Project description:GC-MS is a commonly used metabolomic platform for the analysis of urine. A key step in the preparation of samples for GC-MS is derivatisation, in particular, methoximation and trimethylsilylation. This paper presents an assessment of automated derivatisation protocols for GC-MS-based untargeted metabolomic analysis of rat urine. Automated batch and in-time (a sample ready for injection every 70 minutes) derivatisation protocols were tested using BSTFA and MSTFA. Principal component analysis determined differences based upon protocol tested (PC-1; 19%) and silylation reagent (PC-2; 17%) used. Of 249 compounds, 40 compounds were significantly different (P<0.05) based upon reagent and 154 compounds were significantly different (P<0.05) based upon protocol. A key outcome of this study was the demonstrated effects of derivatisation including reagent and protocol (i.e. reaction duration, temperature and mixing speed) on individual urinary metabolites. It is hoped that the current work will provide a reference on which to base future GC-MS-based untargeted and targeted metabolomic analyses of urine.
Project description:Here we describe a genome-wide analysis of copy number variations (CNVs) in Chinese domestic cattle by using array comparative genomic hybridization (array CGH) and quantitative PCR (qPCR). We conducted array CGH analysis on 30 male cattle individuals, animals from consisting of 12 breeds of Bos taurus/Bos indicus, 1 Bos grunniens and and two ones of Bubalus bubalis breeds for with beef, and/or dairy or dual purpose. We identified over 470 candidate CNV regions (CNVRs) in Bos B. taurus/B. indicus; 118 candidate CNV regions (CNVRs) in B. grunniens, 139 CNVRs in B. bubalis. Furthermore, based on the Y haplotypes of B. taurus/ B. indicus, Wwe also identified 69, 337, and 251 candidate CNV regions (CNVRs) in the sub-groups of Y1, Y2 and Y3 haplotypes.
Project description:Urine passes through the entire kidney and urinary tract system starting from the glomerulus and ending to the urethra. Cells in the kidney and urinary tract could be exfoliated from the epithelium into the urine, while leukocyte could infiltrate from the local tissue into the urine, which makes the urine a useful subject for clinical evaluation of relevant diseases. We performed scRNA-seq on voided urine samples. 50–100 mL middle stream urine samples were collected from 12 Chinese healthy adults and combined for droplet-based single-cell RNA sequencing after flow cytometric sorting of live cells. We presented the first single-cell atlas of adult human urine and identified multiple previously unrecognized cell types. Based on our scRNA-seq analysis data, a SOX9+ cell population was identified in adult human urine which we speculated to have progenitor potential.
Project description:Interstitial cystitis/bladder pain syndrome (IC/BPS) is a chronic and debilitating pain disorder of the bladder and urinary tract with poorly understood etiology. A definitive diagnosis of IC/BPS can be challenging because many symptoms of IC/BPS are shared with other urological disorders. An analysis of urine presents an attractive and non-invasive resource for monitoring and diagnosing IC/BPS. Here, a non-targeted LC-MS and LC-MS/MS-based peptidomics analysis of urine samples collected from IC/BPS patients were compared to urine samples from asymptomatic controls.