Kalman S

References (6)

Title : The diploid genome sequence of Candida albicans - Jones_2004_Proc.Natl.Acad.Sci.U.S.A_101_7329
Author(s) : Jones T , Federspiel NA , Chibana H , Dungan J , Kalman S , Magee BB , Newport G , Thorstenson YR , Agabian N , Magee PT , Davis RW , Scherer S
Ref : Proc Natl Acad Sci U S A , 101 :7329 , 2004
Abstract : We present the diploid genome sequence of the fungal pathogen Candida albicans. Because C. albicans has no known haploid or homozygous form, sequencing was performed as a whole-genome shotgun of the heterozygous diploid genome in strain SC5314, a clinical isolate that is the parent of strains widely used for molecular analysis. We developed computational methods to assemble a diploid genome sequence in good agreement with available physical mapping data. We provide a whole-genome description of heterozygosity in the organism. Comparative genomic analyses provide important clues about the evolution of the species and its mechanisms of pathogenesis.
ESTHER : Jones_2004_Proc.Natl.Acad.Sci.U.S.A_101_7329
PubMedSearch : Jones_2004_Proc.Natl.Acad.Sci.U.S.A_101_7329
PubMedID: 15123810
Gene_locus related to this paper: canal-apth1 , canal-ATG15 , canal-bna7 , canal-c4yl13 , canal-cbpy , canal-LIP1 , canal-LIP2 , canal-LIP3 , canal-LIP4 , canal-LIP5 , canal-LIP6 , canal-LIP7 , canal-LIP8 , canal-LIP9 , canal-LIP10 , canal-ppme1 , canal-q5a0c9 , canal-q5a0i7 , canal-q5a2i9 , canal-q5a2u7 , canal-q5a6l4 , canal-q5a042 , canal-q5a948 , canal-q5aa97 , canal-q5abf2 , canal-q5acl5 , canal-q5ad17 , canal-q5adx4 , canal-q5ady2 , canal-q5aeu3 , canal-q5afp8 , canal-q5ag57 , canal-q5ah37 , canal-q5ai09 , canal-q5ai12 , canal-q5ai87 , canal-q5ajt3 , canal-q5ak09 , canal-q5ak29 , canal-q5ak96 , canal-q5akr2 , canal-q5akz5 , canal-q5amg8 , canal-q5amn4 , canal-q5amn7 , canal-q5ams2 , canal-q5ams7 , canal-q5apu4 , canal-q59k70 , canal-q59kl3 , canal-q59l46 , canal-q59ln6 , canal-q59m48 , canal-q59ng0 , canal-q59nl9 , canal-q59nw6 , canal-q59nx4 , canal-q59nx8 , canal-q59s22 , canal-q59tt5 , canal-q59u61 , canal-q59u64 , canal-q59vf1 , canal-q59vp0 , canal-q59we9 , canal-q59xq6 , canal-q59y42 , canal-q59y97 , canaw-c4yrr3 , canal-hda1

Title : The composite genome of the legume symbiont Sinorhizobium meliloti - Galibert_2001_Science_293_668
Author(s) : Galibert F , Finan TM , Long SR , Puhler A , Abola P , Ampe F , Barloy-Hubler F , Barnett MJ , Becker A , Boistard P , Bothe G , Boutry M , Bowser L , Buhrmester J , Cadieu E , Capela D , Chain P , Cowie A , Davis RW , Dreano S , Federspiel NA , Fisher RF , Gloux S , Godrie T , Goffeau A , Golding B , Gouzy J , Gurjal M , Hernandez-Lucas I , Hong A , Huizar L , Hyman RW , Jones T , Kahn D , Kahn ML , Kalman S , Keating DH , Kiss E , Komp C , Lelaure V , Masuy D , Palm C , Peck MC , Pohl TM , Portetelle D , Purnelle B , Ramsperger U , Surzycki R , Thebault P , Vandenbol M , Vorholter FJ , Weidner S , Wells DH , Wong K , Yeh KC , Batut J
Ref : Science , 293 :668 , 2001
Abstract : The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB megaplasmids. Genome sequence analysis indicates that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution. The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments.
ESTHER : Galibert_2001_Science_293_668
PubMedSearch : Galibert_2001_Science_293_668
PubMedID: 11474104
Gene_locus related to this paper: rhime-PTRB , rhime-R01391 , rhime-R01762 , rhime-R02260 , rhime-RB0025 , rhime-RB0171

