saccharomyces cerevisiae potentialities

[Nick M.]

All, 

Hope everyone had lovely and peaceful holidays. 

I've been lurking the group for ~16 months now. So far I've done a GFP plant, selective breeding on plants, selective breeding on brewer's yeast, and a few other random projects. I want to thank you all for the invaluable depth of knowledge that is available here.

I am a brewer by profession and have recently taken over a brewery with considerable corporate backing, corporate has told me 'Do what you want, don't break anything, and most importantly make great beer.' 

I take this to me I can build my own synbio lab, I am confident that is within my AOR. 

 I was hoping to receive some input from you all on interesting directions to go with S. cerevisiae. 

I have seen the iGEM projects on beer, caffeine, limonene(particularly interesting to me), and kumamolisin, and all of those are things I would like to work towards. 

Any ideas on what I can do in the interim whilst trial running my lab and knowledge base? Looking for projects that would be valuable to me in either an academic or practical regard that would build a good framework of experience to operate on in a professional standard. I also feel indebted to the community and must offer my position to the benefit to the diybio community once it becomes a position of value. 

Cheers,

Nick 

[Cathal Garvey]

Wow, sounds like you just landed a job as microbiology-Willy-Wonka!
Congratulations, can't wait to see what you do with it. :)

As far as "awesome stuff to do with yeast", there's plenty of
neutriceutical hacks you could replicate, like resveratrol beer. There's
also plenty of utilitarian stuff you could try, ways of producing
difficult things, or under difficult conditions.

I was told by someone who ought to know, that a major biofab out there
uses a custom, directed-evolution-bred, strain of yeast that grows as
low as pH 3.X, a startlingly low pH for a yeast! The idea was that you
can avoid contamination by growing things at such low pH, I don't know
how much use it sees however. It is, sadly, proprietary; I wonder how
hard that would be to replicate? Whether by DirEvo or Synbio?

While we're on the subject of "wyrd yeest", what about psychrophilic
yeast? Or thermophilic?

There's already a talented team working on cannabinoid yeast, how about
circumin? Or vitamin B12? Or berberine?

> --
> -- You received this message because you are subscribed to the Google
> Groups DIYbio group. To post to this group, send email to
> diy...@googlegroups.com. To unsubscribe from this group, send email to
> diybio+un...@googlegroups.com. For more options, visit this group
> at https://groups.google.com/d/forum/diybio?hl=en
> Learn more at www.diybio.org
> ---
> You received this message because you are subscribed to the Google
> Groups "DIYbio" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to diybio+un...@googlegroups.com
> <mailto:diybio+un...@googlegroups.com>.
> To post to this group, send email to diy...@googlegroups.com
> <mailto:diy...@googlegroups.com>.
> Visit this group at http://groups.google.com/group/diybio.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/diybio/1cf1d37b-1d7d-4a24-b3a5-8809f8d67cb7%40googlegroups.com
> <https://groups.google.com/d/msgid/diybio/1cf1d37b-1d7d-4a24-b3a5-8809f8d67cb7%40googlegroups.com?utm_medium=email&utm_source=footer>.
> For more options, visit https://groups.google.com/d/optout.

[Mega [Andreas Stuermer]]

Recently a mutation has been found that confers greater ethanol tolerance in yeast. I can look it up if that's interesting. 

You could add exoenzymes such as cellulase and pektinase and lignin degrading(?) and feed your yeast with straw to produce ethanol. pKlac2 plasmid excretes the protein into the medium. 

[Mega [Andreas Stuermer]]

Enhancing ethanol tolerance was conferred by overexpressing a potassium pump

They also found thermotolerant yeast mutations.

http://www.techtimes.com/articles/17128/20141003/thermotolerant-yeast-will-change-the-face-of-biofuel-production.htm

[Mega [Andreas Stuermer]]

Is there a value in producing breberine? It has cool properties, but is there a market? 

All the other berberine analogous substances (epiberberine, sanguarine, ...) may work together in medical plants. By taking just berberine, the effects may not be optimal as they could be by eating a plant that contains analoga. 

[Cathal Garvey]

Actually, pectinases would be directly valuable to brewing as they'd
clarify brews. Pectinases are routinely added to wine brews, for
example, and it was a brand of pectinase designed for home-brew I used
to de-pectinate agar when I experimented way-back-when with making
homebrew agarose.

Also in this vein; anti-bacterial enzymes like lysozyme, which are added
to reduce maltolactic fermentor bacteria which produce off-flavours or
ruin brews entirely. Would probably reduce acetic acid bacteria too,
preventing vinegary brews.

> --
> -- You received this message because you are subscribed to the Google
> Groups DIYbio group. To post to this group, send email to
> diy...@googlegroups.com. To unsubscribe from this group, send email to
> diybio+un...@googlegroups.com. For more options, visit this group
> at https://groups.google.com/d/forum/diybio?hl=en
> Learn more at www.diybio.org
> ---
> You received this message because you are subscribed to the Google
> Groups "DIYbio" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to diybio+un...@googlegroups.com
> <mailto:diybio+un...@googlegroups.com>.
> To post to this group, send email to diy...@googlegroups.com
> <mailto:diy...@googlegroups.com>.
> Visit this group at http://groups.google.com/group/diybio.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/diybio/c54660f5-659d-43a9-940c-20bb1f11d533%40googlegroups.com
> <https://groups.google.com/d/msgid/diybio/c54660f5-659d-43a9-940c-20bb1f11d533%40googlegroups.com?utm_medium=email&utm_source=footer>.

