Hot off the presses! Sep 01 Nat Methods

The Sep 01 issue of the Nat Methods is now up on Pubget (About Nat Methods): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Metagenomics versus Moore's law
  - Nat Methods 6(9):623 (2009)
  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.
• CASD-NMR: critical assessment of automated structure determination by NMR
  - Nat Methods 6(9):625-626 (2009)
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• Targeting ancient DNA
  - Nat Methods 6(9):629 (2009)
  A method that allows precise capture of Neanderthal genome sequences will permit detailed comparison of modern and ancient humans.
• Tethered together
  - Nat Methods 6(9):630-631 (2009)
  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
  - Nat Methods 6(9):630-631 (2009)
  A strategy for selectively disabling activated neurons helps researchers to characterize brain circuitry controlling addiction-related behaviors.
• News in brief
  - Nat Methods 6(9):631 (2009)
  
• Reading between the lines
  - Nat Methods 6(9):632 (2009)
  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
  - Nat Methods 6(9):634 (2009)
  Researchers develop a strategy to improve the intracellular retention of fluorescent probes and thus their imaging sensitivity.
• Google 'EarthWorm'
  - Nat Methods 6(9):635-636 (2009)
  A three-dimensional digital atlas allows cell-by-cell navigation of Caenorhabditis elegans.
• The 'rare biosphere': a reality check
  - Nat Methods 6(9):636-637 (2009)
  Methods for error correction and classification of metagenomic datasets suggest that the rare biosphere is not as large as previously assumed.
• Accurate determination of microbial diversity from 454 pyrosequencing data
  - Nat Methods 6(9):639-641 (2009)
  We present an algorithm, PyroNoise, that clusters the flowgrams of 454 pyrosequencing reads using a distance measure that models sequencing noise. This infers the true sequences in a collection of amplicons. We pyrosequenced a known mixture of microbial 16S rDNA sequences extracted from a lake and found that without noise reduction the number of operational taxonomic units is overestimated but using PyroNoise it can be accurately calculated.
• Modular scanning FCS quantifies receptor-ligand interactions in living multicellular organisms
  Ries J Yu SR Burkhardt M Brand M Schwille P - Nat Methods 6(9):643-645 (2009)
  Analysis of receptor-ligand interactions in vivo is key to biology but poses a considerable challenge to quantitative microscopy. Here we combine static-volume, two-focus and dual-color scanning fluorescence correlation spectroscopy to solve this task at cellular resolution in complex biological environments. We quantified the mobility of fibroblast growth factor receptors Fgfr1 and Fgfr4 in cell membranes of living zebrafish embryos and determined their in vivo binding affinities to their ligand Fgf8.
• Digital transcriptome profiling using selective hexamer priming for cDNA synthesis
  - Nat Methods 6(9):647-649 (2009)
  We developed a procedure for the preparation of whole transcriptome cDNA libraries depleted of ribosomal RNA from only 1 g of total RNA. The method relies on a collection of short, computationally selected oligonucleotides, called 'not-so-random' (NSR) primers, to obtain full-length, strand-specific representation of nonribosomal RNA transcripts. In this study we validated the technique by profiling human whole brain and universal human reference RNA using ultra-high-throughput sequencing.
• Crystallographic ab initio protein structure solution below atomic resolution
  - Nat Methods 6(9):651-653 (2009)
  Ab initio macromolecular phasing has been so far limited to small proteins diffracting at atomic resolution (beyond 1.2 Å) unless heavy atoms are present. We describe a general ab initio phasing method for 2 Å data, based on combination of localizing model fragments such as small á-helices with Phaser and density modification with SHELXE. We implemented this approach in the program Arcimboldo to solve a 222-amino-acid structure at 1.95 Å.
