Biomedical subjects

Xuning Wang

Publications and source records attributed to Xuning Wang.

3 recordsLinked to original sources

PubMed2006

An RNA map predicting Nova-dependent splicing regulation.

Nova proteins are a neuron-specific alternative splicing factors. We have combined bioinformatics, biochemistry and genetics to derive an RNA map describing the rules by which Nova proteins regulate alternative splicing. This map revealed that the position of Nova binding sites (YCAY clusters) in a pre-messenger RNA determines the outcome of splicing. The map correctly predicted Nova's effect to inhibit or enhance exon inclusion, which led us to examine the relationship between the map and Nova's mechanism of action. Nova binding to an exonic YCAY cluster changed the protein complexes assembled on pre-mRNA, blocking U1 snRNP (small nuclear ribonucleoprotein) binding and exon inclusion, whereas Nova binding to an intronic YCAY cluster enhanced spliceosome assembly and exon inclusion. Assays of splicing intermediates of Nova-regulated transcripts in mouse brain revealed that Nova preferentially regulates removal of introns harbouring (or closest to) YCAY clusters. These results define a genome-wide map relating the position of a cis-acting element to its regulation by an RNA binding protein, namely that Nova binding to YCAY clusters results in a local and asymmetric action to regulate spliceosome assembly and alternative splicing in neurons.

Alternative Splicing↗

PubMed2005

Electrochemical synthesis of gold nanocrystals and their 1D and 2D organization.

Size-controlled gold nanocrystals were conveniently synthesized through direct electroreduction of bulk AuCl(4)(-) ions in the presence of poly(N-vinylpyrrolidone) (PVP). PVP greatly enhanced the gold particle formation process and also significantly retarded the gold electrodeposition process, allowing the electrochemical synthesis of gold nanocrystals to be carried out in the form of simple electroreduction. This novel electrochemical method may be extended to synthesis of other noble metal nanoparticles with controllable size on a large scale. The PVPK90-protected gold nanocrystals spontaneously self-assembled into nearly ordered 2D close-packed arrays and interesting 1D nanostructures. The aggregation of unstable PVPK17-protected gold nanocrystals resulted in the formation of ultrathin single-crystalline films. PVP plays multifunctional roles in controlling the size and shape of gold nanocrystals and in inducing individual gold nanocrystals to construct 1D nanostructures. The nanoparticle self-assembling technique based on PVP offers a simple, but effective, path to organize individual gold nanoparticles into various 1D and 2D nanostructured materials.

Crystallization↗

PubMed2002

Mining protein sequences for motifs.

We use methods from Data Mining and Knowledge Discovery to design an algorithm for detecting motifs in protein sequences. The algorithm assumes that a motif is constituted by the presence of a "good" combination of residues in appropriate locations of the motif. The algorithm attempts to compile such good combinations into a "pattern dictionary" by processing an aligned training set of protein sequences. The dictionary is subsequently used to detect motifs in new protein sequences. Statistical significance of the detection results are ensured by statistically determining the various parameters of the algorithm. Based on this approach, we have implemented a program called GYM. The Helix-Turn-Helix motif was used as a model system on which to test our program. The program was also extended to detect Homeodomain motifs. The detection results for the two motifs compare favorably with existing programs. In addition, the GYM program provides a lot of useful information about a given protein sequence.

Algorithms↗