User:Karmella Haynes/BME494 ProjectTemplate: Difference between revisions

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<font face="trebuchet ms" style="color: #808080">[http://openwetware.org '''My Profile''']
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[http://openwetware.org '''My Profile'''] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[[http://openwetware.org/wiki/User:Karmella_Haynes | <font face="trebuchet ms" style="color: #808080"> '''Dr. Haynes''' </font>]]
[http://openwetware.org/wiki/User:Karmella_Haynes '''Dr. Haynes'''] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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[http://openwetware.org '''OpenWetWare'''] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[[BME494_s2013:Schedule | <font face="trebuchet ms" style="color: #808080"> '''OpenWetWare''' </font>]]
[http://openwetware.org/wiki/BME494_s2013 '''Previous Course'''] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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[http://openwetware.org/wiki/BME494_s2013:WikiHelp '''Wiki Editing Help''']  
[[BME494_s2013:Photos | <font face="trebuchet ms" style="color: #808080"> '''Previous Course''' </font>]]  
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==Background & Proposed Application==
==Background & Proposed Application==
'''BACKGROUND'''
<br>
<!-- Incorporate information from Presentation 1. Summarize the classical synthetic device upon which your new design is based. If you post an image of a figure from a paper, include an in-text citation in the text legend. -->
<!-- Below is a template code for making a thumbnail image to embed in your text. See BME494_Wiki_Help for help with uploading images to OpenWetWare and using them on your page.-->
<!-- Below is a template code for making a thumbnail image to embed in your text. See BME494_Wiki_Help for help with uploading images to OpenWetWare and using them on your page.-->
[[Image:CirEmblemHandwriteLogo2.png|thumb|140px||left|Text legend for the figure]]  
[[Image:CirEmblemHandwriteLogo2.png|thumb|140px||left|Text legend for the figure]]  


<!-- summarize the classical synthetic device upon which your design is based. If you post an image of a figure from a paper, include an in-text citation in the text legend


<!-- This is where you can get creative. Think of a practical application for a genetic input/ output switch that is based on the Lac switch you designed. Perhaps it can generate some useful compound instead of RFP/ GFP? Perhaps you could replace the Lac Repressor/ promoter part with something that binds to a different compound to make a sensor? Type a "10,000 foot" overview of your project below this comment line. What is your project's impact on the world? -->
'''APPLICATION OF A NEW DEVICE'''
 
<br>
<!-- In the next paragraph, explain how the IPTG-input/ fluorescent protein-output Lac switch you proposed to build (in Unit 2) serves as a roof-of-concept for the practical application you just described -->


<!-- Incorporate information from Presentation 1. Must be reasonable and clearly relevant to an important health challenge. -->




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<br><br><br><br><br><br><br><br>
<br><br><br><br><br><br><br><br>
<!-- These are lines breaks for spacing purposes. You can add or delete these as needed -->
==Overview & Purpose==
[[Image:CirEmblemHandwriteLogo2.png|thumb|140px|left|Text describing the image]]
<!-- Background information on the on the classical device. This should be based on Presentation 1 -->
<br><br><br><br><br><br><br><br><br><br><br><br>
<!-- These are lines breaks for spacing purposes. You can add or delete these as needed -->
<!-- These are lines breaks for spacing purposes. You can add or delete these as needed -->


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<!-- Show a network/ circuit diagram of your device. Include a paragraph to explain how it works (i.e., how to switch the system from on to off and vice versa, and what happens to each component as the system switches between states) -->
<!-- Show a network/ circuit diagram of your device. Include a paragraph to explain how it works (e.g., how to switch the system from on to off and vice versa, and what happens to each component as the system switches between states) -->


[[Image:CirEmblemHandwriteLogo2.png|300px|Text describing the image]]
[[Image:CirEmblemHandwriteLogo2.png|300px|Text describing the image]]
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<!-- Incorporate information from Presentation 1 and Presentation 2 -->
<!-- Incorporate information from Presentation 1 and Presentation 2 -->


'''Synthetic DNA Layout'''
'''SYNTHETIC DNA LAYOUT'''


