Brown D

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Full name : Brown Derek

First name : Derek

Mail : Department of Psychiatry, Stobhill Hospital, Glasgow

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Country : United Kingdom

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References (14)

Title : Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona - Zhou_2013_PLoS.Genet_9_e1003471
Author(s) : Zhou Z , McCann A , Litrup E , Murphy R , Cormican M , Fanning S , Brown D , Guttman DS , Brisse S , Achtman M
Ref : PLoS Genet , 9 :e1003471 , 2013
Abstract : Salmonella enterica serovar Agona has caused multiple food-borne outbreaks of gastroenteritis since it was first isolated in 1952. We analyzed the genomes of 73 isolates from global sources, comparing five distinct outbreaks with sporadic infections as well as food contamination and the environment. Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and subsequently underwent a major population expansion in the 1960s. Homologous recombination with other serovars of S. enterica imported 42 recombinational tracts (360 kb) in 5/143 nodes within the genealogy, which resulted in 3,164 additional SNPs. In contrast to this paucity of genetic diversity, Agona is highly diverse according to pulsed-field gel electrophoresis (PFGE), which is used to assign isolates to outbreaks. PFGE diversity reflects a highly dynamic accessory genome associated with the gain or loss (indels) of 51 bacteriophages, 10 plasmids, and 6 integrative conjugational elements (ICE/IMEs), but did not correlate uniquely with outbreaks. Unlike the core genome, indels occurred repeatedly in independent nodes (homoplasies), resulting in inaccurate PFGE genealogies. The accessory genome contained only few cargo genes relevant to infection, other than antibiotic resistance. Thus, most of the genetic diversity within this recently emerged pathogen reflects changes in the accessory genome, or is due to recombination, but these changes seemed to reflect neutral processes rather than Darwinian selection. Each outbreak was caused by an independent clade, without universal, outbreak-associated genomic features, and none of the variable genes in the pan-genome seemed to be associated with an ability to cause outbreaks.
ESTHER : Zhou_2013_PLoS.Genet_9_e1003471
PubMedSearch : Zhou_2013_PLoS.Genet_9_e1003471
PubMedID: 23637636
Gene_locus related to this paper: salty-STY1441

Title : NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis - Rusniok_2009_Genome.Biol_10_R110
Author(s) : Rusniok C , Vallenet D , Floquet S , Ewles H , Mouze-Soulama C , Brown D , Lajus A , Buchrieser C , Medigue C , Glaser P , Pelicic V
Ref : Genome Biol , 10 :R110 , 2009
Abstract : BACKGROUND: Genome sequences, now available for most pathogens, hold promise for the rational design of new therapies. However, biological resources for genome-scale identification of gene function (notably genes involved in pathogenesis) and/or genes essential for cell viability, which are necessary to achieve this goal, are often sorely lacking. This holds true for Neisseria meningitidis, one of the most feared human bacterial pathogens that causes meningitis and septicemia.
RESULTS: By determining and manually annotating the complete genome sequence of a serogroup C clinical isolate of N. meningitidis (strain 8013) and assembling a library of defined mutants in up to 60% of its non-essential genes, we have created NeMeSys, a biological resource for Neisseria meningitidis systematic functional analysis. To further enhance the versatility of this toolbox, we have manually (re)annotated eight publicly available Neisseria genome sequences and stored all these data in a publicly accessible online database. The potential of NeMeSys for narrowing the gap between sequence and function is illustrated in several ways, notably by performing a functional genomics analysis of the biogenesis of type IV pili, one of the most widespread virulence factors in bacteria, and by identifying through comparative genomics a complete biochemical pathway (for sulfur metabolism) that may potentially be important for nasopharyngeal colonization.
CONCLUSIONS: By improving our capacity to understand gene function in an important human pathogen, NeMeSys is expected to contribute to the ongoing efforts aimed at understanding a prokaryotic cell comprehensively and eventually to the design of new therapies.
ESTHER : Rusniok_2009_Genome.Biol_10_R110
PubMedSearch : Rusniok_2009_Genome.Biol_10_R110
PubMedID: 19818133
Gene_locus related to this paper: neimb-q9k0t9 , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB1828

