BME494s2013 Project Team1

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'''Building a Sweet Cyan<br>
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Below is the content for our final project for the SPring 2013 Introduction to Synthetic BIology Class at Arizona State University.
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<br>
==Overview & Purpose==
==Overview & Purpose==
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[[Image:CirEmblemHandwriteLogo2.png|thumb|140px||left|Text describing the image]]
 
<!-- 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? -->
<!-- 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? -->
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<!-- 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 -->
<!-- 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 -->
Sarah
Sarah
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</br>What this can be used for
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* What this can be used for
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</br>sensing something  
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* Sensing something  
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[[Image:LacOperon.jpg|thumb|1040px||center|Basic Components of a Lac Operon]]
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==Background==
==Background==
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[[Image:NLacOperon.jpg|thumb|140px||left|Natural Lac Operon Parts/DNA Schematic]]
<!-- Background information on the natural Lac operon. This should be based on Group Presentation 2 -->
<!-- Background information on the natural Lac operon. This should be based on Group Presentation 2 -->
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Sean
 
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The lac operon itself is a set of genes found in certain bacterias' DNA that is required for the transport and metabolism of lactose. Most commonly found in Escherichia coli, the operon was the first example of a group of genes under the control of an operator region to which a lactose repressor binds.
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<br><br>
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The lac operon functions as a single transcription unit and is comprised of an operator, a promoter, and on or more structural genes such as a regulator or terminator that are transcribed into one polycistronic mRNA. When the bacteria are transferred to lactose-containing medium, allolactose (which forms when lactose is present in the cell) binds to the repressor, inhibits the binding of the repressor to the operator, and allows transcription of mRNA for enzymes involved in lactose metabolism and transport across the membrane.
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'''OUR GENE SWITCH''':   
'''OUR GENE SWITCH''':   
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THE PARTS
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<tab>pSB1A3-1 is a high copy number plasmid. The replication origin is a pUC19-derived pMB1 (copy number of 100-300 per cell). The terminators bracketing pSB1A3 MCS are designed to prevent transcription from inside the MCS from reading out into the vector.
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<!-- 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) -->
<!-- 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) -->
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[[Image:Sweet_Cyan_Plasmid_Map.png|300px|Plasmid Map of "Sweet Cyan"]]
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* My name is Julia Smith, and I am a senior majoring in Biomedical Engineering. I am taking BME 494 because I am extremely interested in synthetic biology. An interesting fact about me is that in addition to my nerdy side and love of accademic learning, I train reining horses.  
* My name is Julia Smith, and I am a senior majoring in Biomedical Engineering. I am taking BME 494 because I am extremely interested in synthetic biology. An interesting fact about me is that in addition to my nerdy side and love of accademic learning, I train reining horses.  

Revision as of 18:15, 22 April 2013


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Building a Sweet Cyan
Below is the content for our final project for the SPring 2013 Introduction to Synthetic BIology Class at Arizona State University.


Contents

Overview & Purpose

Sarah

  • What this can be used for
  • Sensing something
Basic Components of a Lac Operon
Basic Components of a Lac Operon






Background

Natural Lac Operon Parts/DNA Schematic
Natural Lac Operon Parts/DNA Schematic


The lac operon itself is a set of genes found in certain bacterias' DNA that is required for the transport and metabolism of lactose. Most commonly found in Escherichia coli, the operon was the first example of a group of genes under the control of an operator region to which a lactose repressor binds.

The lac operon functions as a single transcription unit and is comprised of an operator, a promoter, and on or more structural genes such as a regulator or terminator that are transcribed into one polycistronic mRNA. When the bacteria are transferred to lactose-containing medium, allolactose (which forms when lactose is present in the cell) binds to the repressor, inhibits the binding of the repressor to the operator, and allows transcription of mRNA for enzymes involved in lactose metabolism and transport across the membrane.











Design: Our genetic circuit

Julia

OUR GENE SWITCH:

THE PARTS

<tab>pSB1A3-1 is a high copy number plasmid. The replication origin is a pUC19-derived pMB1 (copy number of 100-300 per cell). The terminators bracketing pSB1A3 MCS are designed to prevent transcription from inside the MCS from reading out into the vector.


Plasmid Map of "Sweet Cyan"












Building: Assembly Scheme

Emily
















Testing: Modeling and GFP Imaging


graphical model (Julia)
graphical model (Julia)


A LAC SWITCH MODEL
Emily
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
Someone
We used a model of the natural Lac operon to understand how changing the parameter values changes the behavior of the system.


COLLECTING IMPERICAL VALUES TO IMPROVE THE MODEL
Someone
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.


- show plot of data and discuss outcome. - include some of the pictures of the raw data - wrap up section to explain how the curves could be improved


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
Danger of Chemicals in Farmlands














Our Team

Your Name
Your Name


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



Sarah K. Halls
Sarah K. Halls


  • My name is Sarah K. Halls, and I am a student majoring in Biomedical Engineering. I am taking BME 494 because I enjoy cell and tissue Engineering work and hope to start my career in this field of study. An interesting fact about me is that I did an internship at Harvard University working on cell patterning.



Sean Hector
Sean Hector





  • My name is Edgil Hector (Sean), and I am a student majoring in biomedical engineering. I am taking BME 494 because the subject is relevant to my interests, and the class counts as a required technical elective. An interesting fact about me is that I am the most indecisive human being on the planet.



Julia Smith
Julia Smith




  • My name is Julia Smith, and I am a senior majoring in Biomedical Engineering. I am taking BME 494 because I am extremely interested in synthetic biology. An interesting fact about me is that in addition to my nerdy side and love of accademic learning, I train reining horses.






Works Cited

[1] Full reference.

[2] Full reference.

[3] Full reference.


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