True bioluminescense in fish

[Vincent]

Could it be possible to influence a fish to produce photoproteins in
it's chromatophores?
My original idea was to use goldfish, but I've been looking at
zebrafish because they are easy to care for and are well documented
scientifically. I also found biobricks for the clemicals used by
fireflies, although they are tuned for use in E. Coli. How difficult
would it be to get those to work in a zebrafish?

[Cathal Garvey]

Really, they would be best entirely recoded. They would need new promoters, ribosomal binding sites, codon usage (you might get away without changing codons), possibly some work on polyadenylation at the end.. (must brush up on that aspect myself).

However, that said the genetic end of things should be pretty well documented. It's delivering the DNA that's challenging.

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[Vincent]

Hmm... That's a lot of work. Might try it anyway if I can't find any
alternatives.
What I'm really trying to do is create an organism that is truly
bioluminescent, as in it produces light in sufficient quantities that
it is easily visible to the naked eye. So far the only things that
come close are the GloFish sold in petshops. However, those only glow
when exposed to UV light. As I understand it so far, I have to get
this organism to produce either photoproteins, or a luciferin-
luciferase coctail. I don't mind starting with single-celled organisms
first, but I do want to eventually try something more complex like a
plant or fish.

On Sep 8, 10:48 am, Cathal Garvey <cathalgar...@gmail.com> wrote:
> Really, they would be best entirely recoded. They would need new promoters,
> ribosomal binding sites, codon usage (you might get away without changing
> codons), possibly some work on polyadenylation at the end.. (must brush up
> on that aspect myself).
>
> However, that said the genetic end of things should be pretty well
> documented. It's delivering the DNA that's challenging.

> On 8 Sep 2011 14:21, "Vincent" <vinhi...@gmail.com> wrote:> Could it be possible to influence a fish to produce photoproteins in

[Nathan McCorkle]

I can't tell if all the fish listed here:
http://en.wikipedia.org/wiki/Bioluminescence
have bacteria that actually make the light... if there are
non-bacterial photophores (photocytes), it might make this problem a
little easier to solve:
http://en.wikipedia.org/wiki/Photocytes

--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

[Mac Cowell]

Anyone feel comfortable estimating the metabolic load on photophore cells to generate "reasonably bright" yields of light via the luciferin system? Relative to skeletal muscle cells for instance? Just as a sanity check...

Obviously fireflies can support it somehow.

231.313.9062 // @100ideas // sent from my rotary phone

[Cathal Garvey]

Well staying warm blooded is surely much more costly, and the luciferase conversion efficiency is in the high nineties?

Also, while most fish use organs full of symbiotic bacteria, at least some have an endogenous pathway instead. Can't find ref now. Typing left-handed in the dark with a baby. :P

letters.cunningprojects.com
twitter.com/onetruecathal
http://www.indiebiotech.com

[Nathan McCorkle]

On Thu, Sep 8, 2011 at 8:14 PM, Cathal Garvey <cathal...@gmail.com> wrote:
> Well staying warm blooded is surely much more costly, and the luciferase
> conversion efficiency is in the high nineties?

Fish nor lighting bugs are warm blooded though, why the warm blooded mention?

> Also, while most fish use organs full of symbiotic bacteria, at least some
> have an endogenous pathway instead. Can't find ref now. Typing left-handed
> in the dark with a baby. :P
>

You type with a baby instead of a keyboard??? DIYbio I guess...

[Cathal Garvey]

> Fish nor lighting bugs are warm blooded though, why the warm blooded mention?

i.e., light-production wouldn't be, in my view, an unlikely addition to a vertebrate, given that they already demonstrate very costly features.

> You type with a baby instead of a keyboard??? DIYbio I guess...

A biological solution to everything! Although, she has a pretty blunt nose, making it awkward to pick out just one key at a time on this netbook..

[Vincent]

Replace your left arm with a baby? There's a gene for that.

Back to topic: what would theoretically be easier, getting a fish to
develope photophores in place of chromatophores, or getting it to
develop photocytes throughout the epidermis?

