistry/genetics ; Chromosomes/genetics ; Conserved Sequence ; Genes, Protozoan/genetics ; Genome, Protozoan/*genetics ; *Genomics ; Humans ; Macaca mulatta/*parasitology ; Malaria/*parasitology ; Molecular Sequence Data ; Plasmodium knowlesi/classification/*genetics/physiology ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry/genetics ; Sequence Analysis, DNA ; Telomere/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1 (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-10-23
    Description: The proto-oncogene KRAS is mutated in a wide array of human cancers, most of which are aggressive and respond poorly to standard therapies. Although the identification of specific oncogenes has led to the development of clinically effective, molecularly targeted therapies in some cases, KRAS has remained refractory to this approach. A complementary strategy for targeting KRAS is to identify gene products that, when inhibited, result in cell death only in the presence of an oncogenic allele. Here we have used systematic RNA interference to detect synthetic lethal partners of oncogenic KRAS and found that the non-canonical IkappaB kinase TBK1 was selectively essential in cells that contain mutant KRAS. Suppression of TBK1 induced apoptosis specifically in human cancer cell lines that depend on oncogenic KRAS expression. In these cells, TBK1 activated NF-kappaB anti-apoptotic signals involving c-Rel and BCL-XL (also known as BCL2L1) that were essential for survival, providing mechanistic insights into this synthetic lethal interaction. These observations indicate that TBK1 and NF-kappaB signalling are essential in KRAS mutant tumours, and establish a general approach for the rational identification of co-dependent pathways in cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783335/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783335/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barbie, David A -- Tamayo, Pablo -- Boehm, Jesse S -- Kim, So Young -- Moody, Susan E -- Dunn, Ian F -- Schinzel, Anna C -- Sandy, Peter -- Meylan, Etienne -- Scholl, Claudia -- Frohling, Stefan -- Chan, Edmond M -- Sos, Martin L -- Michel, Kathrin -- Mermel, Craig -- Silver, Serena J -- Weir, Barbara A -- Reiling, Jan H -- Sheng, Qing -- Gupta, Piyush B -- Wadlow, Raymond C -- Le, Hanh -- Hoersch, Sebastian -- Wittner, Ben S -- Ramaswamy, Sridhar -- Livingston, David M -- Sabatini, David M -- Meyerson, Matthew -- Thomas, Roman K -- Lander, Eric S -- Mesirov, Jill P -- Root, David E -- Gilliland, D Gary -- Jacks, Tyler -- Hahn, William C -- R01 CA129105/CA/NCI NIH HHS/ -- R01 CA129105-03/CA/NCI NIH HHS/ -- R01 CA130988/CA/NCI NIH HHS/ -- R01 CA130988-01A2/CA/NCI NIH HHS/ -- R33 CA128625/CA/NCI NIH HHS/ -- R33 CA128625-01A1/CA/NCI NIH HHS/ -- R33 CA128625-02/CA/NCI NIH HHS/ -- T32 CA009172/CA/NCI NIH HHS/ -- T32 CA09172-33/CA/NCI NIH HHS/ -- T32 GM007753/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Nov 5;462(7269):108-12. doi: 10.1038/nature08460. Epub 2009 Oct 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115 USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847166" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Apoptosis ; Cell Line, Tumor ; Cell Survival ; Gene Expression Profiling ; Genes, Lethal ; Genes, ras/*genetics ; Humans ; Lung Neoplasms/genetics/metabolism/pathology ; Neoplasms/genetics/metabolism/pathology ; Oncogene Protein p21(ras)/*genetics/*metabolism ; Protein-Serine-Threonine Kinases/antagonists & inhibitors/*metabolism ; Proto-Oncogene Proteins c-rel/metabolism ; *RNA Interference ; Signal Transduction ; bcl-X Protein/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    Losartan, an AT1 antagonist, prevents aortic aneurysm in a mouse model of Marfan syndrome (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-04-08
