Team:Carnegie Mellon/HostPhageDynamics

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<h2>Phage-Host Dynamics</h2>
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<h2>Phage-host dynamics model</h2>
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<p><b> What is it? </b></p>
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This is aligned to the center
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<p>
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  This is an agent-based model that was made in Netlogo. The purpose of the model is to illustrate the impact that lambda phages have on a population of E. coli cells. The phages contain a sequence coding for either KillerRed (KR) or Red Fluorescent Protein (RFP). RFP is used as the control in this model because it is 1000 times less phototoxic than KR. Additionally, some phages will contain IPTG to enduce protein expression. The model aims to mimic an experiment that was actually performed by our team in the lab. The general procedure for the experiment is as follows:
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</p><ul>
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<li>Prepare 8 E. coli cultures </li>
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<li>4 cultures will be infected with phages containing KR </li>
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<li>4 cultures will be infected with phages containing RFP </li>
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<li>We apply the following conditions on both sets of cultures: </li>
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<ul><li>Not induced with IPTG, not exposed to light</li>
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<li>Induced with IPTG, not exposed to light </li>
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<li>Not induced with IPTG, exposed to light</li>
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<li>Induced with IPTG, exposed to light</li></ul>
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<li>Determine how many cells have been killed by plating cultures and counting CFUs </li>
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<p> For more information about this experiment, see <a href="https://2013.igem.org/Team:Carnegie_Mellon/Project/Procedure">procedures</a>. </p>
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<p><b>How it works</b></p>
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<p> Phages travel around the environment until they come in contact with a cell. When they attach to the cell, the phage will be removed from the environment. The cell will now change its behavior according to which type of phage infected it (KR or RFP) and the other various conditions put on it. As more KR builds up in the cell, more superoxide is produced. When the superoxide concentration becomes high enough, the cell bursts, producing more phages into the environment. </p>
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<p><b> How to use it</b></p>
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<p> You can download netlogo for free <a href="http://ccl.northwestern.edu/netlogo/">here</a> and the source code for the model <a href="https://static.igem.org/mediawiki/2013/c/c4/Phage_cell_simulation.nlogo.zip">here</a>. Begin by choosing an initial number of cells and phage. Then set up the system’s conditions with the switches. Supply the phage either KR or RFP. If “induced” is turned on, then the protein expression in the cell will be induced by due to the IPTG promotor. If “Induced” is set to off, a very small amount of protein will still accumulate in the cell over time. The “exposed ” switch mimics the effects of exposing the cells to light. Light will activate KR to produce reactive oxygen species (ROS), such as superoxide. Superoxide will kill the cell once it is in high enough concentration. </p>
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<p><b>Things to notice</b></p>
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<p>If the cell is infected by a phage without IPTG, KR production will be very slow. If the cell is infected by a phage with RFP rather than KR, no KR will be produced but some superoxide will be produced very slowly. This is because RFP is 1000 times less phototoxic than KR. Also, light-intensity affects superoxide concentration, but not KR concentration. </p>
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<b>Clip 1:</b> Demonstrating the Effect of KillerRed<br>
<embed src="https://static.igem.org/mediawiki/2013/a/a9/Netlogo_movie1.mov" width="822" height="640">
<embed src="https://static.igem.org/mediawiki/2013/a/a9/Netlogo_movie1.mov" width="822" height="640">
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<b>Clip 2:</b> RFP Control <br>
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<embed src="https://static.igem.org/mediawiki/igem.org/9/92/Netlogo_movie2.mov" width="818" height="639">
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[[image:Healthy_cells_varying_light.png|thumb|600px|right|]]
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<p> One of variables we can change in this model is the light intensity. The following graphs represent simulations at 4 different light intensities. The model suggests that increased light intensity results in faster killing. However, the cells will still die after exposure to less intense light, given enough time. </p>
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[[image:infected_cells_varying_light.png|thumb|600px|center|]]

Latest revision as of 00:47, 28 September 2013

Killer Red




Phage-host dynamics model

What is it?

This is an agent-based model that was made in Netlogo. The purpose of the model is to illustrate the impact that lambda phages have on a population of E. coli cells. The phages contain a sequence coding for either KillerRed (KR) or Red Fluorescent Protein (RFP). RFP is used as the control in this model because it is 1000 times less phototoxic than KR. Additionally, some phages will contain IPTG to enduce protein expression. The model aims to mimic an experiment that was actually performed by our team in the lab. The general procedure for the experiment is as follows:

  • Prepare 8 E. coli cultures
  • 4 cultures will be infected with phages containing KR
  • 4 cultures will be infected with phages containing RFP
  • We apply the following conditions on both sets of cultures:
    • Not induced with IPTG, not exposed to light
    • Induced with IPTG, not exposed to light
    • Not induced with IPTG, exposed to light
    • Induced with IPTG, exposed to light
  • Determine how many cells have been killed by plating cultures and counting CFUs

For more information about this experiment, see procedures.

How it works

Phages travel around the environment until they come in contact with a cell. When they attach to the cell, the phage will be removed from the environment. The cell will now change its behavior according to which type of phage infected it (KR or RFP) and the other various conditions put on it. As more KR builds up in the cell, more superoxide is produced. When the superoxide concentration becomes high enough, the cell bursts, producing more phages into the environment.

How to use it

You can download netlogo for free here and the source code for the model here. Begin by choosing an initial number of cells and phage. Then set up the system’s conditions with the switches. Supply the phage either KR or RFP. If “induced” is turned on, then the protein expression in the cell will be induced by due to the IPTG promotor. If “Induced” is set to off, a very small amount of protein will still accumulate in the cell over time. The “exposed ” switch mimics the effects of exposing the cells to light. Light will activate KR to produce reactive oxygen species (ROS), such as superoxide. Superoxide will kill the cell once it is in high enough concentration.

Things to notice

If the cell is infected by a phage without IPTG, KR production will be very slow. If the cell is infected by a phage with RFP rather than KR, no KR will be produced but some superoxide will be produced very slowly. This is because RFP is 1000 times less phototoxic than KR. Also, light-intensity affects superoxide concentration, but not KR concentration.

Clip 1: Demonstrating the Effect of KillerRed

Clip 2: RFP Control

Healthy cells varying light.png

One of variables we can change in this model is the light intensity. The following graphs represent simulations at 4 different light intensities. The model suggests that increased light intensity results in faster killing. However, the cells will still die after exposure to less intense light, given enough time.

Infected cells varying light.png
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