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Kwong et al. use nanoparticles coated with protease substrates to generate mass-encoded synthetic biomarkers for sensitive detection of fibrosis and cancer in mice.
The Cuffdiff 2 algorithm improves analysis of RNA-Seq data by accounting for sample-to-sample biological variability and the complexity of transcript isoforms.
Petsch et al. apply mRNA vaccination for the first time to infectious disease, demonstrating immunogenicity and/or protective effects against influenza virus in mice, ferrets and pigs.
To facilitate the conversion of maize into biofuels, Shen et al. equip the plant with a thermoregulated intein-modified xylanase that does not compromise yield and allows cell-wall degradation at high temperatures.
Tan et al. use a multiplex screening method to systematically evaluate ∼500,000 drug pairs assembled from a collection of 1,000 FDA-approved or clinically tested compounds, and identify drugs that synergize to inhibit HIV replication.
Komori et al. show that hepatocytes, pancreatic islets and thymocytes flourish in the mouse lymph node, suggesting that lymph nodes could serve as a transplantation site for cell therapies.
By combining two metabolic labeling techniques, Eichelbaum et al. detect and quantify large numbers of secreted proteins, including low-abundance proteins such as cytokines.
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.
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.
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.