    Description: Aortic aneurysm and dissection are manifestations of Marfan syndrome (MFS), a disorder caused by mutations in the gene that encodes fibrillin-1. Selected manifestations of MFS reflect excessive signaling by the transforming growth factor-beta (TGF-beta) family of cytokines. We show that aortic aneurysm in a mouse model of MFS is associated with increased TGF-beta signaling and can be prevented by TGF-beta antagonists such as TGF-beta-neutralizing antibody or the angiotensin II type 1 receptor (AT1) blocker, losartan. AT1 antagonism also partially reversed noncardiovascular manifestations of MFS, including impaired alveolar septation. These data suggest that losartan, a drug already in clinical use for hypertension, merits investigation as a therapeutic strategy for patients with MFS and has the potential to prevent the major life-threatening manifestation of this disorder.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1482474/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1482474/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Habashi, Jennifer P -- Judge, Daniel P -- Holm, Tammy M -- Cohn, Ronald D -- Loeys, Bart L -- Cooper, Timothy K -- Myers, Loretha -- Klein, Erin C -- Liu, Guosheng -- Calvi, Carla -- Podowski, Megan -- Neptune, Enid R -- Halushka, Marc K -- Bedja, Djahida -- Gabrielson, Kathleen -- Rifkin, Daniel B -- Carta, Luca -- Ramirez, Francesco -- Huso, David L -- Dietz, Harry C -- K08 HL067056/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2006 Apr 7;312(5770):117-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16601194" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenergic beta-Antagonists/administration & dosage/therapeutic use ; Angiotensin II Type 1 Receptor Blockers/administration & dosage/*therapeutic use ; Animals ; Antibodies/immunology ; Aorta/pathology ; Aortic Aneurysm/etiology/*prevention & control ; *Disease Models, Animal ; Elastic Tissue/pathology ; Female ; Losartan/administration & dosage/*therapeutic use ; Lung/pathology ; Lung Diseases/drug therapy/pathology ; Marfan Syndrome/complications/*drug therapy/metabolism/pathology ; Mice ; Microfilament Proteins/genetics ; Mutation ; Neutralization Tests ; Pregnancy ; Pregnancy Complications/drug therapy ; Propranolol/administration & dosage/therapeutic use ; Pulmonary Alveoli/pathology ; Receptor, Angiotensin, Type 1/metabolism ; Signal Transduction ; Transforming Growth Factor beta/antagonists & inhibitors/immunology/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-02
    Description: Leguminous plants (such as peas and soybeans) and rhizobial soil bacteria are symbiotic partners that communicate through molecular signaling pathways, resulting in the formation of nodules on legume roots and occasionally stems that house nitrogen-fixing bacteria. Nodule formation has been assumed to be exclusively initiated by the binding of bacterial, host-specific lipochito-oligosaccharidic Nod factors, encoded by the nodABC genes, to kinase-like receptors of the plant. Here we show by complete genome sequencing of two symbiotic, photosynthetic, Bradyrhizobium strains, BTAi1 and ORS278, that canonical nodABC genes and typical lipochito-oligosaccharidic Nod factors are not required for symbiosis in some legumes. Mutational analyses indicated that these unique rhizobia use an alternative pathway to initiate symbioses, where a purine derivative may play a key role in triggering nodule formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Giraud, Eric -- Moulin, Lionel -- Vallenet, David -- Barbe, Valerie -- Cytryn, Eddie -- Avarre, Jean-Christophe -- Jaubert, Marianne -- Simon, Damien -- Cartieaux, Fabienne -- Prin, Yves -- Bena, Gilles -- Hannibal, Laure -- Fardoux, Joel -- Kojadinovic, Mila -- Vuillet, Laurie -- Lajus, Aurelie -- Cruveiller, Stephane -- Rouy, Zoe -- Mangenot, Sophie -- Segurens, Beatrice -- Dossat, Carole -- Franck, William L -- Chang, Woo-Suk -- Saunders, Elizabeth -- Bruce, David -- Richardson, Paul -- Normand, Philippe -- Dreyfus, Bernard -- Pignol, David -- Stacey, Gary -- Emerich, David -- Vermeglio, Andre -- Medigue, Claudine -- Sadowsky, Michael -- New York, N.Y. -- Science. 2007 Jun 1;316(5829):1307-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut de Recherche pour le Developpement, Centre de Cooperation International en Recherche Agronomique pour le Developpement, Institut National de la Recherche Agronomique, Universite Montpellier 2, France. giraud@mpl.ird.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17540897" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/genetics/metabolism ; Amidohydrolases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Bradyrhizobium/*genetics/growth & development/*physiology ; Cytokinins/metabolism ; Fabaceae/*microbiology ; Genes, Bacterial ; Genome, Bacterial ; Genomics ; Lipopolysaccharides/metabolism ; Molecular Sequence Data ; Mutation ; N-Acetylglucosaminyltransferases/genetics/metabolism ; Photosynthesis ; Plant Roots/microbiology ; Plant Stems/*microbiology ; Purines/biosynthesis ; Root Nodules, Plant/microbiology/*physiology ; Signal Transduction ; *Symbiosis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    An integrated genomic analysis of human glioblastoma multiforme (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-09-06
