Volume 5 Issue 9, September 2008

A constant influx of new methods keeps research on microRNA biology fast-paced and can provide divergent vantage points.

Two research groups apply quantitative proteomics to study the effects of microRNAs on cellular proteins.

Two groups describe wiki platforms for community-based curation of gene annotations or biological pathways.

Researchers use tetrad analysis and high-density oligonucleotide tiling arrays to generate a high-resolution map of meiotic recombination events in budding yeast.

A serendipitous discovery reveals that an existing fluorescent protein is actually a specific sensor for superoxide.

Applying a classical solution to a cutting-edge problem, two groups used bacterial conjugation to construct Escherichia coli double mutants on a genome-wide scale. This will allow comprehensive genetic interaction screens in bacteria for the first time.

A decade after the introduction of genetically encoded Ca²⁺ indicator proteins (GECIs), a new generation of improved GECIs demonstrates their usefulness for the functional analysis of the mammalian brain in vivo.

A simplified strategy to enzymatically preadenylate bar-coded oligonucleotides to be used for capturing microRNAs in biological samples is described. This efficient method should greatly facilitate multiplex analysis and profiling of microRNAs.

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.

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.

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.

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.

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.

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.

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

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.

Could the latest high-throughput technologies propel chemical genomics screens forward in academic settings? After 18 months of careful design and planning, scientists at the Broad Institute's chemical biology platform are about to flip the switches and find out.