Proteomics

MaxQuant software for proteomics

Cox and Mann introduce MaxQuant, a software package for managing large quantitative mass spectrometry datasets. MaxQuant efficiently detects peaks, isotope clusters and stable amino acid isotope (SILAC)-labeled peptide pairs. It yields very high mass accuracy information by integrating multiple mass measurements, facilitating more effective database searching and thus greater peptide identifications in complex proteomes. The software is available at http://www.maxquant.org/.

Cox, J. & Mann, M. Nat. Biotechnol. 26, 1367–1372 (2008).

Cell biology

SUPER bilayers

Membrane fission is essential for both organelle and lipid vesicle formation but remains technically challenging to study. Pucadyil and Schmid now report supported bilayers with excess membrane reservoir (SUPER) templates, which are compatible with both real-time microscopy and biochemical assays. They use the SUPER templates to reevaluate the relationship between dynamin and GTP during membrane fission.

Pucadyil T.J & Schmid S.L. Cell 135, 1263–1275 (2008).

Gene transfer

Bypassing the blood-brain barrier

The ability to deliver therapeutic genes to the brain and spinal cord would likely have a great impact on medicine, but it has been very challenging to develop strategies to bypass the blood-brain barrier. Foust et al. discovered that the adeno-associated virus 9 vector effectively bypasses the blood-brain barrier, which they demonstrated by delivering and expressing GFP in the central nervous system in both neonatal and adult mice.

Foust, K.D. et al. Nat. Biotechnol. 27, 59–65 (2009).

Bioinformatics

Finding protein functional regions

Structural genomics efforts have yielded a large number of protein structures for which their functions are unknown. To begin to characterize these proteins, Nimrod et al. present PatchFinder, an algorithm that detects clusters of highly conserved residues on protein surfaces, which likely correspond to functional regions. They also created N-Func, a database containing 757 structures of previously unannotated proteins. PatchFinder and N-Func are available at http://patchfinder.tau.ac.il/.

Nimrod, G. et al. Structure 16, 1755–1763 (2008).

Microfluidics

Paper and tape microfluidics

Cheap, simple and rugged devices are needed for diagnostic applications in the field and in developing countries. Martinez et al. describe the fabrication of three-dimensional microfluidic devices made from layers of paper and water-impermeable double-sided tape, patterned such that fluid is wicked within and between the layers of paper. Such devices cost only 3 cents to make and may find applications in environmental monitoring as well as healthcare.

Martinez, A.W. et al. Proc. Natl. Acad. Sci. USA 105, 19606–19611 (2008).