Volume 5 Issue 11, November 2008

Several studies evaluate high-density single-nucleotide polymorphism (SNP) arrays for the detection of copy-number variations in human genomes.

New findings challenge the assumption that aggregate genotype data, in which the single-nucleotide polymorphism (SNP) profiles of many people are pooled, conceal the identity of the individuals within that pool.

Researchers describe a method for evolving G protein–coupled receptors (GPCRs) with greater stability and enhanced expression.

A co-infection model of two pathogens in a nematode yields insights into the complex interaction between the microbes.

Researchers use microfluidics, a fluorescent reporter and modeling to quantify yeast's response to glucose availability.

A portable fiber-optic epifluorescence microscope allows real-time imaging of brain function with cellular spatial resolution in freely moving mice.

A miniature epifluorescence microscope that can be carried by a freely-moving adult mouse allows cellular-level imaging of neuronal spiking or measurement of microcirculation during normal behavioral activities.

Directed evolution experiments usually rely on high-throughput screening of very large libraries of mutants, but most of the mutants do not even yield stable, functional proteins. The concept of neutral drift can be used to generate small but highly polymorphic and stable mutant libraries as a starting point for further evolution.

A simple yet powerful super-resolution imaging approach based on switching off ordinary fluorophores and localizing those remaining or regaining fluorescence is illustrated using continuous widefield illumination and imaging of fixed and living cells labeled with rhodamine-derived dyes or fluorescent proteins. Biteen et al., also in this issue, describe related work using the ordinary fluorophore of EYFP for super-resolution imaging.

Previous work showed that the commonly used fluorescent protein EYFP can be bleached and reactivated. Exploiting this property allows super-resolution in vivo imaging of EYFP-labeled structures in living bacteria. Fölling et al., also in this issue, describe a related approach for super-resolution imaging using other ordinary fluorophores.

To determine long-range linkage between single-nucleotide polymorphisms (SNPs) and the repeat-containing region of a disease-related gene, Liu et al. develop SNP linkage by circularization (SLiC) and lay the groundwork for using allele-specific RNA interference to target insertion or deletion mutations in disease-associated genes.

Many different red fluorescent proteins display cytotoxicity substantially higher than EGFP when used for whole-cell labeling of bacterial and mammalian cells with standard high-level expression systems. An improved tetrameric red fluorescent protein called DsRed-Express2 allows high-level labeling with minimal cytotoxicity comparable to that of EGFP.

The two major mechanisms for peptide fragmentation by mass spectrometry, collision-activated dissociation (CAD) or a newer method, electron transfer dissociation (ETD), display different efficacies for different peptide chemistries. A decision tree algorithm, which can be embedded into instruments with both CAD and ETD capabilities, selects the optimal fragmentation method to improve the chances of successful peptide identification.

The combination of single-molecule fluorescence resonance energy transfer measurements of multiple dye pairs with probabilistic data analysis allows quantitative measurement of the position of flexible domains in macro-molecular complexes. The method was used to determine the three-dimensional probability density of the position of RNA exiting the transcription elongation complex.

Researchers at two Boston–based neuroscience centers are working to develop new imaging tools and technology with the hope of discovering the secrets behind how the brain functions.