NATURE METHODS
November 2008 Volume 5 Number 11, pp 911 - 988
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EDITORIAL
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Looking back and moving forward p911
The fourth anniversary of Nature Methods' arrival on the publishing
scene and a change in leadership offer an opportunity for reflection
and editorial fine-tuning.
doi:10.1038/nmeth1108-911
http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B8z50EZ
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CORRESPONDENCE
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A database of mass spectrometric assays for the yeast
proteome pp913 - 914
Paola Picotti et al.
doi:10.1038/nmeth1108-913
http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B8z60Ea
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RESEARCH HIGHLIGHTS
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Finding copy-number variants p917
Several studies evaluate high-density single-nucleotide polymorphism
(SNP) arrays for the detection of copy-number variations in human
genomes.
Nicole Rusk
doi:10.1038/nmeth1108-917
http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B8z70Eb
SNPing away at anonymity pp918 - 919
New findings challenge the assumption that aggregate genotype data,
in which the single-nucleotide polymorphism (SNP) profiles of many
people are pooled, conceal the identity of the individuals within
that pool.
Natalie de Souza
doi:10.1038/nmeth1108-918a
http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B8z80Ec
Evolving a better-expressing GPCR pp918 - 919
Researchers describe a method for evolving G protein-coupled
receptors (GPCRs) with greater stability and enhanced expression.
Allison Doerr
doi:10.1038/nmeth1108-918b
http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81A0EY
News in brief p919
doi:10.1038/nmeth1108-919
http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81B0EZ
Fighting fire with fire p920
A co-infection model of two pathogens in a nematode yields insights
into the complex interaction between the microbes.
Nicole Rusk
doi:10.1038/nmeth1108-920
http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81C0Ea
Microfluidics, microscopy and modeling p922
Researchers use microfluidics, a fluorescent reporter and modeling
to quantify yeast's response to glucose availability.
Allison Doerr
doi:10.1038/nmeth1108-922
http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81D0Eb
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NEWS AND VIEWS
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New views into the brain of mice on the move pp925 - 926
A portable fiber-optic epifluorescence microscope allows real-time
imaging of brain function with cellular spatial resolution in freely
moving mice.
Fritjof Helmchen and Carl C H Petersen
doi:10.1038/nmeth1108-925
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PERSPECTIVE
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Native mass spectrometry: a bridge between interactomics and
structural biology pp927 - 933
Albert J R Heck
doi:10.1038/nmeth.1265
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81F0Ed
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81G0Ee
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BRIEF COMMUNICATIONS
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High-speed, miniaturized fluorescence microscopy in freely
moving mice pp935 - 938
A miniature epifluorescence microscope that can be carried by a
freely-moving adult mouse allows cellular-level imaging of neuronal
spiking or measurement of microcirculation during normal behavioral
activities.
Benjamin A Flusberg et al.
doi:10.1038/nmeth.1256
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81H0Ef
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81I0Eg
Directed enzyme evolution via small and effective neutral drift
libraries pp939 - 942
Directed evolution experiments usually rely on high-throughput
screening of very large libraries of mutants, but most of the mutants
do not even yield stable, functional proteins. The concept of neutral
drift can be used to generate small but highly polymorphic and stable
mutant libraries as a starting point for further evolution.
Rinkoo D Gupta and Dan S Tawfik
doi:10.1038/nmeth.1262
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81J0Eh
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81K0Ei
Fluorescence nanoscopy by ground-state depletion and single-molecule
return pp943 - 945
A simple yet powerful super-resolution imaging approach based on
switching off ordinary fluorophores and localizing those remaining or
regaining fluorescence is illustrated using continuous widefield
illumination and imaging of fixed and living cells labeled with
rhodamine-derived dyes or fluorescent proteins. Biteen et al., also
in this issue, describe related work using the ordinary fluorophore
of EYFP for super-resolution imaging.
