Bumgarner R

References (6)

Title : Comparative genomic hybridization and transcriptome analysis with a pan-genome microarray reveal distinctions between JP2 and non-JP2 genotypes of Aggregatibacter actinomycetemcomitans - Huang_2013_Mol.Oral.Microbiol_28_1
Author(s) : Huang Y , Kittichotirat W , Mayer MP , Hall R , Bumgarner R , Chen C
Ref : Mol Oral Microbiol , 28 :1 , 2013
Abstract : It was postulated that the highly virulent JP2 genotype of Aggregatibacter actinomycetemcomitans may possess a constellation of distinct virulence determinants not found in non-JP2 genotypes. This study compared the genome content and the transcriptome of the serotype b JP2 genotype and the closely related serotype b non-JP2 genotype of A. actinomycetemcomitans. A custom-designed pan-genomic microarray of A. actinomycetemcomitans was constructed and validated against a panel of 11 sequenced reference strains. The microarray was subsequently used for comparative genomic hybridization of serotype b strains of JP2 (six strains) and non-JP2 (six strains) genotypes, and for transcriptome analysis of strains of JP2 (three strains) and non-JP2 (two strains). Two JP2-specific and two non-JP2-specific genomic islands were identified. In one instance, distinct genomic islands were found to be inserted into the same locus among strains of different genotypes. Transcriptome analysis identified five operons, including the leukotoxin operon, to have at least two genes with an expression ratio of 2 or greater between genotypes. Two of the differentially expressed operons were members of the membrane-bound nitrate reductase system (nap operon) and the Tol-Pal system of gram-negative bacterial species. This study is the first to demonstrate the differences in the full genome content and gene expression between A. actinomycetemcomitans strains of JP2 and non-JP2 genotypes. The information is essential for designing hypothesis-driven experiments to examine the pathogenic mechanisms of A. actinomycetemcomitans.
ESTHER : Huang_2013_Mol.Oral.Microbiol_28_1
PubMedSearch : Huang_2013_Mol.Oral.Microbiol_28_1
PubMedID: 23194436
Gene_locus related to this paper: aggac-i1xqw9 , aggad-c9r4e8

Title : Genome sequence of a serotype b non-JP2 aggregatibacter actinomycetemcomitans strain, ANH9381, from a periodontally healthy individual - Chen_2012_J.Bacteriol_194_1837
Author(s) : Chen C , Kittichotirat W , Chen W , Downey JS , Bumgarner R
Ref : Journal of Bacteriology , 194 :1837 , 2012
Abstract : Gram-negative Aggregatibacter actinomycetemcomitans can be distinguished (based on the promoter structure of the leukotoxin operon) into JP2 and non-JP2 genotypes, with the former found to be more pathogenic than the latter. Here we report the first complete genome sequence of a serotype b non-JP2 strain of A. actinomycetemcomitans.
ESTHER : Chen_2012_J.Bacteriol_194_1837
PubMedSearch : Chen_2012_J.Bacteriol_194_1837
PubMedID: 22408240
Gene_locus related to this paper: aggac-g3zaa7 , aggac-i1xqw9 , aggad-c9r4e8

Title : Genome sequence of Methyloversatilis universalis FAM5T, a methylotrophic representative of the order Rhodocyclales - Kittichotirat_2011_J.Bacteriol_193_4541
Author(s) : Kittichotirat W , Good NM , Hall R , Bringel F , Lajus A , Medigue C , Smalley NE , Beck D , Bumgarner R , Vuilleumier S , Kalyuzhnaya MG
Ref : Journal of Bacteriology , 193 :4541 , 2011
Abstract : Rhodocyclales are representative of versatile bacteria that are able to utilize a wide variety of organic compounds for growth, but only a few strains have been isolated in pure culture thus far. Here we present the genome sequence of Methyloversatilis universalis FAM5(T), the first cultivable methylotrophic member of the order.
ESTHER : Kittichotirat_2011_J.Bacteriol_193_4541
PubMedSearch : Kittichotirat_2011_J.Bacteriol_193_4541
PubMedID: 21725020
Gene_locus related to this paper: 9rhoo-f5rf80 , metuf-f5rhz8

Title : Genome sequence of naturally competent Aggregatibacter actinomycetemcomitans serotype a strain D7S-1 - Chen_2010_J.Bacteriol_192_2643
Author(s) : Chen C , Kittichotirat W , Chen W , Downey JS , Si Y , Bumgarner R
Ref : Journal of Bacteriology , 192 :2643 , 2010
Abstract : The major clonal lineages of the Gram-negative periodontal pathogen Aggregatibacter actinomycetemcomitans include serotype a, b, and c strains. Here, we report the draft genome sequence of a naturally competent serotype a strain, D7S-1, isolated from a patient with aggressive periodontitis.
ESTHER : Chen_2010_J.Bacteriol_192_2643
PubMedSearch : Chen_2010_J.Bacteriol_192_2643
PubMedID: 20348265
Gene_locus related to this paper: aggac-d4ee60 , aggac-d4ee97 , aggac-g3zaa7 , aggac-i1xqw9 , aggad-c9r4e8

