MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Nature Protocols' source. Mon, 06 Feb 2012 14:01:06 +0100 http://www.medworm.com/index.php?rid=5656206&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Ftj5YaBPbaxA%2Fnprot.2011.451 Authors: Tatjana Trcek, Jeffrey A Chao, Daniel R Larson, Hye Yoon Park, Daniel Zenklusen, Shailesh M Shenoy & Robert H Singer Fluorescent in situ hybridization (FISH) allows the quantification of single mRNAs in budding yeast using fluorescently labeled single-stranded DNA probes, a wide-field epifluorescence microscope and a spot-detection algorithm. Fixed yeast cells are attached to coverslips and hybridized with a mixture of FISH probes, each (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5656206 Thu, 02 Feb 2012 05:00:00 +0100 5656206 http://www.medworm.com/index.php?rid=5656205&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FDsaIaDjTBSg%2Fnprot.2011.449 In this report, we describe a reliable protocol for biocytin labeling of neuronal tissue and diaminobenzidine (DAB)-based processing of brain slices. We describe how to embed tissues in different media and how to subsequently histochemically label the tissues for light or electron microscopic examination. We (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5656205 Thu, 02 Feb 2012 05:00:00 +0100 5656205 http://www.medworm.com/index.php?rid=5656204&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FveTRE1jvhIs%2Fnprot.2011.446 Authors: Lukas E Dow, Prem K Premsrirut, Johannes Zuber, Christof Fellmann, Katherine McJunkin, Cornelius Miething, Youngkyu Park, Ross A Dickins, Gregory J Hannon & Scott W Lowe RNA interference (RNAi) is an extremely effective tool for studying gene function in almost all metazoan and eukaryotic model systems. RNAi in mice, through the expression of short hairpin RNAs (shRNAs), offers something not easily achieved with traditional genetic approaches—inducible and reversible gene silencing. However, (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5656204 Thu, 02 Feb 2012 05:00:00 +0100 5656204 http://www.medworm.com/index.php?rid=5656203&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fkjjj76fnSaw%2Fnprot.2011.448 This article provides an overview of expression and purification (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5656203 Thu, 02 Feb 2012 05:00:00 +0100 5656203 http://www.medworm.com/index.php?rid=5635216&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FU2dP4kcElhI%2Fnprot.2011.442 Authors: Liang Wang & Till Marquardt This protocol describes an optimized method for direct in vitro monitoring of homo- and heterotypic axon-axon interactions involved in the developmental assembly of neural circuits. The assay exploits a classical example of heterotypic axonal interactions by modeling the sequential extension of spinal motor and (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5635216 Thu, 26 Jan 2012 05:00:00 +0100 5635216 http://www.medworm.com/index.php?rid=5635215&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FIWTJavPtDEM%2Fnprot.2011.443 We describe a method for the efficient and selective identification of DNA containing the 5-hydroxymethylcytosine (5-hmC) modification. This protocol takes advantage of two proteins: T4 β-glucosyltransferase (β-gt), which converts 5-hmC to β-glucosyl-5-hmC (β-glu-5-hmC), and J-binding protein 1 (JBP1), which specifically recognizes and binds to β-glu-5-hmC. (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5635215 Thu, 26 Jan 2012 05:00:00 +0100 5635215 http://www.medworm.com/index.php?rid=5635214&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fc3B1Fk1EgXE%2Fnprot.2011.447 Authors: Pattabhiraman Shankaranarayanan, Marco-Antonio Mendoza-Parra, Wouter van Gool, Luisa M Trindade & Hinrich Gronemeyer Linear amplification of DNA (LinDA) by T7 polymerase is a versatile and robust method for generating sufficient amounts of DNA for genome-wide studies with minute amounts of cells. LinDA can be coupled to a great number of global profiling technologies. Indeed, chromatin immunoprecipitation coupled to (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5635214 Thu, 26 Jan 2012 05:00:00 +0100 5635214 http://www.medworm.com/index.php?rid=5635213&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FkTB0KQkkC4s%2Fnprot.2012.003 Authors: Philseok Kim, Wilmer E Adorno-Martinez, Mughees Khan & Joanna Aizenberg We provide a protocol for transforming the structure of an array of high-aspect-ratio (HAR) micro/nanostructures into various new geometries. Polymeric HAR arrays are replicated from a Bosch-etched silicon master pattern by soft lithography. By using various conditions, the original pattern is coated with metal, which (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5635213 Thu, 26 Jan 2012 05:00:00 +0100 5635213 http://www.medworm.com/index.php?rid=5635212&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FjX6XPxFOUGQ%2Fnprot.2011.426 We present a protocol for reliably detecting DNA copy number aberrations in a single human cell. Multiple displacement-amplified DNAs of a cell are hybridized to a 3,000–bacterial artificial chromosome (BAC) array and to an Affymetrix 250,000 (250K)-SNP array. Subsequent copy number calling is based on (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5635212 Thu, 19 Jan 2012 05:00:00 +0100 5635212 http://www.medworm.com/index.php?rid=5635211&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FeOPtE74oKFY%2Fnprot.2011.445 Authors: Vanessa Gil & José Antonio del Río This protocol uses rat tail–derived type I collagen hydrogels to analyze key processes in developmental neurobiology, such as chemorepulsion and chemoattraction. The method is based on culturing small pieces of brain tissue from embryonic or early perinatal mice inside a 3D hydrogel formed by rat (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5635211 Thu, 19 Jan 2012 05:00:00 +0100 5635211 http://www.medworm.com/index.php?rid=5635210&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FUn-deNnxp0s%2Fnprot.2011.444 Authors: Jeremy M Simon, Paul G Giresi, Ian J Davis & Jason D Lieb Eviction or destabilization of nucleosomes from chromatin is a hallmark of functional regulatory elements in eukaryotic genomes. Historically identified by nuclease hypersensitivity, these regulatory elements are typically bound by transcription factors or other regulatory proteins. FAIRE (formaldehyde-assisted isolation of regulatory elements) is an alternative approach (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5635210 Thu, 19 Jan 2012 05:00:00 +0100 5635210 http://www.medworm.com/index.php?rid=5635209&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FoLk9PS_cVcA%2Fnprot.2011.440 We describe here a protocol for culturing epicardial cells from adult zebrafish hearts, which have a unique regenerative capacity after injury. Briefly, zebrafish hearts first undergo ventricular amputation or sham operation. Next, the hearts are excised and explanted onto fibrin gels prepared in advance in (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5635209 Thu, 19 Jan 2012 05:00:00 +0100 5635209 http://www.medworm.com/index.php?rid=5592748&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FcgBQ0-sMpIo%2Fnprot.2011.437 Authors: Jiri Kalabis, Gabrielle S Wong, Maria E Vega, Mitsuteru Natsuizaka, Erle S Robertson, Meenhard Herlyn, Hiroshi Nakagawa & Anil K Rustgi This protocol describes the isolation and characterization of mouse and human esophageal epithelial cells and the application of 3D organotypic culture (OTC), a form of tissue engineering. This model system permits the interrogation of mechanisms underlying epithelial-stromal interactions. We provide guidelines for isolating and cultivating (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5592748 Thu, 12 Jan 2012 05:00:00 +0100 5592748 http://www.medworm.com/index.php?rid=5592747&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fqr73qL_e10w%2Fnprot.2011.438 Authors: Jackson LiangYao Li, Chi Ching Goh, Jo L Keeble, Jim S Qin, Ben Roediger, Rohit Jain, Yilin Wang, Weng Keong Chew, Wolfgang Weninger & Lai Guan Ng Multiphoton (MP) microscopy enables the direct in vivo visualization, with high spatial and temporal resolution, of fluorescently tagged immune cells, extracellular matrix and vasculature in tissues. This approach, therefore, represents a powerful alternative to traditional methods of assessing immune cell function in the skin, (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5592747 Thu, 12 Jan 2012 05:00:00 +0100 5592747 http://www.medworm.com/index.php?rid=5592746&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F2OYjVOzdrnE%2Fnprot.2011.433 We present a protocol for constructing an illumination system capable of dynamic multispectral optical targeting (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5592746 Thu, 12 Jan 2012 05:00:00 +0100 5592746 http://www.medworm.com/index.php?rid=5592745&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F7FDqUBAuU-4%2Fnprot.2011.439 Authors: Juan Carlos Tapia, Narayanan Kasthuri, Kenneth J Hayworth, Richard Schalek, Jeff W Lichtman, Stephen J Smith & JoAnn Buchanan Conventional heavy metal poststaining methods on thin sections lend contrast but often cause contamination. To avoid this problem, we tested several en bloc staining techniques to contrast tissue in serial sections mounted on solid substrates for examination by field emission scanning electron microscopy (FESEM). (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5592745 Thu, 12 Jan 2012 05:00:00 +0100 5592745 http://www.medworm.com/index.php?rid=5568604&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FCneHs-4lZA8%2Fnprot.2011.431 Authors: Neville E Sanjana, Le Cong, Yang Zhou, Margaret M Cunniff, Guoping Feng & Feng Zhang Transcription activator-like effectors (TALEs) are a class of naturally occurring DNA-binding proteins found in the plant pathogen Xanthomonas sp. The DNA-binding domain of each TALE consists of tandem 34–amino acid repeat modules that can be rearranged according to a simple cipher to target new (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5568604 Thu, 05 Jan 2012 05:00:00 +0100 5568604 http://www.medworm.com/index.php?rid=5568603&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FZxX7F0dutc8%2Fnprot.2011.436 Authors: Pei-Hsun Wu, Christopher M Hale, Wei-Chiang Chen, Jerry S H Lee, Yiider Tseng & Denis Wirtz High-throughput ballistic injection nanorheology is a method for the quantitative study of cell mechanics. Cell mechanics are measured by ballistic injection of submicron particles into the cytoplasm of living cells and tracking the spontaneous displacement of the particles at high spatial resolution. The trajectories of (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5568603 Thu, 05 Jan 2012 05:00:00 +0100 5568603 http://www.medworm.com/index.php?rid=5568602&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FKNUopg5Li14%2Fnprot.2011.434 Authors: Martin P Stewart, Yusuke Toyoda, Anthony A Hyman & Daniel J Müller To understand the role of physical forces at a cellular level, it is necessary to track mechanical properties during cellular processes. Here we present a protocol that uses flat atomic force microscopy (AFM) cantilevers clamped at constant height, and light microscopy to measure the resistance (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5568602 Thu, 05 Jan 2012 05:00:00 +0100 5568602 http://www.medworm.com/index.php?rid=5568601&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FNWAUGezE7_w%2Fnprot.2011.424 Authors: Alexander Sasha Krupnick, Vanessa K Tidwell, John A Engelbach, Vamsi V Alli, Arye Nehorai, Ming You, Haris G Vikis, Andrew E Gelman, Daniel Kreisel & Joel R Garbow Primary lung cancer remains the leading cause of cancer-related