Author Report for: Hall NNo contact information in database for Hall N
Liu LN, Faulkner M, Liu X, Huang F, Darby AC, Hall N Ref: Genome Announc, 4:, 2016 : PubMed ESTHER: Liu_2016_Genome.Announc_4_e01520 PubMedSearch: Liu 2016 Genome.Announc 4 e01520 PubMedID: 26798090 Gene_locus related to this paper: blavi-a0a0h5b6a9 Abstract Blastochloris viridis is a unique anaerobic, phototrophic purple bacterium that produces bacteriochlorophyll b. Here we report an improved genome sequence of Blastochloris viridis DSM133, which is instrumental to the studies of photosynthesis, metabolic versatility, and genetic engineering of this microorganism. Title: Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi Bronowski C, Fookes MC, Gilderthorp R, Ashelford KE, Harris SR, Phiri A, Hall N, Gordon MA, Wain J and Winstanley C <3 more author(s)> Bronowski C, Fookes MC, Gilderthorp R, Ashelford KE, Harris SR, Phiri A, Hall N, Gordon MA, Wain J, Hart CA, Wigley P, Thomson NR, Winstanley C (- 3) Ref: PLoS Negl Trop Dis, 7:e2557, 2013 : PubMed ESTHER: Bronowski_2013_PLoS.Negl.Trop.Dis_7_e2557 PubMedSearch: Bronowski 2013 PLoS.Negl.Trop.Dis 7 e2557 PubMedID: 24244782 Abstract BACKGROUND: Invasive Non-typhoidal Salmonella (iNTS) are an important cause of bacteraemia in children and HIV-infected adults in sub-Saharan Africa. Previous research has shown that iNTS strains exhibit a pattern of gene loss that resembles that of host adapted serovars such as Salmonella Typhi and Paratyphi A. Salmonella enterica serovar Bovismorbificans was a common serovar in Malawi between 1997 and 2004. METHODOLOGY: We sequenced the genomes of 14 Malawian bacteraemia and four veterinary isolates from the UK, to identify genomic variations and signs of host adaptation in the Malawian strains. PRINCIPAL FINDINGS: Whole genome phylogeny of invasive and veterinary S. Bovismorbificans isolates showed that the isolates are highly related, belonging to the most common international S. Bovismorbificans Sequence Type, ST142, in contrast to the findings for S. Typhimurium, where a distinct Sequence Type, ST313, is associated with invasive disease in sub-Saharan Africa. Although genome degradation through pseudogene formation was observed in ST142 isolates, there were no clear overlaps with the patterns of gene loss seen in iNTS ST313 isolates previously described from Malawi, and no clear distinction between S. Bovismorbificans isolates from Malawi and the UK. The only defining differences between S. Bovismorbificans bacteraemia and veterinary isolates were prophage-related regions and the carriage of a S. Bovismorbificans virulence plasmid (pVIRBov). Title: Exploring the diversity of Arcobacter butzleri from cattle in the UK using MLST and whole genome sequencing Merga JY, Williams NJ, Miller WG, Leatherbarrow AJ, Bennett M, Hall N, Ashelford KE, Winstanley C Ref: PLoS ONE, 8:e55240, 2013 : PubMed ESTHER: Merga_2013_PLoS.ONE_8_E55240 PubMedSearch: Merga 2013 PLoS.ONE 8 E55240 PubMedID: 23405126 Gene_locus related to this paper: 9prot-e6l4v2, 9prot-a0a0g9kwp1 Abstract Arcobacter butzleri is considered to be an emerging human foodborne pathogen. The completion of an A. butzleri genome sequence along with microarray analysis of 13 isolates in 2007 revealed a surprising amount of diversity amongst A. butzleri isolates from humans, animals and food. In order to further investigate Arcobacter diversity, 792 faecal samples were collected from cattle on beef and dairy farms in the North West of England. Arcobacter was isolated from 42.5% of the samples and the diversity of the isolates was investigated using multilocus sequence typing. An A. butzleri whole genome sequence, obtained by 454 shotgun sequencing of an isolate from a clinically-healthy dairy cow, showed a number of differences when compared to the genome of a human-derived A. butzleri isolate. PCR-based prevalence assays