December 2008 Volume 5 Number 12, pp 989 - 1068
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SPECIAL ADVERTISING SECTION
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Application Notes Collection 2008
Special Feature
http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCY30Eg
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EDITORIAL
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Next-generation genome p989
Sequencing technology is now advanced enough to decode individual
human genomes. Will it prove to be better than existing methods for
discovering the genetic basis of human phenotypic variation?
doi:10.1038/nmeth1208-989
http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCY40Eh
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CORRESPONDENCE
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Much room for improvement in deposition rates of expression
microarray datasets p991
Scott A Ochsner, David L Steffen, Christian J Stoeckert, Jr and
Neil J McKenna
doi:10.1038/nmeth1208-991
http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCY50Ei
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RESEARCH HIGHLIGHTS
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Optical proteomics p993
Researchers describe a method for protein identification and
quantification based on electron-vibration-vibration two-dimensional
infrared spectroscopy.
Allison Doerr
doi:10.1038/nmeth1208-993
http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCY60Ej
DNA nanostructures go 'live' pp994 - 995
To scale up the production and complexity of DNA nanostructures,
researchers enlist the help of Escherichia coli to replicate and
assemble them in vivo.
Nicole Rusk
doi:10.1038/nmeth1208-994a
http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCY70Ek
No sunshine in a spotless mind? pp994 - 995
Chemical-genetic manipulation of enzyme activity allows specific
memory erasure in the mouse.
Natalie de Souza
doi:10.1038/nmeth1208-994b
http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCY80El
News in brief p995
doi:10.1038/nmeth1208-995
http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZA0Ev
Hotwiring protein regulation p996
An algorithm for identifying allosteric mechanisms allows researchers
to assemble a functional multidomain protein and may offer new
evolutionary insights.
Michael Eisenstein
doi:10.1038/nmeth1208-996
http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZB0Ew
Diamonds are a spectroscopist's best friend p998
A diamond impurity holds great promise for nanoscale magneto-optical
resonance imaging.
Allison Doerr
doi:10.1038/nmeth1208-998
http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZC0Ex
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NEWS AND VIEWS
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Proteome expression moves in vitro: resources and tools for
harnessing the human proteome pp1001 - 1002
Comprehensive sets of clones and improved high-throughput methods
for production of functional proteins now allow proteome-scale in
vitro experiments on nearly 15,000 human genes.
James L Hartley, Kourosh Salehi-Ashtiani and David E Hill
doi:10.1038/nmeth1208-1001
http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZD0Ey
On display on a bug: a systematic approach to characterize
antibodies pp1003 - 1004
Efficient methods to characterize the binding properties of affinity
reagents are required. A combination of bacterial surface display,
flow cytometry and pyrosequencing is now used for high-speed
mapping of the epitopes recognized by antibodies.
Thomas Knorpp and Markus F Templin
doi:10.1038/nmeth1208-1003
http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZE0Ez
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PERSPECTIVE
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A large genome center's improvements to the Illumina sequencing
system pp1005 - 1010
Michael A Quail et al.
doi:10.1038/nmeth.1270
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZF0E1
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZG0E2
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RESOURCE
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Human protein factory for converting the transcriptome into an in
vitro-expressed proteome pp1011 - 1017
A collection of 33,275 human Gateway entry clones and complementary
in vitro protein expression methodologies are described that allow
proteome-scale production of human proteins. This 'human protein
factory' was validated by expression of 13,364 human proteins and
assessment of activity in a variety of assays.
Naoki Goshima et al.
doi:10.1038/nmeth.1273
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZH0E3
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZI0E4
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BRIEF COMMUNICATIONS
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Intravital imaging of metastatic behavior through a mammary imaging
window pp1019 - 1021
The combination of a glass window placed on top of a mouse mammary
gland with photoswitchable fluorescent protein labeling of implanted
tumor cells allows tumor-cell tracking over multiple imaging sessions
in orthotopic tumors. Results show the existence of two distinct
microenvironments with different tumor-cell invasion and
intravasation characteristics.
Dmitriy Kedrin et al.
doi:10.1038/nmeth.1269
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZJ0E5
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZK0E6
Detecting microRNA binding and siRNA off-target effects from
expression data pp1023 - 1025
The algorithm Sylamer finds over- or underrepresented nucleotide
motifs, such as microRNA seeds, in a gene list ranked according to
expression levels and thus establishes whether a microRNA is directly
affecting gene expression.
Stijn van Dongen, Cei Abreu-Goodger and Anton J Enright
doi:10.1038/nmeth.1267
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZL0E7
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZM0E8
Nanoscale imaging of molecular positions and
anisotropies pp1027 - 1030
A simple modification to the optical configuration used for
fluorescence photoactivation localization microscopy (FPALM)
allows the fluorescence anisotropies of each individual molecule
in a nanoscale image to be measured. The method was used to
obtain position and orientation information for fluorescently labeled
actin or hemagglutinin molecules in fixed fibroblasts.
Travis J Gould et al.
doi:10.1038/nmeth.1271
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZN0EA
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZO0EB
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ARTICLES
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High-resolution statistical mapping reveals gene territories in live
yeast pp1031 - 1037
The spatial organization of the genome within the eukaryotic cell
nucleus is not random. Automated imaging of thousands of live
yeast is now used to build high-resolution probabilistic maps of
the locations occupied by individual loci.
Axel B Berger et al.
doi:10.1038/nmeth.1266
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZP0EC
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZQ0ED
Epitope mapping of antibodies using bacterial surface
display pp1039 - 1045
An efficient pipeline for mapping antibody epitopes is presented.
Combining bacterial surface display of peptide libraries, flow
cytometric sorting, and pyrosequencing, the approach is amenable
to a high-throughput format and should find future application in
whole-proteome studies.
Johan Rockberg et al.
doi:10.1038/nmeth.1272
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZR0EE
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZS0EF
Whole-cell 3D STORM reveals interactions between cellular structures
with nanometer-scale resolution pp1047 - 1052
Extension of multicolor three-dimensional stochastic optical
reconstruction microscopy (STORM) allows super-resolution
fluorescence imaging of whole cells and quantitative characterization
of subcellular structures and their spatial relationships. This was
demonstrated by imaging the entire mitochondrial and tubulin networks
in cells.
Bo Huang, Sara A Jones, Boerries Brandenburg and Xiaowei Zhuang
doi:10.1038/nmeth.1274
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZT0EG
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZU0EH
Micropatterning for quantitative analysis of protein-protein
interactions in living cells pp1053 - 1060
Co-patterning of a membrane protein bait and a fluorescently labeled
prey is used to examine protein-protein interactions in a
semiautomated fashion in living cells. Photobleaching experiments
and single-molecule imaging further allow dynamic studies of the
interaction.
Michaela Schwarzenbacher et al.
doi:10.1038/nmeth.1268
Abstract: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZV0EI
Article: http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZW0EJ
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TECHNOLOGY FEATURE
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Stem cells: finding the right path pp1061 - 1068
With increasing numbers of well-characterized stem cell lines and
improved culture and differentiation technologies, more scientists
are testing the waters of stem cell research.
Nathan Blow
doi:10.1038/nmeth1208-1061
http://ealerts.nature.com/cgi-bin24/DM/y/eo4q0Xztnp0Hi80CCZX0EK
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