Interim:
Problem Definition: Biologists today can genetically modify bacteria and other organisms to serve for beneficial medical purposes [1]. This can be done either by directly interfering with the genome of the organism (gene transfer through transformation, transduction, conjugation, plasmids, etc.) or by using the procedure we are introducing in our project – letting the organisms evolve under certain controlled conditions and simulating natural selection to choose the fittest organisms. We can control these organisms’ characteristics and genetics by changing the environmental conditions.

The goal of this project is to simulate the bacteria E.coli living under different hostile environments – environments with different gravity levels and different food distribution and amount. The different colonies will develop differently and some will be the fittest - dividing successfully, finding food for survival, and being physically fit in the particular environment with the specific gravity level. Bacteria that are able to survive in an environment with hyper gravity will produce offspring with similar traits and the resulting colony will be potentially well-fit for surviving under normal conditions with no hostile environment. The goal is to find E.coli’s characteristics for surviving under hyper-gravity. Our method will provide scientists with a way to modify bacteria to be physically strong to survive in a human host and be used for medical purposes, such as killing cancer tumors or, in the future, serving as agonists of strong white blood cells.

Problem Solution: A single E.coli bacterium will have certain characteristics which get inherited, with some mutation, to the daughter cells. Some of the traits given to each cell are the minimum and the maximum cell speed, the minimum and the maximum number of flagella and their minimum and maximum lengths, the minimum and the maximum speed of eating, and the number of ATP consumed per second. All of the values will proximate evaluated statistical values, and will be slightly different for each cell. After establishing the basics of the model, we will change the environment’s parameters (gravity level, amount 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 in the different hostile environments. We will simulate natural selection by setting rules for surviving under certain conditions (having enough energy to live and move, etc.) and not surviving under others. For instance, a bacterium needs to have a particular amount of energy to undergo binary fission (to divide), and if it does not have that amount of energy, it will not pass on its traits to the next generation – this is natural selection’s choice for these particular traits to disappear. The rules for survival conditions will be based on biological information about E.coli. Gravity will be simulated by means of decreasing the cell’s speed, using basic physics laws. It will be taken 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 [2]. 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 [3].

Progress to Date: The team managed to develop a program that simulates E.coli. The program was developed in ANSI C using the MPI parallel library. The created program simulates the life of E.coli in different conditions, the environment as well as the E.coli themselves. The conditions could be changed by using defined and precompiled variables. Using the program we were able to confirm results from an actual biological experiment by Jonathan E. Visick.

Expected Results: Natural selection will select the best traits for surviving in hostile environments. We expect that the fastest bacteria will be able to survive under higher gravity levels because they will be the only ones able to reach food sources on time to survive. Natural selection might prefer other traits too, such as a lower amount of ATP needed to reproduce and more cellular flagella. 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.

Citation:
1. Christopher Anderson and colleagues: Tumor-Killing Bacteria, June 02, 2006; Blood Vol. 94, No. 8
2. 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
3. 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
4. Tissenbaum HA, Guarente L. 2002. Model organisms as a guide to mammalian aging. Dev Cell. 2:9–19.
5. Lin ECC, Hirota Y, Jacob F (1971) On the process of cellular division in Escherichia coli. VI. Use of a methocel−autoradiographic method for the study of cellular division in Escherichia coli. J Bacteriol 108:375–385.

Team Members:

  Stoyana Alexandrova
  Iliana Alexandrova
  Paola Jaime

Sponsoring Teacher: Diane Medford

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