Articles in 2008

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.

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

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

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

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

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

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

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

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

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

With its tremendous potential for understanding cellular biology now poised to become a reality, super-resolution fluorescence microscopy is our choice for Method of the Year.

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.

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.

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 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.

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.

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.