October 2008 Volume 5 Number 10, pp 853 - 879
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EDITORIAL
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Elective affinities p851
A feasibility study for the systematic generation of affinity
reagents to human proteins provides an opportunity to test
the merits of recombinant affinity reagents.
doi:10.1038/nmeth1008-851
http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eK0E4
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CORRESPONDENCE
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Large-scale evaluation of protein reductive methylation for improving
protein crystallization pp853 - 854
Youngchang Kim et al.
doi:10.1038/nmeth1008-853
http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eL0E5
A pilot project to generate affinity reagents to human
proteins pp854 - 855
Mathias Uhlen, Susanne Graslund and Michael Sundstrom
doi:10.1038/nmeth1008-854
http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eM0E6
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RESEARCH HIGHLIGHTS
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Microbes right on target p857
Researchers use a targeted metagenomic approach to functionally
characterize complex microbial communities.
Michelle Pflumm
doi:10.1038/nmeth1008-857
http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eN0E7
New twists on photoswitchable proteins pp858 - 859
Fluorescent proteins with new photoswitching properties allow
multilabel imaging at a single detection wavelength and dual-color
superresolution microscopy.
Natalie de Souza
doi:10.1038/nmeth1008-858a
http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eO0E8
Phosphorylation and the cell cycle pp858 - 859
Two groups used quantitative mass spectrometry to look at changes
in protein phosphorylation across the cell cycle.
Allison Doerr
doi:10.1038/nmeth1008-858b
http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eP0EA
News in brief p859
doi:10.1038/nmeth1008-859
http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eQ0EB
Antibodypedia p860
A web portal to share antibody validation data.
Veronique Kiermer
doi:10.1038/nmeth1008-860
http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eR0EC
A surrogate scaffold tested p861
Researchers tested an alternate antibody scaffold, creating so-called
Surrobodies.
Irene Kaganman
doi:10.1038/nmeth1008-861
http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eS0ED
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NEWS AND VIEWS
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Classical genetics goes high-tech pp863 - 864
A combination of automated screening and next-generation sequencing
makes it possible to identify Caenorhabditis elegans mutants
at unprecedented speed and scale.
David S Fay
doi:10.1038/nmeth1008-863
http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eT0EE
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BRIEF COMMUNICATIONS
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Caenorhabditis elegans mutant allele identification by
whole-genome sequencing pp865 - 867
Identifying the molecular lesions in mutants isolated in forward
genetic screens can be a laborious process. A proof-of-principle
study in Caenorhabditis elegans now shows that this can be achieved
rapidly by whole-genome deep sequencing.
Sumeet Sarin et al.
doi:10.1038/nmeth.1249
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eU0EF
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eV0EG
Automated screening for mutants affecting dopaminergic-neuron
specification in C. elegans pp869 - 872
An automated sorting method using the COPAS Biosort machine
allows the isolation of mutant C. elegans displaying differences in
GFP expression in small numbers of cells. Compared to manual methods
this increases the efficiency of the phenotypic selection step in
cell-fate screens.
Maria Doitsidou et al.
doi:10.1038/nmeth.1250
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eW0EH
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eX0EI
Building consensus spectral libraries for peptide identification in
proteomics pp873 - 875
Spectral searching, based on matching experimental peptide spectra
to reference spectral libraries, is gaining interest as an
alternative to traditional sequence-database searching in mass
spectrometry-based proteomics. A software tool, SpectraST, now allows
users to build their own high-quality spectral libraries from raw data.
Henry Lam et al.
doi:10.1038/nmeth.1254
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eY0EJ
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eZ0EK
Imaging individual mRNA molecules using multiple singly labeled
probes pp877 - 879
A strategy using 48 or more singly labeled fluorescent
oligonucleotide probes targeted to individual mRNA molecules allows
the simultaneous localization and quantification of three mRNA
species in fixed cells. mRNA visualization in whole animals and other
organisms is also demonstrated.
Arjun Raj et al.
doi:10.1038/nmeth.1253
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6ea0ER
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eb0ES
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ARTICLES
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Tracking the structural dynamics of proteins in solution using
time-resolved wide-angle X-ray scattering pp881 - 886
Time-resolved wide-angle X-ray scattering (TR-WAXS) using
synchrotron radiation can be used to observe dynamic protein
structural changes with nanosecond time resolution in solution,
complementing time-resolved optical spectroscopy and Laue
crystallography methods.
Marco Cammarata et al.
doi:10.1038/nmeth.1255
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6ec0ET
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6ed0EU
Identification of genetic variants using bar-coded multiplexed
sequencing pp887 - 893
Targeted regions of the human genome are resequenced in multiplex
with Illumina technology, and the pipeline is evaluated for
polymorphism discovery and genotyping.
David W Craig et al.
doi:10.1038/nmeth.1251
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6ee0EV
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6ef0EW
Optogenetic analysis of synaptic function pp895 - 902
Using both behavioral and electrophysiological readouts,
Channelrhodopsin-2, a light-gated cation channel, is applied
to the study of synaptic function in Caenorhabditis elegans.
Jana F Liewald et al.
doi:10.1038/nmeth.1252
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eg0EX
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6eh0EY
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TECHNOLOGY FEATURE
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Scientific software: seeing the SNPs between us pp903 - 908
The results of large genome-wide association studies (GWASs) are
being deposited in public databases with increasing frequency. But
the software to analyze and interpret GWAS datasets can be difficult
to use. Could a new generation of user-friendly programs fill
the gap?
Steven David Buckingham
doi:10.1038/nmeth1008-903
http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6ei0EZ
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ERRATUM
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Erratum: Mass spectrometry and proteomics: hitting the mark p910
Nathan Blow
doi:10.1038/nmeth1008-910
http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6ej0Ea
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APPLICATION NOTES
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Development of an Eg5 assay using the HTRFreg Transcreenerreg ADP kit
Laurence Jacquemart, Marion De Decker and Bastien Caumes
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6ek0Eb
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6el0Ec
Rapid, on-demand protein stabilization and destabilization using the ProteoTunertrade systems
Michael Haugwitz et al.
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6em0Ed
Article: http://ealerts.nature.com/cgi-bin24/DM/y/enp70Xztnp0Hi80B6en0Ee
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