Team:RHIT/Outreach

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<h4>Introduction</h4><br />
<p>Throughout the summer, Rose-Hulman iGEM has been collaborating with <a href="https://2012.igem.org/Team:NTNU_Trondheim">NTNU Trondheim</a>. The teams found each other by luck when a speaker came to Rose-Hulman to meet with students participating in a math REU and talk about network modeling. This speaker was Eivind Almaas, NTNU’s iGEM main advisor.
<p>Throughout the summer, Rose-Hulman iGEM has been collaborating with <a href="https://2012.igem.org/Team:NTNU_Trondheim">NTNU Trondheim</a>. The teams found each other by luck when a speaker came to Rose-Hulman to meet with students participating in a math REU and talk about network modeling. This speaker was Eivind Almaas, NTNU’s iGEM main advisor.
After touching base with our lead advisor, Dr. Anthony, Dr. Almaas provided us with great perspective about being a starting iGEM team because his team was in the same position last year.
After touching base with our lead advisor, Dr. Anthony, Dr. Almaas provided us with great perspective about being a starting iGEM team because his team was in the same position last year.
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We hope that this newly found friendship will continue throughout the years and that we will be lucky enough to meet the whole team in person this November.</p>
We hope that this newly found friendship will continue throughout the years and that we will be lucky enough to meet the whole team in person this November.</p>
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<h4>Rose-Hulman's Dr. Ric Anthony (left) with NTNU's Dr. Almaas at their June meeting on the Rose-Hulman campus.</h4>
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<h4>Rose-Hulman's Dr. Ric Anthony (left) with NTNU's Dr. Almaas at their June meeting on the Rose-Hulman campus.</h4><br /><br />
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<h4>Promoter Characterization</h4><br />
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<p>Our NTNU colleagues requested help characterizing the Lld promoter they cloned from E. coli. strain K12. We received the promoter as a 373 bp EcoRI-SpeI fragment cloned into pSB1C3. The fragment was sequenced in both directions using primers VF2 (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_G00100">BBa_G00100</a>) and VR (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_G00101">BBa_G00101</a>). The sequence obtained matched that which was expected and is given in the Registry (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K822000">BBa_K822000</a>).</p><br />
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<p>We then used standard BioBrick construction methods to clone the EcoRI-SpeI promoter fragment into the EcoRI-XbaI sites upstream of the cyan fluorescent protein cloned into pSB1A3 (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_E0422">BBa_E0422</a>). The putative construct was verified by restriction digest analysis and sequenced in both directions using primers VF2 and VR to validate the expected sequence.</p><br/ >
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<p>NEB5alpha cells harboring the reporter construct were spread on LB plates supplemented with 100 mM lithium lactate and incubated at 37 C. The plates were monitored over a 36 hour period and showed no fluorescence. Similar experiments using liquid media and a spectrofluorometer for measurement also indicated no fluorescence.</p><br />
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Revision as of 00:19, 4 October 2012

Home
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NTNU Collaboration

Terre Haute Children's Museum Synthetic Biology Exhibit


Origins of the Project

The Terre Haute Children's Museum, founded in 1988, features many exhibits on topics ranging from archaeology to architecture. However, the Rose-Hulman team noticed that there are no exhibits on small-scale biology, specifically synthetic biology. Devon and Kristen then took on the project of creating an exhibit to introduce children to the concepts and methods of synthetic biology. The team felt that one of the best ways to get kids interested in synthetic biology was to show them lab equipment that they could touch and play with. The exhibit also gives kids a chance to explore designing DNA sequences. In this way, they can experience a process that synthetic biologists go through.

Exhibit Components

The Design Table, pictured below, introduces children to the idea of putting together DNA sequences. The instructions on the table ask them to think of ways they would use synthetic biology if they could make cells "do anything." The team hopes that this will inspire them to use creativity to explore the possibilities of synthetic biology. Colored magnetic shapes are used to represent DNA. Children can select from different colors, each with a different purpose - the four DNA nucleotide bases, A, T, G, and C, as well as Promoters and Terminators - and align them on the board to create their sequence. They also have the option of putting together various sequences found on cards on the table or create the matching sequence to given DNA sequences. This gives more uncertain children the chance to understand the process. Examples of these cards are seen below.



After creating their sequence, the children move on to the Lab Bench, where they explore four different pieces of lab equipment. The four stations are:

  • Microscope
  • Centrifuge
  • Pipetting
  • Media Plates
    • Each station provides a description of the equipment as well as a procedure for the children to follow in order to gain experience with and understanding of the technology. Questions guide the children along the way and encourage them to think about the purpose or design of each piece of equipment.

