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The Department of Energy's ongoing battle for the clean-up of contaminated environments continues to plague
scientists. There are over 7,000 contaminated sites, over half of which contain metals and radionuclides, many
that are harmful to humans and other forms of life (DOE). What is a cost effective solution for converting these contaminated environments back
to their original form? One solution is bioremediation. Bioremediation involves the use of microorganisms either
native to the site, or newly introduced, to clean up contaminants specific to the microbial organism
Bioremediation).
Certain microbes have evolved the ability to use compounds other than oxygen as the terminal electron acceptor in
the electron transport chain, one of the processes that allows for the production of energy in microbes. This is
very important for those who live in environments devoid of oxygen, like those in the soil and sediments in
contaminated areas.  The anaerobic process
of respiration in these microbes actually reduces certain metals, like uranium, and in this process, turns the
uranium into a form that is insoluble. This insoluble form is less likely to move from the soil into the
groundwater, water that if laced with these contaminants, can potentially harm humans and other organisms.
Shewanella can use uranium and chromium, the same metals contaminating DOE sites, as a terminal electron
acceptor in anaerobic conditions. This coupled with the fact that Shewanella is harmless to humans makes
it an ideal candidate for bioremediation. Shewanella is also a model organism for understanding metal-reducing
bacteria. As soon as we know more about Shewanella, we will also be able to find similarities in other
metal-reducing bacteria. Shewanella is also similar to E. coli in that many of the laboratory tools
developed over the past 30 years to manipulate the genetic code of E. coli will also work in Shewanella
(Shewanella Federation).
I actually spent most of my time working with Shewanella denitrificans OS217. Specifically I worked
on annotating the enzymes that catalyze the chemical reactions within metabolic pathways in Shewanella.
With better annotations of these proteins, one actually can produce better metabolic pathways for an organism.
For building the metabolic pathways in Shewanella, I used the modeling software, Pathway Tools.
The developer of Pathway Tools, Peter Karp, combines all the data on pathways 
from many different organisms, including the information on the highly studied E.coli. Pathway Tools actually
uses the experimental data from E.coli and certain computational approaches to determine pathways for the
organisms you create (Pathway Tools).
I used the manual annotation that I had completed from the first part of this summer to create the complete metabolism
for S. denitrificans OS217. To do this, I used part of the Pathway Tools software, Pathologic, and completed an
automated build with the information I supplied from databases and literature on S. denitrificans. Now that we have
predicted pathways in S. denitrificans, we can compare it with other strains and possibly find those involved in metal reduction.
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