Methods in molecular biology
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Mitochondria are considered as the main source of reactive oxygen species (ROS) in the cell. For this reason, they have been recognized as a source of various pathological conditions as well as aging. Chronic increase in the rate of ROS production is responsible for the accumulation of ROS-associated damages in DNA, proteins, and lipids, and may result in progressive cell dysfunctions and, in a consequence, apoptosis, increasing the overall probability of an organism's pathological conditions. ⋯ In this chapter, we describe a relation between mitochondrial membrane potential and the rate of ROS formation. We present different methods applicable for isolated mitochondria or intact cells. We also present experiments demonstrating that a magnitude and a direction (increase or decrease) of a change in mitochondrial ROS production depends on the metabolic state of this organelle.
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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.
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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.
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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.
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Large numbers of diverse small non-coding RNAs have been discovered and characterized in eukaryotic RNA interference pathways. These small RNAs have distinctive characteristics and are associated with Argonaute family proteins to regulate gene expression and genomes at various levels. These small RNAs include the Dicer-dependent group such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), and the Dicer-independent group such as Piwi-interacting RNAs (piRNAs). This review summarizes the various classes of eukaryotic small RNAs and the general knowledge of their characteristics, biogenesis, and functions, with emphasis on some of the recently identified small RNAs.