Volume 9 Issue 5, May 2012

Labeling proteins for single-molecule studies.

The choice of visual representation of the linear genome is guided by the question being asked.

Two methodological approaches allow researchers to manipulate the formation and reactivation of memories in mice.

A dimerization-dependent red fluorescent protein provides a new strategy for biosensor design.

Tools to study stem cell function in planarians continue to accumulate. Researchers now image growing stem cell clones in these animals and make quantitative phenotypic measurements in vivo.

A milling technique affords researchers a high-resolution glimpse deep into the cell using cryoelectron tomography.

Downregulation of natural antisense transcripts enhances expression of their sense counterparts.

A simple microfluidic device allows long-term imaging of single budding yeast cells.

Proteomics analysis of polyclonal antibodies guides monoclonal production.

Light and chemicals offer precise ways to manipulate proteins.

Current practice for the generation and maintenance of induced pluripotent stem cells (iPSCs) involves static culture in dishes. Two groups now report that mouse iPSCs can be generated efficiently in stirred suspension culture.

A strategy that uses genetically encoded GFP-tagged antibodies allows in vivo imaging of extracellular non–genetically encoded molecules.

Using semiconductor processing to construct integrated circuits that reside close to nanopores, researchers demonstrate high-bandwidth, low-noise measurements of DNA translocation through solid-state nanopores.

Informatics has driven mass spectrometry–based protein analysis to create large-scale methods for proteomics. As software algorithms have developed, comparisons between algorithms are inevitable. We outline steps for fair and objective comparisons that will make true innovations apparent.

Reprogramming of mouse fibroblasts to induced pluripotency is demonstrated in suspension culture. Also in this issue, Fluri et al. report suspension-culture reprogramming of mouse cells and further differentiation, also in suspension, into cardiac cells.

Protein localization changes in cells are monitored at high-throughput applying pulse-shape analysis to flow-cytometry data. The authors use the technique in combination with tetracysteine-based oligomer sensors to monitor toxic protein aggregation in a cellular model of Huntington's disease.

ClusterONE detects overlapping protein complexes from large-scale weighted and unweighted protein-interaction networks.

Segway, a method using dynamic Bayesian network techniques, segments a genome and produces functional labels defined by histone modifications, transcription-factor binding, locations of open chromatin and other genome-wide functional data.

Transgenic expression of secreted antibodies specific for modified heparan sulfates fused to GFP allow the visualization of these modifications in vivo.

The authors compare segregation of a protein into two daughter cells for the wild-type protein and a fluorescently tagged version, by assessing protein activity in the two cells; differences in segregation between the two protein versions indicate mislocalization artifacts caused by the fluorescent tag. Using this system they identify widespread artifacts in the localization of bacterial proteases.

Automated cell segmentation in time-lapse confocal images of growing Arabidopsis combined with ratiometric imaging of fluorescent gene expression reporters permits the correlation of cellular properties with gene expression in the growing plant.

The temporal resolution of current signals from solid-state nanopores is improved by integrating a complementary metal-oxide-semiconductor preamplifier with the nanopores in thin silicon nitride membranes.

The biotin-reversible interaction between a 'hook' protein localized to a particular cellular compartment and a reporter protein of interest is exploited in a simple system to synchronize protein traffic through the secretory pathway.

The combination of a genetically encoded aldehyde tag and optimized labeling method allows high-efficiency, site-specific labeling of tagged proteins after purification or in cell extracts. The authors use the high labeling efficiency for single-molecule measurements of the dynamic interactions between two DNA polymerases and polymerase processivity factor bound to DNA.

An in vitro kinase assay for quantification of site-specific substrate phosphorylation allows identification of kinase-kinase dependencies.

Mouse cells are reprogrammed to induced pluripotency in suspension culture and can be further differentiated into cardiac cells, also in suspension. Also in this issue, Shafa et al. report suspension-culture reprogramming of mouse cells.