death in the Western world, and the lung is a common site for recurrence of extrathoracic malignancies. Small-animal (rodent) models of cancer can have a very valuable role in the development of improved therapeutic strategies. However, (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5568601 Thu, 05 Jan 2012 05:00:00 +0100 5568601 http://www.medworm.com/index.php?rid=5533000&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FkQjnTwcC2go%2Fnprot.2011.430 Authors: Ami Citri, Zhiping P Pang, Thomas C Südhof, Marius Wernig & Robert C Malenka A major challenge in neuronal stem cell biology lies in characterization of lineage-specific reprogrammed human neuronal cells, a process that necessitates the use of an assay sensitive to the single-cell level. Single-cell gene profiling can provide definitive evidence regarding the conversion of one cell type (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5533000 Thu, 22 Dec 2011 05:00:00 +0100 5533000 http://www.medworm.com/index.php?rid=5532999&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FnksS-K0doWI%2Fnprot.2011.425 Authors: William P Heal, Megan H Wright, Emmanuelle Thinon & Edward W Tate A protocol for selective and site-specific enzymatic labeling of proteins is described. The method exploits the protein co-/post-translational modification known as myristoylation, the transfer of myristic acid (a 14-carbon saturated fatty acid) to an N-terminal glycine catalyzed by the enzyme myristoyl-CoA:protein N-myristoyltransferase (NMT). Escherichia (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5532999 Thu, 22 Dec 2011 05:00:00 +0100 5532999 http://www.medworm.com/index.php?rid=5532998&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F_9vixXGA7UI%2Fnprot.2011.435 Authors: Marianne Baker, Stephen D Robinson, Tanguy Lechertier, Paul R Barber, Bernardo Tavora, Gabriela D'Amico, Dylan T Jones, Boris Vojnovic & Kairbaan Hodivala-Dilke Here we provide a protocol for quantitative three-dimensional ex vivo mouse aortic ring angiogenesis assays, in which developing microvessels undergo many key features of angiogenesis over a timescale similar to that observed in vivo. The aortic ring assay allows analysis of cellular proliferation, (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5532998 Thu, 22 Dec 2011 05:00:00 +0100 5532998 http://www.medworm.com/index.php?rid=5512153&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F7ga9pXNDHiA%2Fnprot.2011.432 We describe the application of this method to imaging bacteria by using an automated microscopy system. This protocol has been used to analyze sporulation and competence differentiation in (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5512153 Thu, 15 Dec 2011 05:00:00 +0100 5512153 http://www.medworm.com/index.php?rid=5512152&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F6SRdSY6TSQU%2Fnprot.2011.429 Authors: Mototsugu Eiraku & Yoshiki Sasai Generation of compound tissues with complex structures is a major challenge in cell biology. In this article, we describe a protocol for mouse embryonic stem cell (ESC) culture for in vitro generation of three-dimensional retinal tissue, comparing it with the culture protocol for cortical (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5512152 Thu, 15 Dec 2011 05:00:00 +0100 5512152 http://www.medworm.com/index.php?rid=5512151&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FxgX4CiNQl8I%2Fnprot.2011.428 We describe a strategy for analyzing axonal transport of cytosolic proteins (CPs) using photoactivatable GFP—PAGFP—with modifications of standard imaging components that can be retroactively fitted to a conventional epifluorescence microscope. The photoactivation and visualization are nearly simultaneous, allowing studies of proteins with rapidly mobile fractions. (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5512151 Thu, 15 Dec 2011 05:00:00 +0100 5512151 http://www.medworm.com/index.php?rid=5512150&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F7RleHQyPPjo%2Fnprot.2011.420 Authors: Anaïs F Bardet, Qiye He, Julia Zeitlinger & Alexander Stark Chromatin immunoprecipitation (ChIP) followed by deep sequencing can now easily be performed across different conditions, time points and even species. However, analyzing such data is not trivial and standard methods are as yet unavailable. Here we present a protocol to systematically compare ChIP-sequencing (ChIP-seq) data (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5512150 Thu, 15 Dec 2011 05:00:00 +0100 5512150 http://www.medworm.com/index.php?rid=5492396&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FwcwsnIS91OM%2Fnprot.2011.427 Authors: Gian Maria D'Amici, Sara Rinalducci & Lello Zolla Proteomic analysis of red cells is compromised by the presence of high-abundance proteins (hemoglobin and carbonic anhydrase-1), which completely obscure low-abundance species. The depletion method presented here involves performing native gel electrophoresis in a polyacrylamide gel tube using a modified electroelution cell. The electrophoretic run (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5492396 Thu, 08 Dec 2011 05:00:00 +0100 5492396 http://www.medworm.com/index.php?rid=5492395&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FrJsCYkxWld8%2Fnprot.2011.419 Authors: Dylan M Owen, Carles Rentero, Astrid Magenau, Ahmed Abu-Siniyeh & Katharina Gaus It is now recognized that lipids and proteins in cellular membranes are not homogenously distributed. A high degree of membrane order is the biophysical hallmark of cholesterol-enriched lipid rafts, which may induce the lateral sorting of proteins within the membrane. Here we describe a quantitative (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5492395 Thu, 08 Dec 2011 05:00:00 +0100 5492395 http://www.medworm.com/index.php?rid=5492394&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fv01-DM7j8KI%2Fnprot.2011.413 Authors: Dennis R Sparta, Alice M Stamatakis, Jana L Phillips, Nanna Hovelsø, Ruud van Zessen & Garret D Stuber In vivo optogenetic strategies have redefined our ability to assay how neural circuits govern behavior. Although acutely implanted optical fibers have previously been used in such studies, long-term control over neuronal activity has been largely unachievable. Here we describe a method to construct implantable (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5492394 Thu, 08 Dec 2011 05:00:00 +0100 5492394 http://www.medworm.com/index.php?rid=5492393&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FcvVc2lFyA8c%2Fnprot.2011.421 Authors: Sankha S Basu & Ian A Blair Stable isotope labeling by essential nutrients in cell culture (SILEC) was recently developed to generate isotopically labeled coenzyme A (CoA) and short-chain acyl-CoA thioesters. This was accomplished by modifying the widely used technique of stable isotope labeling by amino acids in cell culture to include (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5492393 Thu, 08 Dec 2011 05:00:00 +0100 5492393 http://www.medworm.com/index.php?rid=5465027&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F5TlrZIZ4IQE%2Fnprot.2011.411 Authors: Christophe Guilluy, Adi D Dubash & Rafael García-Mata We have recently shown that a fraction of the total cellular pool of the small GTPase RhoA resides in the nucleus, and that the nuclear guanine nucleotide exchange factor (GEF) Net1 has a role in the regulation of its activity. In this protocol, we describe (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5465027 Thu, 01 Dec 2011 05:00:00 +0100 5465027 http://www.medworm.com/index.php?rid=5465026&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F15fr0d9CUIc%2Fnprot.2011.423 Authors: Alison A Staton & Antonio J Giraldez MicroRNAs (miRNAs) regulate gene expression by pairing with complementary sequences in the 3′ untranslated regions (UTRs) of transcripts. Although the molecular mechanism underlying miRNA biogenesis and activity is becoming better understood, determining the physiological role of the interaction of an miRNA with its target remains (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5465026 Thu, 01 Dec 2011 05:00:00 +0100 5465026 http://www.medworm.com/index.php?rid=5465025&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F4NTKkg9csWg%2Fnprot.2011.418 We present three assembly protocols to produce two different types of RNA self-assembling functional NPs (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5465025 Thu, 01 Dec 2011 05:00:00 +0100 5465025 http://www.medworm.com/index.php?rid=5465024&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F4uWB9sTzDxE%2Fnprot.2011.416 Authors: Maximiliano L Suster, Gembu Abe, Anders Schouw & Koichi Kawakami Bacterial artificial chromosomes (BACs) are widely used in studies of vertebrate gene regulation and function because they often closely recapitulate the expression patterns of endogenous genes. Here we report a step-by-step protocol for efficient BAC transgenesis in zebrafish using the medaka Tol2 transposon. Using (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5465024 Thu, 01 Dec 2011 05:00:00 +0100 5465024 http://www.medworm.com/index.php?rid=5465023&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FVpgHVxslqm0%2Fnprot.2011.415 Authors: Kishore Baathulaa, Yufang Xu & Xuhong Qian Environment-sensitive fluorophores have different quantum yields in different solvents. 6-Dimethylaminonaphthalimide (6-DMN), for example, has a low quantum yield in aqueous solutions, but is highly fluorescent in nonpolar solvents or when bound to hydrophobic sites in proteins or membranes. 6-DMN has been used to investigate protein-protein (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5465023 Thu, 01 Dec 2011 05:00:00 +0100 5465023 http://www.medworm.com/index.php?rid=5417243&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FHG8TWMtFut8%2Fnprot.2011.412 Authors: Judith Fischer, Ruth Beckervordersandforth, Pratibha Tripathi, Andrea Steiner-Mezzadri, Jovica Ninkovic & Magdalena Götz Neural stem cells (NSCs) have the remarkable capacity to self-renew and the lifelong ability to generate neurons in the adult mammalian brain. However, the molecular and cellular mechanisms contributing to these behaviors are still not understood. Now that prospective isolation of the NSCs has become (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5417243 Thu, 17 Nov 2011 05:00:00 +0100 5417243 http://www.medworm.com/index.php?rid=5417242&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F0lJzgNtIlpQ%2Fnprot.2011.417 Authors: Andrew L Goodman, Meng Wu & Jeffrey I Gordon Insertion sequencing (INSeq) is a method for determining the insertion site and relative abundance of large numbers of transposon mutants in a mixed population of isogenic mutants of a sequenced microbial species. INSeq is based on a modified mariner transposon containing MmeI sites at its (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5417242 Thu, 17 Nov 2011 05:00:00 +0100 5417242 http://www.medworm.com/index.php?rid=5417241&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FJHlRzSHaMkU%2Fnprot.2011.414 Authors: Sarah A Mutch, Jennifer C Gadd, Bryant S Fujimoto, Patricia Kensel-Hammes, Perry G Schiro, Sandra M Bajjalieh & Daniel T Chiu This protocol describes a method for determining both the average number and variance of proteins, in the few to tens of copies, in isolated cellular compartments such as organelles and protein complexes. Other currently available protein quantification techniques either provide an average number, but lack (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5417241 Thu, 17 Nov 2011 05:00:00 +0100 5417241 http://www.medworm.com/index.php?rid=5417240&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FuxhlrFh1MIo%2Fnprot.2011.422 Authors: Mark