Linked by Thom Holwerda on Fri 11th Nov 2011 18:39 UTC, submitted by fran
OSNews, Generic OSes Remember yesterday when I said Solaris 11 goes way over my head? Well, today we're talking about where operating systems and biology intersect. Scientists at the University of Nottingham are trying to develop the in vivo biological cell-equivalent of a computer operating system. The project's name is AUdACiOuS.
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But what is really happening?
by Jondice on Fri 11th Nov 2011 20:22 UTC
Jondice
Member since:
2006-09-20

Even as a computational biologist, I really have no idea what they are planning on doing from reading this.

I can guess that they will be using models of regulation (and maybe metabolism if they are good, like this: https://simtk.org/home/ifba ) to aid in the design of some phenotype (function).

Biologically, they will probably be putting a lot of the transcriptional regulators under control of non-metabolic chemicals like doxycycline, though I wonder how many different chemical regulators they could use. If they really wanted to make this cell very programmable, they would need a lot. However, they could potentially engineer the TFs to use combinations of several such chemicals, and 10 chemicals could give you 2^10 - 1 = 1023 different signals, which is already a large portion of the E. coli genome. This approach would involve the overlap of signals (i.e. a superset would regulate a subset) so it probably wouldn't be so useful.

A eukaryotic cell that could use shRNA to turn off any mRNA signal seems like it may allow more flexibility, though perhaps they could engineer in a DICER complex to E. coli (this was done in a baker's yeast about a year ago, but that is also eukaryotic...). This is probably a pretty inefficient way of programming though, since it would assume the default signals were "ON", which would result in a lot of RNA loss and I think shRNA is probably not so cheap iirc.

As for Solaris 11, I just updated my home server system to it last night while playing Skyrim. There seem to be quite a few differences in Solaris 11 and the last dev release of Nevada I was using. The news threads these days are hitting very close to home ... ;)

Edited 2011-11-11 20:29 UTC

Reply Score: 5

Jondice Member since:
2006-09-20

I saw their preprint ... looks like I was wrong, and they are not currently focusing on whole-genome reprogramming, but on circuit modeling using P systems, which I don't know much about.

Reply Parent Score: 3

Gone fishing Member since:
2006-02-22

Can you link the preprint? As a biologist I found the article unintelligible - but I would like to know what is being attempted.

Reply Parent Score: 3