---

	FORUM ON BEER, HOMEBREWING, AND RELATED ISSUES
		Digest Janitor: pbabcock at hbd.org


***************************************************************
       THIS YEAR'S HOME BREW DIGEST BROUGHT TO YOU BY: 

          Northern  Brewer, Ltd. Home Brew Supplies
Visit http://www.northernbrewer.com  to show your appreciation!
               Or call them at 1-800-681-2739

    Support those who support you! Visit our sponsor's site!
********** Also visit http://hbd.org/hbdsponsors.html *********


Contents:
  Crabtree effect and metabolic overflow at pyruvate branch ("Fredrik")
  secondary fermentation in bottle (KEITH R BUSBY)


* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*           The HBD Logo Store is now open!             *
*            http://www.hbd.org/store.html              *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*  Suppport this service: http://hbd.org/donate.shtml   *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*   Beer is our obsession and we're late for therapy!   *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*  Thank you, Drs. Cone, Fischborn, Waldrop, Lemcke, &  *
* Powell! Fortnight of Yeast Question Sumbission is now *
* closed.  Please save further questions for next year. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * *

Send articles for __publication_only__ to post@hbd.org

If your e-mail account is being deleted, please unsubscribe first!!

To SUBSCRIBE or UNSUBSCRIBE send an e-mail message with the word
  "subscribe" or "unsubscribe" to request@hbd.org FROM THE E-MAIL
  ACCOUNT YOU WISH TO HAVE SUBSCRIBED OR UNSUBSCRIBED!!!**
IF YOU HAVE SPAM-PROOFED your e-mail address, you cannot subscribe to
  the digest as we cannot reach you. We will not correct your address
  for the automation - that's your job.

HAVING TROUBLE posting, subscribing or unsusubscribing? See the HBD FAQ at
http://hbd.org.

LOOKING TO BUY OR SELL USED EQUIPMENT? Please do not post about it here. Go
instead to http://homebrewfleamarket.com and post a free ad there.

The HBD is a copyrighted document. The compilation is copyright 
  HBD.ORG. Individual postings are copyright by their authors. ASK 
  before reproducing and you'll rarely have trouble. Digest content 
  cannot be reproduced by any means for sale or profit.

More information is available by sending the word "info" to 
req@hbd.org or read the HBD FAQ at http://hbd.org.

JANITORs on duty: Pat Babcock (pbabcock at hbd dot org), Jason Henning,
                  and Spencer Thomas



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


Date: Sun, 7 Aug 2005 21:44:05 +0200
From: "Fredrik" <carlsbergerensis at hotmail.com>
Subject: Crabtree effect and metabolic overflow at pyruvate branch

Hello everyone. All recent talks on the crabtree discussions 
is interesting.

FWIW I have some comments on which I would like
to get some feedback.

It seems that many "effects in yeast" take place at different
levels. The basic level is the phenomena that can typically 
appear in any complex dynamical system due to constraints in
the metabolic network, like energy and mass balancing. Ontop
of this there are regulatory control of enzymes and gene 
expression.

If you consider a really simplified view of the main energy and 
carbon flow, it seems that at least to principle, the 
crabtree effect can be understood from (an almost) pure dynamical
point of view? though I'm sure the phenomenon is further be 
tweaked and enhanced by more not so easy to understand regulatory 
responses in the cell. But OTOH I think that even the not so 
easy to understand regulatory behaviours often may have a dynamic
explanation, at least for triggerings.

First there is sugaruptake, then there is glycolysis,
then at the pyruvate branch the flow is put to
competion with pyruvatedecarboxylase(pdc)
(to acetadelhyde/fermentation), 
pyruvatedehydrogenas(pdh)(to acetyl-CoA) and also some 
pipelining directly into misc biosynthesis.

Each of these pipelines has an affinity, and a capacity,
and also a different energy balancing etc. Affect the flow
in one pipeline and the flow in remote places in the network 
might change.

I don't find the refenrece now but I know I read a paper 
claming that, pdh has a factor 10 higher *affinity*(prefenece) 
for pyruvate as compared to pdc. pdc has a factir 10 higher 
*capacity* for purvate as comapared to pdh. (If anyone wants 
it I can look for it, I just have no structure on references 
atm so I have to wade through lots of htings). 

But a general good reference is a really nice thesis on the
"Physiological Roles of pyruvate decarboxylase in Saccharomyces cerevisiae"
by Marcel Flikweert - http://www.xs4all.nl/~marcelf/Thesis.htm
Excellent site I found recently where the articles are free to download. Maybe
these numbers are from there even (I forgot!?), but it's a great thesis and
outstanding bedtime and/or bathtub reading. 

So already here one would expect that at low glycolysis rates, 
the respiratory pathways is *preferred*, given that oxidative 
phosporylation is running and there is O2 etc. (pasteur effect)

At higher glycolysis rates, this branch is saturated, and 
there is an overflow into the pdc.

This alone (so far) however, doesn't seem to explain the 
"suppression" of respiratory pathway, it is just a simple 
"overflow" - so more is needed.

