| The Complete Genome Sequence of Bacillus anthracis, Ames Ancestor. Genome Announcements |
Jan 2009 |
3 pages |
| Authors:
Jacques Ravel; Lingxia Jiang; Scott T Stanley; Mark R Wilson; R S Decker; Timothy D Read; Patricia Worsham; Paul S Keim; Steven L Salzberg; Claire M Fraser-Liggett; David A Rasko; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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 | The pathogenic bacterium Bacillus anthracis has become the subject of intense study as a result of its use as a bioterrorism attack in the United States in September and October 2001. Previous studies suggested that B. anthracis Ames ancestor, the original Ames fully virulent plasmid containing isolate, was the ideal reference. This study describes the complete genome sequence of that original isolate, derived from a sample kept in cold storage ... |
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| Genome Sequence Alterations Detected upon Passage of Burkholderia mallei ATCC 23344 in Culture and in Mammalian Hosts |
05 SEP 2006 |
12 pages |
| Authors:
Claudia M. Romero; David DeShazer; Tamara Feldblyum; Jacques Ravel; Donald Woods; H. S. Kim; Yan Yu; Catherine M. Ronning; William C. Nierman; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| Background: More than 12,000 simple sequence repeats (SSRs) have been identified in the genome of Burkholderia mallei ATCC 23344. As a demonstrated mechanism of phase variation in other pathogenic bacteria, these may function as mutable loci leading to altered protein expression or structure variation. To determine if such alterations are occurring in vivo, the genomes of various single-colony passaged B. mallei ATCC 23344 isolates, one from each source, were sequenced ... |
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| Bacterial Genome Adaptation to Niches: Divergence of the Potential Virulence Genes in Three Burkholderia Species of Different Survival Strategies |
DEC 2005 |
14 pages |
| Authors:
H. S. Kim; Mark A. Schell; Yan Yu; Ricky L. Ulrich; Saul H. Sarria; William C. Nierman; David DeShazer; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| Two closely related species -- Burkholderia mallei (Bm) and Burkholderia pseudomallei (Bp) -- are serious human health hazards and are potential bio-warfare agents, whereas another closely related species -- Burkholderia thailandensis (Bt) -- is a non-pathogenic saprophyte. To investigate the genomic factors resulting in such a dramatic difference, we first identified the Bm genes responsive to the mouse environment, and then examined the divergence of these genes in Bp and ... |
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| Anthrax: Gene Expression Analysis of the Early Stages of Infection |
08 DEC 2004 |
4 pages |
| Authors:
Scott N. Peterson; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| Control of anthrax toxin and capsule synthesis, the two major virulence factors of Bacillus anthracis, has been associated with two regulatory genes, atxA and acpA, located on virulence plasmids pXO I and pXO2, respectively. We used DNA microarrays to determine which genes in the B. anthracis genome are controlled by atxA and/or acpA. The regulation of numerous genes present on the virulence plasmids was documented and both positive and negative ... |
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| Genomics of the Human Gastrointestinal Microbiome |
DEC 2004 |
5 pages |
| Authors:
Steven R. Gill; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| We have used sequencing of targeted 16S rDNA PCR libraries and random metagenomic libraries to examine the phylogenetic and genomic diversity within the human gastrointestinal bacterial community. In one study, we used both 16S and metagenomic analysis in a study of fecal samples from three healthy human subjects. In a second study, we used 16S analysis to compare bacterial diversity between samples obtained from multiple intestinal mucosal sites and companion ... |
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| Macrophage Responses to B. Anthracis |
29 NOV 2004 |
5 pages |
| Authors:
Scott N. Peterson; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| Using DNA microarrays, we have established the gene expression patterns of B. anthracis cells throughout the entire process of sporulation. Over 2,000 genes displayed growth-phase dependent gene expression, 900 of these corresponding to sporulation-specific gene expression events. In a separate study, we compared 19 strains from the B. cereus group to B. anthracis, Ames using comparative genome hybridization (CGH). This comparison indicated that horizontal gene acquisition within this group of ... |
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| Malaria Genome Sequencing Project |
JAN 2004 |
178 pages |
| Authors:
Malcolm J. Gardner; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| The objectives of this Cooperative Agreement were: Specific Aim 1, sequence 3.5 Mb of P. falciparum genomic DNA; Specific Aim 2, annotate the sequence; Specific Aim 3, release the information to the scientific community. Two Specific Aims were added to the Cooperative Agreement: Specific Aim 4, sequencing of P. yoelii to 5X coverage; Specific Aim 5, sequencing of P. vivax to 5X coverage. In 2002 the complete genome sequence of ... |
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| The Genome Sequence of Bacillus cereus ATCC 10987 Reveals Metabolic Adaptations and a Large Plasmid Related to Bacillus anthracis pXO1 |
2004 |
13 pages |
| Authors:
