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:Xylose-utilizing yeasts with tolerances to fermentation inhibitors (such as weak organic acids) and high temperature are needed for cost-effective simultaneous saccharification and co-fermentation (SSCF) of lignocellulosic materials. We constructed a novel xylose-assimilating Saccharomyces cerevisiae strain with improved fermentation performance under heat and acid co-stress using the genome shuffling technique. Two xylose-utilizing diploid yeasts with different genetic backgrounds were used as the parental strains for genome shuffling. The hybrid strain Hyb-8 showed significantly higher xylose fermentation ability than both parental strains (Sun049T-Z and Sun224T-K) under co-stress conditions of heat and acids. To screen for genes that might be important for fermentation under heat and acid co-stress, a transcriptomic analysis of hybrid strain Hyb-8 and its parental strains was performed. Overall design: Total RNA extracted from three Saccharomyces cerevisiae strains (Sun049T-Z, Sun224T-K, and Hyb-8) was used for the transcriptomic analysis by Agilent microarray. Each microarray sample was analyzed in triplicate resulting in total of 9 samples.
Project description:Aneuploidy is a hallmark of tumor cells and yet the precise relationship between aneuploidy and a cell’s proliferative ability, or cellular fitness, has remained elusive. In this study we have combined a detailed analysis of aneuploid clones isolated from laboratory-evolved populations of Saccharomyces cerevisiae with a systematic, genome-wide screen for the fitness effects of telomeric amplifications to address the relationship between aneuploidy and cellular fitness. We found that aneuploid clones rise to high population frequencies in nutrient-limited evolution experiments and show increased fitness relative to wild-type. Direct competition experiments confirmed that three out of four aneuploid events isolated from evolved populations were themselves sufficient to improve fitness. To expand the scope beyond this small number of exemplars, we created a genome-wide collection of >1,800 diploid yeast strains each containing a different telomeric amplicon (Tamp) ranging in size from 0.4 to 1,000kb. Using pooled competition experiments in nutrient-limited chemostats followed by high-throughput sequencing of strain-identifying barcodes, we determined the fitness effects of these >1,800 Tamps under three different conditions. Our data revealed that the fitness landscape explored by telomeric amplifications is much broader than that explored by single-gene amplifications. As also observed in the evolved clones, we found the fitness effects of most Tamps to be condition specific with a minority showing common effects in all three conditions. By integrating our data with previous work that examined the fitness effects of single-gene amplifications genome wide, we found that a small number of genes within each Tamp are centrally responsible for each Tamp’s fitness effects. Our genome-wide Tamp screen confirmed that telomeric amplifications identified in laboratory-evolved populations generally increased fitness. Our results show that Tamps are mutations that produce large, typically condition-dependent changes in fitness that are important drivers of increased fitness in asexually evolving populations. Each of these arrays is a Comparative Genomic Hybridization experiment to detect copy number differences between a reference strain and a strain of interest.