Re: "Surprising experiments"
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Russell Whitaker
Nov 5, 2010, 10:56:48 AM11/5/10
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Anaïs, I am replying to the list, since I'm assuming you mistakenly
replied only to me:
replied only to me:
On Fri, Nov 5, 2010 at 7:34 AM, anais cordoba <cordob...@gmail.com> wrote:
> Hello,
>
> Surprising experiments would be like visually interesting experiments. I'm
> talking about experiments such as glow in the dark food or things or
> food/bacteria/animal changing color
> If you have any other suggestion, if may be helpful!
>
> thanks
>
In other words, something you can catch on camera, yes?
What is the actual scientific value of "glow in the dark food," by the way?
Would this be useful for spelunkers who've misplaced their rations?
--
Russell Whitaker
http://twitter.com/OrthoNormalRuss
http://orthonormalruss.blogspot.com/
anais cordoba
Nov 5, 2010, 11:34:21 AM11/5/10
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Exactly, something I could catch on camera. As it is for TV, it has to be a bit demonstrative...thanks
2010/11/5 Russell Whitaker <russell....@gmail.com>
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Eric Ma
Nov 5, 2010, 1:18:03 PM11/5/10
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Nice humor, Russell!
Cheers,
Eric
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On another note, though, I see value in proof-of-principle toy systems. So... sure, it's useful to know that we can express GFP in a rabbit. But what use might it be of? I'm not too sure, but I think combining it with a viral delivery system might help us visualize certain cells within the human body, which would be of use to surgeons, especially if we can find a way to transiently express the protein for a long enough period without integrating it into the human genome. Part of the premise of that kind of diagnostic tool is that GFP fold properly in mammalian systems.
I can't claim to be a master of mammalian biology, as I only have a B.Sc. behind me, but from my own imagination, I'd think that something eye-catchy to capture the public's imagination can end up being pretty darn useful too!
Cheers,
Eric
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Cathal Garvey
Nov 5, 2010, 1:56:26 PM11/5/10
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I seem to recall the London Hackerspace people discussing a fluorescent beer as a cool idea. I agree! Fluorescent drinks would rock. Of course, you can already do that with chlorophyll, but it's not nearly as cool as a Genengineered drink. This application is almost certainly illegal in EU of course, so for now it's a pipe dream.
Of course, fluorescent or bioluminescent foods need not be for consumption. I can imagine a handful of very entertaining and perhaps lucrative ideas for fluorescent foodstuffs, that I may in fact attempt in coming years. ;) Certainly this year I wanted to have a bioluminescent pumpkin outside my house, though I didn't have time to prepare it because of writing my thesis. :( I'll experiment sometime soon to see how feasible it will be for next year using just the bacteria I have, no engineering needed.. Not nearly as safe as the genetically engineered option, of course.
For the show, Anais, I recommend taking a day trip to the iGEM and interviewing the teams there. iGEM is guaranteed to generate "surprising" stuff.--
letters.cunningprojects.com
twitter.com/onetruecathal
twitter.com/labsfromfabs
Of course, fluorescent or bioluminescent foods need not be for consumption. I can imagine a handful of very entertaining and perhaps lucrative ideas for fluorescent foodstuffs, that I may in fact attempt in coming years. ;) Certainly this year I wanted to have a bioluminescent pumpkin outside my house, though I didn't have time to prepare it because of writing my thesis. :( I'll experiment sometime soon to see how feasible it will be for next year using just the bacteria I have, no engineering needed.. Not nearly as safe as the genetically engineered option, of course.
For the show, Anais, I recommend taking a day trip to the iGEM and interviewing the teams there. iGEM is guaranteed to generate "surprising" stuff.
letters.cunningprojects.com
twitter.com/onetruecathal
twitter.com/labsfromfabs
Nathan McCorkle
Nov 5, 2010, 2:59:52 PM11/5/10
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On Fri, Nov 5, 2010 at 1:56 PM, Cathal Garvey <cathal...@gmail.com> wrote:
> I seem to recall the London Hackerspace people discussing a fluorescent beer
> as a cool idea. I agree! Fluorescent drinks would rock. Of course, you can
> already do that with chlorophyll, but it's not nearly as cool as a
> Genengineered drink. This application is almost certainly illegal in EU of
> course, so for now it's a pipe dream.
> I seem to recall the London Hackerspace people discussing a fluorescent beer
> as a cool idea. I agree! Fluorescent drinks would rock. Of course, you can
> already do that with chlorophyll, but it's not nearly as cool as a
> Genengineered drink. This application is almost certainly illegal in EU of
> course, so for now it's a pipe dream.
quinine is found in tonic water here in the U.S. so that makes for
easily fluorescent bar drinks... It would be damn easy to make GFP
beer though, hmm.....
