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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.
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.
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.
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.
Biological control of the root-knot nematode Meloidogyne incognita, one of the world's most destructive crop pathogens, presents a major opportunity for safely improving global agricultural yields. Its 86-Mb genome—the first to be sequenced for a strictly parthenogenetic species—provides a blueprint to design new strategies for plant protection.
Systemic toxicity associated with heterogeneity in the stoichiometries and sites of drug attachment is a major hurdle to developing antibody-drug conjugates (ADCs) for cancer therapy. Junutula et al. engineer cysteine residues in constant domains to produce near-homogenous ADCs that are better tolerated than conventional ADCs, without any loss of antitumor activity.
Little is known about the regulation of RNA interference (RNAi). Shan et al. constructed a reporter system to monitor RNAi activity and identified a small molecule that increases RNAi by facilitating the interaction between small RNAs and a protein involved in small RNA loading and processing.
An inability to estimate absolute DNA methylation levels has slowed progress in understanding the role of this epigenetic modification in health and disease. Down et al. describe an algorithm for analyzing methylated DNA immunoprecipitation profiles generated using either high-throughput sequencing or oligonucleotide arrays.
Generating induced pluripotent stem (iPS) cells is still an inefficient process, in part because the delivery of reprogramming factors by retroviral vectors yields cell populations that are genetically heterogeneous. Wernig et al. increase efficiency by producing iPS-cell chimeric mice from which they isolate cells bearing identical proviral insertions that support drug-inducible reprogramming.
Therapies that target only one inflammatory cytokine such as tumor necrosis factor α are often insufficient to treat rheumatoid arthritis. Aikawa et al. show that a small molecule targeting c-Fos/AP-1, a transcription factor that regulates both inflammatory cytokines and matrix metalloproteinases, inhibits type II collagen-induced arthritis in mice.
Microarray platforms usually rely on fluorescence detection. Clack et al. present an equally sensitive, label-free technique that electrostatically detects DNA or RNA hybridization after randomly dispersing charged microspheres onto the microarray surface.
Widespread use of antiangiogenic drugs for cancer therapy is limited in part by the requirement for intravenous injection. Benny et al. describe an oral formulation of an antiangiogenic small molecule that inhibits tumor growth and prevents liver metastases in mice.
Existing methods for reprogramming somatic cells to 'induced pluripotent stem cells' are inefficient, with only a small fraction of the starting cell population becoming pluripotent. Working with mouse embryonic fibroblasts, Hunagfu et al. increase reprogramming efficiency by treatment with DNA methyltransferase and histone deacetylase inhibitors.
The targets of a microRNA (miRNA) are usually identified by computational analysis of sequences complementary to the miRNA. Working with inflorescence tissue of Arabidopsis, German et al. devise an experimental approach in which the products of miRNA-mediated cleavage are sequenced and used to identify miRNA–target RNA pairs.