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Editorial

Metagenomics versus Moore's law p623

doi:10.1038/nmeth0909-623

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.


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Correspondence

CASD-NMR: critical assessment of automated structure determination by NMR pp625 - 626

Antonio Rosato, Anurag Bagaria, David Baker, Benjamin Bardiaux, Andrea Cavalli, Jurgen F Doreleijers, Andrea Giachetti, Paul Guerry, Peter Güntert, Torsten Herrmann, Yuanpeng J Huang, Hendrik R A Jonker, Binchen Mao, Thérèse E Malliavin, Gaetano T Montelione, Michael Nilges, Srivatsan Raman, Gijs van der Schot, Wim F Vranken, Geerten W Vuister & Alexandre M J J Bonvin

doi:10.1038/nmeth0909-625


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Research Highlights

Targeting ancient DNA p629

Nicole Rusk

doi:10.1038/nmeth0909-629

A method that allows precise capture of Neanderthal genome sequences will permit detailed comparison of modern and ancient humans.


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Tethered together pp630 - 631

Allison Doerr

doi:10.1038/nmeth0909-630a

Researchers describe a genetic approach to identify the native components responsible for forming molecular transport junctions between the mitochondria and the endoplasmic reticulum.


Location, location, location pp630 - 631

Michael Eisenstein

doi:10.1038/nmeth0909-630b

A strategy for selectively disabling activated neurons helps researchers to characterize brain circuitry controlling addiction-related behaviors.


News in brief p631

doi:10.1038/nmeth0909-631


Reading between the lines p632

Michael Eisenstein

doi:10.1038/nmeth0909-632

A phenotype prediction tool helps 'fill in the blanks' for expression microarrays, extending their predictive power and uncovering once-hidden biases.


Stopping intracellular leakage with chemistry p634

Allison Doerr

doi:10.1038/nmeth0909-634

Researchers develop a strategy to improve the intracellular retention of fluorescent probes and thus their imaging sensitivity.


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News and Views

Google 'EarthWorm' pp635 - 636

William A Mohler

doi:10.1038/nmeth0909-635

A three-dimensional digital atlas allows cell-by-cell navigation of Caenorhabditis elegans.

See also: Article by Long et al.


The 'rare biosphere': a reality check pp636 - 637

Jens Reeder & Rob Knight

doi:10.1038/nmeth0909-636

Methods for error correction and classification of metagenomic datasets suggest that the rare biosphere is not as large as previously assumed.

See also: Brief Communication by Quince et al. | Article by Brady & Salzberg


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Brief Communications

Accurate determination of microbial diversity from 454 pyrosequencing data pp639 - 641

Christopher Quince, Anders Lanzén, Thomas P Curtis, Russell J Davenport, Neil Hall, Ian M Head, L Fiona Read & William T Sloan

doi:10.1038/nmeth.1361

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.

See also: News and Views by Reeder & Knight


Modular scanning FCS quantifies receptor-ligand interactions in living multicellular organisms pp643 - 645

Jonas Ries, Shuizi Rachel Yu, Markus Burkhardt, Michael Brand & Petra Schwille

doi:10.1038/nmeth.1355

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.


Digital transcriptome profiling using selective hexamer priming for cDNA synthesis pp647 - 649

Christopher D Armour, John C Castle, Ronghua Chen, Tomas Babak, Patrick Loerch, Stuart Jackson, Jyoti K Shah, John Dey, Carol A Rohl, Jason M Johnson & Christopher K Raymond

doi:10.1038/nmeth.1360

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.


Crystallographic ab initio protein structure solution below atomic resolution pp651 - 653

Dayté D Rodríguez, Christian Grosse, Sebastian Himmel, César González, Iñaki M de Ilarduya, Stefan Becker, George M Sheldrick & Isabel Usón

doi:10.1038/nmeth.1365

A general approach to address the 'phase problem' in protein crystallography is described, allowing protein structures to be directly solved from 2 Å resolution diffraction data without using heavy atom doping or relying on a preexisting structure model for molecular replacement.


Isolation of deletion alleles by G4 DNA-induced mutagenesis pp655 - 657

Daphne B Pontier, Evelien Kruisselbrink, Victor Guryev & Marcel Tijsterman

doi:10.1038/nmeth.1362

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.


ErythRED, a hESC line enabling identification of erythroid cells pp659 - 662

Tanya Hatzistavrou, Suzanne J Micallef, Elizabeth S Ng, Jim Vadolas, Edouard G Stanley & Andrew G Elefanty

doi:10.1038/nmeth.1364

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.


A customized and versatile high-density genotyping array for the mouse pp663 - 666

Hyuna Yang, Yueming Ding, Lucie N Hutchins, Jin Szatkiewicz, Timothy A Bell, Beverly J Paigen, Joel H Graber, Fernando Pardo-Manuel de Villena & Gary A Churchill

doi:10.1038/nmeth.1359

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.


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Articles

A 3D digital atlas of C. elegans and its application to single-cell analyses pp667 - 672

Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart K Kim & Eugene Myers

doi:10.1038/nmeth.1366

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.

See also: News and Views by Mohler


Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models pp673 - 676

Arthur Brady & Steven L Salzberg

doi:10.1038/nmeth.1358

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.

See also: News and Views by Reeder & Knight


BreakDancer: an algorithm for high-resolution mapping of genomic structural variation pp677 - 681

Ken Chen, John W Wallis, Michael D McLellan, David E Larson, Joelle M Kalicki, Craig S Pohl, Sean D McGrath, Michael C Wendl, Qunyuan Zhang, Devin P Locke, Xiaoqi Shi, Robert S Fulton, Timothy J Ley, Richard K Wilson, Li Ding & Elaine R Mardis

doi:10.1038/nmeth.1363

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.


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Technology Feature

Microfluidics: the great divide pp683 - 686

Nathan Blow

doi:10.1038/nmeth0909-683

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.


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Application Notes





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