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Eppendorf Award Winner 2011
In 2011 the prize was awarded to Assistant Professor Suzan Rooijakkers, PhD, (University Medical Center Utrecht, Department of Medical Microbiology, Utrecht, The Netherlands). Find out more about her research here.
If you want to apply for the Eppendorf Award 2012, click here. | |
| |  | TABLE OF CONTENTS
| December 2011 Volume 8, Issue 12 |  | | |  |  In This Issue
Editorial
This Month
Correspondence
Research Highlights
News in Brief
Technology Feature
News and Views
Perspective
Analysis
Brief Communications
Articles
Erratum
 Recommend to your library
 Web feed
 Available online only
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| | | | Advertisement | | Nature Biotechnology
Reprint collection on transcription activator–like (TAL) effector nucleases
Access this collection of articles describing the state of the TAL effector field by visiting: www.nature.com/nbt/collections/talen/index.html
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| | | | In This Issue |  Top | |  | | PDF
| | Editorial | Top | | | | Training the kit generation p983
doi:10.1038/nmeth.1804
Young scientists must learn not just how to use a kit, but how it works.
Full Text | PDF
| | This Month | Top | | | | The author file: Ernst Bamberg p985
Monya Baker
doi:10.1038/nmeth.1789
Fusing light-activated proteins for precise optogenetic control
Full Text | PDF
| | | | Points of view: The design process p987
Bang Wong
doi:10.1038/nmeth.1783
Full Text | PDF
| | Correspondence | Top | | | | The Human Epigenome Browser at Washington University pp989 - 990
Xin Zhou, Brett Maricque, Mingchao Xie, Daofeng Li, Vasavi Sundaram, Eric A Martin, Brian C Koebbe, Cydney Nielsen, Martin Hirst, Peggy Farnham, Robert M Kuhn, Jingchun Zhu, Ivan Smirnov, W James Kent, David Haussler, Pamela A F Madden, Joseph F Costello and Ting Wang
doi:10.1038/nmeth.1772
Full Text | PDF
| | | | Benchmarking a luciferase complementation assay for detecting protein complexes pp990 - 992
Patricia Cassonnet, Caroline Rolloy, Gregory Neveu, Pierre-Olivier Vidalain, Thibault Chantier, Johann Pellet, Louis Jones, Mandy Muller, Caroline Demeret, Guillaume Gaud, Françoise Vuillier, Vincent Lotteau, Fréderic Tangy, Michel Favre and Yves Jacob
doi:10.1038/nmeth.1773
Full Text | PDF
| | Research Highlights | Top | | | | | | News in Brief | Top | | | | Dark-state exchange saturation transfer | Inverted selective plane illumination microscopy | Oligonucleotide-selective sequencing | Simple xanthene dye synthesis | 'Mutate-and-map' RNA structure characterization
| Technology Feature | Top | | | | Faster frames, clearer pictures pp1005 - 1009
Monya Baker
doi:10.1038/nmeth.1777
Better-performing imaging sensors have arrived, but putting them to use is not easy.
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| | News and Views | Top | | | | The Lego-logic of optogenetics pp1011 - 1013
Thomas G Oertner
doi:10.1038/nmeth.1771
Daisy-chaining light-sensitive ion channels, pumps and fluorescent proteins extends the possibilities for control of neuronal activity.
Full Text | PDF
See also: Article by Kleinlogel et al.
| | | | Recognizing heart cells in a crowd pp1013 - 1016
Timothy J Kamp
doi:10.1038/nmeth.1780
A cardiac-specific reporter genetically engineered into human embryonic stem cells allows the optimization of differentiation protocols and the identification of cell-surface markers—a welcome new tool to help isolate and define cardiac cell lineages.
Full Text | PDF
See also: Brief Communication by Elliott et al.
| | | | Exciting times: bountiful data to facilitate studies of cis-regulatory control pp1016 - 1017
Anil Ozdemir and Angelike Stathopoulos
doi:10.1038/nmeth.1795
Chromatin immunoprecipitation and yeast one-hybrid systems are complementary approaches to identify protein-DNA interactions. Improvements to these methods now make them more versatile and high-throughput, and should lead to the generation of rich datasets for the study of gene regulation.
Full Text | PDF
See also: Article by Reece-Hoyes et al. | Article by Hens et al. | Brief Communication by Reece-Hoyes et al. | Brief Communication by Gaudinier et al. | Brief Communication by Mazzoni et al.
| | Perspective | Top | | | | Directed molecular evolution to design advanced red fluorescent proteins pp1019 - 1026
Fedor V Subach, Kiryl D Piatkevich and Vladislav V Verkhusha
doi:10.1038/nmeth.1776
In this Perspective the authors discuss strategies for the development of improved fluorescent proteins, with a focus on probes at the red end of the spectrum. They synthesize the literature on chromophore photochemistry and protein structure to identify residues for targeted mutagenesis, and consider improvements in molecular evolution methodologies to enable improved screening for desired probes.
