Project description:The opportunistic pathogen Streptococcus gallolyticus is one of the few intestinal bacteria that has been consistently linked to colorectal cancer (CRC). This study aimed to identify S. gallolyticus-induced pathways that could on the long-term add to CRC progression. Transcription profiling of S. gallolyticus-exposed CRC-cells revealed the persistent induction of enzymes involved in biotransformation pathways. Specifically, a diffusible factor of S. gallolyticus (SGF-X) interacts with the aryl hydrocarbon receptor thereby inducing CYP1 enzymes that catalyze the bioactivation of polycyclic aromatic hydrocarbons (PAHs) into toxic intermediates. Importantly, priming CRC-cells with SGF-X containing medium increased the DNA damaging effect of the PAH 3-methylcholanthrene, which was not observed for other intestinal bacteria. In conclusion, this study shows for the first time that bacteria can modulate the biotransformation capacity of CRC-cells that offers a novel theory for a contributing role of S. gallolyticus in the etiology of sporadic CRC. Key words : Colorectal cancer cells, Streptococcus bovis, streptococcus gallolyticus, host-pathogen interactions, Cytochrome P4501A1, DNA-damage, polycyclic aromatic hydrocarbons
Project description:The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here we show that the combined action of Isw1 and Chd1 nucleosome spacing enzymes is required to maintain this organization. In the absence of these enzymes regular positioning of the majority of nucleosomes is lost. Exceptions include the region upstream of the promoter, the +1 nucleosome and a subset of locations distributed throughout coding regions where other factors are likely to be involved. These observations indicated that ATP-dependent remodeling enzymes are responsible for directing the positioning of the majority of nucleosomes within the Saccharomyces cerevisiae genome. Examination of nucleosome positioning in mutants of snf2-related enzymes Other data used in this study are provided in GEO Series GSE31301 and GSE31833.
Project description:Tet enzymes (Tet1/2/3) catalyze the conversion of 5-methylcytosine (5mC) to 5-hydroxy-methylcytosine (5hmC) and are dynamically expressed in various embryonic and adult cell types. While loss of individual Tet enzymes or combined deficiency of Tet1/2 allows for embryogenesis, the effect of complete loss of Tet activity and 5hmC marks in development has not been established. To define the role of Tet enzymes and 5hmC in development we have generated Tet1, Tet2 and Tet3 triple knockout (TKO) mouse embryonic stem cells (ESCs) and examined their developmental potential in vitro and in vivo. Combined deficiency of all three Tet enzymes led to complete depletion of 5hmC and impaired ESC differentiation as seen in poorly differentiated TKO embryoid bodies and teratomas. Consistent with impaired differentiation, TKO ES cells exhibited limited contribution to the chimeric embryos and could not support embryonic development in tetraploid complementation assays. Gene expression profiles and genome wide methylome analyses of TKO embryoid bodies revealed promoter hypermethylation and deregulation of genes implicated in embryonic development and differentiation. These findings suggest a requirement for Tet and 5hmC-mediated DNA demethylation in proper regulation of gene expression during differentiation of embryonic stem cells and development. Methylation patterns in tissue samples from a series of wt and Tet1/Tet2 DKO embryos, neonates and adults were generated using ethylated DNA immunoprecipitation with antibodies against 5mC (MeDIP) and 5hmC (hMeDIP) followed by deep sequencing.
Project description:Antimicrobials have been shown to select for changes in biofilm formation and multidrug susceptibility in common human pathogens. We investigated whether common food preservatives selected for these changes in the food pathogen Salmonella enterica serovar Typhimurium. Bacteria were exposed to four food preservatives in either planktonic cultures or biofilms grown on stainless steel beads. Cultures were passaged into fresh media supplemented with the food preservative every 72 hours. Following approximately 1000 generations of continuous preservative exposure, populations were sequenced to determine the single nucleotide polymorphisms that were selected for over evolutionary time.
Project description:The yeast Saccharomyces cerevisiae is an important component of the wine fermentation process and determines various attributes of the final product. However, lactic acid bacteria (LAB) are also an integral part of the microflora of any fermenting must. Various wine microorganism engineering projects have been endeavoured in the past in order to change certain wine characteristics, namely aroma compound composition, ethanol concentration, levels of toxic/ allergenic compounds etc. Most of these projects focus on a specific gene or pathway, whereas our approach aims to understand the genetically complex traits responsible for these phenotypes in a systematic manner by implementing a transcriptomic analysis of yeast in mixed fermentations with the LAB O. oeni. Our aim is to investigate interactions between yeast and LAB on a gene expression level to identify targets for modification of yeast and O. oeni in a directed manner. Our goal was to identify the impact that the common wine microorganism O. oeni (malolactic bacteria) has on fermenting yeast cells on a gene expression level. To this end we co-inoculated the yeast and bacteria at the start of fermentation in a synthetic wine must, using yeast-only fermentations witout O. oeni as a control.