for variable genes suggested some tentative evidence for source-related distributions. We also found evidence for phenotypic differences relating to growth capabilities between our representative human and cattle isolates. Our genotypic and phenotypic observations suggest that some level of niche adaptation may have occurred in A. butzleri. Title: Analysis of the bread wheat genome using whole-genome shotgun sequencing Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A and Hall N <19 more author(s)> Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N (- 19) Ref: Nature, 491:705, 2012 : PubMed ESTHER: Brenchley_2012_Nature_491_705 PubMedSearch: Brenchley 2012 Nature 491 705 PubMedID: 23192148 Gene_locus related to this paper: aegta-r7w1w2, wheat-w5asu5, wheat-w5caq3, wheat-w5a8u5, wheat-a0a080yuw6, wheat-w5d1z6, wheat-w5d232, wheat-w5fha9, wheat-w5d425, wheat-w5bnf5, wheat-w5dsp5, wheat-w5ia79, wheat-w5f9d9, wheat-w4zq98, wheat-w5cae4, aegta-r7w4e1, wheat-w5gam9, wheat-w5h0x4, wheat-w5bda5, wheat-w5cqa5, wheat-w5ggq1, wheat-w5h2c8, wheat-w5f1j8, wheat-a0a077rex4, wheat-a0a1d5vkr8, wheat-a0a1d5wx81, wheat-a0a1d5zjt9, wheat-a0a1d6adr6, wheat-a0a1d6axb7, wheat-a0a1d6s980, wheat-a0a1d6sag1 Abstract Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop. Title: Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes Hepworth PJ, Ashelford KE, Hinds J, Gould KA, Witney AA, Williams NJ, Leatherbarrow H, French NP, Birtles RJ and Winstanley C <5 more author(s)> Hepworth PJ, Ashelford KE, Hinds J, Gould KA, Witney AA, Williams NJ, Leatherbarrow H, French NP, Birtles RJ, Mendonca C, Dorrell N, Wren BW, Wigley P, Hall N, Winstanley C (- 5) Ref: Environ Microbiol, 13:1549, 2011 : PubMed ESTHER: Hepworth_2011_Environ.Microbiol_13_1549 PubMedSearch: Hepworth 2011 Environ.Microbiol 13 1549 PubMedID: 21418497 Gene_locus related to this paper: camco-q4hhu5, camje-a3zji1, camje-d2n059, camjr-q5ht69 Abstract Although the major food-borne pathogen Campylobacter jejuni has been isolated from diverse animal, human and environmental sources, our knowledge of genomic diversity in C. jejuni is based exclusively on human or human food-chain-associated isolates. Studies employing multilocus sequence typing have indicated that some clonal complexes are more commonly associated with particular sources. Using comparative genomic hybridization on a collection of 80 isolates representing diverse sources and clonal complexes, we identified a separate clade comprising a group of water/wildlife isolates of C. jejuni with multilocus sequence types uncharacteristic of human food-chain-associated isolates. By genome sequencing one representative of this diverse group (C. jejuni 1336), and a representative of the bank-vole niche specialist ST-3704 (C. jejuni 414), we identified deletions of genomic regions normally carried by human food-chain-associated C. jejuni. Several of the deleted regions included genes implicated in chicken colonization or in virulence. Novel genomic insertions contributing to the accessory genomes of strains 1336 and 414 were identified. Comparative analysis using PCR assays indicated that novel regions were common but not ubiquitous among the water/wildlife group of isolates, indicating further genomic diversity among this group, whereas all ST-3704 isolates carried the same novel accessory regions. While strain 1336 was able to colonize chicks, strain 414 was not, suggesting that regions specifically absent from the genome of strain 414 may play an important role in this common route of Campylobacter infection of humans. We suggest that the genomic divergence observed constitutes evidence of adaptation leading to niche specialization. Title: Genetic characterization indicates that a specific subpopulation of Pseudomonas aeruginosa is associated with keratitis infections Stewart RM, Wiehlmann L, Ashelford KE, Preston SJ, Frimmersdorf