Project description:The terminal compartments of Streptomyces are less prone to transcription than the rest of the chromosome. Indeed, the expression of the highly variable regions enriched in those compartments is generally conditional and often requires an empirical approach to characterize the inducing conditions. For instance, in the context of identifying adequate antibiotic production conditions, an OSMAC (“One Strain Many Compounds”) approach is frequently implemented, based on strain cultivation in different environmental conditions (composition of the medium, growth time, temperature, co-cultures, etc.). Likewise, to find the expression conditions of a complete prophage of Streptomyces ambofaciens ATCC 23877 (named 'Samy' phage/prophage), we conducted a similar approach by analyzing the transcriptomes in five solid media (HT, SAF, ONA, MMM, MMM+NAG). The terminal compartments of Streptomyces are less prone to transcription than the rest of the chromosome. Indeed, the expression of the highly variable regions enriched in those compartments is generally conditional and often requires an empirical approach to characterize the inducing conditions. For instance, in the context of identifying adequate antibiotic production conditions, an OSMAC (“One Strain Many Compounds”) approach is frequently implemented, based on strain cultivation in different environmental conditions (composition of the medium, growth time, temperature, co-cultures, etc.). Likewise, to find the expression conditions of a complete prophage of Streptomyces ambofaciens ATCC 23877 (named 'Samy' phage/prophage), we conducted a similar approach by analyzing the transcriptomes in five solid media (HT, SAF, ONA, MMM, MMM+NAG).
Project description:YerA41 is a myoviridae bacteriophage that was originally isolated due its ability to infect Yersinia ruckeri bacteria, the causative agent of enteric redmouth disease of salmonid fish. Several attempts to determine its genomic DNA sequence using traditional and next generation sequencing technologies failed, indicating that the phage genome is modified such way that it is an unsuitable template for PCR amplification and sequencing. To determine the YerA41 genome sequence we isolated RNA from phage-infected Y. ruckeri cells at different time points post-infection, and sequenced it. The host-genome specific reads were substracted and de novo assembly was performed on the unaligned reads.
Project description:Marine Oomycetes: community barcoding results from an early winter plankton bloom (2012) in the Brudenell River (Prince Edward Island)
Project description:Streptomyces bingchenggensis is a soil bacterium that produces a family of macrolide antibiotics, milbemycins, which is commercially important in crop protection, human and veterinary medicine. After the complete genome sequence, and annotation, for further development of our gene expression approach to biosynthesis, we have employed whole genome microarray expression profiling as a discovery platform to obtain improved specificity and sensitivity of gene expression analysis, allowing a global and at the same time detailed picture of how gene clusters for secondary metabolism are modulated. In the result, we confirmed the expression mil and nan gene cluster, furthermore, pks3, pks5 and nrps7, nrps8 also showed significant gene expression, but no obvious products detected. In Streptomyces bingchenggensis, there are also corresponding genes belonging to Defense mechanisms, which is much more than other Streptomyces, for the resistance of own metabolites and dealing with complex environmental factors.
Project description:Salmonella enterica serovar Typhimurium (S. Typhimurium) definitive phage type 104 (DT104) has caused significant morbidity and mortality in humans and animals for almost three decades. We have completed the full DNA sequence of one DT104 strain, NCTC13348 and show that the main differences between the genome of this isolate and the previously sequenced S. Typhimurium LT2 lie in integrated prophage elements and the Salmonella Genomic Island 1 encoding antibiotic resistance genes. Thirteen isolates of S. Typhimurium DT104 with different pulsed field gel electrophoresis (PFGE) profiles were analyzed by multi locus sequence typing (MLST), plasmid profiling, hybridization to a Pan-Salmonella DNA microarray and prophage-based multiplex PCR. All the isolates belonged to a single MLST type ST19. Microarray data demonstrated that the 13 DT104 isolates were remarkably conserved in gene content. The PFGE band-size differences in these isolates could be explained to a great extent by changes in prophage and plasmid content. Thus, here the nature of variation in different S. Typhimurium DT104 isolates is further defined at the genome level illustrating how this phage type is evolving over time.
Project description:Metabolomics profile of Streptomyces sp. 11-1-2, a plant pathogen isolated from common scab lesions on potato in Newfoundland, Canada. Positive and negative ionisation mode. The deposition contains RAW and mzXML.