Author Report for: Larke NNo contact information in database for Larke N
Pain A, Bohme U, Berry AE, Mungall K, Finn RD, Jackson AP, Mourier T, Mistry J, Pasini EM and Berriman M <44 more author(s)> Pain A, Bohme U, Berry AE, Mungall K, Finn RD, Jackson AP, Mourier T, Mistry J, Pasini EM, Aslett MA, Balasubrammaniam S, Borgwardt K, Brooks K, Carret C, Carver TJ, Cherevach I, Chillingworth T, Clark TG, Galinski MR, Hall N, Harper D, Harris D, Hauser H, Ivens A, Janssen CS, Keane T, Larke N, Lapp S, Marti M, Moule S, Meyer IM, Ormond D, Peters N, Sanders M, Sanders S, Sargeant TJ, Simmonds M, Smith F, Squares R, Thurston S, Tivey AR, Walker D, White B, Zuiderwijk E, Churcher C, Quail MA, Cowman AF, Turner CM, Rajandream MA, Kocken CH, Thomas AW, Newbold CI, Barrell BG, Berriman M (- 44) Ref: Nature, 455:799, 2008 : PubMed ESTHER: Pain_2008_Nature_455_799 PubMedSearch: Pain 2008 Nature 455 799 PubMedID: 18843368 Gene_locus related to this paper: plakh-b3kz42, plakh-b3kz45, plakh-b3l0y4, plakh-b3l1r3, plakh-b3l8u5, plakh-b3l336, plakh-b3l571, plakh-b3la01, plakh-b3lb44 Abstract 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. Title: Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes Sebaihia M, Peck MW, Minton NP, Thomson NR, Holden MT, Mitchell WJ, Carter AT, Bentley SD, Mason DR and Parkhill J <24 more author(s)> Sebaihia M, Peck MW, Minton NP, Thomson NR, Holden MT, Mitchell WJ, Carter AT, Bentley SD, Mason DR, Crossman L, Paul CJ, Ivens A, Wells-Bennik MH, Davis IJ, Cerdeno-Tarraga AM, Churcher C, Quail MA, Chillingworth T, Feltwell T, Fraser A, Goodhead I, Hance Z, Jagels K, Larke N, Maddison M, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Sanders M, Simmonds M, White B, Whithead S, Parkhill J (- 24) Ref: Genome Res, 17:1082, 2007 : PubMed ESTHER: Sebaihia_2007_Genome.Res_17_1082 PubMedSearch: Sebaihia 2007 Genome.Res 17 1082 PubMedID: 17519437 Gene_locus related to this paper: clobh-A5I3I2, clobh-A51055, clob1-a7fqm2, clob1-a7fv94, clobl-a7gbn0, clobh-pip, clobh-a5i3m0 Abstract Clostridium botulinum is a heterogeneous Gram-positive species that comprises four genetically and physiologically distinct groups of bacteria that share the ability to produce botulinum neurotoxin, the most poisonous toxin known to man, and the causative agent of botulism, a severe disease of humans and animals. We report here the complete genome sequence of a representative of Group I (proteolytic) C. botulinum (strain Hall A, ATCC 3502). The genome consists of a chromosome (3,886,916 bp) and a plasmid (16,344 bp), which carry 3650 and 19 predicted genes, respectively. Consistent with the proteolytic phenotype of this strain, the genome harbors a large number of genes encoding secreted proteases and enzymes involved in uptake and metabolism of amino acids. The genome also reveals a hitherto unknown ability of C. botulinum to degrade chitin. There is a significant lack of recently acquired DNA, indicating a stable genomic content, in strong contrast to the fluid genome of Clostridium difficile, which can form longer-term relationships with its host. Overall, the genome indicates that C. botulinum is adapted to a saprophytic lifestyle both in soil and aquatic environments. This pathogen relies on its toxin to rapidly kill a wide range of prey species, and to gain access to nutrient sources, it releases a large number of extracellular enzymes to soften and destroy rotting or decayed tissues. Title: The genome of the African trypanosome Trypanosoma brucei Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE and El-Sayed NM <92 more author(s)> Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, Bohme U, Hannick L, Aslett MA, Shallom J, Marcello L, Hou L, Wickstead B, Alsmark UC, Arrowsmith C, Atkin RJ, Barron AJ, Bringaud F, Brooks K, Carrington M, Cherevach I, Chillingworth TJ, Churcher C, Clark LN, Corton CH, Cronin A, Davies RM, Doggett J, Djikeng A, Feldblyum T, Field MC, Fraser A, Goodhead I, Hance Z, Harper D, Harris