E, Campbell BJ, Neal TJ, Hall N, Tuft S and Winstanley C <1 more author(s)> Stewart RM, Wiehlmann L, Ashelford KE, Preston SJ, Frimmersdorf E, Campbell BJ, Neal TJ, Hall N, Tuft S, Kaye SB, Winstanley C (- 1) Ref: J Clin Microbiol, 49:993, 2011 : PubMed ESTHER: Stewart_2011_J.Clin.Microbiol_49_993 PubMedSearch: Stewart 2011 J.Clin.Microbiol 49 993 PubMedID: 21227987 Gene_locus related to this paper: pseae-a3kt39, pseae-clipa, pseae-llipa, pseae-PA0201, pseae-PA0231, pseae-PA0308, pseae-PA0368, pseae-PA0480, pseae-PA0543, pseae-PA0599, pseae-PA1166, pseae-PA1239, pseae-PA1304, pseae-PA1510, pseae-PA1558, pseae-PA1597, pseae-PA2098, pseae-PA2302, pseae-PA2425, pseae-PA2540, pseae-PA2682, pseae-PA2927, pseae-PA2949, pseae-PA3301, pseae-PA3327, pseae-PA3695, pseae-PA3859, pseae-PA4968, pseae-PA5080, pseae-PCHC, pseae-PCHF, pseae-PHAC2, pseae-phaD, pseae-Q8G8C7, pseae-Q8G8T6, pseae-q9i252 Abstract Pseudomonas aeruginosa is a common opportunistic bacterial pathogen that causes a variety of infections in humans. Populations of P. aeruginosa are dominated by common clones that can be isolated from diverse clinical and environmental sources. To determine whether specific clones are associated with corneal infection, we used a portable genotyping microarray system to analyze a set of 63 P. aeruginosa isolates from patients with corneal ulcers (keratitis). We then used population analysis to compare the keratitis isolates to a wider collection of P. aeruginosa from various nonocular sources. We identified various markers in a subpopulation of P. aeruginosa associated with keratitis that were in strong disequilibrium with the wider P. aeruginosa population, including oriC, exoU, katN, unmodified flagellin, and the carriage of common genomic islands. The genome sequencing of a keratitis isolate (39016; representing the dominant serotype O11), which was associated with a prolonged clinical healing time, revealed several genomic islands and prophages within the accessory genome. The PCR amplification screening of all 63 keratitis isolates, however, provided little evidence for the shared carriage of specific prophages or genomic islands between serotypes. P. aeruginosa twitching motility, due to type IV pili, is implicated in corneal virulence. We demonstrated that 46% of the O11 keratitis isolates, including 39016, carry a distinctive pilA, encoding the pilin of type IV pili. Thus, the keratitis isolates were associated with specific characteristics, indicating that a subpopulation of P. aeruginosa is adapted to cause corneal infection. Title: The genome of the simian and human malaria parasite Plasmodium knowlesi 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: Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii Khan A, Bohme U, Kelly KA, Adlem E, Brooks K, Simmonds M, Mungall K, Quail MA, Arrowsmith C and Ajioka JW <29 more author(s)> Khan A, Bohme U, Kelly KA, Adlem E, Brooks K, Simmonds M, Mungall K, Quail MA, Arrowsmith C, Chillingworth T, Churcher C, Harris D, Collins M, Fosker N, Fraser A, Hance Z, Jagels K, Moule S, Murphy L, O'Neil S, Rajandream MA, Saunders D, Seeger K, Whitehead S, Mayr T, Xuan X, Watanabe J, Suzuki Y, Wakaguri H, Sugano S, Sugimoto C, Paulsen I, Mackey AJ, Roos DS, Hall N, Berriman M, Barrell B, Sibley LD, Ajioka JW (- 29) Ref: Genome Res, 16:1119, 2006 : PubMed ESTHER: Khan_2006_Genome.Res_16_1119 PubMedSearch: Khan 2006 Genome.Res 16 1119 PubMedID: 16902086 Gene_locus related to this paper: toxgo-q1jt22 Abstract Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has an unusual population structure dominated by three clonal lineages that predominate in North America and Europe, (Types I, II, and III). These lineages were founded by common ancestors approximately10,000 yr ago. The recent origin and widespread distribution of the clonal lineages is attributed to the circumvention of the sexual cycle