Volume 6 Issue 9, September 2009

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

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

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

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

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.