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  • 1
    Publication Date: 2008-04-25
    Description: Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836516/" 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/PMC2836516/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ming, Ray -- Hou, Shaobin -- Feng, Yun -- Yu, Qingyi -- Dionne-Laporte, Alexandre -- Saw, Jimmy H -- Senin, Pavel -- Wang, Wei -- Ly, Benjamin V -- Lewis, Kanako L T -- Salzberg, Steven L -- Feng, Lu -- Jones, Meghan R -- Skelton, Rachel L -- Murray, Jan E -- Chen, Cuixia -- Qian, Wubin -- Shen, Junguo -- Du, Peng -- Eustice, Moriah -- Tong, Eric -- Tang, Haibao -- Lyons, Eric -- Paull, Robert E -- Michael, Todd P -- Wall, Kerr -- Rice, Danny W -- Albert, Henrik -- Wang, Ming-Li -- Zhu, Yun J -- Schatz, Michael -- Nagarajan, Niranjan -- Acob, Ricelle A -- Guan, Peizhu -- Blas, Andrea -- Wai, Ching Man -- Ackerman, Christine M -- Ren, Yan -- Liu, Chao -- Wang, Jianmei -- Wang, Jianping -- Na, Jong-Kuk -- Shakirov, Eugene V -- Haas, Brian -- Thimmapuram, Jyothi -- Nelson, David -- Wang, Xiyin -- Bowers, John E -- Gschwend, Andrea R -- Delcher, Arthur L -- Singh, Ratnesh -- Suzuki, Jon Y -- Tripathi, Savarni -- Neupane, Kabi -- Wei, Hairong -- Irikura, Beth -- Paidi, Maya -- Jiang, Ning -- Zhang, Wenli -- Presting, Gernot -- Windsor, Aaron -- Navajas-Perez, Rafael -- Torres, Manuel J -- Feltus, F Alex -- Porter, Brad -- Li, Yingjun -- Burroughs, A Max -- Luo, Ming-Cheng -- Liu, Lei -- Christopher, David A -- Mount, Stephen M -- Moore, Paul H -- Sugimura, Tak -- Jiang, Jiming -- Schuler, Mary A -- Friedman, Vikki -- Mitchell-Olds, Thomas -- Shippen, Dorothy E -- dePamphilis, Claude W -- Palmer, Jeffrey D -- Freeling, Michael -- Paterson, Andrew H -- Gonsalves, Dennis -- Wang, Lei -- Alam, Maqsudul -- R01 GM083873/GM/NIGMS NIH HHS/ -- R01 GM083873-05/GM/NIGMS NIH HHS/ -- R01 LM006845/LM/NLM NIH HHS/ -- R01 LM006845-08/LM/NLM NIH HHS/ -- England -- Nature. 2008 Apr 24;452(7190):991-6. doi: 10.1038/nature06856.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18432245" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics ; Carica/*genetics ; Contig Mapping ; Databases, Genetic ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Molecular Sequence Data ; Plants, Genetically Modified/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription Factors/genetics ; Tropical Climate
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2007-01-16
    Description: We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2080659/" 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/PMC2080659/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carlton, Jane M -- Hirt, Robert P -- Silva, Joana C -- Delcher, Arthur L -- Schatz, Michael -- Zhao, Qi -- Wortman, Jennifer R -- Bidwell, Shelby L -- Alsmark, U Cecilia M -- Besteiro, Sebastien -- Sicheritz-Ponten, Thomas -- Noel, Christophe J -- Dacks, Joel B -- Foster, Peter G -- Simillion, Cedric -- Van de Peer, Yves -- Miranda-Saavedra, Diego -- Barton, Geoffrey J -- Westrop, Gareth D -- Muller, Sylke -- Dessi, Daniele -- Fiori, Pier Luigi -- Ren, Qinghu -- Paulsen, Ian -- Zhang, Hanbang -- Bastida-Corcuera, Felix D -- Simoes-Barbosa, Augusto -- Brown, Mark T -- Hayes, Richard D -- Mukherjee, Mandira -- Okumura, Cheryl Y -- Schneider, Rachel -- Smith, Alias J -- Vanacova, Stepanka -- Villalvazo, Maria -- Haas, Brian J -- Pertea, Mihaela -- Feldblyum, Tamara V -- Utterback, Terry R -- Shu, Chung-Li -- Osoegawa, Kazutoyo -- de Jong, Pieter J -- Hrdy, Ivan -- Horvathova, Lenka -- Zubacova, Zuzana -- Dolezal, Pavel -- Malik, Shehre-Banoo -- Logsdon, John M Jr -- Henze, Katrin -- Gupta, Arti -- Wang, Ching C -- Dunne, Rebecca L -- Upcroft, Jacqueline A -- Upcroft, Peter -- White, Owen -- Salzberg, Steven L -- Tang, Petrus -- Chiu, Cheng-Hsun -- Lee, Ying-Shiung -- Embley, T Martin -- Coombs, Graham H -- Mottram, Jeremy C -- Tachezy, Jan -- Fraser-Liggett, Claire M -- Johnson, Patricia J -- 072031/Wellcome Trust/United Kingdom -- G0000508/Medical Research Council/United Kingdom -- G0000508(56841)/Medical Research Council/United Kingdom -- G9722968/Medical Research Council/United Kingdom -- G9722968(65078)/Medical Research Council/United Kingdom -- R01 LM006845/LM/NLM NIH HHS/ -- R01 LM006845-08/LM/NLM NIH HHS/ -- R01 LM007938/LM/NLM NIH HHS/ -- R01 LM007938-04/LM/NLM NIH HHS/ -- U01 AI050913/AI/NIAID NIH HHS/ -- U01 AI050913-01A1/AI/NIAID NIH HHS/ -- U01 AI050913-02/AI/NIAID NIH HHS/ -- UO1 AI50913-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2007 Jan 12;315(5809):207-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, 9712 Medical Research Drive, Rockville, MD 20850, USA. jane.carlton@med.nyu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17218520" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Transport/genetics ; DNA Transposable Elements ; DNA, Protozoan/genetics ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Genome, Protozoan ; Humans ; Hydrogen/metabolism ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Data ; Multigene Family ; Organelles/metabolism ; Oxidative Stress/genetics ; Peptide Hydrolases/genetics/metabolism ; Protozoan Proteins/genetics/physiology ; RNA Processing, Post-Transcriptional ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Sexually Transmitted Diseases/parasitology ; Trichomonas Infections/parasitology/transmission ; Trichomonas vaginalis/cytology/*genetics/metabolism/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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  • 3
    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
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  • 4
    Publication Date: 2005-07-16
    Description: A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉El-Sayed, Najib M -- Myler, Peter J -- Blandin, Gaelle -- Berriman, Matthew -- Crabtree, Jonathan -- Aggarwal, Gautam -- Caler, Elisabet -- Renauld, Hubert -- Worthey, Elizabeth A -- Hertz-Fowler, Christiane -- Ghedin, Elodie -- Peacock, Christopher -- Bartholomeu, Daniella C -- Haas, Brian J -- Tran, Anh-Nhi -- Wortman, Jennifer R -- Alsmark, U Cecilia M -- Angiuoli, Samuel -- Anupama, Atashi -- Badger, Jonathan -- Bringaud, Frederic -- Cadag, Eithon -- Carlton, Jane M -- Cerqueira, Gustavo C -- Creasy, Todd -- Delcher, Arthur L -- Djikeng, Appolinaire -- Embley, T Martin -- Hauser, Christopher -- Ivens, Alasdair C -- Kummerfeld, Sarah K -- Pereira-Leal, Jose B -- Nilsson, Daniel -- Peterson, Jeremy -- Salzberg, Steven L -- Shallom, Joshua -- Silva, Joana C -- Sundaram, Jaideep -- Westenberger, Scott -- White, Owen -- Melville, Sara E -- Donelson, John E -- Andersson, Bjorn -- Stuart, Kenneth D -- Hall, Neil -- AI045039/AI/NIAID NIH HHS/ -- AI45038/AI/NIAID NIH HHS/ -- AI45061/AI/NIAID NIH HHS/ -- R01 AI043062/AI/NIAID NIH HHS/ -- U01 AI040599/AI/NIAID NIH HHS/ -- U01 