Team:BostonU/Project Overview

From 2013.igem.org

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In order for synthetic biologists to be able to use automation technologies, we need a well-characterized library of basic biological components that can then be used to design more complex systems. MoClo is a one-pot digestion-ligation assembly technique developed by Weber in 2011, which enables faster and more efficient construction of genetic circuits when compared to BioBricks, the current iGEM standard. With our project, we are proposing that iGEM teams replace the inefficient BioBricks format with MoClo. We have expanded our library of basic MoClo DNA Parts and characterized devices using various promoter-RBS combinations via flow cytometry. We also designed and implemented a standardized data sheet with a JavaScript software program in order to easily share our library and data with the community. Our MoClo library, characterization data, and data sheet tool fill an essential role in the implementation of automated synthetic biology protocols.</h7>
In order for synthetic biologists to be able to use automation technologies, we need a well-characterized library of basic biological components that can then be used to design more complex systems. MoClo is a one-pot digestion-ligation assembly technique developed by Weber in 2011, which enables faster and more efficient construction of genetic circuits when compared to BioBricks, the current iGEM standard. With our project, we are proposing that iGEM teams replace the inefficient BioBricks format with MoClo. We have expanded our library of basic MoClo DNA Parts and characterized devices using various promoter-RBS combinations via flow cytometry. We also designed and implemented a standardized data sheet with a JavaScript software program in order to easily share our library and data with the community. Our MoClo library, characterization data, and data sheet tool fill an essential role in the implementation of automated synthetic biology protocols.</h7>
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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.
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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-effiecient, two-enzyme system for DNA assembly.  &nbsp;<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 such a standard library and characterizing the parts through 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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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 off of BioBrick parts and making new parts</li>
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<li> building a library of composite (Level 1 and 2) parts to characterize promoter-RBS 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="cidar.bu.edu">CIDAR</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> working with the CIDAR group to design protocols for a TECAN liquid-handling robot</li>
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<li> continuing the <a href="https://2012.igem.org/Team:BostonU/DataSheet">Data Sheet 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 Data Sheets</li>
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This year's work on these projects bring us closer to a more complete MoClo/Clotho platform for designing devices with software, constructing more complex devices in the wetlab by hand or with a liquid-handling robot, and sharing characterization data.
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Revision as of 14:07, 4 September 2013



Abstract

In order for synthetic biologists to be able to use automation technologies, we need a well-characterized library of basic biological components that can then be used to design more complex systems. MoClo is a one-pot digestion-ligation assembly technique developed by Weber in 2011, which enables faster and more efficient construction of genetic circuits when compared to BioBricks, the current iGEM standard. With our project, we are proposing that iGEM teams replace the inefficient BioBricks format with MoClo. We have expanded our library of basic MoClo DNA Parts and characterized devices using various promoter-RBS combinations via flow cytometry. We also designed and implemented a standardized data sheet with a JavaScript software program in order to easily share our library and data with the community. Our MoClo library, characterization data, and data sheet tool fill an essential role in the implementation of automated synthetic biology protocols.

Project Overview

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-effiecient, 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 such a standard library and characterizing the parts through 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 off of BioBrick parts and making new parts
  • building a library of composite (Level 1 and 2) parts to characterize promoter-RBS 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
  • working with the Wellesley Desyne team to develop an easy-to-use visualized programming language to wrap around Eugene
  • working with the CIDAR group to design protocols for a TECAN liquid-handling robot
  • continuing the Data Sheet 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 Data Sheets

This year's work on these projects bring us closer to a more complete MoClo/Clotho platform for designing devices with software, constructing more complex devices in the wetlab by hand or with a liquid-handling robot, and sharing characterization data.

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