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The freely available WormToolbox enables high-throughput image analysis of a variety of phenotypes of Caenorhabditis elegans in liquid culture and should prove useful for image-based screens.
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.
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.
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.
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.
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.
Transgenic expression of secreted antibodies specific for modified heparan sulfates fused to GFP allow the visualization of these modifications in vivo.
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.
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.
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.
The Bowtie 2 software achieves fast, sensitive, accurate and memory-efficient gapped alignment of sequencing reads using the full-text minute index and hardware-accelerated dynamic programming algorithms.
Reported is a method, genome-wide enrichment of seed sequence (GESS), to analyze primary data from siRNA screens to identify major off-targeted transcripts. Using GESS the authors identify off-targeted transcripts in several screens.
The systematic functional dissection of long non-coding RNA (lncRNA) is simplified using a combined knockdown and localization approach based on endoribonuclease-prepared siRNA (esiRNA). A pilot screen reveals lncRNAs involved in the maintenance of pluripotency.
A light-inducible dimerization domain is used to create a genetically encoded, light-switchable transactivator of gene expression. The system allows rapid blue light–mediated activation of transgenes containing an appropriate activation sequence with low background and high induction.
The pairing of bisulfite padlock probes with a probe-design algorithm, library-free sequencing and an analysis pipeline provides a flexible and scalable method for quantifying cytosine methylation.
Lipidic sponge phase crystallization yields membrane protein microcrystals that can be injected into an X-ray free electron laser beam, yielding diffraction patterns that can be processed to recover the crystal structure.
Expression of a protein in Sf9 insect cells at high concentration triggers formation of in vivo crystals that can be analyzed by serial femtosecond X-ray crystallography.
The authors report Alexa Fluor 633 hydrazide to be artery-specific and use it to measure arteriole dilation dynamics in vivo in response to visual stimuli in mouse, rat and cat neocortex. They find that sensory stimulus–evoked arteriole dilation reduces the fluorescence recorded from underlying neurons.
Automated tissue sectioning and two-photon imaging of fluorescently labeled and fixed mouse brains allows high-resolution tomographic imaging of the entire brain. The authors demonstrate performance using multiple GFP mouse lines, dye-based retrograde tracing and viral anterograde tracing.