Jonas Folling et al.
doi:10.1038/nmeth.1257
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81L0Ej
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81M0Ek
Super-resolution imaging in live Caulobacter crescentus cells using
photoswitchable EYFP pp947 - 949
Previous work showed that the commonly used fluorescent protein
EYFP can be bleached and reactivated. Exploiting this property allows
super-resolution in vivo imaging of EYFP-labeled structures in living
bacteria. Folling et al., also in this issue, describe a related approach
for super-resolution imaging using other ordinary fluorophores.
Julie S Biteen et al.
doi:10.1038/nmeth.1258
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81N0El
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81O0Em
Linking SNPs to CAG repeat length in Huntington's disease
patients pp951 - 953
To determine long-range linkage between single-nucleotide
polymorphisms (SNPs) and the repeat-containing region of a
disease-related gene, Liu et al. develop SNP linkage by
circularization (SLiC) and lay the groundwork for using
allele-specific RNA interference to target insertion or deletion
mutations in disease-associated genes.
Wanzhao Liu et al.
doi:10.1038/nmeth.1261
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81P0En
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81Q0Eo
A noncytotoxic DsRed variant for whole-cell labeling pp955 - 957
Many different red fluorescent proteins display cytotoxicity
substantially higher than EGFP when used for whole-cell labeling
of bacterial and mammalian cells with standard high-level expression
systems. An improved tetrameric red fluorescent protein called
DsRed-Express2 allows high-level labeling with minimal cytotoxicity
comparable to that of EGFP.
Rita L Strack et al.
doi:10.1038/nmeth.1264
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81R0Ep
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81S0Eq
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ARTICLES
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Decision tree-driven tandem mass spectrometry for shotgun
proteomics pp959 - 964
The two major mechanisms for peptide fragmentation by mass
spectrometry, collision-activated dissociation (CAD) or a newer
method, electron transfer dissociation (ETD), display different
efficacies for different peptide chemistries. A decision tree
algorithm, which can be embedded into instruments with both CAD
and ETD capabilities, selects the optimal fragmentation method to
improve the chances of successful peptide identification.
Danielle L Swaney, Graeme C McAlister and Joshua J Coon
doi:10.1038/nmeth.1260
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81T0Er
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81U0Es
A nano-positioning system for macromolecular structural
analysis pp965 - 971
The combination of single-molecule fluorescence resonance energy
transfer measurements of multiple dye pairs with probabilistic data
analysis allows quantitative measurement of the position of flexible
domains in macro-molecular complexes. The method was used to
determine the three-dimensional probability density of the position
of RNA exiting the transcription elongation complex.
Adam Muschielok et al.
doi:10.1038/nmeth.1259
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81V0Et
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81W0Eu
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PROTOCOL
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Correlative light-electron microscopy (CLEM) combining live-cell
imaging and immunolabeling of ultrathin cryosections pp973 - 980
Carolien van Rijnsoever, Viola Oorschot and Judith Klumperman
doi:10.1038/nmeth.1263
http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81Y0Ew
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TECHNOLOGY FEATURE
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Neuroscience tools: brain insights pp981 - 987
Researchers at two Boston-based neuroscience centers are working to
develop new imaging tools and technology with the hope of discovering
the secrets behind how the brain functions.
Nathan Blow
doi:10.1038/nmeth1108-981
http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81Z0Ex
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ERRATUM
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Erratum: Tracking the structural dynamics of proteins in solution
using time-resolved wide-angle X-ray scattering p988
Marco Cammarata et al.
doi:10.1038/nmeth1108-988
http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81a0E5
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APPLICATION NOTES
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Transiently produced recombinant proteins to speed up the
decision-making process and limit risks
Andre Sobczyk, Flavien Carpentier and Sebastien Paris
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81b0E6
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81c0E7
Harnessing multimodality to enhance quantification and
reproducibility of in vivo molecular imaging data
Gilbert D Feke et al.
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81d0E8
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81e0EA
Bioluminescence microscopy for cellular level circadian analysis
in the suprachiasmatic nucleus
Werner Kammerloher
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81f0EB
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eoUn0Xztnp0Hi80B81g0EC
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