We report a highly reproducible method to crystallize the RNA-dependent RNA polymerase (RdRp) domain of dengue virus serotype 3 (DENV-3), allowing structure refinement to a 1.79-Å resolution and revealing amino acids not seen previously. We also present a DENV-3 polymerase/inhibitor cocrystal structure at a 2.1-Å resolution. The inhibitor binds to the RdRp… (More)
Software engineering is commonly taught as an upper level course in students in computer science. There are many software development skills that can be taught in a software engineering course that are useful in other courses. The development of this course has greatly influenced the types of projects and assignments that are required in the upper level… (More)
Bacteria respond to environmental stresses using a variety of signaling and gene expression pathways, with translational mechanisms being the least well understood. Here, we identified a tRNA methyltransferase in Pseudomonas aeruginosa PA14, trmJ, which confers resistance to oxidative stress. Analysis of tRNA from a trmJ mutant revealed that TrmJ catalyzes… (More)
Large-scale production of bis-3'-5'-cyclic-di-GMP (c-di-GMP) would facilitate biological studies of numerous bacterial signaling pathways and phenotypes controlled by this second messenger molecule, such as virulence and biofilm formation. C-di-GMP constitutes also a potentially interesting molecule as a vaccine adjuvant. Even though chemical synthesis of… (More)
Dengue is the most common vector-borne viral disease, causing nearly 400 million infections yearly. Currently there are no approved therapies. Antibody epitopes that elicit weak humoral responses may not be accessible by conventional B cell panning methods. To demonstrate an alternative strategy to generating a therapeutic antibody, we employed a… (More)
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VLSI HLS design is a typical design optimization problem with a focus on generating good solutions. Typical expert design systems incorporate a large amount of domain knowledge to generate good initial solutions. These systems are unable to use information gleaned from analysis of the solutions (feedback)to generate better solutions. This paper describes a… (More)
Design optimization problems and VLSI microprocessor design in particular, are complex problems with some characteristics that make them very dierent from the problems that AI researchers have traditionally studied. Case based reasoning is a valuable tool that can be used to make these problems tractable. Traditional case based methods with their use of… (More)