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Author
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Topic: Using Computers, Scientists Successfully Predict Evolution of E. Coli Bacteria
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andyg
Member
Member # 415
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posted 15. November 2002 14:51
I thought this web page press release might be of interest to Brainstorms readers:
NSF Web Page
The press release is for the following paper:
quote:
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth.
Ibarra RU, Edwards JS, Palsson BO.
Annotated genome sequences can be used to reconstruct whole-cell metabolic networks. These metabolic networks can be modelled and analysed (computed) to study complex biological functions. In particular, constraints-based in silico models have been used to calculate optimal growth rates on common carbon substrates, and the results were found to be consistent with experimental data under many but not all conditions. Optimal biological functions are acquired through an evolutionary process. Thus, incorrect predictions of in silico models based on optimal performance criteria may be due to incomplete adaptive evolution under the conditions examined. Escherichia coli K-12 MG1655 grows sub-optimally on glycerol as the sole carbon source. Here we show that when placed under growth selection pressure, the growth rate of E. coli on glycerol reproducibly evolved over 40 days, or about 700 generations, from a sub-optimal value to the optimal growth rate predicted from a whole-cell in silico model. These results open the possibility of using adaptive evolution of entire metabolic networks to realize metabolic states that have been determined a priori based on in silico analysis.
The use of modelling to predict genome-wide responses to selection pressure has been a challenge for complex systems aficionados for some time. It has great implications for drug discovery.
I would be particularly interested to see it applied to more extreme situations than the glycerol-carbon source experiment described above. For example, Steve Finkel at the University of Southern California has done some very interesting work on bacterial evolution under conditions of prolonged starvation:
quote:
Yeiser B, Pepper ED, Goodman MF, Finkel SE.
SOS-induced DNA polymerases enhance long-term survival and evolutionary fitness.
Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8737-41.
Finkel SE, Kolter R. Related Articles, Links
DNA as a nutrient: novel role for bacterial competence gene homologs.
J Bacteriol. 2001 Nov;183(21):6288-93.
Finkel SE, Kolter R. Related Articles, Links
Evolution of microbial diversity during prolonged starvation.
Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):4023-7.
I would be very interested to see if the computer can mimic the tricks used by bacteria when they use DNA as a sole nutrient source, for example.
AndyG
[ 15. November 2002, 20:43: Message edited by: andyg ]
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Moderator
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posted 15. November 2002 15:28
Hey Andy,
We prefer for thread starters to post comments about news stories along with links, rather than just posting the news story. This way the discussion gets going in a certain direction.
Do you think you could make some preliminary comments on this story? What do you see as the relevant implications?
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Mike Gene
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Member # 149
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posted 24. November 2002 10:18
Using Computers, Scientists Successfully Predict Evolution Of E. Coli Bacteria
Yet another indicator of the plausibility of front-loaded evolution. Imagine this approach with 500 years of experimental experience under its belt.
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