Title : Defective thyroglobulin storage in LDL receptor-associated protein-deficient mice - Lisi_2006_Am.J.Physiol.Cell.Physiol_290_C1160
Author(s) : Lisi S , Botta R , Pinchera A , Collins AB , Refetoff S , Arvan P , Bu G , Grasso L , Marshansky V , Bechoua S , Hurtado-Lorenzo A , Marcocci C , Brown D , McCluskey RT , Marino M
Ref : American Journal of Physiology Cell Physiol , 290 :C1160 , 2006
Abstract : The molecular chaperone receptor-associated protein (RAP) is required for biosynthesis of megalin, an endocytic receptor for follicular thyroglobulin (Tg), the thyroid hormone precursor. RAP also binds to Tg itself, suggesting that it may affect Tg trafficking in various manners. To elucidate RAP function, we have studied the thyroid phenotype in RAP-knockout (RAP-KO) mice and found a reduction of Tg aggregates into thyroid follicles. Serum Tg levels were significantly increased compared with those of wild-type (WT) mice, suggesting a directional alteration of Tg secretion. In spite of these abnormalities, hormone secretion was maintained as indicated by normal serum thyroxine levels. Because Tg in thyroid extracts from RAP-KO mice contained thyroxine residues as in WT mice, we concluded that in RAP-KO mice, follicular Tg, although reduced, was nevertheless sufficient to provide normal hormone secretion. Serum TSH was increased in RAP-KO mice, and although no thyroid enlargement was observed, some histological features resembling early goiter were present. Megalin was decreased in RAP-KO mice, but this did not affect thyroid function, probably because of the concomitant reduction of follicular Tg. In conclusion, RAP is required for the establishment of Tg reservoirs, but its absence does not affect hormone secretion.
ESTHER : Lisi_2006_Am.J.Physiol.Cell.Physiol_290_C1160
PubMedSearch : Lisi_2006_Am.J.Physiol.Cell.Physiol_290_C1160
PubMedID: 16306127

Title : The genome sequence of the rice blast fungus Magnaporthe grisea - Dean_2005_Nature_434_980
Author(s) : Dean RA , Talbot NJ , Ebbole DJ , Farman ML , Mitchell TK , Orbach MJ , Thon M , Kulkarni R , Xu JR , Pan H , Read ND , Lee YH , Carbone I , Brown D , Oh YY , Donofrio N , Jeong JS , Soanes DM , Djonovic S , Kolomiets E , Rehmeyer C , Li W , Harding M , Kim S , Lebrun MH , Bohnert H , Coughlan S , Butler J , Calvo S , Ma LJ , Nicol R , Purcell S , Nusbaum C , Galagan JE , Birren BW
Ref : Nature , 434 :980 , 2005
Abstract : Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.
ESTHER : Dean_2005_Nature_434_980
PubMedSearch : Dean_2005_Nature_434_980
PubMedID: 15846337
Gene_locus related to this paper: maggr-a4qqu1 , maggr-a4uuq1 , mago7-g4n0f1 , maggr-a4qy60 , maggr-a4qyj3 , maggr-a4r8c0 , maggr-a4r257 , maggr-a4rd24 , maggr-a4ri35 , maggr-a4rlz4 , maggr-a4rme6 , maggr-q0pnd2 , maggr-q0pnd5 , maggr-q2keh4 , maggr-q2khf5 , mago7-a4qsp1 , mago7-a4qt55 , mago7-a4qua7 , mago7-a4qup0 , mago7-a4qvx8 , mago7-a4qwz1 , mago7-a4qx26 , mago7-a4qxi6 , mago7-a4qz39 , mago7-a4qzg2 , mago7-a4r4e9 , mago7-a4r4n4 , mago7-a4r6f4 , mago7-a4r106 , mago7-a4ra37 , mago7-a4rdm3 , mago7-a4rgp8 , mago7-a4rlj9 , mago7-a4rpg7 , mago7-a4uc22 , mago7-dapb , mago7-g4mk92 , mago7-g4mkc6 , mago7-g4mkk9 , mago7-g4mns9 , mago7-g4ms19 , mago7-g4mvm8 , mago7-g4mvw5 , mago7-g4mvw6 , mago7-g4n6j4 , mago7-g4nal1 , mago7-g4naw0 , mago7-g4nba0 , mago7-g4nbs0 , mago7-g4nc41 , mago7-g4ncz9 , mago7-g4nhn9 , mago7-g4nil3 , mago7-g4nky6 , mago7-g5ehg6 , mago7-g5ehv6 , mago7-q2kh83 , mago7-q2khe7 , mago7-a4qxp0 , mago7-g4nih2 , mago7-g4mr24 , mago7-g4nff5 , mago7-g4n8c3 , mago7-g4ni03 , mago7-g4nhm4 , mago7-g4nfb6 , mago7-g4mmn3 , mago7-g4mqv7 , mago7-g4mzv6 , mago7-g4nbz1 , mago7-g4ms46 , mago7-g4n0h2 , mago7-g4nev7 , mago7-g4msm5 , magoy-l7i6m7 , mago7-g4ne75 , magor-a0a4p7n714 , magor-a0a4p7nig7 , mago7-g4mzi2 , mago7-cbpya , mago7-kex1 , mago7-g4n703

