[BBF Standards] BioHackathon, or Characterization Challenge

[Bryan Bishop]

On Monday 11 February 2008, Drew Endy wrote:
> Meanwhile, Bryan, your comment might be well connected to something I
> was struggling to say...
>
> On Feb 11, 2008, at 9:35 PM, Bryan Bishop wrote:
> > I would like to point out to the list that doubling rate is
> > strongly linked to development cycle time in terms of biobricks and
> > the standards. It seems to be nearly equivalent to waiting for the
> > compiler to finish (except, biobricks are like precompiled
> > bytecode). 
>
> As soon as we start working with doubling times below 40 minutes, for
> many of our systems, the debugging time constant for system
> performance is limited not by cell growth rate, but rather by the
> time it takes for protein (and other molecular) levels to rise and
> fall. Some of the fastest protein production systems around are found
> in phage, the best of which can produce convert most of E.coli into
> phage specific proteins by 10-20 minutes post infection.  Faster than
> this and we have to start thinking carefully about how cell doubling
> time is driving the reset of system state to ground.

The more the cells proliferate, the more there are cells that are near 
ground state in comparison to whatever it is that we want them to be 
doing. Sounds right to me, because replication necessarily splits the 
resources between the two cells. And on top of this, production rates 
on proteins are necessarily linear (per each cell) because ultimately 
there can only be one protein reading the same sequence of DNA at one 
time (a locking system, if you will), although there are multiple 
ribosomes working on protein folding at a time. So maybe it'd be more 
efficient to insert mRNA ready to go and supply it from our own 
external caches, to control the maximum rate of protein production? 
However, mRNA insertion protocols look complex and seriously involved 
from my end, perhaps we should focus on developing a way to coat mRNA 
with a delicious-looking tag that our bacteria will immediately consume  
no matter whether they are prepped or not in the traditional sense? But 
then we have to be able to control deployed mRNA fragments, i.e. if we 
wanted to flush the system without losing very valuable cell states.

Another quick note - even if we have the ability to synthesize mRNA at 
some reasonable rate, at some point the doubling time of the colonies 
*will* outpace the (static) technological ability to produce mRNA. But 
I don't see cases where you need such large colonies.

> Meanwhile, note that we should be able to deploy active mRNA and
> protein degradation systems (e.g., ClpX) to push faster reset times
> independent of the cell growth rate (c/o Bob Sauer et al.).

Looks like you're ahead of me on that one. For flushing, you suggest 
protein degradation systems to do reset times, but what about coating 
the mRNA with something that is both (1) going to be accepted by the 
cells and (2) able to be attracted to a source that the bacteria are 
not, perhaps electrically? This way, we can flush the system, add in 
the protein degradation systems, and keep our bacteria at the same 
time.

So:
* mRNA coating - to allow quick uptake (prereq - a genome mod?)
* mRNA tagging - so that an applied current can bring these to the top 
for cleansing (maybe an mRNA filter .. think fishtank-like setup?)
* Fast mRNA synthesis. Oligo synth protocols seem to take hours??
** This looks like a chemistry problem -- so either bring in a chemist 
for this problem or we all develop massive oligo libraries and hope we 
have a relevant sequence ... ugh. Combinatorial storage space, anyone?
* Protein degradation chemicals (ClpX, etc.)
* 

> So, eventually, my guess would be that we want to consider cell
> doubling times for specific purposes (i.e., production of DNA, cells,
> or other objects), but otherwise figure out how to decouple the
> operation of our engineered biological systems from cell doubling
> time.

I agree re: the importance of decoupling development time from doubling 
time, but this also introduces an interesting coupling of mRNA 
synthesis rates (your dx) in relation to how big a colony you can 
support for massive experiments, but this is a good problem to have.

- Bryan
________________________________________
Bryan Bishop
http://heybryan.org/