BACKGROUND: Radiation is an effective anti-cancer therapy but leads to severe late radiation toxicity in 5%-10% of patients. Assuming that genetic susceptibility impacts this risk, we hypothesized that the cellular response of normal tissue to X-rays could discriminate patients with and without late radiation toxicity. METHODS AND FINDINGS: Prostate carcinoma patients without evidence of cancer 2 y after curative radiotherapy were recruited in the study. Blood samples of 21 patients with severe ...[more]
Project description:The effects of bovine bile and SDS on transcriptional events were studied by means of genome wide microarrays in Enterococcus faecalis V583. Transcriptional profiles were obtained through time series experiments over periods of 120min for cells treated with bile and the combination of SDS and bile, and 360min. for SDS.
Project description:The effects of NaCl on transcriptional events were studied by means of genome wide microarrays in Enterococcus faecalis V583. Transcriptional profiles were obtained through time series experiments over periods of 60min.
Project description:Transcriptional profiling of H37Rv (WT), Mut1 and Comp1 bacteria under aerobic (Aer/0 day, i.e 0 D) and hypoxic conditions (Hyp/5 days standing culture, i.e 5 D). Mut1: H37Rv carrying devR gene disruption by in frame insertion of kanamycin resistance cassette and expressing DevRN-Kan fusion protein. Comp1: Mut1 complemented with low copy number plasmid carrying devR gene expressed from its native constitutive upstream promoter. (Reference: Majumdar et al., 2010, PLoS One 5:e9448). Goal is to compare transcriptional patterns of WT, Mut1 and Comp1 strains under aerobic (0 D) and hypoxic (5 D) conditions in vitro. Two color and One-color experiments,Organism: Mycobacterium tuberculosis, Genotypic Technology designed Custom Mycobacterium tuberculosis H37Rv Whole Genome 8x15k GE Microarray (AMADID-020181)
Project description:Differences in gene content between three test strains were first assessed by comparative genomic hybridization using an E. faecalis V583 oligo array and with E. faecalis V583 as a reference strain . Transcriptional profiles of the same three test strains were then obtained through time series experiments over periods of 30min.
Project description:Total transcript amplification (TTA) from single eukaryotic cells for transcriptome analysis is established, but TTA from a single prokaryotic cell presents additional challenges with much less starting material and lack of poly(A)-tails. We described, here, a novel method for single bacterium TTA, using a Burkholderia thailandensis model exposed to subinhibitory concentration of the antibacterial agent, glyphosate. Utilizing B. thialandensis microarray to assess the TTA method showed little gene bias (< 2 fold-change) and absence (~5-6%) when compared to the larger scale non-amplified RNA samples. B. thailandensis genes important to possibly recuperate and balance the intracellular amino acid pool were induced (or repressed) by the aromatic amino acid biosynthesis inhibitor, glyphosate. We validated our single-cell microarray data at the multi-cells and single-cell levels with lacZ and gfp reporter-gene fusions, respectively. This novel method will rejuvenate and expand the prokaryotic transcriptomic field. Two identical cultures of B. thailandensis wildtype strain E264 were grown in 1x M9 minimal medium supplemented with 1% Brij-58 and 20 mM glucose (MG) to mid-log phase. One culture was induced by final concentration of 0.01% (w/v) glyphosate for 30 minutes. Total RNA was then purified from B. thailandensis uninduced and induced samples, converted to cDNA and hybridized onto B. thailandensis 70mer triplicate array
Project description:comparative genomic hybridization (CGH) analysis was perfromed in order to identify coding regions present in strain T44625 that are either absent or contain a high degree of sequence divergence compared to the RB50 reference strain.
Project description:This project investigates the changes in proteome profiles that occurred in the same set of S. mutans wild-type and lrgAB mutant samples used in our recently published RNA-seq study. To this end, mass spectrometry-based label-free quantitative proteomics, a technology known to enable comprehensive identification and quantification of complete bacterial proteomes, was adapted to study changes in S. mutans intracellular protein levels in response to aeration, heat, and vancomycin stress. Furthermore, the degree of correlation between S. mutans protein abundance profiles and gene expression changes was determined. Further understanding of these combined “-omics” data at the cellular or molecular level will enhance our knowledge of Cid/Lrg-mediated cellular responses of S. mutans to adverse environments. Furthermore, these “-omics” data will serve as a valuable resource that can be mined to help clarify the role of the S. mutans stress response and physiological activity to its dynamic survival in the oral cavity.