Difference between revisions of "Team:Michigan/Modeling"

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           <p style="text-align:center; font-size:20px;"><font face="verdana"> We were invited to participate in the Building with Biology  event at the Michigan Science Center in Detroit, Michigan. This event took place on August 6th, 2016 and is part of a larger national initiative across museums in the country through the National Science Foundation, the NISE Network and the Science Museum of Boston. Its purpose is to provide a space of conversation about synthetic biology between scientists and the general public, ranging from kids to adults, in order to eliminate the “pipeline of doom” kind of polarized thought regarding this topic. Examples of the activities done included a simple DNA isolation, a virus making activity, an activity where people considered the uses of synthetic biology regarding food. As well as an activity where people considered in what kind of research they would invest in, among many others. The interactive activities that people participate in during the event, are designed to educate on the technologies of synthetic biology. Afterwards, a few members of our team gave a presentation on iGEM, our project, and a successful example of the everyday use of synthetic biology in many people's lives: the synthesis of human insulin. We were happy to participate in such an edifying event and were  able to answer many people’s questions and concerns while having fun.</font><br><hr></p>
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           <p style="text-align:center; font-size:20px;"><font face="verdana">Mathematical models greatly aid in the prediction of the outcome of a biological design. Our mathematical model will be employed to test the efficacy of an aptamer based proximity-dependent ligation assay (PLA) in the detection of biomarkers. The proximity dependent ligation assay is an extension to the traditional immunoassay and can be used for protein detection with high specificity and sensitivity. The selectivity of the proximity dependent ligation assay is dramatically enhanced through the double recognition by two oligonucleotide-conjugated aptamers. We sought to optimize the aptamer-protein equilibria to promote the efficient and precise binding of the aptamer with the target molecule.</font><br><hr></p>
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         <p style="text-align:center; font-size:20px;"><font face="verdana">We competed (and won a $500 award) in a health hackathon organized by Ann Arbor Health Hacks from June 14-16, 2016. Hackathons like these bring people with diverse backgrounds together to solve problems that they propose. We took our basic Aptapaper idea and through talking with the other hackathon participants worked to envision a version that could help diagnose heart disease.The hackathon was actually where we came up with the idea to use proximity dependent ligation instead of a toehold switch for our design. As part of the hackathon, we interacted with the other 200 or so participants from all different health related fields, teaching them about synthetic biology as they taught us about aspects of their particular field that were relevant to our project.</font></p>
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         <p style="text-align:center; font-size:20px;"><font face="verdana">Using Wolfram Mathematica 10.4, a symbolic mathematical computation program, we will evaluate the minimum Gibbs Free Energy (G) of the aptamer-protein complex for different concentrations of the initial reactants: aptamer 1 ([A1]), aptamer 2 ([A2]), the connector oligonucleotide ([C]), and the target protein ([P]). By finding the minimum Gibbs Free Energy of the system, we will be able to find the concentrations of the final aptamer-protein complexes at chemical equilibrium. The possible aptamer protein complexes at chemical equilibrium include: unbound aptamer 1 [A1], unbound aptamer 2 [A2], unbound connector [C], unbound protein target [P], aptamer 1 and protein complex [A1P], aptamer 2 and protein complex [A2P], aptamer 1, aptamer 2, and protein complex [A1A2P], aptamer 1 and connector complex [A1C], aptamer 2 and connector complex [A2C],  aptamer 1, aptamer 2, and connector complex [A1A2C], aptamer 1, protein, and connector complex [A1PC], aptamer 2, protein, and connector complex [A2PC], and the aptamer 1, aptamer 2, protein and connector complex [A1A2PC]. By calculating the concentrations of the above aptamer-proteins complexes at chemical equilibrium at different initial concentrations of the reactants, we can optimize the aptamer-protein equilibria to promote the sensitivity of the aptamer in the presence of the target protein, while lowering the formation of an aptamer-protein complex when there is a lack of the target protein (non-specific reaction formation).</font></p>
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<p style="text-align:center; font-size:20px;"><font face="verdana">In mid-June, the team helped out with the University of Michigan's GISE summer camp. We held two sessions where we showed middle-school girls how to extract DNA from strawberries and their own spit--an integral technique in synthetic biology! Aside from the activities, we explained the basics of genetics and synthetic biology. Despite the numerous spills and messes, the girls were intrigued with how the spidery liquid (full of their own DNA) contained in the microcentrifuge tube held all the instructions for their bodies! Hopefully, they'll be the next generation of Michigan Synthetic Biologists!</p>
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<p style="text-align:center; font-size:20px;"><font face="verdana">The ligation of aptamer 1 to the biomarker is independent to the ligation of aptamer 2 to the biomarker; in other words, the binding of an aptamer to the protein would not make the binding of the second aptamer less or more likely. Only one aptamer molecule may bind at a time to a target molecule. We are assume that gibbs free energy of the reaction at equilibrium of the reaction will never exactly be zero. The dozens of aptamer-protein dynamics will although approach zero, will not be exactly zero.</p>
 
