Kombucha as-is or isolated cultures for gel electrophoresis or other DIYbio uses
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Nathan McCorkle
Feb 25, 2013, 8:49:27 PM2/25/13
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I just got a kombucha SCOBY in the mail... I haven't brewed kombucha
for years and the vinegary smell out of the box is a bit unpleasant (I
know brew doesn't need to be so acidic). Other than drinking and
electrophoresis gel+buffer, what other uses can we think of?
Cathal mentioned isolating G.xylinus, presumably in the line of
thinking that we could scale up production and have a nice pure
cellulose/other-ose producer for various uses.
What other ideas are there for kombucha as-is or as isolates? For
instance, I knew a guy who grafted a bunch of cacti, then applied
blended SCOBY to the fresh graft wounds. He said the cacti all healed
with no failures, and thought the SCOBY may have added some antibiotic
factor (or at least antibiotic for plant diseases).
On Wed, Jan 30, 2013 at 4:44 AM, Cathal Garvey
<cathal...@cathalgarvey.me> wrote:
> Sadly I let my Kombucha stale in the fridge for too long and couldn't
> recover it. And, my isolated culture of G.xylinus is long dried out too,
> due to a gap in the parafilm. So, I'll have to re-order Kombucha and
> re-isolate G.xylinus! Thankfully, the latter isn't too challenging.
>
> You make agar containing calcium carbonate powder, stir and pour right
> before solidifying so you get evenly dispersed CaCO4 particles through
> the gel, then streak and re-streak your kombucha on the surface. The
> colonies that create a broad area of clear agar (acid dissolving the
> CaC04) are your Geo/Acetobacter, of which there may be one or two species.
>
> Isolate those and grow to stationary, the plates that form nodules of
> whitish cellulose after a week or so are your guys. :)
>
> I have the agar recipe lying around somewhere, will dig up soon.
>
> On 30/01/13 06:06, Patrik D'haeseleer wrote:
>> Hey Cathal - do you have some Kombucha going right now? I'd love to see
>> what happens if you take a nice thick "mother" SCOBY, cut some wells
>> into it, and use it as an electrophoresis gel. :-). Food dyes
>> electrophorese pretty well.
>>
>> Patrik
>>
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-Nathan
for years and the vinegary smell out of the box is a bit unpleasant (I
know brew doesn't need to be so acidic). Other than drinking and
electrophoresis gel+buffer, what other uses can we think of?
Cathal mentioned isolating G.xylinus, presumably in the line of
thinking that we could scale up production and have a nice pure
cellulose/other-ose producer for various uses.
What other ideas are there for kombucha as-is or as isolates? For
instance, I knew a guy who grafted a bunch of cacti, then applied
blended SCOBY to the fresh graft wounds. He said the cacti all healed
with no failures, and thought the SCOBY may have added some antibiotic
factor (or at least antibiotic for plant diseases).
On Wed, Jan 30, 2013 at 4:44 AM, Cathal Garvey
<cathal...@cathalgarvey.me> wrote:
> Sadly I let my Kombucha stale in the fridge for too long and couldn't
> recover it. And, my isolated culture of G.xylinus is long dried out too,
> due to a gap in the parafilm. So, I'll have to re-order Kombucha and
> re-isolate G.xylinus! Thankfully, the latter isn't too challenging.
>
> You make agar containing calcium carbonate powder, stir and pour right
> before solidifying so you get evenly dispersed CaCO4 particles through
> the gel, then streak and re-streak your kombucha on the surface. The
> colonies that create a broad area of clear agar (acid dissolving the
> CaC04) are your Geo/Acetobacter, of which there may be one or two species.
>
> Isolate those and grow to stationary, the plates that form nodules of
> whitish cellulose after a week or so are your guys. :)
>
> I have the agar recipe lying around somewhere, will dig up soon.
>
> On 30/01/13 06:06, Patrik D'haeseleer wrote:
>> Hey Cathal - do you have some Kombucha going right now? I'd love to see
>> what happens if you take a nice thick "mother" SCOBY, cut some wells
>> into it, and use it as an electrophoresis gel. :-). Food dyes
>> electrophorese pretty well.
>>
>> Patrik
>>
>> --
>> -- You received this message because you are subscribed to the Google
>> Groups DIYbio group. To post to this group, send email to
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>> diybio+un...@googlegroups.com. For more options, visit this group
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>> Learn more at www.diybio.org
>> ---
>> You received this message because you are subscribed to the Google
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>>
>>
>
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>
--
-Nathan
Patrik D'haeseleer
Feb 26, 2013, 7:33:41 AM2/26/13
to diy...@googlegroups.com
You know, I usually try to make things *easier* to degrade, but what if you could engineer G.xylinus to produce something a bit stronger than amorphous cellulose?
Add an acetyltransferase and get it to produce chitin?
Mix in some bioplastics?
Try to secrete silk, spidersilk, or mussel glue proteins, possibly modified with some cellulose binding modules?