Winter, Eric Wait, Badrinath Roysam, Susan K Goderie, Rania Ahmed Naguib Ali, Erzsebet Kokovay, Sally Temple & Andrew R Cohen This protocol and the accompanying software program called LEVER (lineage editing and validation) enable quantitative automated analysis of phase-contrast time-lapse images of cultured neural stem cells. Images are captured at 5-min intervals over a period of 5–15 d as the cells proliferate and differentiate. LEVER (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5417240 Thu, 17 Nov 2011 05:00:00 +0100 5417240 http://www.medworm.com/index.php?rid=5396532&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FfmBRdOuGNkw%2Fnprot.2011.407 Authors: Richard W Cole, Tushare Jinadasa & Claire M Brown This protocol outlines a procedure for collecting and analyzing point spread functions (PSFs). It describes how to prepare fluorescent microsphere samples, set up a confocal microscope to properly collect 3D confocal image data of the microspheres and perform PSF measurements. The analysis of the PSF (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5396532 Thu, 10 Nov 2011 05:00:00 +0100 5396532 http://www.medworm.com/index.php?rid=5396531&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FzeI66szb-Ls%2Fnprot.2011.410 Authors: Kyle W McCracken, Jonathan C Howell, James M Wells & Jason R Spence Here we describe a protocol for generating 3D human intestinal tissues (called organoids) in vitro from human pluripotent stem cells (hPSCs). To generate intestinal organoids, pluripotent stem cells are first differentiated into FOXA2+SOX17+ endoderm by treating the cells with activin (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5396531 Thu, 10 Nov 2011 05:00:00 +0100 5396531 http://www.medworm.com/index.php?rid=5396530&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FXsqEb-5n7H8%2Fnprot.2011.406 Authors: Mirco Fanelli, Stefano Amatori, Iros Barozzi & Saverio Minucci Formalin-fixed, paraffin-embedded (FFPE) samples represent the gold standard for storage of pathology samples. Here we describe pathology tissue chromatin immunoprecipitation (PAT-ChIP), a technique for extraction and high-throughput analysis, by techniques such as ChIP-seq, of chromatin derived from FFPE samples. Technically, the main challenge of PAT-ChIP (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5396530 Thu, 10 Nov 2011 05:00:00 +0100 5396530 http://www.medworm.com/index.php?rid=5396529&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fi1k4UZM9MeI%2Fnprot.2011.408 Authors: Olivier Renaud, Philippe Herbomel & Karima Kissa Confocal live imaging is a key tool for studying cell behavior in the whole zebrafish embryo. Here we provide a detailed protocol that is adaptable for imaging any progenitor cell behavior in live zebrafish embryos. As an example, we imaged the emergence of the first (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5396529 Thu, 10 Nov 2011 05:00:00 +0100 5396529 http://www.medworm.com/index.php?rid=5374822&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fyeode6mr5Jc%2Fnprot.2011.403 Authors: Jan C Koch, Johanna Knöferle, Lars Tönges, Uwe Michel, Mathias Bähr & Paul Lingor In this protocol, we describe the imaging of single axons in the rat optic nerve in vivo. Axons are labeled through the intravitreal injection of adeno-associated viral vectors (AAVs) expressing a fluorophore (duration of the procedure ∼1 h). Two weeks after intravitreal injection, the (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5374822 Thu, 03 Nov 2011 04:00:00 +0100 5374822 http://www.medworm.com/index.php?rid=5374821&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FjcnSQ9_xa_I%2Fnprot.2011.396 Authors: Magdalena Harakalova, Michal Mokry, Barbara Hrdlickova, Ivo Renkens, Karen Duran, Henk van Roekel, Nico Lansu, Mark van Roosmalen, Ewart de Bruijn, Isaac J Nijman, Wigard P Kloosterman & Edwin Cuppen The unprecedented increase in the throughput of DNA sequencing driven by next-generation technologies now allows efficient analysis of the complete protein-coding regions of genomes (exomes) for multiple samples in a single sequencing run. However, sample preparation and targeted enrichment of multiple samples has become a (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5374821 Thu, 03 Nov 2011 04:00:00 +0100 5374821 http://www.medworm.com/index.php?rid=5374820&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FISADm3cvE8k%2Fnprot.2011.409 Authors: Morgane Thomas-Chollier, Andrew Hufton, Matthias Heinig, Sean O'Keeffe, Nassim El Masri, Helge G Roider, Thomas Manke & Martin Vingron The transcription factor affinity prediction (TRAP) method calculates the affinity of transcription factors for DNA sequences on the basis of a biophysical model. This method has proven to be useful for several applications, including for determining the putative target genes of a given factor. This (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5374820 Thu, 03 Nov 2011 04:00:00 +0100 5374820 http://www.medworm.com/index.php?rid=5374819&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FLuXzcQCy028%2Fnprot.2011.404 Authors: Felipe Ortega, Marcos R Costa, Tatiana Simon-Ebert, Timm Schroeder, Magdalena Götz & Benedikt Berninger A comprehensive understanding of the cell biology of adult neural stem cells (aNSCs) requires direct observation of aNSC division and lineage progression in the absence of niche-dependent signals. Here we describe a culture preparation of the adult mouse subependymal zone (SEZ), which allows for continuous (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5374819 Thu, 03 Nov 2011 04:00:00 +0100 5374819 http://www.medworm.com/index.php?rid=5374818&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F3Fz1BzqaT70%2Fnprot.2011.395 Authors: Elena Kardash, Jan Bandemer & Erez Raz Fluorescence resonance energy transfer (FRET)-based molecular biosensors serve as important tools for studying protein activity in live cells and have been widely used for this purpose over the past decade. However, FRET biosensors are rarely used in the context of the live organism because of (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5374818 Thu, 03 Nov 2011 04:00:00 +0100 5374818 http://www.medworm.com/index.php?rid=5355122&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FhkE0Iw-jY_0%2Fnprot.2011.392 Authors: Bi-Huei Hou, Hitomi Takanaga, Guido Grossmann, Li-Qing Chen, Xiao-Qing Qu, Alexander M Jones, Sylvie Lalonde, Oliver Schweissgut, Wolfgang Wiechert & Wolf B Frommer Knowledge of the in vivo levels, distribution and flux of ions and metabolites is crucial to our understanding of physiology in both healthy and diseased states. The quantitative analysis of the dynamics of ions and metabolites with subcellular resolution in vivo poses a (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5355122 Thu, 27 Oct 2011 04:00:00 +0100 5355122 http://www.medworm.com/index.php?rid=5355121&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FHy1yyoitEWo%2Fnprot.2011.391 Authors: Clara Bermejo, Farzad Haerizadeh, Hitomi Takanaga, Diane Chermak & Wolf B Frommer Optical sensors allow dynamic quantification of metabolite levels with subcellular resolution. Here we describe protocols for analyzing cytosolic glucose levels in yeast using genetically encoded Förster resonance energy transfer (FRET) sensors. FRET glucose sensors with different glucose affinities (Kd) covering the low (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5355121 Thu, 27 Oct 2011 04:00:00 +0100 5355121 http://www.medworm.com/index.php?rid=5355120&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FMk4EJYyCaKg%2Fnprot.2011.401 Authors: Jean-Charles Boisset, Charlotte Andrieu-Soler, Wiggert A van Cappellen, Thomas Clapes & Catherine Robin Time-lapse confocal microscopy of mouse embryo slices was developed to access and image the living aorta. In this paper, we explain how to label all hematopoietic and endothelial cells inside the intact mouse aorta with fluorescent directly labeled antibodies. Then we describe the technique to (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5355120 Thu, 27 Oct 2011 04:00:00 +0100 5355120 http://www.medworm.com/index.php?rid=5355119&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FkErhHd5Ef3g%2Fnprot.2011.387 Authors: Norbert Berndt & Saïd M Sebti The importance of the post-translational lipid modifications farnesylation and geranylgeranylation in protein localization and function coupled with the critical role of prenylated proteins in malignant transformation has prompted interest in their biology and the development of farnesyl transferase and geranylgeranyl transferase inhibitors (FTIs and GGTIs) (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5355119 Thu, 27 Oct 2011 04:00:00 +0100 5355119 http://www.medworm.com/index.php?rid=5343397&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fn-wgdRvwjkk%2Fnprot.2011.400 Authors: David C Appleyard, Stephen C Chapin, Rathi L Srinivas & Patrick S Doyle This protocol describes the core methodology for the fabrication of bar-coded hydrogel microparticles, the capture and labeling of protein targets and the rapid microfluidic scanning of particles for multiplexed detection. Multifunctional hydrogel particles made from poly(ethylene glycol) serve as a sensitive, nonfouling and bio-inert suspension (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5343397 Thu, 20 Oct 2011 04:00:00 +0100 5343397 http://www.medworm.com/index.php?rid=5343396&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FXsUYLTQRXAk%2Fnprot.2011.386 Applying label-free dynamic mass redistribution technology to frame signaling of G protein–coupled receptors noninvasively in living cells Nature Protocols 6, 1748 (2011). doi:10.1038/nprot.2011.386 Authors: Ralf Schröder, Johannes Schmidt, Stefanie Blättermann, Lucas Peters, Nicole Janssen, Manuel Grundmann, Wiebke Seemann, Dorina Kaufel, Nicole Merten, Christel Drewke, Jesus Gomeza, Graeme Milligan, Klaus Mohr & Evi Kostenis Label-free dynamic mass redistribution (DMR) is a cutting-edge assay technology that enables real-time detection of integrated cellular responses in living cells. It relies on detection of refractive index alterations on biosensor-coated microplates that originate from stimulus-induced changes in the total biomass proximal to the sensor (... Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5343396 Thu, 20 Oct 2011 04:00:00 +0100 5343396 http://www.medworm.com/index.php?rid=5343395&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FuWGci8U_lbs%2Fnprot.2011.399 Authors: Lira Mamanova & Daniel J Turner The unifying feature of second-generation sequencing technologies is that single template strands are amplified clonally onto a solid surface prior to the sequencing reaction. To convert template strands into a compatible state for attachment to this surface, a multistep library preparation is required, which typically (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5343395 Thu, 20 Oct 2011 04:00:00 +0100 5343395 http://www.medworm.com/index.php?rid=5321265&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F98Khocoi8fg%2Fnprot.2011.394 Authors: Fabian Langenbach, Karin Berr, Christian Naujoks, Andrea Hassel, Michael Hentschel, Rita Depprich, Norbert R Kubler, Ulrich Meyer, Hans-Peter Wiesmann, Gesine Kögler & Jörg Handschel This protocol describes an effective method for the production of spherical microtissues (microspheres), which can be used for a variety of tissue-engineering purposes. The obtained microtissues are well suited for the study of osteogenesis in vitro when multipotent stem cells are used. The dimensions (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5321265 Thu, 13 Oct 2011 04:00:00 +0100 5321265 http://www.medworm.com/index.php?rid=5321264&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F8F5C90ECsN0%2Fnprot.2011.390 Authors: Herman S Gill & Jan Marik An optimized procedure for preparing fluorine-18 (18F)-labeled peptides by the copper-catalyzed azide-alkyne 1,3-dipolar cyloaddition (CuAAC) is presented here. The two-step radiosynthesis begins with the microwave-assisted nucleophilic 18F-fluorination of a precursor containing a terminal p-toluenesulfonyl, terminal azide and polyethylene glycol backbone. The resulting (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5321264 Thu, 13 Oct 2011 04:00:00 +0100 5321264 http://www.medworm.com/index.php?rid=5321263&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FQSROYQuXZmQ%2Fnprot.2011.405 Authors: Robert Krencik & Su-Chun Zhang Regionally and functionally diverse types of astrocytes exist throughout the central nervous system and participate in nearly every aspect of normal and abnormal neural function. Therefore, human astrocyte subtypes are useful tools for understanding brain function, modulating disease processes and promoting neural regeneration. Here we (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5321263 Thu, 13 Oct 2011 04:00:00 +0100 5321263 http://www.medworm.com/index.php?rid=5321262&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FnMlrQg54npg%2Fnprot.2011.388 We describe a protocol for analyzing protein in FFPE-TMAs using matrix-assisted laser desorption/ionization (MALDI) imaging (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5321262 Thu, 13 Oct 2011 04:00:00 +0100 5321262 http://www.medworm.com/index.php?rid=5292630&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FPL_bKlctpOM%2Fnprot.2011.393 Authors: Jean-Francois Taly, Cedrik Magis, Giovanni Bussotti, Jia-Ming Chang, Paolo Di Tommaso, Ionas Erb, Jose Espinosa-Carrasco, Carsten Kemena & Cedric Notredame T-Coffee (Tree-based consistency objective function for alignment evaluation) is a versatile multiple sequence alignment (MSA) method suitable for aligning most types of biological sequences. The main strength of T-Coffee is its ability to combine third party aligners and to integrate structural (or homology) information when (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5292630 Fri, 07 Oct 2011 06:59:45 +0100 5292630 http://www.medworm.com/index.php?rid=5292631&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FxqxJuTuaA-I%2Fnprot.2011.373 Selective 2′-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) for direct analysis of covalent adducts and of nucleotide flexibility in RNA Nature Protocols 6, 1683 (2011). doi:10.1038/nprot.2011.373 Authors: Kady-Ann Steen, Nathan A Siegfried & Kevin M Weeks RNA SHAPE chemistry yields quantitative, single-nucleotide resolution structural information based on the reaction of the 2′-hydroxyl group of conformationally flexible nucleotides with electrophilic SHAPE reagents. However, SHAPE technology has been limited by the requirement that sites of RNA modification be detected by primer extension. Primer (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5292631 Thu, 06 Oct 2011 04:00:00 +0100 5292631 http://www.medworm.com/index.php?rid=5268401&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FAfElU-2zyco%2Fnprot.2011.402 Authors: Mazhar Adli & Bradley E Bernstein Chromatin immunoprecipitation (ChIP) combined with high-throughput sequencing (ChIP-seq) has become the gold standard for whole-genome mapping of protein-DNA interactions. However, conventional ChIP protocols necessitate the use of large numbers of cells, and library preparation steps associated with current high-throughput sequencing platforms require substantial amounts of (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5268401 Thu, 29 Sep 2011 04:00:00 +0100 5268401 http://www.medworm.com/index.php?rid=5268400&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Ft_bPjAlwcrE%2Fnprot.2011.383 Authors: Jordi Vila-Planas, Elisabet Fernández-Rosas, Bergoi Ibarlucea, Stefanie Demming, Carme Nogués, Jose A Plaza, Carlos Domínguez, Stephanus Büttgenbach & Andreu Llobera Here we present a protocol for analyzing cell cultures using a photonic lab-on-a-chip (PhLoC). By using a broadband light source and a spectrometer, the spectrum of a given cell culture with an arbitrary population is acquired. The PhLoC can work in three different regimes: light (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5268400 Thu, 29 Sep 2011 04:00:00 +0100 5268400 http://www.medworm.com/index.php?rid=5268399&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FknDnCGGjwgI%2Fnprot.2011.397 Authors: Joshua D Currie & Stephen L Rogers Cultured Drosophila melanogaster S2 and S2R+ cell lines have become important tools for uncovering fundamental aspects of cell biology as well as for gene discovery. Despite their utility, these cell lines are nonmotile and cannot build polarized structures or cell-cell contacts. Here we outline (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5268399 Thu, 29 Sep 2011 04:00:00 +0100 5268399 http://www.medworm.com/index.php?rid=5246031&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FN8Sa2NxvgCg%2Fnprot.2011.379 Authors: Danielle N Rockwood, Rucsanda C Preda, Tuna Yücel, Xiaoqin Wang, Michael L Lovett & David L Kaplan Silk fibroin, derived from Bombyx mori cocoons, is a widely used and studied protein polymer for biomaterial applications. Silk fibroin has remarkable mechanical properties when formed into different materials, demonstrates biocompatibility, has controllable degradation rates from hours to years and can be chemically modified (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5246031 Thu, 22 Sep 2011 04:00:00 +0100 5246031 http://www.medworm.com/index.php?rid=5246030&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FYIji8hs8ynA%2Fnprot.2011.382 Authors: Oded Kleifeld, Alain Doucet, Anna Prudova, Ulrich auf dem Keller, Magda Gioia, Jayachandran N Kizhakkedathu & Christopher M Overall Analysis of the sequence and nature of protein N termini has many applications. Defining the termini of proteins for proteome annotation in the Human Proteome Project is of increasing importance. Terminomics analysis of protease cleavage sites in degradomics for substrate discovery is a key new (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5246030 Thu, 22 Sep 2011 04:00:00 +0100 5246030 http://www.medworm.com/index.php?rid=5246029&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FkACdePu7Lt0%2Fnprot.2011.398 Nature Protocols 6, 1568 (2011). doi:10.1038/nprot.2011.398 Author: Heather Etchevers A highly enriched population of neural crest cells (NCCs) from amniote embryos, such as from chicks, mice and humans, is desirable for experiments in fate determination. NCCs are also useful for testing the functional effects of molecular changes underlying numerous human diseases of neural crest (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5246029 Thu, 22 Sep 2011 04:00:00 +0100 5246029 http://www.medworm.com/index.php?rid=5233157&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FO1r2c0mWMQ4%2Fnprot.2011.384 Authors: Vadim Zinchuk, Yong Wu, Olga Grossenbacher-Zinchuk & Enrico Stefani Interactions of proteins are examined by detecting their overlap using fluorescent markers. The observed overlap is then quantified to serve as a measure of spatial correlation. A major drawback of this approach is that it can produce false values because of the properties of the (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5233157 Thu, 15 Sep 2011 04:00:00 +0100 5233157 http://www.medworm.com/index.php?rid=5233156&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F-czKkSrWUuM%2Fnprot.2011.381 Authors: Dominik Jańczewski, Nikodem Tomczak, Ming-Yong Han & G Julius Vancso Quantum dots (QDs) need to be attached to other chemical species if they are to be used as biomarkers, therapeutic agents or sensors. These materials also need to disperse well in water and have well-defined functional groups on their surfaces. QDs are most often synthesized (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5233156 Thu, 15 Sep 2011 04:00:00 +0100 5233156 http://www.medworm.com/index.php?rid=5233155&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FVzGziuahLr8%2Fnprot.2011.385 Authors: Maximillian H Bailor, Anthony M Mustoe, Charles L Brooks & Hashim M Al-Hashimi More than 50% of RNA secondary structure is estimated to be A-form helices, which are linked together by various junctions. Here we describe a protocol for computing three interhelical Euler angles describing the relative orientation of helices across RNA junctions. 5′ and 3′ helices, H1 (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5233155 Thu, 15 Sep 2011 04:00:00 +0100 5233155 http://www.medworm.com/index.php?rid=5203906&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FSJN12ZvvG40%2Fnprot.2011.376 Authors: David Entenberg, Jeffrey Wyckoff, Bojana Gligorijevic, Evanthia T Roussos, Vladislav V Verkhusha, Jeffrey W Pollard & John Condeelis Characterizing biological mechanisms dependent upon the interaction of many cell types in vivo requires both multiphoton microscope systems capable of expanding the number and types of fluorophores that can be imaged simultaneously while removing the wavelength and tunability restrictions of existing systems, and enhanced (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5203906 Sun, 11 Sep 2011 03:22:25 +0100 5203906 http://www.medworm.com/index.php?rid=5203907&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FBC4QDIcDq64%2Fnprot.2011.378 We describe an experimental approach for generating mutant alleles in rat spermatogonial stem cells (SSCs) using Sleeping Beauty (SB) transposon–mediated insertional mutagenesis. The protocol is based on mobilization of mutagenic gene-trap transposons from transfected plasmid vectors into the genomes of cultured stem (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5203907 Thu, 08 Sep 2011 04:00:00 +0100 5203907 http://www.medworm.com/index.php?rid=5203905&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FQpdZSjOR94s%2Fnprot.2011.375 Global urinary metabolic profiling procedures using gas chromatography–mass spectrometry Nature Protocols 6, 1483 (2011). doi:10.1038/nprot.2011.375 Authors: Eric Chun Yong Chan, Kishore Kumar Pasikanti & Jeremy K Nicholson The role of urinary metabolic profiling in systems biology research is expanding. This is because of the use of this technology for clinical diagnostic and mechanistic studies and for the development of new personalized health care and molecular epidemiology (population) studies. The methodologies commonly used (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5203905 Thu, 08 Sep 2011 04:00:00 +0100 5203905 http://www.medworm.com/index.php?rid=5191014&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FJLkTMPgS2Pw%2Fnprot.2011.377 Authors: Maximilian J Waldner, Stefan Wirtz, Clemens Neufert, Christoph Becker & Markus F Neurath New endoscopic techniques such as narrow-band imaging (NBI) and confocal laser endomicroscopy (CLE) have improved the in vivo diagnosis of human gastrointestinal diseases in the colon. Whereas NBI may facilitate the identification of neoplastic lesions, CLE permits real-time histology of the inflamed or neoplastic (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5191014 Wed, 31 Aug 2011 23:00:00 +0100 5191014 http://www.medworm.com/index.php?rid=5191013&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FUFG-Lu60zQ0%2Fnprot.2011.371 Authors: Yusuf Tufail, Anna Yoshihiro, Sandipan Pati, Monica M Li & William J Tyler Brain stimulation methods are indispensable to the study of brain function. They have also proven effective for treating some neurological disorders. Historically used for medical imaging, ultrasound (US) has