Team:Stanford

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Revision as of 00:59, 21 July 2010

Welcome to the Stanford team Wiki for iGEM 2010

Stanford iGEM is a student-run, faculty-directed research group at Stanford University. The objective of our interdisciplinary group is to design and build novel engineered biological systems using standardized DNA-based parts to submit to the iGEM (International Genetically Engineered Machines) competition, held annually at MIT. Our research draws from the principles of Synthetic Biology, an emerging interdisciplinary and multidisciplinary area that involves the design and construction of biological systems.
Want to apply for the 2010 team? Please fill out the following [http://igem.stanford.edu/Stanford%20iGEM%20Application.doc form]
If you are looking for our winning 2009 project, check out our old site
Here is our team profile

Our Project

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 decided to design and implement two different varieties of modular ratiometric sensor in order to allow future bioengineers to create more nuanced cellular systems.

The first sensor, which gives a digital readout, 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 order to provide a more analog readout (detect more than one distinct ratio). 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.

Calendar

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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 decided to design and implement two different varieties of modular ratiometric sensor in order to allow future bioengineers to create more nuanced cellular systems.
-The first sensor, which gives a digital readout, uses small RNA interference to calculate the difference in the concentrations of the two input chemicals. One input chemical (chemical A) would bind to a promoter and cause the transcription of an mRNA coding for an output protein. The other input chemical (B) would bind to a promoter and cause transcription of an sRNA, which would be complementary to a target sequence concatenated onto the end of the mRNA sequence promoted by A. The sRNA would then bind to the mRNA, creating a dimer that would be lysed by Dicer, preventing synthesis of the output protein. In the ideal case, this system would mean that no output protein would be produced if less A were present than B, and protein would begin to be produced as soon as the concentration of A surpassed that of B. To change the threshold ratio detected by the sensor, multiple copies of the genes encoding either the mRNA or the sRNA could be placed downstream of the promoters.
+The first sensor, which gives a digital readout, 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 would use a reversible reaction regulated by a pair of enzymes in order to provide a more analog readout (detect more than one distinct ratio). In this system, input A would bind to a promoter and cause the synthesis of either a phosphotase or a kinase. Input B would bind to a promoter to cause the synthesis of the other enzyme in the pair. The two enzymes would then regulate the phosphorylation of a transcription factor, only one form of which (phosphorylated or unphosphorylated) could activate a promoter. The promoter, when activated, would cause transcription of an mRNA coding for our output protein. By testing the concentration of output protein in relation to various concentrations of input chemicals, we could create an algorithm to work backwards from a given concentration of output protein to deduce the ratio of the original concentrations of input chemicals. This system could therefore provide an output indicative of multiple different input ratios. We could tune the sensitivity by mutating the genes coding for the phosphotase and kinase, affecting their efficiency.
+The second sensor uses a transcription factor regulated by a kinase/phosphotase pair in order to provide a more analog readout (detect more than one distinct ratio). 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 first application we envision would be as a detector for preterm labor, the leading cause of infant mortality in the US. A change in vaginal bacteria seems to be an indicator of preterm labor. Our sensor could use quorum-sensing pathways to detect the ratio of normal bacteria to foreign ones in the vagina, releasing a chemical indicator if the ratio  tips too far towards the foreign bacteria. The sensor could also be used to test for other potentially significant ratios, such as that between estrogen and progesterone, helping doctors discover other predictive factors.
+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.
 == Calendar ==