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Revision as of 03:05, 18 October 2016

Home Project Modeling Team BioBrick Human Practices Safety Awards

Modeling

Synthetic biology has a long way to being completely accepted by the public, mainly due to lack of education about the subject. The Michigan Synthetic Biology Team held a few workshops in order to excite and incite younger generations to pursue synthetic biology!

Introduction

Mathematical models greatly aid in the prediction of the outcome of a biological design. Our mathematical model will be employed to test the efficacy of an aptamer based proximity-dependent ligation assay (PLA) in the detection of biomarkers. The proximity dependent ligation assay is an extension to the traditional immunoassay and can be used for protein detection with high specificity and sensitivity. The selectivity of the proximity dependent ligation assay is dramatically enhanced through the double recognition by two oligonucleotide-conjugated aptamers. We sought to optimize the aptamer-protein equilibria to promote the efficient and precise binding of the aptamer with the target molecule.

Methodology

Using Wolfram Mathematica 10.4, a symbolic mathematical computation program, we will evaluate the minimum Gibbs Free Energy (G) of the aptamer-protein complex for different concentrations of the initial reactants: aptamer 1 ([A1]), aptamer 2 ([A2]), the connector oligonucleotide ([C]), and the target protein ([P]). By finding the minimum Gibbs Free Energy of the system, we will be able to find the concentrations of the final aptamer-protein complexes at chemical equilibrium. The possible aptamer protein complexes at chemical equilibrium include: unbound aptamer 1 [A1], unbound aptamer 2 [A2], unbound connector [C], unbound protein target [P], aptamer 1 and protein complex [A1P], aptamer 2 and protein complex [A2P], aptamer 1, aptamer 2, and protein complex [A1A2P], aptamer 1 and connector complex [A1C], aptamer 2 and connector complex [A2C],  aptamer 1, aptamer 2, and connector complex [A1A2C], aptamer 1, protein, and connector complex [A1PC], aptamer 2, protein, and connector complex [A2PC], and the aptamer 1, aptamer 2, protein and connector complex [A1A2PC]. By calculating the concentrations of the above aptamer-proteins complexes at chemical equilibrium at different initial concentrations of the reactants, we can optimize the aptamer-protein equilibria to promote the sensitivity of the aptamer in the presence of the target protein, while lowering the formation of an aptamer-protein complex when there is a lack of the target protein (non-specific reaction formation).

Assumptions


The ligation of aptamer 1 to the biomarker is independent to the ligation of aptamer 2 to the biomarker; in other words, the binding of an aptamer to the protein would not make the binding of the second aptamer less or more likely. Only one aptamer molecule may bind at a time to a target molecule. We are assume that gibbs free energy of the reaction at equilibrium of the reaction will never exactly be zero. The dozens of aptamer-protein dynamics will although approach zero, will not be exactly zero.