Team:BostonU

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<h1><center>Fuse, or Die: The Case for MoClo</center></h1>
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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. Destabilization: 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 output. 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 protocol constructs all sorts of products and reduces the workload of the researcher by adopting a single-pot reaction approach &nbsp;<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016765">(Weber et al., 2011)</a>. Before the products can be mass produced and widely available, the synthetic biology community needs a standardized and well-characterized library of MoClo parts for <i>Escherichia coli</i>. The 2013 Boston University iGEM seeks to bridge this gap in the product development chain by building such standard library and characterizing the parts through flow cytometry.</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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<p>We envision that synthetic biology can be viewed as any other industry. With the right engineering, it can reach its full potential as a tool for improving society across many pressing and global concerns. It is our hope that the process is eventually fully automated and standardized across the synthetic biology community. In order to promote this end-goal, we will be working with other members of Dr. Douglas Densmore&rsquo;s CIDAR Lab Group to test protocols on a liquid-handling robot (TECAN) and providing feedback on Clotho 2.0 software tools, the Eugene CAD language, RavenCAD, and BBN Technologies&rsquo;s TASBE Data Analysis Program. Furthermore, we are working with Wellesley College&rsquo;s Human-Computer Interaction (HCI) team to develop an easy-to-use visualized programming language to wrap around Eugene. We are currently talking with the Purdue iGEM team to coordinate flow cytometry protocols for <i>E. coli</i> systems in an effort to standardize and optimize the flow cytometry experiments.
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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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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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