<!-- Show each DNA fragment in the order in which you propose to assemble them into a single plasmid. This can be a series of connected blocks. You do not have to show the plasmid as a circle. -->
<!-- Show each DNA fragment in the order in which you propose to assemble them into a single plasmid. This can be a series of connected blocks. You do not have to show the plasmid as a circle. -->


'''Resources'''
'''RESOURCES'''


<!-- List pre-existing parts/ Biobricks that you will use. Also list new parts that you will need to get from a natural source. BE SPECIFIC. -->
<!-- List pre-existing parts/ Biobricks that you will use. Also list new parts that you will need to get from a natural source. BE SPECIFIC. -->


'''TYPE IIS ASSEMBLY'''


<!-- Incorporate information from Presentation 2 -->




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==Testing the New Device==
==Testing the New Device==


'''LAC OPERON MODEL SIMULATION'''
<br>
<br>
'''A LAC SWITCH MODEL'''
I used a model of the natural Lac operon to learn how changing the parameter values changes the behavior of the system.
<!-- Continue this paragraph by explaining how you interacted with the MatLab model. Include two or more images showing different output curves that were generated when you altered the IPTG input concentration -->
 
 
'''RELATIONSHIP BETWEEN THE LAC MODEL AND MY NEW DESIGN'''
<br>
<br>
We used a previously published synthetic switch, developed by Ceroni et al., to understand how our system could potentially be modeled and simulated.
<!-- Continue this paragraph by explaining to a non-specialist what a mathematical model is and what parameter values are, in general. Include your network diagram illustration of the Ceroni et al. model and list all of the parameters you were able to map onto the model -->


'''Similarities''': <!-- Describe what aspects of the Lac operon model are related to your system -->


'''AN INTERACTIVE MODEL'''
<br>
<br>
We used a model of the natural Lac operon to understand how changing the parameter values changes the behavior of the system.
<!-- Continue this paragraph by explaining how you interacted with the MatLab model. Include two or more images showing different output curves that were generated when you altered the IPTG concentration -->


'''Differences''': <!-- Describe what aspects of your new device are not accounted for by the Lac operon model, and how this difference would require changes or additions to the Lac operon model. You may write this in general terms if you are not yet familiar with advanced biological modeling. Try your best! --->


'''COLLECTING EMPIRICAL VALUES TO IMPROVE THE MODEL'''
<br>
<br>
We explored how one technique, imaging via microscopy could be used to determine the production rate of an output protein, in this case GFP in yeast, could be used to determine a "real" value for maximum GFP production rate under our own laboratory conditions.


<!-- Describe summarize how you measured GFP intensities, plotted charts in MatLab, make a curve of best fit, and tried to determine the maximum rate of GFP production. You don't have to include your raw values, just the graphs and equations. You may include some small images of the GFP-expressing yeast. If you didn't get a nice peak, explain how your image analysis might be changed to improve your outcome. -->


'''TESTING THE NEW DEVICE'''
<br>
<br>
Ideally, the GFP production rate measured by this method could be entered as a value for [which parameter] in the Ceroni et al. model.
 
<!-- Briefly describe a wet lab experiment you will need to perform to compare the behavior of your device to a mathematical model (based on a type of model that is similar to the Lac operon model). What inputs will you use? How will you measure output? What type of result will confirm that the device works as expected? You do not have to describe the experimental protocol, just the overall approach. -->




Revision as of 12:19, 14 April 2014


My Profile       Dr. Haynes       OpenWetWare       Previous Course       Wiki Editing Help

     


Background & Proposed Application

BACKGROUND

Text legend for the figure


APPLICATION OF A NEW DEVICE











Design of a New Device

Text describing the image












Building the New Device

SYNTHETIC DNA LAYOUT


RESOURCES


TYPE IIS ASSEMBLY















Testing the New Device

LAC OPERON MODEL SIMULATION
I used a model of the natural Lac operon to learn how changing the parameter values changes the behavior of the system.


RELATIONSHIP BETWEEN THE LAC MODEL AND MY NEW DESIGN

Similarities:


Differences:



TESTING THE NEW DEVICE












Human Practices

Danger of Chemicals in Farmlands














About the Designer

Your Name


  • My name is ###, and I am a ### majoring in ###. I am taking BME 494 because ###. An interesting fact about me is that ###.





References

[1] Full reference.

[2] Full reference.

[3] Full reference.


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