Talk:CH391L/S13/Optogenetics

• Gabriel Wu 17:34, 25 February 2013 (EST): In your timeline, add the species name where the rhodopsin was found.
  • Siddharth Das 3:01, 4 March 2013 (EST): done!

• Gabriel Wu 17:40, 25 February 2013 (EST): There's a reasonable amount of history of optogenetics in synthetic biology as well. Here's a few papers to check out (there's even a UT connection!). [1] [2]
  • Siddharth Das 3:01, 4 March 2013 (EST): Thank you. I will attempt to add more synthetic biology related historical information where possible. To be honest, I guess I was biased when it comes to this topic.

• Evan Weaver 17:06, 26 February 2013 (EST): I edited the History section for readability. There were lots of grammar errors in that giant paragraph.
  • Siddharth Das 3:01, 4 March 2013 (EST): Thanks dude! It looks great!

• Alvaro E. Rodriguez M. 21:35, 28 February 2013 (EST): Another comment, it's important to say what an acronym means, example, I don't know what PRC,RBS mean, etc....I googled it but you get the point, I bet. Also in the table you might want to add the wavelength (i.e. ....nm) that each of these rhodopsins absorbs, meaning if it says Yellow (600 nm). Also do all bacteriorhodopsins absorb yellow light only?
  • Siddharth Das 3:01, 4 March 2013 (EST): I previously defined PRC as proton release complex and RBS also was previously defined as the Schiff base lacking the H+. If you read through the paragraph, I believe, I defined everything so that I could use these acronyms. However, I see you're point; These acronyms can be lost in the sea of text. Although, If anyone could figure out what "Asp" stands for, It will be much appreciated. It refers to an amino acid sequence; It might be a genetics shorthand term of some sort. Also, same goes for "M-Intermediate" and "N-Intermediate". Also, yellow isn't exactly 600nm; in fact, yellow is defined to be from around 570-590 nm. BR is activated by initially yellow light only as far as I know. Also, there is an optimal wavelength that ejects the RSBH+. Granted, if you follow the photocycle, the M-intermediate absorbs light around 400nm (red) and N-intermediate absorbs light at 568nm (yellow). In other words, throughout the photocycle, the opsin undergoes changes in its maximal photon absorbance which is irrelevant to the initiation of the opsin. The change of photostates most likely reflect the multiple comformational changes within the opsin at the particular instant of a single photocyle. By the way, I also mention how throughout the photocyle, the maximal absorbance changes. I personally believe that the color is enough for this wiki's purpose. The optimal absorbance is still debated due to a lack of consensus found in my papers which was why I avoided to publish anything concrete and find it to be wrong later on. Nevertheless, I will try to make it more clear to avoid any confusion. Thanks!

• Thomas Wall 23:02, 25 February 2013 (EST): I agree with Gabe, You did a good job outlining the medical importance of this issue, but there is little synthetic biology discussion. This is the sort of thing I expected here (https://www.openwetware.org/images/7/71/2002_Sato.pdf)
  • Siddharth Das 3:01, 4 March 2013 (EST): Sorry, but this is rather vague. What do you particularly want me to address? I truly agree with Gabe that my history is a bit lacking. In addition,I'll probably elaborate on my research section. I would argue synthetic biology and medicine are two sides of the same coin in this case of optogenetics. Medicine had an issue and synthetic biology answered. The purpose of synthetic biology is to create robust and versatile biological entities to be applied to an issue in society, this case being neuroscience.
  • Siddharth Das 6:30, 4 March 2013 (EST): I would like to rectify my previous misunderstanding. I just read you paper and understand where you're coming from. Last year's topic "Light Sensors" contained optogenetics as a separate subtopic. In response, I will try to add a light sensor sub-section in my article. Hopefully, I finish it by the time I update the class! I would like to pose a question: what is the difference between optogenetics and light sensors, if there is any? I personally thought the exclusive use of opsin, a photosensitive channel protein, made optogentics different for the latter. Granted, there are chimeric opsins used to mediate various cell functions. I guess it boils down to a semantics issue. (Possible good class discussion)
    • Gabriel Wu 14:23, 4 March 2013 (EST): I think it's interesting to bring up the neuroscience component of this topic. I certainly think synthetic biology is more than just tinkering with E. coli (at least it should be). It might make more sense to start more general. Discuss the idea of light detection in a biological context and then move toward how light detection can lead to activation of cellular processes in nature. Then, discuss how this natural process can be engineered for other purposes. At that point, you can divide the neuroscience from the microorganism component.
    • Gabriel Wu 14:23, 4 March 2013 (EST): To answer your question, a light sensor is a part of an optogenetic circuit. Optogenetics is simply a genetically encoded light sensor that induces a biological behavior.

