Talk:Optogenetics

Wiki Education Foundation-supported course assignment
This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Le Pensive3. Peer reviewers: Tianxiao3000, Jukakim.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 01:56, 18 January 2022 (UTC)

Wiki Education Foundation-supported course assignment
This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Pizzaman1995.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 05:47, 17 January 2022 (UTC)

Potential Article Reorganization, Looking for Feedback!
Hello All,

I've drafted a short outline in accordance to some of the minute aspects of optogenetics that are overlooked in this piece. Please do let me know what you think!

Optogenetics Outline
 * 1) Expansion of ‘Issues Section’ with a focus on possibilities or room for growth? (Concepts for a, b, c, d adapted from https://www.sfn.org/~/media/SfN/Documents/Short%20Courses/2013%20Short%20Course%20I/SC1%20Deisseroth.ashx )
 * 2) Specificity Issue
 * 3) Subcellular targeting guidance strategies to allow for selective expression in subcellular compartments (dendrites, somata, axon terminals) is difficult to do without confounding expression in axons
 * 4) Connectomic Elucidation
 * 5) Optogenetics has the capability of revealing brainwide wiring networks/projections derived from the stimulation/optogenetic control of some population. fMRI is currently an option however this readout has spatial and temporal resolution issues. The ability to associate a certain cell’s behavior with the rest of its network and possibly “close the loop” to engineer a feedback system spurred by optogenetic control can have far reaching ramifications.
 * 6) Expanding optic spectrum
 * 7) Incorporation of infrared light allows for deeper penetration, increased resolution via scattering reduction. This has proven successful for optogenetics without the use of opsin however expansion into this domain will increase the versatility of this technique.
 * 8) Biochemical signaling
 * 9) Understanding and subsequently influencing/adapting a biochemical pathway via G-protein coupled reecptors, intracellular signaling etc. can open up a completely new field of use for the technique
 * 10) 2.      Illuminating Cell Signaling Pathways ( http://www.nature.com/nrm/journal/v15/n8/full/nrm3837.html )
 * 11) Neuronal optogenetics tool can only influence membrane potentials however the technique has the capability to elucidate processes in cellular and developmental biology
 * 12) Protein Localization
 * 13) Post-translational modification
 * 14) GTP Loading
 * 15) Different Strategies for Optogenetic Inputs (Fig. 1)
 * 16) Inducible Protein Association
 * 17) Gene Expression
 * 18) Clustering-based activation
 * 19) Sequestration-based inhibition
 * 20) Conformation Change+
 * 21) Optogenetic Signal Control over time (Fig. 4)
 * 22) Cellular decision changes (proliferation vs. differentiation)
 * 23) Downstream signaling up/down regulation
 * 24) “Closing the loop”

Le Pensive3 (talk) 09:46, 11 May 2017 (UTC)

NPR
npr-talk of the nation, 16 Oct. 2010 has a discussion with the leading experimenter in the field working on fruit flies.

Intact animals
"This emerging repertoire of optogenetic probes now allows cell-type-specific and temporally precise control of multiple axes of neural function within intact animals". I'm not sure the phrase intact animals is accurate. after all, in order to project light on the receptors introduced into the animal's brain, parts of the skull have to be removed (and if you're doing it deeper than 0.5mm into the brain, an optic fiber has to be inserted into the brain). I would use the phrase behaving animals. OfriRaviv (talk) 13:09, 19 January 2010 (UTC)

Living animals should be the phrasing, as experiments could also be conducted under anaesthesia. Gould80 (talk) 09:14, 5 February 2012 (UTC)

Neurophysiology vs. Neuropsychology
I'm thinking that the topic to be labeled in this article would be neurophysiology rather than neuropsychology? Optogenetics seems to have much more directly to do with physiology than psychology. Doesn't neuropshychology work by means of neurophysiology? —Preceding unsigned comment added by 130.235.170.108 (talk) 15:46, 24 March 2010 (UTC)

Assessment for WikiProject Neuroscience
Following a suggestion on the project page, I am assessing this article. Although there is a lot of referenced material here, I consider it only Start class because there is hardly anything in the article to tell a reader what the method is and how it works. Looie496 (talk) 04:43, 4 May 2011 (UTC)

History of Optogenetics
Would be nice to work in the history of the field. Its quite exciting. http://f1000.com/reports/b/3/11 — Preceding unsigned comment added by 165.124.149.28 (talk) 15:57, 2 November 2011 (UTC)
 * Wow thats a really cool article. Can you create a history page, maybe citing a few more articles? Dont know if they will let you post it because your not signed in, but if you post it on this page someone will do it.Millertime246 (talk) 16:12, 2 November 2011 (UTC)

