Articles in 2008

A framework based on numerous empirical data, including protein-protein interaction reference sets, provides parameters for assessing the quality and coverage of protein-protein interaction datasets and estimation of the size of the human interactome. Braun et al., also in this issue, use the reference sets to help derive confidence scores for individual protein-protein interactions.

Use of the protein-protein interaction reference sets reported in this issue in Venkatesan et al. to benchmark four complementary protein-protein interaction assays, followed by the training of a logistic regression model, allows the assignment of standardized confidence scores to individual protein-protein interactions.

Massively parallel sequencing is a precise way to analyze copy-number variations given the right computational tools. An algorithm now facilitates the detection and fine mapping of copy-number gains and losses from millions of short sequence reads.

An efficient pipeline for mapping antibody epitopes is presented. Combining bacterial surface display of peptide libraries, flow cytometric sorting, and pyrosequencing, the approach is amenable to a high-throughput format and should find future application in whole-proteome studies.

Extension of multicolor three-dimensional stochastic optical reconstruction microscopy (STORM) allows super-resolution fluorescence imaging of whole cells and quantitative characterization of subcellular structures and their spatial relationships. This was demonstrated by imaging the entire mitochondrial and tubulin networks in cells.

Co-patterning of a membrane protein bait and a fluorescently labeled prey is used to examine protein-protein interactions in a semiautomated fashion in living cells. Photobleaching experiments and single-molecule imaging further allow dynamic studies of the interaction.

The spatial organization of the genome within the eukaryotic cell nucleus is not random. Automated imaging of thousands of live yeast is now used to build high-resolution probabilistic maps of the locations occupied by individual loci.

The two major mechanisms for peptide fragmentation by mass spectrometry, collision-activated dissociation (CAD) or a newer method, electron transfer dissociation (ETD), display different efficacies for different peptide chemistries. A decision tree algorithm, which can be embedded into instruments with both CAD and ETD capabilities, selects the optimal fragmentation method to improve the chances of successful peptide identification.

The combination of single-molecule fluorescence resonance energy transfer measurements of multiple dye pairs with probabilistic data analysis allows quantitative measurement of the position of flexible domains in macro-molecular complexes. The method was used to determine the three-dimensional probability density of the position of RNA exiting the transcription elongation complex.

Time-resolved wide-angle X-ray scattering (TR-WAXS) using synchrotron radiation can be used to observe dynamic protein structural changes with nanosecond time resolution in solution, complementing time-resolved optical spectroscopy and Laue crystallography methods.

Targeted regions of the human genome are resequenced in multiplex with Illumina technology, and the pipeline is evaluated for polymorphism discovery and genotyping.

Using both behavioral and electrophysiological readouts, Channelrhodopsin-2, a light-gated cation channel, is applied to the study of synaptic function in Caenorhabditis elegans.

A chromatin immunoprecipitation and sequencing (ChIP-Seq) data analysis package, QuEST, facilitates transcription factor binding site discovery at about 20-base-pair resolution.

A new prediction algorithm for microRNA targets, mirWIP, is presented. The algorithm weights target site features based on their enrichment in an experimentally defined immunoprecipitation dataset and identifies verified miRNA-mRNA interactions in Caenorhabditis elegans with improved specificity compared to current methods.

To study long-term changes in neuronal circuits at single-cell resolution, a Troponin C–based Ca²⁺ indicator protein has been reengineered to increase the signal strength. This allows repeated measurements, over days and weeks, of orientation selective neurons in mouse visual cortex. Hasan et al., also in this issue, describe the use of a similar sensor for recording neuronal activity in vivo.

Measurement of in vivo neuronal activity with single neuron and single action potential resolution is important for studying neuronal function. Delivery of a FRET-based fluorescent Ca²⁺ indicator protein using adeno-associated virus results in high expression levels allowing in vivo detection of single action potentials at low firing rates. Griesbeck et al., also in this issue, describe the use of a similar sensor for recording neuronal activity in vivo.

Holographic illumination allows the production of complex, user-defined, two-dimensional illumination patterns. Used to manipulate light-sensitive molecules in cells, this system permits their simultaneous excitation at multiple locations of arbitrary shape and size—facilitating spatial and temporal regulation of cell function.

An array-based high-throughput approach termed Escherichia coli synthetic genetic array, or eSGA, now allows comprehensive genetic interaction screens in bacteria. The method makes use of bacterial conjugation and robotic technology to generate double mutants on a genome-wide scale. In this issue, another paper presents GIANT-coli, a very similar approach.

An array-based high-throughput approach, genetic interaction analysis technology for Escherichia coli (GIANT-coli), now allows comprehensive genetic interaction screens in bacteria. The method uses bacterial conjugation and robotic technology to generate double mutants on a genome-wide scale. In this issue another paper presents eSGA, a very similar approach.

Cell-cell coupling via gap junctions has been extensively studied in vitro and in heterologous systems, but in vivo studies are still few. A new class of photoactivatable bioconjugates is now used to monitor gap junctional coupling in living Caenorhabditis elegans.