    Description: Glioblastoma multiforme (GBM) is the most common and lethal type of brain cancer. To identify the genetic alterations in GBMs, we sequenced 20,661 protein coding genes, determined the presence of amplifications and deletions using high-density oligonucleotide arrays, and performed gene expression analyses using next-generation sequencing technologies in 22 human tumor samples. This comprehensive analysis led to the discovery of a variety of genes that were not known to be altered in GBMs. Most notably, we found recurrent mutations in the active site of isocitrate dehydrogenase 1 (IDH1) in 12% of GBM patients. Mutations in IDH1 occurred in a large fraction of young patients and in most patients with secondary GBMs and were associated with an increase in overall survival. These studies demonstrate the value of unbiased genomic analyses in the characterization of human brain cancer and identify a potentially useful genetic alteration for the classification and targeted therapy of GBMs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820389/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820389/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Parsons, D Williams -- Jones, Sian -- Zhang, Xiaosong -- Lin, Jimmy Cheng-Ho -- Leary, Rebecca J -- Angenendt, Philipp -- Mankoo, Parminder -- Carter, Hannah -- Siu, I-Mei -- Gallia, Gary L -- Olivi, Alessandro -- McLendon, Roger -- Rasheed, B Ahmed -- Keir, Stephen -- Nikolskaya, Tatiana -- Nikolsky, Yuri -- Busam, Dana A -- Tekleab, Hanna -- Diaz, Luis A Jr -- Hartigan, James -- Smith, Doug R -- Strausberg, Robert L -- Marie, Suely Kazue Nagahashi -- Shinjo, Sueli Mieko Oba -- Yan, Hai -- Riggins, Gregory J -- Bigner, Darell D -- Karchin, Rachel -- Papadopoulos, Nick -- Parmigiani, Giovanni -- Vogelstein, Bert -- Velculescu, Victor E -- Kinzler, Kenneth W -- 5P50-NS-20023/NS/NINDS NIH HHS/ -- CA09547/CA/NCI NIH HHS/ -- CA108786/CA/NCI NIH HHS/ -- CA11898/CA/NCI NIH HHS/ -- CA121113/CA/NCI NIH HHS/ -- CA43460/CA/NCI NIH HHS/ -- CA57345/CA/NCI NIH HHS/ -- CA62924/CA/NCI NIH HHS/ -- NS052507/NS/NINDS NIH HHS/ -- P50 CA062924/CA/NCI NIH HHS/ -- P50 CA062924-160017/CA/NCI NIH HHS/ -- R01 CA121113/CA/NCI NIH HHS/ -- R01 CA121113-04/CA/NCI NIH HHS/ -- R01 CA140316/CA/NCI NIH HHS/ -- R37 CA043460/CA/NCI NIH HHS/ -- R37 CA043460-27/CA/NCI NIH HHS/ -- R37 CA057345/CA/NCI NIH HHS/ -- R37 CA057345-13/CA/NCI NIH HHS/ -- R37 CA057345-17/CA/NCI NIH HHS/ -- R37 CA057345-18/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Sep 26;321(5897):1807-12. doi: 10.1126/science.1164382. Epub 2008 Sep 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ludwig Center for Cancer Genetics and Therapeutics, and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772396" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Brain Neoplasms/*genetics/mortality ; Female ; Gene Amplification ; Gene Dosage ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Genome, Human ; Glioblastoma/*genetics/mortality ; Humans ; Isocitrate Dehydrogenase/chemistry/*genetics ; Male ; Middle Aged ; *Mutation ; Mutation, Missense ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Signal Transduction ; Survival Rate
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Genome of the host-cell transforming parasite Theileria annulata compared with T. parva (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-05
