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A new method called functional ultrasound (fUS) is reported that allows imaging of transient changes in blood volume in the whole rat brain with a spatiotemporal resolution not attained by other functional brain imaging modalities.
The functional role of protein phosphorylation is determined not just by whether a particular site is phosphorylated or not but also by the site's stoichiometry. A method to determine the absolute stoichiometries of protein phosphorylation on a proteomic scale is described.
Membrane protein interactions and conformational changes can be sensitively monitored with two-photon polarization microscopy, a method that takes advantage of the anisotropic absorption properties of fluorescent proteins. The authors applied the method to image G-protein activation and changes in intracellular calcium concentration.
Two sequence-verified, clonal, publicly available collections of human open reading frames are reported. One collection is in a lentiviral vector for expression in mammalian cells; the other is in the Gateway vector system.
A framework and web interface for the large-scale and automated synthesis of human neuroimaging data extracted from the literature is presented. It is used to generate a large database of mappings between neural and cognitive states and to address long-standing inferential problems in the neuroimaging literature.
In this sequencing-by-synthesis approach, the incorporation of a terminal-phosphate labeled fluorogenic nucleotide by DNA polymerase results in the generation of a fluorescent dye that is trapped in a sealed microreactor and does not require real-time detection.
Quantitative analysis of Caenorhabditis elegans chemosensory behavior is achieved in a structured arena with microfluidic delivery of stimuli with precise spatial and temporal control. Also in this issue, Swierczek et al. report software for real-time behavioral analysis in worms.
Fiducial marks that can be visualized by both light and electron microscopy are generated by 'branding' fixed tissue with a near-infrared laser and will facilitate correlative light and electron microscopy.
The performance of low-power, continuous-wave stimulated emission depletion microscopy is improved by combining pulsed excitation with time-gated detection. This combination also simplifies super-resolution fluorescence correlation spectroscopy.
A linear, one-tube amplification procedure generates sufficient amounts of material from chromatin immunoprecipitation (ChIP) and reChIP experiments to allow high-throughput sequencing.
The Multi-Worm Tracker permits real-time, high-throughput, quantitative analysis of behavior in Caenorhabditis elegans. It should enable screens for genes implicated in complex worm behaviors. Also in this issue, Albrecht and Bargmann apply microfluidics to study worm chemosensory behavior with high spatial and temporal precision.
A microfluidic setup for nanoliter-volume perfused clonal culture and imaging of thousands of nonadherent cells is applied to study signaling and proliferation in hematopoietic stem cells.
A multilaboratory pilot project demonstrates that hybridoma and phage display technologies can be applied to produce high-affinity, high-specificity renewable antibodies to a set of 20 human SH2 domain proteins in a reasonable time frame, suggesting that a systematic, large-scale effort to generate renewable protein binders will be feasible.
Both identified and unidentified peptide mass spectra can be clustered and represented as consensus spectra in a spectral archive, offering new ways of interpreting proteomics data. A software tool for clustering billions of spectra is presented, as is a 1.18-billion spectra spectral archive.
The comparison of cross-linking and immunoprecipitation (CLIP) and photoactivatable ribonucleoside–enhanced CLIP (PAR-CLIP) protocols shows specific biases of each method in enriching subsets of binding sites of RNA-binding proteins and shows ways around these biases.
An algorithm to combine the results of different quantitative proteomics data processing workflows is presented. The method substantially increases the number of proteins that can be quantified in a proteomics experiment.
Three-dimensional structural RNA modules, defined as ensembles of stacked arrays of ordered non-Watson-Crick base pairs, are found in many RNAs and play important functional roles. The presented computational tool, RMDetect, allows the identification of common RNA modules from sequence alone.
Judicious choice of probes and imaging conditions allows two-dimensional super-resolution imaging of live cells at speeds up to 2 Hz with ~25-nm resolution and three-dimensional super-resolution imaging at ~1 Hz with ~30 nm x-y and ~50 nm z dimension resolution using stochastic optical reconstruction microscopy (STORM).
A protein-trap mutagenesis system efficiently disrupts expression and reports endogenous expression patterns of genes in the zebrafish. The authors used it to generate an initial collection of 350 freely available fish lines.
