September 2009 Volume 6 Number 9, pp 623 - 686
Visit Nature Methods online to browse the journal.
Now available at http://links.ealert.nature.com/ctt?kn=134&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Please note that you need to be a subscriber to enjoy full text
access to Nature Methods online. To purchase a subscription,
please visit:
http://links.ealert.nature.com/ctt?kn=44&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Alternatively, to recommend a subscription to your library,
please visit
http://links.ealert.nature.com/ctt?kn=167&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
=========================== ADVERTISEMENT ===========================
small - your journal of choice in Nano and Micro
With its increased Impact Factor of 6.525, Small http://links.ealert.nature.com/ctt?kn=152&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
nal.org/
continues to be among the top multidisciplinary journals covering a
broad spectrum of topics at the nano- and microscale at the interface
of materials science, chemistry, physics, engineering, medicine, and b
iology.
See for yourself and read the current issue FOR FREE
http://links.ealert.nature.com/ctt?kn=100&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
=========================== ADVERTISEMENT ===========================
Welcome to more choice. Buy 4, get 2 FREE.
Choose from 200 newly released reagents, more sizes, and
fast, free, expert support in under 4 hours. Now choose any
4 fluorochrome or biotin-labeled antibodies from our entire
portfolio and choose 2 more FREE with no quantity limit.
Welcome to a more colorful world(SM). Visit bdbiosciences.com/choice
for more information.
http://links.ealert.nature.com/ctt?kn=77&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
=========================== ADVERTISEMENT ===========================
YOUR SCIENCE CAREER: WHAT NEXT?
Explore your options at The Source Event: London 25/09/2009 and Berlin 04/12/09. Throughout the day conference sessions and workshops will tackle a range of science career issues. Running alongside this is a FREE career fair where you can meet employers who are actively looking to recruit scientists.
Register now at: http://links.ealert.nature.com/ctt?kn=80&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
=====================================================================
----------------------
EDITORIAL
----------------------
Metagenomics versus Moore's law p623
Metagenomics sprang from advances in sequencing technology,
and continued improvements are providing data in quantities
unimaginable a few years ago. But without concerted efforts,
the amount of data will quickly outpace the ability of scientists
to analyze it.
doi:10.1038/nmeth0909-623
http://links.ealert.nature.com/ctt?kn=51&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
----------------------
CORRESPONDENCE
----------------------
CASD-NMR: critical assessment of automated structure determination
by NMR pp625 - 626
Antonio Rosato et al.
doi:10.1038/nmeth0909-625
http://links.ealert.nature.com/ctt?kn=52&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
----------------------
RESEARCH HIGHLIGHTS
----------------------
Targeting ancient DNA p629
A method that allows precise capture of Neanderthal genome sequences
will permit detailed comparison of modern and ancient humans.
Nicole Rusk
doi:10.1038/nmeth0909-629
http://links.ealert.nature.com/ctt?kn=53&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Tethered together pp630 - 631
Researchers describe a genetic approach to identify the native
components responsible for forming molecular transport junctions
between the mitochondria and the endoplasmic reticulum.
Allison Doerr
doi:10.1038/nmeth0909-630a
http://links.ealert.nature.com/ctt?kn=54&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Location, location, location pp630 - 631
A strategy for selectively disabling activated neurons helps
researchers to characterize brain circuitry controlling
addiction-related behaviors.
Michael Eisenstein
doi:10.1038/nmeth0909-630b
http://links.ealert.nature.com/ctt?kn=49&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
News in brief p631
doi:10.1038/nmeth0909-631
http://links.ealert.nature.com/ctt?kn=50&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Reading between the lines p632
A phenotype prediction tool helps 'fill in the blanks' for expression
microarrays, extending their predictive power and uncovering
once-hidden biases.
Michael Eisenstein
doi:10.1038/nmeth0909-632
http://links.ealert.nature.com/ctt?kn=75&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Stopping intracellular leakage with chemistry p634
Researchers develop a strategy to improve the intracellular retention
of fluorescent probes and thus their imaging sensitivity.
Allison Doerr
doi:10.1038/nmeth0909-634
http://links.ealert.nature.com/ctt?kn=73&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
----------------------
NEWS AND VIEWS
----------------------
Google 'EarthWorm' pp635 - 636
A three-dimensional digital atlas allows cell-by-cell navigation of
Caenorhabditis elegans.
