Team:BostonU/Project Overview

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<li><a href="https://2012.igem.org/Team:BostonU/Project_Overview">Project Overview and Abstract</a></li>  
<li><a href="https://2012.igem.org/Team:BostonU/Project_Overview">Project Overview and Abstract</a></li>  
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<li><a href="https://2012.igem.org/Team:BostonU/Characterization">Introduction to Characterization</a></li>  
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                        <li><a href="https://2012.igem.org/Team:BostonU/MoClo2">Introduction to MoClo</a></li>
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<li><a href="https://2012.igem.org/Team:BostonU/Characterization">Introduction to Characterization</a></li>
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                        <li><a href="https://2012.igem.org/Team:BostonU/DataSheet">Introduction to Data Sheets</a></li> 
<li><a href="https://2012.igem.org/Team:BostonU/Methodology ">Methodology Overview</a></li>  
<li><a href="https://2012.igem.org/Team:BostonU/Methodology ">Methodology Overview</a></li>  
<li><a href="https://2012.igem.org/Team:BostonU/Results ">Results Summary</a></li>  
<li><a href="https://2012.igem.org/Team:BostonU/Results ">Results Summary</a></li>  
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<li><a href="#">Considerations</a>  
<li><a href="#">Considerations</a>  
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<li><a href="https://2012.igem.org/Team:BostonU/Advancement">Synthetic Biology Advancement</a></li>  
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<li><a href="https://2012.igem.org/Team:BostonU/NEGEM">New England iGEM Regional Meeting</a></li>
<li><a href="https://2012.igem.org/Team:BostonU/Human Practices">Human Practices</a></li>  
<li><a href="https://2012.igem.org/Team:BostonU/Human Practices">Human Practices</a></li>  
<li><a href="https://2012.igem.org/Team:BostonU/Safety">Safety</a></li>
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<h4>Project Overview</h4>
<h4>Project Overview</h4>
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Our project has two major goals: 1. To introduce MoClo as an alternative assembly method for use by iGEM teams and 2. To develop a standard protocol for the characterization of genetic circuits containing fluorescent proteins and share this protocol with the synthetic biology community.
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In order to achieve these goals, there many steps must be taken. First, we must convert BioBrick Parts into MoClo Parts using PCR. Upon converting basic parts, our project will have three thrusts:
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<li><a href="https://2012.igem.org/Team:BostonU/MoClo2">Building:</a> Build Genetic Circuits with MoClo Parts
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<li><a href="https://2012.igem.org/Team:BostonU/Characterization">Characterizing:</a> Characterize Circuits using Flow Cytometry
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<li><a href="https://2012.igem.org/Team:BostonU/DataSheet">Sharing:</a> Generate Data Sheet for MoClo Parts</ul>
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<h3>SAFETY OVERVIEW
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Despite the great expansibility potential of the synthetic biology, the productions of unwilling genetically modified organisms (GMOs) are the main obstacle that slows down the expansion of SynBio. For this concern, safety in environment is the very first issue when scientists come up with a new project. In the case of studying on the assays that involve in vivo media or include biological components, this safety issue becomes necessary. Considering the media that we aim to use in our first module, the possibility of the production of GMO through the conjugation or horizontal gene transfer must be taken into account.
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As we worked towards our first goal over the summer months, we ran into difficulties with some of our PCR and cloning reactions. This has unfortunately delayed our other goals, but we're still working hard towards generating a characterization workflow and a MoClo data sheet format for the Jamboree.  
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Regarding all of these, we designed a third module in our project that poses a promising solution for involuntary GMO production. Halorhodopsin is an ion channel that is activated by direct emission of light. After activation, it transfers chloride ions into the cell. In our design, we aim to use this mechanism to induce our chloride inducible promoter system which we plan to use as a second mechanism to produce bacterium lysis device. Thus, we intend to induce a self-destruction throughout our bacteria by emitting light.  
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<h4>Abstract</h4>
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<h9>Title</h9>
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<p dir="ltr">Abandon All Hope, Ye Who PCR: MoClo and the Quest for Genetic Circuit Characterization</h6>
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<h9>Authors</h9>
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<p dir="ltr">Monique De Freitas&#185;, Shawn Jin&#185;, Evan Appleton&#178;, Swati Carr&#178;, Sonya Iverson&#178;, Traci Haddock&#179;, and Douglas Densmore<SUP>&#167;</SUP></h7>
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<h9>Affiliations</h9>
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<p dir="ltr">&#185;iGEM Team Member, &#178;iGEM Team Mentor, &#179;iGEM Team Advisor, <SUP>&#167;</SUP>Faculty Sponsor,  Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA</h7>
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The first module aims to detect the possible circulating tumor cells (CTC) in the bloodstream. However, to be able to identify the presence of CTC through synthetic biology approach, we would need to amplify the signal with a second mechanism due to the prospective weak signal yield of the first module. Hence, we designed an enrichment system to solve this problem. LuxR/AHL duo is one of the main components of quorum sensing mechanism in bacteria. We plan to link this complex to the induction system by TEV protease which we intend to use in the first module. Therefore, the CTC detector bacterium becomes a “sender” to induce a chain reaction for signal amplification. The “message”, which features the knowledge of the detection of CTC, activates the “receiver” system in the rest of the bacteria in the media which ends up with a serial production of signaling molecules. (Here we want to use fluorescent proteins, LacZ and XylE.)
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Our project has three aims: to introduce MoClo as an alternative assembly technique to BioBricks, to develop a standardized protocol for the characterization of genetic circuits using flow cytometry, and to share our MoClo Kit with the iGEM community. MoClo is an assembly technique developed by <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016765"> Weber et al., 2011</a>, which involves a multi-way, one-pot digestion-ligation reaction, enabling faster and more efficient construction of genetic circuits. We converted a large subset of BioBricks from the <a href="http://partsregistry.org/Main_Page">Registry</a> into MoClo Parts using PCR and cloning strategies. We are in the process of building and characterizing various genetic circuits using MoClo Parts, which we will compare to their BioBrick counterparts. A characterization workflow will be shared once this is complete. We also developed a data sheet using Clotho to be included in the Registry of Standard Biological Parts for each Part we characterized to easily share our data with the synthetic biology community.  
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Latest revision as of 20:08, 25 October 2012

