Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain
the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in
Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles
and JavaScript.
A microfluidic embryo-trap array for large-scale end-on imaging of Drosophila melanogaster embryos permits quantitative analysis of dorsoventral gradients during development.
The Network-Free Stochastic Simulator (NFsim) allows the representation of complex biological systems as rule-based models and facilitates coarse-graining of the reaction mechanisms.
Context-dependent assembly (CoDA) of zinc finger nucleases is reported. Starting from an archive of zinc finger modules known to function well together, effective multifinger arrays can be constructed using standard techniques. Also in this issue, Doyon et al. report rational design of nucleases with improved cleavage activity.
Fast, two-photon intravital imaging of a mechanically stabilized and physiologically intact preparation of the mouse lung is reported. It is used to monitor immune cells in the lung under normal and injured conditions.
A statistical framework for assigning confidence scores for protein-protein interaction data generated via affinity purification–mass spectrometry, called significance analysis of interactome (SAINT) is described.
Derivatizing glycosphingolipids, extracted from bovine brain or human erythrocytes, with a fluorescent tag allows their immobilization on an array which can be probed with glycan binding proteins.
Identification of residues critical for dimerization of the Fok1 nuclease domain of zinc-finger nucleases permits rational design of enzymes with improved cleavage activity and retained obligate heterodimerization. Also in this issue, Sander et al. report context-dependent assembly (CoDA), a simple method for designing zinc-finger nucleases.
Methods are reported for the combination of fluorescence nanoscopy using either stimulated emission depletion microscopy (STED) or photoactivated localization microscopy (PALM) with electron microscopy, to achieve correlative imaging in which the super-resolved fluorescence signal is placed in the context of cellular ultrastructure.
Tracking the displacement of fluorescent beads surrounding a cell embedded in a hydrogel matrix allows quantitative measurement of the three-dimensional traction forces exerted by the cell.
A soft X-ray microscope design using partially incoherent light and a sample holder that can be tilted permits three-dimensional ultrastructural imaging of cryopreserved adherent mammalian cells without chemical fixation.
Defined surfaces displaying heparin-binding peptides support long-term culture of multiple human embryonic and induced pluripotent stem cell lines in defined media.
A statistical approach to quantitatively derive single and double mutant fitness from colony-based growth assays is described. The resultant SGA score permits assessment of yeast fitness and genetic interactions on the genome scale.
The mixture of isoforms model (MISO) assesses the confidence in estimates of the abundance of spliced exons or isoforms from paired-end RNA-seq data and detects their differential expression.
High-throughput sequencing of RNA fragments generated from a single-strand RNA-specific nuclease followed by novel computational analysis yields structural insights into noncoding RNA at the transcriptome level.
Protein modules that dimerize rapidly upon exposure to light are reported. They permit light-induced control of dimerization of fused protein targets and can be manipulated with two-photon illumination for experiments in thick samples and in vivo.
Readily synthesized maltose–neopentyl glycol (MNG) amphiphiles are useful reagents for stabilizing, extracting and crystallizing a variety of integral membrane proteins and have favorable properties relative to conventional detergents.
A polished and reinforced thinned-skull procedure is used to create a large, chronically stable window in the skull that allows repeated imaging of cortical structures as well as optically guided physiological manipulation. It is proposed as an alternative to the craniotomy and current thinned-skull methods.
An efficient one-step method for re-engineering mouse mutant alleles harboring loxP and FRT sites is reported. It may be applied to the large collection of targeted alleles from the International Knockout Mouse Consortium.
By pooling barcoded genomes of thirty rats before enrichment of a 1.4-megabase target sequence, mutation discovery in 770 genes is achieved with high accuracy.