Articles in 2010

Two new approaches to neurochemical monitoring in vivo—an improved real-time microsensor and genetically engineered cells that sense neurotransmitter levels—address the critical issue of brain reactivity to implanted devices.

A surprisingly simple method provides an effective way of correcting optical distortions in two-photon fluorescence microscopy and recovers nearly ideal images of inhomogeneous thick samples.

Mobile computing platforms such as the iPhone are beginning to make inroads into the laboratory—serious prospect or fairy tale?

Adapting optics: techniques for seeing stars scale to cells.

An in-depth, systems biology approach to analyzing a 'reduced genome' bacterium reveals startling complexity.

By sampling a two-dimensional diffraction pattern on a spherical detector, three-dimensional structure determination of single molecules should be possible from a single measurement.

By grouping short reads derived from the same long genomic fragment, the reads can easily be assembled into fragments that approach the length of capillary sequencing reads.

Mass spectrometry–based proteomics is still rapidly expanding, not just in terms of the methods and instruments but also the biological questions.

Conventional extracellular electrode recordings are generally limited to monitoring action potentials. But use of extracellular gold microelectrodes with microspines that are engulfed by a neuron generates efficient electrical coupling and allows detection of both action potentials and subthreshold synaptic potentials with a signal-to-noise ratio similar to that of conventional intracellular recordings.

Single-molecule fluorescence resonance energy transfer (smFRET) is applied in live cells and reveals the conformational changes of individual SNARE proteins upon entering a SNARE complex.

Microwestern arrays combine the advantages of scalability of reverse phase protein arrays and the information content of western blotting for analyzing protein abundance and modification state with high sensitivity and throughput. The method is demonstrated for analyzing phosphorylation state changes in the EGF receptor signaling network using Bayesian network modeling.

Lifetime screening of fluorescent protein variants by fluorescent lifetime imaging microscopy of bacterial colonies identifies bright, high-quantum-yield fluorescent protein variants including a cyan fluorescent protein named mTurquoise that is 1.5-fold brighter than mCerulean and has a mono-exponential fluorescence decay.

By using a reverse transcriptase for the bridge-amplification step on the Illumina Genome Analyzer, RNA conversion to cDNA and sequencing take place directly in the flowcell and yield highly accurate strand-specific sequences.

Short sequence reads are grouped based on the long genomic fragments from which they derive, enabling efficient local assembly of the long fragments and therefore accurate de novo genome assembly and metagenome sequencing.

Reduced-representation bisulfite sequencing, optimized for DNA amounts as low as 30 nanograms and robust enough to process DNA extracted from formalin-fixed, paraffin-embedded tissue, allows genome-scale mapping of DNA methylation in many samples.

The Negatome is a database of non-interacting protein pairs that can be used for training protein-protein interaction prediction algorithms.