Project description:Feature reduction of microarray data from mycobacteria treated with a variety of various clinical and investigational drugs We are using feature reduction to demonstrate that subsets of biomarker genes representative of the whole genome are sufficient for MOA classification and deconvolution in a medium-throughput microfluidic format ultimately leading to a cost effective and rapid tool for routine antibacterial drug-discovery programs.
Project description:Mycobacteria are known to be non-spore forming but very hardy: the bacilli can for instance survive starvation in zero-nutrient saline in a non-replicating state. Recently we reported that mycobacteria in fact can undergo cellular differentiation when exposed to different starvation conditions. The presence of traces of nutrients triggers the development of a new, ‘small resting cell’ form (SMRCs). Saline shock-starved large resting cells (LARCs), which did not show cell size or surface changes when observed by scanning electron microscopy, remodeled their internal structure to the septated, multi-nucleoided cells seen during differentiation to SMRCs. Here we conduct RNA-seq to gain greater insights into whether starvation elicited a distinct developmental pathway. Comparative transcriptome analysis of SMRC and LARC development revealed largely overlapping sets of differentially expressed regulatory and metabolic genes. These transcriptome data are consistent with a mycobacterial starvation-induced differentiation program in which at first septated, multi-nuceloided cells are generated. Under zero-nutrient conditions bacteria terminate development at this stage as LARCs. In the presence of traces of a carbon source, these multi-nucleoided cells continue differentiation into mono-nuleoided SMRCs.
Project description:In this study, we report the identification of a five-locus copper-inducible regulon in Mycobacterium tuberculosis. The identification of a copper responsive regulon unique to pathogenic Mycobacteria suggests copper homeostasis must be maintained during an infection.
Project description:In this study, we report the identification of a five-locus copper-inducible regulon in Mycobacterium tuberculosis. The identification of a copper responsive regulon unique to pathogenic Mycobacteria suggests copper homeostasis must be maintained during an infection.
Project description:During our efforts to isolate potantial binding partners of Esat6, we isolated few peptides rich in phenylalanine residues that strongly interacted with Esat6. All peptides were less than fifty amino acids in length, One of them, Hcl1, when expressed in mycobacteria showed significant retardation in growth and survival within macrophages. Microarray analysis showed that Hcl1 affects a host of genes and cellular pathways. RNA was isolated from exponentially growing mycobacteria containing either plasmid vector pVV16 encoding peptide or vector pVV16 alone. Comparisons were made between Experimental (Mtb/Hcl1) and control (Mtb/pVV16) samples by extracting raw intensity values from multiple arrays.