Abstract | Full Text | PDF
| | Analysis | Top | | | | Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging pp1027 - 1036
Graham T Dempsey, Joshua C Vaughan, Kok Hao Chen, Mark Bates and Xiaowei Zhuang
doi:10.1038/nmeth.1768
A quantitative characterization of the switching properties of 26 organic dyes relates these properties to the quality of localization-based super-resolution images they generate. The data are a useful resource for selecting dyes and point to avenues for future analysis.
Abstract | Full Text | PDF
| | Brief Communications | Top | | | | NKX2-5eGFP/w hESCs for isolation of human cardiac progenitors and cardiomyocytes pp1037 - 1040
David A Elliott, Stefan R Braam, Katerina Koutsis, Elizabeth S Ng, Robert Jenny, Ebba L Lagerqvist, Christine Biben, Tanya Hatzistavrou, Claire E Hirst, Qing C Yu, Rhys J P Skelton, Dorien Ward-van Oostwaard, Sue Mei Lim, Ouda Khammy, Xueling Li, Susan M Hawes, Richard P Davis, Adam L Goulburn, Robert Passier, Owen W J Prall, John M Haynes, Colin W Pouton, David M Kaye, Christine L Mummery, Andrew G Elefanty and Edouard G Stanley
doi:10.1038/nmeth.1740
A human embryonic stem cell line expressing a fluorescent reporter of cardiac differentiation is described. The authors use this tool to optimize differentiation methods and to identify cell-surface markers in the cardiac lineage.
Abstract | Full Text | PDF
See also: News and Views by Kamp
| | | | Rapid empirical discovery of optimal peptides for targeted proteomics pp1041 - 1043
Andrew B Stergachis, Brendan MacLean, Kristen Lee, John A Stamatoyannopoulos and Michael J MacCoss
doi:10.1038/nmeth.1770
An empirical approach for identifying optimal proteotypic peptides and fragmentation patterns from in vitro-synthesized proteins, for targeted proteomics applications, is described.
Abstract | Full Text | PDF
| | | | Super-resolution 3D microscopy of live whole cells using structured illumination pp1044 - 1046
Lin Shao, Peter Kner, E Hesper Rego and Mats G L Gustafsson
doi:10.1038/nmeth.1734
Live-cell volumetric super-resolution imaging with 120-nm lateral and 360-nm axial resolution using structured-illumination microscopy at speeds of up to 5 s per cell volume over >50 time points captures fine cellular dynamics using only low illumination intensities.
Abstract | Full Text | PDF
| | | | Live-cell 3D super-resolution imaging in thick biological samples pp1047 - 1049
Francesca Cella Zanacchi, Zeno Lavagnino, Michela Perrone Donnorso, Alessio Del Bue, Laura Furia, Mario Faretta and Alberto Diaspro
doi:10.1038/nmeth.1744
The combination of light-sheet microscopy and localization-based super-resolution imaging allows deep subdiffraction resolution imaging in thick scattering specimens as demonstrated by three-dimensional super-resolution imaging of proteins in live 150-μm-diameter cell spheroids.
Abstract | Full Text | PDF
| | | | Yeast one-hybrid assays for gene-centered human gene regulatory network mapping pp1050 - 1052
John S Reece-Hoyes, A Rasim Barutcu, Rachel Patton McCord, Jun Seop Jeong, Lizhi Jiang, Andrew MacWilliams, Xinping Yang, Kourosh Salehi-Ashtiani, David E Hill, Seth Blackshaw, Heng Zhu, Job Dekker and Albertha J M Walhout
doi:10.1038/nmeth.1764
A sequence-verified collection of human transcription factors is reported. The authors used it in the enhanced yeast-one hybrid (eY1H) assay to map human gene regulatory networks. Also in this issue, Reece-Hoyes et al. describe the eY1H pipeline.
Abstract | Full Text | PDF
See also: News and Views by Ozdemir & Stathopoulos
| | | | Enhanced Y1H assays for Arabidopsis pp1053 - 1055
Allison Gaudinier, Lifang Zhang, John S Reece-Hoyes, Mallorie Taylor-Teeples, Li Pu, Zhijie Liu, Ghislain Breton, Jose L Pruneda-Paz, Dahae Kim, Steve A Kay, Albertha J M Walhout, Doreen Ware and Siobhan M Brady
doi:10.1038/nmeth.1750
An almost-complete, sequence-verified collection of Arabidopsis thaliana root stele transcription factors is reported. The authors use it in the enhanced yeast-one hybrid (eY1H) assay to map gene regulatory interactions in the plant. Also in this issue, Reece-Hoyes et al. describe the eY1H pipeline.
