Team:Carnegie Mellon

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<i><b>Welcome to Carnegie Mellon University's 2012 iGEM Team Wiki!</b></i>
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<p><h1 align="center" /><div class="glow1"><b>Quantitative <i>In Vivo</i> Promoter Characterization Using<br /><br /> Fluorescent Biosensors</b></div><br /><br /></h1>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon">Home</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon">Overview</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hom-Introduction">Introduction</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hom-Team">Team</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hom-Attributions">Attributions</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hom-Acknowledgements">Acknowledgements</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Bio-Overview">BioBricks</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Bio-Overview">Overview</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Bio-Submitted">Submitted Parts</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Met-Overview">Methods and Results</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Met-Overview">Overview</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Met-Results">Results</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Met-Protocols">Protocols</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Met-Challenges">Challenges</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Met-Notebook">Notebook</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Met-Safety">Safety</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Overview">Modeling</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Overview">Overview</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Matlab">Matlab</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Expanded">Expanded</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Overview">Human Practices</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Circuit">Circuit Kit</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Software">Software</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Team">Team Presentation</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Teaching">Teaching Presentation</a>
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<i>Using fluorescent technology to analyze new promoters</i>
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<i><div class="glow-title">Real-time quantitative measurement of RNA and protein levels using fluorogen-activated biosensors </div></i>
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<i>Note: This wiki is still under construction. Please visit often for updates.</i>
 
