Team:BostonU

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<h11><center>Fuse, or Die: The Case for the MoClo Revolution</center></h11>
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      <a href="https://2013.igem.org/Team:BostonU/Project_Overview">
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<p  style="text-align:center;"><a href="https://2013.igem.org/Team:BostonU"><img src="https://static.igem.org/mediawiki/2012/f/f0/GreenLine.png" width="800px"></a></p>
 
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<li><a href="#">Our Team</a>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Team">Team</a></li>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Social">Summer Fun</a></li>
 
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<li><a href="#">Project</a>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Project_Overview">Project Overview and Abstract</a></li>
 
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                        <li><a href="https://2013.igem.org/Team:BostonU/MoClo2">Introduction to MoClo</a></li>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Characterization">Introduction to Characterization</a></li>
 
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                        <li><a href="https://2013.igem.org/Team:BostonU/DataSheet">Introduction to Data Sheets</a></li> 
 
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<li><a href="https://2013.igem.org/Team:BostonU/Methodology ">Methodology Overview</a></li>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Results ">Results Summary</a></li>
 
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<li><a href="#">Achievements</a>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Data">Data Collected</a></li>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Parts">Parts Submitted</a></li>
 
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<li><a href="https://2013.igem.org/Team:BostonU/MoClo">MoClo Kit</a></li>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Gold">Medal Fulfillment</a></li>
 
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<li><a href="#">Notebook</a>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Protocols">Protocols</a></li>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Clotho">Clotho and Eugene</a></li>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Notebook">Weekly Notebook</a></li>
 
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<li><a href="#">Considerations</a>
 
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<li><a href="https://2013.igem.org/Team:BostonU/NEGEM">New England iGEM Regional Meeting</a></li>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Human Practices">Human Practices</a></li>
 
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<li><a href="https://2013.igem.org/Team:BostonU/Safety">Safety</a></li>
 
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<li><a href="#">Acknowledgements</a>
 
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                    <li><a href="https://2013.igem.org/Team:BostonU/Collaborations">Collaborations</a></li>
 
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                    <li><a href="https://2013.igem.org/Team:BostonU/Acknowledgements">Acknowledgements</a></li>
 
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<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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<h7><p>Synthetic biology exists more as a form of art than a reproducible, well-defined production chain. From laboratory to laboratory, the experiments vary in procedure, characterization, and yield. The main product of synthetic biology — engineered organisms, are available only to the highly-experienced researcher and are not without the costs of timely preparation and low product yield. Consequently, the lack of standardization across the field has impeded the product from ever reaching a wide industry audience. More recent engineering efforts in the assembly of gene circuits has provided a pathway to a modular view of genetic parts. Termed the Modular Cloning Assembly Method (MoClo), this novel single-pot reaction protocol is a time-efficient, two-enzyme system for DNA assembly <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016765">(Weber et al., 2011)</a>. Before MoClo can reach its full potential across research and industry interests, the synthetic biology community needs a standardized and well-characterized library of MoClo parts for <i>Escherichia coli</i> to enable protocol automation and informed device designing. The 2013 Boston University iGEM Team seeks to bridge this gap in the product development chain by building a standard library and characterizing the parts via flow cytometry. To further efforts to develop foundational advancements for synthetic biology, we are taking a multi-faceted approach and working at several aspects and levels of design automation by:</p>
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<li><a href="https://2013.igem.org/Team:BostonU/MoClo2">Building:</a> Build Genetic Circuits with MoClo Parts
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<li>expanding a library of basic Level 0 MoClo parts by cloning from BioBrick parts and making new parts</li>
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<li><a href="https://2013.igem.org/Team:BostonU/Characterization">Characterizing:</a> Characterize Circuits using Flow Cytometry
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<li>building a library of composite Level 1 and 2 devices to characterize promoter-5' Untranslated Region combinations and demonstrate the library's usefulness</li>
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<li><a href="https://2013.igem.org/Team:BostonU/DataSheet">Sharing:</a> Generate Data Sheet for MoClo Parts</ul>
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<li>providing feedback on Clotho 2.0 software tools including the EugeneCAD language to a team of developers in the <a href="http://wiki.bu.edu/ece-cidar/index.php/Main_Page">CIDAR Lab</a></li>
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<li>working with the <a href="https://2013.igem.org/Team:Wellesley_Desyne">Wellesley Desyne</a> team to develop an easy-to-use visualized programming language to wrap around Eugene</li>
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<li>continuing the <a href="https://2012.igem.org/Team:BostonU/DataSheet">Datasheet project from the 2012 BostonU team</a> by finalizing a format for sharing information with <a href="https://2013.igem.org/Team:Purdue">Purdue Biomaker's iGEM Team</a> and programming a web app to generate the standardized datasheets</li>
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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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<h4>Abstract</h4>
 
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<h9>Authors</h9>
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<h6><center>Our Sponsors</center></h6><br>
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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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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 03:46, 28 September 2013



Fuse, or Die: The Case for the MoClo Revolution



Synthetic biology exists more as a form of art than a reproducible, well-defined production chain. From laboratory to laboratory, the experiments vary in procedure, characterization, and yield. The main product of synthetic biology — engineered organisms, are available only to the highly-experienced researcher and are not without the costs of timely preparation and low product yield. Consequently, the lack of standardization across the field has impeded the product from ever reaching a wide industry audience. More recent engineering efforts in the assembly of gene circuits has provided a pathway to a modular view of genetic parts. Termed the Modular Cloning Assembly Method (MoClo), this novel single-pot reaction protocol is a time-efficient, two-enzyme system for DNA assembly (Weber et al., 2011). Before MoClo can reach its full potential across research and industry interests, the synthetic biology community needs a standardized and well-characterized library of MoClo parts for Escherichia coli to enable protocol automation and informed device designing. The 2013 Boston University iGEM Team seeks to bridge this gap in the product development chain by building a standard library and characterizing the parts via flow cytometry. To further efforts to develop foundational advancements for synthetic biology, we are taking a multi-faceted approach and working at several aspects and levels of design automation by:

  • expanding a library of basic Level 0 MoClo parts by cloning from BioBrick parts and making new parts
  • building a library of composite Level 1 and 2 devices to characterize promoter-5' Untranslated Region combinations and demonstrate the library's usefulness
  • providing feedback on Clotho 2.0 software tools including the EugeneCAD language to a team of developers in the CIDAR Lab
  • working with the Wellesley Desyne team to develop an easy-to-use visualized programming language to wrap around Eugene
  • continuing the Datasheet project from the 2012 BostonU team by finalizing a format for sharing information with Purdue Biomaker's iGEM Team and programming a web app to generate the standardized datasheets

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