Team:Dundee
From 2012.igem.org
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<center><h2>Clostridium Difficile</h2></center> | <center><h2>Clostridium Difficile</h2></center> | ||
- | <em>Clostridium difficile (C. diff)</em> is a gram- positive bacterium that lives naturally in the gut. In healthy individuals, the levels of <em>C. diff</em> are kept constant as it is outcompeted by other species in the gut flora. However, when patients receive large doses of antibiotics, competing gut flora can be wiped out. This can allow numbers of <em>C. diff</em> to increase to a level where infection can be caused, resulting in severe colitis. <em>C. diff</em> has therefore become a major cause of hospital acquired infections, with, for example, some 2645 patients in hospitals in England and Wales found suffering from <em>C. diff</em> induced colitis in March- May 2010. Infection rates have also been high at Dundee's Ninewells Hospital, which is affiliated with the University of Dundee, and so for us, this is also a very local health problem. Up until now, there have been two ways of treating this problem: prescribe more antibiotics, with the added difficulty of possibly causing more resistance to build-up, or by means of faecal transplant. A faecal transplant | + | <em>Clostridium difficile (C. diff)</em> is a gram- positive bacterium that lives naturally in the gut. In healthy individuals, the levels of <em>C. diff</em> are kept constant as it is outcompeted by other species in the gut flora. However, when patients receive large doses of antibiotics, competing gut flora can be wiped out. This can allow numbers of <em>C. diff</em> to increase to a level where infection can be caused, resulting in severe colitis. <em>C. diff</em> has therefore become a major cause of hospital acquired infections, with, for example, some 2645 patients in hospitals in England and Wales found suffering from <em>C. diff</em> induced colitis in March- May 2010. Infection rates have also been high at Dundee's Ninewells Hospital, which is affiliated with the University of Dundee, and so for us, this is also a very local health problem. Up until now, there have been two ways of treating this problem: prescribe more antibiotics, with the added difficulty of possibly causing more resistance to build-up, or by means of faecal transplant. A faecal transplant involves the faeces of another person being inserted directly into the patient's colon. This has been proven to be effective in test cases, but is obviously an unsavoury form of treatment for many patients and so the idea of creating an alternative gave rise to this project. |
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<center><h2>Mathematical Modelling</h2></center> | <center><h2>Mathematical Modelling</h2></center> | ||
- | The depth and range of the mathematical modelling will evolve throughout this project, from models of growth for <em>Salmonella</em> and the strain of <em>E. | + | The depth and range of the mathematical modelling will evolve throughout this project, from models of growth for <em>Salmonella</em> and the strain of <em>E. coli</em> that we will engineer, to systems ordinary and partial differential equations that will show us not only how two populations interact, but how the shape and natural processes of the colon affect this interaction. |
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- | Other aspects that we will look at modelling are the number of "needles" that we can engineer the <em>E. | + | Other aspects that we will look at modelling are the number of "needles" that we can engineer the <em>E. coli</em> to create and the amount of endolysin that must be secreted to lyse all of the <em>C. diff</em> bacteria. Using software such as MATLAB® and COMSOL® we are able to create visual representations of population interactions such as graphs and animations of the colon as we introduce the <em>E. coli</em> to lyse the excessive levels of <em>C. diff</em>. |
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Beyond the team's Wiki and blog site, ongoing work is taking place to develop an Android based application framework. It shall encompass any tools that the team finds useful, and will be released at the end of the project so that it may be utilised as a starting point for other similar projects. | Beyond the team's Wiki and blog site, ongoing work is taking place to develop an Android based application framework. It shall encompass any tools that the team finds useful, and will be released at the end of the project so that it may be utilised as a starting point for other similar projects. | ||
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- | The team is also working on a desktop modelling tool that utilises the principles of cellular automata to graphically illustrate the cell interactions that are taking place between the modified <em>E. | + | The team is also working on a desktop modelling tool that utilises the principles of cellular automata to graphically illustrate the cell interactions that are taking place between the modified <em>E. coli</em> and <em>C. diff</em> cells. The application currently models cell mitosis, movement, lysis and flow. Work on the application is continuing to encompass further aspects such as nutrients, colony sizes and initial placement of cells within the model. The completed application, including source code, will be released for Windows and Linux development environments to be used by others in the future for practical and educational purposes. |
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Revision as of 11:05, 23 July 2012
Dundee University
iGem 2012
Clostridium Difficile
Type VI Secretion System
Project Summary
Mathematical Modelling
Other aspects that we will look at modelling are the number of "needles" that we can engineer the E. coli to create and the amount of endolysin that must be secreted to lyse all of the C. diff bacteria. Using software such as MATLAB® and COMSOL® we are able to create visual representations of population interactions such as graphs and animations of the colon as we introduce the E. coli to lyse the excessive levels of C. diff.
Software Development
The team is also working on a desktop modelling tool that utilises the principles of cellular automata to graphically illustrate the cell interactions that are taking place between the modified E. coli and C. diff cells. The application currently models cell mitosis, movement, lysis and flow. Work on the application is continuing to encompass further aspects such as nutrients, colony sizes and initial placement of cells within the model. The completed application, including source code, will be released for Windows and Linux development environments to be used by others in the future for practical and educational purposes.