ABSTRACT
Objective Urine is a promising biomarker source for clinical proteomics studies. Regional physiological differences are common in multi-center clinical studies. In this study, we investigate whether significant differences are present in the urinary proteomes of individuals from different regions in China. Methods In this study, morning urine samples were collected from healthy urban residents in three regions of China (Haikou, Xi'an and Xining) and urinary proteins were preserved using a membrane-based method (Urimem). The urine proteomes of 27 normal samples were analyzed using LC-MS/MS and compared among three regions. Functional annotation of the differential proteins among the three areas was analyzed using the DAVID online database, and pathway enrichment of the differential urinary proteins was analyzed using KEGG. Results We identified 1898 proteins from Urimem samples using label-free proteome quantification, of which 56 urine proteins were differentially expressed among the three regions ( < 0.05). Hierarchical clustering analysis showed that inter-regional differences caused less significant changes in the urine proteome than inter-sex differences. After gender stratification, 16 differential proteins were identified in male samples and 84 differential proteins were identified in female samples. Among these differential proteins, several proteins have been previously reported as urinary disease biomarkers. Conclusions Urimem will facilitate urinary protein storage for large-scale urine sample collection. Regional differences are a confounding factor influencing the urine proteome and should be considered in future multi-center biomarker studies.
ABSTRACT
We developed a novel method for constructing nearly random peptide library. Genomic DNAs extracted from tissue or cells of large genome species were digested with frequent cutter to produce short DNA fragments. These short fragments can be considered nearly random. Nearly random peptide libraries can be constructed by cloning the short fragments into appropriate expression vectors and transformation into host cells. Genomic DNA from one species can be digested with different restriction enzymes and ligated to different reading frames to produce several different libraries. In this study, we digested tobacco genomic DNA with two enzymes and cloned into three different reading frames to make totally six nearly random peptide libraries.
Subject(s)
DNA, Plant , Genetics , Genome, Plant , Genetics , Peptide Library , Tobacco , GeneticsABSTRACT
<p><b>OBJECTIVE</b>To deduce all potential ligands undiscovered experimentally by searching all the proteins containing same C-termini, which can bind a certain PDZ domain.</p><p><b>METHODS</b>We developed a JAVA program for searching short exact sequence matches at C-terminus. According to the known C-termini, which PDZ domains recognized experimentally, Swissprot database has been searched by this program for all potential ligands.</p><p><b>RESULTS</b>Some PDZ domains may have more potential ligand proteins, which are undiscovered yet experimentally. These bioinformatic results also provide clues for studying functions of hypothetical proteins and PDZ domains' protein interactions in many different organisms.</p><p><b>CONCLUSION</b>The results may provide useful clues for discovering potential functions of hypothetical proteins and new functions of known proteins.</p>