recently been shown to be capable of noninvasively stimulating brain activity. Here we provide a general (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5191013 Wed, 31 Aug 2011 23:00:00 +0100 5191013 http://www.medworm.com/index.php?rid=5191012&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FnCQzpvOr0K4%2Fnprot.2011.370 Authors: Theeraporn Puntheeranurak, Isabel Neundlinger, Rolf K H Kinne & Peter Hinterdorfer Atomic force microscopy (AFM) has proven to be a powerful tool in biological sciences. Its particular advantage over other high-resolution methods commonly used is that biomolecules can be investigated not only under physiological conditions but also while they perform their biological functions. Single-molecule force spectroscopy (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5191012 Wed, 31 Aug 2011 23:00:00 +0100 5191012 http://www.medworm.com/index.php?rid=5168741&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FCELeRK-M1HQ%2Fnprot.2011.372 Authors: Sohyun Hwang, Seung Y Rhee, Edward M Marcotte & Insuk Lee AraNet is a functional gene network for the reference plant Arabidopsis and has been constructed in order to identify new genes associated with plant traits. It is highly predictive for diverse biological pathways and can be used to prioritize genes for functional screens. Moreover, (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5168741 Wed, 24 Aug 2011 23:00:00 +0100 5168741 http://www.medworm.com/index.php?rid=5168740&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FBADtVZfgphw%2Fnprot.2011.363 We describe here a highly efficient procedure for conditional mutagenesis in Plasmodium. The procedure uses the site-specific recombination FLP-FRT system of yeast and targets the pre-erythrocytic stages of the rodent Plasmodium parasite P. berghei, including the sporozoite stage and the (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5168740 Wed, 24 Aug 2011 23:00:00 +0100 5168740 http://www.medworm.com/index.php?rid=5168739&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F7SiiQJbbkNo%2Fnprot.2011.389 Authors: Dani Dumitriu, Alfredo Rodriguez & John H Morrison Morphological features such as size, shape and density of dendritic spines have been shown to reflect important synaptic functional attributes and potential for plasticity. Here we describe in detail a protocol for obtaining detailed morphometric analysis of spines using microinjection of fluorescent dyes, high-resolution confocal (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5168739 Wed, 24 Aug 2011 23:00:00 +0100 5168739 http://www.medworm.com/index.php?rid=5155364&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F-ZgjAP63cXU%2Fnprot.2011.358 We describe here the development of a mass spectrometry protocol based on (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5155364 Wed, 17 Aug 2011 23:00:00 +0100 5155364 http://www.medworm.com/index.php?rid=5155363&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FTb9akV-pOUw%2Fnprot.2011.369 We describe a protocol for construction and quantification of libraries for emulsion PCR (emPCR)-based sequencing platforms such as Roche 454 or Ion Torrent PGM. The protocol involves library construction using customized Y adapters, quantification using TaqMan-MGB (minor groove binder) probe–based quantitative PCR (qPCR) and calculation (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5155363 Wed, 17 Aug 2011 23:00:00 +0100 5155363 http://www.medworm.com/index.php?rid=5155362&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F2-jREvAV2t4%2Fnprot.2011.349 Authors: Gregory M Palmer, Andrew N Fontanella, Siqing Shan, Gabi Hanna, Guoqing Zhang, Cassandra L Fraser & Mark W Dewhirst Optical techniques for functional imaging in mice have a number of key advantages over other common imaging modalities such as magnetic resonance imaging, positron emission tomography or computed tomography, including high resolution, low cost and an extensive library of available contrast agents and reporter genes. (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5155362 Wed, 17 Aug 2011 23:00:00 +0100 5155362 http://www.medworm.com/index.php?rid=5116936&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FZkBKGLuulxM%2Fnprot.2011.367 Authors: Nurcan Tuncbag, Attila Gursoy, Ruth Nussinov & Ozlem Keskin Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. We provide a protocol (termed PRISM, protein interactions by structural matching) for large-scale (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5116936 Wed, 10 Aug 2011 23:00:00 +0100 5116936 http://www.medworm.com/index.php?rid=5116935&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F9s0t_098CxM%2Fnprot.2011.364 Authors: Yuansheng Sun, Richard N Day & Ammasi Periasamy Fluorescence lifetime imaging microscopy (FLIM) is now routinely used for dynamic measurements of signaling events inside living cells, including detection of protein-protein interactions. An understanding of the basic physics of fluorescence lifetime measurements is required to use this technique. In this protocol, we describe both (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5116935 Wed, 10 Aug 2011 23:00:00 +0100 5116935 http://www.medworm.com/index.php?rid=5116934&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F5FWVdtGaMwE%2Fnprot.2011.368 Authors: Rohith Srivas, Gregory Hannum, Johannes Ruscheinski, Keiichoro Ono, Peng-Liang Wang, Michael Smoot & Trey Ideker To take full advantage of high-throughput genetic and physical interaction mapping projects, the raw interactions must first be assembled into models of cell structure and function. PanGIA (for physical and genetic interaction alignment) is a plug-in for the bioinformatics platform Cytoscape, designed to integrate physical (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5116934 Wed, 10 Aug 2011 23:00:00 +0100 5116934 http://www.medworm.com/index.php?rid=5094020&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FjBQ_4rph1-o%2Fnprot.2011.308 Authors: Jan Schellenberger, Richard Que, Ronan M T Fleming, Ines Thiele, Jeffrey D Orth, Adam M Feist, Daniel C Zielinski, Aarash Bordbar, Nathan E Lewis, Sorena Rahmanian, Joseph Kang, Daniel R Hyduke & Bernhard Ø Palsson Over the past decade, a growing community of researchers has emerged around the use of constraint-based reconstruction and analysis (COBRA) methods to simulate, analyze and predict a variety of metabolic phenotypes using genome-scale models. The COBRA Toolbox, a MATLAB package for implementing COBRA methods, was (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5094020 Wed, 03 Aug 2011 23:00:00 +0100 5094020 http://www.medworm.com/index.php?rid=5094019&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FHWDUQIhSdSw%2Fnprot.2011.362 We describe a protocol for the derivation of clonal populations (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5094019 Wed, 03 Aug 2011 23:00:00 +0100 5094019 http://www.medworm.com/index.php?rid=5094018&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F6LsR6l3eMZc%2Fnprot.2011.374 We describe a protocol for the generation of human iPSCs using a single polycistronic lentiviral vector (pLM-fSV2A) coexpressing OCT4, SOX2, KLF4 (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5094018 Wed, 03 Aug 2011 23:00:00 +0100 5094018 http://www.medworm.com/index.php?rid=5076221&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FrKalobLrpeQ%2Fnprot.2011.366 Authors: Christopher A Sellick, Rasmus Hansen, Gill M Stephens, Royston Goodacre & Alan J Dickson Metabolite profiling of industrially important suspension-cultured mammalian cells is being increasingly used for rational improvement of bioprocesses. This requires the generation of global metabolite profiles that cover a broad range of metabolites and that are representative of the cells at the time of sampling. The (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5076221 Wed, 27 Jul 2011 23:00:00 +0100 5076221 http://www.medworm.com/index.php?rid=5076220&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FNpKFTz4vgIE%2Fnprot.2011.380 Authors: S R L Stacpoole, B Bilican, D J Webber, A Luzhynskaya, X L He, A Compston, R Karadottir, R J M Franklin & S Chandran This protocol has been designed to generate neural precursor cells (NPCs) from human embryonic stem cells (hESCs) using a physiological oxygen (O2) level of 3% (previously termed hypoxia) and chemically defined conditions. The first stage involves suspension culture of hESC colonies at 3% (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5076220 Wed, 27 Jul 2011 23:00:00 +0100 5076220 http://www.medworm.com/index.php?rid=5076219&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FFJr8roMcClY%2Fnprot.2011.365 Slide preparation for single-cell–resolution imaging of fluorescent proteins in their three-dimensional near-native environment Nature Protocols 6, 1221 (2011). doi:10.1038/nprot.2011.365 Authors: Hugo J Snippert, Arnout G Schepers, Gabriele Delconte, Peter D Siersema & Hans Clevers In recent years, many mouse models have been developed to mark and trace the fate of adult cell populations using fluorescent proteins. High-resolution visualization of such fluorescent markers in their physiological setting is thus an important aspect of adult stem cell research. Here we describe (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5076219 Wed, 27 Jul 2011 23:00:00 +0100 5076219 http://www.medworm.com/index.php?rid=5076218&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FIV8_V2t5X3c%2Fnprot.2011.357 Continuous-flow reactor–based synthesis of carbohydrate and dihydrolipoic acid–capped quantum dots Nature Protocols 6, 1209 (2011). doi:10.1038/nprot.2011.357 Authors: Paola Laurino, Raghavendra Kikkeri & Peter H Seeberger A detailed protocol for the large-scale synthesis of carbohydrate and dihydrolipoic acid (DHLA)-coated CdSe/ZnS and CdTe/ZnS nanoparticles using continuous flow reactors is described here. Three continuous flow microreaction systems, operating at three different temperatures, are used for the synthesis of mannose-, galactose- or DHLA-functionalized quantum (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5076218 Wed, 27 Jul 2011 23:00:00 +0100 5076218 http://www.medworm.com/index.php?rid=5048108&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FXbURUgtTdnc%2Fnprot.2011.360 Authors: Tao Geng, Yihong Zhan, Jun Wang & Chang Lu Electroporation is a high-efficiency and low-toxicity physical gene transfer method. Classical electroporation protocols are limited by the small volume of cell samples processed (less than 107 cells per reaction) and low DNA uptake due to partial permeabilization of the cell membrane. Here we (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5048108 Wed, 20 Jul 2011 23:00:00 +0100 5048108 http://www.medworm.com/index.php?rid=5048107&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FDfZZ9KUL32Y%2Fnprot.2011.361 Authors: Sam A Golden, Herbert E Covington, Olivier Berton & Scott J Russo A major impediment to novel drug development has been the paucity of animal models that accurately reflect symptoms of affective disorders. In animal models, prolonged social stress has proven to be useful in understanding the molecular mechanisms underlying affective-like disorders. When considering experimental approaches for (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5048107 Wed, 20 Jul 2011 23:00:00 +0100 5048107 http://www.medworm.com/index.php?rid=5048106&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FISPFOV84UGQ%2Fnprot.2011.354 Authors: Steven W Cotten, Jianwei Zou, C Alexander Valencia & Rihe Liu mRNA display is a powerful yet challenging in vitro selection technique that can be used to identify proteins with desired properties from both natural proteome and combinatorial