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<h1> Introduction: Motivation and Background </h1>
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  <h2 class="current">Introduction: Motivation and Background</h2>
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  <div class="pane" style="display:block"><h3><a href="#Introduction:_Motivation_and_Background">Learn about the science behind our project!</a><br /><a href="#Project_description">Read our project description</a>
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  <h2>Primary Objective: A New Set of Well-Characterized Promoters</h2>
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  <h2>The Team</h2>
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<b> Our primary goal is to develop new promoters that can be measured with fluorescent technology.</b>  
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  <h2>Further Considerations</h2>
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<li><p> We seek to develop a system that will allow researchers in the field of synthetic biology to accurately measure a variety of metrics in gene expression networks including translational efficiency and transcriptional strength.
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<li><p> We hypothesize that we can use Spinach (a fluorogen-activating RNA sequence) and a FAP (fluorogen activating protein) as biosensors to measure these gene expression metrics <i>in vivo</i> (in living cells), rather than <i>in vitro</i> (in a test tube), which can be very costly and labor intensive.
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<li><p> We aim to characterize the relationship between synthesis rates of Spinach and transcription rates and the relationship between synthesis rates of FAP and translation rates.
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<a name="Introduction:_Motivation_and_Background"></a><h2> <span class="mw-headline"> Introduction: Motivation and Background</span></h2>
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<ul><li><b> Our primary goal is to develop new promoters that can be measured with fluorescent technology.</b>
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<a name="Project_description"></a>Project Description</h1>
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</li><li> We seek to develop a system that will allow researchers in the field of synthetic biology to accurately measure a variety of metrics in gene expression networks including translational efficiency and transcriptional strength.
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<h3><b>Experimental</b></h3>
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<ul><li> We hypothesize that we can use Spinach (a fluorescent RNA sequence) and a FAP (fluorogen activating protein) as biosensors to reflect these metrics <i>in vivo</i> (in living cells), rather than <i>in vitro</i> (in a test tube), which can be very costly and impractical.
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<ul><li> We will characterize the relationship between the rates of production of Spinach and FAP and the gene's translational efficiency and transcription rate. <br />
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<a name="Project_description"></a><b>Project Description</b></h3>
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<h4><b>Experimental</b></h4>
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The design and implementation of synthetic biological systems often require information on transcription and translation rates and on the impact of both RNA and protein levels on metabolic activities of host cells. Such information is needed when both strong and low levels of expression are desired, depending on the biologists’ goal, e.g. high production or cell localization of a protein, respectively. To date, however, quantitative information about the expression strength of a promoter is difficult to obtain due to the lack of noninvasive and quick approaches to measure the levels of RNA and protein in cells.  
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The design and implementation of synthetic biological systems often require information on transcription and translation rates and on the impact of both RNA and protein levels on metabolic activities of host cells. Such information is needed when both strong and low levels of expression are desired, depending on the biologists’ goal, e.g., high production or single-molecule localization of a protein, respectively. To date, however, quantitative information about the expression strength of a promoter is difficult to obtain due to the lack of noninvasive and quick approaches to measure levels of RNA and protein in cells.  
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Here, we engineer a fluorescence-based sensor that can provide information on both transcription strength and translation efficiency that is noninvasive, easily applied to a variety of promoters, and capable of providing results in a time frame that is short when compared to current technologies.  The sensor is based on the use of an RNA aptamer (termed Spinach) and a fluorogen activating protein (FAP). Both the Spinach and FAP become fluorescent in response to binding with dye molecules. The combination of FAP and Spinach will allow us to quantitatively determine relationships involving mRNA and protein, such as translational efficiency.
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Here, we engineer a fluorescence-based biosensor that can provide information on both transcription strength and translation efficiency that is noninvasive, easily applied to a variety of promoters, and capable of providing results in a time frame that is short when compared to current technologies.  The sensor is based on the use of an RNA aptamer (termed Spinach) and a fluorogen activating protein (FAP). Both the Spinach and FAP become fluorescent in response to binding with dye molecules. The combination of FAP and Spinach will allow us to quantitatively determine relationships involving mRNA and protein, such as translational efficiency.
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To demonstrate the utility of the sensor, we will construct and characterize several T7/Lac promoters. For each of the promoters, we will measure the mRNA and protein fluorescence during synthesis and after the synthesis ceased as a function of the concentration of dyes added to the cells. The time dependent fluorescence measurements of mRNA and protein levels will be used in a model that allows one to calculate two important characteristics of gene expression, namely the polymerase per second (PoPS) and translational efficiency. Information about other characteristics of the cell, such as degradation constants for mRNA and protein, and transcriptional efficiency, will be obtained indirectly.
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To demonstrate the utility of the sensor, we have constructed and characterized four T7Lac promoters. For each of the promoters, we have measured both mRNA and protein fluorescence over time. The time-lapse fluorescence levels of mRNA and protein were used in a mathematical model for the estimation of transcription and translation rate constants.
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We have submitted these promoters to the parts registry, whose strength is measured by the newly developed biosensor.
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The outcome of this project will consist of a family of promoters, whose strength is measured by the newly developed sensor, which covers a relatively broad range of strengths.
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<i><a href="https://2012.igem.org/Team:Carnegie_Mellon/Met-Overview"> Learn more here</a></i>
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Human Practices
Human Practices
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The realization of the potential of synthetic biology depends on the number and quality of scientists making significant contributions to the field.  Hence, we plan to contribute to raising the awareness of high school students, who may become future scientists, of the interdisciplinary field synthetic biology and of the preparation one needs to become a synthetic biologist.
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The impact of synthetic biology depends on the number and quality of scientists making significant contributions to the field.  To this end, we contributed to raising the awareness of high school students, who may become future scientists, about the interdisciplinary field of synthetic biology, and about the preparation one needs to become a synthetic biologist.