Title : Acetylcholine muscarinic receptors and response to anti-cholinesterase therapy in patients with Alzheimer's disease - Brown_2003_Eur.J.Nucl.Med.Mol.Imaging_30_296
Author(s) : Brown D , Chisholm JA , Owens J , Pimlott S , Patterson J , Wyper D
Ref : Eur J Nucl Med Mol Imaging , 30 :296 , 2003
Abstract : An acetylcholine deficit remains the most consistent neurotransmitter abnormality found in Alzheimer's disease and various therapeutic agents have been targeted at this. In this study we investigated the action of Donepezil, a cholinesterase inhibitor that has few side-effects. In particular we set out to investigate whether muscarinic acetylcholine receptor (mAChR) availability influences the response to this therapy. We used the novel single-photon emission tomography (SPET) tracer (R, R)[(123)I]I-quinuclidinyl benzilate (R, R[(123)I]I-QNB), which has high affinity for the M1 subtype of mAChR. Regional cerebral perfusion was also assessed using technetium-99m hexamethylpropylene amine oxime. We investigated 20 patients on Donepezil treatment and ten age-matched controls. The results showed a reduction in (R, R)[(123)I]I-QNB binding in the caudal anterior cingulate in patients compared with controls and relatively high binding in the putamen and rostral anterior cingulate, suggesting a relative sparing of mAChR in these regions. The main finding of the study was that mAChR availability as assessed by (R, R)[(123)I]I-QNB binding did not distinguish responders from non-responders. Interestingly, we found that the extent of cognitive improvement showed no positive correlation with (R, R)[(123)I]I-QNB binding in any brain region but was inversely related to binding in the insular cortex. This suggests that, within the advised cognitive performance band for use of Donepezil, response is greater in those patients with evidence of a more marked cholinergic deficit. A larger study should investigate this.
ESTHER : Brown_2003_Eur.J.Nucl.Med.Mol.Imaging_30_296
PubMedSearch : Brown_2003_Eur.J.Nucl.Med.Mol.Imaging_30_296
PubMedID: 12552349

Title : Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reesei - Foreman_2003_J.Biol.Chem_278_31988
Author(s) : Foreman PK , Brown D , Dankmeyer L , Dean R , Diener S , Dunn-Coleman NS , Goedegebuur F , Houfek TD , England GJ , Kelley AS , Meerman HJ , Mitchell T , Mitchinson C , Olivares HA , Teunissen PJ , Yao J , Ward M
Ref : Journal of Biological Chemistry , 278 :31988 , 2003
Abstract : The filamentous fungus Trichoderma reesei produces and secretes profuse quantities of enzymes that act synergistically to degrade cellulase and related biomass components. We partially sequenced over 5100 random T. reesei cDNA clones. Among the sequences whose predicted gene products had significant similarity to known proteins, 12 were identified that encode previously unknown enzymes that likely function in biomass degradation. Microarrays were used to query the expression levels of each of the sequences under different conditions known to induce cellulolytic enzyme synthesis. Most of the genes encoding known and putative biomass-degrading enzymes were transcriptionally co-regulated. Moreover, despite the fact that several of these enzymes are not thought to degrade cellulase directly, they were coordinately overexpressed in a cellulase overproducing strain. A variety of additional sequences whose function could not be ascribed using the limited sequence available displayed analogous behavior and may also play a role in biomass degradation or in the synthesis of biomass-degrading enzymes. Sequences exhibiting additional regulatory patterns were observed that might reflect roles in regulation of cellulase biosynthesis. However, genes whose products are involved in protein processing and secretion were not highly regulated during cellulase induction.
ESTHER : Foreman_2003_J.Biol.Chem_278_31988
PubMedSearch : Foreman_2003_J.Biol.Chem_278_31988
PubMedID: 12788920
Gene_locus related to this paper: hypjq-cip2 , hypje-q7z9m3

