Team:MoWestern Davidson

From 2009.igem.org

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=Project Summary=
 
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Our team was interested in advancing bacterial computing by harnessing the parallel processing capabilities of E. coli to tackle the SAT problem from a biological perspective.  The SAT problem was the first mathematical problem proven to be among a class of computationally challenging problems called NP-complete.  Problems of this class exceed modern computer limitations because as the problems grow in size, the time it takes computers to solve these problems increases exponentially.  The SAT problem groups true-false variables into logical clauses linked together to form decision problems.  The task is to assign true or false to each variable in such a way that the problem is satisfied and reports true.
 
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We constructed logical clauses of a SAT problem by designing a DNA sequence that includes combinations of 5-base pair codons that represent different variables.  These logical clauses are located directly upstream of a reporter gene so that the original sequence is out of frame.  In order to express the reporter, we need suppressor tRNAs to fix the frameshift created by these 5-base pair codons.  We engineered these suppressor 5-base pair anticodon tRNAs to represent the corresponding inputs for our variables.  If a tRNA suppresses a mutation and a problem is satisfied, then the reporter gene will be expressed. 
 
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Our project extends the understanding of synthetic biology through educational surveys and models.  Our team collaborated with psychology students to receive public opinion of synthetic biology based on provided summaries of the field.  Through paper and online surveys, these students collected and analyzed responses to see how individual knowledge of the field affects support of its inclusion in high school curriculums.  The descriptions of the field that were provided corresponded with the prior knowledge reported by the participants.  We also designed and constructed physical models of our 5 nucleotide anticodon tRNAs to understand and communicate their functions.
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==Project Description==
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Our team research goal was to advance the developing field of bacterial computing by harnessing the inherent biological properties of <i>E. coli</i> to tackle computationally challenging mathematical problems from a class known as NP-complete.  As NP-complete problems grow in size, the time required to solve them increases rapidly.  The Satisfiability (SAT) logic problem was the first mathematical problem proven to be NP-complete.  Logical clauses are composed of two (2-SAT) or three (3-SAT) true-false variables connected by OR operators.  A series of logical clauses are linked together by AND operators to form a SAT problem.  A problem is satisfied if true or false can be assigned to each variable in such a way that the overall value of the logical expression is true. 
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Our system is designed to use frameshift suppressor tRNAs as inputs that can be processed by frameshift suppressor leaders (FSLs) that enable the translation of reporter constructs only when an appropriate combination of inputs is present.  Accordingly, we designed and constructed FSLs as logical clauses in reporter genes encoding antibiotic resistance and fluorescent proteins.  Once logical clauses are satisfied, a given reporter gene is expressed, and our bacterial computers report the result of the SAT problem.  The results of this project promise to illustrate the use of engineered living cells to evaluate challenging mathematical problems.
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=Medal Criteria=
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In our project, we also sought to explore two specific aspects of synthetic biology education.  Our project explored, through surveys, how the general public as well as high school teachers understand synthetic biology.  Our team collaborated with psychology and sociology students to construct, distribute, collect, and analyze surveys of public opinion and knowledge of synthetic biology based on provided summaries of the field.  We also designed and constructed physical models of our frameshift suppressor tRNAs to better understand and communicate their role in our project.
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==Medal Criteria==
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'''Bronze'''
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'''[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=MoWestern_Davidson New Parts Contributed to the Registry]''' - We designed, built, and contributed 60 new parts and intermediates to the Registry. We also submitted our summary by August 1st and presented our PPT and poster at iGEM 2009.
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'''[[Team:MoWestern Davidson/parts|New Parts Contributed to the Registry]]''' - we designed, built, and contributed 25 new parts to the Registry.
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'''Silver'''
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'''[[Team:MoWestern Davidson/project wetlab|Experience Gained on New Registry Parts]]''' - We measured the function of several new parts we designed, and some worked as expected.
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'''[[Team:MoWestern Davidson/project wetlab|Experience Gained on New Registry Parts]]''' - we measured the function of several new parts we designed, and some expectations were met.
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'''Gold'''
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'''[[Team:MoWestern Davidson/human practice|Human Practice: Public opinion on Synthetic Biology]]''' - We learned more about public views on synthetic biology and potentially garnered support for its inclusion in high school curricula.
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Improvement of pre-existing Registry Parts - we redesigned the lacIQ1 promoter.
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'''[[Team:MoWestern Davidson/human practice|Human Practice: Physical modeling]]''' - We designed and constructed physical models of various molecules to serve as visual educational tools.
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Human Practice: Public opinion on Synthetic Biology - we learned more about public views on synthetic biology and potentially garnered support for its in inclusion in high school curriculums.
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'''[http://partsregistry.org/Part:BBa_K091112:Experience Characterized an existing BioBrick part]''' (K091112) and found ''E. coli'' can spontaneously insert a 35 bp segment that inactivates the promoter that is very strong when not mutated.  
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Human Practice: Physical modeling - we designed and constructed physical models of various molecules to serve as visual educational tools.
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Latest revision as of 02:48, 21 October 2009

Project Description

Our team research goal was to advance the developing field of bacterial computing by harnessing the inherent biological properties of E. coli to tackle computationally challenging mathematical problems from a class known as NP-complete. As NP-complete problems grow in size, the time required to solve them increases rapidly. The Satisfiability (SAT) logic problem was the first mathematical problem proven to be NP-complete. Logical clauses are composed of two (2-SAT) or three (3-SAT) true-false variables connected by OR operators. A series of logical clauses are linked together by AND operators to form a SAT problem. A problem is satisfied if true or false can be assigned to each variable in such a way that the overall value of the logical expression is true.

Our system is designed to use frameshift suppressor tRNAs as inputs that can be processed by frameshift suppressor leaders (FSLs) that enable the translation of reporter constructs only when an appropriate combination of inputs is present. Accordingly, we designed and constructed FSLs as logical clauses in reporter genes encoding antibiotic resistance and fluorescent proteins. Once logical clauses are satisfied, a given reporter gene is expressed, and our bacterial computers report the result of the SAT problem. The results of this project promise to illustrate the use of engineered living cells to evaluate challenging mathematical problems.

In our project, we also sought to explore two specific aspects of synthetic biology education. Our project explored, through surveys, how the general public as well as high school teachers understand synthetic biology. Our team collaborated with psychology and sociology students to construct, distribute, collect, and analyze surveys of public opinion and knowledge of synthetic biology based on provided summaries of the field. We also designed and constructed physical models of our frameshift suppressor tRNAs to better understand and communicate their role in our project.

Medal Criteria

Bronze New Parts Contributed to the Registry - We designed, built, and contributed 60 new parts and intermediates to the Registry. We also submitted our summary by August 1st and presented our PPT and poster at iGEM 2009.

Silver Experience Gained on New Registry Parts - We measured the function of several new parts we designed, and some worked as expected.

Gold Human Practice: Public opinion on Synthetic Biology - We learned more about public views on synthetic biology and potentially garnered support for its inclusion in high school curricula.

Human Practice: Physical modeling - We designed and constructed physical models of various molecules to serve as visual educational tools.

Characterized an existing BioBrick part (K091112) and found E. coli can spontaneously insert a 35 bp segment that inactivates the promoter that is very strong when not mutated.

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