BR, Hauser H, Hostetler J, Ivens A, Jagels K, Johnson D, Johnson J, Jones K, Kerhornou AX, Koo H, Larke N, Landfear S, Larkin C, Leech V, Line A, Lord A, MacLeod A, Mooney PJ, Moule S, Martin DM, Morgan GW, Mungall K, Norbertczak H, Ormond D, Pai G, Peacock CS, Peterson J, Quail MA, Rabbinowitsch E, Rajandream MA, Reitter C, Salzberg SL, Sanders M, Schobel S, Sharp S, Simmonds M, Simpson AJ, Tallon L, Turner CM, Tait A, Tivey AR, Van Aken S, Walker D, Wanless D, Wang S, White B, White O, Whitehead S, Woodward J, Wortman J, Adams MD, Embley TM, Gull K, Ullu E, Barry JD, Fairlamb AH, Opperdoes F, Barrell BG, Donelson JE, Hall N, Fraser CM, Melville SE, El-Sayed NM (- 92) Ref: Science, 309:416, 2005 : PubMed ESTHER: Berriman_2005_Science_309_416 PubMedSearch: Berriman 2005 Science 309 416 PubMedID: 16020726 Gene_locus related to this paper: tryb2-q6h9e3, tryb2-q6ha27, tryb2-q38cd5, tryb2-q38cd6, tryb2-q38cd7, tryb2-q38dc1, tryb2-q38de4, tryb2-q38ds6, tryb2-q38dx1, tryb2-q380z6, tryb2-q382c1, tryb2-q382l4, tryb2-q383a9, tryb2-q386e3, tryb2-q387r7, tryb2-q388n1, tryb2-q389w3, trybr-PEPTB, trycr-q4cq28, trycr-q4cq94, trycr-q4cq95, trycr-q4cq96, trycr-q4csm0, trycr-q4cwv3, trycr-q4cx66, trycr-q4cxr6, trycr-q4cyc5, trycr-q4cyf6, trycr-q4d3a2, trycr-q4d3x3, trycr-q4d3y4, trycr-q4d6h1, trycr-q4d8h8, trycr-q4d8h9, trycr-q4d8i0, trycr-q4d786, trycr-q4d975, trycr-q4da08, trycr-q4dap6, trycr-q4dbm2, trycr-q4dbn1, trycr-q4ddw7, trycr-q4de42, trycr-q4dhn8, trycr-q4dkk8, trycr-q4dkk9, trycr-q4dm56, trycr-q4dqa6, trycr-q4dt91, trycr-q4dvp2, trycr-q4dw34, trycr-q4dwm3, trycr-q4dy49, trycr-q4dy82, trycr-q4dzp6, trycr-q4e3m8, trycr-q4e4t5, trycr-q4e5d1, trycr-q4e5z2 Abstract African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma brucei. The 26-megabase genome contains 9068 predicted genes, including approximately 900 pseudogenes and approximately 1700 T. brucei-specific genes. Large subtelomeric arrays contain an archive of 806 variant surface glycoprotein (VSG) genes used by the parasite to evade the mammalian immune system. Most VSG genes are pseudogenes, which may be used to generate expressed mosaic genes by ectopic recombination. Comparisons of the cytoskeleton and endocytic trafficking systems with those of humans and other eukaryotic organisms reveal major differences. A comparison of metabolic pathways encoded by the genomes of T. brucei, T. cruzi, and Leishmania major reveals the least overall metabolic capability in T. brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified. Title: Extensive DNA inversions in the B. fragilis genome control variable gene expression Cerdeno-Tarraga AM, Patrick S, Crossman LC, Blakely G, Abratt V, Lennard N, Poxton I, Duerden B, Harris B and Parkhill J <15 more author(s)> Cerdeno-Tarraga AM, Patrick S, Crossman LC, Blakely G, Abratt V, Lennard N, Poxton I, Duerden B, Harris B, Quail MA, Barron A, Clark L, Corton C, Doggett J, Holden MT, Larke N, Line A, Lord A, Norbertczak H, Ormond D, Price C, Rabbinowitsch E, Woodward J, Barrell B, Parkhill J (- 15) Ref: Science, 307:1463, 2005 : PubMed ESTHER: Cerdeno-Tarraga_2005_Science_307_1463 PubMedSearch: Cerdeno-Tarraga 2005 Science 307 1463 PubMedID: 15746427 Gene_locus related to this paper: bacfn-q5l8p8, bacfn-q5lef1, bacfn-q5lh43, bacfn-q5lhv2, bacfr-q64mh3, bacfr-q64n33, bacfr-q64qs3, bacfr-q64t24, bacfr-q64uj8, bacfr-q64vx6, bacfr-q64wh2, bacfr-q64xp9, bacfr-q650j0 Abstract The obligately anaerobic bacterium Bacteroides fragilis, an opportunistic pathogen and inhabitant of the normal human colonic microbiota, exhibits considerable within-strain phase and antigenic variation of surface components. The complete genome sequence has revealed an unusual breadth (in number and in effect) of DNA inversion events that potentially control expression of many different components, including surface and secreted components, regulatory molecules, and restriction-modification proteins. Invertible promoters of two different types (12 group 