Brief Communications in 2010

Robust and accurate quantification of human tumor tissue proteomes is made possible by combining the tissue sample with an 'internal standard' mixture of five relevant, stable isotope–labeled cell lines, followed by mass spectrometry analysis.

A theoretical and experimental treatment of fitting methods for localizing the centers of diffraction-limited spots is presented. Use of an analytical point spread function shows that maximum likelihood fitting is superior to both unweighted and weighted least squares Gaussian fitting.

An iterative algorithm implemented on a graphics processing unit determines maximum likelihood estimates of the positions of isolated fluorophores at a rate of 10⁵ localizations per second and allows real-time generation of super-resolution images with high precision.

Comparing the haplotypes of a few randomly microdissected chromosomes to a full genome-wide haplotype allows one to determine the long-range haplotype of chromosomes for which only one copy was captured.

A side-view endoscope permits the imaging of large fields of gastrointestinal and respiratory mucosa at high resolution in the mouse. The approach is applied to imaging changes during inflammation and tumor progression in the living mouse.

Fast protein interaction dynamics can be observed in cells via a fluorescence correlation spectroscopy–based method. Endogenous bait proteins are captured via quantum dots, and their interaction with fluorescently tagged prey proteins is monitored with high temporal resolution.

A Toxoplasma gondii strain that efficiently secretes Cre recombinase into infected host cells permits the deletion of genes specifically in the infected cells. It should facilitate the study of host-pathogen interactions in vitro and in vivo.

Using DNA microarray–derived gene expression data from complex tissues and the relative frequencies of cell types in the tissue as input the algorithm csSAM finds cell type–specific differentially expressed genes.

A Rosetta full-atom framework, called fragment assembly of RNA with full-atom refinement (FARFAR), allows the de novo structure prediction and design of noncanonical RNA motifs with near-atomic resolution.

Chemically inducible dimerization probes selectively target proteins to the surface of specific organelles or tether organelles to each other, thus allowing precise spatiotemporal analysis of signaling events.

By subdividing a charge-coupled device (CCD) array into subgroups using a digital micromirror device and offsetting exposure times, temporal pixel multiplexing allows simultaneous high-speed and high-resolution imaging using a single CCD. This imaging modality allows 250 Hz microscopic imaging of fast cellular responses with a 10-Hz 1.3 megapixel camera

Simple minicircle vectors carrying four reprogramming factors induce pluripotency in adult human adipose stem cells and in neonatal fibroblasts without integration into the genome.

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.

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.