Project description:Diluted urine for biomarker discovery.
Processed in MZmine 2.37.corr17.7_kei_merge2
GNPS link for IIN paper:
https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=a5480529261b4a13bb867f2edad1dcbe
Project description:19 men were split into two groups. 10 were provided with a diet of twice the recommended daily intake of protein and 9 were provided meals with the recommended dietary intake of protein. Faecal samples were collected after 10 weeks on the diet. This project looked at determining any qualitative differences present in the self-proteins from each group.
Project description:The type and the amount of dietary fat have a significant influence on the metabolic pathways involved in the development of obesity, metabolic syndrome, diabetes type 2 and cardiovascular diseases. However, it is unknown to what extent this modulation is achieved through DNA methylation. We assessed the effects of cholesterol intake, the proportion of energy intake derived from fat, the ratio of polyunsaturated fatty acids (PUFA) to saturated fatty acids (SFA), the ratio of monounsaturated fatty acids (MUFA) to SFA, and the ratio of (MUFA+PUFA) to SFA on genome-wide DNA methylation patterns in normal-weight and obese children. We determined the genome-wide methylation profile in blood of 69 Greek preadolescents (~10 y old), as well as their dietary intake for two consecutive weekdays and one weekend day. The methylation levels of four sites and a CpG island were significantly correlated with total fat intake. The methylation levels of 13 islands and 16 sites were significantly correlated with PUFA/SFA; of 35 islands and 158 sites with MUFA/SFA; and of 50 islands and 130 sites with (MUFA+PUFA)/SFA. We found significant gene enrichment in 26 pathways for PUFA/SFA, including the leptin pathway, and a significant enrichment in three pathways for (MUFA+PUFA)/SFA. Our results suggest that the quality, and to a lesser extent the quantity of fat intake, influences DNA methylation, including genes involved in metabolism. Thus, specific changes in DNA methylation may play an important role in the mechanisms involved in the physiological responses to different types of dietary fat.
Project description:CYP monooxygenase-mediated conversion of LA to EpOMEs plays critical roles in the health effects of dietary LA, implicating a unique mechanistic linkage between dietary fatty acid intake and cancer risks.
Project description:The type and the amount of dietary fat have a significant influence on the metabolic pathways involved in the development of obesity, metabolic syndrome, diabetes type 2 and cardiovascular diseases. However, it is unknown to what extent this modulation is achieved through DNA methylation. We assessed the effects of cholesterol intake, the proportion of energy intake derived from fat, the ratio of polyunsaturated fatty acids (PUFA) to saturated fatty acids (SFA), the ratio of monounsaturated fatty acids (MUFA) to SFA, and the ratio of (MUFA+PUFA) to SFA on genome-wide DNA methylation patterns in normal-weight and obese children. We determined the genome-wide methylation profile in blood of 69 Greek preadolescents (~10 y old), as well as their dietary intake for two consecutive weekdays and one weekend day. The methylation levels of four sites and a CpG island were significantly correlated with total fat intake. The methylation levels of 13 islands and 16 sites were significantly correlated with PUFA/SFA; of 35 islands and 158 sites with MUFA/SFA; and of 50 islands and 130 sites with (MUFA+PUFA)/SFA. We found significant gene enrichment in 26 pathways for PUFA/SFA, including the leptin pathway, and a significant enrichment in three pathways for (MUFA+PUFA)/SFA. Our results suggest that the quality, and to a lesser extent the quantity of fat intake, influences DNA methylation, including genes involved in metabolism. Thus, specific changes in DNA methylation may play an important role in the mechanisms involved in the physiological responses to different types of dietary fat. Bisulphite converted DNA from 22 boys were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2.Both obese and normal-weight indiviudals were included.
Project description:Cell state determination is apparent within the endometrium during the mid-luteal window of implantation. Using previously identified biomarkers of cell states (SCARA5 and DIO2) we performed bulk RNA sequencing on 6 pairs of endometrial biopsies characterised by either normal biomarker expression in both biopsies, or abnormal biomarker expression in one biopsy (low SCARA5 and high DIO2) and normal expression in a second biopsy. We demonstrate that “abnormal cycles” are associated with a distinct gene expression profile when compared to “normal cycles” and have utilised this dataset for biomarker discovery.
Project description:Even though the importance of adequate zinc intake has been known for around half a century, a reliable diagnostic tool to assess the dietary zinc status of individual humans or populations is in absence. The specific aim of this study was to examine differential expression of specific gene transcripts that occur when the dietary intake of zinc is acutely reduced below the dietary requirement for a period of ten days. Gene expression profiles of whole blood collected before and after dietary zinc restriction were determined by microarray analyses. The data provide potential signature genes of suboptimal zinc consumption and relevant bioinformatic interpretation indicate immune response and cell cycle regulation as biological processes associated with the zinc-responsive genes.
Project description:Biomarker discovery approaches in urine have been hindered by concerns for reproducibility and inadequate standardization of proteomics protocols. In this study, we describe an optimized quantitative proteomics strategy for urine biomarker discovery, which is applicable to fresh or long frozen samples. We used urine from healthy controls to standardize iTRAQ (isobaric tags for relative and absolute quantitation) for variation induced by protease inhibitors, starting protein and iTRAQ label quantities, protein extraction methods, and depletion of albumin and immunoglobulin G (IgG). We observed the following: (a) Absence of protease inhibitors did not affect the number or identity of the high confidence proteins. (b) Use of less than 20 μg of protein per sample led to a significant drop in the number of identified proteins. (c) Use of as little as a quarter unit of an iTRAQ label did not affect the number or identity of the identified proteins. (d) Protein extraction by methanol precipitation led to the highest protein yields and the most reproducible spectra. (e) Depletion of albumin and IgG did not increase the number of identified proteins or deepen the proteome coverage. Applying this optimized protocol to four pairs of long frozen urine samples from diabetic Pima Indians with or without nephropathy, we observed patterns suggesting segregation of cases and controls by iTRAQ spectra. We also identified several previously reported candidate biomarkers that showed trends toward differential expression, albeit not reaching statistical significance in this small sample set.