Team:Carnegie Mellon/Hum-Overview

From 2012.igem.org

(Difference between revisions)
Line 165: Line 165:
<p>
<p>
   </p>
   </p>
-
Our goal was to create a model of our biosensor (link to the description)that clearly represents its main components and makes clear how the biosensor works.  We also planned to enable the students to simulate changes in the “environment” and to observe the outcome of these changes.  To achieve this goal, we built an affordable, microcontroller-based, hardware platform and also developed an associated, open-source, digital simulation software.  
+
</p>
 +
<p>
 +
Our goal was to create a model of our <b><a href="http://2012.igem.org/Team:Carnegie_Mellon/Mod-Derivations"> biosensor</a></b>that clearly represents its main components and makes clear how the biosensor works.  We also planned to enable the students to simulate changes in the “environment” and to observe the outcome of these changes.  To achieve this goal, we built an affordable, microcontroller-based, hardware platform and also developed an associated, open-source, digital simulation software.  
 +
</p>
<p>
<p>
-
  </p>
 
In order to present features of the <b><a href="http://2012.igem.org/Team:Carnegie_Mellon/Mod-Derivations"> biosensor</a></b> that we designed, and to make it more accessible to others, we built an affordable, microcontroller-based, <a href="http://2012.igem.org/Team:Carnegie_Mellon/Hum-Documentation"> hardware platform</a>, and developed associated, open-source, digital simulation <a href="http://2012.igem.org/Team:Carnegie_Mellon/Hum-Software"> software</a>.  
In order to present features of the <b><a href="http://2012.igem.org/Team:Carnegie_Mellon/Mod-Derivations"> biosensor</a></b> that we designed, and to make it more accessible to others, we built an affordable, microcontroller-based, <a href="http://2012.igem.org/Team:Carnegie_Mellon/Hum-Documentation"> hardware platform</a>, and developed associated, open-source, digital simulation <a href="http://2012.igem.org/Team:Carnegie_Mellon/Hum-Software"> software</a>.  
</p>
</p>

Revision as of 22:57, 2 October 2012

Image:CMU_image6.jpeg




The impact of synthetic biology depends on the number and quality of scientists making significant contributions to the field. Future scientists will rise from current high school students who are excited about science and gain a solid background in math and science in their formative years. To this end, we decided to raise the awareness of high school students about the interdisciplinary field of synthetic biology and to also teach them about the process of scientific research.

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 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 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. In designing the demonstration platform, we exploited the relationship between biological networks in synthetic biology and electronic circuits in electrical engineering. Specifically, we created a circuit kit that emulates in hardware our biological construct and in software both the response of the biological construct to specific cell conditions and the fluorescence measurement.

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 is based on the same model created for the analysis of the experimental data collected in our research. A GUI facilitates the manipulation of the circuit kit.

System implemented with the kit

As described here, our team engineered a fluorescence-based sensor that provides information on both transcription strength and translation efficiency of a promoter. The sensor 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 for the characterization of promoters.

The sensor is based on the use of an RNA aptamer (termed Spinach) and a fluorogen activating protein (FAP). The complexes of Spinach (mRNA-DMHBI in the Figure) and FAP (FAF-MG in the Figure) with specific dyes, DFHBI and MG, respectively, are fluorescent. Measurements of the fluorescence intensity of these complexes enables one to determine the concentration of mRNA and expressed protein for a given promoter. Analysis of the fluorescence data with an appropriate model leads to the transcription strength and translation efficiency for each promoter.

Our goal was to create a model of our biosensorthat clearly represents its main components and makes clear how the biosensor works. We also planned to enable the students to simulate changes in the “environment” and to observe the outcome of these changes. To achieve this goal, we built an affordable, microcontroller-based, hardware platform and also developed an associated, open-source, digital simulation software.

In order to present features of the biosensor that we designed, and to make it more accessible to others, we built an affordable, microcontroller-based, hardware platform, and developed associated, open-source, digital simulation software.

We gave several presentations about synthetic biology and our project to high school students enrolled in the Summer Academy of Math and Science. To bridge the gap between the background of a high school student and the complexity of our project, we built and demonstrated 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, by changing the current and/or voltage. These electronic components are formal equivalents of the BioBricks used in building the sensor, such as the promoter, the FAP, and the Spinach. Manipulating the electronic components allows for measuring with our kit the electronic equivalents of PoPS and translational efficiency. The microscope is simulated using LEDs and a photoresistor.

The software that is used in the platform is based on the model that we derived for the analysis of the sensor. We have also created a GUI that allows users to interact with the components of the model and read the results from the table and graphical output representing fluorescence of mRNA and protein over time.

The hardware/software platform allows for comparing different promoters and observing which ones are the strongest. The kit allows for a convenient hands-on experience that helps students understand how all parts of the model affect the mRNA and protein production, without working in the wet lab.

Image:TartanFooter.jpeg