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Supercomputing Challenge

E.Coli in Hostile Environments

Team: 52


Area of Science: Microbiology

Proposal: E.Coli in Hostile Environments
Stoyana Alexandrova, Paola Jaime and Iliana Alexandrova - Los Alamos High School

Our scientific problem is to explore the effects of different hostile environments on the evolution of the inherited characteristics of bacteria E.Coli. The problem is important because of its connection with a recent research showing that E.Coli may be eventually used for a cancer treatment, if one can change its usual characteristics (Christopher Anderson and colleagues: Tumor-Killing Bacteria, June 02, 2006; Blood Vol. 94, No. 8).

We will model a bacterial colony developing in a hostile environment with different food levels and different gravity levels. We will take under consideration that under low food levels and/or with a low probability of encountering food due to hyper gravity, new genes can be expressed. Researchers have shown that in a starving environment a special gene is expressed in E.Coli to accommodate to the new environment (Claude Saint-Ruf, François Taddei, and Ivan Matic: Genetics. 2004 September; 168(1): 541–546; also - Steven E. Finkel and Roberto Kolter: Vol. 96, Issue 7, 4023-4027, March 30, 1999). We will also take into account that when a bacterium divides, the two daughter cells will not receive identical genetic material from the parent cell, but they will have slightly different heritable characteristics. It was recently proven that E.Coli does not divide completely symmetrically, and therefore does not exhibit a functional immortality. Genetic defects are transferred to the daughter cells when the parent cell divides (Stewart EJ, Madden R, Paul G, Taddei F (2005) Aging and Death in an Organism That Reproduces by Morphologically Symmetric Division. PLoS Biol 3(2): e45).

First, we will simulate a real experiment with E.Coli’s growth in a starving environment by Jonathan E. Visick’s experiment. We will aim to repeat his experimental data, and to establish our mathematical procedure with the parameters and the time scale of the model. We will construct an agent-based model, written on ANSI C using MPI, to have the possibility to run the code on different Linux clusters, and simulating more than 107 bacteria growing in a bigger than 10^4x10^4 lattice with random distribution of the food. After establishing the model we will change the environment’s parameters (gravity level, amount of food, and type of food) to obtain our results. We will show how the growth and the average inherited characteristics of E.Coli evolve and change with time in every next generation at different hostile environments.

We conducted, and will keep doing extensive research on E.Coli’s growth and evolution in different environments. We have started on our model and we will continue to modify it based on the information of our research. After having enough data, we will analyze the averaged results over all the runs, and realizations of the initial conditions, to obtain statistically average values of the E.Coli’s characteristics. Finally, we will compare E.Coli’s behavior in the different hostile environments.

Project Mentors:

Anny Usheva
Associate Professor
Harvard University
Harvard Medical School
Director Basic Science Research

Ludmil Alexandrov, Neumont University

Sponsoring Teacher: Diane Medford, Los Alamos High School

Team Members:

  Stoyana Alexandrova
  Iliana Alexandrova
  Paola Jaime

Sponsoring Teacher: Diane Medford

Mail the entire Team