NATURE METHODS
August 2009 Volume 6 Number 8, pp 547 - 622
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EDITORIALS
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Method of the Year 2009 voting begins p547
We are now accepting nominations and collecting votes
for the Method of the Year 2009.
doi:10.1038/nmeth0809-547a
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Software by any name pp547 - 548
Computational biologists are often tempted to avoid providing
a named software implementation of their new algorithm, but
resisting this temptation helps avoid difficulties later on and
benefits the wider community of biologists.
doi:10.1038/nmeth0809-547b
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CORRESPONDENCE
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MAQGene: software to facilitate C. elegans mutant genome sequence
analysis p549
Henry Bigelow, Maria Doitsidou, Sumeet Sarin and Oliver Hobert
doi:10.1038/nmeth.f.260
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SHOREmap: simultaneous mapping and mutation identification by deep
sequencing pp550 - 551
Korbinian Schneeberger et al.
doi:10.1038/nmeth0809-550
http://links.ealert.nature.com/ctt?kn=79&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Sub-angstrom accuracy in protein loop reconstruction by
robotics-inspired conformational sampling pp551 - 552
Daniel J Mandell, Evangelos A Coutsias and Tanja Kortemme
doi:10.1038/nmeth0809-551
http://links.ealert.nature.com/ctt?kn=74&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
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RESEARCH HIGHLIGHTS
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Mass spectrometers on a chip p555
A prototype for a mass spectrometer with single-molecule sensitivity
has prospects for single-cell proteomics.
Allison Doerr
doi:10.1038/nmeth0809-555
http://links.ealert.nature.com/ctt?kn=55&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Actions speak louder pp556 - 557
A fluorescence resonance energy transfer (FRET)-based biosensor
helps scientists monitor the activation of an essential signaling
protein over the course of embryogenesis in Drosophila melanogaster.
Michael Eisenstein
doi:10.1038/nmeth0809-556a
http://links.ealert.nature.com/ctt?kn=130&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
New shapes of prions pp556 - 557
Modification of a system for rapid amplification of misfolded prion
proteins allows de novo generation of these infectious molecules
and provides a glimpse of the diverse range of possible misfolded
prion strains.
Irene Kaganman
doi:10.1038/nmeth0809-556b
http://links.ealert.nature.com/ctt?kn=71&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
News in brief p557
doi:10.1038/nmeth0809-557
http://links.ealert.nature.com/ctt?kn=113&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Network countdown p558
Researchers lay the foundation for networks that will self-destruct
after being exposed to a predetermined number of stimuli.
Nicole Rusk
doi:10.1038/nmeth0809-558
http://links.ealert.nature.com/ctt?kn=14&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Clinical proteomics on target p560
A multilaboratory study designed to assess the reproducibility of
multiple reaction monitoring (MRM) mass spectrometry-based proteomics
demonstrates the promise of this technology for disease biomarker
verification.
Allison Doerr
doi:10.1038/nmeth0809-560
http://links.ealert.nature.com/ctt?kn=110&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
A good nose for stem cells p562
Cells can be delivered to the rodent brain noninvasively, via the
nasal cavity.
Natalie de Souza
doi:10.1038/nmeth0809-562
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NEWS AND VIEWS
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Probing the basis for genotype-phenotype relationships pp565 - 566
Transposon mutagenesis coupled with microarray analysis helps to
rapidly generate information about changing genotype-phenotype
relationships in laboratory-evolved bacteria.
Byung-Kwan Cho and Bernhard O Palsson
doi:10.1038/nmeth0809-565
http://links.ealert.nature.com/ctt?kn=92&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
New genetic tools for cell lineage analysis in
Drosophila pp566 - 568
Real-time lineage tracing in flies gets a boost with three techniques
to specifically label a progenitor's daughter cells.
Tzumin Lee
doi:10.1038/nmeth0809-566
http://links.ealert.nature.com/ctt?kn=121&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
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REVIEW
----------------------
Statistical methods for analysis of high-throughput RNA interference
screens pp569 - 575
Amanda Birmingham et al.
doi:10.1038/nmeth.1351
Abstract: http://links.ealert.nature.com/ctt?kn=32&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
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BRIEF COMMUNICATIONS
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Conditional and reversible disruption of essential herpesvirus
proteins pp577 - 579
A system for inducible protein degradation, originally developed
for mammalian cells, is applied to essential viral proteins and will
allow functional studies in a wide range of viruses.
Mandy Glasz et al.
doi:10.1038/nmeth.1346
Abstract: http://links.ealert.nature.com/ctt?kn=138&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
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Global discovery of adaptive mutations pp581 - 583
This array-based discovery tool creates linkage between functional
mutations and selectable markers across a bacterial genome and can
thus distinguish between adaptive and neutral mutations.