polypeptide libraries. The physical conjugation between a protein and its own RNA presents unique challenges in manipulating (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5048106 Wed, 20 Jul 2011 23:00:00 +0100 5048106 http://www.medworm.com/index.php?rid=5026701&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FE6CZZmkTX4M%2Fnprot.2011.353 Authors: Mario Engelmann, Jana Hädicke & Julia Noack Testing declarative memory in laboratory rodents can provide insights into the fundamental mechanisms underlying this type of learning and memory processing, and these insights are likely to be applicable to humans. Here we provide a detailed description of the social discrimination procedure used to investigate (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5026701 Wed, 13 Jul 2011 23:00:00 +0100 5026701 http://www.medworm.com/index.php?rid=5026700&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F7n6zjjf0ndA%2Fnprot.2011.352 Synthesis of magnetic resonance–, X-ray– and ultrasound-visible alginate microcapsules for immunoisolation and noninvasive imaging of cellular therapeutics Nature Protocols 6, 1142 (2011). doi:10.1038/nprot.2011.352 Authors: Brad P Barnett, Aravind Arepally, Matthias Stuber, Dian R Arifin, Dara L Kraitchman & Jeff W M Bulte Cell therapy has the potential to treat or cure a wide variety of diseases. Non-invasive cell tracking techniques are, however, necessary to translate this approach to the clinical setting. This protocol details methods to create microcapsules that are visible by X-ray, ultrasound (US) or magnetic (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5026700 Wed, 13 Jul 2011 23:00:00 +0100 5026700 http://www.medworm.com/index.php?rid=5026699&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F3vsztDAjvi4%2Fnprot.2011.355 Authors: An Staes, Francis Impens, Petra Van Damme, Bart Ruttens, Marc Goethals, Hans Demol, Evy Timmerman, Joël Vandekerckhove & Kris Gevaert In recent years, procedures for selecting the N-terminal peptides of proteins with analysis by mass spectrometry have been established to characterize protease-mediated cleavage and protein α-N-acetylation on a proteomic level. As a pioneering technology, N-terminal combined fractional diagonal chromatography (COFRADIC) has been used (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5026699 Wed, 13 Jul 2011 23:00:00 +0100 5026699 http://www.medworm.com/index.php?rid=5026698&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FTTRQuy0uN4Q%2Fnprot.2011.346 Knockout and pullout recombineering for naturally transformable Burkholderia thailandensis and Burkholderia pseudomallei Nature Protocols 6, 1085 (2011). doi:10.1038/nprot.2011.346 Authors: Yun Kang, Michael H Norris, Bruce A Wilcox, Apichai Tuanyok, Paul S Keim & Tung T Hoang Phage λ-Red proteins are powerful tools for pulling and knocking out chromosomal fragments but have been limited to the γ-proteobacteria. Procedures are described here to easily knock out (KO) and pull out (PO) chromosomal DNA fragments from naturally transformable Burkholderia thailandensis and Burkholderia pseudomallei (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5026698 Wed, 06 Jul 2011 23:00:00 +0100 5026698 http://www.medworm.com/index.php?rid=5006180&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fd4CAcIF-QhQ%2Fnprot.2011.351 Authors: Daniel Razansky, Andreas Buehler & Vasilis Ntziachristos Multispectral optoacoustic tomography (MSOT) has recently been developed to enable visualization of optical contrast and tissue biomarkers, with resolution and speed representative of ultrasound. In the implementation described here, MSOT enables operation in real-time mode by capturing single cross-sectional images in (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5006180 Wed, 06 Jul 2011 23:00:00 +0100 5006180 http://www.medworm.com/index.php?rid=5006179&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fr0NB2QFufEY%2Fnprot.2011.347 Authors: Christopher J Potter & Liqun Luo In Drosophila, the GAL4/UAS/GAL80 repressible binary expression system is widely used to manipulate or mark tissues of interest. However, complex biological systems often require distinct transgenic manipulations of different cell populations. For this purpose, we recently developed the Q system, a second repressible binary (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5006179 Wed, 06 Jul 2011 23:00:00 +0100 5006179 http://www.medworm.com/index.php?rid=5006178&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FTTRQuy0uN4Q%2Fnprot.2011.346 Authors: Yun Kang, Michael H Norris, Bruce A Wilcox, Apichai Tuanyok, Paul S Keim & Tung T Hoang Phage λ-Red proteins are powerful tools for pulling and knocking out chromosomal fragments but have been limited to the γ-proteobacteria. Procedures are described here to easily knock out (KO) and pull out (PO) chromosomal DNA fragments from naturally transformable Burkholderia thailandensis and Burkholderia pseudomallei (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=5006178 Wed, 06 Jul 2011 23:00:00 +0100 5006178 http://www.medworm.com/index.php?rid=4991600&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FFcUBx7vb5Zo%2Fnprot.2011.335 Authors: Warwick B Dunn, David Broadhurst, Paul Begley, Eva Zelena, Sue Francis-McIntyre, Nadine Anderson, Marie Brown, Joshau D Knowles, Antony Halsall, John N Haselden, Andrew W Nicholls, Ian D Wilson, Douglas B Kell & Royston Goodacre Metabolism has an essential role in biological systems. Identification and quantitation of the compounds in the metabolome is defined as metabolic profiling, and it is applied to define metabolic changes related to genetic differences, environmental influences and disease or drug perturbations. Chromatography–mass spectrometry (MS) platforms (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4991600 Wed, 29 Jun 2011 23:00:00 +0100 4991600 http://www.medworm.com/index.php?rid=4991599&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FGcnTiD3KgM0%2Fnprot.2011.356 Authors: Haruko Obokata, Masayuki Yamato, Satoshi Tsuneda & Teruo Okano Perfecting tissue engineering and cell sheet transplantation is an important step toward realizing regenerative medicine and is a growing area of research. Before being applied to clinical settings, it is important that these approaches are evaluated in vivo. Here we provide a detailed protocol (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4991599 Wed, 29 Jun 2011 23:00:00 +0100 4991599 http://www.medworm.com/index.php?rid=4991598&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fbedit1oiiJM%2Fnprot.2011.350 Authors: Nam-Young Kang, Seong-Wook Yun, Hyung-Ho Ha, Sung-Jin Park & Young-Tae Chang Detecting and isolating specific types of cells is crucial to understanding a variety of biological processes, including development, aging, regeneration and pathogenesis; this understanding, in turn, allows the use of cells for therapeutic purposes, for which stem cells have emerged recently as invaluable materials. The (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4991598 Wed, 29 Jun 2011 23:00:00 +0100 4991598 http://www.medworm.com/index.php?rid=4967394&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F5M2vu0GiHXU%2Fnprot.2011.342 Authors: Himabindu Nandivada, Luis G Villa-Diaz, K Sue O'Shea, Gary D Smith, Paul H Krebsbach & Joerg Lahann The culture of human embryonic stem (hES) cells in defined and xenogeneic-free conditions will contribute substantially to future biotechnological and medical applications. To achieve this goal, we developed the first fully defined synthetic polymer coating poly[2-(methacryloyloxy)ethyl dimethyl-(3-sulfopropyl)ammonium hydroxide] (PMEDSAH) that sustains long-term growth of hES (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4967394 Wed, 22 Jun 2011 23:00:00 +0100 4967394 http://www.medworm.com/index.php?rid=4967393&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FoL5_9Zo-6So%2Fnprot.2011.345 Authors: Wieteke A M Hoeijmakers, Richárd Bártfai, Kees-Jan Françoijs & Hendrik G Stunnenberg Linear amplification for deep sequencing (LADS) is an amplification method that produces representative libraries for Illumina next-generation sequencing within 2 d. The method relies on attaching two different sequencing adapters to blunt-end repaired and A-tailed DNA fragments, wherein one of the adapters is extended with (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4967393 Wed, 22 Jun 2011 23:00:00 +0100 4967393 http://www.medworm.com/index.php?rid=4967392&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Flzb13Fua6Io%2Fnprot.2011.337 Authors: Xue Li, Bin Hu, Jianhua Ding & Huanwen Chen In this protocol, the sample (which could be a bulk or heterogeneous fluid, or a greasy surface) is treated with a neutral desorption (ND) sampling gas beam, and the resulting analyte mixtures are directly characterized by extractive electrospray ionization mass spectrometry (EESI-MS). The ND device (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4967392 Wed, 22 Jun 2011 23:00:00 +0100 4967392 http://www.medworm.com/index.php?rid=4931970&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FtOAuUGj2Ji0%2Fnprot.2011.336 Authors: Sebastian van de Linde, Anna Löschberger, Teresa Klein, Meike Heidbreder, Steve Wolter, Mike Heilemann & Markus Sauer Direct stochastic optical reconstruction microscopy (dSTORM) uses conventional fluorescent probes such as labeled antibodies or chemical tags for subdiffraction resolution fluorescence imaging with a lateral resolution of ∼20 nm. In contrast to photoactivated localization microscopy (PALM) with photoactivatable fluorescent proteins, dSTORM experiments (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4931970 Wed, 15 Jun 2011 23:00:00 +0100 4931970 http://www.medworm.com/index.php?rid=4931969&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FqBZUpS3TPjw%2Fnprot.2011.343 Authors: Jizhe Hao & Patrick Delmas Mechanotransduction constitutes the basis of a variety of physiological processes, such as the senses of touch, balance, proprioception and hearing. In vertebrates, mechanosensation is mediated by mechanosensory receptors. The aptitude of these mechanoreceptors for detecting mechanical information relies on the presence of mechanosensitive channels that (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4931969 Wed, 15 Jun 2011 23:00:00 +0100 4931969 http://www.medworm.com/index.php?rid=4931968&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FtxzSjt0B4dU%2Fnprot.2011.348 Authors: Andrea E M Seiler & Horst Spielmann In the embryonic stem cell test (EST), differentiation of mouse embryonic stem cells (mESCs) is used as a model to assess embryotoxicity in vitro. The test was successfully validated by the European Center for the Validation of Alternative Methods (ECVAM) and models fundamental mechanisms (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4931968 Wed, 15 Jun 2011 23:00:00 +0100 4931968 http://www.medworm.com/index.php?rid=4919895&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FDDydLTeA5Ag%2Fnprot.2011.344 Authors: Matthew H Cato, Irene W Yau & Robert C Rickert Detailed biochemical analysis of unmanipulated germinal center (GC) B cells has not been achieved. Previously, we designed and used a simple, economical and new magnetic bead separation scheme for the purification of 'untouched' mature GC and non-GC B cells from the spleens of immunized mice (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4919895 Wed, 08 Jun 2011 23:00:00 +0100 4919895 http://www.medworm.com/index.php?rid=4919894&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FfahNS-hgpeI%2Fnprot.2011.339 Authors: Peter C Simons, Susan M Young, Mark B Carter, Anna Waller, Dayong Zhai, John C Reed, Bruce S Edwards & Larry A Sklar The B-cell