David A. Rasko; Jacques Ravel; Ole A. Okstad; Erlendur Helgason; Regina Z. Cer; Lingxia Jiang; Kelly A. Shores; Derrick E. Fouts; Nicolas J. Tourasse; Samuel V. Angiuoli; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| We sequenced the complete genome of Bacillus cereus ATCC 10987, a non-lethal dairy isolate in the same genetic subgroup as Bacillus anthracis. Comparison of the chromosomes demonstrated that B.cereus ATCC 10987 was more similar to B.anthracis Ames than B.cereus ATCC 14579, while containing a number of unique metabolic capabilities such as urease and xylose utilization and lacking the ability to utilize nitrate and nitrite. Additionally, genetic mechanisms for variation of ... |
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| Malaria Genome Sequencing Project |
JAN 2003 |
52 pages |
| Authors:
Malcolm J. Gardner; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| The objectives of this 5-year Cooperative Agreement between TTGR and the Malaria Program, NMRC, were to: Specific Aim 1, sequence 3.5 Mb of P. falciparum genomic DNA; Specific Aim 2, annotate the sequence; Specific Aim 3, release the information to the scientific community. Two additional Specific Aims were added to the Cooperative Agreement: Specific Aim 4, sequencing of P. yoelii to 5X coverage; Specific Aim 5, sequencing of P. vivax ... |
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| Malaria Genome Sequencing Project |
JAN 2002 |
25 pages |
| Authors:
Malcolm J. Gardner; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| The objectives of this 5-year Cooperative Agreement between TIGR and the Malaria Program, NMRC, were to: Specific Aim 1, sequence 3.5 Mb of P. falciparum genomic DNA; Specific Aim 2, annotate the sequence; Specific Aim 3, release the information to the scientific community. Two additional Specific Aims were added to the Cooperative Agreement: Specific Aim 4, sequencing of P. yoelii to 3x coverage; Specific Aim 5, sequencing of P. vivax ... |
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| Shotgun Sequencing of Plasmids from Marine Sediment Bacteria - Genetic Exploration |
30 SEP 2001 |
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| Authors:
Jonathan Eisen; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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 | We have generated DNA libraries from 10+ plasmids (some samples contained more than one plasmid) and have performed enough DNA sequencing reactions on these estimated to yield approximately 5x sequence coverage. Sequence assemblies were generated for each of these and gap closure performed so far on five plasmids. These five have been analyzed using TIGR's automated bioinformatics tools. All the results are available internally and to our collaborators through a ... |
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| Malaria Genome Sequencing Project |
JAN 2001 |
25 pages |
| Authors:
Malcolm J. Gardner; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| The objectives of this 5-year Cooperative Agreement between TICR and the Malaria Program, NMPC, were to: Specific Aim 1, sequence 3.5 Mb of P. ralciparum genomic DNA; Specific Aim 2, annotate the sequence; Specific Aim 3, release the information to the scientific community. Two additional Specific Aims have been added: Specific Aim 4, sequencing if P. yoeiii to 3x coverage; Specific Aim 5, sequencing of P. vi vax to 3x ... |
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| Malaria Genome Sequencing Project |
JAN 2000 |
53 pages |
| Authors:
Malcolm J. Gardner; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| The objectives of this 5-year Cooperative Agreement between TIGR and the Malaria Program, NMRC, were to: Specific Aim 1, sequence 3.5 Mb of P. falciparum genomic DNA; Specific Aim 2, annotate the sequence; Specific Aim 3, release the information to the scientific community. To date, we have published the first complete sequence of a malarial chromosome (chromosome 2 4 ), completed the random phase sequencing ... |
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| Malaria Genome Sequence Project |
JAN 1999 |
102 pages |
| Authors:
J. C. Venter; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| The objectives of this 5-year Cooperative Agreement between TIGR and the USAMRMC, were to: Specific Aim 1, sequence 3.5 Mb) of P. falciparum gnomonic DNA; Specific Aim 2, annotate the sequence; Specific Aim 3, release the information to the scientific community. Excellent progress was made towards achievement of these goals. The complete sequence of P. falciparum chromosome 2(1 Mb) was determined, published in Science, and released on the TIGR web ... |
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| DNA Microarray Workshop |
JAN 1999 |
10 pages |
| Authors:
Bernie Lauro; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| On Monday, November 9 and Tuesday, November 10, 1998, The Institute for Genomic Research hosted along with The Department of Defense, a Workshop on Functional Analysis of the Malaria Genome. The workshop was the first of three planned workshops that arose from discussions at the Malaria Genome Project meeting held in Cambridge, UK on 1-3 July 1998. Funding for the workshop was provided by the ... |
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| Genetic Regulation in the Aiptasia pallida Symbiosis - Performance Report, Year 1 |
FEB 97 |
3 pages |
| Authors:
Jean-Francois Tomb; INSTITUTE FOR GENOMIC RESEARCH ROCKVILLE MD
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| This report describes the progress of the project 'Genetic Regulation in A. pallida Symbiosis'. The main goal of the project in year 1 was to identify sequence tags for differentially expressed genes using the SAGE approach. The initial protocal we followed to compare gene expression in cultured and symbiotic zooxanthellae is one developed for serial analysis of gene expression (SAGE). We initially tested the SAGE protocol with cDNA generated from ... |
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