--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics
Russell Whitaker
Nov 5, 2010, 3:21:16 PM11/5/10
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On Fri, Nov 5, 2010 at 11:59 AM, Nathan McCorkle <nmz...@gmail.com> wrote:
> On Fri, Nov 5, 2010 at 1:56 PM, Cathal Garvey <cathal...@gmail.com> wrote:
>> I seem to recall the London Hackerspace people discussing a fluorescent beer
>> as a cool idea. I agree! Fluorescent drinks would rock. Of course, you can
>> already do that with chlorophyll, but it's not nearly as cool as a
>> Genengineered drink. This application is almost certainly illegal in EU of
>> course, so for now it's a pipe dream.
>
> quinine is found in tonic water here in the U.S. so that makes for
> easily fluorescent bar drinks...
> --> On Fri, Nov 5, 2010 at 1:56 PM, Cathal Garvey <cathal...@gmail.com> wrote:
>> I seem to recall the London Hackerspace people discussing a fluorescent beer
>> as a cool idea. I agree! Fluorescent drinks would rock. Of course, you can
>> already do that with chlorophyll, but it's not nearly as cool as a
>> Genengineered drink. This application is almost certainly illegal in EU of
>> course, so for now it's a pipe dream.
>
> quinine is found in tonic water here in the U.S. so that makes for
> easily fluorescent bar drinks...
Really? Cool... do you have a formula for me to enhance my customary
G&T?
sgt york
Nov 8, 2010, 10:27:15 AM11/8/10
to DIYbio
GFP beer for St Patrick's day...hey, that could be fun.
It's easy to get yeast to express something. You could put GFP under
some anaerobic promoter, that way it doesn't interfere with the
initial oxygen depletion in fermentation. GFP will glow pretty well
under standard blacklight bulbs.
Not a problem at all for someone with even rudimentary knowledge of
molecular biology & brewing. Let me know if you want to take a crack
at this, I'd love to help out if I can. I don't have a whole lot of
experience with yeast specifically and have no home lab, but I have a
solid foundation in general molecular biology and I've been a
homebrewer for years.
On Nov 5, 1:59 pm, Nathan McCorkle <nmz...@gmail.com> wrote:
It's easy to get yeast to express something. You could put GFP under
some anaerobic promoter, that way it doesn't interfere with the
initial oxygen depletion in fermentation. GFP will glow pretty well
under standard blacklight bulbs.
Not a problem at all for someone with even rudimentary knowledge of
molecular biology & brewing. Let me know if you want to take a crack
at this, I'd love to help out if I can. I don't have a whole lot of
experience with yeast specifically and have no home lab, but I have a
solid foundation in general molecular biology and I've been a
homebrewer for years.
On Nov 5, 1:59 pm, Nathan McCorkle <nmz...@gmail.com> wrote:
Nathan McCorkle
Nov 8, 2010, 12:58:49 PM11/8/10
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first we need to find a good promoter, Sgt... got a gene name?
I have pYES2, but its episomal... if we used the ADH promoter rather
than what Sgt was suggesting, we could incorporate into the genome by
cutting the plasmid somewhere in the middle of the promoter and
transforming with a linear strand.
I also have pKLAC2, which has amdS for selection with acetamide, which
is pretty cheap to come by. I'm in process of modifying pKLAC2 now, so
I should have more experience with the molecular side of things in the
next few months, as well as having a ton of compatible restriction
enzymes.
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John Griessen
Nov 8, 2010, 1:36:26 PM11/8/10
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On 11/08/2010 11:58 AM, Nathan McCorkle wrote:
> I'm in process of modifying pKLAC2 now, so
> I should have more experience with the molecular side of things in the
> next few months, as well as having a ton of compatible restriction
> enzymes.
> I'm in process of modifying pKLAC2 now, so
> I should have more experience with the molecular side of things in the
> next few months, as well as having a ton of compatible restriction
> enzymes.
You'll qualify for videography interest and hit the popular news
with fluorescing green? yellow? red? beer!
JG
sgt york
Nov 8, 2010, 3:53:21 PM11/8/10
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Will pKLAC2 incorporate into Saccharomyces? Most brewer's yeast are
Saccharomyces.
Selection of some kind during application would be useful, but not
terribly necessary. Any gene loss would likely be due to random
mutation in response to the high stress environment of fermentation,
so a separate gene wouldn't give a whole lot of advantage. Some, but
not much. It wouldn't be hard to test, though, and we'd need some kind
of marker for screening anyway. Might as well be something we can use
later.
Problem, though. I forgot about this in my initial post. Although GFP
doesn't require oxygen to glow, it does require oxygen in processing.
You usually get a nonfunctional (nonglowing) protein if it's grown
anaerobically.
With this in mind, it's probably best to just make it constituitive,
or find a gene that is constituitive but is HAP1p dependent (HAP1p is
heme-dependent and shuts down in low oxygen) in order to not hurt the
efficiency of the yeast too much. I'm not really that familiar with
the tools used in yeast genetics, but probably anything from the ROX1
or HAP1p systems would work. I'll look around a bit.