History issue
The history section of the Optogenetics article states: "An early use of light to activate neurons was carried out by Richard Fork[7] and later Rafael Yuste,[8] who demonstrated laser activation of neurons within intact tissue, although not in a genetically-targeted manner." It may not be accurate to describe the Yuste result as experiments in an intact tissue. The experiments were done in living brain slices. This is a slab of tissue removed from the brain and therefore not really intact. At any rate, those experiments using two-photon uncaging of caged glutamate to photoactivate neurons were preceded by experiments using essentially the same approach - glutamate uncaging - conducted 14 years earlier by Callaway and Katz. E M Callaway and L C Katz. Photostimulation using caged glutamate reveals functional circuitry in living brain slices. PNAS 1993 90 (16) 7661-7665. This photostimulation approach has been used extensively since 1993 to probe connections in the brain. — Preceding unsigned comment added by 198.202.68.151 (talk) 19:55, 21 November 2012 (UTC)

Optogenetics movies
There are two movies in the Wikimedia Commons which illustrate optogenetic tools and subsequent behavioral responses for C. elegans, and I would like to include the movies in the main article. Any comments on this? Ptrrupprecht (talk) 16:32, 29 April 2013 (UTC)
 * If they are accompanied by a proper explanation, maybe. Just looking at them I have no idea what is going on. Looie496 (talk) 21:14, 5 July 2013 (UTC)

Description
There needs to be an introductory paragraph in this section that explains what optogenetics is, and does. I surmise that it inhibits or induces the firing of neurons, or groups of neurons that have been identified or selected in some way, genetically. I also surmise that the previous sentence is wrong, and a correct paragraph needs to start this section. JFistere (talk) 05:49, 6 October 2013 (UTC)

Error in description of Tecuapetla et al. (2010)
The Wikipedia article talks about "cholinergic" synapses in nucleus accumbens, but the Tecuapetla et al. paper is about glutamatergic synapses, not cholinergic ones. Laura.Freberg (talk) 23:27, 18 December 2013 (UTC)

In the news
Headline-1: Scientists have built an 'off switch' for the brain QUOTE: "Research could help towards developing treatment for neurological disorders such as epilepsy" -- Charles Edwin Shipp (talk) 16:49, 27 April 2014 (UTC) -- PS:FYI for future editing.
 * http://www.independent.co.uk/news/science/scientists-have-built-an-off-switch-for-the-brain-9291690.html

Expanding subsections on Applications
Greetings,

I was planning on expanding on some of the current subsections under Applications, and I have a couple sources from which I will be attaining my information. I would appreciate any tips or critiques on my choice of sources.

http://www.pnas.org/content/110/35/E3340.full

http://www.nature.com/nbt/journal/v33/n7/full/nbt.3268.html?cookies=accepted

http://www.sciencedirect.com/science/article/pii/S0306452216304821

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752823/

http://www.sciencedirect.com/science/article/pii/S0959438815000136

In addition, I would like to change the section title of Atrial Fibrilation to Cardiovascular as there are few sources for the former. Finally, the current subtitle perturbs the flow of the section Applications due to the subtitles pertaining to structures rather than specific diseasesPizzaman1995 (talk) 03:59, 24 October 2016 (UTC).

Further Expansions
Greetings,

I am currently working on adding to the article a section to try to explain how does optogenetics get introduced into the animal species and how researchers then manipulate this targeted area. I believe the article currently has some basic details on how optogenetics is used and what are its main constituents, but it appears to lack a section on how do all the separate constituents (i.e transgenic mice, optical neural interfaces, Cre-recombinase, promoters, and opsins) come together to create this methodology.

In addition to adding a basic process as to how it all comes together, I plan on adding a section on some of the variety of tools currently at the disposal of researchers to use on the transgenic mice. More importantly, I want to describe the techniques researchers use in trying to better focus in on their area of interest.

Finally, I plan to add a small section on some of the downfalls or areas in which optogenetics is still improving upon.

Here are my sources from which I will be gathering my information:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4163158/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756725/

https://www.ncbi.nlm.nih.gov/pubmed/25850004

As always I would appreciate any corrections or criticisms.Pizzaman1995 (talk) 04:29, 7 November 2016 (UTC)

Peer Edit
Dear fellow Wiki Editor. I really enjoyed reading your article on optogenetics and was impressed at the amount of editing you must have done since this topic is pretty difficult and the technique relatively new. Before choosing to peer review this article I had no idea what optogenetics was let alone how important its implications were. Thanks to your contributions I now have a better understanding of what optogenetics is.

A few recommendations in regards to the structure of the article is that I would recommend trying to expand on the introduction section with a little more background information on optogenetics and its general uses in science. I also would recommend you possibly adding a couple of reasons and specific benefits for using optogenetics in the same paragraph. In regards to the last two paragraphs (Description and Technique), I think you can somehow combine these two paragraphs into one cohesive section labeled (technique/method?) so that it makes it more clear and allows for more flow in the transition from the history of optogenetics to its uses/techniques. Other than those mentioned the article looks great and again very happy to have been able to read such a fascinating topic. Rehman94 (talk) 01:12, 22 November 2016 (UTC)Rehman94

Peer Edit
I really appreciate the content you added, especially regarding the methodology of optogenetics. It clarifies the article and answers several questions I had regarding optogenetics. The content is clearly organized and explained which helps the reader understand a rather technical process. However, I feel the content may still be too technical for readers unfamiliar with the topic or without a strong science background. For example, what is a microbial opsin or what is an optogenetic actuator? I would recommend adding a few sentences or two after specific scientific terms to improve understanding for the reader. I would also recommend writing in a more active tense rather than the passive tense to improve readability and perhaps changing the title "How does it Work?" to a more technical title. I think the content added so far is very helpful and relevant and would greatly benefit by changing some writing and adding basic descriptions. Nina.juansing (talk) 18:07, 22 November 2016 (UTC)

Major Gap in the article
The lead sentence in this article only refers to optogenetics as it applies to ion channels. And if my impression is correct, the whole article, in fact, only covers ion channels. But this is only half the story, for optogenetics has also been used to modify gene expression. If you have doubts, here is a link to an excellent review article on gene expression and optogenetics, from 2018.