Abstract | Full Text | PDF
See also: News and Views by Ozdemir & Stathopoulos
| | | | Embryonic stem cell-based mapping of developmental transcriptional programs pp1056 - 1058
Esteban O Mazzoni, Shaun Mahony, Michelina Iacovino, Carolyn A Morrison, George Mountoufaris, Michael Closser, Warren A Whyte, Richard A Young, Michael Kyba, David K Gifford and Hynek Wichterle
doi:10.1038/nmeth.1775
Presented is a study of gene regulation during development using a combination of chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq) and directed differentiation of mouse embryonic stem cells inducibly expressing epitope-tagged transcription factors.
Abstract | Full Text | PDF
See also: News and Views by Ozdemir & Stathopoulos
| | | Advertisement | | | | | | Articles | Top | | | | Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping pp1059 - 1064
John S Reece-Hoyes, Alos Diallo, Bryan Lajoie, Amanda Kent, Shaleen Shrestha, Sreenath Kadreppa, Colin Pesyna, Job Dekker, Chad L Myers and Albertha J M Walhout
doi:10.1038/nmeth.1748
The authors describe the enhanced yeast one-hybrid platform for large-scale screening of protein-DNA interactions and test its performance by mapping Caenorhabditis elegans gene regulatory networks. Also in this issue, Hens et al. describe an alternative platform for this purpose and apply it to screen for transcription factor-DNA interactions in Drosophila melanogaster.
Abstract | Full Text | PDF
See also: News and Views by Ozdemir & Stathopoulos
| | | | Automated protein-DNA interaction screening of Drosophila regulatory elements pp1065 - 1070
Korneel Hens, Jean-Daniel Feuz, Alina Isakova, Antonina Iagovitina, Andreas Massouras, Julien Bryois, Patrick Callaerts, Susan E Celniker and Bart Deplancke
doi:10.1038/nmeth.1763
Described is a high-throughput yeast one-hybrid platform for mapping protein-DNA interactions and a sequence-verified clone collection of Drosophila transcription factors. Also in this issue, Reece-Hoyes et al. report enhanced yeast one-hybrid assays, an alternative system for large-scale protein-DNA interaction screens.
Abstract | Full Text | PDF
See also: News and Views by Ozdemir & Stathopoulos
| | | | A homozygous mutant embryonic stem cell bank applicable for phenotype-driven genetic screening pp1071 - 1077
Kyoji Horie, Chikara Kokubu, Junko Yoshida, Keiko Akagi, Ayako Isotani, Akiko Oshitani, Kosuke Yusa, Ryuji Ikeda, Yue Huang, Allan Bradley and Junji Takeda
doi:10.1038/nmeth.1739
This paper describes a method to enrich for homozygous mutant mouse embryonic stem cells without an inherently selectable phenotype. It is used to construct a bank of homozygous and heterozygous mutant cells and should prove useful for cellular phenotypic screens.
Abstract | Full Text | PDF
| | | | A scalable pipeline for highly effective genetic modification of a malaria parasite pp1078 - 1082
Claudia Pfander, Burcu Anar, Frank Schwach, Thomas D Otto, Mathieu Brochet, Katrin Volkmann, Michael A Quail, Arnab Pain, Barry Rosen, William Skarnes, Julian C Rayner and Oliver Billker
doi:10.1038/nmeth.1742
Reported is a recombineering pipeline for efficient and large-scale gene modification in the mouse malarial parasite Plasmodium berghei.
Abstract | Full Text | PDF
| | | | A gene-fusion strategy for stoichiometric and co-localized expression of light-gated membrane proteins pp1083 - 1088
Sonja Kleinlogel, Ulrich Terpitz, Barbara Legrum, Deniz Gökbuget, Edward S Boyden, Christian Bamann, Phillip G Wood and Ernst Bamberg
doi:10.1038/nmeth.1766
Molecular engineering allows stoichiometric and co-localized expression of two optogenetic actuators, spaced by a fluorescent protein and an additional transmembrane helix in a single protein fusion. The method provides modular optogenetic tools for bidirectional membrane potential control or synergistic effects on neuronal activity.
Abstract | Full Text | PDF
See also: News and Views by Oertner
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| | | | Erratum | Top | | | | Sorting out sequencing data p1089
Monya Baker
doi:10.1038/nmeth1211-1089
Full Text | PDF
| | | Top | |  | | Advertisement | | Nature Reprint Collection
Technology Features
This Collection offers a special compilation of popular Technology Features that have appeared in Nature and Nature Methods throughout the year.
To access the Collection and Articles online for free, click here. |
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