News & Comment

Sequencing-based technologies for RNA discovery are playing a key role in deciphering the transcriptome and hold the potential to provide us with a census of RNAs and their functions.

The potential of mass spectrometry–based proteomics to advance biology and biomedicine is nearly unlimited but so is its potential for generating bad data. Apart from the pursuit of technological progress in protocols and instruments, stringent comparative analyses of different approaches are critical for fully developing the discipline.

Despite expansion of the fluorescent protein and optical highlighter palette into the orange to far-red range of the visible spectrum, achieving performance equivalent to that of EGFP has continued to elude protein engineers.

A wide range of methodology will be needed to bridge the gap between genome sequence and mechanistic understanding in biology. Recent advances in high-throughput genetic screening address this task.

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.

Here we introduce a new shorthand nomenclature for designating the disaccharide subunit structure of all glycosaminoglycans as a way to compare compositions and describe linear sequences. Each disaccharide structural code (DSC) comprises four alphanumeric characters that reflect the actual substituents and isomeric characteristics of each component sugar. Larger structures can be represented easily by forming concatamers. The structural transparency of this new nomenclature eliminates the need for ambiguous acronyms or difficult numeric representations.

Next-generation sequencing technologies are beginning to facilitate genome sequencing. But in addition, new applications and new assay concepts have emerged that are vastly increasing our ability to understand genome function.

A new generation of non-Sanger-based sequencing technologies has delivered on its promise of sequencing DNA at unprecedented speed, thereby enabling impressive scientific achievements and novel biological applications. However, before stepping into the limelight, next-generation sequencing had to overcome the inertia of a field that relied on Sanger-sequencing for 30 years.

When generating novel tailor-made proteins, protein engineers routinely apply the principles of 'Darwinian' evolution. However, laboratory evolution of proteins also has the potential to test evolutionary theories and reproduce evolutionary scenarios, thus reconstructing putative protein intermediates and providing a glimpse of 'protein fossils'. This commentary describes research at the interface of applied and fundamental molecular evolution, and provides a personal view of how synergy between fundamental and applied experiments indicates novel and more efficient ways of generating new proteins in the laboratory.

To characterize the contributions of individual amino acids to the structure or function of a protein, researchers have adopted directed evolution approaches, which use iterated cycles of mutagenesis and selection or screening to search vast areas of sequence space for sets of mutations that provide insights into the protein of interest.

Research performed where epidemics hit the hardest is necessary to bring solutions to the major health crises that plague poverty-stricken areas. Far from being limited to these areas, 'research in situ' can benefit health management worldwide. There are pressing technological needs to be addressed in order to facilitate such research.

Mass spectrometry has been rapidly maturing as the core technology at the heart of proteomics. The application of these powerful methods to the study of human diseases and their translation to the clinic, however, has been beset with unique challenges.

ProteomeBinders is a new European consortium aiming to establish a comprehensive resource of well-characterized affinity reagents, including but not limited to antibodies, for analysis of the human proteome. Given the huge diversity of the proteome, the scale of the project is potentially immense but nevertheless feasible in the context of a pan-European or even worldwide coordination. NOTE: In the version of the article originally published, Manfred Koegl’s name was misspelled. Additionally, Zoltan Konthur's affiliation was listed incorrectly; it should be Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany. These errors have been corrected in the HTML and PDF versions of the article.

Large-scale RNA interference (RNAi)-based analyses, very much as other 'omic' approaches, have inherent rates of false positives and negatives. The variability in the standards of care applied to validate results from these studies, if left unchecked, could eventually begin to undermine the credibility of RNAi as a powerful functional approach. This Commentary is an invitation to an open discussion started among various users of RNAi to set forth accepted standards that would insure the quality and accuracy of information in the large datasets coming out of genome-scale screens. Please visit methagora to view and post comments on this article

Fluorescence microscopy has undergone a renaissance in the last decade. The introduction of green fluorescent protein (GFP) and two-photon microscopy has allowed systematic imaging studies of protein localization in living cells and of the structure and function of living tissues. The impact of these and other new imaging methods in biophysics, neuroscience, and developmental and cell biology has been remarkable. Further advances in fluorophore design, molecular biological tools and nonlinear and hyper-resolution microscopies are poised to profoundly transform many fields of biological research.

Standard controls and best practice guidelines advance acceptance of data from research, preclinical and clinical laboratories by providing a means for evaluating data quality. The External RNA Controls Consortium (ERCC) is developing commonly agreed-upon and tested controls for use in expression assays, a true industry-wide standard control.