BME494s2013 Project Template: Difference between revisions

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==Genetic Switch Designs==
==Design: Our genetic circuit==


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'''OUR GENE SWITCH''':   
'''OUR GENE SWITCH''':   
<!-- Show a network/ circuit diagram of your team's Lac switch. Include a paragraph to explain how it works -->


* '''Key Pre-existing Part''': We are currently using biobrick parts that was used for a similar project. The Pu and Pr promoters was created by the Michigan 2009 iGEM team. Because the projects are very similar, we hope to differentiate our project in the long-term by incorporating our constructed biobrick into a plant. When toulene or other aromatic compounds bind to the xylr protein, the plant would turn red. Right now, we are just testing our proof-of-concept in E.coli.
<!-- Show a network/ circuit diagram of your team's Lac switch. 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) -->


*'''Primers''':
[[Image:CirEmblemHandwriteLogo2.png|300px|Text describing the image]]
Forward Primer :5'->GAATTCGCGGCCGCTTCTAG ATGTCGCTTACATACAAACC->3’
<br>
Reverse Primer: 3’->TCGAACTGGGGTCGAATAGA TACTAGTAGCGGCCGCTGCAG->5’
<br>
Silent Mutagenesis Primer: '''5’->TACGAGCTACAGACCCAG->3'''
 
[[Image:group1proofofconcept.jpg|300px]]
<br>
 
<!--Draw out plasmids, restriction digests, antibiotics used, etc. -->


'''Assembly Scheme'''


[[Image:group1assembly001.jpg|400px]] [[Image:group1assembly02.jpg|400px]]


<br>


<br><br><br><br><br><br><br><br><br><br><br><br>
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<!-- Illustrate and describe how you will build your lac switch. Incorporate information from Group Presentation 2 -->
<!-- Illustrate and describe how you will build your lac switch. Incorporate information from Group Presentation 2 -->


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==Testing: Modeling and GFP Imaging==
==Testing: Modeling and GFP Imaging==


<br>
<br>
'''Measurement'''
'''A LAC SWITCH MODEL'''
<br>
<br>
<!--How are you measuring function? Which fluorescence system? Describe procedure-->
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 -->


For our testing, we will examine the relationship between the level of concentration of the chemical compound toulene and the level of fluorescence. The fluorescence from DH5α cells harboring the constructed biobrick with the xylr protein will be measured at various concentrations of toluene.


'''AN INTERACTIVE MODEL'''
<br>
<br>
'''Expected Observations [4]'''
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 -->
 
 
'''COLLECTING EMPIRICAL VALUES TO IMPROVE THE MODEL'''
<br>
<br>
<!--Make some "mock data" to demonstrate sound experimental design (controls, significance, etc.)-->
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.
[[Image:group1testing01.jpg|400px]] [[Image:group1testing02.jpg|400px]]
 
<!-- 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. -->


<br>
<br>
'''Tuning Our System'''
Ideally, the GFP production rate measured by this method could be entered as a value for [which parameter] in the Ceroni et al. model.
 
 
 


For tuning our system, we hope to make it more effective by increasing the efficiency of the ribosome binding site. The RBS controls the accuracy and efficiency with which the translation of mRNA begins. Therefore, we hope to use this important variable to tune our system.
<br>
<!--Explain how you have built in "tunability". Explain expected changes in data. Draw how the graphs would change -->
[[Image:group1testing2.jpg|400px]]  [[Image:group1testing03.jpg|400px]]


<br>
<br><br><br><br><br><br><br><br>


==Human Practices==
==Human Practices==
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<!--Wait until Unit 3 to fill this in. Demonstrate that you have considered the societal aspects of your project - what could go wrong? Is it implementable? Etc.-->
<!--Wait until Unit 3 to fill this in. Demonstrate that you have considered the societal aspects of your project - what could go wrong? Is it implementable? Etc.-->
The human practices of our project is important because it seeks to identify where these carcinogens are located in farmland areas. If these chemicals are getting into the groundwater, it poses an extreme risk to people in those areas. Problems of concern also involve the farmland animals, who eat the plants from the soil and drink the water. This is a serious issue because these chemicals get into the food that is produced.
 
 
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==Our Team==
==Our Team==
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<div style="color: #808080; background-color: #ffffff; width: 600px; padding: 5px">
<div style="color: #808080; background-color: #ffffff; width: 600px; padding: 5px">
[[Image:bradylaughlin.jpg|thumb|noframe|130px|left|'''Brady Laughlin''']]  
[[Image:BME194_profile.jpg |thumb|noframe|130px|left|'''Your Name''']]  




 
* My name is ###, and I am a ### majoring in ###. I am taking BME 494 because ###. An interesting fact about me is that ###.  
*My name is Brady Laughlin, and I am a freshman majoring in biomedical engineering. I am taking BME 494 because I am interested in synthetic biology and its many applications. I'm also a member of the Haynes Lab at ASU and I have my own research project. An interesting fact about me is that I have a twin brother.  


