RESUMO
BACKGROUND: The comprehensive analysis of human kidney glomerulus we previously performed using highly purified glomeruli, provided a dataset of 6,686 unique proteins representing 2,966 distinct genes. This dataset, however, contained considerable redundancy resulting from identification criteria under which all the proteins matched with the same set of peptides and its subset were reported as identified proteins. In this study we reanalyzed the raw data using the Mascot search engine and highly stringent criteria in order to select proteins with the highest scores matching peptides with scores exceeding the "Identity Threshold" and one or more unique peptides. This enabled us to exclude proteins with lower scores which only matched the same set of peptides or its subset. This approach provided a high-confidence, non-redundant dataset of identified proteins for extensive profiling, annotation, and comparison with other proteome datasets that can provide biologically relevant knowledge of glomerulus proteome. RESULTS: Protein identification using the Mascot search engine under highly stringent, computational strategy generated a non-redundant dataset of 1,817 proteins representing 1,478 genes. These proteins were represented by 2-D protein array specifying observed molecular weight and isoelectric point range of identified proteins to demonstrate differences in the observed and calculated physicochemical properties. Characteristics of glomerulus proteome could be illustrated by GO analysis and protein classification. The depth of proteomic analysis was well documented via comparison of the dynamic range of identified proteins with other proteomic analyses of human glomerulus, as well as a high coverage of biologically important pathways. Comparison of glomerulus proteome with human plasma and urine proteomes, provided by comprehensive analysis, suggested the extent and characteristics of proteins contaminated from plasma and excreted into urine, respectively. Among the latter proteins, several were demonstrated to be highly or specifically localized in the glomerulus by cross-reference analysis with the Human Protein Atlas database, and could be biomarker candidates for glomerular injury. Furthermore, comparison of ortholog proteins identified in human and mouse glomeruli suggest some biologically significant differences in glomerulus proteomes between the two species. CONCLUSIONS: A high-confidence, non-redundant dataset of proteins created by comprehensive proteomic analysis could provide a more extensive understanding of human glomerulus proteome and could be useful as a resource for the discovery of biomarkers and disease-relevant proteins.
RESUMO
Unsaturated free fatty acids (FFAs), such as palmitoleic, oleic, linoleic, linolenic and arachidonic acids, have inhibitory actions on mutagenesis. These FFAs in bile may play a role in preventing cholecystopathy and their levels may be influenced by diet. However, the effects of dietary intake on biliary FFAs levels are not known. In order to examine possible associations between dietary habits and biliary FFAs levels, bile samples were collected from resected gallbladders of 114 Chilean female patients with gallstones, and FFAs were measured with an HPLC system. The long-term dietary intake of the patients was investigated through a semi-quantitative food frequency questionnaire. A high intake of vegetables was negatively correlated with the total FFA level (r = -0.264, P = 0.010). Positive correlations were found between fruit consumption and the lauric acid level (r = 0.200, P = 0.041), fish consumption and the levels of oleic (r = 0.370, P <0.0001), linolenic (r = 0.197, P = 0.038) and arachidonic (r = 0.200, P =0.035) acids, and consumption of foods fried in vegetable oil and the linoleic acid level (r = 0.269, P =0.004). Linoleic, linolenic, and arachidonic acids which may have an inhibitory effect on actions of unknown mutagens in bile appear to be increased by consumption of high levels of fish and fried foods.