by a new mode of transmission-asexual transmission between intermediate hosts. Asexual transmission appears to be multigenic and although the specific genes mediating this trait are unknown, it is predicted that all members of the clonal lineages should share the same alleles. Genetic mapping studies suggested that chromosome Ia was unusually monomorphic compared with the rest of the genome. To investigate this further, we sequenced chromosome Ia and chromosome Ib in the Type I strain, RH, and the Type II strain, ME49. Comparative genome analyses of the two chromosomal sequences revealed that the same copy of chromosome Ia was inherited in each lineage, whereas chromosome Ib maintained the same high frequency of between-strain polymorphism as the rest of the genome. Sampling of chromosome Ia sequence in seven additional representative strains from the three clonal lineages supports a monomorphic inheritance, which is unique within the genome. Taken together, our observations implicate a specific combination of alleles on chromosome Ia in the recent origin and widespread success of the clonal lineages of T. gondii. 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: The genome of the social amoeba Dictyostelium discoideum Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K and Kuspa A <87 more author(s)> Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A (- 87) Ref: Nature, 435:43, 2005 : PubMed ESTHER: Eichinger_2005_Nature_435_43 PubMedSearch: Eichinger 2005 Nature 435 43 PubMedID: 15875012 Gene_locus related to this paper: dicdi-abhd, dicdi-ACHE, dicdi-apra, dicdi-cinbp, dicdi-CMBL, dicdi-crysp, dicdi-DPOA, dicdi-P90528, dicdi-ppme1, dicdi-Q8MYE7, dicdi-q54cf7, dicdi-q54cl7, dicdi-q54cm0, dicdi-q54ct5, dicdi-q54cu1, dicdi-q54d54, dicdi-q54d66, dicdi-q54dj5, dicdi-q54dy7, dicdi-q54ek1, dicdi-q54eq6, dicdi-q54et1, dicdi-q54et7, dicdi-q54f01, dicdi-q54g24, dicdi-q54g47, dicdi-q54gi7, dicdi-q54gw5, dicdi-q54gx3, dicdi-q54h23, dicdi-q54h73, dicdi-q54i38, dicdi-q54ie5, dicdi-q54in4, dicdi-q54kz1, dicdi-q54l36, dicdi-q54li1, dicdi-q54m29, dicdi-q54n21, dicdi-q54n35, dicdi-q54n85, dicdi-q54qe7, dicdi-q54qi3, dicdi-q54qk2, dicdi-q54rl3, dicdi-q54rl8, dicdi-q54sy6, dicdi-q54sz3, dicdi-q54t49, dicdi-q54t91, dicdi-q54th2, dicdi-q54u01, dicdi-q54vc2, dicdi-q54vw1, dicdi-q54xe3, dicdi-q54xl3, dicdi-q54xu1, dicdi-q54xu2, dicdi-q54y48, dicdi-q54yd0, dicdi-q54ye0, dicdi-q54yl1, dicdi-q54yr8, dicdi-q54z90, dicdi-q55bx3, dicdi-q55d01, dicdi-q55d81, dicdi-q55du6, dicdi-q55eu1, dicdi-q55eu8, dicdi-q55fk4, dicdi-q55gk7, dicdi-Q54ZA6, dicdi-q86h82, dicdi-Q86HC9, dicdi-Q86HM5, dicdi-Q86HM6, dicdi-q86iz7, dicdi-q86jb6, dicdi-Q86KU7, dicdi-q550s3, dicdi-q552c0, dicdi-q553t5, dicdi-q555e5, dicdi-q555h0, dicdi-q555h1, dicdi-q557k5, dicdi-q558u2, dicdi-Q869Q8, dicdi-u554, dicdi-y9086, dicdi-q54r44, dicdi-f172a Abstract The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi. Title: Comparative genomics of trypanosomatid parasitic protozoa El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA and Hall N <35 more author(s)> El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, Wortman JR, Alsmark UC, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, Hall N (- 35) Ref: Science, 309:404, 2005 : PubMed ESTHER: El-Sayed_2005_Science_309_404 PubMedSearch: El-Sayed 2005 Science 309 404 PubMedID: 16020724 Gene_locus related to this paper: tryb2-q382c1, trycr-q4dhv2, trycr-q4dpt2, trycr-q4dpy4 Abstract 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. Title: Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A and Nene V <34 more author(s)> Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M, Wilson RJ, Sato S, Ralph SA, Mann DJ, Xiong Z, Shallom SJ, Weidman J, Jiang L, Lynn J, Weaver B, Shoaibi A, Domingo AR, Wasawo D, Crabtree J, Wortman JR, Haas B, Angiuoli SV, Creasy TH, Lu C, Suh B, Silva JC, Utterback TR, Feldblyum TV, Pertea