Motif Recognition

The problem of recognizing motifs from biological data has been well-studied and numerous algorithms, both exact and approximate, have been proposed to address the underlying issue. We strongly believe that open availability and ease of accessibility of quality implementations for such algorithms are critical to the research community, in order to directly reproduce and utilize the results from other studies, so as not to reinvent the wheel. Moreover, it is also important for the implementation to be as generic as possible so that any researcher can to extend it with minimal effort to test a newly implemented algorithmic extension or heuristic. With this motivation, we choose to focus an existing algorithm, PatternBranching and, to a lesser degree, Yang2004. We analyze these approaches for minor heuristical changes & speed-ups by adjusting certain thresholds, and finally, implement the variant in high-level language (Java) using thought through programming practices and generic, extensible interfaces. We also analyze the performance of PatternBranching using a synthetically generated test-suite for a variety of sequence lengths and report the results. Code from this project will be made freely available online to the research community

Involvement of Actin-Regulating Factor Cofilin in the Inclusion Body Formation and RNA Synthesis of Human Parainfluenza Virus Type 3 via Interaction With the Nucleoprotein

Human parainfluenza virus type 3 (HPIV3) is one of the primary pathogens that causing severe respiratory tract diseases in newborns and infants. It could induce inclusion bodies (IBs) in infected cells. Comprised of viral nucleoprotein (N) and phosphoprotein (P), as well as some cellular factors, HPIV3 IBs are unique platform for efficient viral synthesis. Although several studies have demonstrated the formation of IBs, little is known about cellular proteins involved in HPIV3 IBs formation. By quantitative real-time PCR assays after cytochalasin D treatment, we found actin microfilaments of the cytoskeleton were indispensible for HPIV3 RNA synthesis. Using co-immunoprecipitation and immunofluorescence assays, an actin-modulating protein, cofilin was found to involve in the IBs formation through interaction with the N protein in N–P induced IBs complex. Viral IBs formation reduced upon RNA interference knockdown of cellular cofilin, thus viral RNA synthesis and protein expression level were also suppressed. What’s more, the inactive form of cofilin, p-cofilin was increased after HPIV3 infection, and phosphorylation of cofilin was required for interacting with N–P complex and IBs formation. We further identified that the regions in cofilin interacting with N protein lies in the C-terminus. Our findings for the first time to state that cellular cofilin involves in HPIV3 IBs and interaction with N is critical for cofilin to aid IBs formation and enhancing viral RNA synthesis

Roll-to-Roll Manufacturing of Robust Superhydrophobic Coating on Metallic Engineering Materials

Creating a robust superhydrophobic surface on the conventional engineering materials at mass production is of great importance for self–cleaning, anti–icing, non–wetting surface and low flow resistance in industrial applications. Herein, we report a roll–to–roll strategy to create durable and robust superhydrophobic surfaces with designed micro–/nano– scale hierarchical structures on many conventional engineering materials by combining electrical discharge machining, coating of carbon nanoparticles, and followed by oil penetration and drying. The treated surface shows good superhydrophobic properties with static water contact angle of 170±2o and slide angle of 3±1o. The treated surface also exhibits good resilience and maintains the performance after tested in various harsh conditions including water flushing for several days, sand abrasion, scratching with sandpapers and corrosive solution. Significantly, the superhydrophobic surfaces also shows a high efficiency of self–cleaning properties even after oil–contamination during applications