Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Comparative genomic hybridization of Burkholderia mallei strain ATCC 23344 before and after passage in human host cells

ABSTRACT: A whole genome PCR amplicon DNA microarray for B. mallei were fabricated as previously described [7]. Total RNA was isolated from in vitro cultures in LBG medium of B. mallei ATCC 23344, FMH, and JHU. The OD600 of the samples at harvest were all 0.55. The RNAs from FMH and JHU were labeled and hybridized to the array using the ATCC 23344 RNA as the reference using protocols as described. Flip-dye replicates were performed for all analyses. Two B. mallei ATCC 23344 samples grown to an O.D.600 of 1.0 on separate days and total RNA was extracted. These RNA samples were hybridized against each other as a control for the JHU vs. ATCC 23344 hybridization and the FMH vs. ATCC 23344 hybridization.

ORGANISM(S): Burkholderia mallei

DISEASE(S): normal

SUBMITTER: Claudia Romero

PROVIDER: E-MEXP-853 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts.

Romero Claudia M CM DeShazer David D Feldblyum Tamara T Ravel Jacques J Woods Donald D Kim H Stanley HS Yu Yan Y Ronning Catherine M CM Nierman William C WC

BMC genomics 20060905

<h4>Background</h4>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 from culture, a mou ...[more]

PMID: 16953889

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Project description:Background: Thellungiella salsuginea is an important model plant due to its natural tolerance to abiotic stresses including salt, cold, and water deficits. Microarray and metabolite profiling have shown that Thellungiella undergoes stress-responsive changes in transcript and organic solute abundance when grown under controlled environmental conditions. However, few reports assess the capacity of plants to display stress-responsive traits in natural habitats where concurrent stresses are the norm. Results: To determine whether stress-responsive changes observed in cabinet-grown plants are recapitulated in the field, we analyzed leaf transcript and metabolic profiles of Thellungiella growing in its native Yukon habitat during two years of contrasting meteorological conditions. We found 673 genes showing differential expression between field and unstressed, chamber-grown plants. There were comparatively few overlaps between genes expressed under field and cabinet treatment-specific conditions. Only 20 of 99 drought-responsive genes were expressed both in the field during a year of low precipitation and in plants subjected to drought treatments in cabinets. There was also a general pattern of lower abundance among metabolites found in field plants relative to control or stress-treated plants in growth cabinets. Nutrient availability may explain some of the observed differences. For example, proline accumulated to high levels in cold and salt-stressed cabinet-grown plants but proline content was, by comparison, negligible in plants at a saline Yukon field site. We show that proline accumulated in a stress-responsive manner in Thellungiella plants salinized in growth cabinets and in salt-stressed seedlings when nitrogen was provided at 1.0 mM. In seedlings grown on 0.1 mM nitrogen medium, the proline content was low while carbohydrates increased. The relatively higher content of sugar-like compounds in field plants and seedlings on low nitrogen media suggests that Thellungiella shows metabolic plasticity in response to environmental stress and that resource availability can influence the expression of stress tolerance traits under field conditions. Conclusion: Comparisons between Thellungiella plants responding to stress in cabinets and in their natural habitats showed differences but also overlap between transcript and metabolite profiles. The traits in common offer potential targets for improving crops that must respond appropriately to multiple, concurrent stresses. A custom cDNA mcroarray was used for transcript profiling. Cauline leaves from individual plants collected at a Yukon, Canada field site were used in this study. Three samples were obtained in 2003 (Field 2003 A, B and C) and three harvested in 2005 (Field 2005 A, B and D). Cauline leaves from 12 week old chamber grown plants served as controls. For each microarray experiment a technical replicate (dye swap) was performed resulting in a total of 12 hybridizations.

Dataset Information

Comparative genomic hybridization of Burkholderia mallei strain ATCC 23344 before and after passage in human host cells

Publications

Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts.

Similar Datasets

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