Team:MoWestern Davidson/conclusion

From 2009.igem.org

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==Training of Undergraduate Researchers==
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==Laying the Foundation for an Innovative Project==
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Our iGEM team worked across disciplinary and institutional boundaries to conceive of an innovative approach to the use of bacterial cells to evaluate the satisfiability, or SAT, problem.  We designed a unique system for the project and carried out a number of mathematical analyses in support of the design.  We designed and built parts that enabled us to demonstrate the basic molecular mechanism for the project, frameshift suppression.  The important milestone that we have achieved is that we have laid the foundation for a very innovative approach to the use of bacterial computers that can evaluate an important class of logical problems. 
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==Exploration of Bio-Math Connections==
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==Parts Contributed to the Registry==
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Add text here
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Our team contributed 66 parts to the Registry this year.  The methods by which we constructed basic parts included direct synthesis by DNA oligonucleotides, site directed mutagenesis of existing parts, and PCR amplification from genomic sources.  Our new basic parts that should prove to be of general use, including 5 base suppressor tRNAs and cognate reporter genes to test their function.  We also constructed a number of intermediate from combinations of new and existing parts and several devices designed to test frameshift suppression.
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==Laying a Foundation for an Innovative Project==
+
==Training of Undergraduate Researchers==
-
Add text here
+
An important goal of our iGEM team was to enable us as undergraduate students to have a valuable education experience.  By taking ownership of the conception, design, construction, and presentation of our project, we learned valuable lessons about conducting scientific research.  We learned to work as a team on significant challenges, to communicate across disciplines and distance, to troubleshoot experimental methods, and to communicate our progress in diverse ways.
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==Parts Contributed to Registry==
+
==Exploration of BioMath Connections==
-
Add text here
+
Our iGEM is mentored by faculty with backgrounds in both Biology and Mathematics and is composed of students from each of these disciplines.  From the beginning of the year, we sought to explore BioMath Connections in the choice of a project and in the way we pursued it.  We have found synthetic biology and the iGEM experience to be a very effective way to carry out this type of multidisciplinary research.  Mathematical modeling of the satsifiability problem in general and of our specific approach to carrying out SAT problems in bacterial cells informed our biological designs.  We also made significant connections between mathematics and biology in the design and construction of physical models of our frameshift suppressor tRNA molecules.
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==Presentations to a Broader Audience==
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==Human Practice==
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Since the 2008 iGEM Jamboree, team members have presented synthetic biology and the work of the team in the following venues.
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The multidisciplinary nature of our iGEM team is also illustrated by a part of our project in which students at Davidson College researched public opinion of synthetic biology based on provided summaries of the field. Citizens in North Carolina were randomly assigned to one of two groups. One group used the word '''"create"''' and similar terms to see if this had an impact on their view of synthetic biology. The other group used words such as '''"build", "construct"''', etc.  
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Truman State University Mathematical Biology Seminar, January 2009
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We also measured each person's '''"religiosity"''' and analyzed the impact religiosity had on the manipulation. We found that more religious people were more likely to view synthetic biology in a favorable light which was not what we had predicted.
-
Mathematical Association of America Missouri Section, April 2009
+
Faculty at high schools and colleges/universities from across the country were asked how much they presently know about synthetic biology and its implementation in course curricula. The survey revealed that 16% of college faculty reported adequate knowledge of synthetic biology while only 8% of high school teachers reported adequate knowledge of the field. Surveys given to general public were used to study public opinion based on the influence of different descriptions of synthetic biology.
-
Genome Consortium for Active Teaching (GCAT) workshop, July 2009
+
==Presentations to a Broader Audience==
 +
During 2009, our iGEM team members have presented their project and synthetic biology in general at the following local, regional, and national venues.
-
Western Summer Research Institute Symposium, July 2009
+
*Truman State University Mathematical Biology Seminar, January 2009
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+
*Mathematical Association of America Missouri Section, April 2009
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Davidson Research Initiative Symposium, September 2009
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*Genome Consortium for Active Teaching (GCAT) workshop, July 2009
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+
*Missouri Western Summer Research Institute Symposium, July 2009
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Association of College and University Biology Educators (ACUBE), October 2009
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*Davidson Research Initiative Symposium, September 2009
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*Association of College and University Biology Educators (ACUBE), October 2009
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Foundation for the Carolinas, October 2009
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*Foundation for the Carolinas, November 2009
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*Undergraduate Research Conference at the Interface Between Biology and Mathematics, October 2009
Upcoming presentations include:
Upcoming presentations include:
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*Missouri Western Computer Science, Math, and Physics Colloquium, November 2009
