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://2012.igem.org/Team:BostonU"><img src="https://static.igem.org/mediawiki/2012/d/d5/Nightsky.gif" width="800px"></a></p>
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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>expanding a library of basic Level 0 MoClo parts by cloning from BioBrick parts and making new parts</li>
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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>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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<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://2012.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://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/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> 
 
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<li><a href="https://2012.igem.org/Team:BostonU/Methodology ">Methodology Overview</a></li>
 
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<li><a href="https://2012.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://2012.igem.org/Team:BostonU/Data">Data Collected</a></li>
 
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<li><a href="https://2012.igem.org/Team:BostonU/Parts">Parts Submitted</a></li>
 
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<li><a href="https://2012.igem.org/Team:BostonU/MoClo">MoClo Kit</a></li>
 
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<li><a href="https://2012.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://2012.igem.org/Team:BostonU/Protocols">Protocols</a></li>
 
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<li><a href="https://2012.igem.org/Team:BostonU/Clotho">Clotho and Eugene</a></li>
 
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<li><a href="https://2012.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://2012.igem.org/Team:BostonU/Human Practices">Human Practices</a></li>
 
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<li><a href="https://2012.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://2012.igem.org/Team:BostonU/Collaborations">Collaborations</a></li>
 
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                    <li><a href="https://2012.igem.org/Team:BostonU/Acknowledgements">Acknowledgements</a></li>
 
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<a href="https://2012.igem.org/Team:BostonU/Social">Summer Fun</a>
 
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<a href="https://2012.igem.org/Team:BostonU/Project_Overview">Project Overview and Abstract</a>
 
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<br>
 
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<a href="https://2012.igem.org/Team:BostonU/Characterization">Introduction to Characterization</a>
 
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<a href="https://2012.igem.org/Team:BostonU/Methodology ">Methodology Overview</a>
 
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<h7><p dir="ltr">We're pleased to announce that our team has advanced to the World Championship Jamboree that will be held at MIT in November!</h7>
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<left>The scope of synthetic biology is limitless, but there are challenges within the field that slow progress.  One of these major aspects is the ability to accurately predict the function of genetic circuits. The ideal goal is to have basic parts available with their functions  well characterized which then can be combined to create genetic circuits with complex behavior. <p>
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<p>This year, the BU iGEM team aims to introduce not only a standardized method for the characterization of genetic circuits in synthetic biology but also a new method for cloning in iGEM called MoClo <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016765">(Weber et al., 2011)</a>. In order to achieve this goal we are working on converting various BioBrick parts into MoClo parts, which we will make available for future iGEM teams to use.  We are focusing on building a vast number of both simple and complex genetic circuits manually and automatically with a liquid handling robot using the principles of MoClo, and then characterizing these circuits using various methodologies, including flow cytometry. <p>
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<p>A further goal for us is to create a standardized data sheet to be included in the parts registry for each part submitted and characterized, thus allowing anyone who would like to use the parts to have a comprehensive understanding of the behaviors of the parts.<p>
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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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