Methods in molecular biology
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Homologous recombination is the most precise way to manipulate the genome. As a tool it has been used extensively in bacteria, yeast, murine embryonic stem cells, and a few other specialized cell lines but has not been available to researchers in other systems, such as for mammalian somatic cell genetics. ⋯ ZFNs are artificial proteins in which a zinc finger DNA-binding domain is fused to a nonspecific nuclease domain. This chapter describes how to identify potential targets for ZFN cutting, to make ZFNs to cut this target site, and how to test whether the newly designed ZFNs are active in a mammalian cell culture-based system.
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The systematic study of proteins and protein networks, that is, proteomics, calls for qualitative and quantitative analysis of proteins and peptides. Mass spectrometry (MS) is a key analytical technology in current proteomics and modern mass spectrometers generate large amounts of high-quality data that in turn allow protein identification, annotation of secondary modifications, and determination of the absolute or relative abundance of individual proteins. Advances in mass spectrometry-driven proteomics rely on robust bioinformatics tools that enable large-scale data analysis. This chapter describes some of the basic concepts and current approaches to the analysis of MS and MS/MS data in proteomics.
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Molecular imaging offers many unique opportunities to study biological processes in intact organisms. Bioluminescence is the emission of light from biochemical reactions that occur within a living organism. Luciferase has been used as a reporter gene in transgenic mice but, until bioluminescence imaging was described, the detection of luciferase activity required either sectioning of the animal or excision of tissue and homogenization to measure enzyme activities in a conventional luminometer. ⋯ This imaging modality has proven to be a very powerful methodology to detect luciferase reporter activity in intact animal models. This form of optical imaging is low cost and noninvasive and facilitates real-time analysis of disease processes at the molecular level in living organisms. Bioluminescence provides a noninvasive method to monitor gene expression in vivo and has enormous potential to elucidate the pathobiology of lung diseases in intact mouse models, including models of inflammation/injury, infection, and cancer.
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Regulation of blood flow in tissues such as skeletal muscle, liver, and adipose tissue is needed to meet the changing local metabolic and physiological demands under varying conditions. In healthy individuals, adipose tissue blood flow (ATBF) is remarkably responsive to meal ingestion, but changes in ATBF in response to other physiological stimuli, such as stress and physical exercise, have also been noted. ⋯ A better understanding of the physiological basis for (nutritional) regulation of ATBF may therefore give insight to the relationship between disturbances in ATBF and the metabolic disturbances observed in response to insulin resistance. In this chapter, we describe some different approaches to quantify human ATBF, with a particular emphasis on the 133xenon wash-out technique and a method by which regulatory properties of subcutaneous ATBF can be studied by pharmacological micromanipulation (microinfusion).
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The development of trans-splicing vectors opens the door for delivering a large therapeutic gene with adeno-associated viral vectors (AAV). One potential application is to deliver the 6 kb mini-dystrophin gene for Duchenne muscular dystrophy (DMD) gene therapy. However, early attempts have been very disappointing because of low transduction efficiency. ⋯ This barrier can be overcome by rational selection of the gene splitting site. Here we outline a detailed RNase protection assay-based strategy to determine the optimal gene splitting site for the mini-dystrophin gene. We also provide methods to evaluate transduction efficiency of the mini-dystrophin trans-splicing vectors in mdx mouse, a model for DMD.