Volume 10 Issue 7, July 2013

Inspired by his son, an electrical engineer brings microchip technology and portability to biology.

Visually organize complex data by mapping them onto familiar representations of biological systems.

X-ray imaging using synchrotron radiation reveals the cellular choreography of a developing frog embryo in spectacular detail.

Two methodological advances enable tracking of the walking behavior of fruit flies at single-leg resolution.

Reagents that recognize specific chemical modifications while ignoring the surrounding protein offer valuable proteomic insights.

Methodological optimization makes possible the long-awaited derivation of human embryonic stem cells from embryos obtained with somatic cell nuclear transfer.

A large library of peptides and phosphopeptides, along with their tandem mass spectra, serves as a resource for the proteomics field.

Binning based on differential read coverage, rather than sequence composition, allows separation of metagenomic sequence reads into species-level clusters that can be assembled into single chromosomes.

Being sure is good; being uncertain is not necessarily bad. Research teams are working to render uncertainty visual.

More than 40 years after the invention of semiconductor pH microtransducers known as ISFETs, this transistor-based technology may revolutionize quantitative PCR.

A synthetic biology terminator toolkit enables more sophisticated circuit design and gives insight into the mechanism of transcriptional termination.

Two approaches to serially enrich protein post-translational modifications allow the detection of multiple modifications in a single biological sample using mass spectrometry.

This comparison of five RNA-seq library preparation methods highlights metrics for assessing the suitability of the methods for samples with low amounts of RNA and/or those with low-quality RNA.

The integration of microRNA target sequence features and data from cross-linking and immunoprecipitation of Argonaute proteins, implemented in the hidden Markov model–based framework MUMMIE, provides accurate prediction of microRNA targets.

A mass spectrometry–based method using serial enrichments of different post-translational modifications (SEPTM) enables high-coverage proteomic analysis of multiple PTMs from a single biological sample.

Conditional genetic knockout is achieved in the rat by using zinc-finger nucleases to place loxP sites at specific genomic locations and introducing Cre recombinase under the control of a native promoter.

A semiconductor chip, coupled to an ion-sensitive field effect transistor (ISFET) pH sensor, can amplify and quantitate DNA in real time without dyes, cameras and external heating devices.

A method for enzymatically producing long, high-purity, single-stranded DNA oligonucleotides should find many applications in basic research, in DNA nanotechnology and in clinical fields.

Algorithms that account for and overcome the intrinsic pixel-dependent readout noise from scientific complementary metal-oxide semiconductor (sCMOS) cameras prevent localization artifacts and avoid substantial compromises in localization uncertainty in single-molecule imaging. When combined with multi-emitter fitting, sCMOS cameras allow video-rate single-molecule switching nanoscopy.

For genetically engineered circuits, the movement of RNA polymerase across the DNA during transcription needs to be tightly controlled. A large library of strong terminators will make circuit design easier and more efficient.

Automated methods are described for the determination of survival curves in C. elegans, enabling rapid and statistically rigorous studies of lifespan in this organism.

Barcode-enabled sequencing of tetrads (BEST) allows isolation and genotyping of individual yeast spores while maintaining their tetrad relationships.

Two methods for identifying protein isoforms that are concurrently phosphorylated and ubiquitylated are applied in yeast to identify phosphorylation sites that regulate ubiquitin proteasome–mediated proteome degradation.

RNA-seq of blood-derived RNA can aid discovery of the cause of disease, as well as preclinical research. However, the high content of globin mRNA and ribosomal RNA (rRNA) in blood samples limits the detection of rare transcripts and splice variants. The ScriptSeq^™ Complete Kit (Blood) is a new method to prepare directional RNA-seq libraries that are virtually free of globin mRNA and rRNA contamination and exhibit high detection of reference and novel genes.