Title : The genome sequence of Schizosaccharomyces pombe - Wood_2002_Nature_415_871
Author(s) : Wood V , Gwilliam R , Rajandream MA , Lyne M , Lyne R , Stewart A , Sgouros J , Peat N , Hayles J , Baker S , Basham D , Bowman S , Brooks K , Brown D , Brown S , Chillingworth T , Churcher C , Collins M , Connor R , Cronin A , Davis P , Feltwell T , Fraser A , Gentles S , Goble A , Hamlin N , Harris D , Hidalgo J , Hodgson G , Holroyd S , Hornsby T , Howarth S , Huckle EJ , Hunt S , Jagels K , James K , Jones L , Jones M , Leather S , McDonald S , McLean J , Mooney P , Moule S , Mungall K , Murphy L , Niblett D , Odell C , Oliver K , O'Neil S , Pearson D , Quail MA , Rabbinowitsch E , Rutherford K , Rutter S , Saunders D , Seeger K , Sharp S , Skelton J , Simmonds M , Squares R , Squares S , Stevens K , Taylor K , Taylor RG , Tivey A , Walsh S , Warren T , Whitehead S , Woodward J , Volckaert G , Aert R , Robben J , Grymonprez B , Weltjens I , Vanstreels E , Rieger M , Schafer M , Muller-Auer S , Gabel C , Fuchs M , Dusterhoft A , Fritzc C , Holzer E , Moestl D , Hilbert H , Borzym K , Langer I , Beck A , Lehrach H , Reinhardt R , Pohl TM , Eger P , Zimmermann W , Wedler H , Wambutt R , Purnelle B , Goffeau A , Cadieu E , Dreano S , Gloux S , Lelaure V , Mottier S , Galibert F , Aves SJ , Xiang Z , Hunt C , Moore K , Hurst SM , Lucas M , Rochet M , Gaillardin C , Tallada VA , Garzon A , Thode G , Daga RR , Cruzado L , Jimenez J , Sanchez M , del Rey F , Benito J , Dominguez A , Revuelta JL , Moreno S , Armstrong J , Forsburg SL , Cerutti L , Lowe T , McCombie WR , Paulsen I , Potashkin J , Shpakovski GV , Ussery D , Barrell BG , Nurse P
Ref : Nature , 415 :871 , 2002
Abstract : We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.
ESTHER : Wood_2002_Nature_415_871
PubMedSearch : Wood_2002_Nature_415_871
PubMedID: 11859360
Gene_locus related to this paper: schpo-APTH1 , schpo-be46 , schpo-BST1 , schpo-C2E11.08 , schpo-C14C4.15C , schpo-C22H12.03 , schpo-C23C4.16C , schpo-C57A10.08C , schpo-dyr , schpo-este1 , schpo-KEX1 , schpo-PCY1 , schpo-pdat , schpo-PLG7 , schpo-ppme1 , schpo-q9c0y8 , schpo-SPAC4A8.06C , schpo-C22A12.06C , schpo-SPAC977.15 , schpo-SPAPB1A11.02 , schpo-SPBC14C8.15 , schpo-SPBC530.12C , schpo-SPBC1711.12 , schpo-SPBPB2B2.02 , schpo-SPCC5E4.05C , schpo-SPCC417.12 , schpo-SPCC1672.09 , schpo-yb4e , schpo-yblh , schpo-ydw6 , schpo-ye7a , schpo-ye63 , schpo-ye88 , schpo-yeld , schpo-yk68 , schpo-clr3 , schpo-ykv6

