Volume 6 Issue 1, January 2009

The maturation of large-scale protein-protein interaction methodologies calls for improved methods to assess performance and data quality.

Tagging ribosomes in a cell type–specific way allows the isolation of mRNAs that are being translated in these cells.

A new generation of brilliant X-ray laser sources will be coming online within the next few years. Researchers now show that using these lasers to determine the structures of single molecules should be possible.

Scientists create a high-throughput platform for proteome-scale assessment of protein stability.

A new spin on a popular imaging technique allows researchers to accurately visualize tumors deep within the tissues of live mice.

A device to cool localized areas of the zebra finch brain allows researchers to investigate how the timing of birdsong is controlled.

After a long period of measured development and a recent surge of technical advances driven by physicists, super-resolution fluorescence microscopy emerged in 2008 as a powerful tool for biologists. Kelly Rae Chi reports.

A brief description of the theory and methods behind super-resolution fluorescence imaging.

Super-resolution microscopy is poised to revolutionize our understanding of the workings of the cell. But the technology still has some limitations, and these must be taken into consideration if widespread application is to yield biological insight.

Methods to reprogram somatic cells to pluripotency have improved and will improve further; more biological studies of these cells are forthcoming.

After constructing a synthetic genome, the challenge is to prove its functionality.

Automated imaging has the power to transform microscopy into a more quantitative technique with new capabilities.

Quantitative mass spectrometry–based proteomics is now being applied on a large scale to address interesting biological questions.

New methods addressing the challenges in membrane protein expression, solubilization and crystallization promise to yield many more atomic structures.

Optical methods to image deep into thick samples make it increasingly possible to watch biological processes in vivo.

Although microRNA target predictions are continually improving, high-throughput validation of direct interaction is still needed.

The use of light for active cellular control rather than just passive observation continues to make headway.

A new strategy is presented to functionally knock down microRNAs in a mouse.

High-throughput yeast two-hybrid screening is used to generate the largest C. elegans interactome resource available thus far. Using an empirical quality control framework presented in Venkatesan et al., also online, the data set is evaluated for quality and is used to estimate the total size of the worm interactome.

Different experimental designs for protein interaction mapping are modeled to compare their efficiency in completing an interactome map. Testing of the strategy that minimized the final experimental cost in an ongoing Drosophila melanogaster interactome project found 450 high-confidence interactions using only 47 microtiter plates.

To study microRNA function in vivo, the authors optimize lentiviral-driven expression of microRNA target sequences in mice and show dose-dependent inhibition of microRNA-mediated regulation of reporter constructs as well as of natural microRNA targets. With the inhibition of a miR-223, they can phenocopy the knockout of this microRNA.

This variant ascertainment algorithm, or VAAL, uses short sequence reads of haploid bacterial genomes to first locally assemble the reads and then compare these assemblies to the reference genome. This allows VAAL to detect all types of variants ranging from single-nucleotide polymorphisms to large insertions or deletions.

A combination of in vitro protein synthesis and microfluidics is used to measure protein-protein interactions between 43 proteins in Streptococcus pneumoniae. The method does not require expression within cells and is amenable to large-scale experiments.

A web-based protein-protein interaction (PPI) analysis platform called PINA integrates PPI data from six public databases and provides tools to aid in the construction and analysis of PPI networks, including local recuration and annotation of existing records and manual addition of new records.

An infrared laser is used to activate gene expression from a heat shock promoter in single cells in Caenorhabditis elegans, and is shown to be more effective and less detrimental to cells than a visible laser used for this purpose.

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.

Some researchers say an eighty-year-old statistical method can make setting up and analyzing high-throughput screens and large-scale experiments faster and more efficient. So why are more biologists not flocking to use this tool?

Nature Methods' Method of the Year 2008 goes to super-resolution fluorescence microscopy. This series of articles—and the related movie—showcase how these novel imaging methods came into their own in 2008 and the incredible impact they promise to have in biological research.