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Missouri Western Computer Science, Math, adn Physics Colloquium, November 2009
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*National Academies Keck Future Initiatives (NAKFI) Conference on Synthetic Biology, November 2009
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*National Joint Meetings of the American Mathematics Society, Mathematical Association of America, and the Society for Industrial and Applied Mathematics, January 2010
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National Academies Keck Future Initiatives (NAKFI) Conference on Synthetic Biology, November 2009
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+
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National Joint Meetings of the American Mathematics Society, Mathematical Association of America, and the Society for Industrial and Applied Mathematics, January 2010
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+
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==Human Factors==
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Add text here
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==Directions for Future Research==
==Directions for Future Research==
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Add text here
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We have developed a design for the use of frameshift suppression to enable bacterial cells to analyze and report the results of a SAT problem. We have develeped mathematical models for our system that can be used to inform our choices for constructing SAT problems in bacteria. We have constructed the frameshift suppressor tRNA genes that will serve as inputs for the SAT problem and have tested their ability to provide frameshift suppression resulting in expression of reporter genes. Our next step is to determine the ability of bacterial cells to accommodate multiple frameshift suppressor tRNAs and to test combinations of them in cells. Then we will design and construct reporter genes that will carry out simple OR logical operations, which can then be combined in to a 2-SAT problem with multiple reporters for multiple clauses. The following task will be to encode 3-SAT problems in a similar fashion.
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==Alternative Format==
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1. Single Literal: In this approach, the reporter gene has a FSL of one literal, or 5 base pair insertion. The bacteria are given a set of tRNA variables as inputs to evaluate that literal, and if the bacteria receive that literal's tRNA compliment, then it will express a gene. To evaluate the logical clauses and MAX SAT, we must look plates to see if the gene was expressed. The design of the FSL in the reporter genes in this example is relatively simple. Immediately after the start codon, ATG, we insert a single the 5 base pair insertion. Then every possible 5mer is exposed to a common set of tRNAs
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2. Single Clause: In this approach, the reporter gene has a FSL of one logical clause (a OR b), consisting of two 5 base pair insertions. Bacteria are given a set of tRNA variables as inputs to evaluate that clause. If the clause is satisfied and suppression occurs, then the gene will be expressed. In order to compute the problem we must then determine how many colonies expressed the gene, thus satisfying the clauses. In this design, the FSL has two 5 base pair insertions. If one tRNA binds to either insertion, the reading frame is restored. However, these insertions are designed in such a manner that if one tRNA binds, another tRNA could not bind to the second 5 base pair insertion.
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3. Automated Population with One Reporter Type: This approach uses 4 different FSLs ranging from 1 to 4 clauses (a or b) in the same reporter gene. These reporter genes are then divided into colonies representing the number of clauses (1, 2, 3, or 4) in their reporter gene. Bacteria are given a set of tRNA variables as inputs and evaluate the logical clauses and MAX SAT by reporting the gene expression. This set up allows us to determine the maximum number of clauses the tRNA is able to solve. The FSL length and design varies according to the number of clauses inserted. However, the clauses are designed in the same way as in the previous single clause line. These single clauses are then strung together so that in order for the proper reading frame to be restored, exactly one 5 base pair insertion in each clause must be satisfied.
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4. Automated Population with Individual Reporter Types: This approach is basically the same as the previous, except that the each clause has its own reporter gene. For example, the first clone tests for 1 clause satisfied and if satisfied, the clone will produce GFP. The second clone tests for 2 clauses satisfied and will produce RFP if satisfied. The third clone tests for 3 clauses satisfied and will produce Chloramphenicol resistance. The last clone tests for 4 clauses satisfied and will produce Tetracycline resistance.  
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5. Automated Population with Individual Reporter Types in a Single Clone: In this approach, 4 different FSLs that test for at least 1, 2, 3, and 4 clauses satisfied are inserted in the beginning of different reporter genes used in a single clone. The first reporter gene tests for at least 1 clause satisfied, and if satisfied, the gene GFP will be expressed. The second reporter gene tests for at least 2 clauses satisfied and will express RFP if satisfied. The third reporter gene tests for at least 3 clauses satisfied and will produce Chloramphenicol resistance. Tetracycline resistance is the last reporter gene that tests for all 4 clauses satisfied. Each FSL design has the same SAT problem, (a OR b) AND (b OR cā€™) for example, encoded in it. Bacteria are given a set of tRNA variables as inputs and evaluate the logical clauses and MAX SAT.
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{{Template:MoWestern_Davidson2009_end}}

Latest revision as of 18:31, 20 October 2009

Contents

Laying the Foundation for an Innovative Project

Our iGEM team worked across disciplinary and institutional boundaries to conceive of an innovative approach to the use of bacterial cells to evaluate the satisfiability, or SAT, problem. We designed a unique system for the project and carried out a number of mathematical analyses in support of the design. We designed and built parts that enabled us to demonstrate the basic molecular mechanism for the project, frameshift suppression. The important milestone that we have achieved is that we have laid the foundation for a very innovative approach to the use of bacterial computers that can evaluate an important class of logical problems.

