Volume 8 Issue 7, July 2011

Single-molecule studies lead to high-throughput sequencing.

A new flow cytometry technology based on mass detection allows a very large number of parameters to be simultaneously measured in single cells.

Phenotypic screens of a complex in vivo structure predict function for essential genes in the worm.

Two complementary methods facilitate genome-wide enrichment of hydroxymethylated DNA.

A single-molecule pull-down method provides a simple way for biologists to examine their favorite protein at the single-molecule level.

A combination of techniques is used to measure and model RNA dynamics in dendritic cells.

Researchers adapt split-GFP complementation to single-molecule imaging.

Forays into information technology can make lab work easier to manage.

A large-scale, multifaceted screening and validation strategy combining traditional and recombinant antibody technologies yielded a broad spectrum of validated protein binders with high binding affinity and specificity applicable to many fields in proteome research.

A method for clustering billions of unidentified tandem mass spectra from shotgun proteomics experiments offers new ways of storing, organizing and analyzing proteomics data, with potential benefits to the entire proteomics community.

A technique that combines the speed of pyrosequencing with the sensitivity of fluorescent detection may lead to faster sequencing with smaller quantities of DNA.

A multilaboratory pilot project demonstrates that hybridoma and phage display technologies can be applied to produce high-affinity, high-specificity renewable antibodies to a set of 20 human SH2 domain proteins in a reasonable time frame, suggesting that a systematic, large-scale effort to generate renewable protein binders will be feasible.

The comparison of cross-linking and immunoprecipitation (CLIP) and photoactivatable ribonucleoside–enhanced CLIP (PAR-CLIP) protocols shows specific biases of each method in enriching subsets of binding sites of RNA-binding proteins and shows ways around these biases.

A linear, one-tube amplification procedure generates sufficient amounts of material from chromatin immunoprecipitation (ChIP) and reChIP experiments to allow high-throughput sequencing.

Fiducial marks that can be visualized by both light and electron microscopy are generated by 'branding' fixed tissue with a near-infrared laser and will facilitate correlative light and electron microscopy.

The performance of low-power, continuous-wave stimulated emission depletion microscopy is improved by combining pulsed excitation with time-gated detection. This combination also simplifies super-resolution fluorescence correlation spectroscopy.

In this sequencing-by-synthesis approach, the incorporation of a terminal-phosphate labeled fluorogenic nucleotide by DNA polymerase results in the generation of a fluorescent dye that is trapped in a sealed microreactor and does not require real-time detection.

A microfluidic setup for nanoliter-volume perfused clonal culture and imaging of thousands of nonadherent cells is applied to study signaling and proliferation in hematopoietic stem cells.

Both identified and unidentified peptide mass spectra can be clustered and represented as consensus spectra in a spectral archive, offering new ways of interpreting proteomics data. A software tool for clustering billions of spectra is presented, as is a 1.18-billion spectra spectral archive.

The Multi-Worm Tracker permits real-time, high-throughput, quantitative analysis of behavior in Caenorhabditis elegans. It should enable screens for genes implicated in complex worm behaviors. Also in this issue, Albrecht and Bargmann apply microfluidics to study worm chemosensory behavior with high spatial and temporal precision.

Quantitative analysis of Caenorhabditis elegans chemosensory behavior is achieved in a structured arena with microfluidic delivery of stimuli with precise spatial and temporal control. Also in this issue, Swierczek et al. report software for real-time behavioral analysis in worms.