M, Allen J, Nierman WC, Taracha EL, Salzberg SL, White OR, Fitzhugh HA, Morzaria S, Venter JC, Fraser CM, Nene V (- 34) Ref: Science, 309:134, 2005 : PubMed ESTHER: Gardner_2005_Science_309_134 PubMedSearch: Gardner 2005 Science 309 134 PubMedID: 15994558 Gene_locus related to this paper: thepa-q4mzr2, thepa-q4n0b4, thepa-q4n2i4, thepa-q4n4i8, thepa-q4n5d6, thepa-q4n5m4, thepa-q4n006, thepa-q4n9g7, thepa-q4n315, thepa-q4n349, thepa-q4n803 Abstract We report the genome sequence of Theileria parva, an apicomplexan pathogen causing economic losses to smallholder farmers in Africa. The parasite chromosomes exhibit limited conservation of gene synteny with Plasmodium falciparum, and its plastid-like genome represents the first example where all apicoplast genes are encoded on one DNA strand. We tentatively identify proteins that facilitate parasite segregation during host cell cytokinesis and contribute to persistent infection of transformed host cells. Several biosynthetic pathways are incomplete or absent, suggesting substantial metabolic dependence on the host cell. One protein family that may generate parasite antigenic diversity is not telomere-associated. Title: A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses Hall N, Karras M, Raine JD, Carlton JM, Kooij TW, Berriman M, Florens L, Janssen CS, Pain A and Sinden RE <20 more author(s)> Hall N, Karras M, Raine JD, Carlton JM, Kooij TW, Berriman M, Florens L, Janssen CS, Pain A, Christophides GK, James K, Rutherford K, Harris B, Harris D, Churcher C, Quail MA, Ormond D, Doggett J, Trueman HE, Mendoza J, Bidwell SL, Rajandream MA, Carucci DJ, Yates JR, 3rd, Kafatos FC, Janse CJ, Barrell B, Turner CM, Waters AP, Sinden RE (- 20) Ref: Science, 307:82, 2005 : PubMed ESTHER: Hall_2005_Science_307_82 PubMedSearch: Hall 2005 Science 307 82 PubMedID: 15637271 Gene_locus related to this paper: plaba-q4ymx5, plaba-q4ysr8, plaba-q4ytp7, plaba-q4yy11, plaba-q4z0q9, plaba-q4z5y0, plaba-q4z5z8, plaba-q4z215, plach-q4x817, plach-q4xb56, plach-q4xbi1, plach-q4xd64, plach-q4xfc7, plach-q4xm16, plach-q4xmx8, plach-q4xmy0, plach-q4xsf9, plach-q4xsg4, plach-q4xsw6, plach-q4xvc8, plach-q4xxw0, plach-q4xxy1, plach-q4y0k9, plach-q4y5u9, plach-q4y6j0, plach-q4y638, plach-q4y740, playo-PY05572, playo-q7rq09 Abstract Plasmodium berghei and Plasmodium chabaudi are widely used model malaria species. Comparison of their genomes, integrated with proteomic and microarray data, with the genomes of Plasmodium falciparum and Plasmodium yoelii revealed a conserved core of 4500 Plasmodium genes in the central regions of the 14 chromosomes and highlighted genes evolving rapidly because of stage-specific selective pressures. Four strategies for gene expression are apparent during the parasites' life cycle: (i) housekeeping; (ii) host-related; (iii) strategy-specific related to invasion, asexual replication, and sexual development; and (iv) stage-specific. We observed posttranscriptional gene silencing through translational repression of messenger RNA during sexual development, and a 47-base 3' untranslated region motif is implicated in this process. Title: The genome of the protist parasite Entamoeba histolytica Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP and Hall N <44 more author(s)> Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Ponten T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA, Jr., Clark CG, Embley TM, Barrell B, Fraser CM, Hall N (- 44) Ref: Nature, 433:865, 2005 : PubMed ESTHER: Loftus_2005_Nature_433_865 PubMedSearch: Loftus 2005 Nature 433 865 PubMedID: 15729342 Gene_locus related to this paper: entds-b0efg6, entds-b0egj2, enthi-b1n4x1, enthi-b1n449, enthi-b1n456, enthi-c4lsp4, enthi-c4lte6, enthi-c4lu03, enthi-c4lu54, enthi-c4lve4, enthi-c4lwe1, enthi-c4m0c3, enthi-c4m0e4, enthi-c4m1e7, enthi-c4m2a9, enthi-c4m2i4, enthi-c4m3r1, enthi-c4m4l3, enthi-c4m6g0, enthi-c4m6k3, enthi-c4m7k7, enthi-c4m7n4, enthi-c4m7v0, enthi-c4m8y5, enthi-c4m793, enthi-c4mb48, enthi-DPP, enthi-q50rh1, enthi-q50ya6, enthi-q51a37, enthi-q51aw6, enthi-q51ch3, enthi-q51cz6, enthi-q51ds3, enthi-q513q8, enthi-q513w3, enthi-q519v1 