This is a pretty massive problem with this article. I don’t have the Wiki know-how to fix it, in fact I’m not sure I can successfully attach the link. Here goes.

https://www.frontiersin.org/articles/10.3389/fgene.2018.00518/full

Here's a quote from the end of the intro to the linked article: "In this review we will address the most recent advances in the design and utilization of optogenetic tools to control gene transcription in both unicellular and multicellular organisms."

If I am right, I could rewrite the lead sentences--but then the rest of the article would ignore them! Maybe I can just insert the link as a footnote at the end of the rewrite. I have to look up how to do that. Obviously it would be good if others lent a hand in this. — Preceding unsigned comment added by HHHEB3 (talk • contribs) 14:34, 3 June 2021 (UTC)

Partial Retraction, new edit
I found paragraphs at the very end of the article that referred to gene expression. My bad! In an Edit I did just now, I added a brief reference to them in the lead section, not changing claims about what the term "optogenetics" is restricted to. I still feel that the article as a whole is unbalanced, but at least there is no major gap as I had first thought. HHHEB3 (talk) 14:41, 6 June 2021 (UTC)

Discussion on manipulation-only vs encompassing meanings of optogenetics
The lead and body of this article could benefit, I think, from a clearer definition of optogenetics, and a more explicit distinction between the use of the term to refer to optogenetic neuromodulation as opposed to optogenetic recording or control of neural signals. Critically, that should include information about the prevalence of each meaning across contexts and across time. It might even be worth having a disambiguation notice at the top of the article with a link to a page on optical methods to record neural activity that links together other articles like calcium imaging and synapto-pHluorin. To me, it is clear that the term optogenetics most commonly refers nowadays to manipulation exclusively. I believe that the more encompassing meaning still needs to be mentioned in this article, but it should come as a warning or a heads-up for readers rather than an integral part of the definition of optogenetics. I think the allusion to both meanings throughout the article is at best confusing and at worst misleading and a disservice to the average reader. I'm looking forward to discussing these potential modifications in a little more depth here with anyone interested. Does anyone disagree that the term optogenetics has come to mean primarily neuromodulation rather than both control and interrogation? Please reply below with your thoughts on this matter. I'm sure we can finding consensus without too much trouble. Cffisac (talk) 07:17, 7 October 2021 (UTC)

I think this is an excellent suggestion, why don't you go ahead and do it? Neuromodulation tools could be structured: channels, pumps, enzymes, opto-GPCRs, dimerizers/gene transcription. Getting rid of all the brain area stuff and gazillion application examples. Have a general section on gene delivery and on light delivery methods. End with upcoming medial applications. Millencolin (talk) 21:15, 25 October 2021 (UTC)

I took the first step, created a new page Optogenetic methods to record cellular activity. There is still a lot of work left to clean up Optogenetics and make it less of a patchwork. --Millencolin (talk) 21:26, 26 October 2021 (UTC)

Splitting proposal
I propose that the article be split into neuronal optogenetics and optical control of intracellular proteins which is primarily non-neuronal in application. The reason is that most of this entry is not relevant to the latter topic, or reads as if the latter topic does not exist. For example the history and technique sections do not include any content on non-neuronal photocontrol methods. If the history and technique sections were to add that content, it would be a lot of work (for which there seem to be no volunteers), and it would make each of those sections unwieldy. The simplest solution is to split off the last section on "cellular biology/cell signaling pathways" into its own page (name to be determined). This will also allow the intro to the optogenetics page to be confined to opsin-based control of neuronal excitability (references to cell biology and biochemical pathways can be removed). A new disambiguation link to the new page on optical control of intracellular proteins may then be useful. — Preceding unsigned comment added by 171.66.160.89 (talk) 21:19, 14 November 2022 (UTC)


 * I fully agree. I would go a bit further. This article should be renamed "optogenetics in neurological studies". This would enable the creation of a more general article on optogenetics. Said general article would indeed reference this one and emphesize the historical importance of neurology in optogenetics.
 * The new article would ideally be located in the "biotechnology" section. It could detail the different modes of activation and activities possible with current tools . And encompass the various fields using this technology (i.e. metabolism, morphogenesis , signalling pathways ).
 * I would gladly contribute to the new page but I would like to know if the name change is fine for everyone. PolloSama (talk) 13:38, 26 November 2022 (UTC)