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| |  | TABLE OF CONTENTS
| October 2011 Volume 8, Issue 10 |  | | |  |  In This Issue
Editorial
This Month
Correspondence
Research Highlights
News in Brief
Technology Feature
News and Views
Review
Resource
Brief Communications
Articles
Application Notes
 Recommend to your library
 Web feed
 Available online only
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| | | | In This Issue |  Top | |  | | PDF
| | Editorial | Top | | | | From lab bench to product catalog p779
doi:10.1038/nmeth.1728
Commercialization of academic research is increasing and provides important benefits, but it remains difficult, and recent developments bring new challenges.
Full Text | PDF
| | This Month | Top | | | | The author file: Abbas El Gamal and Mark Schnitzer p781
Monya Baker
doi:10.1038/nmeth.1713
Two-gram microscopes make brain images in moving mice.
Full Text | PDF
| | | | Points of view: Layout p783
Bang Wong
doi:10.1038/nmeth.1711
Full Text | PDF
| | Correspondence | Top | | | | SignalP 4.0: discriminating signal peptides from transmembrane regions pp785 - 786
Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne and Henrik Nielsen
doi:10.1038/nmeth.1701
Full Text | PDF
| | Research Highlights | Top | | | | | | News in Brief | Top | | | | A palette of calcium indicators | Manipulating genomes with new recombinases | Freely orbiting magnetic tweezers | Growth-factor immobilization in hydrogels | Protein origami
| Technology Feature | Top | | | | Sorting out sequencing data pp799 - 803
Monya Baker
doi:10.1038/nmeth.1702
The toughest work is not sequencing a genome: it is finding the mutations that matter.
Full Text | PDF
| | News and Views | Top | | | | Induced pluripotent stem cells for conserving endangered species? pp805 - 807
Vimal Selvaraj, David E Wildt and Budhan S Pukazhenthi
doi:10.1038/nmeth.1715
Induced pluripotent stem cells have been derived from two endangered wildlife species. There are exciting possibilities, yet formidable challenges, for these cells to contribute to real-life species preservation.
Full Text | PDF
See also: Brief Communication by Friedrich Ben-Nun et al.
| | | | The proteomes of native and induced pluripotent stem cells pp807 - 808
Martin F Pera
doi:10.1038/nmeth.1707
A comparison of embryonic stem cells and induced pluripotent stem cells on the proteome level reveals subtle distinctions between these cell types that might explain differences in their ability to differentiate into specific lineages.
Full Text | PDF
See also: Resource by Phanstiel et al.
| | | | Cells see the light to bring signaling under control pp808 - 809
Jason M Haugh
doi:10.1038/nmeth.1708
The combination of optogenetics with feedback control counteracts variability in cellular signaling responses to promote a deeper understanding of the biochemical mechanisms involved.
Full Text | PDF
See also: Brief Communication by Toettcher et al.
| | Review | Top | | | | Optical sectioning microscopy with planar or structured illumination pp811 - 819
Jerome Mertz
doi:10.1038/nmeth.1709
Presented is a Review of the principles and practice of optical sectioning microscopy using planar illumination or structured illumination with descriptions of the advantages and disadvantages of these techniques.
Abstract | Full Text | PDF
| | Resource | Top | | | | Proteomic and phosphoproteomic comparison of human ES and iPS cells pp821 - 827
Douglas H Phanstiel, Justin Brumbaugh, Craig D Wenger, Shulan Tian, Mitchell D Probasco, Derek J Bailey, Danielle L Swaney, Mark A Tervo, Jennifer M Bolin, Victor Ruotti, Ron Stewart, James A Thomson and Joshua J Coon
doi:10.1038/nmeth.1699
A comparison of the proteomes and phosphoproteomes of four human embryonic stem cell lines and four induced pluripotent stem cell lines is reported, revealing subtle differences in these cell types at the protein level. Also introduced is the Stem Cell-Omics Repository (SCOR), a database of quantitative information for transcripts, proteins and post-translational modifications.