Abstract Entamoeba histolytica is an intestinal parasite and the causative agent of amoebiasis, which is a significant source of morbidity and mortality in developing countries. Here we present the genome of E. histolytica, which reveals a variety of metabolic adaptations shared with two other amitochondrial protist pathogens: Giardia lamblia and Trichomonas vaginalis. These adaptations include reduction or elimination of most mitochondrial metabolic pathways and the use of oxidative stress enzymes generally associated with anaerobic prokaryotes. Phylogenomic analysis identifies evidence for lateral gene transfer of bacterial genes into the E. histolytica genome, the effects of which centre on expanding aspects of E. histolytica's metabolic repertoire. The presence of these genes and the potential for novel metabolic pathways in E. histolytica may allow for the development of new chemotherapeutic agents. The genome encodes a large number of novel receptor kinases and contains expansions of a variety of gene families, including those associated with virulence. Additional genome features include an abundance of tandemly repeated transfer-RNA-containing arrays, which may have a structural function in the genome. Analysis of the genome provides new insights into the workings and genome evolution of a major human pathogen. Title: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB and Denning DW <87 more author(s)> Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J, Bowyer P, Chen D, Collins M, Coulsen R, Davies R, Dyer PS, Farman M, Fedorova N, Feldblyum TV, Fischer R, Fosker N, Fraser A, Garcia JL, Garcia MJ, Goble A, Goldman GH, Gomi K, Griffith-Jones S, Gwilliam R, Haas B, Haas H, Harris D, Horiuchi H, Huang J, Humphray S, Jimenez J, Keller N, Khouri H, Kitamoto K, Kobayashi T, Konzack S, Kulkarni R, Kumagai T, Lafon A, Latge JP, Li W, Lord A, Lu C, Majoros WH, May GS, Miller BL, Mohamoud Y, Molina M, Monod M, Mouyna I, Mulligan S, Murphy L, O'Neil S, Paulsen I, Penalva MA, Pertea M, Price C, Pritchard BL, Quail MA, Rabbinowitsch E, Rawlins N, Rajandream MA, Reichard U, Renauld H, Robson GD, Rodriguez de Cordoba S, Rodriguez-Pena JM, Ronning CM, Rutter S, Salzberg SL, Sanchez M, Sanchez-Ferrero JC, Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, Vazquez de Aldana CR, Weidman J, White O, Woodward J, Yu JH, Fraser C, Galagan JE, Asai K, Machida M, Hall N, Barrell B, Denning DW (- 87) Ref: Nature, 438:1151, 2005 : PubMed ESTHER: Nierman_2005_Nature_438_1151 PubMedSearch: Nierman 2005 Nature 438 1151 PubMedID: 16372009 Gene_locus related to this paper: aspfc-b0xp50, aspfc-b0xu40, aspfc-b0xzj6, aspfc-dpp5, aspfu-apth1, aspfu-axe1, aspfu-CBPYA, aspfu-faec, aspfu-kex1, aspfu-ppme1, aspfu-q4wa39, aspfu-q4wa78, aspfu-q4wf56, aspfu-q4wg73, aspfu-q4wk44, aspfu-q4wkh6, aspfu-q4wnx3, aspfu-q4wpb9, aspfu-q4wqv2, aspfu-q4wub2, aspfu-q4wxr1, aspfu-q4x0n6, aspfu-q4x1n0, aspfu-q5vjg7, neofi-a1cwa6, neofi-a1dfr9, aspfm-a0a084bf80, aspfu-fmac Abstract Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen. Its conidia production is prolific, and so human respiratory tract exposure is almost constant. A. fumigatus is isolated from human habitats and vegetable compost heaps. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus. 