Team:Stanford/Research

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Revision as of 21:46, 24 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 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 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.
Successfully complete and submit a Project Summary form.
Create and share a Description of the team's project via the iGEM wiki
Present a Poster and Talk at the iGEM Jamboree
Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Parts
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.
Submit DNA for at least one new BioBrick Part or Device to the Registry of Parts.

Silver Medal

Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected.
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

Gold Medal

Characterize or improve an existing BioBrick Part or Device and enter this information back on the Registry.
Help another iGEM team by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.

detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.

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 === Bronze Medal ===
 #Register the team, have a great summer, and have fun attending the Jamboree.
-Successfully complete and submit a Project Summary form.
+#Successfully complete and submit a Project Summary form.
-Create and share a Description of the team's project via the iGEM wiki (see TUDelft 2008 for a great example).
+#Create and share a Description of the team's project via the iGEM wiki
-Present a Poster and Talk at the iGEM Jamboree (watch the Heidelberg 2008 video for a great example).
+#Present a Poster and Talk at the iGEM Jamboree
-Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Parts
+#Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Parts
-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. Consider BBa_J45004 as one example (be sure to check Main, Design Page, and Experiences sub-pages for this part).
+#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.
-Teams are currently expected to design and contribute standard biological parts that conform to the accepted BioBrick standards for physical assembly. Non-BioBrick parts will not be recognized by iGEM 2010 judges unless they have specific approval. The two specific BioBrick physical assembly schemes that the judges will recognize by default are (i) Tom Knight's original assembly standard and (ii) Ira Phillips fusion assembly standard.
+#Submit DNA for at least one new BioBrick Part or Device to the Registry of Parts.
-[Special Note. A discussion has been initiated by the BioBricks Standards Working Group to consider updating the BioBrick assembly standard in time for June 1. Check back for any updates on acceptable BioBrick assembly standards.]
-Any new Devices that are based on gene expression are expected to conform to the PoPS device boundary standard. See chapter 3 of the book, Adventures in Synthetic Biology, for more information about common signal carriers and PoPS.
+=== Silver Medal ===
-Submit DNA for at least one new BioBrick Part or Device to the Registry of Parts.
+#Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected.
-The submitted DNA must be associated with a Part or Device for which you have entered information describing the part or device, and must conform to the BioBrick standards for Parts or Devices (see above).
+#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
-The requirements to earn a Silver Medal, in addition to the Bronze Medal requirements, are:
-Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected.
+=== Gold Medal ===
-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 (see BBa_F2620 for an exemplar).
+#Characterize or improve an existing BioBrick Part or Device and enter this information back on the Registry.
-The requirements to earn a Gold Medal, in addition to the Silver Medal requirements, are any one OR more of the following:
+#Help another iGEM team by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.
-Characterize or improve an existing BioBrick Part or Device and enter this information back on the Registry.
+ detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.
-Help another iGEM team by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.
-Develop and document a new technical standard that supports the (i) design of BioBrick Parts or Devices, or (ii) construction of BioBrick Parts or Devices, or (iii) characterization of BioBrick Parts or Devices, or (iv) analysis, modeling, and simulation of BioBrick Parts or Devices, or (v) sharing BioBrick Parts or Devices, either via physical DNA or as information via the internet.
-Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.