BostonU iGEM Team: Welcome


Project Overview


    Our project has two major goals: 1. To introduce MoClo as an alternative assembly method for use by iGEM teams and 2. To develop a standard protocol for the characterization of genetic circuits containing fluorescent proteins and share this protocol with the synthetic biology community.

    In order to achieve these goals, there many steps must be taken. First, we must convert BioBrick Parts into MoClo Parts using PCR. Upon converting basic parts, our project will have three thrusts:


    As we worked towards our first goal over the summer months, we ran into difficulties with some of our PCR and cloning reactions. This has unfortunately delayed our other goals, but we're still working hard towards generating a characterization workflow and a MoClo data sheet format for the Jamboree.

Abstract


Title

    Abandon All Hope, Ye Who PCR: MoClo and the Quest for Genetic Circuit Characterization


Authors

    Monique De Freitas¹, Shawn Jin¹, Evan Appleton², Swati Carr², Sonya Iverson², Traci Haddock³, and Douglas Densmore§


Affiliations

    ¹iGEM Team Member, ²iGEM Team Mentor, ³iGEM Team Advisor, §Faculty Sponsor, Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA


Abstract

    Our project has three aims: to introduce MoClo as an alternative assembly technique to BioBricks, to develop a standardized protocol for the characterization of genetic circuits using flow cytometry, and to share our MoClo Kit with the iGEM community. MoClo is an assembly technique developed by Weber et al., 2011, which involves a multi-way, one-pot digestion-ligation reaction, enabling faster and more efficient construction of genetic circuits. We converted a large subset of BioBricks from the Registry into MoClo Parts using PCR and cloning strategies. We are in the process of building and characterizing various genetic circuits using MoClo Parts, which we will compare to their BioBrick counterparts. A characterization workflow will be shared once this is complete. We also developed a data sheet using Clotho to be included in the Registry of Standard Biological Parts for each Part we characterized to easily share our data with the synthetic biology community.



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