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>At present, the cost to synthesize oligonucleotides has been continually declining and therefore their availability is exponentially growing.  However, the current technique to ligate pieces of DNA together is outdated. 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.  This 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 a structured manner within hours rather than days. Our hope is to see this method 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 utilized to miniaturize construction allowing for additional validation for automated production of constructs.</p>
<p align=right><p align=right><a href="https://2009.igem.org/Team:Alberta/Project/assemblyoverview"> Click here for more...</a> </P>
<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>The 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>
<p align=right><p align=right><a href="https://2009.igem.org/Team:Alberta/Project/Bioinformatics"> Click here for more...</a> </P>
<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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<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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<font size="2"><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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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. We then intend to remove the host chromosome by making it incapable of division, thus allowing only the artificially inserted chromosome to propagate through multiple generations as the cells grow and divide. 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 minimal <i>E. coli</i> genome.</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>188 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>Validated the method with the use of microfluidics which can be employed for Biofabrication
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<li>Hosting a debate involving synthetic biology
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<li>We have hosted a debate 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 presentation to discuss iGEM and promote knowledge of synthetic biology  
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Revision as of 04:54, 21 October 2009

University of Alberta - BioBytes










































































































BioBytes

At present, the cost to synthesize oligonucleotides has been continually declining and therefore their availability is exponentially growing. However, the current technique to ligate pieces of DNA together is outdated. 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. This 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 a structured manner within hours rather than days. Our hope is to see this method 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 utilized to miniaturize construction allowing for additional validation for automated production of constructs.

Click here for more...

The 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.

Click here for more...

The Minimal Genome Project

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.

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. We then intend to remove the host chromosome by making it incapable of division, thus allowing only the artificially inserted chromosome to propagate through multiple generations as the cells grow and divide. 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 minimal E. coli genome.

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
  • 188 essential genes have been amplified and their primers added to the registry
  • A robot has been developed demonstrating the potential of automation for BioBytes
  • Validated the method with the use of microfluidics which can be employed for Biofabrication
  • We have hosted a debate involving synthetic biology
  • We have constructed and completed a series of presentation to discuss iGEM and promote knowledge of synthetic biology

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