Methods in molecular biology
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The intestine is often examined histologically in connection with allergies and in search for pathological changes. To be able to examine the intestine histologically with a microscope, it must be sampled and processed correctly. For microscopic analysis, the samples have to be cut into thin sections, stained, and mounted on slides. ⋯ This chapter describes the method of processing intestinal tissue for paraffin-embedding, sectioning, and staining with H&E. Tissue processing can be done in tissue processing machines or manually. We describe the manual processing that is often used for smaller batches of samples.
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Mouse models of allergic asthma have been utilized to establish the role of T helper type 2 (Th2) cells in driving lung inflammation, airway hyperresponsiveness, and obstruction. Here, we present the allergic asthma models, in which mice are hypersensitized to ovalbumin (OVA) and house dust mite (HDM). These models mimic the major characteristics of human asthma including the eosinophilic inflammation and hyperactivity of the airway, overproduction of Th2 cytokines in the lung, and elevated total and allergen-specific immunoglobulin E (IgE) in serum.
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DNA methylation is extensively reprogrammed during mammalian embryogenesis and germ cell development. Protocols for genome-wide bisulfite sequencing enable the quantification of DNA methylation with high precision and single base-pair resolution; however they can be limited by the necessity for high amounts of DNA. Here we describe optimized reduced representation bisulfite sequencing (RRBS) and whole genome bisulfite sequencing (WGBS) protocols for low amounts of DNA, which include steps to estimate the minimal number of PCR cycles needed for the final library preparation to minimize PCR biases. These protocols require no more than 5 ng DNA and can easily be applied to mammalian cells available in small quantities such as early embryos or primordial germ cells.
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Optogenetic calcium sensors enable the imaging in real-time of the activities of single or multiple neurons in brain slices and in vivo. Bioluminescent probes engineered from the natural calcium sensor aequorin do not require illumination, are virtually devoid of background signal, and exhibit wide dynamic range and low cytotoxicity. These probes are thus well suited for long-duration, whole-field recordings of multiple neurons simultaneously. Here, we describe a protocol for monitoring and analyzing the dynamics of neuronal ensembles using whole-field bioluminescence imaging of an aequorin-based sensor in brain slice.