Research articles

Frei et al. show that a new tri-functional reagent identifies unknown cell-surface receptors bound by known ligands on living cells.

Bacchus et al. describe the first experiments in mammalian cells that distribute complex behavior across several types of engineered cells, thereby mimicking natural multicellular systems.

Wong et al. differentiate human pluripotent stem cells into mature airway epithelial cells expressing CFTR, a gene involved in cystic fibrosis. Applying the method to induced pluripotent stem cells derived from cystic fibrosis patients provides a renewable source of cells for drug screening.

No mucosal adjuvant formulation is approved for clinical use, even though boosting immunity at sites of pathogen entry should increase the efficacy of nonreplicating vaccines. Wegmann et al. report that polyethyleneimine (PEI) acts as a potent mucosal adjuvant for protein antigens from influenza and herpes simplex virus, protecting mice against otherwise lethal infections.

López-Arredondo and Herrera-Estrella produce transgenic plants that express a bacterial phosphite-oxidoreductase gene to enable use of phosphite as a sole phosphorus source. This technology could reduce the amount of non-renewable phosphorus used as fertilizer and control weeds.

Mass cytometry can measure up to 34 markers on cells, but samples cannot be multiplexed. Bodenmiller et al. use metal ion tags to facilitate multiplexed mass cytometry analysis of human blood cell samples treated with 27 kinase inhibitors and 12 stimuli across a range of dosages and time points.

Bacterial attachment and biofilm formation are problematic for medical devices. Hook et al. present a high-throughput method to find materials that resist bacterial attachment and colonization.

Nawroth et al. combine rat cardiomyocytes and silicone polymer to make a jellyfish replica that mimics the propulsive behavior of its live counterpart. The design principles guiding this feat may facilitate tissue engineering of muscular organs.

Sequencing a genome and identifying genetic markers lays the groundwork for genome-wide association studies, but can be difficult to achieve for polyploid species. Harper et al. present an approach for performing association studies using genetic maps and markers generated from transcriptome sequencing data alone and apply it to the polyploid crop Brassica napus.

RNA-Seq of single cells has been limited by biases in transcript coverage and unknown technical variability. Ramsköld et al. describe a protocol to reproducibly recover full-length transcripts and use it to quantitatively analyze splice isoforms in single cells.

Optical maps of a genome, which are generated by imaging labeled single molecules of DNA, facilitate structural variation analysis and sequence assembly. Lam et al. immobilize DNA molecules in nanoscale channels, increasing the accuracy and throughput of the mapping process.

Chambers et al. use a combination of small-molecule pathway inhibitors to rapidly differentiate human pluripotent stem cells into nociceptors, a type of sensory neuron. The conversion occurs about three-fold faster than during development, suggesting that pathway inhibition may offer a general approach for speeding up the generation of specific cell types in vitro.

The multikilobase reads that can be produced by single-molecule sequencing technologies may span complex, repetitive genomic regions but have high error rates. Bashir et al. use these reads to organize contigs assembled from accurate, short-read data, facilitating the analysis of clinically important regions of an outbreak strain of cholera.

Single-molecule sequencing technologies can produce multikilobase-long reads, which are more useful than short reads for assembling genomes and transcriptomes, but their error rates are too high. Koren et al. correct long reads from a PacBio instrument using high-fidelity, short reads from complementary technologies, facilitating assembly of previously intractable sequences.

Khmelinskii et al. describe tandem fluorescent protein timers for measuring protein turnover and trafficking in living cells. Data from a single time point are used to determine protein stability, allowing the authors to screen for components of protein degradation pathways.

Lippmann et al. present a protocol for differentiating human pluripotent stem cells into blood-brain barrier endothelial cells. The cells should be useful for studying this endothelial barrier, including screening for drugs that can cross from the blood to the brain.

Drukker and colleagues differentiated human embryonic stem (ES) cells for 3 days and screened the cells for labeling by >400 antibodies. They identified cell-surface markers expressed on four classes of early progenitor cell.

To increase the affinity of designed protein inhibitors for influenza hemagglutinin, Whitehead et al. use yeast display and deep sequencing to measure the effects on binding of ~1,000 amino-acid substitutions. Rare beneficial mutations are then combined and screened, yielding inhibitors with ~25-fold lower dissociation constants.

Analyzing the effects of multiple promoter motifs on gene expression can be a laborious process. Sharon et al. present a high-throughput method to measure the expression of thousands of designed yeast promoters in a single experiment and use it to reveal new features of transcriptional regulation.

Completion of genome sequences for the diploid Setaria italica reveals features of C₄ photosynthesis that could enable improvement of the polyploid biofuel crop switchgrass (Panicum virgatum). The genetic basis of biotechnologically relevant traits, including drought tolerance, photosynthetic efficiency and flowering control, is also highlighted.