Project description:Runs used for retention time matching between 5-ASA (combinatorial synthesis and single reaction compound) and biological sample (Rheumatoid arthritis stool). Samples were either run on timsTOF Pro 2 or on Thermo Q Exactive.
Project description:This dataset is created for retention time matching for the conjugated metabolome project, including lactic acid-amino acid conjugates, phenylacetic acid-amino acid conjugates, phenylpropionic acid-amino acid conjugates and others.
Project description:Runs used for retention time matching between N-acyl lipids (combinatorial synthesis) and biological samples (HNRC - stool; Salmonella infection - cecum; Dead bodies - skin swab; Microbial monocultures - extracts). Two gradients were used (LC1 - total 11 min; LC2 - total 14 min) and a Kinetex 1.6 um polar C18 column (100 x 2.1 mm) was employed . Two spiking levels were used for coinjection (high - 1:3 sample:reaction pool; low - 3:1 sample:reaction pool).
Project description:A re-analysis of published data-dependent acquisition glycoproteomics datasets to demonstrate relative retention time prediction on glycopeptide identification and disambiguation of adduct states.
Project description:Matching sets of RfxCasR and shRNAs targeting ANXA4 and B4GALNT1 plus non-targeting (NT) controls were profiled by mRNA sequencing to compare non-specific transcriptome perturbations for both shRNA and RfxCasR technologies.
Project description:Conversion of the primary bile acids cholic acid (CA) and chenodeoxycholic acid (CDCA) to the secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA) is performed by a few species of intestinal bacteria in the genus Clostridium through a multistep biochemical pathway that removes a 7α-hydroxyl group. The rate-determining enzyme in this pathway is bile acid 7α-dehydratase (baiE). In this study, crystal structures of apo-BaiE and its putative product-bound [3-oxo-Δ(4,6) -lithocholyl-Coenzyme A (CoA)] complex are reported. BaiE is a trimer with a twisted α + β barrel fold with similarity to the Nuclear Transport Factor 2 (NTF2) superfamily. Tyr30, Asp35, and His83 form a catalytic triad that is conserved across this family. Site-directed mutagenesis of BaiE from Clostridium scindens VPI 12708 confirm that these residues are essential for catalysis and also the importance of other conserved residues, Tyr54 and Arg146, which are involved in substrate binding and affect catalytic turnover. Steady-state kinetic studies reveal that the BaiE homologs are able to turn over 3-oxo-Δ(4) -bile acid and CoA-conjugated 3-oxo-Δ(4) -bile acid substrates with comparable efficiency questioning the role of CoA-conjugation in the bile acid metabolism pathway.