Team:Stanford/Research

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Revision as of 06:20, 25 October 2010

Our Project: Detecting the Ratio of Two Chemicals

The detection of a ratio of input chemicals is an important biological information processing application that has so far not been realized in a BioBrick standard device or, for the most part, within the larger synthetic biology community. While some sensors have been developed to detect pH (references), such sensors are highly limited in both their application and their output. For our project this year, the Stanford iGEM team designed and implemented two different modular ratiometric sensors in order to allow future bioengineers to create more nuanced cellular systems.

The first sensor uses small RNA interference to calculate the difference in the concentrations of the two input chemicals. One input chemical (chemical A) binds to a promoter and causes the transcription of an mRNA coding for an output protein. The other input chemical (B) binds to a promoter and causes transcription of an sRNA, which is complementary to a target sequence overlapping the ribosome binding site of the mRNA sequence promoted by A. The sRNA then binds to the mRNA, preventing the ribosome from binding and synthesizing the output protein. In the ideal case, no output protein is produced if less A is present than B, and protein begins to be produced as soon as the concentration of A surpasses that of B. To change the threshold ratio detected by the sensor, multiple copies of the genes encoding either the mRNA or the sRNA can be placed downstream of the promoters.

The second sensor uses a transcription factor regulated by a kinase/phosphotase pair. In this system, the phosphorylated form of the transcription factor causes transcription of a gene coding for our output protein. The production of the transcription factor is under the control of a constitutive promoter, which maintains a basal concentration. The kinase that acts on the transcription factor is under the control of a promoter positively regulated by A. A phosphotase is similarly controlled by input B. By testing the concentration of output protein in relation to various concentrations of input chemicals, we plan to create an algorithm that will allow us to work backwards from a given concentration of output protein to deduce the ratio of the original concentrations of input chemicals.

Both sensors are modular in that the input and output molecules can be changed without affecting the interior mechanism of the device. We see many applications for this device, including more efficiently regulated metabolic engineering, targeted drug delivery, detection of preterm labor (the ratio of different types of vaginal bacteria has been linked to spontaneous preterm birth, reference), and the discovery of other significant biological ratios.

Research

Research and Development

Modeling

Medal Requirements

Bronze Medal

Register the team, have a great summer, and have fun attending the Jamboree.
Done!
Successfully complete and submit a Project Summary form.
Done!
Create and share a Description of the team's project via the iGEM wiki
Done!
Present a Poster and Talk at the iGEM Jamboree
Booked our plane tickets!
Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Parts
Done?
Entered information for each new part or device should at least include primary nucleic acid sequence, description of function, authorship, any relevant safety notes, and an acknowledgement of sources and references.
Done?
Submit DNA for at least one new BioBrick Part or Device to the Registry of Parts.
Done?

Silver Medal

Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected.
Waiting for lab results...
Characterize the operation of at least one new BioBrick Part or Device and enter this information on the Parts or Device page via the Registry of Parts
Waiting for lab results...

Gold Medal

Characterize or improve an existing BioBrick Part or Device and enter this information back on the Registry.
When sequencing one of our ligations, we noticed an unexpected sequence in our results. After more investigation, we determined that that sequence came from the Distribution part BBa_E1010, and that the part sequence listed on the Parts Registry was incomplete.
Help another iGEM team by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.
With our Twitter project, we hope to help all iGEM teams by facilitating collaboration between teams. Read more about it here!

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 The detection of a ratio of input chemicals is an important biological information processing application that has so far not been realized in a BioBrick standard device or, for the most part, within the larger synthetic biology community. While some sensors have been developed to detect pH (references), such sensors are highly limited in both their application and their output. For our project this year, the Stanford iGEM team designed and implemented two different modular ratiometric sensors in order to allow future bioengineers to create more nuanced cellular systems.
-The '''[[Digital Sensor|first sensor]] uses small RNA interference''' to calculate the difference in the concentrations of the two input chemicals. One input chemical (chemical A) binds to a promoter and causes the transcription of an mRNA coding for an output protein. The other input chemical (B) binds to a promoter and causes transcription of an sRNA, which is complementary to a target sequence overlapping the ribosome binding site of the mRNA sequence promoted by A. The sRNA then binds to the mRNA, preventing the ribosome from binding and synthesizing the output protein. In the ideal case, no output protein is produced if less A is present than B, and protein begins to be produced as soon as the concentration of A surpasses that of B. To change the threshold ratio detected by the sensor, multiple copies of the genes encoding either the mRNA or the sRNA can be placed downstream of the promoters.
+The '''[[Team:Stanford/Digital Sensor|first sensor]] uses small RNA interference''' to calculate the difference in the concentrations of the two input chemicals. One input chemical (chemical A) binds to a promoter and causes the transcription of an mRNA coding for an output protein. The other input chemical (B) binds to a promoter and causes transcription of an sRNA, which is complementary to a target sequence overlapping the ribosome binding site of the mRNA sequence promoted by A. The sRNA then binds to the mRNA, preventing the ribosome from binding and synthesizing the output protein. In the ideal case, no output protein is produced if less A is present than B, and protein begins to be produced as soon as the concentration of A surpasses that of B. To change the threshold ratio detected by the sensor, multiple copies of the genes encoding either the mRNA or the sRNA can be placed downstream of the promoters.
-The '''[[Analog Sensor|second sensor]] uses a transcription factor regulated by a kinase/phosphotase pair'''. In this system, the phosphorylated form of the transcription factor causes transcription of a gene coding for our output protein. The production of the transcription factor is under the control of a constitutive promoter, which maintains a basal concentration. The kinase that acts on the transcription factor is under the control of a promoter positively regulated by A. A phosphotase is similarly controlled by input B. By testing the concentration of output protein in relation to various concentrations of input chemicals, we plan to create an algorithm that will allow us to work backwards from a given concentration of output protein to deduce the ratio of the original concentrations of input chemicals.
+The '''[[Team:Stanford/Analog Sensor|second sensor]] uses a transcription factor regulated by a kinase/phosphotase pair'''. In this system, the phosphorylated form of the transcription factor causes transcription of a gene coding for our output protein. The production of the transcription factor is under the control of a constitutive promoter, which maintains a basal concentration. The kinase that acts on the transcription factor is under the control of a promoter positively regulated by A. A phosphotase is similarly controlled by input B. By testing the concentration of output protein in relation to various concentrations of input chemicals, we plan to create an algorithm that will allow us to work backwards from a given concentration of output protein to deduce the ratio of the original concentrations of input chemicals.
 Both sensors are modular in that the input and output molecules can be changed without affecting the interior mechanism of the device. We see many applications for this device, including more efficiently regulated metabolic engineering, targeted drug delivery, detection of preterm labor (the ratio of different types of vaginal bacteria has been linked to spontaneous preterm birth, reference), and the discovery of other significant biological ratios.