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In this Protocol, data obtained from optical projection tomography and confocal microscopy is analyzed with Tree Surveyor and Imaris to obtain information about branching morphogenesis. Mouse kidneys are used as an example, but the method is applicable to other branched organs.
Biochemical methods have typically been underused in Drosophila research owing to technical challenges. Here Depner et al. describe a simple CNS fractionation method that yields ∼4 mg of synaptic membrane protein per 1 g of adult fly heads.
This protocol describes how to prepare mouse, rat, human and porcine pancreas tissue slices and how to use them to investigate cellular mechanisms underlying the function, pathology and interaction of endocrine and exocrine components of the pancreas.
This protocol describes how to maintain the gastrointestinal nematode Heligmosomoides polygyrus bakeri and generate excretory-secretory products for identification, cloning, and immunological characterization of the modulatory molecules.
This protocol describes how to rapidly anchor pipettes to the head of a rat, enabling reliable whole-cell recording of neurons from freely moving rats and facilitating studies of neuronal integration and plasticity in identified cells during natural behaviors.
This protocol recreates the in vivo condition of latently infected, resting CD4+ T lymphocytes and can be used for drug screening, studying CTL responses to HIV-1, comparing viral alleles, or growth of cells from HIV-1–infected individuals.
Predicting the structure of antibodies on the basis of their sequences is a key objective in medical and biotechnology research. Marcatili et al. describe the use of their online system PIGS for the automated modeling of the 3D structure of antibodies.
The morphogenetic and signaling events during blastocyst to egg cylinder transition at the peri-implantation stages are largely unexplored. This protocol supports development of mouse embryos beyond the blastocyst stage in vitro.
Murine inner-medullary collecting duct cells grown in a matrigel mixture grow into spheroids with apicobasal polarity to model renal disease and test the functional relevance of new gene mutations.
Pancreatic ductal infusion enables the delivery of dyes or viruses directly to specific pancreatic cell types, permitting their manipulation. This manipulation is helpful for the study of diabetes, pancreatitis and pancreatic cancer.
Magnetic resonance colonography (MRC) can be used to monitor colonic tumors and mucosal inflammation. This protocol describes the use of a Fluorinert enema that distends the colon and forms a black homogeneous background in MRC images.
This protocol describes how to differentiate human pluripotent cells into ureteric bud progenitor–like cells, which then self-assemble into chimeric 3D structures in combination with embryonic mouse kidney cells.
Recurrent aggression occurs in many psychiatric and neurological disorders. This protocol describes how to set up a mouse model of repeated aggression.
Dionicio Siegel et al. provide detailed instructions on implementing their facile, scalable, catalyst-free and functional group–tolerant approach to hydroxylating arenes.
A protocol for processing exome genotyping array data that proceeds by targeting the exome plus rare SNPs and provides a feasible, cheaper alternative to exome sequencing when analyzing data from large genome-wide association studies.
Equipping an electron microscope with Zernike phase-contrast optics dramatically increases the contrast of the images. Dai et al. describe how to successfully apply this technology for the acquisition and analysis of electron tomograms.
This protocol describes how to process samples potentially containing influenza A virus (IAV), amplify the samples in chicken eggs or mammalian cells and identify whether and which IAV is present.
The high error rate of NGS methods has limited the ability to accurately detect ultra-low-frequency mutations. Duplex Sequencing reduces the error rate of NGS such that a single nucleotide mutation can be detected in >1×107 wild-type nucleotides.
Kumar et al. describe how to build a diSPIM from commercially available parts and use it to live-image cultured cells or worm embryogenesis. The inverted setup enables samples to be mounted directly on microscope slides, avoiding agarose embedding.