Biomedical subjects

Liping Wei

Publications and source records attributed to Liping Wei.

24 records · Page 2Linked to original sources

PubMed2003

Gene identification and expression analysis of 86,136 Expressed Sequence Tags (EST) from the rice genome.

Expressed Sequence Tag (EST) analysis has pioneered genome-wide gene discovery and expression profiling. In order to establish a gene expression index in the rice cultivar indica, we sequenced and analyzed 86,136 ESTs from nine rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars. We assembled these ESTs into 13,232 contigs and leave 8,976 singletons. Overall, 7,497 sequences were found similar to existing sequences in GenBank and 14,711 are novel. These sequences are classified by molecular function, biological process and pathways according to the Gene Ontology. We compared our sequenced ESTs with the publicly available 95,000 ESTs from japonica, and found little sequence variation, despite the large difference between genome sequences. We then assembled the combined 173,000 rice ESTs for further analysis. Using the pooled ESTs, we compared gene expression in metabolism pathway between rice and Arabidopsis according to KEGG. We further profiled gene expression patterns in different tissues, developmental stages, and in a conditional sterile mutant, after checking the libraries are comparable by means of sequence coverage. We also identified some possible library specific genes and a number of enzymes and transcription factors that contribute to rice development.

Arabidopsis↗

PubMed2003

Recognizing complex, asymmetric functional sites in protein structures using a Bayesian scoring function.

The increase in known three-dimensional protein structures enables us to build statistical profiles of important functional sites in protein molecules. These profiles can then be used to recognize sites in large-scale automated annotations of new protein structures. We report an improved FEATURE system which recognizes functional sites in protein structures. FEATURE defines multi-level physico-chemical properties and recognizes sites based on the spatial distribution of these properties in the sites' microenvironments. It uses a Bayesian scoring function to compare a query region with the statistical profile built from known examples of sites and control nonsites. We have previously shown that FEATURE can accurately recognize calcium-binding sites and have reported interesting results scanning for calcium-binding sites in the entire Protein Data Bank. Here we report the ability of the improved FEATURE to characterize and recognize geometrically complex and asymmetric sites such as ATP-binding sites and disulfide bond-forming sites. FEATURE does not rely on conserved residues or conserved residue geometry of the sites. We also demonstrate that, in the absence of a statistical profile of the sites, FEATURE can use an artificially constructed profile based on a priori knowledge to recognize the sites in new structures, using redoxin active sites as an example.

Adenosine Triphosphate↗

PubMed2002

Adrenalectomy enhances the insulin sensitivity of muscle protein synthesis.

After confirming that adrenalectomy per se does not affect skeletal muscle protein synthesis rates, we examined whether endogenously produced glucocorticoids modulate the effect of physiological insulin concentrations on protein synthesis in overnight-fasted rats 4 days after either a bilateral adrenalectomy (ADX), ADX with dexamethasone treatment (ADX + DEX), or a sham operation (Sham; n = 6 each). Rats received a 3-h euglycemic insulin clamp (3 mU. min(-1). kg(-1)). Rectus muscle protein synthesis was measured at the end of the clamp, and the phosphorylation states of protein kinase B (Akt), eukaryotic initiation factor 4E-binding protein 1 (4E-BP1), and ribosomal protein S6 kinase (p70(S6K)) were quantitated before and after the insulin clamp. The basal phosphorylation states of Akt, 4E-BP1, and p70(S6K) were similar between ADX and Sham rats. Insulin significantly enhanced the phosphorylation of Akt (P < 0.03), 4E-BP1 (P = 0.003), and p70(S6K) (P < 0.002) in ADX but not in Sham rats. Protein synthesis was significantly greater after insulin infusion in ADX than in Sham rats (P = 0.01). Glucocorticoid replacement blunted the effect of insulin on Akt, 4E-BP1, and p70(S6K) phosphorylation and protein synthesis. In conclusion, glucocorticoid deficiency enhances the insulin sensitivity of muscle protein synthesis, which is mediated by increased phosphorylation of translation initiation-regulatory proteins.

Adrenalectomy↗

PubMed2002

Comparative genomics approaches to study organism similarities and differences.

Comparative genomics is a large-scale, holistic approach that compares two or more genomes to discover the similarities and differences between the genomes and to study the biology of the individual genomes. Comparative studies can be performed at different levels of the genomes to obtain multiple perspectives about the organisms. We discuss in detail the type of analyses that offer significant biological insights in the comparisons of (1) genome structure including overall genome statistics, repeats, genome rearrangement at both DNA and gene level, synteny, and breakpoints; (2) coding regions including gene content, protein content, orthologs, and paralogs; and (3) noncoding regions including the prediction of regulatory elements. We also briefly review the currently available computational tools in comparative genomics such as algorithms for genome-scale sequence alignment, gene identification, and nonhomology-based function prediction.

Animals↗

PubMed2002

UniBLAST: a system to filter, cluster, and display BLAST results and assign unique gene annotation.

MOTIVATION: More and more often, a gene is epitomized by a large number of sequences in GenBank. This high redundancy makes it very difficult to identify a unique best match for a query sequence from its BLAST results. We developed a novel program UniBLAST that filters out uninformative hits, clusters the redundant hits, groups the hits by LocusLink, and graphically displays the results. We also implemented a scoring function in UniBLAST to assign a unique gene name to a query sequence. UniBLAST significantly increases the efficiency of gene annotation. AVAILABILITY: The program is available at http://south.genomics.org.cn/software/uniblast/index.html CONTACT: uniblast@genomics.org.cn; wei@nexusgenomics.com

Cluster Analysis↗

PubMed2002

Amino acids stimulate translation initiation and protein synthesis through an Akt-independent pathway in human skeletal muscle.

Studies in vitro as well as in vivo in rodents have suggested that amino acids (AA) not only serve as substrates for protein synthesis, but also as nutrient signals to enhance mRNA translation and protein synthesis in skeletal muscle. However, the physiological relevance of these findings to normal humans is uncertain. To examine whether AA regulate the protein synthetic apparatus in human skeletal muscle, we infused an AA mixture (10% Travesol) systemically into 10 young healthy male volunteers for 6 h. Forearm muscle protein synthesis and degradation (phenylalanine tracer method) and the phosphorylation of protein kinase B (or Akt), eukaryotic initiation factor 4E-binding protein 1, and ribosomal protein S6 kinase (p70(S6K)) in vastus lateralis muscle were measured before and after AA infusion. We also examined whether AA affect urinary nitrogen excretion and whole body protein turnover. Postabsorptively all subjects had negative forearm phenylalanine balances. AA infusion significantly improved the net phenylalanine balance at both 3 h (P < 0.002) and 6 h (P < 0.02). This improvement in phenylalanine balance was solely from increased protein synthesis (P = 0.02 at 3 h and P < 0.003 at 6 h), as protein degradation was not changed. AA also significantly decreased whole body phenylalanine flux (P < 0.004). AA did not activate Akt phosphorylation at Ser(473), but significantly increased the phosphorylation of both eukaryotic initiation factor 4E-binding protein 1 (P < 0.04) and p70(S6K) (P < 0.001). We conclude that AA act directly as nutrient signals to stimulate protein synthesis through Akt-independent activation of the protein synthetic apparatus in human skeletal muscle.

Adaptor Proteins, Signal Transducing↗