Abstract | Full Text | PDF
See also: News and Views by Pera
| | Brief Communications | Top | | | | Induced pluripotent stem cells from highly endangered species pp829 - 831
Inbar Friedrich Ben-Nun, Susanne C Montague, Marlys L Houck, Ha T Tran, Ibon Garitaonandia, Trevor R Leonardo, Yu-Chieh Wang, Suellen J Charter, Louise C Laurent, Oliver A Ryder and Jeanne F Loring
doi:10.1038/nmeth.1706
Reprogramming to induced pluripotency of cells from the endangered silver-maned drill and the northern white rhinoceros is reported. Induced pluripotent stem cells from endangered species may prove useful for species preservation in the future.
Abstract | Full Text | PDF
See also: News and Views by Selvaraj et al.
| | | | FaST linear mixed models for genome-wide association studies pp833 - 835
Christoph Lippert, Jennifer Listgarten, Ying Liu, Carl M Kadie, Robert I Davidson and David Heckerman
doi:10.1038/nmeth.1681
An algorithm for linear mixed models substantially reduces memory usage and run time for genome-wide association studies. The improved algorithm scales linearly in cohort size, allowing the application of these models to much larger samples.
Abstract | Full Text | PDF
| | | | Light-based feedback for controlling intracellular signaling dynamics pp837 - 839
Jared E Toettcher, Delquin Gong, Wendell A Lim and Orion D Weiner
doi:10.1038/nmeth.1700
Feedback control of a light-gated protein-protein interaction is used to deliver precisely tuned intracellular signals to cultured cells.
Abstract | Full Text | PDF
See also: News and Views by Haugh
| | | | Toward the blood-borne miRNome of human diseases pp841 - 843
Andreas Keller, Petra Leidinger, Andrea Bauer, Abdou ElSharawy, Jan Haas, Christina Backes, Anke Wendschlag, Nathalia Giese, Christine Tjaden, Katja Ott, Jens Werner, Thilo Hackert, Klemens Ruprecht, Hanno Huwer, Junko Huebers, Gunnar Jacobs, Philip Rosenstiel, Henrik Dommisch, Arne Schaefer, Joachim Müller-Quernheim, Bernd Wullich, Bastian Keck, Norbert Graf, Joerg Reichrath, Britta Vogel, Almut Nebel, Sven U Jager, Peer Staehler, Ioannis Amarantos, Valesca Boisguerin, Cord Staehler, Markus Beier, Matthias Scheffler, Markus W Büchler, Joerg Wischhusen, Sebastian F M Haeusler, Johannes Dietl, Sylvia Hofmann, Hans-Peter Lenhof, Stefan Schreiber, Hugo A Katus, Wolfgang Rottbauer, Benjamin Meder, Joerg D Hoheisel, Andre Franke and Eckart Meese
doi:10.1038/nmeth.1682
Expression profiles of several hundred microRNAs in the blood of individuals with disease, including autoimmune disease, cancers, cardiovascular disease and chronic inflammatory disease are reported.
Abstract | Full Text | PDF
| | | | Quantitative proteomics by amino acid labeling in C. elegans pp845 - 847
Julius Fredens, Kasper Engholm-Keller, Anders Giessing, Dennis Pultz, Martin Røssel Larsen, Peter Højrup, Jakob Møller-Jensen and Nils J Færgeman
doi:10.1038/nmeth.1675
A method for performing quantitative proteomics experiments in Caenorhabditis elegans using stable-isotope labeling of lysine is described. The method can be coupled with RNA interference to examine global effects on the proteome. Also in this issue, Larance et al. describe a very similar method.
Abstract | Full Text | PDF
| | | | Stable-isotope labeling with amino acids in nematodes pp849 - 851
Mark Larance, Aymeric P Bailly, Ehsan Pourkarimi, Ronald T Hay, Grant Buchanan, Sarah Coulthurst, Dimitris P Xirodimas, Anton Gartner and Angus I Lamond
doi:10.1038/nmeth.1679
A method for performing quantitative proteomics experiments in Caenorhabditis elegans using stable-isotope labeling with amino acids in cell culture (SILAC) is described. The authors used the method to identify heat shock-responsive proteins in worms. Also in this issue, Fredens et al. describe a very similar method.