Title : Massive gene decay in the leprosy bacillus - Cole_2001_Nature_409_1007
Author(s) : Cole ST , Eiglmeier K , Parkhill J , James KD , Thomson NR , Wheeler PR , Honore N , Garnier T , Churcher C , Harris D , Mungall K , Basham D , Brown D , Chillingworth T , Connor R , Davies RM , Devlin K , Duthoy S , Feltwell T , Fraser A , Hamlin N , Holroyd S , Hornsby T , Jagels K , Lacroix C , Maclean J , Moule S , Murphy L , Oliver K , Quail MA , Rajandream MA , Rutherford KM , Rutter S , Seeger K , Simon S , Simmonds M , Skelton J , Squares R , Squares S , Stevens K , Taylor K , Whitehead S , Woodward JR , Barrell BG
Ref : Nature , 409 :1007 , 2001
Abstract : Leprosy, a chronic human neurological disease, results from infection with the obligate intracellular pathogen Mycobacterium leprae, a close relative of the tubercle bacillus. Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted every effort at culture in the laboratory. Comparing the 3.27-megabase (Mb) genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus with that of Mycobacterium tuberculosis (4.41 Mb) provides clear explanations for these properties and reveals an extreme case of reductive evolution. Less than half of the genome contains functional genes but pseudogenes, with intact counterparts in M. tuberculosis, abound. Genome downsizing and the current mosaic arrangement appear to have resulted from extensive recombination events between dispersed repetitive sequences. Gene deletion and decay have eliminated many important metabolic activities including siderophore production, part of the oxidative and most of the microaerophilic and anaerobic respiratory chains, and numerous catabolic systems and their regulatory circuits.
ESTHER : Cole_2001_Nature_409_1007
PubMedSearch : Cole_2001_Nature_409_1007
PubMedID: 11234002
Gene_locus related to this paper: mycle-a85a , mycle-a85b , mycle-a85c , mycle-lipG , mycle-LPQC , mycle-metx , mycle-ML0314 , mycle-ML0370 , mycle-ML0376 , mycle-ML1339 , mycle-ML1444 , mycle-ML1632 , mycle-ML1633 , mycle-ML1921 , mycle-ML2269 , mycle-ML2297 , mycle-ML2359 , mycle-ML2603 , mycle-mpt5 , mycle-PKS13 , mycle-PTRB , mycle-q9cc62 , mycle-q9cdb3

Title : The anterior\/posterior polarity of somites is disrupted in paraxis-deficient mice - Johnson_2001_Dev.Biol_229_176
Author(s) : Johnson J , Rhee J , Parsons SM , Brown D , Olson EN , Rawls A
Ref : Developmental Biology , 229 :176 , 2001
Abstract : Establishing the anterior/posterior (A/P) boundary of individual somites is important for setting up the segmental body plan of all vertebrates. Resegmentation of adjacent sclerotomes to form the vertebrae and selective migration of neural crest cells during the formation of the dorsal root ganglia and peripheral nerves occur in response to differential expression of genes in the anterior and posterior halves of the somite. Recent evidence indicates that the A/P axis is established at the anterior end of the presomitic mesoderm prior to overt somitogenesis in response to both Mesp2 and Notch signaling. Here, we report that mice deficient for paraxis, a gene required for somite epithelialization, also display defects in the axial skeleton and peripheral nerves that are consistent with a failure in A/P patterning. Expression of Mesp2 and genes in the Notch pathway were not altered in the presomitic mesoderm of paraxis(-/-) embryos. Furthermore, downstream targets of Notch activation in the presomitic mesoderm, including EphA4, were transcribed normally, indicating that paraxis was not required for Notch signaling. However, genes that were normally restricted to the posterior half of somites were present in a diffuse pattern in the paraxis(-/-) embryos, suggesting a loss of A/P polarity. Collectively, these data indicate a role for paraxis in maintaining somite polarity that is independent of Notch signaling.
ESTHER : Johnson_2001_Dev.Biol_229_176
PubMedSearch : Johnson_2001_Dev.Biol_229_176
PubMedID: 11133162