William A Mohler
doi:10.1038/nmeth0909-635
http://links.ealert.nature.com/ctt?kn=74&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
The 'rare biosphere': a reality check pp636 - 637
Methods for error correction and classification of metagenomic
datasets suggest that the rare biosphere is not as large as
previously assumed.
Jens Reeder and Rob Knight
doi:10.1038/nmeth0909-636
http://links.ealert.nature.com/ctt?kn=71&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
----------------------
BRIEF COMMUNICATIONS
----------------------
Accurate determination of microbial diversity from 454 pyrosequencing
data pp639 - 641
PyroNoise, an algorithm that preclusters the flowgrams generated on a
454 GS FLX with DNA extracted from microbial samples can distinguish
between noise and genuine sequence diversity in a metagenomic
dataset.
Christopher Quince et al.
doi:10.1038/nmeth.1361
Abstract: http://links.ealert.nature.com/ctt?kn=72&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=69&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Modular scanning FCS quantifies receptor-ligand interactions in
living multicellular organisms pp643 - 645
A combination of static-volume, two-focus and dual-color scanning
fluorescence correlation spectroscopy is used for the in vivo
analysis of receptor-ligand interactions in living zebrafish embryos.
The measured binding affinities suggest that Fgf8 binds to both
Fgfr1 and Fgfr4 during gastrulation.
Jonas Ries et al.
doi:10.1038/nmeth.1355
Abstract: http://links.ealert.nature.com/ctt?kn=70&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=67&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Digital transcriptome profiling using selective hexamer priming for
cDNA synthesis pp647 - 649
To deplete abundant rRNA from total RNA during cDNA library
generation, hexamer primers that perfectly match rRNA are removed.
These 'not so randomly primed' cDNA libraries can be generated from
small amount of total RNA, preserve strand orientation and are
equally enriched in polyadenylated and non-polyadenylated
transcripts.
Christopher D Armour et al.
doi:10.1038/nmeth.1360
Abstract: http://links.ealert.nature.com/ctt?kn=68&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=65&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Crystallographic ab initio protein structure solution below atomic
resolution pp651 - 653
A general approach to address the 'phase problem' in protein
crystallography is described, allowing protein structures to be
directly solved from 2 A resolution diffraction data without using
heavy atom doping or relying on a preexisting structure model
for molecular replacement.
Dayte D Rodriguez et al.
doi:10.1038/nmeth.1365
Abstract: http://links.ealert.nature.com/ctt?kn=12&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=13&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Isolation of deletion alleles by G4 DNA-induced
mutagenesis pp655 - 657
Deletions of polyguanine tracts in Caenorhabditis elegans deficient
in the DOG-1 DNA helicase can be exploited to generate deletion
alleles of several genes for which no such alleles exist in this
organism.
Daphne B Pontier, Evelien Kruisselbrink, Victor Guryev and Marcel
Tijsterman
doi:10.1038/nmeth.1362
Abstract: http://links.ealert.nature.com/ctt?kn=14&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=16&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
ErythRED, a hESC line enabling identification of erythroid
cells pp659 - 662
A human embryonic stem cell line, ErythrRED, harbors a red
fluorescent protein under the control of regulatory sequences
from the beta-globin locus, as a reporter for erythroid
differentiation.
Tanya Hatzistavrou et al.
doi:10.1038/nmeth.1364
Abstract: http://links.ealert.nature.com/ctt?kn=17&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=18&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
A customized and versatile high-density genotyping array for the
mouse pp663 - 666
This array with 623,124 SNP probes and 916,269 probes to query
structural variants opens the door to a detailed characterization
of genetic diversity in laboratory mouse strains. This will allow
genome-wide association studies in mice.
Hyuna Yang et al.
doi:10.1038/nmeth.1359
Abstract: http://links.ealert.nature.com/ctt?kn=4&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=6&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
----------------------
ARTICLES
----------------------
A 3D digital atlas of C. elegans and its application to single-cell
analyses pp667 - 672
A digital atlas of C. elegans at the post-embryonic L1 stage is
presented, along with automated methods for nucleus segmentation
and annotation. These resources will enable quantitative analyses
of nuclear spatial arrangements as well as high-throughput
single-cell analyses in this organism.
