• I feel like this has potential to cross with the techniques used in the ce6 project (ongoing and happening i swear!). I'll start researching.

    Extracting things from birds you say.... ;)
  • tehehe i'll take the eye you take the other fun bits? nothing goes to waste right? maybe even a chicken nugget or two out of all this :P go for three and extract the HA from it's bones lol. i'll post a few articles i found. one was a masters thesis detailing the whole process of nanoparticle drug delivery in the retina
  • Send me the links and i'll drop them in the documents in case anyone wants to read them (and remembers how to find the documents section...)
  • For those who don't, Here's the link, I believe.
  • Ok so just as an update. I've done a massive look into all of this. For those interested: color vision is controlled by 4 proteins. 1 for each cone and then 1 for rods. To each a cofactor attaches. Each protein has a unique gene rather than  intron/exon shinanigans. I ran blast analysis on the green and red proteins (i was gonna do blue too but the program cacked and i was gonna murder it so I stopped) which tells you how similiar the sequences are. They are identical except one gap in the red protein around 750bp into the sequence. So the only real difference is the missing letter. So I figured that colorblindness was likely caused by a different mutation in the green protein so it once again has a gap and instead pick up red rather than green. Turns out I was right. So tetrachromes have a normal red green and blue and then a mutant green pigment that gives them a second red wavelength. all of which is easy enough with decent funding to replicate and insert into a living person since the pigments are constantly being damaged and replaced and only 1 gene would have to be put in.

    Ok so with that aside, unless someone has access to a lab to work on this, i'll be saving this project for the thought emporium once our lab has the funding to allow for this. I'll be preforming mutations on the various genes to produce pigments of various wavelengths, selecting the mutants that produce pigments with useful wavelengths and then working that into either a nanoparticle or more likely a genetic vector to grant tetrachromancy to normal people. 

    Now community time. If you want in on this let me know and i'll let you know how you can help out but fair warning unless you are already comfortable with genetics and genetic vectoring and mutations, it will require a lot of reading. 
  • I'm not ready to offer anything helpful to this endeavour except that I'd definitely be interesting in volunteering to be a test subject (although I'm based in Australia). You'd probably have no shortage of that though.
  • I want to help but don't have technical knowledge but can do some research.  I'd volunteer but I'm far away from the lab as I'm on the east coast. 

    I have experience with making manuka honey, MSM, and even lemon eyedrops (heavily diluted in distilled water of course, but if there's no very minor burning sensation you've diluted too much, if it's major you didn't dilute enough) to get rid of the eye film that develops over the years and greatly reduce future risk of cataracts. 

    Though working with pigments is probably far more complicated than cooking up a simple manuka honey eyedrop mixture. 
  • edited February 2015
    @agemfrostmage Ya just bit... :P

    So what needs doing is this. We need to find as many versions of the color pigment genes that we can that aren't the same as the normal gene. So colorblind ideally. Not non functional. The gene must still produce protein just of the wrong color. Then we compare these copies to the original normal functional ones. I need to see where the changes are and what they are. If we're lucky it may even list what wavelength the mutant proteins absorb at. the genes we're looking at are:
    OPN1LW (RED)
    OPN1MW (green)
    OPN1SW (blue)

    Once we have candidates for sequences that will produce functional proteins at the wavelengths we're hoping for, we can either isolate or get the sequence printed, stick it in a bacteria and then isolate the protein and run it through a spec to see what it's absorbing at. Once we have our final choice protein we design a gene vector to get it into place. But that's more complicated and will need more work. So first things first, start comparing sequences then list the NCBI reference numbers here if you find something interesting.