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Specifically we will give several presentations about synthetic biology (including the iGEM competition) and our project to high school students enrolled in the Summer Academy of Math and Science.  To bridge the natural intellectual gap between the background of a high school student and the complexity of our project, we will build and use in the demonstrations an affordable, microcontroller-based, hardware platform and associated, open-source, digital simulation software.   The combined hardware/software platform will allow the students to directly manipulate electronic components, which are formal equivalents of the Biobricks used in building our sensor, to affect the current and/or voltage, which are formally the equivalent of the PoPs and translational efficiency measured with the sensor.  The software, which is based on the same model we create for the analysis of the sensor, will ensure that the data generated by the students is physiologically accurate.
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We decided to create teaching materials for high school students inspired by our team’s research project.  Our goal was that these materials can be easily used by a science teacher in a lecture in a Biology or Chemistry course to (1) explain what Synthetic Biology is, and (2) enable the students to understand how our <a href="https://2012.igem.org/Team:Carnegie_Mellon/Met-Overview"> biosensor</a> works.  The teaching materials we have created, specifically a power point presentation and an <a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Circuit"> electronic circuit kit</a>, have become part of the Lending Library of Kits of <a href="http://www.cmu.edu/cnast/DNAZone/index"> DNAZone</a>, the outreach program of the <a href="http://www.cmu.edu/cnast/"> Center of Nucleic Acids Science and Technology (CNAST)</a> at Carnegie Mellon.  The kits in the Library are loaned to high school teachers in the Pittsburgh area to be used in teaching Math and Science.  We have also tested the kit in several demonstrations in the Summer of 2012 to high school students enrolled in the <a href="http://www.cmu.edu/enrollment/summerprogramsfordiversity/sams.html"> Summer Academy of Math and Science (SAMS)</a> at Carnegie Mellon.
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To bridge the gap between the background of a high school student and the complexity of our project, we built an affordable, microcontroller-based, <a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Circuit"> hardware platform</a> and associated, open-source, digital simulation <a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Software"> software</a>. The combined hardware/software platform allows the students to directly manipulate electronic components, which are formal equivalents of the BioBricks used in our sensor, and to observe the effect of changing these components on the current or voltage output, which is the equivalent of the fluorescence intensity in our lab experiments. The software part of the platform includes the same model we created for the analysis of the sensor, and the GUI that facilitates the manipulation of the circuit kit.
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<i><a href="/Overview"> Learn more here</a></i>
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<a name="Primary_Objective:_A_New_Set_of_Well-Characterized_Promoters"></a><h2> <span class="mw-headline"> Primary Objective: A New Set of Well-Characterized Promoters </span></h2>
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<div class="thumb tright"><div class="thumbinner" style="width:152px;"><a href="/Image:Carnegie_Mellon-MicroMaize.jpg" class="image" title="Fluorescence Microscopy"><img alt="Fluorescence Mircroscopy" src="/wiki/images/thumb/0/08/Carnegie_Mellon-MicroMaize.jpg/150px-Carnegie_Mellon-MicroMaize.jpg" width="150" height="301" border="0" class="thumbimage" /></a>  <div class="thumbcaption"><div class="magnify"><a href="/Image:Carnegie_Mellon-MicroMaize.jpg" class="internal" title="Enlarge"><img src="/wiki/skins/common/images/magnify-clip.png" width="15" height="11" alt="" /></a></div>Fluorescence Microscopy</div></div></div>
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<i><a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Overview"> Learn more here</a></i>
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<font size="4"><p><b>Our primary objective is to develop a series of BioBricks that are well characterized based on our methods of measurement.</b></p></font>
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<p>We assert that our new method of analyzing promoters can quantify certain properties such as:
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<a name="Objective_1:_A_New_Set_of_Well-Characterized_Promoters"></a><h1> <span class="mw-headline"> Objective 1: Novel Well-Characterized Promoters </span></h1>
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<p><b>Our first objective is to develop a series of BioBricks that are well characterized based on our methods of measurement.</b></p></font>
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<p>We assert that our new method of analyzing promoters can quantify certain properties such as: </p>
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<ol><li> Translational efficiency <i>in vivo </i>
<ol><li> Translational efficiency <i>in vivo </i>
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</li><li> <i>in vivo</i> transcription rates
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</li><li> <i>In vivo</i> transcription rates
</li><li> Promoter strength
</li><li> Promoter strength
</li><li> <i>In vivo</i> mRNA and protein half-lives in real time
</li><li> <i>In vivo</i> mRNA and protein half-lives in real time
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</ol> The promoters we submit will be characterized with these properties.
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<a name="Secondary_Objective:_Humanistic_Practice"></a><h2> <span class="mw-headline"> Secondary Objective: Humanistic Practice</span></h2>
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<p> <a href="https://2012.igem.org/Team:Carnegie_Mellon/FAQ" class="external text" title="https://2012.igem.org/Team:Carnegie_Mellon/FAQ" rel="nofollow">FAQ/Terminology</a> in engineering <i>Escherichia coli</i> to <b>monitor these variables via fluorescence</b>. Find out more about Carnegie Mellon: (<a href="http://www.cmu.edu" class="external text" title="http://www.cmu.edu" rel="nofollow">CMU Home Page</a>).
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<p>The promoters we submit were characterized with these properties. </p>
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<img src="https://static.igem.org/mediawiki/2012/d/de/Ts.png" height="300" width="380" align="center"/>
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<img src="https://static.igem.org/mediawiki/2012/9/9b/Tl.png" height="300" width="380" >
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<strong>Figure 1: Measured transcription (left panel) and translation (right panel) rate constants of three new promoters using a new fluorogen-activated biosensor. </strong>
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<br> Based on established parts, we have developed a new biosensor that can report levels of both RNA and protein in a single cell. This biosensor enables non-invasive and real-time measurements of RNA and protein expression rates. We have applied the biosensor in the characterization of three new T7Lac promoters, which yielded high quality time-lapse data of both RNA and protein levels (see details in <a href = "https://2012.igem.org/Team:Carnegie_Mellon/Met-Overview"> Methods & Results </a>). The data was used to estimate transcription and translation rate constants (see details in <a href =" https://2012.igem.org/Team:Carnegie_Mellon/Mod-Overview"> Modeling </a>).  
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<a name="Objective_2:_Human_Practices"></a><h1> <span class="mw-headline"> Objective 2: Human Practices</span></h1>
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<p> As part of our project, we seek to intrigue high school students about synthetic biology and engineering. In this pursuit, we developed an electrical analog of our BioBricks (with a simulated microscope using LEDs and a photoresistor) to teach high school students about:
<p> As part of our project, we seek to intrigue high school students about synthetic biology and engineering. In this pursuit, we developed an electrical analog of our BioBricks (with a simulated microscope using LEDs and a photoresistor) to teach high school students about:
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<ol><li> The iGEM competitions and how iGEM works
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<ol><li> Synthetic biology and its relationship to biology, science, and engineering in general
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</li><li> Gene expression and the central dogma of molecular biology
</li><li> Gene expression and the central dogma of molecular biology
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</li><li> How our project measures properties of promoters
 
