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.     

Receptor-associated protein facilitates proper folding and maturation of the low-density lipoprotein receptor and its class 2 mutants

Familial hypercholesterolemia is the consequence of various mutations in the low-density lipoprotein receptor (LDLR). In the current study, we show that a specialized molecular chaperone, the receptor-associated protein (RAP), promotes proper folding and subsequent exocytic trafficking of the wild-type LDLR and several of its class 2 mutants. Co-immunoprecipitation with anti-RAP antibody demonstrates that RAP interacts with the LDLR. Kinetic analyses of LDLR posttranslational folding and maturation in the absence or presence of RAP coexpression show that RAP prevents aggregation and promotes the maturation of the LDLR. Additionally, depletion of Ca(2+) in intact cells impairs LDLR folding, and coexpression of RAP partially corrects this misfolding. Finally, we show that the increased mature cell surface LDLR in the presence of RAP coexpression is functional in its ability to endocytose and degrade (125)I-LDL. Taken together, our results show that the folding, trafficking, and maturation of the LDLR and its class 2 mutants are promoted by RAP.     

Fish parasite communities in tropical reservoirs along the Perak River, Malaysia

The parasite communities of fish in three reservoirs (Temengor, Kenering and Cenderuh) along the Perak River, as well as in the lower Perak, are compared. A total of 36 species, 51 species, 61 species and 58 species of metazoan parasites from six types of fishes common in all studied locations, were obtained in Temengor, Kenering, Cenderuh Reservoirs, and downstream Perak River, respectively. The various criteria (prevalence, mean intensity, diversity index, similarity index and evenness) of the parasite community were highest at the Cenderuh Reservoir, followed by the downstream river, Kenering, and Temengor Reservoirs. Monogeneans were the most common parasites in all species of fish examined from all study sites. Fish of the same species showed a high degree of similarity of its parasite fauna regardless of study site, but different hosts had a low similarity of their parasite fauna, even within the same study site. This revised version was published online in August 2006 with corrections to the Cover Date.     

Inhibition of cleavage of a plant viral polyprotein by an inhibitor activity present in wheat germ and cowpea embryos

In rabbit reticulocyte lysate, the bottom component RNA of cowpea mosaic virus directs the synthesis of a 200,000-molecular-weight precursor protein (200K protein) that is cleaved during synthesis by a reticulocyte enzyme to form a 32K protein and a 170K protein. Cleavage of the 200K protein was found to be effectively inhibited by inhibitor activity in wheat germ and cowpea embryo extracts. The inhibitor was nondialyzable, precipitatable by ammonium sulfate, and partially stable at high temperatures. The activity appeared to be specific in that it caused no inhibition of the secondary cleavage reactions (cleavage of the 170K protein) at concentrations that were sufficient to cause complete inhibition of the primary cleavage reaction (cleavage of the 200K protein).     

SIMPLE: a simplifying-ensembling framework for parallel community detection from large networks

Community detection is a classic and very difficult task in complex network analysis. As the increasingly explosion of social media, scaling community detection methods to large networks has attracted considerable recent interests. In this paper, we propose a novel SIMPLifying and Ensembling (SIMPLE) framework for parallel community detection. It employs the random link sampling to simplify the network and obtain basic partitionings on every sampled graphs. Then, the K-means-based Consensus Clustering is used to ensemble a number of basic partitionings to get high-quality community structures. All of phases in SIMPLE, including random sampling, sampled graph partitioning, and consensus clustering, are encapsulated into MapReduce for parallel execution. Experiments on six real-world social networks analyze key parameters and factors inside SIMPLE, and demonstrate both effectiveness and efficiency of the SIMPLE.