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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Mycobacterium tuberculosis using a transposon mutagenesis approach to elucidate pe/ppe regulation

ABSTRACT: Data is also available from BuG@Sbase

INSTRUMENT(S): Bioanalyser

ORGANISM(S): Mycobacterium tuberculosis

SUBMITTER:

PROVIDER: E-BUGS-91 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence.

Goldstone Rachael M RM Goonesekera Sunali D SD Bloom Barry R BR Sampson Samantha L SL

Infection and immunity 20090803 10

The pe and ppe genes are unique to mycobacteria and are widely speculated to play a role in tuberculosis pathogenesis. However, little is known about how expression of these genes is controlled. Elucidating the regulatory control of genes found exclusively in mycobacteria, such as the pe and ppe gene families, may be key to understanding the success of this pathogen. In this study, we used a transposon mutagenesis approach to elucidate pe and ppe regulation. This resulted in the identification o ...[more]

PMID: 19651861

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Transcription profiling by array of Mycobacterium smegmatis response to nitrogen stress using bipartite active modules

Project description:BACKGROUND: The ability to adapt to environments with fluctuating nutrient availability is vital for bacterial survival. Although essential for growth, few nitrogen metabolism genes have been identified or fully characterised in mycobacteria and nitrogen stress survival mechanisms are unknown. RESULTS: A global transcriptional analysis of the mycobacterial response to nitrogen stress, showed a significant change in the differential expression of 16% of the Mycobacterium smegmatis genome. Gene expression changes were mapped onto the metabolic network using Active Modules for Bipartite Networks (AMBIENT) to identify metabolic pathways showing coordinated transcriptional responses to the stress. AMBIENT revealed several key features of the metabolic response not identified by KEGG enrichment alone. Down regulated reactions were associated with the general reduction in cellular metabolism as a consequence of reduced growth rate. Up-regulated modules highlighted metabolic changes in nitrogen assimilation and scavenging, as well as reactions involved in hydrogen peroxide metabolism, carbon scavenging and energy generation. CONCLUSIONS: Application of an Active Modules algorithm to transcriptomic data identified key metabolic reactions and pathways altered in response to nitrogen stress, which are central to survival under nitrogen limiting environments. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-140]

2013-06-10 | E-BUGS-140 | biostudies-arrayexpress

Transcription profiling of Staphylococcus aureus treated with tigecycline to determine the effect of the expression of virulence factors in biofilm-associated cells

Project description:Data is also available from <ahref=http://bugs.sgul.ac.uk/E-BUGS-81 target=_blank>BuG@Sbase</a>

2009-11-25 | E-BUGS-81 | biostudies-arrayexpress

cGMP modulates responses to queen mandibular pheromone in worker honey bees

Project description:Responses to social cues, such as pheromones, can be modified by genotype, physiology, or environmental context. Honey bee queens produce a pheromone (queen mandibular pheromone; QMP) which regulates many aspects of worker bee behavior and physiology. Forager honey bees are less responsive to QMP than young nurse bees engaged in brood care, suggesting that physiological changes associated with behavioral maturation may modulate response to this pheromone. Since cGMP is a major regulator of behavioral maturation in honey bee workers, we examined its role in modulating worker responses to QMP. Treatment with a cGMP analog, 8-Br-cGMP, resulted in significant reductions in both behavioral and physiological responses to QMP in young caged workers. Treatment significantly reduced attraction to QMP (the retinue response) and inhibited the QMP-mediated increase in vitellogenin levels in the fat bodies of worker bees. Genome-wide analysis of brain gene expression patterns demonstrated that cGMP has a larger effect on expression levels than QMP, and that QMP has specific effects in the presence of cGMP, suggesting that some responses to QMP may be dependent on an individual beesM-^R physiological state. Several functional gene categories were significantly differentially expressed, including genes involved in regulating GTPase activity, phototransduction, immunity, and carboxylic acid transmembrane transporter activity. Overall, our data suggest that cGMP-mediated processes play a large role in modulating responses to queen pheromone in honey bees, at the behavioral, physiological and molecular levels.

2011-06-15 | E-MEXP-3135 | biostudies-arrayexpress

Comparative genomic hybridization by array of Streptococcus pneumoniae isolates from the Mitis group to identify pneumococcal virulance genes

Project description:Data is also available from <ahref=http://bugs.sgul.ac.uk/E-BUGS-82 target=_blank>BuG@Sbase</a>

2010-07-22 | E-BUGS-82 | biostudies-arrayexpress

Impact of Nosema apis and Nosema ceranae co-infection on worker fat body gene expression

Project description:Newly emerged adult workers (24 hours old) were infected with 25,000 Nosema apis spores and 25,000 Nosema ceranae spores in sucrose solution. Controls were fed sucrose. Workers were maintained in cages in an incubator and collected at 14 days post-infection. Fat bodies (eviscerated abdomens) were dissected and whole genome expression in this tissue was compared across treatments using microarrays.

