Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of RNA from mouse liver or spleen was vs a sample from cultures or to genomic DNA

ABSTRACT: In each experiment, RNA from mouse liver or spleen was compared to a sample from cultures or to genomic DNA.

ORGANISM(S): Burkholderia mallei

SUBMITTER: H. Stanley Kim

PROVIDER: E-MEXP-334 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies.

Kim H Stanley HS Schell Mark A MA Yu Yan Y Ulrich Ricky L RL Sarria Saul H SH Nierman William C WC DeShazer David D

BMC genomics 20051207

<h4>Background</h4>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 Bt.<h4>Results ...[more]

PMID: 16336651

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Project description:Wounding due to mechanical injury or insect feeding causes a wide array of damage to the cell including cell disruption, desiccation, metabolite oxidation, and disruption of primary metabolism. In response, plants regulate a variety of genes and metabolic pathways to cope with injury. Tomato (Solanum lycopersicum) is a model for wound signaling but few studies have examined the comprehensive gene expression profiles in response to injury. A cross-species microarray approach using the TIGR potato 10-K cDNA array was analyzed for large-scale temporal (early and late) and spatial (locally and systemically) responses to mechanical wounding in tomato leaves. These analyses demonstrated that tomato regulates many primary and secondary metabolic pathways and this regulation is dependent on both timing and location. To determine if LAP-A, a known modulator of wound signaling, influences gene expression beyond the core of late wound-response genes, changes in RNAs from healthy and wounded Leucine aminopeptidase A-silenced (LapA-SI) and wild-type (WT) leaves were examined. While most of the changes in gene expression after wounding in LapA-SI leaves were similar to WT, overall responses were delayed in the LapA-SI leaves. Moreover, two pathogenesis-related 1 (PR-1c and PR-1a2) and two dehydrin (TAS14 and Dhn3) genes were negatively regulated by LAP-A. Collectively, this study has shown that tomato wound responses are complex and that LAP-A's role in modulation of wound responses extends beyond the well-described late-wound gene core. A reference design hybridization strategy was used with WT (0-hr) being the reference RNA. The reference RNA was a pool from five WT 0-hr RNAs. RNAs from wounded or unwounded leaves labeled with Cy3 and the reference RNA labeled with Cy5 were co-hybridized to the potato cDNA array. Three dye bias experiments were performed in which WT 0-hr RNAs were labeled with Cy3 and co-hybridized with the Cy5-labeled reference RNA (WT 0-hr RNAs from a different pool). After normalization, no dye bias was detected on these experiments (p-value<0.05).

Dataset Information

Transcription profiling of RNA from mouse liver or spleen was vs a sample from cultures or to genomic DNA

Publications

Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies.

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