Volume 6 Issue 6, June 2009

Researchers develop an approach to selectively isolate and profile cell-surface proteins by targeting the glycopeptides, a strategy that could be used to generate an atlas of cell-surface protein 'barcodes'.

Researchers use microRNAs to more efficiently generate induced pluripotent stem cells in the mouse.

Researchers integrate proteomics data with genomic-context analysis and develop a protein-function prediction tool to annotate functional orphans in Escherichia coli.

A new pH nanosensor changes color in acidic cell compartments by forming an unusual four-stranded DNA structure.

By combining methods for selective genome capture, allele enrichment and array resequencing, researchers create a pipeline for high-throughput variant detection.

Flying animals ranging from bugs to bats use a common mechanism to maintain control in turns a discovery that reveals hidden advantages of flapping-wing flight.

A multilaboratory study attempts to dispel some of the notions of the irreproducibility of mass spectrometry–based proteomics by pinpointing where the methodological problems are and where challenges remain.

Applying modern machine-vision techniques to the study of animal behavior, two groups developed systems that quantify many aspects of the complex social behaviors of Drosophila melanogaster. These software tools will enable high-throughput screens that seek to uncover the cellular and molecular underpinnings of behavior.

A multilaboratory analysis characterized the ability of 27 different labs to identify 20 proteins at equimolar concentrations in a highly purified test sample mixture using mass spectrometry. The results show that while the technology is reproducible, many common experimental problems arise, and improved search engines and databases are still needed.

Two bacterial artificial chromosome (BAC) libraries, spanning almost the entire D. melanogaster genome in insert sizes of 20 and 80 kb, that allow easy integration into the fruit fly genome at defined docking sites provide a rich resource to study gene expression and function.

Genomic fosmid libraries for Drosophila melanogaster and Drosophila pseudoobscura with an average insert size of 36 kilobases can easily be tagged and inserted into the fly genome. These resources will be valuable for evolutionary and developmental studies in the fly.

Expressing uracil phosphoribosyltransferase in specific tissues in the fly allows the incorporation of 4-thiouracil into newly synthesized RNA in vivo. The thio-labeled RNA can then be isolated and analyzed by routine procedures allowing the cell type–specific measure of RNA synthesis and decay rates.

On-array synthesis of over 20,000 shRNAs at a coverage of ∼30 shRNAs per gene, followed by cloning into lentiviral shRNA libraries and deconvolution of the complex libraries by deep sequencing, ensures high confidence in the observed knockdown phenotypes with low false-negative rates and few off-target hits.

A modular, automatable system using recombineering to facilitate multigene assembly, called Acembl, provides a streamlined approach for expressing multiprotein complexes in Escherichia coli.

An automated system for tracking large numbers of fruit flies over time and for detecting their behaviors is presented, and should allow high-throughput quantitative studies of fly behavior.

As tissues mature, they undergo shape changes that are the result of individual and collective cell movement triggered by cell-autonomous behavior or external forces. By measuring patterns of strain rates the authors can model these forces and quantify tissue shaping behavior.

In a short period of time, in vivo molecular imaging systems have become indispensable research tools in many clinical and basic research laboratories. But developers are now pushing the technology further in the hopes of making a new generation of platforms with greater accuracy and sensitivity for a wider array of applications.