Title : Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491 - Parkhill_2000_Nature_404_502
Author(s) : Parkhill J , Achtman M , James KD , Bentley SD , Churcher C , Klee SR , Morelli G , Basham D , Brown D , Chillingworth T , Davies RM , Davis P , Devlin K , Feltwell T , Hamlin N , Holroyd S , Jagels K , Leather S , Moule S , Mungall K , Quail MA , Rajandream MA , Rutherford KM , Simmonds M , Skelton J , Whitehead S , Spratt BG , Barrell BG
Ref : Nature , 404 :502 , 2000
Abstract : Neisseria meningitidis causes bacterial meningitis and is therefore responsible for considerable morbidity and mortality in both the developed and the developing world. Meningococci are opportunistic pathogens that colonize the nasopharynges and oropharynges of asymptomatic carriers. For reasons that are still mostly unknown, they occasionally gain access to the blood, and subsequently to the cerebrospinal fluid, to cause septicaemia and meningitis. N. meningitidis strains are divided into a number of serogroups on the basis of the immunochemistry of their capsular polysaccharides; serogroup A strains are responsible for major epidemics and pandemics of meningococcal disease, and therefore most of the morbidity and mortality associated with this disease. Here we have determined the complete genome sequence of a serogroup A strain of Neisseria meningitidis, Z2491. The sequence is 2,184,406 base pairs in length, with an overall G+C content of 51.8%, and contains 2,121 predicted coding sequences. The most notable feature of the genome is the presence of many hundreds of repetitive elements, ranging from short repeats, positioned either singly or in large multiple arrays, to insertion sequences and gene duplications of one kilobase or more. Many of these repeats appear to be involved in genome fluidity and antigenic variation in this important human pathogen.
ESTHER : Parkhill_2000_Nature_404_502
PubMedSearch : Parkhill_2000_Nature_404_502
PubMedID: 10761919
Gene_locus related to this paper: neima-metx , neimb-q9k0t9 , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB1877 , neimf-a1kta9 , neime-r0tza2

Title : The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum - Bowman_1999_Nature_400_532
Author(s) : Bowman S , Lawson D , Basham D , Brown D , Chillingworth T , Churcher CM , Craig A , Davies RM , Devlin K , Feltwell T , Gentles S , Gwilliam R , Hamlin N , Harris D , Holroyd S , Hornsby T , Horrocks P , Jagels K , Jassal B , Kyes S , McLean J , Moule S , Mungall K , Murphy L , Oliver K , Quail MA , Rajandream MA , Rutter S , Skelton J , Squares R , Squares S , Sulston JE , Whitehead S , Woodward JR , Newbold C , Barrell BG
Ref : Nature , 400 :532 , 1999
Abstract : Analysis of Plasmodium falciparum chromosome 3, and comparison with chromosome 2, highlights novel features of chromosome organization and gene structure. The sub-telomeric regions of chromosome 3 show a conserved order of features, including repetitive DNA sequences, members of multigene families involved in pathogenesis and antigenic variation, a number of conserved pseudogenes, and several genes of unknown function. A putative centromere has been identified that has a core region of about 2 kilobases with an extremely high (adenine + thymidine) composition and arrays of tandem repeats. We have predicted 215 protein-coding genes and two transfer RNA genes in the 1,060,106-base-pair chromosome sequence. The predicted protein-coding genes can be divided into three main classes: 52.6% are not spliced, 45.1% have a large exon with short additional 5' or 3' exons, and 2.3% have a multiple exon structure more typical of higher eukaryotes.
ESTHER : Bowman_1999_Nature_400_532
PubMedSearch : Bowman_1999_Nature_400_532
PubMedID: 10448855
Gene_locus related to this paper: plafa-PFC0950C

