Project description:Leishmania donovani WHO reference strain MHOM/IN/80/DD8 and Leptomonas seymouri isolates Ld 2001 and Ld39 were used for proteome analysis which were originally isolated from clinical cases of kala azar patients with different inherent antimonial sensitivities. Ld 2001 was Sb-S and Ld 39 was Sb-R. The genome sequencing of these isolates had confirmed co-infection with Leptomonas.
Project description:Most proteogenomic approaches for mapping single amino acid polymorphisms (SAPs) require construction of a sample-specific database containing protein variants predicted from the next-generation sequencing (NGS) data. We present a new strategy for direct SAP detection without relying on NGS data. Among the 348 putative SAP peptides identified in an industrial yeast strain, 85.6% of SAP sites were validated by genomic sequencing.
Project description:Gene content comparison of control C.j. strain 11168 which colonizes and causes disease in a murine model versus strain NW which colonizes but does not elicit disease symptomology in the mouse model. Keywords: DNA/DNA comparison Overall design: Two genome comparison of disease strain versus non disease strain of C.j., Biological replicates - 2, independently grown and harvested, Technical replicates 2, also independent, 3 ORF replicates per array.
Project description:Whole transcriptome analysis of N. gonorrhoeae FA19 and isogenic NGEG_00293 (misR) mutant using RNA-Seq (note that NGO0177 is the misR ORF designation in mapping strain FA1090) Examination of total transcriptomes in N. gonorrhoeae FA19 WT and an FA19 misR::kan isogenic mutant to determine the regulatory impact of the MisR response regulator on cells grown under laboratory conditions. Illumina HiSeq-2000 next generation sequencing was used to sequence the transcriptomes of each strain. Reads were mapped against the N. gonorrhoeae FA1090 genome (NCBI accession number NC_002946) because at the time this experiment was run the FA19 genome was incomplete.
Project description:The most important approach to the development of platform organisms for recombinant protein production relies on random mutagenesis and phenotypic selection. Complex phenotypes, including those associated with significant elevated expression and secretion of heterologous proteins, are the result of multiple genomic mutations. Using next generation sequencing, a parent and derivative hypersecreter strain (B41) of Escherichia coli were sequenced with an average coverage of 52.8X and 55X, respectively. A new base-pair calling program, revealed a single nucleotide polymorphism in the B41 genome at position 1,074,787, resulting in translation termination near the N-terminus of a transcriptional regulator protein, RutR, coded by the ycdC gene. We verified the hypersecretion phenotype in a ycdC::Tn5 mutant and observed a 3.4-fold increase in active hemolysin secretion, consistent with the increase observed in B41. mRNA expression profiling showed decreased expression of tRNA-synthetases and some amino acid transporters in the ycdC::Tn5 mutant. This study demonstrates that power of next generation sequencing to characterize mutants leading to successful metabolic engineering strategies for strain improvement. Overall design: 6 samples were analyzed with three biological replicates for each strain. Hly-ycdC+ is the control strain.