Volume 9 Issue 6, June 2012

Making direct conversion pure and efficient

Techniques are at hand for taming the ever-growing number of data tracks.

Fly rhythms under natural light and temperature differ from those in the lab.

With the help of engineered polymerases and reverse transcriptases, synthetic nucleic acids can encode and pass on genetic information.

Bioinformatic discrimination of siRNAs that perturb cells via direct versus indirect effects can improve data quality and change hit lists in image-based screens.

Recombineering between two linear molecules enables long sequences to be efficiently cloned from a genomic mixture.

Radio waves and iron nanoparticles could hold the key to targeted perturbation of cells deep inside living tissue.

A flurry of recent papers report refinements to the activity and the assembly of engineered nucleases.

Bisulfite sequencing of chromatin-immunoprecipitated material allows a direct assessment of cytosine methylation in histone-modified regions of DNA.

As the less familiar cousin of quantitative PCR moves mainstream, researchers have more options to choose from.

Fluorescence recording of neural activity in the magnetic resonance scanner is a new strategy for examining the cellular underpinnings of blood oxygenation level–dependent (BOLD) functional magnetic resonance imaging (fMRI).

Researchers describe an approach to predict microbial-community composition across broad spatial and temporal gradients, an important step to bringing microbial ecology into the 21^st century.

Integrating biochemical footprinting data with molecular dynamics yields more accurate RNA three-dimensional structure predictions.

In this Review, the authors provide a guide through to the different steps involved in selected reaction monitoring as well as discuss its applications.

To increase the efficiency of direct neuronal conversion of postnatal human fibroblasts, the authors combine two-factor neuronal programming with small molecules. This method increases the yield and purity of functional neuron-like cells by more than 15-fold.

A computational framework is reported for the accurate and sensitive identification of RNA editing sites from whole-genome DNA and RNA sequences from the same individual.

Nanobodies that bind to fluorescent proteins with high affinity and are coupled to bright organic dyes allow simple efficient labeling of fusion proteins for super-resolution microscopy.

A robot, algorithm and software for automated in vivo intracellular electrophysiology are reported that can automatically perform whole-cell patch clamping in the living mouse brain with quality comparable to that for a trained human experimenter.

The range of genomic sequences accessible by zinc-finger nucleases is expanded by this archive of validated two-finger modules.

The use of marker coselection in combination with multiplex automated genome engineering (MAGE) is reported to improve the efficiency of engineered changes in bacterial genomes. The authors use the method to insert twelve 20-base-pair T7 promoters to control indirubin and indigo production.

A proximity assay based on methylation of interacting 'prey' proteins by a 'bait' fused to the histone lysine methyltransferase permits the detection of enzyme-substrate protein-protein interactions in yeast.

Simultaneous functional magnetic resonance imaging (fMRI) and fiber-optic–based calcium recordings in rats allow investigation of the relationship between blood oxygen level–dependent (BOLD) fMRI signals and the underlying neural activity. The study uncovers prolonged BOLD signal components involving glial activation.

Hydroxyl radical probing measurements of large RNA molecules drive molecular dynamics simulations to generate three-dimensional structural models.

The authors analyze how sequencing depth, choice of control sample, paired-end versus single-end reads and the selection of peak-calling algorithm influence the interpretation of chromatin immunoprecipitation–sequencing (ChIP-seq) experiments.

A hybrid fluorescence molecular tomography–X ray computed tomography system is applied for in vivo imaging of multiple mouse models, and its performance is validated on post-mortem cryosection data.

Microbial Assemblage Prediction is a predictive model for the climate-dependent abundance of microbial taxa in space and time. It takes potential interactions between taxa into account and is used on longitudinal metagenomic and climate data from the Western English Channel.