> > For more options, visit this group athttp://groups.google.com/group/diybio?hl=en.
Saccharomyces.
Selection of some kind during application would be useful, but not
terribly necessary. Any gene loss would likely be due to random
mutation in response to the high stress environment of fermentation,
so a separate gene wouldn't give a whole lot of advantage. Some, but
not much. It wouldn't be hard to test, though, and we'd need some kind
of marker for screening anyway. Might as well be something we can use
later.
Problem, though. I forgot about this in my initial post. Although GFP
doesn't require oxygen to glow, it does require oxygen in processing.
You usually get a nonfunctional (nonglowing) protein if it's grown
anaerobically.
With this in mind, it's probably best to just make it constituitive,
or find a gene that is constituitive but is HAP1p dependent (HAP1p is
heme-dependent and shuts down in low oxygen) in order to not hurt the
efficiency of the yeast too much. I'm not really that familiar with
the tools used in yeast genetics, but probably anything from the ROX1
or HAP1p systems would work. I'll look around a bit.
Cathal Garvey
Nov 8, 2010, 4:10:29 PM11/8/10
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That's an interesting trait I wasn't aware of, why is it that GFP won't fold in low-oxygen? Is it a redox-thing relating to the amino acids in GFP? Would recoding the protein for low-oxygen environs be a possibility? (Warning: potential DIY-GEM project taking form)
Cathal Garvey
Nov 8, 2010, 4:13:11 PM11/8/10
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Hey Nathan,
If I'd known yeast episomes were floating around DIYbio I'd have asked for a sample already! :) I wonder could I get a sample dried on blotting paper, so I can test yeast transfection protocols? I've got a kilogram of Miralax and infinite sodium chloride, I just lack a plasmid to test it out with!
Alternatively, I'd love a look at an annotated plasmid map, so I can learn more about the necessary sequences Yeast episomes need. I'm hoping to get into total plasmid synthesis in the coming year, and making IP-free plasmids for bacteria and yeast is on the cards!
All the best,
Cathal
Cory Tobin
Nov 8, 2010, 4:15:52 PM11/8/10
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> Alternatively, I'd love a look at an annotated plasmid map, so I can learn
> more about the necessary sequences Yeast episomes need.
> more about the necessary sequences Yeast episomes need.
map of pKLAC2:
http://www.neb.com/nebecomm/products/productN3742.asp
-Cory
Nathan McCorkle
Nov 8, 2010, 4:27:33 PM11/8/10
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pKLAC2(K.lactis expression vector with secretion tag, no yeast ORI):
http://www.ncbi.nlm.nih.gov/nuccore/196122458
http://www.ncbi.nlm.nih.gov/nuccore/196122458
pYES2(Invitrogen, saccharomyces and maybe others, yeast ORI is 2micron
region, E.coli is from pBR322):
http://www.lablife.org/p?a=vdb_view&old_id=3193&id=
http://genome-www.stanford.edu/vectordb//vector_descrip/PYES2.html
sgt york
Nov 8, 2010, 4:49:20 PM11/8/10
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I don't know why.
As far as I'm aware, it's just an observation at this point. I only
know because I tried to grow some GFP-expressing cells in an anaerobic
chamber. When the time came to test them, they just barely glowed
(only detectable with a PMT). We thought we had a weird phenotype
until another guy in the department told me about this. I checked with
an anti-GFP antibody and lo and behold, GFP was there, just non-
glowing.
But I've never looked into it; the cause may be well known for all I
know. As far as I was concerned, it was just a broken model system and
I moved on.
> > diybio+un...@googlegroups.com<diybio%2Bunsu...@googlegroups.com>
> > .
> > .
As far as I'm aware, it's just an observation at this point. I only
know because I tried to grow some GFP-expressing cells in an anaerobic
chamber. When the time came to test them, they just barely glowed
(only detectable with a PMT). We thought we had a weird phenotype
until another guy in the department told me about this. I checked with
an anti-GFP antibody and lo and behold, GFP was there, just non-
glowing.
But I've never looked into it; the cause may be well known for all I
know. As far as I was concerned, it was just a broken model system and
I moved on.
> > .
> > > --
> > > Nathan McCorkle
> > > Rochester Institute of Technology
> > > College of Science, Biotechnology/Bioinformatics
>
> > --
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> > > Nathan McCorkle
> > > Rochester Institute of Technology
> > > College of Science, Biotechnology/Bioinformatics
>
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Cory Tobin
Nov 8, 2010, 4:57:34 PM11/8/10
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GFP maturation has an oxidation step. Check out this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC45466/ Fig 2 shows the
step that requires oxygen.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC45466/ Fig 2 shows the
step that requires oxygen.
-Cory
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