Title : Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence - Cole_1998_Nature_393_537
Author(s) : Cole ST , Brosch R , Parkhill J , Garnier T , Churcher C , Harris D , Gordon SV , Eiglmeier K , Gas S , Barry CE, 3rd , Tekaia F , Badcock K , Basham D , Brown D , Chillingworth T , Connor R , Davies R , Devlin K , Feltwell T , Gentles S , Hamlin N , Holroyd S , Hornsby T , Jagels K , Krogh A , McLean J , Moule S , Murphy L , Oliver K , Osborne J , Quail MA , Rajandream MA , Rogers J , Rutter S , Seeger K , Skelton J , Squares R , Squares S , Sulston JE , Taylor K , Whitehead S , Barrell BG
Ref : Nature , 393 :537 , 1998
Abstract : Countless millions of people have died from tuberculosis, a chronic infectious disease caused by the tubercle bacillus. The complete genome sequence of the best-characterized strain of Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve our understanding of the biology of this slow-growing pathogen and to help the conception of new prophylactic and therapeutic interventions. The genome comprises 4,411,529 base pairs, contains around 4,000 genes, and has a very high guanine + cytosine content that is reflected in the biased amino-acid content of the proteins. M. tuberculosis differs radically from other bacteria in that a very large portion of its coding capacity is devoted to the production of enzymes involved in lipogenesis and lipolysis, and to two new families of glycine-rich proteins with a repetitive structure that may represent a source of antigenic variation.
ESTHER : Cole_1998_Nature_393_537
PubMedSearch : Cole_1998_Nature_393_537
PubMedID: 9634230
Gene_locus related to this paper: myctu-a85a , myctu-a85b , myctu-a85c , myctu-bpoC , myctu-cut3 , myctu-cutas1 , myctu-cutas2 , myctu-d5yk66 , myctu-ephA , myctu-ephB , myctu-ephc , myctu-ephd , myctu-ephE , myctu-ephF , myctu-hpx , myctu-linb , myctu-lipG , myctu-lipJ , myctu-LIPS , myctu-lipv , myctu-LPQC , myctu-LPQP , myctu-MBTB , myctu-metx , myctu-mpt51 , myctu-MT1628 , myctu-MT3441 , myctu-p71654 , myctu-p95011 , myctu-PKS6 , myctu-PKS13 , myctu-ppe42 , myctu-ppe63 , myctu-Rv1430 , myctu-RV0045C , myctu-Rv0077c , myctu-Rv0151c , myctu-Rv0152c , myctu-Rv0159c , myctu-Rv0160c , myctu-rv0183 , myctu-Rv0217c , myctu-Rv0220 , myctu-Rv0272c , myctu-RV0293C , myctu-RV0421C , myctu-RV0457C , myctu-RV0519C , myctu-RV0774C , myctu-RV0782 , myctu-RV0840C , myctu-Rv1069c , myctu-Rv1076 , myctu-RV1123C , myctu-Rv1184c , myctu-Rv1190 , myctu-Rv1191 , myctu-RV1192 , myctu-RV1215C , myctu-Rv1399c , myctu-Rv1400c , myctu-Rv1426c , myctu-RV1639C , myctu-RV1683 , myctu-RV1758 , myctu-Rv1800 , myctu-Rv1833c , myctu-RV2054 , myctu-RV2296 , myctu-Rv2385 , myctu-Rv2485c , myctu-RV2627C , myctu-RV2672 , myctu-RV2695 , myctu-RV2765 , myctu-RV2800 , myctu-RV2854 , myctu-Rv2970c , myctu-Rv3084 , myctu-Rv3097c , myctu-rv3177 , myctu-Rv3312c , myctu-RV3452 , myctu-RV3473C , myctu-Rv3487c , myctu-Rv3569c , myctu-Rv3591c , myctu-RV3724 , myctu-Rv3802c , myctu-Rv3822 , myctu-y0571 , myctu-y963 , myctu-Y1834 , myctu-y1835 , myctu-y2079 , myctu-Y2307 , myctu-yc88 , myctu-ym23 , myctu-ym24 , myctu-YR15 , myctu-yt28

