Volume 9 Issue 1, January 2012

Measuring single-molecule forces with light.

Enhancement of pattern discovery through graphical representation of data.

Synthetic clusters of membrane-bound droplets may provide a useful means for simulating tissues or transporting therapeutic payloads.

A combination of chromosome conformation capture carbon copy (5C), modeling and automated imaging renders an empirical three-dimensional model of a bacterial genome.

Targeting portions of the transcriptome for deep sequencing reveals very rare transcripts.

An analysis of over 100 human embryonic stem cell lines reveals a genetic change that might confer a growth advantage.

A new fluorination approach enables the synthesis of diverse PET probes.

Combining experiments and calculations makes it possible to measure the prognostic value of toxic protein species in the cell.

Precise ways to modify the genome arose from unexpected places. Monya Baker reports.

A brief description of tools for targeted cleavage and tailored modification of genomes is presented.

Engineered nucleases have advanced the field of gene therapy with the promise of targeted genome modification as a treatment for human diseases. Here we discuss why engineered nucleases are an exciting research tool for gene editing and consider their applications to a range of biological questions.

Zinc-finger nuclease dimers are more difficult to engineer than single DNA-binding domains, but the development of new methods could help.

Improved single-cell methods are helping to unravel biological complexity.

Tools to manipulate murine genes on a genome-wide scale and to phenotype their effects in animals are maturing.

Methods for tackling the enormously complex glycoproteome are sorely needed.

Sequencing a haploid genome and understanding the impact of its variants requires technical and computational improvements.

The revival of light-sheet microscopy opens new possibilities for the imaging of living processes.

Next-generation sequencing is broadening the application of genetic and genomic studies to the panoply of life.

Genetically encoded voltage sensors are finally measuring up.

Accurate methods for RNA-structure determination are being developed.

Adaptive technologies are helping researchers combine and organize experimental results.

Microbial rhodopsins convert light into ion flux; in neurons, this can be used to control activity. New work shows that the opposite is also true: rhodopsins can be used to visualize neural activity.

A method uses single-molecule, real-time DNA sequencing to detect the modified base 5-hydroxymethylcytosine, an epigenetic mark recently suspected of having essential roles in genome regulation.

This Review covers recent technological developments to label and manipulate genes in selected populations of cells in Drosophila melanogaster. The Review is intended as a user guide to help with the selection of the best expression systems and clonal analysis techniques for developmental studies in the fly.

Authors present workflows for the analysis of metabolism phenotypes in mice and recommend analysis of covariance to asses body composition effects.

A fluorescent molecular tension sensor for spatially and temporally mapping the mechanical strain exerted by cell-surface receptors in living cells is described.

Conjugation of triplet-state quenchers to the small organic cyanine fluorophore, Cy5, increases photostability without affecting its spectral characteristics. This allows longer fluorescence imaging with a concomitant reduction in blinking both in vitro and in living cells.

Unique molecular identifiers (UMIs) associate distinct sequences with every DNA or RNA molecule and can be counted after amplification to quantify molecules in the original sample. Using UMIs, the authors obtain a digital karyotype of an individual with Down's syndrome and quantify mRNA in Drosophila melanogaster cells.

The DNA modification 5-hydroxymethylcytosine has recently been implicated in several biological processes. Enrichment by selective chemical labeling in combination with single-molecule, real-time sequencing provides sensitive detection of this epigenetic mark in genomic DNA at base-pair resolution.

Mutations at arbitrarily sampled genomic positions are identified using next-generation sequencing and are used to infer the lineage of DNA damage–prone 'mutator' mouse cells in culture.

The controlled overexpression or knockdown of gene expression in primary organoid cultures of mouse endodermal epithelia is described. This should enable ex vivo studies of mammalian gene function.

A quantitative proteomics approach to characterize protein palmitoylation dynamics on a global scale in cells, as well as to identify enzymes responsible for the regulation of palmitoylation, is described.

The microbial rhodopsin protein, Archaerhodopsin 3, can function as a rapid and highly sensitive genetically encoded voltage indicator in mammalian cells that is capable of detecting single action potentials with a signal-to-noise ratio greater than 10. A mutant lacking proton pumping displays greater sensitivity but a slowed response.

In this paper, the authors report GFP reconstitution across synaptic partners (GRASP) adapted for synapse visualization in the mammalian brain.

Site-directed seamless modification of bacterial artificial chromosomes is enhanced more than tenfold in efficiency by improving the counterselection step. A set of plasmids and oligonucleotide design software also make this E. coli recombineering approach markedly faster and easier.

Nature Methods' choice for Method of the Year 2011 is genome editing with engineered nucleases. This collection of articles—and the related video—highlights how the ability to use engineered nucleases to make precise, tailored and specific changes to coding and noncoding sequences of the genome, in cells and in organisms of many species, could revolutionize the study of gene function.