Project description:Single-molecule read technologies allow for detection of epigenomic base modifications during routine sequencing by analysis of kinetic data during the reaction, including the duration between base incorporations at the elongation site (the "inter-pulse duration.") Methylome data associated with a closed de novo bacterial genome of Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992 was produced and submitted to the Gene Expression Omnibus. Single-sample sequencing and base modification detection of cultured isolate of a foodborne pathogen.
Project description:Strain Cad16T was previously shown to fix a major fraction of the bulk CO2 under both light and dark conditions and was suggested to be involved in Fe(II) driven aerobic metabolism in the lake Cadagno chemocline. However evidence on genomic and proteomic level was only fragmentary . In order to understand the biological functions expressed under phototrophic and chemotrophic growth conditions of str. Cad16T an in situ experiment conceived. It included cultures of str. Cad16T incubated in dialysis bags for three months while physiochemical conditions were monitored longitudinally. Upon sampling, physiological differences of str. Cad16T were compared utilizing quantitative proteomics in combination with CO2-uptake measurements.
Project description:Neomegalonema perideroedes (formerly Meganema perideroedes) str. G1 is the type strain and only described isolate of the genus Neomegalonema (formerly Meganema). N. perideroedes is distinguished by the ability to accumulate high amounts of polyhydroxyalkanoates and has been associated with bulking problems in wastewater treatment plants due to its filamentous morphology. In 2013, its genome was sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which aims to improve the sequencing coverage of the poorly represented regions of the bacterial and archaeal branches of the tree of life. As N. perideroedes str. G1 is relatively distantly related to well described species – being the only sequenced member of its proposed family - the in silico prediction of genes by nucleotide homology to reference genes might be less reliable. The aim of this study was to improve the genome annotation by usage of proteomic data. Besides the identification of novel and overlooked genes, the N-terminal cleavage pattern and the differences between databases were considered. Proteogenomic approaches, such as is described here, complements the GEBA initiative well - by providing important refinement of reference genome annotations.