Team:Alberta

From 2009.igem.org

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<p>At present, the cost to synthesize DNA has been continually dropping and therefore its availability has been exponentially growing. However, the ability to put pieces of DNA together has not been able to keep up.  Present methods take a considerable amount of time to piece DNA together, making large constructs incredibly difficult to build. The University of Alberta 2009 iGEM team would like to introduce the BioBytes Chromosome Assembly System.  The method refers to a mechanism for rapid and reliable construction of plasmids (i.e. artificial gene sets) in vitro.  It allows for the assembly of components in hours rather than in days and we hope to see it become a valuable tool for any molecular biologist. Furthermore we have adapted our approach for Biofabrication by developing a robot which can use our method for automated assembly. Finally, microfluidics have been used to miniaturize construction allowing for additional validation for automated production of constructs.</p>
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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 align=right><p align=right><a href="https://2009.igem.org/Team:Alberta/Project/assemblyoverview"> Click here for more...</a> </P>
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<p>The method can be applied to numerous different applications. However, its greatest application is to the assembly of entire genomes. For this reason we have provided a detailed explanation on 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 genome.</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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<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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<b>BioBytes is the only method that is fast, modular, sequential and in vitro:</b></P>
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<ul>
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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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</ul>
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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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     <h2>The Minimal Genome Project</h2>
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     <h2>Organism Design and The Minimal Genome Project</h2>
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<font size="2"><P>The minimal <i>E. coli</i> genome has been a 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, in principle, preferred as a chassis for experimentation. To reduce the <i>E. coli</i> genome to roughly 10% of its original size shows a great simplification of this model organism.</P>
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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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<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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To create 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>. We then intend to remove the host chromosome by making it incapable of division. This allows only the artificial, inserted chromosome to propagate through multiple generations as the cells grow and divide. This is markedly different than 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 minimal <i>E. coli</i> genome.</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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     <h2>Our Team's Achievements</h2>
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     <h2>Team Achievements</h2>
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<font size="2"><P> Throughout our efforts we have made many accomplishments.  These include:</p>
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<font size="2"><P> Through our efforts we have made the following accomplishments:</p>
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<li>Developing the BioBytes Assembly Method and producing a proof of concept of the design
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<li>Developed the BioBytes Assembly Method and produced a proof of concept of the design
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<li>Adding a kit of components to the registry allowing for use of our system by anyone
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<li>A kit of components has been added to the registry allowing for use of our system by anyone
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<li>Producing a series of modeling programs which can be used to determine the essential genes in any organism
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<li>Produced a series of modeling programs which can be used to determine the essential genes in any organism
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<li>Amplifying 188 essential genes and their primers and adding them to the registry
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<li>185 essential genes have been amplified and their primers added to the registry
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<li>Developing a robot demonstrating the potential of automation for BioBytes
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<li>A robot has been developed demonstrating the potential of automation for BioBytes
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<li>Validating the method with use of microfluidics which can be used for Biofabrication
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<li>Used microfluidics to show the biofabrication potential of our design
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<li>Hosting a debate involving synthetic biology
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<li>We have hosted debates involving synthetic biology
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<li>Multiple presentations to discuss iGEM and encourage knowledge of 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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<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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