Optogenetics Resources, Guides, and Protocols

We would like to share some of the many resources our customers have found useful for planning their optogenetics projects. Please post comments if you know of more resources we should include – we will update this list regularly.

Starting From Scratch

For neuroscientists, Karl Deisseroth’s Optogenetics Resource Center is perhaps the best first stop when planning your experiment. The Deisseroth lab provides optogenetics related  DNA cassettes and vectors to the optogenetic research community, as well as training and workshops for in in-vivo optogenetics on campus at Stanford University.

The Deisseroth lab (d-lab) website also hosts

  • A light power vs distance attenuation calculator for brain tissue,
  • Chromophore, DNA sequence, and vector databases,
  • Information on requesting the many viruses and DNA provided by D-lab to other researchers.
  • Links to protocols for many optogenetics based methods.

Mapping Neural Circuits

Karl Deisseroth’s 2016 Cell paper serves as both a primer on mapping neural circuits via optogenetics and a review of the many optogenetic switches available for the task.

Finding the Best Switch

If you are hunting for the right optogenetic switch for your project, the OptoBase website provides curated databases of optogenetic techniques, but the true value is in the indexing, tagging, and online tools the BIOSS team created to accelerate your search. For example, In the publication search, filters such as “multichromatic” return only papers which combine multiple optogenetic switches within a single optogenetic system and “Exclude Background” let you exclude basic research on photoreceptors.

The OptoBase’s “Find the Application” tool is a publication selector allowing you to tick off  optogenetic uses (e.g. “Control of vesicular transport” AND “control of second messengers”) and returns only those publications which actually used those methods – as opposed to just mentioning them in the discussion section. Publications are tagged and updated weekly. The Optobase is a collaborative project of the BIOSS Centre for Biological Signalling Studies.

Preventing Phototoxicity during in-vitro Experiments

Phototoxicity presents the risk of introducing artifacts or cell death in both in-vitro and in-vivo experiments, particularly when the illumination wavelength is lower than 500 nm. For in-vitro experiments,  Káradóttir et. al. found that careful choice of the culture media components can prevent many of the issues from occurring in neuronal cell cultures. In particular, removing riboflavin, thyroxine, and triiodo-1-thyronine and including additional antioxidants increases cell survival considerably.

These media and supplements are now available from Cell Guidance.

Non-neuronal Optogenetics

For non-neuronal optogenetics, EMBL has placed a short introductory course online.

Transgenic Models – Ready to Go

While many companies supply strains of mice and rats ready for transgenic manipulation to introduce optogenetic switches, the Jackson Laboratory provide many strains of transgenic mice already expressing channelrhodopsin (CHR2), archaerhodopsin (Arch), and halorhodopsin (NpHR).

Turnkey In-Vitro and wireless In-Vivo Optogenetics Systems

Amuza provides Teleopto wireless systems for in-vivo optogenetics in mice and rats as well as LED arrays for in-vitro optogenetics in culture plates.

Teleopto wireless comprises a detachable, rechargeable headstage (receiver) and LED fiber optic implants which together weigh as little as 1.3 grams. Our starter kits are turnkey solutions for your first experiment, including receivers, LED implants, remote control, charger, and stereotaxic adapters.

Teleopto LED arrays are normally made for illuminating 96 well plates inside incubators, but can be customized to many different sizes and well configurations.

Both systems are available in colors across the spectrum including UV, violet, blue, yellow, green, red, far red, and IR. Multicolor options are also available. Please visit the Amuza site for more information:

Categories: Blog, Optogenetics

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