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Using Computers, Scientists Successfully Predict Evolution of E. coli Bacteria
NSF ^ | 11/14/2002 | staff

Posted on 11/14/2002 9:19:45 PM PST by Nebullis

For more than a decade, researchers have been trying to create accurate computer models of Escherichia coli (E. coli), a bacterium that makes headlines for its varied roles in food poisoning, drug manufacture and biological research.

By combining laboratory data with recently completed genetic databases, researchers can craft digital colonies of organisms that mimic, and even predict, some behaviors of living cells to an accuracy of about 75 percent.

Now, NSF-supported researchers at the University of California at San Diego have created a computer model that accurately predicts how E. coli metabolic systems adapt and evolve when the bacteria are placed under environmental constraints. Bernhard Palsson, Rafael Ibarra (now at GenVault Corporation in Carlsbad, California) and Jeremy Edwards (now at the University of Delaware at Newark) report their findings in the November 14 issue of Nature.

"Ours is the only existing genome-scale model of E. coli," says Palsson. In addition, while many approaches to genetics experiments "knock out" individual genes and track the results, the new model takes a whole-system approach. Changing one aspect of a genetic code could be irrelevant if an organism adapts and evolves, says Palsson. The constraints-based models allow the E. coli to evolve more naturally along several possible paths.

Scientists may use the approach to design new bacterial strains on the computer by controlling environmental parameters and predicting how microorganisms adapt over time. Then, by recreating the environment in a laboratory, researchers may be able to coax living bacteria into evolving into the new strain.

The resulting strains may be more efficient at producing insulin or cancer-fighting drugs than existing bacterial colonies engineered by researchers using standard techniques.

"Now we have a better tool to predict how bacteria evolve and adapt to changes," says National Science Foundation program director Fred Heineken. "As a result, this constraints-based approach could lead to better custom-built organisms," he says.

The researchers based their digital bacteria on earlier laboratory studies and E. coli genome sequences, detailed genetic codes that have been augmented with experimental information about the function of every gene.

Such digital models are known as "in silico" experiments.

In the first days of testing on living organisms, the bacteria did not adapt into the strain predicted by the simulation. Yet, with more time (40 days, or 500-1000 generations), the E. coli growing in the laboratory flasks adapted and evolved into a strain like the one the in silico model predicted.

"The novelty of the constraints-based approach is that it accounts for changes in cellular properties over time," says Palsson. "Fortunately," he adds, "the other advantage is that it actually works surprisingly often."

For many years, drug manufacturers have manipulated the genetic code in E. coli strains, creating species that can produce important substances, such as the hormone insulin for use by people with diabetes or the experimental cancer drug angiostatin.

Using the new constraints-based techniques Palsson and his colleagues developed, drug manufacturers and bioprocessing companies could use computers to determine the genetic code that could yield the most efficient and productive versions of E. coli, and then use adaptive evolution to create bacterial strains that have the desired properties.

Says Palsson, "This development potentially opens up a revolutionary new direction in the design of new production strains." In addition, says Palsson, "now that we have gained a greater understanding of this process in E. coli, developing similar simulations of other organisms should take less time."


TOPICS: Culture/Society; News/Current Events
KEYWORDS: crevolist

1 posted on 11/14/2002 9:19:45 PM PST by Nebullis
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To: *crevo_list
Bump
2 posted on 11/14/2002 9:20:33 PM PST by Nebullis
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To: Nebullis
Alright you poly-sci majors, get cracking on predicting the evolution of E. Carville and Clinton.
3 posted on 11/14/2002 9:34:05 PM PST by ctonious
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To: ctonious
>Alright you poly-sci majors, get cracking on predicting the evolution of E. Carville and Clinton.

The left turning proteins found in E. Carville are unnatural.

