June 2009 Volume 6 Number 6, pp 395 - 469
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FREE ARTICLE
Novel strategies for HIV therapy
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Two research teams are proposing the use of known compounds-the mild surfactant glycerol monolaurate and a protein called griffithsin that could be scaled up in tobacco-be used to block distinct steps in the early stages of HIV infection. Both teams already have commercial links but what challenges lay ahead?
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EDITORIAL
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No fruit fly an island? p395
Methods to study the behavior of Drosophila sp. in the context
of a group may deepen our understanding of the neural mechanisms
underlying social behavior.
doi:10.1038/nmeth0609-395
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CORRESPONDENCE
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Predicting microRNA targets and functions: traps for the
unwary pp397 - 398
William Ritchie, Stephane Flamant and John E J Rasko
doi:10.1038/nmeth0609-397
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RESEARCH HIGHLIGHTS
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Snapshots of the cell surface p401
Researchers develop an approach to selectively isolate and profile
cell-surface proteins by targeting the glycopeptides, a strategy that
could be used to generate an atlas of cell-surface protein
'barcodes'.
Allison Doerr
doi:10.1038/nmeth0609-401
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Micro-reprogramming pp402 - 403
Researchers use microRNAs to more efficiently generate induced
pluripotent stem cells in the mouse.
Natalie de Souza
doi:10.1038/nmeth0609-402a
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A functional blueprint of E. coli pp402 - 403
Researchers integrate proteomics data with genomic-context analysis
and develop a protein-function prediction tool to annotate functional
orphans in Escherichia coli.
Allison Doerr
doi:10.1038/nmeth0609-402b
http://links.ealert.nature.com/ctt?kn=33&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
News in brief p403
doi:10.1038/nmeth0609-403
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Nature's pH meter p404
A new pH nanosensor changes color in acidic cell compartments by
forming an unusual four-stranded DNA structure.
Wayne Peng
doi:10.1038/nmeth0609-404
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TACLing rare genetic variants p406
By combining methods for selective genome capture, allele enrichment
and array resequencing, researchers create a pipeline for
high-throughput variant detection.
Nicole Rusk
doi:10.1038/nmeth0609-406
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Flight patterns p408
Flying animals ranging from bugs to bats use a common mechanism to
maintain control in turns a discovery that reveals hidden advantages
of flapping-wing flight.
Michael Eisenstein
doi:10.1038/nmeth0609-408
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NEWS AND VIEWS
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A stress test for mass spectrometry-based proteomics pp411 - 412
A multilaboratory study attempts to dispel some of the notions of the
irreproducibility of mass spectrometry-based proteomics by
pinpointing where the methodological problems are and where
challenges remain.
Ruedi Aebersold
doi:10.1038/nmeth.f.255
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The ethomics era? pp413 - 414
Applying modern machine-vision techniques to the study of animal
behavior, two groups developed systems that quantify many aspects
of the complex social behaviors of Drosophila melanogaster. These
software tools will enable high-throughput screens that seek to
uncover the cellular and molecular underpinnings of behavior.
Michael Reiser
doi:10.1038/nmeth0609-413
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REVIEW
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Transposon-mediated genome manipulation in vertebrates pp415 - 422
Zoltan Ivics et al.
doi:10.1038/nmeth.1332
Abstract: http://links.ealert.nature.com/ctt?kn=102&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
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ANALYSIS
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A HUPO test sample study reveals common problems in mass
spectrometry-based proteomics pp423 - 430
A multilaboratory analysis characterized the ability of 27 different
labs to identify 20 proteins at equimolar concentrations in a highly
purified test sample mixture using mass spectrometry. The results
show that while the technology is reproducible, many common
experimental problems arise, and improved search engines
and databases are still needed.
Alexander W Bell et al.
doi:10.1038/nmeth.1333
Abstract: http://links.ealert.nature.com/ctt?kn=127&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
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BRIEF COMMUNICATIONS
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Versatile P[acman] BAC libraries for transgenesis studies in
Drosophila melanogaster pp431 - 434
Two bacterial artificial chromosome (BAC) libraries, spanning almost
the entire D. melanogaster genome in insert sizes of 20 and 80 kb,
that allow easy integration into the fruit fly genome at defined
docking sites provide a rich resource to study gene expression
and function.