lymphoma-2 (Bcl-2) family contains six antiapoptotic members, each with a hydrophobic pocket in which Bcl-2 homology region 3 (BH3) helices bind. This binding quenches apoptotic signals from activated BH3 family members. Many tumor cells either have increased expression of one of these six (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4919894 Wed, 08 Jun 2011 23:00:00 +0100 4919894 http://www.medworm.com/index.php?rid=4919893&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FqXuXqmHfgj0%2Fnprot.2011.340 We describe an effective and simple protocol that uses click chemistry to attach native β-cyclodextrin (β-CD) to silica particles, resulting in a chiral stationary phase (CCNCSP) that can be used for the enantioseparation of chiral drugs by high-performance liquid chromatography (HPLC). Starting from β-CD, the (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4919893 Wed, 08 Jun 2011 23:00:00 +0100 4919893 http://www.medworm.com/index.php?rid=4891421&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FeDOdclRrk18%2Fnprot.2011.330 A time-of–drug addition approach to target identification of antiviral compounds Nature Protocols 6, 925 (2011). doi:10.1038/nprot.2011.330 Authors: Dirk Daelemans, Rudi Pauwels, Erik De Clercq & Christophe Pannecouque Insight into the mode of action of newly discovered antiviral agents is now almost a prerequisite for clinical development. This protocol describes a method that provides information on the target of inhibitors of the human immunodeficiency virus (HIV); it can also be adapted to other (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4891421 Wed, 01 Jun 2011 23:00:00 +0100 4891421 http://www.medworm.com/index.php?rid=4891420&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FCWeQnUPEXRk%2Fnprot.2011.329 Authors: Heather L Lord, Xu Zhang, F Marcel Musteata, Dajana Vuckovic & Janusz Pawliszyn This protocol for in vivo solid-phase microextraction (SPME) can be used to monitor and quantify intravenous concentrations of drugs and metabolites without the need to withdraw a blood sample for analysis. The SPME probe is inserted directly into a peripheral vein of a living (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4891420 Wed, 01 Jun 2011 23:00:00 +0100 4891420 http://www.medworm.com/index.php?rid=4891419&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fv0V8H4KKUc8%2Fnprot.2011.328 Authors: Tyrone Ryba, Dana Battaglia, Benjamin D Pope, Ichiro Hiratani & David M Gilbert Replication timing profiles are cell type–specific and reflect genome organization changes during differentiation. In this protocol, we describe how to analyze genome-wide replication timing (RT) in mammalian cells. Asynchronously cycling cells are pulse labeled with the nucleotide analog 5-bromo-2-deoxyuridine (BrdU) and sorted into S-phase fractions (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4891419 Wed, 01 Jun 2011 23:00:00 +0100 4891419 http://www.medworm.com/index.php?rid=4870585&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FUBlmE8bcHX0%2Fnprot.2011.333 Authors: Katharina Bluemlein & Markus Ralser Targeted quantification of proteins is a daily task in biological research but often relies on techniques such as western blotting that are only barely quantitative. Here we present a broadly applicable workflow for protein quantification from unpurified whole-cell extracts that can be completed in less (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4870585 Wed, 25 May 2011 23:00:00 +0100 4870585 http://www.medworm.com/index.php?rid=4870584&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F-cUsnUpWc0k%2Fnprot.2011.332 Authors: Andrew J Bushby, Kenneth M Y P'ng, Robert D Young, Christian Pinali, Carlo Knupp & Andrew J Quantock In this protocol, we describe a 3D imaging technique known as 'volume electron microscopy' or 'focused ion beam scanning electron microscopy (FIB/SEM)' applied to biological tissues. A scanning electron microscope equipped with a focused gallium ion beam, used to sequentially mill away the sample surface, (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4870584 Wed, 25 May 2011 23:00:00 +0100 4870584 http://www.medworm.com/index.php?rid=4870583&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FPR-_b7Fd12U%2Fnprot.2011.338 We describe here a detailed protocol for generating gene knockout rats by homologous recombination in embryonic stem (ES) cells. This protocol comprises the following procedures: derivation and expansion of rat ES cells, construction of gene-targeting vectors, generation of gene-targeted rat ES cells and, finally, production (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4870583 Wed, 25 May 2011 23:00:00 +0100 4870583 http://www.medworm.com/index.php?rid=4839484&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FLcENcYpG0L4%2Fnprot.2011.359 Authors: Renhai Cao, Sharon Lim, Hong Ji, Yin Zhang, Yunlong Yang, Jennifer Honek, Eva-Maria Hedlund & Yihai Cao This protocol describes a powerful in vivo method to quantitatively study the formation of new lymphatic vessels in the avascular cornea without interference of pre-existing lymphatics. Implantation of 100 ng of lymphangiogenic factors such as vascular endothelial growth factor (VEGF)-A, VEGF-C or fibroblast growth (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4839484 Wed, 18 May 2011 23:00:00 +0100 4839484 http://www.medworm.com/index.php?rid=4839483&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FoHHtELRqba8%2Fnprot.2011.327 A simple, versatile and efficient method to genetically modify human monocyte-derived dendritic cells with HIV-1–derived lentiviral vectors Nature Protocols 6, 806 (2011). doi:10.1038/nprot.2011.327 Authors: Grégory Berger, Stéphanie Durand, Caroline Goujon, Xuan-Nhi Nguyen, Stéphanie Cordeil, Jean-Luc Darlix & Andrea Cimarelli Lentiviral vectors derived from the human immunodeficiency type 1 virus (HIV-1 LV) are among the finest tools available today for the genetic modification of human monocyte-derived dendritic cells (MDDCs). However, this process is largely inefficient because MDDCs show a strong resistance to HIV-1 transduction. Here (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4839483 Wed, 18 May 2011 23:00:00 +0100 4839483 http://www.medworm.com/index.php?rid=4839482&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FSKdO9_blCBs%2Fnprot.2011.321 We describe micromanipulation and microinjection procedures for the fabrication of soft-matter networks consisting of lipid bilayer nanotubes and surface-immobilized vesicles. These biomimetic membrane systems feature unique structural flexibility and expandability and, unlike solid-state microfluidic and nanofluidic devices prepared by top-down fabrication, they allow network designs (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4839482 Wed, 18 May 2011 23:00:00 +0100 4839482 http://www.medworm.com/index.php?rid=4819485&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FvgTSIJLfmIo%2Fnprot.2011.331 Authors: Yuki Goto, Takayuki Katoh & Hiroaki Suga Genetic code reprogramming is a method for the reassignment of arbitrary codons from proteinogenic amino acids to nonproteinogenic ones; thus, specific sequences of nonstandard peptides can be ribosomally expressed according to their mRNA templates. Here we describe a protocol that facilitates genetic code reprogramming using (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4819485 Wed, 11 May 2011 23:00:00 +0100 4819485 http://www.medworm.com/index.php?rid=4819484&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FCe9QTMsH6po%2Fnprot.2011.326 Authors: Ashley R Connolly & Matt Trau This protocol describes a new and rapid isothermal reaction process designed to amplify and detect a specific DNA sequence in purified DNA extracted from cultured cells. The protocol uses a DNA nanomachine that comprises two molecular switches that function in concert to isothermally amplify and (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4819484 Wed, 11 May 2011 23:00:00 +0100 4819484 http://www.medworm.com/index.php?rid=4819483&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FBXkFsaRI6RA%2Fnprot.2011.324 Synthesis of all-hydrocarbon stapled α-helical peptides by ring-closing olefin metathesis Nature Protocols 6, 761 (2011). doi:10.1038/nprot.2011.324 Authors: Young-Woo Kim, Tom N Grossmann & Gregory L Verdine This protocol provides a detailed procedure for the preparation of stapled α-helical peptides, which have proven their potential as useful molecular probes and as next-generation therapeutics. Two crucial features of this protocol are (i) the construction of peptide substrates containing hindered α-methyl, α-alkenyl amino acids (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4819483 Wed, 11 May 2011 23:00:00 +0100 4819483 http://www.medworm.com/index.php?rid=4788023&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FjwhKCWgxx8Y%2Fnprot.2011.319 Authors: Jianguo Xia & David S Wishart MetaboAnalyst is an integrated web-based platform for comprehensive analysis of quantitative metabolomic data. It is designed to be used by biologists (with little or no background in statistics) to perform a variety of complex metabolomic data analysis tasks. These include data processing, data normalization, statistical (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4788023 Wed, 04 May 2011 23:00:00 +0100 4788023 http://www.medworm.com/index.php?rid=4788022&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FaPAH2YJNLFA%2Fnprot.2010.144 Authors: Natali R Mustafa, Ward de Winter, Frank van Iren & Robert Verpoorte Methods described in this paper are confined to in vitro dedifferentiated plant cell suspension cultures, which are convenient for the large-scale production of fine chemicals in bioreactors and for the study of cellular and molecular processes, as they offer the advantages of a simplified (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4788022 Wed, 04 May 2011 23:00:00 +0100 4788022 http://www.medworm.com/index.php?rid=4788021&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FPV5c_A1nVgo%2Fnprot.2011.320 Authors: Emily Dick, Elena Matsa, Lorraine E Young, David Darling & Chris Denning The protocols described here address methods used in two crucial stages in the retroviral reprogramming of somatic cells to produce human induced pluripotent stem cell (hiPSC) lines. The first is an optimized method for producing lentivirus at an efficiency 600-fold greater than previously published, and (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4788021 Wed, 04 May 2011 23:00:00 +0100 4788021 http://www.medworm.com/index.php?rid=4762157&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FxxWqUEUvWZw%2Fnprot.2011.318 Authors: Robert Zweigerdt, Ruth Olmer, Harmeet Singh, Axel Haverich & Ulrich Martin Routine commercial and clinical applications of human pluripotent stem cells (hPSCs) and their progenies will require increasing cell quantities that cannot be provided by conventional adherent culture technologies. Here we describe a straightforward culture protocol for the expansion of undifferentiated human embryonic stem cells (hESCs) (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4762157 Wed, 27 Apr 2011 23:00:00 +0100 4762157 http://www.medworm.com/index.php?rid=4762156&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FMIZSziuyOhE%2Fnprot.2011.316 Chemical toxicity testing in vitro using cytochrome P450–expressing cell lines, such as human CYP1B1 Nature Protocols 6, 677 (2011). doi:10.1038/nprot.2011.316 Authors: Robert Landsiedel, Eric Fabian, Tewes Tralau & Andreas Luch This protocol describes how to use cytochrome P450–dependent monooxygenase (CYP)-expressing cell lines in toxicity testing of chemicals in vitro. Selected cells amenable to permanently grow