    BioPioneer: Synthetic Biology

    Overview

    With goal of education in mind, the RHIT team developed a board game that teaches its participants as they play it. The game is called BioPioneer: Synthetic Biology. Players try to solve major world problems by selecting one of five laboratories, each having a special laboratory technique. Every player has to meet the world problem’s requirements while obtaining the correct DNA sequence that will code for the solution to the problem. Players take turns hiring people, buying equipment, and producing papers to help grow the knowledge pool and capabilities of the lab. The game was designed to incorporate actual procedures, resources, and equipment that are used in synthetic biology, creating a realistic laboratory experience.



    Educational Ties

    The main focus of the board game is education through fun. The game was designed to be intriguing and interactive, but still involve a large portion of strategy. Through the wide array of techniques, equipment, and paper combinations, players can find a play style that fits their personality. This will link to players to the game and will lead players not familiar with synthetic biology to search deeper about what it is. To help facilitate this, an educational pamphlet with simple descriptions will be included with the board game that has simple descriptions of terms and processes and how they apply to synthetic biology.



    What makes this game different from many other games out there is how realistic the gameplay is to the actual science. The creation of sequence is analogous to the actual process that biologists use for plasmid design. The shapes signify different DNA sequences that code for different functional units, whereas the colors represent the different choices between the available units with similar function. For example, there are many different types of restriction sites that can be used, but in order to follow certain protocols a specialized site is selected for use.



    In addition, the idea of limited resources plays a vital role in teaching players about how research is done. Actions are determined by the number of people in your lab, but become useless when there is nothing to spend the actions on. Following the same lines, a player can have all of the pieces of equipment with no one in the lab to work them. These both show the importance of keeping the size of laboratories manageable to optimize production of advancements. Finally, papers in the game help players to obtain pieces of equipment and lab members, showing that the knowledge pool of the laboratory must be kept up to date in order to be successful.



    Gameplay

    The goal of Bio-Pioneer is to solve the World Problem through the use of synthetic biology. To do so, your lab must achieve all prerequisites of the World Problem, synthesize your DNA sequence, and reach the Knowledge Pool Requirement of the World Problem.



    Each player selects the lab of their choice. Every lab has a unique technique found in synthetic biology. Each player then collects the starting resources found on their Lab Play Mat and places their Lab token on the start location of the game board.



    A turn consists of the following phases:

    1. Movement and Shape Card Selection Phase
    2. Lab Personnel and Equipment Phase
    3. World Problem Phase


    Players acquire cards during the first phase, modify them and add to their lab during the second, and try to win during their third. The key to winning the game is using the equipment, techniques, and actions to their fullest capability.



    Sample Game Pieces


    Game Board


    World Problem Cards


    Equipment Cards

    Introduction


    Throughout the summer, Rose-Hulman iGEM has been collaborating with NTNU Trondheim. The teams found each other by luck when a speaker came to Rose-Hulman to meet with students participating in a math REU and talk about network modeling. This speaker was Eivind Almaas, NTNU’s iGEM main advisor. After touching base with our lead advisor, Dr. Anthony, Dr. Almaas provided us with great perspective about being a starting iGEM team because his team was in the same position last year. He suggested that we should video conference in the near future.


    On 7/23/2012, the two teams met for the first time via video conferencing to talk about their projects and to offer advice to the other team. In efforts to help each other out, RHIT agreed to help to characterize their lactate promote. In exchange, the NTNU team agreed to help critique our Mathematical Model and produce a stochastic model. We hope that this newly found friendship will continue throughout the years and that we will be lucky enough to meet the whole team in person this November.

    Rose-Hulman's Dr. Ric Anthony (left) with NTNU's Dr. Almaas at their June meeting on the Rose-Hulman campus.



    Promoter Characterization


    Our NTNU colleagues requested help characterizing the Lld promoter they cloned from E. coli. strain K12. We received the promoter as a 373 bp EcoRI-SpeI fragment cloned into pSB1C3. The fragment was sequenced in both directions using primers VF2 (BBa_G00100) and VR (BBa_G00101). The sequence obtained matched that which was expected and is given in the Registry (BBa_K822000).


    We then used standard BioBrick construction methods to clone the EcoRI-SpeI promoter fragment into the EcoRI-XbaI sites upstream of the cyan fluorescent protein cloned into pSB1A3 (BBa_E0422). The putative construct was verified by restriction digest analysis and sequenced in both directions using primers VF2 and VR to validate the expected sequence.


    NEB5alpha cells harboring the reporter construct were spread on LB plates supplemented with 100 mM lithium lactate and incubated at 37 C. The plates were monitored over a 36 hour period and showed no fluorescence. Similar experiments using liquid media and a spectrofluorometer for measurement also indicated no fluorescence.


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