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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.
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.
Functional genomics requires facile methods to recover sequences of interest. Fu et al. show that the phage proteins RecE and RecT mediate recombination between linear DNA fragments and can facilitate natural product discovery.
The ability to identify antibodies circulating in the bloodstream would advance immunology and vaccinology research and the development of therapeutics. Cheung et al. couple proteomics with next-generation sequencing of RNA from B cells to clone antibodies directly from the sera of immunized rabbits and mice.
Methods for specific gene silencing have advanced as far as clinical trials, but a similar set of tools does not exist for increasing gene expression. Modarresi et al. demonstrate gene-specific upregulation in vivo by treating mice with oligonucleotides that inhibit the function of natural antisense transcripts.
Vaccination with a virus-expressed cDNA library derived from normal prostate cells can cure established prostate cancer in mouse models. Pulido et al. extend this approach and identify specific tumor-associated antigens from tumor-derived virus-expressed cDNA libraries that can be used in combination to cure established melanoma in mice.
Two groups describe approaches for synthesizing and assaying the function of thousands of variants of mammalian DNA regulatory elements. Melnikov et al. use their results to engineer short optimized regulatory elements in human cells, whereas Patwardhan et al. study enhancers hundreds of bases long in mice.
An improved understanding of enhancers in mammalian genomes could facilitate the design of new regulatory elements. Melnikov et al. synthesize thousands of ~90 nt enhancer variants, assay their activity in human cells and use the data to rationally optimize synthetic enhancers.
Genetic analysis of agronomic traits in crops is complicated by the long generation times and challenges of growing and phenotyping plants in large field trials. Abe et al. show how whole genome resequencing can be used to identify the genetic basis of subtle phenotypic traits in rice.
Vascular smooth muscle cells have multiple embryological origins. Cheung et al. present a chemically defined protocol for differentiating human pluripotent stem cells into vascular smooth muscle subtypes arising from neuroectoderm, lateral plate mesoderm and paraxial mesoderm.