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The mouse cancer model 'Multi-Hit' allows for the evaluation of oncogene cooperativities in tumor development based on stochastic Cre-recombination events. Cells with cooperating oncogenes are positively selected and give rise to tumors. The approach is used to study Ras downstream effector pathways in tumorigenesis.
pLink, software for data analysis of cross-linked proteins coupled with mass spectrometry, estimates false discovery rate and enables analysis of protein complexes without extensive purification.
This method achieves simultaneous and spatially colocalized excitation of three fluorophores with distinct spectra, doing so via two-photon microscopy using a femtosecond laser and an optical parametric oscillator and by temporally overlapping the beams. Imaging of 'Brainbow'-labeled mouse and chicken nervous tissue and of developing fly embryos is shown.
A machine learning–based structural-variant discovery approach that incorporates prior knowledge shows high sensitivity and specificity even on single genomes.
Due to an unexpected cell-penetrating property, zinc-finger nucleases (ZFNs) can be delivered to several mammalian cell types as proteins. Dose-dependent disruption of an endogenous gene was achieved with reduced activity at known off-target sites.
This paper reports a fluorescence imaging method based on interference contrast in which the incidence angle of the excitation light is actively scanned. The high axial precision and temporal resolution are used for dynamic nanoscale imaging of cytoskeleton and adhesion proteins in living cells.
A rare cutting protease that creates large peptides is well suited for differentiating protein isoforms and detecting combinations of post-translational modifications by tandem mass spectrometry.
An analytically exact approach that determines the radial symmetry center of the image of any radially symmetric particle allows faster localization than iterative methods while also giving localization accuracies approaching theoretical limits.
MetaPhlAn (metagenomic phylogenetic analysis) allows the rapid and accurate identification of microbial species and higher clades from shotgun sequencing data.
The authors describe a method for realigning images from serially sectioned biological specimens that minimizes the effect of artificial deformations in the alignment by applying global elastic constraints. The method is applied to transmission electron microscopy and array tomography image series and is made available through the Fiji platform.
A selective-plane illumination microscope with two illumination and two detection objectives rapidly records four three-dimensional images of an entire developing fly embryo and processes them into a single high-content image in real time. This allows for cell tracking and quantification of cell shape changes across the embryo. A related paper by Tomer et al. is also in this issue.
The authors present a bioinformatic method for the accurate unsupervised classification of time-lapse images. This method should enable reproducible and unbiased annotation of large-scale image data sets.
Genotyping based on restriction site7ndash;associated (RAD) sequencing around type IIB enzyme recognition sites is reported. The streamlined reduced-representation approach features even and tunable genome coverage and enables large-scale genotyping studies by maximizing the amount of genotypic information that can be obtained from individuals for a given amount of sequencing.
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.
Structure determination followed by targeted engineering of the popular photoactivatable fluorescent protein monomeric (m)Eos2 yields mEos3 versions that are more monomeric and less disruptive in protein fusions and also exhibit higher labeling density, brightness and other beneficial properties.
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.
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.
Global optimization of single-molecule localizations using compressed sensing allows stochastic optical reconstruction microscopy (STORM) at high molecular densities and live cell super-resolution imaging with a temporal resolution of 3 seconds.