Abstract | Full Text | PDF
| | | Advertisement | | Intravital Imaging of a Mouse Ventral Skin-Flap Using the iBox® Explorer™ Imaging Microscope
Minimally invasive techniques allow macro to micro visualization of cellular behavior in vivo, enabling the understanding of metastasis in animal cancer models. With amazing resolution, the iBox® Explorer™ Imaging Microscope shows the transit of individual as well as clusters of fluorescent protein-expressing cancer cells within the systemic circulation of a live mouse. www.uvp.com/intravitalimagining |  |
| | | | Articles | Top | | | | Antiviral restriction factor transgenesis in the domestic cat pp853 - 859
Pimprapar Wongsrikeao, Dyana Saenz, Tommy Rinkoski, Takeshige Otoi and Eric Poeschla
doi:10.1038/nmeth.1703
This paper reports transgenesis by genetic modification of gametes in the domestic cat. The approach is used to generate transgenic cats expressing a virus restriction factor from rhesus macaque.
Abstract | Full Text | PDF
| | | | Site-specific integration and tailoring of cassette design for sustainable gene transfer pp861 - 869
Angelo Lombardo, Daniela Cesana, Pietro Genovese, Bruno Di Stefano, Elena Provasi, Daniele F Colombo, Margherita Neri, Zulma Magnani, Alessio Cantore, Pietro Lo Riso, Martina Damo, Oscar M Pello, Michael C Holmes, Philip D Gregory, Angela Gritti, Vania Broccoli, Chiara Bonini and Luigi Naldini
doi:10.1038/nmeth.1674
Presented is an experimental analysis of the stability of transgene expression, the perturbation of endogenous expression and the perturbation of epigenetic organization upon site-directed delivery of transgenes to the CCR5 and AAVS1 loci in human cells. It provides guidelines for optimal cassette design for stable and nonperturbative gene transfer.
Abstract | Full Text | PDF
| | | | Miniaturized integration of a fluorescence microscope pp871 - 878
Kunal K Ghosh, Laurie D Burns, Eric D Cocker, Axel Nimmerjahn, Yaniv Ziv, Abbas El Gamal and Mark J Schnitzer
doi:10.1038/nmeth.1694
An integrated, miniature (1.9 g) fluorescence microscope containing light source, optics and sensor allows high-speed, wide field of view imaging of calcium spiking in hundreds of neurons in freely moving mice. The mass-producible portable microscope is also useful for a variety of fluorescence assays for which size, cost and portability can be concerns.
Abstract | Full Text | PDF
| | | | Firefly luciferase mutants as sensors of proteome stress pp879 - 884
Rajat Gupta, Prasad Kasturi, Andreas Bracher, Christian Loew, Min Zheng, Adriana Villella, Dan Garza, F Ulrich Hartl and Swasti Raychaudhuri
doi:10.1038/nmeth.1697
Destabilized mutants of firefly luciferase are characterized as sensors for protein homeostasis (proteostasis). Their use as tools for comparisons of proteostasis capacity is demonstrated in cells and in Caenorhabditis elegans.
Abstract | Full Text | PDF
| | | Advertisement | | | | | | Application Notes | Top | | | | Stellaris™ fluorescence in situ hybridization (FISH) probes: a powerful tool for mRNA detection
Arturo Orjalo Jr., Hans E Johansson and Jerry L Ruth
Abstract | Full Text | PDF
| | | | EndoLISA®: a novel and reliable method for endotoxin detection
Holger Grallert, Sonja Leopoldseder, Maike Schuett, Peter Kurze and Bernd Buchberger
Abstract | Full Text | PDF
| | | Top | |  | | Advertisement | | Nature Reviews Molecular Cell Biology
Poster − From teratomas to embryonic stem cells: discovering pluripotency
This Poster provides a timeline overview of the history of pluripotency, starting from early studies of teratocarcinomas in 1954, which preceded the isolation of mouse and human ES cells, and ending with the generation of iPS cells. In doing so, it highlights how our understanding of the pluripotent state has evolved over almost 60 years.
Access the Poster FREE online!
Produced with support from:
Abcam Plc |
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