Title : Genome sequence of Aggregatibacter actinomycetemcomitans serotype c strain D11S-1 - Chen_2009_J.Bacteriol_191_7378
Author(s) : Chen C , Kittichotirat W , Si Y , Bumgarner R
Ref : Journal of Bacteriology , 191 :7378 , 2009
Abstract : Aggregatibacter actinomycetemcomitans is a major etiological agent of periodontitis. Here we report the complete genome sequence of serotype c strain D11S-1, which was recovered from the subgingival plaque of a patient diagnosed with generalized aggressive periodontitis.
ESTHER : Chen_2009_J.Bacteriol_191_7378
PubMedSearch : Chen_2009_J.Bacteriol_191_7378
PubMedID: 19820097
Gene_locus related to this paper: aggac-d4ee60 , aggac-g3zaa7 , aggad-c9r4e8 , aggad-c9r728

Title : Evolutionary and biomedical insights from the rhesus macaque genome - Gibbs_2007_Science_316_222
Author(s) : Gibbs RA , Rogers J , Katze MG , Bumgarner R , Weinstock GM , Mardis ER , Remington KA , Strausberg RL , Venter JC , Wilson RK , Batzer MA , Bustamante CD , Eichler EE , Hahn MW , Hardison RC , Makova KD , Miller W , Milosavljevic A , Palermo RE , Siepel A , Sikela JM , Attaway T , Bell S , Bernard KE , Buhay CJ , Chandrabose MN , Dao M , Davis C , Delehaunty KD , Ding Y , Dinh HH , Dugan-Rocha S , Fulton LA , Gabisi RA , Garner TT , Godfrey J , Hawes AC , Hernandez J , Hines S , Holder M , Hume J , Jhangiani SN , Joshi V , Khan ZM , Kirkness EF , Cree A , Fowler RG , Lee S , Lewis LR , Li Z , Liu YS , Moore SM , Muzny D , Nazareth LV , Ngo DN , Okwuonu GO , Pai G , Parker D , Paul HA , Pfannkoch C , Pohl CS , Rogers YH , Ruiz SJ , Sabo A , Santibanez J , Schneider BW , Smith SM , Sodergren E , Svatek AF , Utterback TR , Vattathil S , Warren W , White CS , Chinwalla AT , Feng Y , Halpern AL , Hillier LW , Huang X , Minx P , Nelson JO , Pepin KH , Qin X , Sutton GG , Venter E , Walenz BP , Wallis JW , Worley KC , Yang SP , Jones SM , Marra MA , Rocchi M , Schein JE , Baertsch R , Clarke L , Csuros M , Glasscock J , Harris RA , Havlak P , Jackson AR , Jiang H , Liu Y , Messina DN , Shen Y , Song HX , Wylie T , Zhang L , Birney E , Han K , Konkel MK , Lee J , Smit AF , Ullmer B , Wang H , Xing J , Burhans R , Cheng Z , Karro JE , Ma J , Raney B , She X , Cox MJ , Demuth JP , Dumas LJ , Han SG , Hopkins J , Karimpour-Fard A , Kim YH , Pollack JR , Vinar T , Addo-Quaye C , Degenhardt J , Denby A , Hubisz MJ , Indap A , Kosiol C , Lahn BT , Lawson HA , Marklein A , Nielsen R , Vallender EJ , Clark AG , Ferguson B , Hernandez RD , Hirani K , Kehrer-Sawatzki H , Kolb J , Patil S , Pu LL , Ren Y , Smith DG , Wheeler DA , Schenck I , Ball EV , Chen R , Cooper DN , Giardine B , Hsu F , Kent WJ , Lesk A , Nelson DL , O'Brien W E , Prufer K , Stenson PD , Wallace JC , Ke H , Liu XM , Wang P , Xiang AP , Yang F , Barber GP , Haussler D , Karolchik D , Kern AD , Kuhn RM , Smith KE , Zwieg AS
Ref : Science , 316 :222 , 2007
Abstract : The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.
ESTHER : Gibbs_2007_Science_316_222
PubMedSearch : Gibbs_2007_Science_316_222
PubMedID: 17431167
Gene_locus related to this paper: macmu-3neur , macmu-ACHE , macmu-BCHE , macmu-f6rul6 , macmu-f6sz31 , macmu-f6the6 , macmu-f6unj2 , macmu-f6wtx1 , macmu-f6zkq5 , macmu-f7aa58 , macmu-f7ai42 , macmu-f7aim4 , macmu-f7buk8 , macmu-f7cfi8 , macmu-f7cnr2 , macmu-f7cu68 , macmu-f7flv1 , macmu-f7ggk1 , macmu-f7hir7 , macmu-g7n054 , macmu-KANSL3 , macmu-TEX30 , macmu-Y4neur , macmu-g7n4x3 , macmu-i2cy02 , macmu-f7ba84 , macmu-CES2 , macmu-h9er02 , macmu-a0a1d5rbr3 , macmu-a0a1d5q4k5 , macmu-g7mxj6 , macmu-f7dn71 , macmu-f7hkw9 , macmu-f7hm08 , macmu-g7mke4 , macmu-a0a1d5rh04 , macmu-h9fud6 , macmu-f6qwx1 , macmu-f7h4t2 , macmu-h9zaw9 , macmu-f7h550 , macmu-a0a1d5q9w1 , macmu-f7gkb9 , macmu-f7hp78 , macmu-a0a1d5qvu5