</li><li> How synthetic biologists tackle real-world problems
</li><li> How synthetic biologists tackle real-world problems
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</li><li> The iGEM competition and how our iGEM team's project enables one to measures the properties of promoters
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</li><li> The interdisciplinary nature of synthetic biology
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</li><li> The advantages and challenges of interdisciplinary work
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<a name="The_Team"></a><h2><span class="mw-headline"> The Team</span></h2>
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<p>The 2012 Carnegie Mellon University iGEM team consists of students from Biological Sciences, Electrical and Computer Engineering, Biomedical Engineering and Chemical Engineering.
<p>The 2012 Carnegie Mellon University iGEM team consists of students from Biological Sciences, Electrical and Computer Engineering, Biomedical Engineering and Chemical Engineering.
<ul><li>Peter Wei (ECE, BME)
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Advisors for the team are from the Chemistry, Biomedical Engineering, Electrical and Computer Engineering, Computational Biology, and Biological Science Departments.  
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<a name="Further_Considerations"></a><h2> <span class="mw-headline"> Further Considerations </span></h2>
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Latest revision as of 03:26, 27 October 2012

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Real-time quantitative measurement of RNA and protein levels using fluorogen-activated biosensors



Introduction: Motivation and Background

Our primary goal is to develop new promoters that can be measured with fluorescent technology.

  • We seek to develop a system that will allow researchers in the field of synthetic biology to accurately measure a variety of metrics in gene expression networks including translational efficiency and transcriptional strength.

  • We hypothesize that we can use Spinach (a fluorogen-activating RNA sequence) and a FAP (fluorogen activating protein) as biosensors to measure these gene expression metrics in vivo (in living cells), rather than in vitro (in a test tube), which can be very costly and labor intensive.

  • We aim to characterize the relationship between synthesis rates of Spinach and transcription rates and the relationship between synthesis rates of FAP and translation rates.



    • Project Description

    Experimental

    The design and implementation of synthetic biological systems often require information on transcription and translation rates and on the impact of both RNA and protein levels on metabolic activities of host cells. Such information is needed when both strong and low levels of expression are desired, depending on the biologists’ goal, e.g., high production or single-molecule localization of a protein, respectively. To date, however, quantitative information about the expression strength of a promoter is difficult to obtain due to the lack of noninvasive and quick approaches to measure levels of RNA and protein in cells.