Title : The nucleotide sequence of Saccharomyces cerevisiae chromosome IV - Jacq_1997_Nature_387_75
Author(s) : Jacq C , Alt-Morbe J , Andre B , Arnold W , Bahr A , Ballesta JP , Bargues M , Baron L , Becker A , Biteau N , Blocker H , Blugeon C , Boskovic J , Brandt P , Bruckner M , Buitrago MJ , Coster F , Delaveau T , del Rey F , Dujon B , Eide LG , Garcia-Cantalejo JM , Goffeau A , Gomez-Peris AC , Granotier C , Hanemann V , Hankeln T , Hoheisel JD , Jager W , Jimenez A , Jonniaux JL , Kramer C , Kuster H , Laamanen P , Legros Y , Louis E , Muller-Rieker S , Monnet A , Moro M , Muller-Auer S , Nussbaumer B , Paricio N , Paulin L , Perea J , Perez-Alonso M , Perez-Ortin JE , Pohl TM , Prydz H , Purnelle B , Rasmussen SW , Remacha M , Revuelta JL , Rieger M , Salom D , Saluz HP , Saiz JE , Saren AM , Schafer M , Scharfe M , Schmidt ER , Schneider C , Scholler P , Schwarz S , Soler-Mira A , Urrestarazu LA , Verhasselt P , Vissers S , Voet M , Volckaert G , Wagner G , Wambutt R , Wedler E , Wedler H , Wolfl S , Harris DE , Bowman S , Brown D , Churcher CM , Connor R , Dedman K , Gentles S , Hamlin N , Hunt S , Jones L , McDonald S , Murphy L , Niblett D , Odell C , Oliver K , Rajandream MA , Richards C , Shore L , Walsh SV , Barrell BG , Dietrich FS , Mulligan J , Allen E , Araujo R , Aviles E , Berno A , Carpenter J , Chen E , Cherry JM , Chung E , Duncan M , Hunicke-Smith S , Hyman R , Komp C , Lashkari D , Lew H , Lin D , Mosedale D , Nakahara K , Namath A , Oefner P , Oh C , Petel FX , Roberts D , Schramm S , Schroeder M , Shogren T , Shroff N , Winant A , Yelton M , Botstein D , Davis RW , Johnston M , Hillier L , Riles L , Albermann K , Hani J , Heumann K , Kleine K , Mewes HW , Zollner A , Zaccaria P
Ref : Nature , 387 :75 , 1997
Abstract : The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome IV has been determined. Apart from chromosome XII, which contains the 1-2 Mb rDNA cluster, chromosome IV is the longest S. cerevisiae chromosome. It was split into three parts, which were sequenced by a consortium from the European Community, the Sanger Centre, and groups from St Louis and Stanford in the United States. The sequence of 1,531,974 base pairs contains 796 predicted or known genes, 318 (39.9%) of which have been previously identified. Of the 478 new genes, 225 (28.3%) are homologous to previously identified genes and 253 (32%) have unknown functions or correspond to spurious open reading frames (ORFs). On average there is one gene approximately every two kilobases. Superimposed on alternating regional variations in G+C composition, there is a large central domain with a lower G+C content that contains all the yeast transposon (Ty) elements and most of the tRNA genes. Chromosome IV shares with chromosomes II, V, XII, XIII and XV some long clustered duplications which partly explain its origin.
ESTHER : Jacq_1997_Nature_387_75
PubMedSearch : Jacq_1997_Nature_387_75
PubMedID: 9169867
Gene_locus related to this paper: yeast-dlhh , yeast-ECM18 , yeast-YDL109C , yeast-YDR428C , yeast-YDR444W

Title : The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII - Bowman_1997_Nature_387_90
Author(s) : Bowman S , Churcher C , Badcock K , Brown D , Chillingworth T , Connor R , Dedman K , Devlin K , Gentles S , Hamlin N , Hunt S , Jagels K , Lye G , Moule S , Odell C , Pearson D , Rajandream M , Rice P , Skelton J , Walsh S , Whitehead S , Barrell B
Ref : Nature , 387 :90 , 1997
Abstract : Systematic sequencing of the genome of Saccharomyces cerevisiae has revealed thousands of new predicted genes and allowed analysis of long-range features of chromosomal organization. Generally, genes and predicted genes seem to be distributed evenly throughout the genome, having no overall preference for DNA strand. Apart from the smaller chromosomes, which can have substantially lower gene density in their telomeric regions, there is a consistent average of one open reading frame (ORF) approximately every two kilobases. However, one of the most surprising findings for a eukaryote with approximately 6,000 genes was the amount of apparent redundancy in its genome. This redundancy occurs both between individual ORFs and over more extensive chromosome regions, which have been duplicated preserving gene order and orientation. Here we report the entire nucleotide sequence of chromosome XIII, the sixth-largest S. cerevisiae chromosome, and demonstrate that its features and organization are consistent with those observed for other S. cerevisiae chromosomes. Analysis revealed 459 ORFs, 284 have not been identified previously. Both intra- and interchromosomal duplications of regions of this chromosome have occurred.
ESTHER : Bowman_1997_Nature_387_90
PubMedSearch : Bowman_1997_Nature_387_90
PubMedID: 9169872
Gene_locus related to this paper: yeast-FSH2 , yeast-ym60 , yeast-ymc0