Volume 5 Issue 8, August 2008

Ongoing efforts show promise in replacing reprogramming factors with small molecules for making induced pluripotent stem cells.

A new protein tag simplifies labeling and visualization of newly synthesized target proteins in tissue and whole animals.

Using chemically assembled ubiquitylated histone H2B, researchers demonstrate that direct cross-talk results in methylation of a lysine on another histone.

Researchers demonstrate a method for observing intact membrane protein complexes by mass spectrometry.

Next-generation sequencing–based studies locate nucleosomes at high resolution throughout several genomes.

By engineering magnetic microstructures, researchers demonstrate the potential for multiplexed MRI.

Algorithms for analyzing single-particle tracking images to obtain the paths of individual particles are challenged by high-density data. Improvements in algorithms help to overcome these limitations.

A new base caller for the Illumina Genome Analyzer uses machine learning to compensate for noise factors and improves accuracy for up to 78-base-pair sequencing reads.

Designing fluorescent protein-based sensors that display large changes in fluorescence resonance energy transfer (FRET) is challenging. Redesign of a FRET-based voltage sensor using new fluorescent proteins increased the sensor response to changes in membrane voltage and measurements at warmer temperatures displayed faster kinetics comparable to action potentials.

Single-particle tracking methods allow detailed analysis of protein movement in cells, but existing tracking algorithms have substantial limitations, particularly at high particle densities. A new software tool overcomes some of these limitations and can be used to track high-density particles in cell membranes. Also in this issue, Jaqaman et al. describe an alternative software tool for high-density single-particle tracking.

Single-particle tracking methods allow detailed analysis of protein movement in cells, but existing tracking algorithms have substantial limitations, particularly at high particle densities. A new software tool overcomes some of these limitations and is used to track CD36 receptors and assay the lifetime of clathrin-coated pits. Also in this issue, Sergé et al. describe an alternative software tool for high-density single-particle tracking.

Automated imaging of the Caenorhabditis elegans embryo now allows monitoring of the timing and relative expression of individual reporter genes at single-cell resolution over almost all of embryonic development. Future systematic analysis could be used to reveal gene expression patterns of every cell during development.

To increase the range and precision of genetic interaction studies in Saccharomyces cerevisiae, a collection of hypomorphic alleles of essential yeast genes and a highly sensitive flow cytometry–based growth competition assay are presented. Also in this issue, Yan et al. present a similar strain collection, tagged with unique bar-code identifiers, and use this collection in pooled chemical genetic screens.

A library of universal Saccharomyces cerevisiae Barcoder strains for efficient tagging is presented. It is used to tag a collection of hypomorphic alleles of essential yeast genes and applied to chemical genetic screens. Also in this issue, Breslow et al. present a similar collection of hypomorphic alleles, coupled with a sensitive growth assay for improved genetic interaction studies.

Many proteins, including G protein–coupled receptors (GPCRs), interact to form oligomers at the cell surface. A combination of bioluminescence resonance energy transfer (BRET) and fluorescence resonance energy transfer (FRET) in a technique called sequential resonance energy transfer (SRET) extends these methods to study higher-order oligomers of GPCRs or other proteins.

In vitro studies of neuronal function have mainly been limited to two-dimensional networks of cultured neurons. Use of transparent colloids as a moveable support for neuronal growth allows user-guided construction of optically accessible three-dimensional networks whose function can be manipulated and measured.

Mass spectrometry instrumentation has made strides in recent years in terms of dynamic range and sensitivity, putting researchers in a better position to use the technology to tackle the challenges of disease biomarker discovery and validation.