    Here, we engineer a fluorescence-based biosensor that can provide information on both transcription strength and translation efficiency that is noninvasive, easily applied to a variety of promoters, and capable of providing results in a time frame that is short when compared to current technologies. The sensor is based on the use of an RNA aptamer (termed Spinach) and a fluorogen activating protein (FAP). Both the Spinach and FAP become fluorescent in response to binding with dye molecules. The combination of FAP and Spinach will allow us to quantitatively determine relationships involving mRNA and protein, such as translational efficiency.

    To demonstrate the utility of the sensor, we have constructed and characterized four T7Lac promoters. For each of the promoters, we have measured both mRNA and protein fluorescence over time. The time-lapse fluorescence levels of mRNA and protein were used in a mathematical model for the estimation of transcription and translation rate constants. We have submitted these promoters to the parts registry, whose strength is measured by the newly developed biosensor.

    Learn more here

    Human Practices

    The impact of synthetic biology depends on the number and quality of scientists making significant contributions to the field. To this end, we contributed to raising the awareness of high school students, who may become future scientists, about the interdisciplinary field of synthetic biology, and about the preparation one needs to become a synthetic biologist.

    We decided to create teaching materials for high school students inspired by our team’s research project. Our goal was that these materials can be easily used by a science teacher in a lecture in a Biology or Chemistry course to (1) explain what Synthetic Biology is, and (2) enable the students to understand how our biosensor works. The teaching materials we have created, specifically a power point presentation and an electronic circuit kit, have become part of the Lending Library of Kits of DNAZone, the outreach program of the Center of Nucleic Acids Science and Technology (CNAST) at Carnegie Mellon. The kits in the Library are loaned to high school teachers in the Pittsburgh area to be used in teaching Math and Science. We have also tested the kit in several demonstrations in the Summer of 2012 to high school students enrolled in the Summer Academy of Math and Science (SAMS) at Carnegie Mellon.

    To bridge the gap between the background of a high school student and the complexity of our project, we built an affordable, microcontroller-based, hardware platform and associated, open-source, digital simulation software. The combined hardware/software platform allows the students to directly manipulate electronic components, which are formal equivalents of the BioBricks used in our sensor, and to observe the effect of changing these components on the current or voltage output, which is the equivalent of the fluorescence intensity in our lab experiments. The software part of the platform includes the same model we created for the analysis of the sensor, and the GUI that facilitates the manipulation of the circuit kit.

    Learn more here



    Objective 1: Novel Well-Characterized Promoters

    Our first objective is to develop a series of BioBricks that are well characterized based on our methods of measurement.

    We assert that our new method of analyzing promoters can quantify certain properties such as:

    1. Translational efficiency in vivo
    2. In vivo transcription rates
    3. Promoter strength
    4. In vivo mRNA and protein half-lives in real time


    The promoters we submit were characterized with these properties.


    Figure 1: Measured transcription (left panel) and translation (right panel) rate constants of three new promoters using a new fluorogen-activated biosensor.
    Based on established parts, we have developed a new biosensor that can report levels of both RNA and protein in a single cell. This biosensor enables non-invasive and real-time measurements of RNA and protein expression rates. We have applied the biosensor in the characterization of three new T7Lac promoters, which yielded high quality time-lapse data of both RNA and protein levels (see details in Methods & Results ). The data was used to estimate transcription and translation rate constants (see details in Modeling ).



    Objective 2: Human Practices

    As part of our project, we seek to intrigue high school students about synthetic biology and engineering. In this pursuit, we developed an electrical analog of our BioBricks (with a simulated microscope using LEDs and a photoresistor) to teach high school students about:

    1. Synthetic biology and its relationship to biology, science, and engineering in general
    2. Gene expression and the central dogma of molecular biology
    3. How synthetic biologists tackle real-world problems
    4. The iGEM competition and how our iGEM team's project enables one to measures the properties of promoters
    5. The interdisciplinary nature of synthetic biology
    6. The advantages and challenges of interdisciplinary work



    Further Considerations

    In the pursuit of our project we:

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