[John Griessen]

On 12/26/2014 11:29 AM, Nick M. wrote:
> Any ideas on what I can do in the interim whilst trial running my lab and knowledge base? Looking for projects that would be
> valuable to me in either an academic or practical regard that would build a good framework of experience to operate on in a
> professional standard

If you imagine any equipment projects would help, that's my focus and I would
help with development.

I'm thinking of tools like incubator, thermocycler,
pH meter, conductivity meter, pressured bioreactor, optical density, mass density -- all with an automation
mindset -- ethernet or plastic optical fiber connected, no galvanic connections:
battery/indoor photovoltaic powered and with design for automation with handler bots
to carry material from station to station. Radio is another interconnection method
to consider for the data depending on RF noise allowable in your lab. Ethernet is
a simpler starting point though. USB seems too limited to me, especially when ethernet is
everywhere already, and eases development of instrument apps -- they're just web apps then.

On 12/29/2014 11:02 AM, Cathal Garvey wrote:
> Also in this vein; anti-bacterial enzymes like lysozyme, which are added to reduce maltolactic fermentor bacteria which produce
> off-flavours or ruin brews entirely. Would probably reduce acetic acid bacteria too, preventing vinegary brews.

Cathal's suggestion seems like a natural to develop an anti-bacterial enzyme producer along
with some instrumentation to tell how much of the enzyme is produced and being effective
in a culture by measuring presence of the unwanted bacteria somehow. The vinegar bacteria presence
could be inferred by pH alone. What is a good indicator or maltolactic fermentor bacteria presence
in a culture broth?

[Mega [Andreas Stuermer]]

Make the yeast produce nisin, so you get ride of lactobacilli which may destroy beer quality? Or some vinegar bacterium-antimicrobial peptide?

[Mega [Andreas Stuermer]]

Ah, I think I came across a glucanase which destroys gram+ bacteria in literature research in my bee project. I didn't look closer at it, because bacteria seem to be much much  lesser a problem to bees than fungi and viruses and pesticides. 

[mostromundo]

I work in wine production, we want yeast that will consume all of the hexose sugars (especially fructose) and will do so while producing more glycerol and less ethanol. If you can make  a fructophilic wine yeast with below-average ethanol production and acceptable sensory characters, you will make a lot of winemakers very happy :)

[Mega [Andreas Stuermer]]

That actually seems doable, but the yeast would grow slower. All the enzymes have been known for a long time. Unless you add methane production for energy making

[Mega [Andreas Stuermer]]

Hm, maybe you can inhibit the krebs cycle thus the yeast never oxidizes your ethanol to CO2? You could grow it in a standard atmosphere then (not sure if that makes any difference)

[Patrik D'haeseleer]

Awesome- that sounds like a dream job!

Whereabouts are you located? We've been looking forward to doing some brew hacking.

One fun thing to follow up on would be the symbiosis between aromatic beer yeasts and fruit flies. Use some of your favorite beer to attract fruit flies, capture some of the wild yeasts the flies carry, sequence their ATF1 gene, and make a library of ATF1 mutant yeasts with different aromatic properties.

You could do the same with a bunch of other known aromatic compound producing enzymes. Or you could use subtractive techniques to sequence the parts of the genome that differ from standard S. cerevisiae.

Patrik

On Friday, December 26, 2014 9:29:46 AM UTC-8, Nick M. wrote:

[Jeswin]

On Mon, Jan 5, 2015 at 4:48 AM, Patrik D'haeseleer <pat...@gmail.com> wrote:
> One fun thing to follow up on would be the symbiosis between aromatic beer
> yeasts and fruit flies. Use some of your favorite beer to attract fruit
> flies, capture some of the wild yeasts the flies carry, sequence their ATF1
> gene, and make a library of ATF1 mutant yeasts with different aromatic
> properties.
>
> You could do the same with a bunch of other known aromatic compound
> producing enzymes. Or you could use subtractive techniques to sequence the
> parts of the genome that differ from standard S. cerevisiae.
>
> Patrik
>

Do fruit flies spread yeast, similar to how bees spread pollen?

[Patrik D'haeseleer]

On Monday, January 5, 2015 6:04:57 AM UTC-8, phillyj wrote:

Do fruit flies spread yeast, similar to how bees spread pollen?

That's the idea. Fruit flies are attracted by the aroma compounds produced by yeast. Yeast lure fruit flies to help them spread to new fruit. So you can use fruit flies to select for yummy smelling wild yeasts...

Patrik

[Brian Degger]

ATF1 sequencing sounds like fun, and a nice proxy for diversity of yeasts :) 

More of a Summer Sport though ;) 

cheers

Brian

--

-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+un...@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.

To unsubscribe from this group and stop receiving emails from it, send an email to diybio+un...@googlegroups.com.

To post to this group, send email to diy...@googlegroups.com.

Visit this group at http://groups.google.com/group/diybio.

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/4eba5159-9685-4615-b2ec-1e171df31c14%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

--

----------------------------------------
Brian Degger

twitter: @drbrian

http://makerspace.org.uk

http://transitlab.org

----------------------------------------