2014-05-01 | E-MEXP-3889 | biostudies-arrayexpress

Impact of Nosema apis infection on worker honey bee midgut gene expression

Project description:Newly emerged adult workers (24 hours old) were infected with 50,000 Nosema apis spores in sucrose solution. Controls were fed sucrose. Workers were maintained in cages in an incubator and collected at 1 and 2 days post-infection. Midguts were dissected and whole genome expression in this tissue was compared across treatments and collection time points using microarrays.

2014-05-03 | E-MEXP-3891 | biostudies-arrayexpress

Symmetric Bis-benzimidazoles Are Potent Anti-Staphylococcal Agents with Dual Inhibitory Mechanisms against DNA Gyrase

Project description:Various bis-benzimidazole derivatives have been reported to possess activity against Gram-positive pathogens. No mechanism of action has been elucidated to fully account for the antibacterial activity of this class of compounds. A group of symmetric bis-benzimidazoles (BBZ) designed as anticancer agents have previously been shown to possess moderate antiproliferative activity. We sought to assess the antibacterial activity and mechanism of action of BBZ compounds against Staphylococcus aureus. Antibacterial activities were assessed by determination of minimal inhibitory concentrations (MICs), time-kill curves, and scanning electron microscopy. Transcriptional responses to BBZ treatment were determined using whole genome microarrays. Activities against bacterial type II topoisomerases were investigated using in vitro supercoiling, decatenation, DNA binding, and DNA cleavage inhibition assays. MICs for EMRSA-16 were between 0.03 and 0.5 μg/mL. The compounds showed concentration-dependent bactericidal activity and induced cell swelling and lysis. Transcriptional responses to BBZ were consistent with topoisomerase inhibition and DNA damage. A subset of BBZ compounds inhibited S. aureus DNA gyrase supercoiling activity with IC50 values in the range of 5−10 μM. This inhibition was subsequently shown to operate through both inhibition of binding of DNA gyrase to DNA and accumulation of single-stranded DNA breaks. We conclude that BBZ compounds are potent antistaphylococcal agents and operate at least in part through DNA gyrase inhibition, leading to the accumulation of single-stranded DNA breaks, and by preventing the binding of gyrase to DNA. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-106]

2012-10-14 | E-BUGS-106 | biostudies-arrayexpress

Transcription profiling of honey bee queens treated with carbon dioxide and physical manipulation vs virgin controls

Project description:Mating is a complex process that causes many behavioral and physiological changes, but the factors triggering these changes and the underlying molecular processes are not well characterized. Honey bee queens provide a convenient system for dissecting these factors (e.g., physical manipulation, insemination volume, insemination substance) via instrumental insemination. We examined the effects of carbon dioxide (CO2), a commonly used anesthetic in instrumental insemination that causes changes similar to those observed after mating, and physical manipulation, which presumably mimics the act of copulation, on the brain transcriptional changes in honey bee queens. We found significant gene overlap between our study and previous mating studies in honey bee queens and Drosophila. This suggests that molecular pathways regulating the mating process are conserved across different mating regimes of honey bees as well as across insect orders.

2011-01-30 | E-MEXP-2646 | biostudies-arrayexpress

Transcription profiling by array of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis

Project description:BACKGROUND: Nitrogen is an essential element for bacterial growth and an important component of biological macromolecules. Consequently, responding to nitrogen limitation is critical for bacterial survival and involves the interplay of signalling pathways and transcriptional regulation of nitrogen assimilation and scavenging genes. In the soil dwelling saprophyte Mycobacterium smegmatis the OmpR-type response regulator GlnR is thought to mediate the transcriptomic response to nitrogen limitation. However, to date only ten genes have been shown to be in the GlnR regulon, a vastly reduced number compared to other organisms. RESULTS: We investigated the role of GlnR in the nitrogen limitation response and determined the entire GlnR regulon, by combining expression profiling of M. smegmatis wild type and glnR deletion mutant, with GlnR-specific chromatin immunoprecipitation and high throughput sequencing. We identify 53 GlnR binding sites during nitrogen limitation that control the expression of over 100 genes, demonstrating that GlnR is the regulator controlling the assimilation and utilisation of nitrogen. We also determine a consensus GlnR binding motif and identify key residues within the motif that are required for specific GlnR binding. CONCLUSIONS: We have demonstrated that GlnR is the global nitrogen response regulator in M. smegmatis, directly regulating the expression of more than 100 genes. GlnR controls key nitrogen stress survival processes including primary nitrogen metabolism pathways, the ability to utilise nitrate and urea as alternative nitrogen sources, and the potential to use cellular components to provide a source of ammonium. These studies further our understanding of how mycobacteria survive nutrient limiting conditions. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-143]

2013-04-24 | E-BUGS-143 | biostudies-arrayexpress

Expression profiling of BORIS knockout mice testis

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2010-06-05 | E-GEOD-19162 | biostudies-arrayexpress

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