[Avery louie]

Why not just get a translucent mutant of zebrafish (like the clear ones they use for research) and extract some of its gut bacteria, transform a plasmid into them, and try to reintroduce them?

[Vincent]

That's actually a great idea! Not exactly what I'm trying to
accomplish, but still worth trying. Would also be interesting to see
what effect aquarium medications have on their intestinal flora/fauna.

On Sep 9, 1:09 pm, Avery louie <inactiv...@gmail.com> wrote:
> Why not just get a translucent mutant of zebrafish (like the clear ones they
> use for research) and extract some of its gut bacteria, transform a plasmid
> into them, and try to reintroduce them?

[Nathan McCorkle]

On Fri, Sep 9, 2011 at 12:09 PM, Avery louie <inact...@gmail.com> wrote:
> Why not just get a translucent mutant of zebrafish (like the clear ones they
> use for research) and extract some of its gut bacteria, transform a plasmid
> into them, and try to reintroduce them?

I'd say the only advantage of a photophore would be that its closer to
the skin, would that be correct?

--

[Vincent Hilversum]

That's actually a great idea! Not exactly what I'm trying to accomplish, but still worth trying. Would also be interesting to see what effect aquarium medications have on their intestinal flora/fauna.

[Vincent]

What's the best recipe for a homebrew agar culture medium?

On Sep 10, 11:55 am, Vincent Hilversum <vinhi...@gmail.com> wrote:
> That's actually a great idea! Not exactly what I'm trying to accomplish, but
> still worth trying. Would also be interesting to see what effect aquarium
> medications have on their intestinal flora/fauna.
>
>
>
>
>
>
>
> On Fri, Sep 9, 2011 at 1:09 PM, Avery louie <inactiv...@gmail.com> wrote:
> > Why not just get a translucent mutant of zebrafish (like the clear ones
> > they use for research) and extract some of its gut bacteria, transform a
> > plasmid into them, and try to reintroduce them?

[Nathan McCorkle]

On Tue, Sep 13, 2011 at 11:47 AM, Vincent <vinh...@gmail.com> wrote:
> What's the best recipe for a homebrew agar culture medium?
>

for growing what? PDA is easy, googleable, cheap. Find agar at asian,
particularly southeast asian, food stores. I get 'Telephone' brand
around here, about $1 a packet.

We've never tried it on this mailing list, but we've speculated that
chicken broth (probably need homemade or Organic canned) would be a
good place to start trying to recreate LB broth media, a media that E.
coli likes to grow on.

--

[Mega]

http://www.glowingsushi.com/

Just dound something "nice" :D 

[Patrik D'haeseleer]

Keep in mind that the luciferin biosynthesis pathway for firefly is not known yet, so if you use the firefly luciferase, you'll have to keep your goldfish swimming in an aquarium of expensive purchased firefly luciferin...

The bacterial bioluminescence pathways are fully known, which is why most people are focusing on those. Now you're dealing with 5-6 genes that you all have to express in approximately the right ratios and locations. Chances are engineering a bioluminescent goldfish would be equally or more difficult as engineering a bioluminescent plant - at least with a plant, you can target the chloroplasts, which are essentially mini bacterial organelles.

If you would like to go that route, your best approach would be to try replicate the GFP goldfish first. At least you only need to express a single gene for that.

There's also a big hurdle in getting the genes into the germ line. Sure, you could engineer single fish cells, but there's a big distance from having a single engineered cell to having a live fish that expresses the bioluminescence pathway.

Patrik

[Patrik D'haeseleer]

A nice workaround to all this fish engineering hassle might be to take advantage of the fact that cyanobacteria can apparently live symbiotically inside zebra fish tissues without too much trouble! Look at this lovely work by Pam Silver's group:

An Injection of Symbiotic Cyanobacteria Gives Fish the Power of Photosynthesis (Sort Of)

Towards a Synthetic Chloroplast

So now the problem has been reduced to engineering bioluminescent cyanobacteria (entirely feasible, and a really cool project I think!), and then injecting those cyanobacteria inside fish embryos...

Patrik