Title : Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid - Barnett_2001_Proc.Natl.Acad.Sci.U.S.A_98_9883
Author(s) : Barnett MJ , Fisher RF , Jones T , Komp C , Abola AP , Barloy-Hubler F , Bowser L , Capela D , Galibert F , Gouzy J , Gurjal M , Hong A , Huizar L , Hyman RW , Kahn D , Kahn ML , Kalman S , Keating DH , Palm C , Peck MC , Surzycki R , Wells DH , Yeh KC , Davis RW , Federspiel NA , Long SR
Ref : Proc Natl Acad Sci U S A , 98 :9883 , 2001
Abstract : The symbiotic nitrogen-fixing soil bacterium Sinorhizobium meliloti contains three replicons: pSymA, pSymB, and the chromosome. We report here the complete 1,354,226-nt sequence of pSymA. In addition to a large fraction of the genes known to be specifically involved in symbiosis, pSymA contains genes likely to be involved in nitrogen and carbon metabolism, transport, stress, and resistance responses, and other functions that give S. meliloti an advantage in its specialized niche.
ESTHER : Barnett_2001_Proc.Natl.Acad.Sci.U.S.A_98_9883
PubMedSearch : Barnett_2001_Proc.Natl.Acad.Sci.U.S.A_98_9883
PubMedID: 11481432
Gene_locus related to this paper: rhime-RA0091 , rhime-RA0138 , rhime-RA0313 , rhime-RA0428 , rhime-RA0633 , rhime-RA0724 , rhime-RA0950 , rhime-RA0980 , rhime-RA1008 , rhime-RA1044 , rhime-RA1075 , rhime-RA1107

Title : Comparative genomes of Chlamydia pneumoniae and C. trachomatis - Kalman_1999_Nat.Genet_21_385
Author(s) : Kalman S , Mitchell W , Marathe R , Lammel C , Fan J , Hyman RW , Olinger L , Grimwood J , Davis RW , Stephens RS
Ref : Nat Genet , 21 :385 , 1999
Abstract : Chlamydia are obligate intracellular eubacteria that are phylogenetically separated from other bacterial divisions. C. trachomatis and C. pneumoniae are both pathogens of humans but differ in their tissue tropism and spectrum of diseases. C. pneumoniae is a newly recognized species of Chlamydia that is a natural pathogen of humans, and causes pneumonia and bronchitis. In the United States, approximately 10% of pneumonia cases and 5% of bronchitis cases are attributed to C. pneumoniae infection. Chronic disease may result following respiratory-acquired infection, such as reactive airway disease, adult-onset asthma and potentially lung cancer. In addition, C. pneumoniae infection has been associated with atherosclerosis. C. trachomatis infection causes trachoma, an ocular infection that leads to blindness, and sexually transmitted diseases such as pelvic inflammatory disease, chronic pelvic pain, ectopic pregnancy and epididymitis. Although relatively little is known about C. trachomatis biology, even less is known concerning C. pneumoniae. Comparison of the C. pneumoniae genome with the C. trachomatis genome will provide an understanding of the common biological processes required for infection and survival in mammalian cells. Genomic differences are implicated in the unique properties that differentiate the two species in disease spectrum. Analysis of the 1,230,230-nt C. pneumoniae genome revealed 214 protein-coding sequences not found in C. trachomatis, most without homologues to other known sequences. Prominent comparative findings include expansion of a novel family of 21 sequence-variant outer-membrane proteins, conservation of a type-III secretion virulence system, three serine/threonine protein kinases and a pair of parologous phospholipase-D-like proteins, additional purine and biotin biosynthetic capability, a homologue for aromatic amino acid (tryptophan) hydroxylase and the loss of tryptophan biosynthesis genes.
ESTHER : Kalman_1999_Nat.Genet_21_385
PubMedSearch : Kalman_1999_Nat.Genet_21_385
PubMedID: 10192388
Gene_locus related to this paper: chlpn-CPN0161 , chlpn-CPN0271 , chlpn-q9k1u7 , chlpn-q9z6x7 , chlpn-q9z6x9 , chlpn-q9z7z1

