Methods in molecular biology
-
Cocaine self-administration provides a methodology allowing researchers to study changes in distinct aspects of drug-taking behavior that model behaviors observed in drug addicts. Traditionally, self-administration schedules were designed to independently study changes in drug-taking behaviors (e.g., rate of responding, reinforcing efficacy, etc.). The threshold self-administration procedure was developed to measure two distinct dependent measures within the same experimental session that are important in the study of drug addiction: the maximal price an animal expends to self-administer cocaine and an animal's preferred level of cocaine consumption when available at a low behavioral cost.
-
Serglycin is a proteoglycan composed of a relatively small (~17 kDa) core protein to which sulfated glycosaminoglycans of either heparin, heparan sulfate or chondroitin sulfate types are attached. Serglycin is expressed in many cell types, including in particular cells of hematopoietic origin. ⋯ Moreover, the absence of serglycin caused a dramatic effect on the ability of mast cells to store a number of granule compounds, including several mast cell-specific proteases as well as biogenic amines. Hence, serglycin has a major function in maintaining mast cell secretory granule homeostasis.
-
Osteoarthritis (OA) is one form of degenerative joint disease characterized by progressive loss of articular cartilage, decreased function and is frequently accompanied by chronic pain. Given the success of arthroplasty as a treatment for late-stage OA, there is considerable interest in developing therapies pertaining to the management of pain associated with OA as well as therapies designed to slow or reverse the progression of the disease. ⋯ Here, we describe a model of OA-related pain in which progressive joint destruction is induced by injection of monosodium iodoacetate into the articular space of the knee of the rat. Further, we describe three different methods to measure pain-related behaviors in this model: hind limb weight bearing, primary mechanical hyperalgesia, and hind limb grip strength.
-
Phosphoproteomics, the systematic study of protein phosphorylation events and cell signaling networks in cells and tissues, is a rapidly evolving branch of functional proteomics. Current phosphoproteomics research provides a large toolbox of strategies and protocols that may assist researchers to reveal key regulatory events and phosphorylation-mediated processes in the cell and in whole organisms. ⋯ We then discuss various tandem mass spectrometry approaches for phosphopeptide sequencing and quantification, and we consider aspects of phosphoproteome data analysis and interpretation. Efficient integration of these stages of phosphoproteome analysis is highly important to ensure a successful outcome of large-scale experiments for studies of phosphorylation-mediated protein regulation.
-
In the past decades, a variety of publicly available data repositories and resources have been developed to support protein related information management, data-driven hypothesis generation and biological knowledge discovery. However, there is also an increasing confusion for the researchers who are trying to quickly find the appropriate resources to help them solve their problems. In this chapter, we present a comprehensive review (with categorization and description) of major protein bioinformatics databases and resources that are relevant to comparative proteomics research. We conclude the chapter by discussing the challenges and opportunities for developing new protein bioinformatics databases.