Hani Goodarzi, Alison K Hottes and Saeed Tavazoie
doi:10.1038/nmeth.1352
Abstract: http://links.ealert.nature.com/ctt?kn=94&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
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Mass spectrometry of membrane transporters reveals subunit
stoichiometry and interactions pp585 - 587
A generally applicable approach to analyze intact membrane protein
complexes by mass spectrometry is reported. This method allows
subunit stoichiometry, lipid binding and the effects of
post-translational modifications on complex formation to be explored.
Nelson P Barrera et al.
doi:10.1038/nmeth.1347
Abstract: http://links.ealert.nature.com/ctt?kn=128&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
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Metabolic network analysis integrated with transcript verification
for sequenced genomes pp589 - 592
Iterative cycles of metabolic modeling and experimental open reading
frame verification in Chlamydomonas reinhardtii lay the groundwork
for more accurate gene annotation and provide resources for metabolic
engineering.
Ani Manichaikul et al.
doi:10.1038/nmeth.1348
Abstract: http://links.ealert.nature.com/ctt?kn=114&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
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Virtual terminator nucleotides for next-generation DNA
sequencing pp593 - 595
Nucleotide analogs modified with a free 3' hydroxyl,
maintaining the interactions at the polymerase active site,
and a cleavable linker, attaching a fluorescent dye and an
inhibitor, are efficient at reading homopolymer runs in a
single-molecule sequencing reaction.
Jayson Bowers et al.
doi:10.1038/nmeth.1354
Abstract: http://links.ealert.nature.com/ctt?kn=78&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
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Dereplication and de novo sequencing of nonribosomal
peptides pp596 - 599
Multistage mass spectrometry and algorithms for spectral alignment
and dereplication allow sequencing of nonribosomal peptides,
pharmacologically important compounds that are not encoded in the
genome but built by nonribosomal peptide synthetases.
Julio Ng et al.
doi:10.1038/nmeth.1350
Abstract: http://links.ealert.nature.com/ctt?kn=53&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=45&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
The twin spot generator for differential Drosophila lineage
analysis pp600 - 602
This technique, adapted from mosaic analysis with double markers in
mice, relies on mitotic recombination to reconstitute sequences
encoding EGFP or mRFP1. After cell division, each daughter cell
contains one fluorescent marker, causing a green and a red twin
spot that can be traced through development.
Ruth Griffin et al.
doi:10.1038/nmeth.1349
Abstract: http://links.ealert.nature.com/ctt?kn=109&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=8&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
G-TRACE: rapid Gal4-based cell lineage analysis in
Drosophila pp603 - 605
A Gal4-based system in Drosophila reports on gene expression
at a given developmental stage combined with lineage information
on expression at earlier developmental stages.
Cory J Evans et al.
doi:10.1038/nmeth.1356
Abstract: http://links.ealert.nature.com/ctt?kn=117&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=105&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
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ARTICLES
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Robust, high-throughput solution structural analyses by small angle
X-ray scattering (SAXS) pp606 - 612
High-throughput analyses of macromolecular shape and oligomeric
state at ~15 A resolution are possible with a partially automated
small angle X-ray scattering (SAXS) pipeline. Though X-ray
crystallography provides higher-resolution structural information
than SAXS, SAXS analysis is faster and has a higher success rate,
which may have implications for how structural genomics research
is performed.
Greg L Hura et al.
doi:10.1038/nmeth.1353
Abstract: http://links.ealert.nature.com/ctt?kn=88&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=118&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Digital RNA allelotyping reveals tissue-specific and allele-specific
gene expression in human pp613 - 618
Padlock probes, synthesized in large scale on programmable
microarrays, capture expressed single-nucleotide polymorphisms
for high-throughput sequencing in this method for RNA allelotyping.
The approach combines the sensitivity of digital expression
measurements with the efficiency of targeted resequencing to
quantify allele specific gene expression in various tissues across
several individuals.
Kun Zhang et al.
doi:10.1038/nmeth.1357
Abstract: http://links.ealert.nature.com/ctt?kn=126&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=100&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
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TECHNOLOGY FEATURE
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Cell culture: building a better matrix pp619 - 622
With the realization that cells interact extensively with their
surrounding microenvironments during growth and development,
the challenge for researchers has become designing three-dimensional
culture systems that more closely mimic those relationships.
Nathan Blow
doi:10.1038/nmeth0809-619
http://links.ealert.nature.com/ctt?kn=123&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
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APPLICATION NOTES
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RNA amplification and cDNA synthesis for qRT-PCR directly from a
single cell
Judith E Meis and Anupama Khanna
Abstract: http://links.ealert.nature.com/ctt?kn=11&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=111&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Thermo Scientific products enable cutting-edge stem cell application
John Meech
Abstract: http://links.ealert.nature.com/ctt?kn=28&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=33&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
Real-time, label-free monitoring of cellular invasion and migration
with the xCELLigence system
Christopher Bird and Shelli Kirstein
Abstract: http://links.ealert.nature.com/ctt?kn=151&m=33756433&r=MTc2NjExMzUwMAS2&b=2&j=NTQ0MzQyMTYS1&mt=1&rt=0
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