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Nutiu et al. repurpose an Illumina sequencer to quantitatively measure binding affinities between protein and DNA. The data reveal the complex interdependency among binding motif positions and allow improved prediction of gene expression.
Analyzing the dynamics of protein-protein interactions remains a key challenge in systems biology. Bisson et al. combine affinity purification with SRM mass spectrometry to monitor the assembly and dissolution of complexes containing the adaptor protein GRB2 after growth factor stimulation.
Prioritizing candidate biomarkers for verification remains a formidable obstacle to the translation of protein diagnostics to clinical applications. Whiteaker et al. assemble a multistage, targeted proteomics pipeline to relieve this bottleneck and use a mouse cancer model to demonstrate its analytical performance.
Rational strategies to prioritize candidate biomarkers should save resources and accelerate progress in diagnostics development. Addona et al. integrate proteomics into a pipeline for biomarker validation and use it to identify markers of cardiovascular injury in a scenario where patients serve as their own biological controls.
Widely applicable methods for mapping protein-RNA interactions by crosslinking achieve a resolution of ∼30–60 nucleotides. Zhang and Darnell analyze sites of mutation induced by the crosslinking to map binding at single-nucleotide resolution.
Carette et al. use a retroviral gene-trap vector to disrupt and tag >98% of all genes in a haploid human cancer cell line. Cells selected for a phenotype of interest are pooled and characterized by parallel DNA sequencing to circumvent time- and labor-intensive screening of individual clones.
Unlike most plants, date palms are either male or female. Assembly of a draft date palm genome, the first for a member of the order Arecales, reveals loci linked to gender and provides markers for improving traits such as fruit quality and ripening time.
Krencik et al. present a chemically defined system for differentiating human pluripotent stem cells to large numbers of immature astrocytes, which mature further after transplantation to the neonatal mouse brain. By applying regional patterning factors at the neuroepithelial stage, the authors also succeed in generating different astrocytes subtypes.
Larman et al. create a phage library containing >400,000 sequences encoding peptides that cover all open reading frames in the human genome. They then use this synthetic peptidome to discover novel autoantigens targeted by antibodies in the cerebrospinal fluid of individuals with a neurological autoimmune disease.
Magtanong et al. describe the first study to systematically analyze dosage suppression, a type of genetic interaction in which increased dosage of one gene compensates for mutation in another. The authors also develop reagents for future large-scale studies of dosage suppression.
Reconstructing full-length transcripts from high-throughput RNA sequencing data is difficult without a reference genome sequence. Grabherr et al. describe Trinity, an algorithm for assembling full-length transcripts from short reads without first mapping the reads to a genome sequence.
When embarking on a microarray-based study of genomic copy number variation, what's helpful for navigating the myriad of available array platforms and data analysis approaches? Pinto et al. evaluate six samples from healthy controls in triplicate on commonly used combinations of commercial arrays and analytic tools, providing realistic comparisons of performance.
High-throughput synthesis of long DNA molecules would open up new experimental paradigms in synthetic biology and functional genomics. Quan et al. take a step toward this goal by integrating oligonucleotide synthesis, amplification and gene assembly on a single microarray, and apply the technology to optimization of protein translation in a heterologous host.
The experiences of patients who try drugs that aren't approved for their disease have the potential to be mined for insights into drug efficacy. Wicks et al. rapidly monitored the efficacy of lithium treatment for 149 patients with amyotrophic lateral sclerosis using an online data collection tool and a patient-matching algorithm.
The relative contributions of RNA production, processing and degradation rates to cellular RNA levels are not well understood. Using pulsed metabolic RNA labeling of stimulated dendritic cells in conjunction with nCounter RNA quantification, RNA sequencing and computer modeling, Regev and colleagues unravel principles that determine RNA expression levels.
Frontini et al. propose to improve therapeutic angiogenesis by targeting perivascular smooth muscle cells rather than endothelial cells. They show that FGF9 causes smooth muscle cells to wrap around nascent endothelial tubes, generating blood vessels that are longer lasting and vasoreactive.
Much work remains to be done to understand the ‘black box’ of reprogramming, which involves changes in the expression of thousands of genes. Subramanyam et al. identify microRNAs that promote human cell reprogramming and use them to identify key cellular pathways and processes.
It has been extremely challenging to simultaneously improve both the yield and quality of cotton by conventional breeding. Extensive field trials indicate that regulated expression of an auxin biosynthesis gene in the epidermis of cotton ovules improves both the number and fineness of cotton fibers.
The sialic acid–dependent interaction of the co-inhibitory receptors CD24 and SiglecG prevents excessive inflammatory responses to pathogen infection. Chen et al. show that microbial sialidases exacerbate sepsis by disrupting this interaction and that sialidase inhibitors reduce mortality in an intestinal perforation mouse model of sepsis.
Essential genes have been effectively studied using temperature-sensitive alleles in yeast. Li et al. construct a large collection of temperature-sensitive yeast mutants and show how it enables high-throughput analyses of the function of essential genes.