Team:BostonU/Project Overview

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The growth in interest and potential applications of synthetic biology necessitates more efficient methods for developing an idea from conception to a realized product. The integration of design automation into the planning, execution, and sharing of synthetic biology products provides a solution that could easily translate into the industrialization of synthetic biology; in order for the synthetic biologists to be able to use automation technologies, we will ultimately need a well-characterized library of biological components in order to have a basis for designing more complex systems. Currently, synthetic biologists either work from scratch, cloning their own parts, or use the inefficient BioBrick assembly method to assemble parts from the Biobrick registry, which often lacks characterization data and a standard format.We expanded the  library for a more efficient assembly method, characterized the parts, and organized the data in a standardized data sheet for distribution.Using the modular cloning (MoClo) assembly method, we constructed a library of bacterial promoters and ribosomal-binding sites, then constructed devices with fluorescent proteins to characterize the promoter-RBS combinations via flow cytometry and designed standard data sheets for the parts with a javascript software program. The library, characterization data, and data sheets fill an essential role in the implementation of automated synthetic biology protocols which will pave the way to industrialized synthetic biology products.</p></h7>
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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 <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016765">(Weber et al., 2011)</a>, which enables faster and more efficient construction of genetic circuits compared to BioBricks, the current iGEM standard. With our project, we are proposing that iGEM teams replace the inefficient BioBricks cloning method with MoClo. We have expanded our library of basic MoClo DNA Parts and characterized devices using various promoter-5' Untranslated Region combinations via flow cytometry. We also are designing and implementing a standardized data sheet using Java and JavaScript 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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<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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<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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<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>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 wet laboratory by hand or with a liquid-handling robot, and sharing characterization data.</p>
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Latest revision as of 01:15, 28 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 et al., 2011), which enables faster and more efficient construction of genetic circuits compared to BioBricks, the current iGEM standard. With our project, we are proposing that iGEM teams replace the inefficient BioBricks cloning method with MoClo. We have expanded our library of basic MoClo DNA Parts and characterized devices using various promoter-5' Untranslated Region combinations via flow cytometry. We also are designing and implementing a standardized data sheet using Java and JavaScript 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-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

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 wet laboratory by hand or with a liquid-handling robot, and sharing characterization data.

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