Methods in molecular biology
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This book is part of the Methods in Molecular Biology series, and provides a general overview of computational approaches used in proteome research. In this chapter, we give an overview of the scope of the book in terms of current proteomics experimental techniques and the reasons why computational approaches are needed. We then give a summary of each chapter, which together provide a picture of the state of the art in proteome bioinformatics research.
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Protein functions rely on their ability to engage in specific protein-protein interactions and form complexes that are dynamically regulated by stimuli. Bioluminescence resonance energy transfer (BRET) is a highly sensitive technique, which allows monitoring of interaction between two proteins: one tagged with the luminescent donor Renilla luciferase, the other with a fluorescent acceptor such as YFP. ⋯ To this aim, we tag proteins of interest, transfect cells with these fusions, and use the high-sensitivity microscopy, combined with electron multiplying cooled charge-coupled device (EMCCD) cameras and improved bioluminescence probes. We thus achieve rapid acquisition of high-resolution BRET images and study the localization and dynamics of protein-protein interactions in individual live cells.
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The results of clinical studies on the value of preemptive analgesia are far from being unanimous. There are a number of potential problems related to preemptive analgesia that could lead to controversy regarding its clinical significance. The following potential problems are analyzed: (1) terminology, (2) approach to reveal the effect of preemptive analgesia, (3) verification of the direct pharmacological effect of a treatment, (4) partial preemptive effect in control, (5) intensity of noxious stimuli, (6) difference in a drug concentration between study groups during postoperative period, and (7) outcome measures.
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The cold pressor test is a reliable pain model in which subjects submerge their hands and forearms into ice water while onset to pain, pain intensity, and tolerance are assessed. Although originally developed as a model for hypertension, the paradigm leads to development of reproducible pain responses allowing assessment to analgesic medications. ⋯ A recent study suggests that methodological discrepancies may contribute to such inconsistencies. The model may be more reproducible by utilizing consistent protocols.
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Clostridium difficile is a spore-forming, toxin-producing, anaerobic bacterium abundant in soils and water. Frequent and early colonization of the human intestinal flora is common and often asymptomatic. Antimicrobials given commonly disrupt the intestinal microflora and through proliferation in colon and production of toxin A and B it precipitates C. difficile infection (CDI). ⋯ Both the current epidemic like this and other local outbreaks from resistant or virulent strains warrant culture to be routinely performed enabling susceptibility testing and typing of the pathogen. Genotyping is most commonly done today by pulse-field gel electrophoresis (PFGE) or PCR ribotyping but multilocus variable-number tandem-repeat analysis (MLVA) seems promising. Epidemiological surveillance using all these tools will help us to better understand the global spread of C. difficile.