Research articles

Recombinant SV40 viral vectors intravenously injected into mice pretreated with mannitol effectively deliver transgenes to adult neurons in several regions of the central nervous system.

Retroviral integration is used to mark clones in human embryonic stem cell cultures and clonal distribution is assessed after functionally testing the cells with different methods. Distinct subsets of clones are detected after in vitro differentiation versus teratoma formation in vivo.

Using 600 oligonucleotides with 60 bases each and three enzymes, the authors assemble the entire mouse mitochondrial genome in four isothermal reactions.

Proteins can be transferred between cells in contact, such as via trogocytosis in lymphocytes, or acquired via bacteria-host interactions during infection. A quantitative proteomics approach to identify such non-cell-autonomous proteins is described.

The Trans-ABySS pipeline is an integrated approach for transcript assembly and analysis to identify new mRNA isoforms and structures.

A targeting method for lentiviral vectors relying on the use of single-chain antibodies recognizing cell-surface antigens is applied to generate lentiviral vectors specific for endothelial cells, hematopoietic progenitors and neurons.

Stimulation of the light-activated cation channel channelrhodopsin-2 can depolarize heart muscle in vitro and in vivo, resulting in precise localized stimulation and constant prolonged depolarization of genetically targeted cardiomyocytes and cardiac tissue.

Adaptations to total internal reflection microscopy permit visualization of the 'footprint' of rolling cells. Applied to neutrophils rolling in whole blood at physiological levels of shear stress, this approach reveals previously unappreciated features of rolling cell biology.

Generalized phase contrast and temporal focusing are combined to shape two-photon excitation patterns that elicit large photocurrents in ChR2-expressing neurons in culture and slices. This method allows precise aiming of the stimulating light at single neuronal processes, neurons or groups of neurons and can elicit simultaneous excitation of multiple cells using optogenetics.

Compared in this Analysis are two widely used procedures for ribosomal RNA removal in metatranscriptomic samples, and the authors present recommendations to prevent misleading analyses of microbial communities.

This resource describes a human MAP kinase interactome. Yeast two hybrid-derived protein interaction maps of MAP kinase pathway members are refined using multiple criteria, tested against reference sets, and functionally validated using knockdown with siRNA.

Mice handled by their tails show high levels of anxiety and stress compared to mice handled in cupped hands or in a transparent tunnel.

Alternative expression analysis by sequencing (ALEXA-seq) aligns RNA-seq reads from different cell types to a database of alternative expression sequence features and quantifies isoforms that are differentially expressed between samples.

MicroRNA targets predicted by a variety of computational tools can be validated using a quantitative targeted proteomics approach, using stable isotope labeling and selected reaction monitoring mass spectrometry. The authors used this method to confirm predicted let-7 and miR-58 targets in Caenorhabditis elegans.

Random and targeted mutagenesis of the far-red fluorescent protein Katushka followed by screening for low toxicity and red-shifted emission resulted in two near-infrared fluorescent proteins, eqFP650 and eqFP670, that display desirable properties for in vivo imaging compared to existing near-infrared fluorescent proteins.

A comparison of ordination analysis methods used to reveal gradients or clusters in sequence data from microbial communities reveals which methods are best suited for which community structure at different sequencing depth.

Single-molecule fluorescence resonance energy transfer (FRET) is a useful technique for monitoring biomolecular dynamics. A new method, termed switchable FRET, facilitates monitoring of multiple distances in single molecules, using a single donor and multiple spectrally identical acceptors that are switched on and off between a fluorescent state and a dark state.

A gene conferring neomycin resistance can be used for antibiotic selection in C. elegans and C. briggsae. This will permit easy maintenance of transgenic lines and facilitate single-copy insertion of transgenes. Also in this issue, a related paper reports nematode selection using puromycin.

A gene conferring puromycin resistance can be used for antibiotic selection in C. elegans and C. briggsae. This will permit easy maintenance of transgenic lines and facilitate single-copy insertion of transgenes. Also in this issue, a related paper reports nematode selection using neomycin.

A computational approach to both measure and infer microtubule dynamics from time-lapse images of end-labeled microtubules is described. It permits intracellular spatial patterns in microtubule behavior to be monitored.