Team:Alberta

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     <h1>RE. coli</h1>
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     <h1>BioBytes</h1>
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<p>Synthetic biology needs more than minor modifications to existing evolutionary plans. We’ve developed a method of gene assembly allowing complete genome re-design. The speed and automation of the Biobytes method makes possible the maximization of modularity on a grand scale. Imagine a synthetic genome grouping common pathway components and components with similar levels of expression. This degree of organism control would be a milestone marking synthetic biology as a mature field. The Biobytes method of gene assembly allows us to efficiently test, optimize and correct genome scale design principles. </p>
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<p>There are currently two alternatives for gene assembly. The first, BioBricks, is modular but slow. The second, the use of unique long sticky ends for each piece, is fast but non-modular. </p>
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<b>BioBytes is the only method that is fast, modular, sequential and in vitro:</b></P>
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<li> <b>Fast: </b> The addition of each DNA segment takes only 20min, a roughly 200-fold increase in speed from traditional cloning. Moreover, we’ve demonstrated that the Biobytes method is automatable and can be performed on microfluidic chips.</li>
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<li> <b> Modular: </b> Our method allows standard parts such as the backbone plasmids and USER primers to be reused, greatly reducing expenses for large scale projects. Once parts are in pAB or pBA, they can be rapidly assembled in any order, allowing easy testing of alternative designs.  </li>
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<li><b>Sequential: </b> Biobytes allows tight control over the order of gene assembly. New DNA segments can add only to the unanchored end, and in only one orientation. Moreover, using two different sets of complementary ends prevents concatamerization of parts before assembly.  </li>
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<li><b>In vitro: </b>Using an organism as an intermediate is time-consuming and limits one’s ability to control and assess the changes being made. For this reason, an in vitro method such as Biobytes is essential. Genome-sized constructs can be transformed into an organism after construction is complete. </li>
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<p> Overall, the BioBytes method gives synthetic biology the tools to understand and organize complexity, standardize  robust parts, use modular strategies and rapidly test rational designs and computational models. With BioBytes we can start asking the most fundamental questions: to what extent do the rules of engineering hold true for biology? To what degree does life equal the sum of its parts?  </P>
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<p align=right><a href="https://2009.igem.org/Team:Alberta/Project/assemblyoverview"> Click here for more...</a> </P>
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    <div align="justify" style="padding-left:20px; padding-right:20px"><font size="2">Team RE. coli is the University of Alberta's 2009 International Genetically Engineered Machines (iGEM) team.  We are dedicated to the advancement of Synthetic Biology through the development of a reduced-genome model organism, Escherichia coli, via novel DNA assembly techniques.</font></div>
 
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<p>The BioBytes gene assembly method can be applied to numerous different applications, however, its greatest application is for the assembling of entire genomes.  For this reason we have provided a detailed explanation regarding the requirements of constructing a minimal genome including an in-silico method for identifying essential genes in any organism, and a theoretical design of replacing the host chromosome with the new synthetic genome.</p>
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  <div align="justify" style="padding-left:20px; padding-right:20px"><font size="2">Synthetic Biology sits at the interface between biology and engineering.  Its goal is to produce modular biological circuits of increasing sophistication and usefulness.  Its guiding principle is to avoid biochemical complexity in favour of well-understood, well-characterized, and well-behaved molecular components that can be reliably assembled in a variety of ways. Synthetic Biology sits at the interface between biology and engineering.  Its goal is to produce modular biological circuits of increasing sophistication and usefulness.  Its guiding principle is to avoid biochemical complexity in favour of well-understood, well-characterized, and well-behaved molecular components that can be reliably assembled in a variety of ways.</font></div>
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<BR><div align="justify" style="padding-left:20px; padding-right:20px"><font size="2">Remarkably, the rapid rise of "SynBio" to prominence has been catalysed by an international undergraduate competition held annually at the Massachusetts Institute of Technology (MIT) in Boston called the International Genetically Engineered Machines (iGEM) Jamboree.  At iGEM, student teams are evaluated not only on the originality and execution of their projects but also on a variety of other criteria that include: the ability to communicate complicated ideas effectively, adherence to ethical and legal principles, and the relevance of their work to real-world problems. This year our team will explore the extent to which E. coli can be driven by a simplified artificial chromosome that incorporates features of design that include modularity of gene organization, standardization of gene expression, and simplification of the genetic code. </font></div>
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<P>The minimal <i>Escherichia coli</i> genome has been the holy grail of biology for a number of years. <i>E. coli</i> is the most widely used cellular research tool by the molecular biology community. Since scientific research is based upon reductionism and simplification for understanding, a simplified version of an experimental model organism such as <i>E. coli</i> is ideally preferred as a chassis for experimentation. Reducing the <i>E. coli</i> genome to roughly 10% of its original size, demonstrates a great simplification of this model organism.</P>
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<p align=right><p align=right><a href="https://2009.igem.org/Team:Alberta/Project/Bioinformatics"> Click here for more...</a> </P>
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<P>
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To reconstruct such an organism, we plan on building an artificial <i>E. coli</i> chromosome using the BioBytes chromosome assembly system and inserting it into living <i>E. coli</i> cells. At the same time, the original host chromosome is displaced, effectively rebooting an <i>E.coli</i> cell with the synthetic chromosome. This is markedly different from the current, time-consuming method of knocking out inessential genes, one at a time, in an effort to produce the minimal genome. It is this difference that we hope to exploit in our attempt to win the race to produce the ideal model organism</p>
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<p align=right><p align=right><a href="https://2009.igem.org/Team:Alberta/Project/Chromosome_Assembly"> Click here for more...</a> </P>
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     <h1>University of Alberta</h1>
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     <h2>Team Achievements</h2>
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<div align="justify" style="padding-left:20px; padding-right:20px"><font size="2">The University of Alberta was founded in 1908 in Alberta's beautiful capital city: Edmonton.  On its 100th birthday it has proven to be one of the finest Universities in promoting excellence in a variety of scientific and humanities fields.  Through innovations and frontiers of knowledge and skills, the University of Alberta allows for global recognition of its talented student body.  It provides a challenging and exciting learning environment that applies new knowledge throughout all disciplines whether through teaching, research, or creative pursuits.</font></div>
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<font size="2"><P> Through our efforts we have made the following accomplishments:</p>
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<li>Developed the BioBytes Assembly Method and produced a proof of concept of the design
 +
<li>A kit of components has been added to the registry allowing for use of our system by anyone
 +
<li>Produced a series of modeling programs which can be used to determine the essential genes in any organism
 +
<li>185 essential genes have been amplified and their primers added to the registry
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<li>A robot has been developed demonstrating the potential of automation for BioBytes
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<li>Used microfluidics to show the biofabrication potential of our design
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<li>We have hosted debates involving synthetic biology
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<li>We have constructed and completed a series of presentations to discuss iGEM and promote knowledge of synthetic biology
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</ul>
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<p align=right><p align=right><a href="https://2009.igem.org/Team:Alberta/MedalRequirements"> Click here for more...</a> </P>
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Latest revision as of 03:59, 22 October 2009

