Methods in molecular biology
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This chapter describes the main issues that genetic epidemiologists usually consider in the design of linkage and association studies. For linkage, we briefly consider the situation of rare, highly penetrant alleles showing a disease pattern consistent with Mendelian inheritance investigated through parametric methods in large pedigrees or with autozygosity mapping in inbred families, and we then turn our focus to the most common design, affected sibling pairs, of more relevance for common, complex diseases. Theoretical and more practical power and sample size calculations are provided as a function of the strength of the genetic effect being investigated. ⋯ The estimates of locus contribution to disease risk from genome-wide scans are often biased, and relying on them might result in an underpowered replication study. Population structure has so far caused less spurious associations than initially feared, thanks to systematic ethnicity matching and application of standard quality control measures. Differential bias could be a more serious threat and must be minimised by strictly controlling all the aspects of DNA acquisition, storage, and processing.
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The spinal nerve ligation model of neuropathic pain in rats, as originally described by Kim and Chung (Pain 50:355-363, 1992), provides an excellent venue to study the antinociception and modulation effects of pulsed radiofrequency (PRF) current in pain processing. We describe the procedure of application of PRF current near the exposed L5 dorsal root ganglion (DRG) in rats with L5 spinal nerve ligation injury-induced behavioral hypersensitivity. This method employs the direct visualization of the L5 DRG, allowing for confirmation of the location of the PRF probe adjacent to the DRG.
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Orofacial pain remains an understudied area in pain research given that most attention has been focused on the spinal system. In this chapter, animal models of neuropathic and inflammatory orofacial pain are presented. Four different types of pain behavior tests are then described for assessing evoked and spontaneous pain behavior in addition to conditional reward behavior. The use of a combination of different pain models and behavior assessments is needed to aid in understanding the mechanisms contributing to orofacial pain in humans for developing effective therapy.
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Mass spectrometry-based quantitative proteomics can identify and quantify thousands of proteins in complex biological samples. Improved instrumentation, quantification strategies and data analysis tools now enable protein analysis on a genome-wide scale. ⋯ The spectrum of applications ranges from bacteria and eukaryotic cell culture systems to multicellular organisms. Here, we provide a step-by-step protocol on how to plan and perform large-scale quantitative proteome analysis using SILAC, from sample preparation to final data analysis.
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The spared nerve injury (SNI) model mimics human neuropathic pain related to peripheral nerve injury and is based upon an invasive but simple surgical procedure. Since its first description in 2000, it has displayed a remarkable development. ⋯ Besides, variants of the SNI model have been developed in rats, mice and neonatal/young rodents, resulting in several possible angles of analysis. Therefore, the purpose of this chapter is to provide a detailed guidance regarding the SNI model and its variants, highlighting its surgical and behavioural testing specificities.