Team:BostonU

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<h11><center>Fuse, or Die: The Case for the MoClo Revolution</center></h11>
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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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<p  style="text-align:center;"><a href="https://2013.igem.org/Team:BostonU"><img src="https://static.igem.org/mediawiki/2013/2/2c/Marsh.png" width="800px" length="200px"></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/MoCloChara">Introduction to MoClo and Characterization</a></li>
 
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                        <li><a href="https://2013.igem.org/Team:BostonU/QS">Quorum Sensing</a></li>
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                        <li><a href="https://2013.igem.org/Team:BostonU/ML">MoClo Library</a></li>
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                        <li><a href="https://2013.igem.org/Team:BostonU/DataSheet">Data Sheets App</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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<h6><center>Our Sponsors</center></h6><br>
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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/PR">Pigeon and Raven</a></li>
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<li><a href="https://2013.igem.org/Team:BostonU/NotebookQS">Quorum Sensing Notebook</a></li>
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                        <li><a href="https://2013.igem.org/Team:BostonU/NotebookML">MoClo Library Notebook</a></li>
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                        <li><a href="https://2013.igem.org/Team:BostonU/TroubleShooting">Trouble Shooting</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="#">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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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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