AI043062/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):404-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. nelsayed@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16020724" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; Chromosomes/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Protozoan ; *Genome, Protozoan ; Genomics ; Leishmania major/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Mutation ; Phylogeny ; Plastids/genetics ; *Proteome ; Protozoan Proteins/chemistry/*genetics/physiology ; Recombination, Genetic ; Retroelements ; Species Specificity ; Symbiosis ; Synteny ; Telomere/genetics ; Trypanosoma brucei brucei/chemistry/*genetics/metabolism ; Trypanosoma cruzi/chemistry/*genetics/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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  • 5
    Publication Date: 2007-09-22
    Description: Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the approximately 90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict approximately 11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during approximately 350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613796/" 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/PMC2613796/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ghedin, Elodie -- Wang, Shiliang -- Spiro, David -- Caler, Elisabet -- Zhao, Qi -- Crabtree, Jonathan -- Allen, Jonathan E -- Delcher, Arthur L -- Guiliano, David B -- Miranda-Saavedra, Diego -- Angiuoli, Samuel V -- Creasy, Todd -- Amedeo, Paolo -- Haas, Brian -- El-Sayed, Najib M -- Wortman, Jennifer R -- Feldblyum, Tamara -- Tallon, Luke -- Schatz, Michael -- Shumway, Martin -- Koo, Hean -- Salzberg, Steven L -- Schobel, Seth -- Pertea, Mihaela -- Pop, Mihai -- White, Owen -- Barton, Geoffrey J -- Carlow, Clotilde K S -- Crawford, Michael J -- Daub, Jennifer -- Dimmic, Matthew W -- Estes, Chris F -- Foster, Jeremy M -- Ganatra, Mehul -- Gregory, William F -- Johnson, Nicholas M -- Jin, Jinming -- Komuniecki, Richard -- Korf, Ian -- Kumar, Sanjay -- Laney, Sandra -- Li, Ben-Wen -- Li, Wen -- Lindblom, Tim H -- Lustigman, Sara -- Ma, Dong -- Maina, Claude V -- Martin, David M A -- McCarter, James P -- McReynolds, Larry -- Mitreva, Makedonka -- Nutman, Thomas B -- Parkinson, John -- Peregrin-Alvarez, Jose M -- Poole, Catherine -- Ren, Qinghu -- Saunders, Lori -- Sluder, Ann E -- Smith, Katherine -- Stanke, Mario -- Unnasch, Thomas R -- Ware, Jenna -- Wei, Aguan D -- Weil, Gary -- Williams, Deryck J -- Zhang, Yinhua -- Williams, Steven A -- Fraser-Liggett, Claire -- Slatko, Barton -- Blaxter, Mark L -- Scott, Alan L -- R01 AI048562/AI/NIAID NIH HHS/ -- R01 AI048562-09/AI/NIAID NIH HHS/ -- R01 LM006845/LM/NLM NIH HHS/ -- R01 LM006845-08/LM/NLM NIH HHS/ -- R01 LM007938/LM/NLM NIH HHS/ -- R01 LM007938-04/LM/NLM NIH HHS/ -- R15 ES013128/ES/NIEHS NIH HHS/ -- R15 ES013128-01/ES/NIEHS NIH HHS/ -- U01 AI048828/AI/NIAID NIH HHS/ -- U01-AI50903/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 21;317(5845):1756-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA. GhedinE@dom.pitt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17885136" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brugia malayi/*genetics/physiology ; Caenorhabditis/genetics ; Drosophila melanogaster/genetics ; Drug Resistance/genetics ; Filariasis/parasitology ; *Genome, Helminth ; Humans ; Molecular Sequence Data
    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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