http://www.cshblogs.org/cshprotocols Mon, 08 Mar 2010 20:01:43 +0000 http://backend.userland.com/rss092 en The recent explosion in the availability and variety of fluorescent proteins, new organic dyes and quantum dots has been a driving force in the growing use of Total Internal Reflection Fluorescence Microscopy (TIRFM). TIRFM only illuminates molecules that are within a thin volume near the coverslip surface of a ... http://www.cshblogs.org/cshprotocols/2010/03/08/total-internal-reflection-fluorescence-microscopy-tirfm/ The use of recombinant proteins, antibodies, small molecules, or nucleic acids as affinity reagents is a simple yet powerful strategy to study the protein/bait interactions that drive biological processes. Analysis via mass spectrometry rather than western blotting extends the identification of interactors, often allowing detection of thousands of proteins from ... http://www.cshblogs.org/cshprotocols/2010/03/01/proteinbait-interactions/ The incorporation of thymidine analogues, such as 5-bromo-2'-deoxyuridine (BrdU), into newly synthesized DNA is a powerful tool for analysis of DNA replication, repair and other aspects of DNA metabolism. In Genome-Wide Analysis of DNA Synthesis by BrdU Immunoprecipitation on Tiling Microarrays (BrdU-IP-chip) in Saccharomyces cerevisiae, Oscar Aparicio and colleagues from ... http://www.cshblogs.org/cshprotocols/2010/02/18/high-throughput-analysis-of-dna-synthesis/ mRNA in situ hybridization is a standard laboratory technique for analyzing gene expression. In a small, transparent specimen like a zebrafish embryo, this technique is straightforward and works well. Cold Spring Harbor Protocols has a set of protocols (here, here and here) describing the method from Cecilia Moens. ... http://www.cshblogs.org/cshprotocols/2010/02/09/gene-expression-in-the-zebrafish-brain/ Mapping DNase I hypersensitive sites has long been the standard method for identifying genetic regulatory elements such as promoters, enhancers, silencers, insulators, and locus control regions. Sequences that are nucleosome-depleted, presumably to provide access for transcription factors, are selectively digested by DNase I. Traditional low-throughput methods use Southern blots ... http://www.cshblogs.org/cshprotocols/2010/02/01/high-throughput-analysis-of-gene-regulation/ January's issue of Cold Spring Harbor Protocols wraps up the second volume of our ongoing Emerging Model Organisms series. The idea behind the series is that technical advances have allowed for great expansion in the range of organisms used for research. Each set of articles is meant to ... http://www.cshblogs.org/cshprotocols/2010/01/26/emerging-model-organisms-january-completes-volume-2/ Metagenomics, the study of DNA isolated from naturally occurring populations and samples, is rapidly growing. Improvements to cloning and sequencing techniques are allowing researchers to study organism in environmental samples, and new knowledge of species interactions and community dynamics is emerging. The identification of microorganisms in these samples ... http://www.cshblogs.org/cshprotocols/2010/01/19/fishing-for-microbes/ As the cost of sequencing declines, more and more laboratories are extending their research into metagenomics. The Metagenomics RAST Server (MG-RAST) is one of the leading tools for metagenomic analysis, and in January's issue of Cold Spring Harbor Protocols, Folker Meyer and colleagues from the Argonne National Laboratory present ... http://www.cshblogs.org/cshprotocols/2010/01/11/mg-rast-for-analyzing-shotgun-metagenomes/ The enzyme-linked immunospot (ELISPOT) assay is considered by many to be the gold standard for monitoring cellular immune responses. The method is highly sensitive, quantitative, easy to use and amenable to high throughput screening. Until recently, the ELISPOT assay has been limited to the characterization of only ... http://www.cshblogs.org/cshprotocols/2010/01/04/monitoring-cellular-immune-response/ I wanted to point out an excellent thought-provoking article by my Scholarly Kitchen colleague Michael Clarke, titled Why Hasn’t Scientific Publishing Been Disrupted Already? I know many readers here are interested in the future of scientific communication, and Clarke makes some interesting arguments for why journals are likely to ... http://www.cshblogs.org/cshprotocols/2010/01/04/disruption-and-scientific-publishing/