Title : Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis - Stephens_1998_Science_282_754
Author(s) : Stephens RS , Kalman S , Lammel C , Fan J , Marathe R , Aravind L , Mitchell W , Olinger L , Tatusov RL , Zhao Q , Koonin EV , Davis RW
Ref : Science , 282 :754 , 1998
Abstract : Analysis of the 1,042,519-base pair Chlamydia trachomatis genome revealed unexpected features related to the complex biology of chlamydiae. Although chlamydiae lack many biosynthetic capabilities, they retain functions for performing key steps and interconversions of metabolites obtained from their mammalian host cells. Numerous potential virulence-associated proteins also were characterized. Several eukaryotic chromatin-associated domain proteins were identified, suggesting a eukaryotic-like mechanism for chlamydial nucleoid condensation and decondensation. The phylogenetic mosaic of chlamydial genes, including a large number of genes with phylogenetic origins from eukaryotes, implies a complex evolution for adaptation to obligate intracellular parasitism.
ESTHER : Stephens_1998_Science_282_754
PubMedSearch : Stephens_1998_Science_282_754
PubMedID: 9784136
Gene_locus related to this paper: chltr-CT073 , chltr-CT136 , chltr-CT149 , chltr-CT206

Title : The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI - Bussey_1997_Nature_387_103
Author(s) : Bussey H , Storms RK , Ahmed A , Albermann K , Allen E , Ansorge W , Araujo R , Aparicio A , Barrell B , Badcock K , Benes V , Botstein D , Bowman S , Bruckner M , Carpenter J , Cherry JM , Chung E , Churcher C , Coster F , Davis K , Davis RW , Dietrich FS , Delius H , DiPaolo T , Dubois E , Dusterhoft A , Duncan M , Floeth M , Fortin N , Friesen JD , Fritz C , Goffeau A , Hall J , Hebling U , Heumann K , Hilbert H , Hillier L , Hunicke-Smith S , Hyman R , Johnston M , Kalman S , Kleine K , Komp C , Kurdi O , Lashkari D , Lew H , Lin A , Lin D , Louis EJ , Marathe R , Messenguy F , Mewes HW , Mirtipati S , Moestl D , Muller-Auer S , Namath A , Nentwich U , Oefner P , Pearson D , Petel FX , Pohl TM , Purnelle B , Rajandream MA , Rechmann S , Rieger M , Riles L , Roberts D , Schafer M , Scharfe M , Scherens B , Schramm S , Schroder M , Sdicu AM , Tettelin H , Urrestarazu LA , Ushinsky S , Vierendeels F , Vissers S , Voss H , Walsh SV , Wambutt R , Wang Y , Wedler E , Wedler H , Winnett E , Zhong WW , Zollner A , Vo DH , Hani J
Ref : Nature , 387 :103 , 1997
Abstract : The nucleotide sequence of the 948,061 base pairs of chromosome XVI has been determined, completing the sequence of the yeast genome. Chromosome XVI was the last yeast chromosome identified, and some of the genes mapped early to it, such as GAL4, PEP4 and RAD1 (ref. 2) have played important roles in the development of yeast biology. The architecture of this final chromosome seems to be typical of the large yeast chromosomes, and shows large duplications with other yeast chromosomes. Chromosome XVI contains 487 potential protein-encoding genes, 17 tRNA genes and two small nuclear RNA genes; 27% of the genes have significant similarities to human gene products, and 48% are new and of unknown biological function. Systematic efforts to explore gene function have begun.
ESTHER : Bussey_1997_Nature_387_103
PubMedSearch : Bussey_1997_Nature_387_103
PubMedID: 9169875
Gene_locus related to this paper: yeast-MCFS1 , yeast-YPR147C