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A microfluidic affinity analysis device with > 7,000 valves is capable of performing thousands of parallel experiments. Einav et al. use this device to isolate a small molecule against the HCV target NS4B (p 1019). Credit: Doron Gerber.
Disease-orientated consumer online communities radically change the way in which individuals monitor their health, but they could also create new ways of testing treatments and speed patient recruitment into clinical trials.
The FDA's Office of Oncology Products has come in for stinging criticism from drug developers, advocates and even a US legislator over the use of surrogate endpoints. Has the agency struck the right balance between speed and caution? Malorye Allison investigates.
Metabolic network modeling in multicellular organisms is confounded by the existence of multiple tissues with distinct metabolic functions. By integrating a genome-scale metabolic network with tissue-specific gene- and protein-expression data, Shlomi et al. adapt constraint-based approaches used for microorganisms to predicting metabolism in ten human tissues. Their computational approach should facilitate interpretation of expression data in the context of metabolic disorders.
Decision trees have been applied to problems such as assigning protein function and predicting splice sites. How do these classifiers work, what types of problems can they solve and what are their advantages over alternatives?
Backbone fragments of the Agrobacterium tumor-inducing (Ti) plasmid that bears transgenes of interest have occasionally been reported to be transferred to plant genomes. Now, Ülker et al. show that Agrobacterium chromosomal DNA can also be integrated into transgenic plants at a low frequency. Gene-bearing chromosomal fragments as large as 18 kb are found in T-DNA–tagged populations of Arabidopsis thaliana.
New hepatitis C treatments are urgently needed. Working with a high-throughput microfluidic affinity assay for RNA-protein interactions, Quake and colleagues identify a small molecule that negatively affects HCV replication in cell culture by inhibiting the binding between the nonstructural protein 4B and the viral RNA genome.
Metagenomics, or shotgun sequencing of environmental DNA, is used to study complex microbial communities. Kalyuzhnaya et al. describe a method for targeting specific microbial subpopulations in environmental samples and use it to analyze microbes that metabolize C1 compounds.
The current reversibly switchable fluorescent proteins (RSFPs) can not be multiplexed. Jakobs and colleagues create two RSFPs with novel switching characteristics that can be used simultaneously in fluorescence microscopy experiments using only one detection color.
PDZ domains represent one of the largest families of interaction domains. Chen et al. develop a scoring matrix that enables prediction of peptide–PDZ domain interactions. Unlike previous methods, the model works to some extent for PDZ domains that were not part of the training set.