    Edit: I'll make a video on how to do this for those lacking the technical background that still want to help.
  • My first question, if you don't plan to include it in the video, is how does one gather samples of these genetic sequences?
  • they're online. Lets just start with the NCBI data base and then go from there. Maybe even look into non-human homologs of the protein. If we run out then we start "taking samples" from colorblind people XD
  • edited February 2015
    I can't make any promises, but I might be able to write a rudimentary search program that would comb that database and log links to relevant sequences. Might take a couple weeks to set up, but it'd speed things up a lot after it was done.
    On further examination, designing a database "spider" to automate the process could be a bit... Tricky. Anything that would help me familiarize myself with the formatting of the databases, without spending multiple hours just clicking around, would be appreciated.
  • the formating of that particular database is horrifying. It's easier to go through it manually since it is fairly inconsistent 
  • well, here are the notes @Rubix had on SWS1
    It's a little bit of leg-work out of the way, maybe. I'd really like to try this too. 
  • oh sweet. took a sec to figure what i was looking at but that's actually pretty helpful. i'll have to look at it in more detail though but a quick scan it's the blue pigment and comparing it to the mouse version. so basically what we'd have to do

  • If computing power is needed for something I can contribute.  I have a Haswell i7 and have used Boinc before.

    Just in case it's needed.
  • Shouldn't be but who knows where this goes. thanks for the offer!
  • @thegreyknight if you're familiar with the R language at all, there is an enormous community of bioinformaticians who've made a large number of functions and tools to allow you to quickly access databases. (Here's a link to a quick google search result about using R to access NCBI databases

    I thought you might be able to pull out opsin related genes by searching for gene-ontology terms on

    Here's the list of (mouse) genes for the GO-term GO:0009881

    So you could access the genes you wanted to in that way. You can also get ALL the genes that are associated with that GO term (across all species), and download a FASTA protein sequence file that contains all the sequences you want (this kind of format:

    I reckon you're missing out on all of the interesting photopigments that algae use though; the optogenetics people are really good at pulling those out, and I suspect that there are a huge number of weird pigments in there that would be of interest to you.

  • edited February 2015
    K all we'd need is w could get this into a quick database is compare them all with BLAST to see where the differences and then show what they are. Whoever is good with coding want to run with this? So whoever steps up for that I'll give more instructions to on what will be required. 
  • I can't say that I'm GOOD at coding, but I can probably manage. I'll give it a go.
  • Ok well whoever is running with that lets start with getting a collection of reference numbers for the genes we want. So we want 2 things for each gene, the regular chromosomal sequence and the mRNA sequence. And we only want ones that have both. So build the code to troll for those genes, find copies that have both forms and then crap that out into a table that also lists which species each copy is from
  • so @thegreyknight, is that you? or is someone else gonna step up? or more fun still are we doing thi the manual way?
  • I say we'd start off manually, unless someone has a tool for this already, and I'll try to get an automated method working.
  • ok so then in the next day or 3 when i have time i'll get that video up.
  • I'm no expert on any of this, still new, still reading up, but I AM colour-blind, so if that's of any use for samples etc, let me know.
  • well it's rough around the edges (been a long day and i filmed this late) but here it is. How to run blast analysis on the genes we need. I left out one thing which is, i need you to also put if the thing you're working on is colorblind. I forgot to mention that in the video. i'll be tinkering with this a lot more in the coming months but im swamped now so begin gathering data and i'll work on processing it shortly.

  • Sorry updated link. Uploaded to wrong channel.

  • It looks like this project has legs in the Biotech field too. Anything we can learn from this?

    Being red green color blind myself this is something I'm really curious about. Also - my biotech friend that sent me the link say's that once we have a platform for delivering DNA for visual augmentation it could be pushed beyond RG and into tetra-chromatic territory.

  • You mean that gaining the 'red', 'green' or'blue' genes can prevent us from being colorblind? The gene therapy is available to monkeys now. But how long it takes to be suitable to human?
  • Exactly.  But think bigger than that.  We are colorblind compared to many species of birds, but with gene therapy we could potentially negate that.  Some of them (such as pigeons) even have five cones!  That would be too much of a jump, I'd rather spend a year or so as a tetrachrome before making the jump to five, if I even want to, five sounds too overwhelming.  There are potential and actual regulations against gene therapy, so getting such operations done needs some loophole exploiting at best or travel to other countries at worst.  

    Bionic eyes are already out there, but from what I've read they're abysmal, but there's obvious potential to greatly exceed organic human eyes, especially as far as color is concerned.  Though I'd prefer gene therapy over surgery involving my eyes being removed.  
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