Cumming School of Medicine
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The University of Calgary Faculty of Medicine was established in 1967 and renamed the Cumming School of Medicine in 2014. The Cumming School of Medicine is a national research leader in brain and mental health, chronic diseases and cardiovascular sciences.
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Browsing Cumming School of Medicine by Department "Biochemistry and Molecular Biology"
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Item Open Access Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking(BioMed Central, 2008) Soh, Jung; Gordon, Paul M. K.; Taschuk, Morgan L.; Dong, Anguo; Ah-Seng, Andrew C.; Turinsky, Andrei L; Sensen, Christoph W.Item Open Access Building generic anatomical models using virtual model cutting and iterative registration(BioMed Central, 2010-02-08) Xiao, Mei; Soh, Jung; Meruvia-Pastor, Oscar; Schmidt, Eric; Hallgrímsson, Benedikt; Sensen, Christoph W.Item Open Access Characterization of the C. elegans erlin homologue(BioMed Central, 2012-01-23) Hoegg, Maja B.; Robbins, Stephen M.; McGhee, James D.Item Open Access Evaluation of yellow pea fibre supplementation on weight loss and the gut microbiota: a randomized controlled trial(BioMed Central, 2014-04-08) Lambert, Jennifer E.; Parnell, Jill A.; Han, Jay; Sturzenegger, Troy; Paul, Heather A.; Vogel, Hans J.; Reimer, Raylene A.Item Open Access Function of Oxygen Resistance Proteins in the Anaerobic, Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough(Journal of Bacteriology, 2003-01) Fournier, Marjorie; Zhang, Yi; Wildschut, Janine D.; Dolla, Alain; Voordouw, Johanna K.; Schriemer, David C.; Vourdouw, GerritTwo mutant strains of Desulfovibrio vulgaris Hildenborough lacking either the sod gene for periplasmic superoxide dismutase or the rbr gene for rubrerythrin, a cytoplasmic hydrogen peroxide (H2O2) reductase, were constructed. Their resistance to oxidative stress was compared to that of the wild-type and of a sor mutant lacking the gene for the cytoplasmic superoxide reductase. The sor mutant was more sensitive to exposure to air or to internally or externally generated superoxide than was the sod mutant, which was in turn more sensitive than the wild-type strain. No obvious oxidative stress phenotype was found for the rbr mutant, indicating that H2O2 resistance may also be conferred by two other rbr genes in the D. vulgaris genome. Inhibition of Sod activity by azide and H2O2, but not by cyanide, indicated it to be an iron-containing Sod. The positions of Fe-Sod and Sor were mapped by two-dimensional gel electrophoresis (2DE). A strong decrease of Sor in continuously aerated cells, indicated by 2DE, may be a critical factor in causing cell death of D. vulgaris. Thus, Sor plays a key role in oxygen defense of D. vulgaris under fully aerobic conditions, when superoxide is generated mostly in the cytoplasm. Fe-Sod may be more important under microaerophilic conditions, when the periplasm contains oxygen-sensitive, superoxide-producing targets.Item Open Access Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses(BMC Bioinformatics, 2009-05-27) Slysz, Gordon W.; Baker, Charles A.H.; Bozsa, Benjamin M.; Dang, Anthony; Percy, Andrew J.; Bennett, Melissa; Schriemer, David C.Background Hydrogen/deuterium exchange mass spectrometry (H/DX-MS) experiments implemented to characterize protein interaction and protein folding generate large quantities of data. Organizing, processing and visualizing data requires an automated solution, particularly when accommodating new tandem mass spectrometry modes for H/DX measurement. We sought to develop software that offers flexibility in defining workflows so as to support exploratory treatments of H/DX-MS data, with a particular focus on the analysis of very large protein systems and the mining of tandem mass spectrometry data. Results We present a software package ("Hydra") that supports both traditional and exploratory treatments of H/DX-MS data. Hydra's software architecture tolerates flexible data analysis procedures by allowing the addition of new algorithms without significant change to the underlying code base. Convenient user interfaces ease the organization of raw data files and input of peptide data. After executing a user-defined workflow, extracted deuterium incorporation values can be visualized in tabular and graphical formats. Hydra also automates the extraction and visualization of deuterium distribution values. Manual validation and assessment of results is aided by an interface that aligns extracted ion chromatograms and mass spectra, while providing a means of rapidly reprocessing the data following manual adjustment. A unique feature of Hydra is the automated processing of tandem mass spectrometry data, demonstrated on a large test data set in which 40,000 deuterium incorporation values were extracted from replicate analysis of approximately 1000 fragment ions in one hour using a typical PC. Conclusion The customizable workflows and user-friendly interfaces of Hydra removes a significant bottleneck in processing and visualizing H/DX-MS data and helps the researcher spend more time executing new experiments and interpreting results. This increased efficiency will encourage the analysis of larger protein systems. The ability to accommodate the tandem MS dimension supports alternative data collection and analysis strategies, as well as higher resolution localization of deuteration where permitted by the fragmentation mechanism.Item Open Access Interspecies data mining to predict novel ING-protein interactions in human(BioMed Central, 2008) Gordon, Paul; Soliman, Mohamed A; Bose, Pinaki; Sensen, Christoph W; Riabowol, Karl T.Item Open Access Multi-tyrosine kinase inhibitors in preclinical studies for pediatric CNS AT/RT: Evidence for synergy with Topoisomerase-I inhibition(BioMed Central, 2011-12-29) Jayanthan, Aarthi; Bernoux, Delphine; Bose, Pinaki; Riabowol, Karl; Narendran, AruItem Open Access Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping(Dove Medical Press, 2009-04-01) Soh, Jung; Turinsky, Andrei L.; Trinh, Quang M.; Chang, Jasmine; Sabhaney, Ajay; Dong, Xiaoli; Gordon, Paul M. K.; Janzen, Ryan P. W.; Hau, David; Xia, Jianguo; Wishart, David S.; Sensen, Christoph W.Item Open Access Survivin as a Preferential Target for Cancer Therapy(Multidisciplinary Digital Publishing Institute, 2014-02-13) Mobahat, Mahsa; Narendran, Aru; Riabowol, Karl