in culture are genetically manipulated to stably express single CYP enzymes originating from any species of interest. This expression (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4762156 Wed, 27 Apr 2011 23:00:00 +0100 4762156 http://www.medworm.com/index.php?rid=4762155&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fr8QylrRAkPk%2Fnprot.2011.322 Authors: Aishun Jin, Tatsuhiko Ozawa, Kazuto Tajiri, Tsutomu Obata, Hiroyuki Kishi & Atsushi Muraguchi Here we report a new method for isolating antigen-specific antibody-secreting cells (ASCs) using a microwell array chip, which offers a rapid, efficient and high-throughput (up to 234,000 individual cells) system for the detection and retrieval of cells that secrete antibodies of interest on a single-cell (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4762155 Wed, 27 Apr 2011 23:00:00 +0100 4762155 http://www.medworm.com/index.php?rid=4741664&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FQsMfFeEE4bY%2Fnprot.2011.317 Authors: Andrew S Goldstein, Justin M Drake, Daina L Burnes, David S Finley, Hong Zhang, Robert E Reiter, Jiaoti Huang & Owen N Witte Epithelial cell transformation has been demonstrated in numerous animal models for the study of solid tumor biology. However, little evidence exists for human epithelial cell transformation without previous immortalization via genetic influences such as SV40 T-antigen, thus limiting our knowledge of the events that can (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4741664 Wed, 20 Apr 2011 23:00:00 +0100 4741664 http://www.medworm.com/index.php?rid=4741663&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FjhOWGVt_rbs%2Fnprot.2011.310 Authors: Ying Liu, Peng Jiang & Wenbin Deng Pluripotent stem cells can be genetically labeled to facilitate differentiation studies. In this paper, we describe a gene-targeting protocol to knock in a GFP cassette into key gene loci in human pluripotent stem cells (hPSCs), and then use the genetically tagged hPSCs to guide in (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4741663 Wed, 20 Apr 2011 23:00:00 +0100 4741663 http://www.medworm.com/index.php?rid=4741662&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F4k1jOi7hij4%2Fnprot.2011.307 Authors: Lingbo Kong, Pengfei Zhang, Guiwen Wang, Jing Yu, Peter Setlow & Yong-qing Li This protocol describes a method combining phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers to characterize the germination of single bacterial spores. The characterization consists of the following steps: (i) loading heat-activated dormant spores into a temperature-controlled microscope sample holder containing a germinant solution (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4741662 Wed, 20 Apr 2011 23:00:00 +0100 4741662 http://www.medworm.com/index.php?rid=4713919&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FKJGo4KwN5uU%2Fnprot.2010.191 Authors: Nancy Stralis-Pavese, Guy C J Abell, Angela Sessitsch & Levente Bodrossy Microbial diagnostic microarrays (MDMs) are highly parallel hybridization platforms containing multiple sets of immobilized oligonucleotide probes used for parallel detection and identification of many different microorganisms in environmental and clinical samples. Each probe is approximately specific to a given group of organisms. Here we describe (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4713919 Wed, 13 Apr 2011 23:00:00 +0100 4713919 http://www.medworm.com/index.php?rid=4713918&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FippnhemBtYU%2Fnprot.2011.334 Authors: Martin Miguel Casco-Robles, Shouta Yamada, Tomoya Miura, Kenta Nakamura, Tracy Haynes, Nobuyasu Maki, Katia Del Rio-Tsonis, Panagiotis A Tsonis & Chikafumi Chiba The great regenerative abilities of newts provide the impetus for studies at the molecular level. However, efficient methods for gene regulation have historically been quite limited. Here we describe a protocol for transgenically expressing exogenous genes in the newt Cynops pyrrhogaster. This method is (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4713918 Wed, 13 Apr 2011 23:00:00 +0100 4713918 http://www.medworm.com/index.php?rid=4713917&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FnS0giNT91ak%2Fnprot.2011.341 Authors: Panagiotis A Tsonis, Tracy Haynes, Nobuyasu Maki, Kenta Nakamura, Martin Miguel Casco-Robles, Shouta Yamada, Tomoya Miura, Chikafumi Chiba & Katia Del Rio-Tsonis Here we describe a protocol for gene loss of function during regeneration in newts, specifically applied to lens regeneration. Knockdown with the use of morpholinos can be achieved both in vitro and in vivo, depending on the experimental design. These methods achieve desirable (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4713917 Wed, 13 Apr 2011 23:00:00 +0100 4713917 http://www.medworm.com/index.php?rid=4692409&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FybR9RiXAYKg%2Fnprot.2011.306 Authors: Matthias D Erlacher, Anna Chirkova, Paul Voegele & Norbert Polacek The protocol describes the site-specific chemical modification of 23S rRNA of Thermus aquaticus ribosomes. The centerpiece of this 'atomic mutagenesis' approach is the site-specific incorporation of non-natural nucleoside analogs into 23S rRNA in the context of the entire 70S ribosome. This technique exhaustively makes (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4692409 Wed, 06 Apr 2011 23:00:00 +0100 4692409 http://www.medworm.com/index.php?rid=4692408&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FC1zeNi4gasM%2Fnprot.2011.325 Authors: Michal Amit, Ilana Laevsky, Yael Miropolsky, Kohava Shariki, Meital Peri & Joseph Itskovitz-Eldor Human pluripotent (embryonic or induced) stem cells (hPSCs) have many potential applications, not only for research purposes but also for clinical and industrial uses. While culturing these cells as undifferentiated lines, an adherent cell culture based on supportive layers or matrices is most often used. (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4692408 Wed, 06 Apr 2011 23:00:00 +0100 4692408 http://www.medworm.com/index.php?rid=4692407&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FPZXKoAhR6bM%2Fnprot.2011.314 Authors: Aurélie M Rakotondrafara & Matthias W Hentze Much of the regulation of gene expression occurs at the level of protein synthesis. In addition to the canonical translation factors, a multitude of proteins and microRNAs (miRNAs) act as regulatory trans-acting factors. Mechanistic analysis of translational control benefits from functional cell-free systems that (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4692407 Wed, 06 Apr 2011 23:00:00 +0100 4692407 http://www.medworm.com/index.php?rid=4663132&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FH9FjvXsX4wQ%2Fnprot.2011.313 Authors: Philip J Spence, Deirdre Cunningham, William Jarra, Jennifer Lawton, Jean Langhorne & Joanne Thompson The rodent malaria parasite Plasmodium chabaudi chabaudi shares many features with human malaria species, including P. falciparum, and is the in vivo model of choice for many aspects of malaria research in the mammalian host, from sequestration of parasitized erythrocytes, to antigenic (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4663132 Wed, 30 Mar 2011 23:00:00 +0100 4663132 http://www.medworm.com/index.php?rid=4663131&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fk5Sfsh926p0%2Fnprot.2011.312 Nature Protocols 6, 540 (2011). doi:10.1038/nprot.2011.312 Author: Burckhard Seelig The mRNA display technology enables the in vitro selection and directed evolution of functional proteins from libraries of more than 1012 different mutants in a single test tube. The size of these libraries is well beyond the limit of screening technologies and (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4663131 Wed, 30 Mar 2011 23:00:00 +0100 4663131 http://www.medworm.com/index.php?rid=4663130&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FBDf2vv0nbvs%2Fnprot.2011.302 Authors: Pradeep M Nair, Khalid Salaita, Rebecca S Petit & Jay T Groves Physical inputs, both internal and external to a cell, can directly alter the spatial organization of cell surface receptors and their associated functions. Here we describe a protocol that combines solid-state nanolithography and supported lipid membrane techniques to trigger and manipulate specific receptors on the (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4663130 Wed, 30 Mar 2011 23:00:00 +0100 4663130 http://www.medworm.com/index.php?rid=4630791&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2F-l9HZ4qG8QY%2Fnprot.2011.311 Authors: Morten Dræby Sørensen & Peter Kristensen Here we describe a new method applying phage-displayed antibody libraries to the selection of antibodies against a single identified cell on a glass slide. This is the only described method that has successfully achieved selection of antibodies against a single rare cell in a heterogeneous (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4630791 Thu, 24 Mar 2011 00:00:00 +0100 4630791 http://www.medworm.com/index.php?rid=4630790&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FPfhrlsrIkd0%2Fnprot.2011.315 Authors: Brian B Theyel, Daniel A Llano, Naoum P Issa, Atul K Mallik & S Murray Sherman Imaging of 300–500 μm mouse brain slices by laser photostimulation with flavoprotein autofluorescence (LFPA) allows the rapid and sensitive mapping of neuronal connectivity. It is accomplished using UV laser-based photo-uncaging of glutamate and imaging neuronal activation by capturing changes in green light (∼520 nm) emitted (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4630790 Thu, 24 Mar 2011 00:00:00 +0100 4630790 http://www.medworm.com/index.php?rid=4630789&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FM2-lsFufxOw%2Fnprot.2011.301 Authors: Iram F Khan, Roli K Hirata & David W Russell Gene targeting with adeno-associated virus (AAV) vectors has been demonstrated in multiple human cell types, with targeting frequencies ranging from 10−5 to 10−2 per infected cell. These targeting frequencies are 1–4 logs higher than those obtained by conventional transfection or electroporation (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4630789 Thu, 24 Mar 2011 00:00:00 +0100 4630789 http://www.medworm.com/index.php?rid=4605119&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2Fcxea6koIpmw%2Fnprot.2010.190 Authors: Hongcang Gu, Zachary D Smith, Christoph Bock, Patrick Boyle, Andreas Gnirke & Alexander Meissner Genome-wide mapping of 5-methylcytosine is of broad interest to many fields of biology and medicine. A variety of methods have been developed, and several have recently been advanced to genome-wide scale using arrays and next-generation sequencing approaches. We have previously reported reduced representation bisulfite sequencing (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4605119 Fri, 18 Mar 2011 00:00:00 +0100 4605119 http://www.medworm.com/index.php?rid=4605118&cid=s_37895_61_f&fid=37895&url=http%3A%2F%2Ffeeds.nature.com%2F%7Er%2Fnprot%2Frss%2Fcurrent%2F%7E3%2FTWdDqiM_OeQ%2Fnprot.2010.202 Authors: Jeffrey C Hanson, Michael A Tangrea, Skye Kim, Michael D Armani, Thomas J Pohida, Robert F Bonner, Jaime Rodriguez-Canales & Michael R Emmert-Buck Laser-based microdissection facilitates the isolation of specific cell populations from clinical or animal model tissue specimens for molecular analysis. Expression microdissection (xMD) is a second-generation technology that offers considerable advantages in dissection capabilities; however, until recently the method has not been accessible to investigators. This (Source: Nature Protocols) Nature Protocols journals http://www.medworm.com/rss/comments.php?id=4605118 Fri, 18 Mar 2011 00:00:00 +0100 4605118