Letters in 2011

Rare transcripts remain enigmatic in part because they are difficult to detect robustly on a large scale. Mercer et al. show that targeted RNA sequencing after array capture can reach saturating depth at the targeted loci and reveal unprecedented levels of rare noncoding transcripts and previously unrecognized spliced variants from important loci such as p53 and HOX.

Mass-release of sterile male mosquitoes is a promising option for controlling dengue and malaria, but it has never been shown that lab-raised transgenic males can compete effectively with their wild counterparts outside laboratory conditions. Promising results from a restricted field trail now suggest the feasibility of extending the approach for large-scale mosquito-control programs.

With the cost of DNA sequencing falling rapidly, sample preparation is becoming a bottleneck to surveying genetic variation across large populations or performing clinical diagnostics. Myllykangas et al. present an efficient approach for targeted sequencing in which genomic regions of interest are captured and sequenced inside a flow cell using a common oligonucleotide probe.

Factor Xa would be ideally suited to control unregulated bleeding were it not for its extremely short half-life and tendency to overactivate clotting mechanisms. Ivanciu et al. show that a longer lived but less active variant of the protease restores hemostasis in mouse models of hemophilia without thrombotic complications.

The cynomolgus and Chinese rhesus macaques are used as animal models in biomedical research. Yan et al. sequence their genomes and compare the sequences to that of the Indian rhesus macaque, providing a genetic foundation for interpreting research results.

The benefits of crops that produce insecticidal toxins from Bacillus thuringiensis (Bt) are threatened by the emergence of insect resistance. Working with five major crop pests, Tabashnik et al. show that previously described variant Bt toxins kill pests rendered resistant to native Bt toxins by multiple mechanisms.

Using cells derived from human pluripotent stem cells for therapeutic applications carries a risk that rare undifferentiated cells in the transplant will give rise to teratomas. Tang et al. identify a new antigen on the surface of human pluripotent cells that, combined with other antigens, enables complete depletion of teratoma-initiating cells.

The similarities and differences between the disease mechanisms underlying the sporadic and familial forms of amyotrophic lateral sclerosis (ALS; Lou Gehrig's disease) are poorly characterized. Using human astrocytes derived from neural progenitor cells obtained from cadaveric spinal cords, Haidet-Phillips et al. propose that sporadic and familial ALS share common pathogenic pathways involving astrocyte-mediated damage.

Imaging the spatial and temporal complexity of molecules in living cells and tissues could provide important data for a quantitative understanding of biology. Capoulade et al. introduce a light sheet–based microscope that performs fluorescence correlation spectroscopy at each pixel of an image to provide spatially resolved maps of protein dynamics.

Fluorescent proteins with excitation and emission maxima in the near-infrared would be especially useful because of the low light absorbance of mammalian tissues in this optical window. Verkhusha and colleagues present a bright, photostable fluorescent protein with optimized near-infrared spectra that does not require the addition of exogenous co-factors.

Cost-effective analysis of allelic variation can be problematic for polyploid crops. By sequencing leaf transcriptomes from a mapping population of oilseed rape and its progenitors, Bancroft et al. provide a general strategy to construct linkage maps for comparative genome analysis.

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.

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.

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.

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.

Delivery of therapeutic siRNA to specific tissues is a major challenge. Alvarez-Erviti et al. show that exosomes—small vesicles that are naturally secreted by many animal cells—can be engineered to transport siRNA specifically to the brain in mice.

Methods to measure affinities of membrane proteins and soluble ligands are cumbersome and often rely on truncations or other modifications of the membrane protein or ligand. Baksh et al. show that backscattering interferometry is a sensitive and accurate technology for the label-free quantification of ligand–membrane receptor interactions.

Proteins have been largely unexplored as feedstocks for synthesizing fuels and chemicals in microbes, in part because their degradation is not thermodynamically favored in the cell. Huo et al. overcome this by engineering nitrogen flux in E. coli, creating microbes that generate biofuels when grown in protein-rich medium.