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Imaging with better than 200-nanometer resolution brings new subcellular-scale details into focus. Practitioners share how they weigh trade-offs in speed, resolution and phototoxicity.
For allele-specific expression and RNA editing studies, targeted RNA sequencing using microfluidic multiplexed PCR (mmPCR-seq) gives robust high-throughput measurements of allelic ratios across the dynamic range of gene expression, even for low-quantity or low-quality RNA.
A line-scanning method is applied to obtain onset times of fMRI responses in rats. The authors show that onset time of the fMRI response can be used to infer information about which cortical layers receive the connectivity input from other brain areas.
High-resolution isoelectric focusing (HiRIEF) of peptides followed by mass spectrometry analysis, combined with accurate peptide pI prediction, allows a reduction of protein database search space, enabling deep proteome coverage and the discovery of protein-coding loci in human and mouse.
A chemically defined diet for Drosophila melanogaster is described. It should enable a variety of behavioral, metabolic and fitness studies where controlled nutrition is important.
An approach is presented for predicting the nature of the relationship (activating or inhibiting) between interacting proteins via integration of phenotypic information with protein-protein interaction networks.
A system to monitor translation regulation in living cells is reported. By fusing a fluorescent reporter that has a controllable destabilization domain to translation regulatory motifs, the authors analyze the contribution of these motifs to changes in translation in individual cells under different experimental situations.
Discrepancies between model prediction and experimental measurements enable molecular-level discovery with a whole-cell model of Mycoplasma genitalium.
By separately sequencing and mapping smaller and larger DNase I fragments from the same DNase I digestion experiment, the approach allows simultaneous profiling of transcription factor footprints relative to nucleosome occupancy.
The RGASP consortium compared 25 RNA-seq analysis programs in their ability to identify exons, reconstruct transcripts and quantify expression levels. Assembly of isoforms and their expression levels in higher eukaryotes remains a challenge.
Authors compare RNA-seq aligners on mouse and human data sets using benchmarks such as alignment yield, splice junction accuracy and suitability for transcript reconstruction. The work highlights the strength of each program and discusses outstanding needs in RNA-seq analysis.