    Description: Theileria annulata and T. parva are closely related protozoan parasites that cause lymphoproliferative diseases of cattle. We sequenced the genome of T. annulata and compared it with that of T. parva to understand the mechanisms underlying transformation and tropism. Despite high conservation of gene sequences and synteny, the analysis reveals unequally expanded gene families and species-specific genes. We also identify divergent families of putative secreted polypeptides that may reduce immune recognition, candidate regulators of host-cell transformation, and a Theileria-specific protein domain [frequently associated in Theileria (FAINT)] present in a large number of secreted proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pain, Arnab -- Renauld, Hubert -- Berriman, Matthew -- Murphy, Lee -- Yeats, Corin A -- Weir, William -- Kerhornou, Arnaud -- Aslett, Martin -- Bishop, Richard -- Bouchier, Christiane -- Cochet, Madeleine -- Coulson, Richard M R -- Cronin, Ann -- de Villiers, Etienne P -- Fraser, Audrey -- Fosker, Nigel -- Gardner, Malcolm -- Goble, Arlette -- Griffiths-Jones, Sam -- Harris, David E -- Katzer, Frank -- Larke, Natasha -- Lord, Angela -- Maser, Pascal -- McKellar, Sue -- Mooney, Paul -- Morton, Fraser -- Nene, Vishvanath -- O'Neil, Susan -- Price, Claire -- Quail, Michael A -- Rabbinowitsch, Ester -- Rawlings, Neil D -- Rutter, Simon -- Saunders, David -- Seeger, Kathy -- Shah, Trushar -- Squares, Robert -- Squares, Steven -- Tivey, Adrian -- Walker, Alan R -- Woodward, John -- Dobbelaere, Dirk A E -- Langsley, Gordon -- Rajandream, Marie-Adele -- McKeever, Declan -- Shiels, Brian -- Tait, Andrew -- Barrell, Bart -- Hall, Neil -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2005 Jul 1;309(5731):131-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. ap2@sanger.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15994557" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Cattle ; Cell Proliferation ; Chromosome Mapping ; Chromosomes/genetics ; Conserved Sequence ; Genes, Protozoan ; *Genome, Protozoan ; Life Cycle Stages ; Lipid Metabolism ; Lymphocytes/cytology/parasitology ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Protein Sorting Signals/genetics ; Protein Structure, Tertiary ; Proteome ; Protozoan Proteins/chemistry/*genetics/physiology ; Sequence Analysis, DNA ; Species Specificity ; Synteny ; Telomere/genetics ; Theileria annulata/*genetics/growth & development/immunology/pathogenicity ; Theileria parva/*genetics/growth & development/immunology/pathogenicity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-05-30
    Description: Transcribing RNA polymerases oscillate between three stable states, two of which, pre- and posttranslocated, were previously subjected to x-ray crystal structure determination. We report here the crystal structure of RNA polymerase II in the third state, the reverse translocated, or "backtracked" state. The defining feature of the backtracked structure is a binding site for the first backtracked nucleotide. This binding site is occupied in case of nucleotide misincorporation in the RNA or damage to the DNA, and is termed the "P" site because it supports proofreading. The predominant mechanism of proofreading is the excision of a dinucleotide in the presence of the elongation factor SII (TFIIS). Structure determination of a cocrystal with TFIIS reveals a rearrangement whereby cleavage of the RNA may take place.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718261/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718261/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Dong -- Bushnell, David A -- Huang, Xuhui -- Westover, Kenneth D -- Levitt, Michael -- Kornberg, Roger D -- GM036559/GM/NIGMS NIH HHS/ -- GM041455/GM/NIGMS NIH HHS/ -- GM049985/GM/NIGMS NIH HHS/ -- K99 GM085136/GM/NIGMS NIH HHS/ -- K99 GM085136-01/GM/NIGMS NIH HHS/ -- R00 GM085136/GM/NIGMS NIH HHS/ -- R01 GM036659/GM/NIGMS NIH HHS/ -- R01 GM041455/GM/NIGMS NIH HHS/ -- R01 GM049985/GM/NIGMS NIH HHS/ -- R01 GM049985-16/GM/NIGMS NIH HHS/ -- R37 GM036659/GM/NIGMS NIH HHS/ -- R37 GM036659-22/GM/NIGMS NIH HHS/ -- R37 GM041455/GM/NIGMS NIH HHS/ -- R37 GM041455-20/GM/NIGMS NIH HHS/ -- U54 GM072970/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 May 29;324(5931):1203-6. doi: 10.1126/science.1168729.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478184" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pair Mismatch ; Crystallography, X-Ray ; Guanosine Monophosphate/chemistry/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Oligoribonucleotides/chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/chemistry/*metabolism ; RNA Polymerase II/*chemistry/*metabolism ; Saccharomyces cerevisiae/*enzymology ; *Transcription, Genetic ; Transcriptional Elongation Factors/chemistry/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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