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TALEs (transcription activator-like effectors) are transcription factors from the plant pathogen Xanthomonas that can be readily engineered to bind new DNA sequences of interest. Miller et al. use a truncated TALE linked to a nuclease domain to edit and regulate endogenous genes in human cells.
DNA molecules that are read by a next-generation sequencer have been discarded after the sequencing reaction, until now. By retrieving oil-emulsified beads encapsulating DNA with a known sequence, Matzas et al. obtain high-quality input material for DNA synthesis.
Long DNA molecules, such as those encoding genes, can be assembled from short oligonucleotides created on a microarray. Kosuri et al. improve the fidelity and scalability of this process, enabling synthesis of 40 antibody fragments having repetitive regions and other challenging sequence features.
Minicircle DNA vectors are superior to plasmids for long-term transgene expression but are not in widespread use because of a laborious production process. Kay et al. present an improved protocol for generating minicircles that makes them a viable alternative to plasmids for gene transfer studies.
The metabolism of tissues often involves interactions between several types of cell. Lewis et al. model metabolism within and between neurons in the human brain, gaining insight into energy metabolism and Alzheimer's disease.
Nanoparticles are under study for pulmonary drug delivery and are continually in contact with the lungs through air pollution. Choi et al. study the effects of size, charge and chemical composition on the behavior of nanoparticles in the rat lung.
Adaptation of insect pests to tolerate Bacillus thuringiensis (Bt) insecticidal proteins threatens to reduce the efficacy of Bt crops. Evidence from an extensive four-year field trial indicates that the release of sterile pink bollworm moths suppresses the emergence of resistance to transgenic Bt cotton, while helping to eradicate the pest.
The simultaneous detection of multiple mRNA species in thick tissues or whole-mount embryos has remained technically challenging. Choi et al. present a method based on the triggered polymerization of RNA stem-loop structures that allows the distribution of up to five mRNAs in intact zebrafish embryos to be imaged at the same time.
Antibodies that modulate the activity of a target are difficult to discover with display-based approaches, which select only high-affinity binders. Mao et al. identify antibodies with a range of affinities using a small-molecule discovery method that involves one-by-one screening of an optimized small library of antibody fragments with known sequences.
The culture of dedifferentiated plant cells to produce commercially important chemicals has met with limited success. Lee et al. demonstrate the potential of innately undifferentiated cells from Taxus cuspidata as an industrial source of the anticancer drug paclitaxel.
Degeneration of articular cartilage in the joints may be amenable to tissue engineering solutions. Oldershaw et al. present an efficient, chemically defined protocol for differentiating human ES cells to chondrocyte-like cells.
The typical therapeutic antibody binds only two target antigen molecules during its lifetime. Igawa et al. describe a method for engineering antibody recycling in vivo, suggesting an approach to reduce the size and/or frequency of dosage with therapeutic antibodies.
The grading systems used by in vitro fertilization clinics cannot determine reliably whether a given embryo will lead to a successful pregnancy. Wong et al. address one part of this problem by showing that development of an embryo to the blastocyst stage can be predicted with high confidence at day 2 post fertilization.
Biomechanical forces may be an effective approach for controlling the behavior of stem cells in vitro. Holst et al. show that the elasticity of a tropoelastin matrix expands hematopoietic stem and progenitor cells.
Methods for profiling DNA methylation differ in the physical principles used to detect modified cytosines. Harris et al. compare the performances of four sequencing-based technologies for genome-wide analysis of DNA methylation and combine two methods to enable detection of allelic differences in epigenetic marks.
Comparison of the methylation patterns of cells in different developmental or disease states can help to elucidate both normal and pathological regulatory mechanisms. Bock et al. evaluate the ability of three sequencing-based methods and one microarray-based technology to detect differentially methylated regions on a genome-wide scale.
Fordyce et al. measure the sequence specificity and affinity of DNA-binding proteins using an improved microfluidic device. They characterize binding of 28 yeast transcription factors, several of which had proved intractable to previous approaches.
Reconstructing a metabolic model from the genome sequence of an organism is a useful but arduous approach for predicting phenotypes. Henry et al. describe a resource that automates most of this process and apply it to create >100 new metabolic models of microbes.
Isolation of antigen-specific antibodies or antibody fragments, whether through B-cell immortalization or recombinant libraries, generally requires laborious screening. Reddy et al. circumvent this step using high-throughput sequencing of plasma cells and bioinformatic analysis of the variable-gene repertoire.
Castor beans are best known as a source of industrial lubricants and the toxic bioterror threat, ricin, and they have potential to provide biofuel. Chan et al. present the draft sequence of the Ricinus communis genome, the first for a member of the Euphorbiaceae.