• Dwight Tyler Fields 01:18, 1 March 2013 (EST): You could also make a connection to bioprospecting and conservation, as I'm reading that many of the "tools" in optogenetics come from microbes found in specialized environments [3]
  • Siddharth Das 3:01, 4 March 2013 (EST): Thanks! I'll add this to my research section.
  • Siddharth Das 7:07, 4 March 2013 (EST): Nevermind, I thought you linked me a bioprospecting research paper, but in actuality you wanted me to really critically think! This would have been a interesting talk topic conversation. I'll make sure to bring this up in class and talk to Andre. You are very right. Personally, I am more interested in the direct protein evolution connection rather than the bioprospecting connection. Bioprospecting is like thrift shopping, you take what you find- most likely its useless. In contrast, direct evolution would modify the already known opsin to yield interesting characteristics.

• Catherine I. Mortensen 13:55, 2 March 2013 (EST): Concerning the iGEM project that was done last year, I'm a bit confused about the purpose... Please correct me if I'm wrong, so this is my understanding: this iGEM team used Ccas or LavTAP as regulatory genes which were placed in front of lacZ so that when certain colored lights were shined on the cell, these regulatory genes would either inhibit or activate the expression of lacZ?
  • Siddharth Das 6:30, 4 March 2013 (EST):Not exactly. Both Ccas and LavTAP are transmembrane photoreceptors. When light is shined on either of these receptors, the proteins undergo a conformational change that leads to autophosphorylation. Increased autophosphorylation leads to activation of the response regulator. This response regulatory acts as a secondary messanger and bind to the promoter sequence of the LacZ. Also, the response regulatory molecule is CcaR that binds to the specific promoter sequences of cpcG2. CcaR contains an N-terminal receiver domain that is phosphorylated by CcaS, and a C-terminal DNA binding domain that selectively couples to the cpcG2 promoter when in a phosphorylated state. And the breakdown of galactose reveal whether the activation of green light and inhibition of red light perturbed genetic regulation. Furthermore, the cells wouldn't normally breakdown lactose because the promoter of the operon has exchanged for the cpcG2. Even thought lactose binds to the repressor unbinding from the operon, the transcription can not take place with out the promoter-regulator interaction. To be honest, I am also confused as to why the RNA polymerase is waiting for the CcaR coupling in order to continue transcription. Nevertheless, the function is somehow halted to depend on whether or not CcaR has coupled. Hopefully, this issue can get resolved in class.

• Catherine I. Mortensen 14:06, 2 March 2013 (EST):Could Ccas and LavTAP be used to regulate other genes besides lacZ?
  • Siddharth Das 6:30, 4 March 2013 (EST): In theory yes, but in practice I am not sure.

• Catherine I. Mortensen 15:24, 2 March 2013 (EST): There are genes found in algae that produce light-sensitive proteins that can be used to help regulate nerve impulses. The idea is that light-sensistive proteins increase receptiveness of neurons in combination with LED lights. They added this gene from algae to the mice's genome and placed LED lights around certain nerves and found an increase in the fluidity of muscle movement. LED lights have been placed around sciatic nerves to increase fluidity in movement in people suffering from cerebral palsy and have had some success. If this gene from algae were successfully added to the human genome, complete muscle control could be regained in those suffering from cerebral palsy, paralysis, and such. [4]
  • Siddharth Das 6:30, 4 March 2013 (EST):Is this question? I find this topic really interesting, but I wouldn't think too much about their big claims. It isn't as simple as integrating the foreign dna into the human brain. Based on current research, planned movements such as waving you right arm above your head are optimally coded in population neurons in the cerebellum or motor cortex. In other words, particular neurons are associated with particular movements. We see know of this relationship but not much else. Which cells would be choosen to be genetically altered? Is there a way to control the area 4 of the cortex to mediate such actions? What goes between the basal ganglion and the cerebellum? Neuroscience is really complicated with more questions than answers. The goal for optogenetics is eventually create neuroprothetics.