Compiler and Runtime Optimizations for Fine-Grained Distributed Shared Memory Systems

Bal, H.E. [Promotor

The distributed ASCI supercomputer project

The Distributed ASCI Supercomputer (DAS) is a homogeneous wide-area distributed system consisting of four cluster computers at different locations. DAS has been used for research on communication software, parallel languages and programming systems, schedulers, parallel applications, and distributed applications. The paper gives a preview of the most interesting research results obtained so far in the DAS project

Real-Time Pcr Detection Of Paenibacillus To Predict The Shelf- Life Of Fluid Milk And Development Of A Pcr And Sequence Based Method To Serotype Salmonella

To improve the quality of commercial dairy ingredients and consumer products, including cheese, fluid milk, milk powders and others, it is important to identify and then control factors that contribute to their degradation. Tracking and eliminating sporeforming bacteria is a particular concern, as these organisms can resist many processing hurdles. Psychrotolerant sporeformers, specifically Paenibacillus spp., are important spoilage bacteria for pasteurized, refrigerated foods such as fluid milk. A real-time PCR assay targeting 16S rDNA was designed to detect Paenibacillus spp. in fluid milk and to discriminate between Paenibacillus and other closely related sporeforming bacteria. Specificity was confirmed using 16 Paenibacillus and 17 Bacillus isolates. All 16 Paenibacillus isolates were detected with a mean cycle threshold (Ct) of 19.14 ± 0.54. While 14/17 Bacillus isolates showed no signal (Ct > 40), 3 Bacillus isolates showed very weak positive signals (Ct = 38.66 ± 0.65). The assay provided a detection limit of approximately 3.25 ! 10 1 CFU/ml using total genomic DNA extracted from raw milk samples inoculated with Paenibacillus. Application of the TaqMan PCR to colony lysates obtained from heattreated and enriched raw milk provided fast and accurate detection of Paenibacillus. Heat-treated milk samples where Paenibacillus (" 1 CFU/ml) were detected by this colony TaqMan PCR showed high bacterial counts (> 4.30 log CFU/ml) after refrigerated storage (6°C) for 21 days. We thus developed a tool for rapid detection of Paenibacillus that has the potential to identify raw milk with microbial spoilage potential as a pasteurized product. Replacement of traditional serotyping methods with molecular approaches is particularly important for Salmonella, which includes >2,500 different serotypes. We evaluated the ability of PFGE, rep-PCR, ribotyping, and MLST to predict serotypes for a set of 46 isolates, which were identified to represent the top 40 reported Salmonella from human and non-human sources reported by the Centers for Disease Control and World Health Organization. MLST was most reliable and able to accurately predict serotypes for 42/46 isolates representing the top 40 serotypes. PFGE, ribotyping, and rep-PCR were able to accurately predict 35/46, 34/46 and 30/46 serotypes, respectively. We also integrated a number of available data sources to develop and validate a PCR-based O-antigen screen with sequencing of internal fliC (H1 antigen) and fljB (H2 antigen) fragments to characterize Salmonella isolates to the serotype level. PCR and sequence based serotyping correctly identified 42/46 common serotypes. We continued to test our method against a selection of 70 less common Salmonella serotypes and were able to accurately predict 62/70 Salmonella serotypes. This study provides an initial comparison of the ability to identify Salmonella serotypes using (i) different molecular methods that predict serotypes based on banding patterns or phylogenetic relationships and (ii) a combined PCR and sequencing based approach that directly targets O and H antigen encoding genes