Research articles

Glycan structure, attachment site and the glycoprotein from which it came can be identified with a method to enrich for glycoproteins from complex biological samples, digest them on a bead and release the glycopeptides for mass spectrometry analysis.

A cocktail of three small molecules improves the efficiency of reprogramming human fibroblasts to induced pluripotent stem cells and allows survival of the cells after trypsinization.

Protein complexes can be detected, counted and localized within the bacterium Leptospira interrogans by combining quantitative mass spectrometry–based proteomics analysis with cryo-electron tomography, with the aid of an improved template-matching method.

Activity of yeast cytosine deaminase can be both positively and negatively selected by adjusting growth conditions. Adapting this life-death selection to a protein complementation assay based on the enzyme allows dissection of protein-protein interactions and protein functions in yeast.

Chromatin conformation capture on chip, or 4C, a technique developed to investigate the interaction of one chromosomal region with the rest of the chromatin, can also provide high resolution mapping of translocations and inversions in selected chromosomal regions.

Engineered splicing factors, consisting of an RNA recognition motif and a functional splicing module, can target a specific mRNA sequence and activate or suppress splicing of endogenous mRNAs.

Optically trapping an individual E. coli cell allows the long-term quantification of bacterial swimming phenotype: the stochastic transitions between 'running' and 'tumbling' as well as changes in swimming speed and direction.

Computational compensation for the loss of information from a cellular marker visualized in one fluorescence channel increases the number of markers that can be used to study a population of cells. This should allow a more detailed molecular understanding of heterogeneity in a cellular population.

High-throughput sequencing of Mariner transposon insertion libraries is used for quantitative studies of fitness and of genetic interactions in Streptococcus pneumoniae. The approach should allow similar studies in several microorganismal species.

By targeting a mutant Flp recombinase that forms a covalent protein-DNA complex to a single FRT site placed anywhere in the yeast genome, the authors can study repair pathways activated by a single genomic insult as well as events at the site of damage.

Quantitative information is necessary to determine which protein interactions are the most relevant in a cellular context. A defined set of affinity purification experiments combined with quantitative mass spectrometry analysis allows the determination of dissociation constants for all protein targets interacting with an introduced ligand.

Fluorescence-activated cell sorting of worm embryos promises to replace manual sorting of staged embryos and yields large populations highly enriched in specific developmental stages, allowing high-throughput genomic analysis.

Using an axial detector, scanning transmission electron microscopy allows three-dimensional tomographic reconstruction of micrometer-thick sections of biological samples, at a resolution comparable to that obtained on thin sections.

Technical modifications of existing methods lead to a somatic cell nuclear transfer method in the zebrafish, which yields adult cloned fish with healthy offspring that carry donor traits.

A series of genetically encoded fluorescent sensors for intracellular Zn²⁺ with binding affinities spanning the picomolar and nanomolar ranges show that cytosolic Zn²⁺ is buffered at ∼0.4 nM. Targeting of the sensors to insulin-containing secretory granules indicates a free Zn²⁺ concentration between 1 and 100 μM in these organelles.

A human embryonic stem cell line, ErythrRED, harbors a red fluorescent protein under the control of regulatory sequences from the beta-globin locus, as a reporter for erythroid differentiation.

A general approach to address the 'phase problem' in protein crystallography is described, allowing protein structures to be directly solved from 2 Å resolution diffraction data without using heavy atom doping or relying on a preexisting structure model for molecular replacement.

Deletions of polyguanine tracts in Caenorhabditis elegans deficient in the DOG-1 DNA helicase can be exploited to generate deletion alleles of several genes for which no such alleles exist in this organism.

A digital atlas of C. elegans at the post-embryonic L1 stage is presented, along with automated methods for nucleus segmentation and annotation. These resources will enable quantitative analyses of nuclear spatial arrangements as well as high-throughput single-cell analyses in this organism.

PyroNoise, an algorithm that preclusters the flowgrams generated on a 454 GS FLX with DNA extracted from microbial samples can distinguish between noise and genuine sequence diversity in a metagenomic dataset.