• Isolation of deletion alleles by G4 DNA-induced mutagenesis
  - Nat Methods 6(9):655-657 (2009)
  Metazoan genomes contain thousands of sequence tracts that match the guanine-quadruplex (G4) DNA signature G3NxG3NxG3NxG3, a motif that is intrinsically mutagenic, probably because it can form secondary structures during DNA replication. Here we show how and to what extent this feature can be used to generate deletion alleles of many Caenorhabditis elegans genes.
• ErythRED, a hESC line enabling identification of erythroid cells
  - Nat Methods 6(9):659-662 (2009)
  A human embryonic stem cell (hESC) line that enabled globin-expressing cells to be easily recognized would facilitate optimization of erythroid differentiation in vitro and aid in the identification of hESC-derived erythroid cells in transplanted animals. We describe a genetically modified hESC line, ErythRED, in which expression of RFP, controlled by regulatory sequences from the human -globin locus control region, is restricted to maturing erythroid cells.
• A customized and versatile high-density genotyping array for the mouse
  - Nat Methods 6(9):663-666 (2009)
  We designed a high-density mouse genotyping array containing 623,124 single-nucleotide polymorphisms that captures the known genetic variation present in the laboratory mouse. The array also contains 916,269 invariant genomic probes targeted to functional elements and regions known to harbor segmental duplications. The array opens the door to the characterization of genetic diversity, copy-number variation, allele-specific gene expression and DNA methylation, and will extend the successes of human genome-wide association studies to the mouse.
• A 3D digital atlas of C. elegans and its application to single-cell analyses
  - Nat Methods 6(9):667-672 (2009)
  We built a digital nuclear atlas of the newly hatched, first larval stage (L1) of the wild-type hermaphrodite of Caenorhabditis elegans at single-cell resolution from confocal image stacks of 15 individual worms. The atlas quantifies the stereotypy of nuclear locations and provides other statistics on the spatial patterns of the 357 nuclei that could be faithfully segmented and annotated out of the 558 present at this developmental stage. We then developed an automated approach to assign cell names to each nucleus in a three-dimensional image of an L1 worm. We achieved 86% accuracy in identifying the 357 nuclei automatically. This computational method will allow high-throughput single-cell analyses of the post-embryonic worm, such as gene expression analysis, or ablation or stimulation of cells under computer control in a high-throughput functional screen.
• Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
  Brady A Salzberg SL - Nat Methods 6(9):673-676 (2009)
  Metagenomics projects collect DNA from uncharacterized environments that may contain thousands of species per sample. One main challenge facing metagenomic analysis is phylogenetic classification of raw sequence reads into groups representing the same or similar taxa, a prerequisite for genome assembly and for analyzing the biological diversity of a sample. New sequencing technologies have made metagenomics easier, by making sequencing faster, and more difficult, by producing shorter reads than previous technologies. Classifying sequences from reads as short as 100 base pairs has until now been relatively inaccurate, requiring researchers to use older, long-read technologies. We present Phymm, a classifier for metagenomic data, that has been trained on 539 complete, curated genomes and can accurately classify reads as short as 100 base pairs, a substantial improvement over previous composition-based classification methods. We also describe how combining Phymm with sequ! ence alignment algorithms improves accuracy.
• BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
  - Nat Methods 6(9):677-681 (2009)
  Detection and characterization of genomic structural variation are important for understanding the landscape of genetic variation in human populations and in complex diseases such as cancer. Recent studies demonstrate the feasibility of detecting structural variation using next-generation, short-insert, paired-end sequencing reads. However, the utility of these reads is not entirely clear, nor are the analysis methods with which accurate detection can be achieved. The algorithm BreakDancer predicts a wide variety of structural variants including insertion-deletions (indels), inversions and translocations. We examined BreakDancer's performance in simulation, in comparison with other methods and in analyses of a sample from an individual with acute myeloid leukemia and of samples from the 1,000 Genomes trio individuals. BreakDancer sensitively and accurately detected indels ranging from 10 base pairs to 1 megabase pair that are difficult to detect via a single convention! al approach.
• Microfluidics: the great divide
  - Nat Methods 6(9):683-686 (2009)
  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.