Volume 9 Issue 11, November 2012

Zeroing in on single DNA strands

A unique set of tools facilitate thinking and hypothesis generation.

Two different mass spectrometry–based approaches are applied to analyze protein complexes on a global scale.

A freely accessible transcriptional atlas offers unprecedented possibilities for exploring the human brain.

Researchers describe a multifunctional reagent for identifying extracellular interactions.

The second, genome-wide phase of the Encyclopedia of DNA Elements (ENCODE) project is being reported.

Computational processing allows sub–diffraction-limit resolution imaging with a standard wide-field microscope.

Single-stranded small interfering RNA offers a potent and simple way to silence gene expression in the body.

Synthetic networks in mammalian cells can regulate cellular behavior.

The menu of maturing, diversifying methods calls for careful selections in experimental design.

Work from two independent groups opens the door to designing gene circuits with advanced regulatory functions.

Researchers adapt a popular Orbitrap-based mass spectrometer to detect and analyze large, intact protein complexes, accelerating a new frontier in structural biology.

This Perspective discusses the registered and publicly available set of Cytoscape plugins to guide potential users to suitable tools.

A unique multiple cloning site (MCS) and defined genetic components without MCS restriction sites allow for the rapid construction and iterative tuning of synthetic genetic circuits.

This paper presents AVeMap, a method and software for automated analysis of cell migration in dense monolayers.

Modifications to an Orbitrap-based mass spectrometer enable analysis of large protein complexes in native-like states by mass spectrometry with very high sensitivity and mass resolution.

A genetic tool that converts bacterial regulators of translational initiation into regulators of transcriptional elongation is described. This adaptor is used to engineer several transcriptional attenuators and activators that can be predictably assembled into higher-order gene regulatory functions.

A synthetic peptide library in conjunction with liquid chromatography–tandem mass spectrometry identifies the specificities of endo- and exopeptidases without requiring enrichment of substrates or products.

RootArray and RootArray Controller comprise a robust pipeline for acquisition and analysis of gene expression data in plant roots over time.

The Strand-seq method independently sequences each parental strand of template DNA from single proliferating cells. It can be used to detect sister chromatid exchange and other chromosomal abnormalities at high resolution and to correct contig misorientations in genome assemblies, with potential for strand-inheritance and haplotyping studies.

Cells are dosed with magnetic nanoparticles and patterned onto micromagnetic substrates, enabling the application of controlled and variable mechanical force to tens of thousands of cells.

The probe selection for imputation (PSI) approach accurately imputes global gene expression profiles from a small subset of probes that it chooses based on a training set of full profiles, allowing many more combinatorial experiments to be performed given the same resources.