Koen J T Venken et al.
doi:10.1038/nmeth.1331
Abstract: http://links.ealert.nature.com/ctt?kn=53&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
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A toolkit for high-throughput, cross-species gene engineering in
Drosophila pp435 - 437
Genomic fosmid libraries for Drosophila melanogaster and Drosophila
pseudoobscura with an average insert size of 36 kilobases can easily
be tagged and inserted into the fly genome. These resources will be
valuable for evolutionary and developmental studies in the fly.
Radoslaw K Ejsmont et al.
doi:10.1038/nmeth.1334
Abstract: http://links.ealert.nature.com/ctt?kn=131&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=97&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
TU-tagging: cell type-specific RNA isolation from intact complex
tissues pp439 - 441
Expressing uracil phosphoribosyltransferase in specific tissues in
the fly allows the incorporation of 4-thiouracil into newly
synthesized RNA in vivo. The thio-labeled RNA can then be isolated
and analyzed by routine procedures allowing the cell type-specific
measure of RNA synthesis and decay rates.
Michael R Miller, Kristin J Robinson, Michael D Cleary and Chris
Q Doe
doi:10.1038/nmeth.1329
Abstract: http://links.ealert.nature.com/ctt?kn=144&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
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Rapid creation and quantitative monitoring of high coverage shRNA
libraries pp443 - 445
On-array synthesis of over 20,000 shRNAs at a coverage of ~30
shRNAs per gene, followed by cloning into lentiviral shRNA libraries
and deconvolution of the complex libraries by deep sequencing,
ensures high confidence in the observed knockdown phenotypes
with low false-negative rates and few off-target hits.
Michael C Bassik et al.
doi:10.1038/nmeth.1330
Abstract: http://links.ealert.nature.com/ctt?kn=27&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
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Automated unrestricted multigene recombineering for multiprotein
complex production pp447 - 450
A modular, automatable system using recombineering to facilitate
multigene assembly, called Acembl, provides a streamlined approach
for expressing multiprotein complexes in Escherichia coli.
Christoph Bieniossek et al.
doi:10.1038/nmeth.1326
Abstract: http://links.ealert.nature.com/ctt?kn=174&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
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ARTICLES
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High-throughput ethomics in large groups of Drosophila pp451 - 457
An automated system for tracking large numbers of fruit flies over
time and for detecting their behaviors is presented, and should allow
high-throughput quantitative studies of fly behavior.
Kristin Branson et al.
doi:10.1038/nmeth.1328
Abstract: http://links.ealert.nature.com/ctt?kn=82&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=166&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
Tissue tectonics: morphogenetic strain rates, cell shape change and
intercalation pp458 - 464
As tissues mature, they undergo shape changes that are the result of
individual and collective cell movement triggered by cell-autonomous
behavior or external forces. By measuring patterns of strain rates
the authors can model these forces and quantify tissue shaping
behavior.
Guy B Blanchard et al.
doi:10.1038/nmeth.1327
Abstract: http://links.ealert.nature.com/ctt?kn=179&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=79&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
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TECHNOLOGY FEATURE
----------------------
In vivo molecular imaging: the inside job pp465 - 469
In a short period of time, in vivo molecular imaging systems have
become indispensable research tools in many clinical and basic
research laboratories. But developers are now pushing the technology
further in the hopes of making a new generation of platforms with
greater accuracy and sensitivity for a wider array of applications.
Nathan Blow
doi:10.1038/nmeth0609-465
http://links.ealert.nature.com/ctt?kn=96&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
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APPLICATION NOTES
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Characterization of phosphoprotein signaling in limited biological
samples using the Cell Biosciences CB1000
David W Voehringer and Walter A Ausserer
Abstract: http://links.ealert.nature.com/ctt?kn=116&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
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Automated selection and collection of pluripotent stem cell colonies
using the CellCelectorTM
Simone Haupt et al.
Abstract: http://links.ealert.nature.com/ctt?kn=160&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=176&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
Kodak X-Sight 761 Nanospheres effectively label living cells for
longitudinal cell tracking in mice
W Matthew Leevy et al.
Abstract: http://links.ealert.nature.com/ctt?kn=146&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
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Mutation profiling in tumor samples using the Sequenom
OncoCartaTM Panel
Marisa Pearce et al.
Abstract: http://links.ealert.nature.com/ctt?kn=136&m=33324821&r=MTc2NjExMzUwMAS2&b=2&j=NTA2MDUyMzMS1&mt=1&rt=0
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