Research articles

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.

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.

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.

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.

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 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.

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.

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.

High-throughput analyses of macromolecular shape and oligomeric state at ∼15 Å 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.

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.

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.

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.

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.

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.

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.

Combinations of fluorescently labeled peptide–major histocompatability (pMHC) tetramers are used to simultaneously detect T cells with multiple antigen specificities from human blood samples. Also in this issue, Hadrup et al. present a very similar combinatorial encoding approach.

Concatenated PCR products serve as subgenomic traps in this targeted genome capture technique; subsequent high-throughput sequencing allows the detection of nucleotide and structural variations in the captured genomic regions.

Using combinations of fluorescently labeled peptide–major histocompatability complex (pMHC) tetramers, T-cell populations with multiple antigen specificities can be monitored in parallel from small samples of human blood. Also in this issue, Newell et al. present a very similar combinatorial encoding method for this purpose.

There have been many attempts to measure gene expression in single cells but counting several different mRNAs in the same cell has been a challenge. A reusable single-cell cDNA library immobilized on beads allows quantitative measurement of multiple mRNAs in a single cell with a large dynamic range and small experimental error.

Mouse embryonic stem cell lines from the C57BL/6 strain are reported. The lines are highly germline competent, suitable for high-throughput genetic manipulation and will enable the generation of large knockout mouse resources.