</div>
</div>
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<div style="color: #808080; background-color: #ffffff; width: 600px; padding: 5px">
<div style="color: #808080; background-color: #ffffff; width: 600px; padding: 5px">
[[Image:christinaforrey.jpg|thumb|noframe|140px|left|'''Christina Forrey''']]
[[Image:BME194_profile.jpg |thumb|noframe|130px|left|'''Your Name''']]  




* Hello, I am Christina and I am a sophomore in biomedical engineering. I decided to sign up for this course because synthetic biology is truly interesting to me and I wanted to further enhance my education on the subject. An interesting fact about me is that I am a tae-kwon-do black belt.</div>
* My name is ###, and I am a ### majoring in ###. I am taking BME 494 because ###. An interesting fact about me is that ###.  
 
</div>
<br>
<br>


<div style="color: #808080; background-color: #ffffff; width: 600px; padding: 5px">
<div style="color: #808080; background-color: #ffffff; width: 600px; padding: 5px">
[[Image:davidmedina.jpg|thumb|noframe|140px|left|'''David Medina''']]
[[Image:BME194_profile.jpg |thumb|noframe|130px|left|'''Your Name''']]  




* My name is ###, and I am a ### majoring in ###. I am taking BME 494 because ###. An interesting fact about me is that ###.
</div>
<br>


* My name is David Medina, I am a senior biomedical engineering major at Arizona State University. I decided to take this introductory course to synthetic biology because it sounded like an interesting topic and I wanted to learn more about this up and coming field. An interesting fact about me is that me and my youngest brother were born on the same day, five years apart.




<div style="color: #808080; background-color: #ffffff; width: 600px; padding: 5px">
<div style="color: #808080; background-color: #ffffff; width: 600px; padding: 5px">
[[Image:benjaminschmitz.jpg|thumb|noframe|130px|left|'''Benjamin Schmitz''']]  
[[Image:BME194_profile.jpg |thumb|noframe|130px|left|'''Your Name''']]  


* Hey all, I'm Ben Schmitz. I am a mega-senior nearing completion of my biomedical engineering bachelors at ASU. I am taking this course as the penultimate technical elective course of my educational career. An interesting fact about me is that I am getting married in Oregon in September.


* My name is ###, and I am a ### majoring in ###. I am taking BME 494 because ###. An interesting fact about me is that ###.
</div>
<br>




</div>
<br><br><br>
<br><br><br>


==Works Cited==
==Works Cited==
[1] "EARTHWORKS." EARTHWORKS. Web. 11 Mar. 2012. <http://www.earthworksaction.org/issues/detail/hydraulic_fracturing_101>.
[1] Full reference.


[2] "Team:Michigan/Project." IGEM 2009/Team Michigan:Project. Web. 12 Mar. 2012. <http://2009.igem.org/Team:Michigan/Project>.
[2] Full reference.


[3] "Water Contamination From Fracking (Hydraulic Fracturing)." Water Contamination From Shale. Web. 7 Mar. 2012. <http://www.water-contamination-from-shale.com/>.
[3] Full reference.


[4] "American Society for MicrobiologyApplied and Environmental Microbiology." Development and Testing of a Bacterial Biosensor for Toluene-Based Environmental Contaminants. Web. 12 Mar. 2012. <http://aem.asm.org/content/64/3/1006.full>.


[5] "xylr." National Center for Biotechnology Information. U.S. National Library of Medicine. Web. 8 Mar. 2012. <http://www.ncbi.nlm.nih.gov/gene/?term=1218757>.
|}

Latest revision as of 15:36, 22 April 2013


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Overview & Purpose

Text describing the image












Background

Text describing the image














Design: Our genetic circuit

OUR GENE SWITCH:


Text describing the image












Building: Assembly Scheme













Testing: Modeling and GFP Imaging


A LAC SWITCH MODEL
We used a previously published synthetic switch, developed by Ceroni et al., to understand how our system could potentially be modeled and simulated.


AN INTERACTIVE MODEL
We used a model of the natural Lac operon to understand how changing the parameter values changes the behavior of the system.


COLLECTING EMPIRICAL VALUES TO IMPROVE THE MODEL
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.



Ideally, the GFP production rate measured by this method could be entered as a value for [which parameter] in the Ceroni et al. model.











Human Practices

Danger of Chemicals in Farmlands














Our Team

Your Name


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



Your Name


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



Your Name


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



Your Name


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






Works Cited

[1] Full reference.

[2] Full reference.

[3] Full reference.


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