But then at a closer look, what happens if the glycolysis 
rate increase? Then the growth rate typically increase too right? 
And so does the demand for building blocks. The puruvate brach 
is then also more drained for carbon, and the acetyl pool is 
also drained for carbon to.

This seems to imply that, given that the pdh is saturated, 
then acetyl-CoA production is in a simple estimate, at max. At 
this point there seems to be a competition for acetyl-CoA between 
respiratory energy transduction pathways and biosynthesis of for 
example fatty acids.

So, at this point - if the growth rate is to be able to 
increase - it seems that the respiratory consumption of acetyl-CoA 
must be not only "saturated and overflowed", it must also be 
*downregulated* to maintain the mass balance.

I have no idea how far this effect lats to explain things when 
you start to put numbers on it, but it seems to me it could at 
least help understand the pasteur and crabtree effects, and any
additional regulatory things probably enhance these dynamic effects.

So from this possibly oversimplified and even incorrect description
it seems to me put simple

The "Crabtree effect" can be roughly understood the combined effect of 

1) saturation of the acetyl-CoA production at high glycolysis rates, 
causing metabolic overflow at hte pyruvate branch

2) downregulation of the respiratory activity, due to growth related
mass flow competition at the acetyl-CoA branch?

The "pasteur effect" would as it seems caused by pdh winning the 
competition for pyruvate, when there is oxygen. The pasteur effect
will exist only if pdh is not near saturation, because then in despited
of the higher affinity, there is an overflow to alcoholic fermentation.

This is admittedly an oversimplification, there are more draining 
going on in the flow, pentose pathways, and also a shunting via 
acetate back to acetyl-CoA. But from papers I've read this shunting 
while highly significant also limited capacity, so it is likely 
insufficient(?) to regenerate enough acetyl-CoA to prevent biosynthesis 
from draining the acetyl-CoA pool. Even if you add these things, 
and the redox balancing I suspect the general conclusion holds to principle.
Though if you were to put numbers on things all pathways probably has to
be accounted for.

Quick simplified pic I made 
http://hem.bredband.net/frerad/beer/modelling/pictures/crabtree.jpg

So it seems to me that the "crabtree" breaking point, seems to be
related to the ratio of the pdh pathway "bandwidth" and the rate 
of glycolysis but also the energy consumption of biosynthesis. So
another complication may be thta the cost for growth increases as
stress factors accumulate (maybe likely in when alcohol anc acids 
are produced and osmosis increase?) Too much to keep
in the head at once. I'd need a computer. 

Since glucose as far as I understnad is the quickest sugar to uptake, 
it is also expected to generate one of the higest glycolytic rates?

Of course, if this is not so, the idea fails. Does anyone
know if this is so or ot? 

Once migth wonder, if the capacity of the pdh pathway is so limiting,
why doesn't the cell just synthesise more pdh?? I don't know. But I
figure that a general thing is that would increase various pool
sizes too, and would also probably affect the steady state redox 
balance? So while I have no idea why, there seems to be many 
possible understandable reasons?? Comments??

These reasoning may well be flawed, as I'm still no biologist, but it's
how I personally currently think of these things where I am
constantly trying to improve my understanding. I'd love to get 
some comments on this or if anyone see any obvious flaws in the 
reasoning.

( I posted about a simplified computer simulations of metabolism 
before, and while I'm still working on it. The more I learn the 
more do I see how much computing power I am going to need due to 
the :-( So right now, it looks like my original strategy is not 
going to work so well due to limited computing power. So I am 
currently trying to figure out how to try to implement even this 
very limited model in a way that it will work on a normal PC.

The basic dynamics will probably be workable, though it is probably 
going to take many hours on a PC. The other problem I recently 
found out is that the mimicing of regulation intelligence seems to 
require probably even more computing power than the "kinetics" alone
unless i simplifiy it even more. So it is definitly going to take a 
little longer than I first thought. I had to make the regulation
more intelligent. My first idea to use set regulation functions
are not good enough mainly because they would most certainly be able
to work, but I would end up with way too many parameters and they
would require constant tweaking. )

I'd like comments from the other of you on this list, if you think this
makes sense, or you see some flaws I missed?

 /Fredrik



Return to table of contents


Date: Sun, 07 Aug 2005 20:18:22 -0500
From: KEITH R BUSBY <kbusby at wisc.edu>
Subject: secondary fermentation in bottle

Does anyone have experience of secondary fermentation of Tripels in
bottle? While in Brussels last week, I read that Tongerlo adds yeast at
bottling to heighten flavors and aromas. Would one use the same yeast as
for primary or a different one (the text I read mentioned primary yeasts
in the plural)? How would one do it? Add with priming sugar? If so, how
much? Or perhaps a drop per bottle? Is there a risk of gushers or bottle
bombs?

Keith

Keith Busby
Douglas Kelly Professor of Medieval French
Department of French and Italian
The University of Wisconsin
618 Van Hise Hall
Madison, WI 53706
(608) 262-3941
(608) 265-3892 (fax)


Return to table of contents

---