Parts Contributed to the Registry

Our team contributed 66 parts to the Registry this year. The methods by which we constructed basic parts included direct synthesis by DNA oligonucleotides, site directed mutagenesis of existing parts, and PCR amplification from genomic sources. Our new basic parts that should prove to be of general use, including 5 base suppressor tRNAs and cognate reporter genes to test their function. We also constructed a number of intermediate from combinations of new and existing parts and several devices designed to test frameshift suppression.

Training of Undergraduate Researchers

An important goal of our iGEM team was to enable us as undergraduate students to have a valuable education experience. By taking ownership of the conception, design, construction, and presentation of our project, we learned valuable lessons about conducting scientific research. We learned to work as a team on significant challenges, to communicate across disciplines and distance, to troubleshoot experimental methods, and to communicate our progress in diverse ways.

Exploration of BioMath Connections

Our iGEM is mentored by faculty with backgrounds in both Biology and Mathematics and is composed of students from each of these disciplines. From the beginning of the year, we sought to explore BioMath Connections in the choice of a project and in the way we pursued it. We have found synthetic biology and the iGEM experience to be a very effective way to carry out this type of multidisciplinary research. Mathematical modeling of the satsifiability problem in general and of our specific approach to carrying out SAT problems in bacterial cells informed our biological designs. We also made significant connections between mathematics and biology in the design and construction of physical models of our frameshift suppressor tRNA molecules.

Human Practice

The multidisciplinary nature of our iGEM team is also illustrated by a part of our project in which students at Davidson College researched public opinion of synthetic biology based on provided summaries of the field. Citizens in North Carolina were randomly assigned to one of two groups. One group used the word "create" and similar terms to see if this had an impact on their view of synthetic biology. The other group used words such as "build", "construct", etc.

We also measured each person's "religiosity" and analyzed the impact religiosity had on the manipulation. We found that more religious people were more likely to view synthetic biology in a favorable light which was not what we had predicted.

Faculty at high schools and colleges/universities from across the country were asked how much they presently know about synthetic biology and its implementation in course curricula. The survey revealed that 16% of college faculty reported adequate knowledge of synthetic biology while only 8% of high school teachers reported adequate knowledge of the field. Surveys given to general public were used to study public opinion based on the influence of different descriptions of synthetic biology.

Presentations to a Broader Audience

During 2009, our iGEM team members have presented their project and synthetic biology in general at the following local, regional, and national venues.

  • Truman State University Mathematical Biology Seminar, January 2009
  • Mathematical Association of America Missouri Section, April 2009
  • Genome Consortium for Active Teaching (GCAT) workshop, July 2009
  • Missouri Western Summer Research Institute Symposium, July 2009
  • Davidson Research Initiative Symposium, September 2009
  • Association of College and University Biology Educators (ACUBE), October 2009
  • Foundation for the Carolinas, November 2009
  • Undergraduate Research Conference at the Interface Between Biology and Mathematics, October 2009

Upcoming presentations include:

  • Missouri Western Computer Science, Math, and Physics Colloquium, November 2009
  • National Academies Keck Future Initiatives (NAKFI) Conference on Synthetic Biology, November 2009
  • National Joint Meetings of the American Mathematics Society, Mathematical Association of America, and the Society for Industrial and Applied Mathematics, January 2010

Directions for Future Research

We have developed a design for the use of frameshift suppression to enable bacterial cells to analyze and report the results of a SAT problem. We have develeped mathematical models for our system that can be used to inform our choices for constructing SAT problems in bacteria. We have constructed the frameshift suppressor tRNA genes that will serve as inputs for the SAT problem and have tested their ability to provide frameshift suppression resulting in expression of reporter genes. Our next step is to determine the ability of bacterial cells to accommodate multiple frameshift suppressor tRNAs and to test combinations of them in cells. Then we will design and construct reporter genes that will carry out simple OR logical operations, which can then be combined in to a 2-SAT problem with multiple reporters for multiple clauses. The following task will be to encode 3-SAT problems in a similar fashion.

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