Patrik
Add an acetyltransferase and get it to produce chitin?
Mix in some bioplastics?
Try to secrete silk, spidersilk, or mussel glue proteins, possibly modified with some cellulose binding modules?
Patrik
Cathal Garvey
Feb 26, 2013, 1:44:28 PM2/26/13
to diy...@googlegroups.com
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
@Nathan
I wanted a pure line of Xylinus so I could mix it with a lab strain of
yeast and have a "lab strain" kombucha. It wouldn't be as robust or as
good for brewing, probably, but might be interesting as a
kitchen-friendly "model organism"! :)
As to antibiotics, there's loads of supposition out there that, in
addition to the acid production, one or more of the species in
kombucha SCOBYs produce bacteriocins or other antibiotics. You could
test this by doing an exclusion assay, of course! Filter-sterilise
some freshly brewed kombucha (or wait til it's a bit stale to check
for stationary phase secretion), soak some sterile discs of filter
paper in that and normal boiled (and filter sterilised) vinegar, and
apply the two discs to separate freshly streaked agar plates of a test
species, like E.coli.
Preferably pick a few test species from different genuses, as
bacteriocins are rarely broad spectrum.
Compare growth exclusion radius, if any, to establish whether there's
cause to suspect more than just the pH is to blame (would want to
ensure by dilution that the pH of either sample is the same, and the
buffering capacity of the agar is the same; same batch for e.g)
@Patrik:
Spider silk requires spinning to form polymers, whether by
electrospinning or spinneret, but glue proteins or chitin sound like
nice leads!
Another thought is: I found some patents for cellulose binding
peptides, and separate patents for calcium carbonate-binding peptides.
Possibly there was a compromise patent involving combining the two to
make cheap bio-bleach for paper industry. Can't recall!
But, there were libraries in each patent of artificially-evolved small
peptides for binding to calcium carbonate and cellulose; could
conjugate those to one another to make cellulose/calcium adaptors to
perhaps help precipitate calcium carbonate into a crust over the
cellulose fibers.
If it worked, you'd probably end up with something that looked a bit
like spongy coral, provided enough CaCl to build up a sufficient crust..
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>>
>>
>
>
>
> -- -Nathan
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@Nathan
I wanted a pure line of Xylinus so I could mix it with a lab strain of
yeast and have a "lab strain" kombucha. It wouldn't be as robust or as
good for brewing, probably, but might be interesting as a
kitchen-friendly "model organism"! :)
As to antibiotics, there's loads of supposition out there that, in
addition to the acid production, one or more of the species in
kombucha SCOBYs produce bacteriocins or other antibiotics. You could
test this by doing an exclusion assay, of course! Filter-sterilise
some freshly brewed kombucha (or wait til it's a bit stale to check
for stationary phase secretion), soak some sterile discs of filter
paper in that and normal boiled (and filter sterilised) vinegar, and
apply the two discs to separate freshly streaked agar plates of a test
species, like E.coli.
Preferably pick a few test species from different genuses, as
bacteriocins are rarely broad spectrum.
Compare growth exclusion radius, if any, to establish whether there's
cause to suspect more than just the pH is to blame (would want to
ensure by dilution that the pH of either sample is the same, and the
buffering capacity of the agar is the same; same batch for e.g)
@Patrik:
Spider silk requires spinning to form polymers, whether by
electrospinning or spinneret, but glue proteins or chitin sound like
nice leads!
Another thought is: I found some patents for cellulose binding
peptides, and separate patents for calcium carbonate-binding peptides.
Possibly there was a compromise patent involving combining the two to
make cheap bio-bleach for paper industry. Can't recall!
But, there were libraries in each patent of artificially-evolved small
peptides for binding to calcium carbonate and cellulose; could
conjugate those to one another to make cellulose/calcium adaptors to
perhaps help precipitate calcium carbonate into a crust over the
cellulose fibers.
If it worked, you'd probably end up with something that looked a bit
like spongy coral, provided enough CaCl to build up a sufficient crust..
>>> this
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> -- -Nathan
>
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Patrik D'haeseleer
Feb 26, 2013, 4:17:14 PM2/26/13
to diy...@googlegroups.com, cathal...@cathalgarvey.me
On Tuesday, February 26, 2013 10:44:28 AM UTC-8, Cathal Garvey wrote:
@Patrik:
Spider silk requires spinning to form polymers, whether by
electrospinning or spinneret, but glue proteins or chitin sound like
nice leads!
Actually, I think spinning is primarily required to form *fibers*. But if we're just creating a sheet of reinforced cellulose++ material, that may be irrelevant.
There's a wide variety of carbohydrate binding modules that have been characterized and/or patented to various degrees. I doubt anyone has ever used them to crosslink amorphous cellulose though, so that would be an entirely novel application ot covered by any preexisting patents.
The CAZy database contains 66 different carbohydrate binding module families, although not all of those are specific for cellulose:
http://www.cazy.org/Carbohydrate-Binding-Modules.html
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