Methods in molecular biology
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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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Peptides scanned from whole protein sequences are the core information for many peptide bioinformatics research such as functional site prediction, protein structure identification, and protein function recognition. In these applications, we normally need to assign a peptide to one of the given categories using a computer model. ⋯ Among various machine learning approaches, including neural networks, peptide machines have demonstrated excellent performance in many applications. This chapter discusses the basic concepts of peptide classification, commonly used feature extraction methods, three peptide machines, and some important issues in peptide classification.
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There are various types of liposomes used for cancer therapy, but these can all be placed into three distinct categories based on the surface charge of vesicles: neutral, anionic and cationic. This chapter describes the more rigorous and easy methods used for liposome manufacture, with references, to aid the reader in preparing these formulations in-house.
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Zinc-finger nucleases (ZFNs) are promising new tools for enhancing the efficiency of gene targeting in many organisms. Because of the flexibility of zinc finger DNA recognition, ZFNs can be designed to bind many different genomic sequences. ⋯ In addition, the breaks can be repaired by homologous recombination with an exogenous donor DNA, allowing the experimenter to introduce designed sequence alterations. We describe the construction of ZFNs for novel targets and their application to targeted mutagenesis and targeted gene replacement in Drosophila melanogaster and Caenorhabditis elegans.
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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.