4 posted on 11/14/2002 9:45:17 PM PST by Dialup Llama
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To: Dialup Llama
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To: Owl_Eagle


10 posted on 11/14/2002 8:28 AM PST by Stand Watch Listen

5 posted on 11/14/2002 9:46:16 PM PST by razorbak
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To: Nebullis
This is BS. They can't even model a protein properly yet...how on earth do they make this quantum leap?
6 posted on 11/14/2002 9:49:13 PM PST by ImaGraftedBranch
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Comment #7 Removed by Moderator

To: Nebullis
Now, NSF-supported researchers at the University of California at San Diego have
created a computer model that accurately predicts how E. coli metabolic systems
adapt and evolve when the bacteria are placed under environmental constraints.


This should feed plenty of lively discussions between Darwinian random evolutionists
and intelligent design proponents.

Does the ability to design a computer program that can predict evolution mean that
the scientists have successfully modeled the random walk of evolution...
or shown that "the grand designer" has created a system that even a computer program
can imitate...

I've got no opinion either way...can just see this being batted about...
8 posted on 11/14/2002 9:51:42 PM PST by VOA
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To: ImaGraftedBranch
This is BS. They can't even model a protein properly yet...how on earth do they make this quantum leap?

Probably done by the same computer modelers who tell us our weather will be 5 degrees hotter
in 100 years, but can't tell us if it will rain tomorrow more than 50% of the time.
9 posted on 11/14/2002 9:54:27 PM PST by VOA
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To: Nebullis
Nice teaser. I want to see the program.
10 posted on 11/14/2002 9:56:52 PM PST by AndrewC
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To: Nebullis
This looks like the subject, from Nature.

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.

11 posted on 11/14/2002 10:07:42 PM PST by AndrewC
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To: AndrewC; Nebullis
Nice teaser.

Better than average teaser!

I want to see the program evidence.

12 posted on 11/14/2002 10:09:03 PM PST by scripter
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To: razorbak
My 2-year-old saw that picture and said: "Scawy monsta." I'm not kidding.
13 posted on 11/14/2002 10:14:26 PM PST by scripter
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To: VOA; ImaGraftedBranch
Posted by ImaGraftedBranch:
"They can't even model a protein properly yet...how on earth do they make this quantum leap?"

It's apples and oranges. That is like saying, "they can't even travel through time, yet. How on Earth do they know how to make a computer program that predicts genetic mutations in bacteria?"

Posted by VOA:
"Does the ability to design a computer program that can predict evolution mean that the scientists have successfully modeled the random walk of evolution."

I don't think so. Obviously I don't have access to the program, but I assume that the program determines which genetic mutations would actually be expressed and then which of those that would be expressed would allow the organism to live and reproduce.
14 posted on 11/14/2002 10:25:28 PM PST by Schmedlap
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To: Nebullis
Now THAT is really interesting! (If it means what I think it means.)

Are they saying that they can predict what are the most viable evolutionary paths - such as which metabolic systems are more likely to change in what ways - in response to a given environment change?

15 posted on 11/14/2002 11:15:19 PM PST by jennyp
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To: ImaGraftedBranch
This is BS.

And you make this claim based upon what? Seems to me, personal incredulity does not an argument make.

16 posted on 11/18/2002 8:25:06 AM PST by Junior
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To: balrog666; Condorman; *crevo_list; general_re; Gumlegs; jennyp; longshadow; PatrickHenry; ...
Ping
17 posted on 11/18/2002 8:26:18 AM PST by Junior
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To: Junior
Seems to me, personal incredulity does not an argument make.

Well, there goes ID.

18 posted on 11/18/2002 8:50:00 AM PST by Gumlegs
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To: Junior
Placemarker.
19 posted on 11/18/2002 8:53:31 AM PST by PatrickHenry
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To: Condorman
You are here.
20 posted on 11/18/2002 10:19:07 AM PST by Condorman
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Waiting for the program bump

Splifford the bat says: Always remember:

A mind is a terrible thing to waste; especially on just-so stories
Just say no to narcotic drugs, alcohol abuse, and corrupt ideological doctrines.

21 posted on 11/19/2002 8:29:15 AM PST by AndrewC
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To: Nebullis
I hope it was written in Ada,
22 posted on 11/27/2002 2:12:28 PM PST by ContentiousObjector
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