1 and 11 group 2) were identified. One group has inversion crossover (fix) sites similar to the hix sites of Salmonella typhimurium. There are also four independent intergenic shufflons that potentially alter the expression and function of varied genes. The composition of the 10 different polysaccharide biosynthesis gene clusters identified (7 with associated invertible promoters) suggests a mechanism of synthesis similar to the O-antigen capsules of Escherichia coli. Title: The genome of the kinetoplastid parasite, Leishmania major Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Rajandream MA, Adlem E and Myler PJ <91 more author(s)> Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Rajandream MA, Adlem E, Aert R, Anupama A, Apostolou Z, Attipoe P, Bason N, Bauser C, Beck A, Beverley SM, Bianchettin G, Borzym K, Bothe G, Bruschi CV, Collins M, Cadag E, Ciarloni L, Clayton C, Coulson RM, Cronin A, Cruz AK, Davies RM, De Gaudenzi J, Dobson DE, Duesterhoeft A, Fazelina G, Fosker N, Frasch AC, Fraser A, Fuchs M, Gabel C, Goble A, Goffeau A, Harris D, Hertz-Fowler C, Hilbert H, Horn D, Huang Y, Klages S, Knights A, Kube M, Larke N, Litvin L, Lord A, Louie T, Marra M, Masuy D, Matthews K, Michaeli S, Mottram JC, Muller-Auer S, Munden H, Nelson S, Norbertczak H, Oliver K, O'Neil S, Pentony M, Pohl TM, Price C, Purnelle B, Quail MA, Rabbinowitsch E, Reinhardt R, Rieger M, Rinta J, Robben J, Robertson L, Ruiz JC, Rutter S, Saunders D, Schafer M, Schein J, Schwartz DC, Seeger K, Seyler A, Sharp S, Shin H, Sivam D, Squares R, Squares S, Tosato V, Vogt C, Volckaert G, Wambutt R, Warren T, Wedler H, Woodward J, Zhou S, Zimmermann W, Smith DF, Blackwell JM, Stuart KD, Barrell B, Myler PJ (- 91) Ref: Science, 309:436, 2005 : PubMed ESTHER: Ivens_2005_Science_309_436 PubMedSearch: Ivens 2005 Science 309 436 PubMedID: 16020728 Gene_locus related to this paper: leima-e9ady6, leima-L2464.12, leima-L2802.02, leima-OPB, leima-q4fw33, leima-q4fwg8, leima-q4fwj0, leima-q4fya7, leima-q4q0a1, leima-q4q0t5, leima-q4q0v0, leima-q4q1h9, leima-q4q2c9, leima-q4q4j7, leima-q4q4t6, leima-q4q5j1, leima-q4q6e9, leima-q4q7v8, leima-q4q8a8, leima-q4q9g9, leima-q4q080, leima-q4q398, leima-q4q615, leima-q4q819, leima-q4q871, leima-q4q942, leima-q4qae7, leima-q4qb85, leima-q4qdz7, leima-q4qe26, leima-q4qe31, leima-q4qe85, leima-q4qe86, leima-q4qe87, leima-q4qe90, leima-q4qec8, leima-q4qgz4, leima-q4qgz5, leima-q4qhs0, leima-q4qj45 Abstract Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The organization of protein-coding genes into long, strand-specific, polycistronic clusters and lack of general transcription factors in the L. major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryp) genomes suggest that the mechanisms regulating RNA polymerase II-directed transcription are distinct from those operating in other eukaryotes, although the trypanosomatids appear capable of chromatin remodeling. Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression. Title: Genome of the host-cell transforming parasite Theileria annulata compared with T. parva Pain A, Renauld H, Berriman M, Murphy L, Yeats CA, Weir W, Kerhornou A, Aslett M, Bishop R and Hall N <40 more author(s)> Pain A, Renauld H, Berriman M, Murphy L, Yeats CA, Weir W, Kerhornou A, Aslett M, Bishop R, Bouchier C, Cochet M, Coulson RM, Cronin A, de Villiers EP, Fraser A, Fosker N, Gardner M, Goble A, Griffiths-Jones S, Harris DE, Katzer F, Larke N, Lord A, Maser P, McKellar S, Mooney P, Morton F, Nene V, O'Neil S, Price C, Quail MA, Rabbinowitsch E, Rawlings ND, Rutter S, Saunders D, Seeger K, Shah T, Squares R, Squares S, Tivey A, Walker AR, Woodward J, Dobbelaere DA, Langsley G, Rajandream MA, McKeever D, Shiels B, Tait A, Barrell B, Hall N (- 40) Ref: Science, 309:131, 2005 : PubMed ESTHER: Pain_2005_Science_309_131 PubMedSearch: Pain 2005 Science 309 131 PubMedID: 15994557 Gene_locus related to this paper: thean-q4u9u6, thean-q4ub48, thean-q4ubz1, thean-q4uc78, thean-q4uc93, thean-q4uck1, thean-q4udw9, thean-q4ue56, thean-q4uf06, thean-q4ug98, thean-q4uhj9, thepa-q4n349 Abstract 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. Title: Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster Pain A, Woodward J, Quail MA, Anderson MJ, Clark R, Collins M, Fosker N, Fraser A, Harris D and Hall N <15 more author(s)> Pain A, Woodward J, Quail MA, Anderson MJ, Clark R, Collins M, Fosker N, Fraser A, Harris D, Larke N, Murphy L, Humphray S, O'Neil S, Pertea M, Price C, Rabbinowitsch E, Rajandream MA, Salzberg S, Saunders D, Seeger K, Sharp S, Warren T, Denning DW, Barrell B, Hall N (- 15) Ref: Fungal Genet Biol, 41:443, 2004 : PubMed ESTHER: Pain_2004_Fungal.Genet.Biol_41_443 PubMedSearch: Pain 2004 Fungal.Genet.Biol 41 443 PubMedID: 14998527 Gene_locus related to this paper: aspfu-q6my76, aspfu-q6myf7, aspfu-q6myz3 Abstract Aspergillus fumigatus is the most ubiquitous opportunistic filamentous fungal pathogen of human. As an initial step toward sequencing the entire genome of A. fumigatus, which is estimated to be approximately 30 Mb in size, we have sequenced a 922 kb region, contained within 16 overlapping bacterial artificial chromosome (BAC) clones. Fifty-four percent of the DNA is predicted to be coding with 341 putative protein coding genes. Functional classification of the proteins showed the presence of a higher proportion of enzymes and membrane transporters when compared to those of Saccharomyces cerevisiae. In addition to the nitrate assimilation gene cluster, the quinate utilisation gene cluster is also present on this 922 kb genomic sequence. We observed large scale synteny between A. fumigatus and Aspergillus nidulans by comparing this sequence to the A. nidulans genetic map of linkage group VIII. Title: Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13 Hall N, Pain A, Berriman M, Churcher C, Harris B, Harris D, Mungall K, Bowman S, Atkin R and Barrell BG <70 more author(s)> Hall N, Pain A, Berriman M, Churcher C, Harris B, Harris D, Mungall K, Bowman S, Atkin R, Baker S, Barron A, Brooks K, Buckee CO, Burrows C, Cherevach I, Chillingworth C, Chillingworth T, Christodoulou Z, Clark L, Clark R, Corton C, Cronin A, Davies R, Davis P, Dear P, Dearden F, Doggett J, Feltwell T, Goble A, Goodhead I, Gwilliam R, Hamlin N, Hance Z, Harper D, Hauser H, Hornsby T, Holroyd S, Horrocks P, Humphray S, Jagels K, James KD, Johnson D, Kerhornou A, Knights A, Konfortov B, Kyes S, Larke N, Lawson D, Lennard N, Line A, Maddison M, McLean J, Mooney P, Moule S, Murphy L, Oliver K, Ormond D, Price C, Quail MA, Rabbinowitsch E, Rajandream MA, Rutter S, Rutherford KM, Sanders M, Simmonds M, Seeger K, Sharp S, Smith R, Squares R, Squares S, Stevens K, Taylor K, Tivey A, Unwin L, Whitehead S, Woodward J, Sulston JE, Craig A, Newbold C, Barrell BG (- 70) Ref: Nature, 419:527, 2002 : PubMed ESTHER: Hall_2002_Nature_419_527 PubMedSearch: Hall 2002 Nature 419 527 PubMedID: 12368867 Gene_locus related to this paper: plaf7-c0h4q4, plafa-MAL6P1.135, plafa-PFD0185C, plafa-PFI1775W, plafa-PFI1800W Abstract Since the sequencing of the first two chromosomes of the malaria parasite, Plasmodium falciparum, there has been a concerted effort to sequence and assemble the entire genome of this organism. Here we report the sequence of chromosomes 1, 3-9 and 13 of P. falciparum clone 3D7--these chromosomes account for approximately 55% of the total genome. We describe the methods used to map, sequence and annotate these chromosomes. By comparing our assemblies with the optical map, we indicate the completeness of the resulting sequence. During annotation, we assign Gene Ontology terms to the predicted gene products, and observe clustering of some malaria-specific terms to specific chromosomes. We identify a highly conserved sequence element found in the intergenic region of internal var genes that is not associated with their telomeric counterparts. | |||||||
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