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==Training of Undergraduate Researchers== | ==Training of Undergraduate Researchers== | ||
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==Directions for Future Research== | ==Directions for Future Research== | ||
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| + | ==Alternative Format== | ||
| + | 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 c’) for example, encoded in it. Bacteria are given a set of tRNA variables as inputs and evaluate the logical clauses and MAX SAT. | ||
Revision as of 16:53, 14 October 2009
Contents |
Training of Undergraduate Researchers
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Exploration of Bio-Math Connections
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Laying a Foundation for an Innovative Project
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Parts Contributed to Registry
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Presentations to a Broader Audience
Since the 2008 iGEM Jamboree, team members have presented synthetic biology and the work of the team in the following 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
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, October 2009
Upcoming presentations include:
Missouri Western Computer Science, Math, adn 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
Human Factors
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Directions for Future Research
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Alternative Format
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
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.
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.
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.
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 c’) for example, encoded in it. Bacteria are given a set of tRNA variables as inputs and evaluate the logical clauses and MAX SAT.