Fuhui Long et al.
doi:10.1038/nmeth.1366
Abstract: http://links.ealert.nature.com/ctt?kn=8&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=9&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Phymm and PhymmBL: metagenomic phylogenetic classification
with interpolated Markov models pp673 - 676
This algorithm for the assignment of phylogenetic groups to
fragments generated by metagenomic sequencing projects improves
on the currently required 1 kb fragment length for classification.
Trained on 539 complete genomes, Phymm can classify reads as
short as 100 bp. Combining Phymm with the sequence alignment
algorithm BLAST further improves accuracy.
Arthur Brady and Steven L Salzberg
doi:10.1038/nmeth.1358
Abstract: http://links.ealert.nature.com/ctt?kn=39&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=35&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
BreakDancer: an algorithm for high-resolution mapping of genomic
structural variation pp677 - 681
This software package provides genome-wide detection of structural
variants (insertions, deletions, inversions and inter- and
intrachromosomal translocations) from 50-base-pair paired-end
reads. The sizes of the detected variants vary from 10 base pairs
to 1 megabase pair.
Ken Chen et al.
doi:10.1038/nmeth.1363
Abstract: http://links.ealert.nature.com/ctt?kn=37&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=43&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
----------------------
TECHNOLOGY FEATURE
----------------------
Microfluidics: the great divide pp683 - 686
Although many intricate microfluidic devices have been created in
academic laboratories around the world, far fewer have been
commercialized for wider use. But several efforts are underway
to bridge this divide.
Nathan Blow
doi:10.1038/nmeth0909-683
http://links.ealert.nature.com/ctt?kn=45&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
----------------------
APPLICATION NOTES
----------------------
Analysis of 5' transcript heterogeneity by high-throughput
sequencing of cDNA
Pietro D Spanu and Ken Doyle
Abstract: http://links.ealert.nature.com/ctt?kn=41&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=42&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Functional isolation of staurosporine binding protein kinases using
CCMS technology
Erik Dulsner, Jenny J Fischer, Christian Jurinke and Hubert Koster
Abstract: http://links.ealert.nature.com/ctt?kn=32&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=33&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
HybSelect: high-throughput access to genomic regions of interest
for targeted next-generation sequencing
Daniel Summerer
Abstract: http://links.ealert.nature.com/ctt?kn=30&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=164&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Highly specific detection of phosphorylated proteins by Duolink
Mats Gullberg and Ann-Catrin Andersson
Abstract: http://links.ealert.nature.com/ctt?kn=147&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
Article: http://links.ealert.nature.com/ctt?kn=145&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
=========================== ADVERTISEMENT ===========================
Nature Genetics
Focus on Copy Number Variation
Individual genomes vary, not only in sequence, but in both their structural organization and in the number of sequence copies they contain. We now have the technology to understand the mechanisms by which genomes diverge, and to investigate the consequences of copy number variation for gene expression and clinical phenotypes.
With sponsorship from Agilent Technologies, Nature Genetics presents a Focus on copy number variation highlighting the complementary roles of paired-end sequencing and oligonucleotide array technology in research discovery.
Free access to the articles is available by visiting: http://links.ealert.nature.com/ctt?kn=29&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
=====================================================================
You have been sent this Table of Contents Alert because you have
opted in to
receive it. You can change or discontinue your e-mail alerts at
any time,
by modifying your preferences on your nature.com account at:
http://links.ealert.nature.com/ctt?kn=106&m=33940600&r=MTc2NjExMzUwMAS2&b=2&j=NTczMDM2MzUS1&mt=1&rt=0
(You will need to log in to be recognised as a nature.com
registrant).
For further technical assistance, please contact our registration
department:
registration@nature.com
For print subscription enquiries, please contact our subscription
department:
subscriptions@nature.com
For other enquiries, please contact our customer feedback
department:
feedback@nature.com
Nature Publishing Group | 75 Varick Street, 9th Floor | New York |
NY 10013-1917 | USA
Nature Publishing Group's worldwide offices:
London - Paris - Munich - New Delhi - Tokyo - Melbourne -
San Diego - San Francisco - Washington - New York - Boston
(c) Copyright 2009 Nature Publishing Group
=====================================================================
