Volume 6 Issue 10, October 2009

Channelrhodopsin-2 can be efficiently activated by infrared two-photon excitation light and stimulates action potentials in cultured neurons.

By fusing a light-sensitive domain of an oat plant protein to Rac1, researchers created a genetically encoded protein fusion that can be reversibly activated with blue light and control cell movement—an attractive alternative to current caging tools.

The development of leader sequences that stimulate mRNA translation in a species-independent manner could offer new possibilities for eukaryotic protein production and proteomic research.

Visualization of choline-containing phospholipids in cells and in vivo is made possible by the metabolic incorporation of a choline analog with an alkyne handle for click chemistry–based labeling.

Bacterial genomes shuttled into yeast can be easily altered before transplantation back into bacteria.

Conceptual breakthroughs in science tend to garner accolades and attention. But, as the invention of tissue culture and the development of isotopic tracers show, innovative methods open up new fields and enable the solution of longstanding problems.

From histology to microcinematography, from cytochemistry to live cell imaging, the history of visualization technology in the life sciences may be understood as a series of cycles of action and reaction between static and dynamic modes of representing life.

Sequencing-based technologies for RNA discovery are playing a key role in deciphering the transcriptome and hold the potential to provide us with a census of RNAs and their functions.

Despite expansion of the fluorescent protein and optical highlighter palette into the orange to far-red range of the visible spectrum, achieving performance equivalent to that of EGFP has continued to elude protein engineers.

The potential of mass spectrometry–based proteomics to advance biology and biomedicine is nearly unlimited but so is its potential for generating bad data. Apart from the pursuit of technological progress in protocols and instruments, stringent comparative analyses of different approaches are critical for fully developing the discipline.

A wide range of methodology will be needed to bridge the gap between genome sequence and mechanistic understanding in biology. Recent advances in high-throughput genetic screening address this task.

Automated stage-specific sorting of Caenorhabditis elegans embryos enables next-generation molecular and biochemical analysis of development.

Using an axial detector, scanning transmission electron microscopy allows three-dimensional tomographic reconstruction of micrometer-thick sections of biological samples, at a resolution comparable to that obtained on thin sections.

Technical modifications of existing methods lead to a somatic cell nuclear transfer method in the zebrafish, which yields adult cloned fish with healthy offspring that carry donor traits.

A series of genetically encoded fluorescent sensors for intracellular Zn²⁺ with binding affinities spanning the picomolar and nanomolar ranges show that cytosolic Zn²⁺ is buffered at ∼0.4 nM. Targeting of the sensors to insulin-containing secretory granules indicates a free Zn²⁺ concentration between 1 and 100 μM in these organelles.

Quantitative information is necessary to determine which protein interactions are the most relevant in a cellular context. A defined set of affinity purification experiments combined with quantitative mass spectrometry analysis allows the determination of dissociation constants for all protein targets interacting with an introduced ligand.

Fluorescence-activated cell sorting of worm embryos promises to replace manual sorting of staged embryos and yields large populations highly enriched in specific developmental stages, allowing high-throughput genomic analysis.

By targeting a mutant Flp recombinase that forms a covalent protein-DNA complex to a single FRT site placed anywhere in the yeast genome, the authors can study repair pathways activated by a single genomic insult as well as events at the site of damage.

Computational compensation for the loss of information from a cellular marker visualized in one fluorescence channel increases the number of markers that can be used to study a population of cells. This should allow a more detailed molecular understanding of heterogeneity in a cellular population.

High-throughput sequencing of Mariner transposon insertion libraries is used for quantitative studies of fitness and of genetic interactions in Streptococcus pneumoniae. The approach should allow similar studies in several microorganismal species.

Neuroscientists are taking advantage of powerful new tools for fluorescence imaging that enable detailed visualization of the structure and activity of neuronal circuits within the living brain.

Nature Methodscelebrates its five year anniversary with commentaries discussing the impact and progress of methodological developments in the life sciences. We also include a fun selection of papers and covers from our pages.