Research articles

Du et al. describe a bead-based method for high-throughput detection of phosphorylated tyrosine kinases and use it to profile 130 human cancer lines. They show that the tyrosine kinase SRC is frequently activated in glioblastoma cells and that a SRC inhibitor blocks the growth of glioblastoma tumors.

Foust et al. describe a viral vector that crosses the blood-brain barrier, providing a non-invasive method for delivering therapeutic genes to the central nervous system. A single intravascular injection of AAV9 results in widespread transduction of astrocytes in adult mice and of astrocytes and neurons in neonatal mice.

The physical properties that determine the propensity of a protein to form a well-ordered crystal suitable for structure determination are poorly understood. An analysis of large-scale crystallization results generated by a structural genomics consortium highlights the importance of low-entropy surface features capable of mediating protein-protein interactions.

Foudi et al. report a method for monitoring the turnover of hematopoietic stem cells that has several advantages over BrdU labeling. Using drug-inducible expression of a histone 2B–GFP fusion protein, which permits a more sensitive analysis of division history, the authors detect hematopoietic stem cells that cycle at a very slow rate.

Cox and Mann describe MaxQuant, a suite of algorithms for the analysis of high-resolution mass spectrometry data. The approach achieves substantial improvements in the accuracy of mass measurements and the peptide identification rate.

During long-term culture, human embryonic stem (hES) cells may acquire chromosomal abnormalities that compromise their potential clinical utility. A study of 17 hES cell lines reveals various genomic changes, including trisomies and monosomies, an amplification at 20q11.21 and a derivative chromosome 18.

During long-term culture, human embryonic stem (hES) cells may acquire chromosomal abnormalities that compromise their potential clinical utility. Lefort et al. show that an amplification at 20q11.21 arose at relatively late passage number in three of five hES cell lines.

Gene silencing by siRNA generally relies on short RNA duplexes containing two strands of the same length. Sun et al. show that an asymmetric duplex with a shortened passenger strand silences its target gene effectively while reducing off-target effects mediated by this strand.

Critical considerations in the design and analysis of ChIP-seq experiments include how to align sequenced tags to the genome, how to detect binding sites and how to estimate the number of tags needed to confidently determine where a protein binds DNA. Using data set for three transcription factors, Kharchenko et al. address these considerations by comparing three novel algorithms with published computational methods.

Fan et al. describe a microfluidic chip for multiplexed analysis of proteins in a finger prick of blood. The chip separates plasma from diluted whole blood and quantifies panels of serum proteins in about 10 minutes, minimizing protein degradation.

Analyzing the massive and heterogenous datasets from genome-wide chromatin immunoprecipitation (ChIP) datasets presents several computational and statistical challenges. Ji et al. present a software suite that integrates all steps in ChIP-chip and ChIP-seq data analyses and illustrate the use of these tools by comparing the ability of the two platforms to identify transcription factor binding sites.

Chechik et al. define activity motifs, which extend the concept of a network motif from the static to the dynamic realm. Mapping functional data onto network structure enables them to reveal new systems-level principles describing how yeast cells integrate exogenous signals and use transcriptional regulation to optimize metabolic responses to environmental perturbations.

Fruit-specific overexpression of a pair of snapdragon transcription factors produces tomatoes that uniformly accumulate anthocyanins at levels unprecedented for metabolic engineering. When included as a dietary supplement, the purple tomatoes increase the life spans of tumorigenic p53 knockout mice.

The picomolar sensitivity of fluorescence-based protein detection limits the use of protein arrays in research and clinical diagnosis. Chen et al. use antibody-tagged single-walled carbon nanotubes as multicolor Raman labels to detect femtomolar levels of serum analytes over a wide dynamic range.

Aasen et al. boost the efficiency of human induced pluripotent stem (iPS) cell generation 100-fold by starting with keratinocytes rather than fibroblasts. They also produce iPS cells from plucked adult hair, an easily accessible source of cells that avoids the need for a biopsy.

One strategy for advancing induced pluripotent stem (iPS) cell technology toward the clinic is to replace the reprogramming genes with small molecules. Huangfu et al. show that the HDAC inhibitor valproic acid can substitute for the reprogramming gene Klf4, allowing human iPS cells to be generated with only two transgenes, Oct4 and Sox2.

The development of effective methods for generating cardiomyocytes from embryonic stem cells may prove useful in cell replacement therapies and drug screening. Chen et al. show that activation of Notch signaling efficiently converts hematopoietic progenitors derived from mouse embryonic stem cells into cardiovascular progenitors that give rise to large numbers of cardiomyocytes.

Munger et al. show that infection with human cytomegalovirus upregulates fatty acid biosynthesis and that pharmacological inhibition of this pathway inhibits replication of both this virus and influenza A. This approach, the first to reliably map major carbon fluxes in mammalian cells, extends the promise of metabolomics from diagnostic applications to identification of new therapeutic concepts.

Penicillins and derived β-lactam antibiotics are essential in healthcare. To gain more insight into penicillin synthesis van den Berg and colleagues sequence and analyze the genome and transcriptome of the filamentous fungus Penicillium chrysogenum.

The HIV-1 protein Vif, which promotes degradation of the host cell's antiviral APOBEC3 proteins, has yet to be targeted for therapeutic intervention. Nathans et al. use a high-throughput fluorescence screen to identify a small molecule that inhibits HIV replication in cultured cells by antagonizing Vif in an APOBEC3-dependent manner.