Neuroscience sees the light

After many years of steady but seemingly slow progress, the development and use of light-based methods for investigating the function of the brain is really accelerating. Part of this is undoubtedly due to the excitement surrounding the use of light-activated channels for neuronal stimulation. This has been highlighted as one of our “”https://www.nature.com/nmeth/focus/moy2008/index.html#mtw">Methods to Watch" for the past two years. But probe development has also overcome some big hurdles recently, from the bolus loading of small calcium dyes to the development of genetically-encoded calcium indicators capable of providing usable signals in living animals.

An editorial in the December issue discusses the advances taking place in optical probes for measuring neuronal function and calls for the use of more standardized procedures for evaluating new probes.

Nature Methods has been requiring a basic set of evaluation tests on new fluorescent proteins that we publish for a few years now and it is possible we could try and do something similar for genetically-encoded sensors but this would obviously be complicated by the greater complexity of sensors and the fact that they respond to different stimuli and have diverse applications.

We encourage the community to tell us what they think about the value and feasibility of standardized tests for new fluorescent probes and sensors.

Highlights of methods in the literature

By now you have probably checked out our most recent selection of Research Highlights in our November issue. Here are some other interesting methods papers up for consideration that we weren’t able to feature in the journal.

Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators

PNAS 106, 15651 – 15656 (2009)

The yeast Wsc1 cell surface sensor behaves like a nanospring in vivo

Nature Chemical Biology 5, 857 – 862 (2009)

Genetic address book for retinal cell types

Nature Neuroscience 12, 1197 – 1204 (2009)

Protein quantification across hundreds of experimental conditions

PNAS 106, 15544 – 15548 (2009)

Biocompatible Functionalized Polyglycerol Microgels with Cell Penetrating Properties

Angewandte Chemie International Edition 48, 7540 – 7545 (2009)

Single-molecule sequencing of an individual human genome

Nature Biotechnology 27, 847 – 850 (2009)

Cell-selective metabolic labeling of proteins

Nature Chemical Biology 5, 715 – 717 (2009)

Generation of Functional Eyes from Pluripotent Cells

PLoS Biology 7, e1000174 (2009)

RNAMATE: a recursive mapping strategy for high-throughput RNA-sequencing data

Bioinformatics 25, 2615 – 2616 (2009)

Targeted capture and massively parallel sequencing of 12 human exomes

Nature 461, 272 – 276 (2009)

Sensitive digital quantification of DNA methylation in clinical samples

Nature Biotechnology 27, 858 – 863 (2009)