University of Alberta - BioBytes










































































































BioBytes

Synthetic biology needs more than minor modifications to existing evolutionary plans. We’ve developed a method of gene assembly allowing complete genome re-design. The speed and automation of the Biobytes method makes possible the maximization of modularity on a grand scale. Imagine a synthetic genome grouping common pathway components and components with similar levels of expression. This degree of organism control would be a milestone marking synthetic biology as a mature field. The Biobytes method of gene assembly allows us to efficiently test, optimize and correct genome scale design principles.

There are currently two alternatives for gene assembly. The first, BioBricks, is modular but slow. The second, the use of unique long sticky ends for each piece, is fast but non-modular.

BioBytes is the only method that is fast, modular, sequential and in vitro:

  • Fast: The addition of each DNA segment takes only 20min, a roughly 200-fold increase in speed from traditional cloning. Moreover, we’ve demonstrated that the Biobytes method is automatable and can be performed on microfluidic chips.
  • Modular: Our method allows standard parts such as the backbone plasmids and USER primers to be reused, greatly reducing expenses for large scale projects. Once parts are in pAB or pBA, they can be rapidly assembled in any order, allowing easy testing of alternative designs.
  • Sequential: Biobytes allows tight control over the order of gene assembly. New DNA segments can add only to the unanchored end, and in only one orientation. Moreover, using two different sets of complementary ends prevents concatamerization of parts before assembly.
  • In vitro: Using an organism as an intermediate is time-consuming and limits one’s ability to control and assess the changes being made. For this reason, an in vitro method such as Biobytes is essential. Genome-sized constructs can be transformed into an organism after construction is complete.

Overall, the BioBytes method gives synthetic biology the tools to understand and organize complexity, standardize robust parts, use modular strategies and rapidly test rational designs and computational models. With BioBytes we can start asking the most fundamental questions: to what extent do the rules of engineering hold true for biology? To what degree does life equal the sum of its parts?

Click here for more...

Organism Design and The Minimal Genome Project

The BioBytes gene assembly method can be applied to numerous different applications, however, its greatest application is for the assembling of entire genomes. For this reason we have provided a detailed explanation regarding the requirements of constructing a minimal genome including an in-silico method for identifying essential genes in any organism, and a theoretical design of replacing the host chromosome with the new synthetic genome.

The minimal Escherichia coli genome has been the holy grail of biology for a number of years. E. coli is the most widely used cellular research tool by the molecular biology community. Since scientific research is based upon reductionism and simplification for understanding, a simplified version of an experimental model organism such as E. coli is ideally preferred as a chassis for experimentation. Reducing the E. coli genome to roughly 10% of its original size, demonstrates a great simplification of this model organism.

Click here for more...

To reconstruct such an organism, we plan on building an artificial E. coli chromosome using the BioBytes chromosome assembly system and inserting it into living E. coli cells. At the same time, the original host chromosome is displaced, effectively rebooting an E.coli cell with the synthetic chromosome. This is markedly different from the current, time-consuming method of knocking out inessential genes, one at a time, in an effort to produce the minimal genome. It is this difference that we hope to exploit in our attempt to win the race to produce the ideal model organism

Click here for more...

Team Achievements

Through our efforts we have made the following accomplishments:

  • Developed the BioBytes Assembly Method and produced a proof of concept of the design
  • A kit of components has been added to the registry allowing for use of our system by anyone
  • Produced a series of modeling programs which can be used to determine the essential genes in any organism
  • 185 essential genes have been amplified and their primers added to the registry
  • A robot has been developed demonstrating the potential of automation for BioBytes
  • Used microfluidics to show the biofabrication potential of our design
  • We have hosted debates involving synthetic biology
  • We have constructed and completed a series of presentations to discuss iGEM and promote knowledge of synthetic biology

Click here for more...

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