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: The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism Hall N, Berriman M, Lennard NJ, Harris BR, Hertz-Fowler C, Bart-Delabesse EN, Gerrard CS, Atkin RJ, Barron AJ and Melville SE <30 more author(s)> Hall N, Berriman M, Lennard NJ, Harris BR, Hertz-Fowler C, Bart-Delabesse EN, Gerrard CS, Atkin RJ, Barron AJ, Bowman S, Bray-Allen SP, Bringaud F, Clark LN, Corton CH, Cronin A, Davies R, Doggett J, Fraser A, Gruter E, Hall S, Harper AD, Kay MP, Leech V, Mayes R, Price C, Quail MA, Rabbinowitsch E, Reitter C, Rutherford K, Sasse J, Sharp S, Shownkeen R, MacLeod A, Taylor S, Tweedie A, Turner CM, Tait A, Gull K, Barrell B, Melville SE (- 30) Ref: Nucleic Acids Research, 31:4864, 2003 : PubMed ESTHER: Hall_2003_Nucleic.Acids.Res_31_4864 PubMedSearch: Hall 2003 Nucleic.Acids.Res 31 4864 PubMedID: 12907729 Gene_locus related to this paper: trybr-CHR1.244, trybr-CHR1.412, trybr-Q4GYA0 Abstract The African trypanosome, Trypanosoma brucei, causes sleeping sickness in humans in sub-Saharan Africa. Here we report the sequence and analysis of the 1.1 Mb chromosome I, which encodes approximately 400 predicted genes organised into directional clusters, of which more than 100 are located in the largest cluster of 250 kb. A 160-kb region consists primarily of three gene families of unknown function, one of which contains a hotspot for retroelement insertion. We also identify five novel gene families. Indeed, almost 20% of predicted genes are members of families. In some cases, tandemly arrayed genes are 99-100% identical, suggesting an active process of amplification and gene conversion. One end of the chromosome consists of a putative bloodstream-form variant surface glycoprotein (VSG) gene expression site that appears truncated and degenerate. The other chromosome end carries VSG and expression site-associated genes and pseudogenes over 50 kb of subtelomeric sequence where, unusually, the telomere-proximal VSG gene is oriented away from the telomere. Our analysis includes the cataloguing of minor genetic variations between the chromosome I homologues and an estimate of crossing-over frequency during genetic exchange. Genetic polymorphisms are exceptionally rare in sequences located within and around the strand-switches between several gene clusters. Title: Genome sequence of the human malaria parasite Plasmodium falciparum Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE and Barrell B <35 more author(s)> Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B (- 35) Ref: Nature, 419:498, 2002 : PubMed ESTHER: Gardner_2002_Nature_419_498 PubMedSearch: Gardner 2002 Nature 419 498 PubMedID: 12368864 Gene_locus related to this paper: plaf7-c0h4q4, plaf7-q8i5y6, plaf7-q8iik5, plafa-PF10.0018, plafa-PF10.0020, plafa-PF10.0379, plafa-PF11.0211, plafa-PF11.0276, plafa-PF11.0441, plafa-PF14.0015, plafa-PF14.0017, plafa-PF14.0099, plafa-PF14.0250, plafa-PF14.0395, plafa-PF14.0737, plafa-PF14.0738, plafa-PFL2530W Abstract The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria. 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. Title: Interaction of tacrine and velnacrine with neocortical synaptosomal membranes: relevance to Alzheimer's disease Butterfield DA, Hensley K, Hall N, Umhauer S, Carney J Ref: Neurochem Res, 18:989, 1993 : PubMed ESTHER: Butterfield_1993_Neurochem.Res_18_989 PubMedSearch: Butterfield 1993 Neurochem.Res 18 989 PubMedID: 8232727 Abstract The acridine-based, potential Alzheimer's disease therapeutic agents, tacrine and velnacrine, were incubated with rat or gerbil neocortical synaptosomal membranes. Electron paramagnetic resonance employing a protein-specific spin label was used to monitor this interaction. Analogous to their effects in erythrocyte membranes [Butterfield and Rangachari (1992) Biochem. Biophys. Res. Commun. 185: 596-603], in the present studies both agents decreased segmental motion of spin labeled synaptosomal membrane proteins, consistent with increased cytoskeletal protein-protein interactions (0.001 < P < 0.005), and tacrine was more potent than velnacrine. These results are discussed with possible relevance to molecular actions of the agents and molecular alterations in Alzheimer's disease. | |||||||
|
