Research articles

Label-free methods for assaying GPCR signaling promise to illuminate the effects of drugs in therapeutically relevant primary cells. Kostenis and colleagues demonstrate the utility of one such method, dynamic mass redistribution, in comparison with traditional second messenger–based assays.

The Microarray Quality Control consortium pitted 36 teams against each other to evaluate methods for creating genomic classifiers, computational tools for interpreting gene expression profiles. The performance of the classifiers on blinded validation data—and metadata on the analytic methods—reveal the challenges facing the field.

Recombinant glycoproteins produced in animal cell lines often bear the nonhuman sialic acid N-glycolylneuraminic acid (Neu5Gc). Ghaderi et al. show that two monoclonal antibodies in clinical use differ with respect to addition of Neu5Gc and propose that drug developers should consider the consequences of the Neu5Gc modification.

Which of the possible combinations of epigenetic marks have biological significance is a major question in epigenetics. Analyzing data from human T-cells, Ernst and Kellis discover 51 distinct, recurring combinations of histone modifications that can be correlated with the functional annotations of the underlying DNA sequences.

Polo et al. show that early-passage induced pluripotent stem cells retain an epigenetic memory of their cell type of origin. These epigenetic differences affect the cells’ differentiation potential and might be exploited to generate particular cell types of interest.

To identify genes affecting traits of interest in E. coli, Warner et al. describe a method to rapidly create and assay rationally mutated versions of every gene. The approach is applied to several traits, including tolerance to cellulosic hydrolysate, a biofuel precursor.

Efforts to study ubiquitination have been hampered by the large size of ubiquitin relative to other post-translational modifications. Xu et al. use a monoclonal antibody specific for the adduct left after proteolysis of ubiquitinated proteins to analyze the differential regulation of ubiquitination at distinct sites within the same proteins.

Much remains to be learned about the biology of mushrooms, which are an important source of food as well as secondary metabolites and enzymes of biotechnological importance. Ohm et al. report the sequence of the genetically tractable species Schizophyllum commune and identify genes involved in the formation of fruiting bodies and the degradation of lignocellulose.

Holt et al. describe an anti-HIV strategy in which human hematopoietic stem/progenitor cells are modified with zinc-finger nucleases to knock out the viral co-receptor CCR5. Transplantation of these cells into mice confers resistance to HIV, as shown by higher human T-cell counts and lower viral loads compared with animals that received unmodified cells.

Although general inhibitors of the ubiquitin-proteasome system have been reported, compounds targeting specific ubiquitylation enzymes should be beneficial in clinical applications and basic research. Orlicky et al. present an allosteric inhibitor specific to the yeast SCF^Cdc4 E3 ligase that prevents binding of the target protein to the WD40 domain of the complex.

The ability to control the activity of cellular signaling pathways is useful for dissecting their functions. Using a short protein insert, Karginov et al. engineer protein kinases that can be specifically activated by the small-molecule rapamycin.

Although general inhibitors of the ubiquitin-proteasome system have been reported, compounds targeting specific ubiquitylation enzymes should be beneficial in clinical applications and basic research. Aghajan et al. present an inhibitor of the yeast SCF^Met30 E3 ligase that prevents the binding of the Met30 F-box protein to the core ligase complex.

Complex combinations of simultaneous stimuli control cellular responses, and cross-talk between signaling pathways makes it even more difficult to predict these responses. Chatterjee et al. demonstrate in human platelets that neural networks trained with measurements of pairwise stimuli can predict combinations of many signaling inputs.

Tang et al. present the first large-scale, gene-specific library of knockout mice. They disrupt 472 genes encoding secreted or transmembrane proteins and report the results of a comprehensive phenotypic analysis.

Live attenuated viruses make more effective vaccines than newer protein subunit or recombinant DNA vaccines, but the traditional passaging methods used to generate them often fail to produce a suitable mutant. Mueller et al. improve the production of live attenuated influenza virus by extensive manipulation of codon-pair bias across the genome, which minimizes the risk of reversion to a virulent form.

The development of fully defined culture conditions for human embryonic stem cells (hESCs) should enhance experimental reproducibility, reduce unwanted contaminants and facilitate scale-up production. Villa-Diaz et al. show that a substrate made of the synthetic polymer PMEDSAH supports long-term culture of hESCs.

The development of fully defined culture conditions for human embryonic stem cells (hESCs) should enhance experimental reproducibility, reduce unwanted contaminants and facilitate scale-up production. Melkoumian et al. show that a substrate made of peptides derived from extracellular matrix proteins supports long-term culture of hESCs and differentiation to cardiomyocytes.

The development of fully defined culture conditions for human embryonic stem cells (hESCs) should enhance experimental reproducibility, reduce unwanted contaminants and facilitate scale-up production. Rodin et al. show that a substrate made of human recombinant laminin-511 supports long-term culture of hESCs and human induced pluripotent stem cells.

The spread of influenza virus strains resistant to the current generation of anti-viral drugs makes the identification of new druggable targets and lead compounds of prime importance. Kao et al. show that the influenza A nucleoprotein can be targeted by a small molecule that protects mice from lethal viral challenges.

Mining information from genomes often begins by aligning the sequences to identify evolutionarily conserved regions. Chen et al. assess the performance of four commonly used multiple sequence alignment tools.