Project description:System-wide metabolic homeostasis is crucial for maintaining physiological functions of living organisms. Stable-isotope tracing metabolomics allows to unravel metabolic activity quantitatively by measuring the isotopically labeled metabolites, but has been largely restricted by coverage. Yet, delineating system-wide metabolic homeostasis at the whole-organism level remains non-trivial. Here, we develop a global isotope tracing metabolomics technology to measure labeled metabolites with a metabolome-wide coverage. Using Drosophila as an aging model organism, we probe the in vivo tracing kinetics with quantitative information on labeling patterns, extents and rates on a metabolome-wide scale. We curate a system-wide metabolic network to characterize metabolic homeostasis and disclose a system-wide loss of metabolic coordinations that impacts both intra- and inter-tissue metabolic homeostasis significantly during Drosophila aging. Importantly, we reveal an unappreciated metabolic diversion from glycolysis to serine metabolism and purine metabolism as Drosophila aging. The developed technology facilitates a system-level understanding of metabolic regulation in living organisms.
Project description:Mining of fungal genomes uncovered their great potential for the production of novel secondary metabolites (SMs). However most of them stay silent under standard laboratory cultivation conditions. Co-cultivation of fungi with organism that occur in their natural habitat has shown to be trigger for the activation of such silent SM gene clusters. Recently, we showed that the cultivation of Aspergillus nidulans with the bacterium Streptomyces rapamycinicus leads to the activation of the orsellinic acid gene cluster. Hence we decided to study this interaction further to gain insight into the regulation of SM gene clusters and more specifically to study the chromatin remodelling network actuve upon co-cultivation of the two organisms. This study gives novel insight into the regulation of the orsellinic acid gene cluster and the interaction of the two organisms. To the best of our knowledge this is the first report of mapping the chromatin landscape of microbial interactions, making this study a role model for the analysis of similar systems.
Project description:Transcription factors have to distinguish proper targets from a large pool of potential binding sites. Here we explore how MSL2 and CLAMP cooperate to bind their specific targets. Using an in vitro chromatin reconstitution system and by mutating the interaction domain of CLAMP we show how direct and indirect cooperation of TF binding influence binding specificity.
2023-07-27 | GSE224981 | GEO
Project description:Plant defense metabolites influence the interaction between an insect herbivore and an entomovirus
Project description:Transcriptional cofactors communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression, which is a hallmark of all multicellular organisms. However, the extent to which different cofactors display intrinsic specificity for distinct promoters is unclear. Testing intrinsic COF – core promoter (CP) compatibilities requires the systematic assessment of transcriptional activation for many CPs in the presence or absence of a given COF in an otherwise constant standardized reporter system. We therefore combined a plasmid-based high-throughput reporter assay, Self-Transcribing Active Core Promoter-sequencing (STAP-seq), with the specific recruitment of individual COFs to create a high-throughput activator bypass-like assay. Using this assay, we tested whether 5 different individually tethered human COFs (MED15, BRD4, EP300, MLL3 and EMSY) activate transcription from a selection of 12,000 candidate sequences encompassing different types of gene core promoters, enhancers and control sequences. In addition, we used the strong transcriptional activator P65 as a positive control and GFP as a negative control. We found that different COFs preferentially activate different CPs. For instance, MED15 prefers TATA-box containing CPs, while MLL3 preferentially activates CpG island promoters. The observed compatibilities between cofactors and promoters can explain how different enhancers specifically activate distinct sets of genes or alternative promoters within the same gene, and may underlie distinct transcriptional programs in human cells.
Project description:Using microarray analysis, 219 differentially expressed genes were isolated between the LPS group and LPS/PBHA treatment-group (fold change > or < 1.5). These genes were analyzed by KEGG system to reveal the important issues. The analyses of gene ontology were shown that the genes of the specific classes “Chemokine signaling pathway”, ”Cytokine-cytokine receptor interaction”, ”RIG-I-like receptor signaling pathway”, ”Leukocyte transendothelial migration”, and “MAPK signaling pathway” showed markedly different patterns between both groups by KEGG analysis system.
Project description:We are testing the ability of spironolactone as a NADPH oxidase inhibitor during an induced dietary oxalate overload by Ethylene Glycol in Sprague Dawley rats at two different time points. We looked into the development of hyperoxaluria and crystal deposition at two different time points and into differences between hyperoxaluria and crystal induced alterations in the kidneys. Eventually, we are expecting to see the role of spironolactone as an inhibitor of NADPH oxidase which is involved in the production of reactive oxygen species (ROS) which leads to oxidative stress in the living organisms leading to a plethora of vascular diseases, hypertension, and kidney diseases.