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An imaging and registration framework called Virtual Brain Explorer for Zebrafish (ViBE-Z) allows mapping of gene expression patterns and anatomical structures in the zebrafish larval brain. ViBE-Z is provided via a web interface and contains software for image processing, data sets from several developmental stages and a brain atlas.
Simultaneous multiview light-sheet microscopy using two illumination and two detection arms with one- or two-photon illumination is coupled to a fast data acquisition framework and analysis pipeline for quantitative imaging and tracking of individual cells and the developing nervous system throughout a living fly embryo. A related paper by Krzic et al. is also in this issue.
Super-resolution microscopy of fluorescently labeled oligonucleotides bound to individual mRNA transcripts is used for highly multiplexed imaging and quantification of transcripts in single cells. The method is used to profile transcripts from 32 stress-response genes in single yeast cells in response to extracellular stress.
The combination of cell-free protein expression and combinatorial dual labeling–aided NMR analysis allows for the rapid backbone structure assessment of human membrane proteins.
Structured illumination using multifocal patterned illumination via a digital micromirror device integrated into a conventional wide-field microscope, followed by digital processing, allows resolution-doubled three-dimensional imaging of live organisms with two-color capability.
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.
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.
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.
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.
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.
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.
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 binary 'Q system' for controlling gene expression in Caenorhabditis elegans is reported. The system affords reversible activation of either extrachromosomal or single-copy integrated transgenes; a complementation-based 'split Q' system also permits specific expression in desired cell types.
In this proof of principle the authors use magnetic tweezers to unzip a DNA hairpin and then measure the molecule extension during rezipping in the presence of oligomers that transiently block the rezipping process. The extent of these blockages allows them to determine the DNA sequence.
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.
Light-inducible dimerization tags are engineered to rapidly recruit proteins to precise points in living yeast and mammalian cells. The affinities and response time of the interactions are tunable, and the authors used the system to activate cell signaling and to direct cell polarization in yeast.
We describe software, MiceProfiler, for automatic tracking of two interacting mice and analysis of their social interactions without the need of animal tagging. The program allows the identification of key elements that trigger social contact in different mouse strains.
Tough decoy microRNA inhibitor, shown to be the most effective of several designs, is packaged in recombinant adeno-associated virus and used for prolonged microRNA inhibition in living mice. A single injection effectively reduces miR-122 in the liver and serum cholesterol for at least 25 weeks.