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Sekulovic O.,Universite de Sherbrooke | Ospina Bedoya M.,Universite de Sherbrooke | Fivian-Hughes A.S.,Imperial College London | Fivian-Hughes A.S.,Synthace | And 2 more authors.
Molecular Microbiology | Year: 2015

Bacteriophages are present in virtually all ecosystems, and bacteria have developed multiple antiphage strategies to counter their attacks. Clostridium difficile is an important pathogen causing severe intestinal infections in humans and animals. Here we show that the conserved cell-surface protein CwpV provides antiphage protection in C.difficile. This protein, for which the expression is phase-variable, is classified into five types, each differing in their repeat-containing C-terminal domain. When expressed constitutively from a plasmid or the chromosome of locked 'ON' cells of C.difficileR20291, CwpV conferred antiphage protection. Differences in the level of phage protection were observed depending on the phage morphological group, siphophages being the most sensitive with efficiency of plaquing (EOP) values of <5×10-7 for phages ϕCD38-2, ϕCD111 and ϕCD146. Protection against the myophages ϕMMP01 and ϕCD52 was weaker, with EOP values between 9.0×10-3 and 1.1×10-1. The C-terminal domain of CwpV carries the antiphage activity and its deletion, or part of it, significantly reduced the antiphage protection. CwpV does not affect phage adsorption, but phage DNA replication is prevented, suggesting a mechanism reminiscent of superinfection exclusion systems normally encoded on prophages. CwpV thus represents a novel ubiquitous host-encoded and phase-variable antiphage system in C.difficile. © 2015 John Wiley & Sons Ltd.


Bhat A.,MathWorks | Lenharth A.,University of Texas at Austin | Nguyen D.,Synthace | Yi Q.,University of Colorado at Colorado Springs | Pingali K.,University of Texas at Austin
Advances in Parallel Computing | Year: 2016

The performance of multi-threaded applications depends on efficient scheduling of parallel tasks. Manually selecting schedulers is difficult because the best scheduler depends on the application, machine and input. We present a framework that automatically selects the best scheduler based on empirical tuning results. We applied our framework to tune eleven applications parallelized using OpenMP, TBB or the Galois system. Depending on the application and machine, we observed up to 4X performance improvement over the default scheduler.We were also able to prune the search space by an order of magnitude while still achieving performance within 16% of the best scheduler. © 2016 The authors and IOS Press.


Lenharth A.,University of Texas at Austin | Nguyen D.,Synthace | Pingali K.,University of Texas at Austin
Communications of the ACM | Year: 2016

Data-centric abstractions and execution strategies are needed to exploit parallelism in large-scale graph analytics. © 2016 ACM.


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Synthace | Date: 2016-04-26

Computer programs and downloadable computer programs that implement a procedural computer programming language, and a laboratory equipment control language for codifying experimental protocols and biological, biochemical and chemical data; computer programs and downloadable computer programs that implement a procedural computer programming language, and a laboratory equipment control language for defining the physical implementation of the protocols on laboratory equipment including data acquisition; computer programs and downloadable computer programs that implement a procedural computer programming language, and a laboratory equipment control language for collating, storing, displaying and processing such data; computer software for automating biological and life science research and development processes; all the aforementioned goods being for use in biological, biotechnological and life science research and development processes.


Synthace | Entity website

Synthetic Biology is set to drive one of the most transformational revolutions in history. The potential benefits, ranging from improved human health, cleaner sources of chemicals and fuels, and the sequestering of pollution, are tremendous ...

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