Team:Alberta

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     <h1>BioBytes</h1>
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<font size="2">Team RE. coli is the University of Alberta's 2009 International Genetically Engineered Machines (iGEM) team. This year's iGEM project can be subdivided into two sub-projects. The first and most important of which is the Life Bytes chromosome assembly system. This system refers to a mechanism for rapid and reliable construction of plasmids (i.e.: artificial gene sets) in vitro. The second, the minimal genome project, refers to the ultimate goal of rapid and reliable DNA assembly, that is, the construction of an artificial <i>E. coli</i> chromosome. Furthermore, it includes the strategy of gene selection, arrangement, artificial chromosome insertion and the destruction of the host's chromosome.</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>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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</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>Life Bytes Chromosome Assembly</h2>
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     <h2>Organism Design and The Minimal Genome Project</h2>
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<P>Current methods for DNA assembly are incredulously slow and complicated, and tend to break down with large scale additions. The current method, in brief, is to incorporate genes constructed in the form of "bricks", put them into a helper plasmid, amplify them within the bacterial host <i>E. coli</i>, and purify them before beginning the next cycle of additions. At each addition step, the construct must be structurally and functionally evaluated. The entire cycle is routinely completed over three to four days, while troubleshooting and correction require considerable effort. It is also pertinent to know that the system has a tendency to break down after five or more additions.
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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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These issues have left a void in genetic engineering that the Life Bytes chromosome assembly system hopes to fill. Our system involves the linking of Streptavidin to a carefully structured set of magnetic beads. Streptavidin strongly binds to biotin, a moiety that can be synthetically added to double stranded DNA molecules. This Bead-Streptavidin-Biotin-Double Stranded DNA platform provides a secure base for genetic information to be added sequentially. Genes are to be created in a standardized format so that they can added one after another, with each gene binding to the last, to form a long chain of DNA as per Figure 1 (See below). This is a far simpler method than the current method of inserting single genes into an already circular piece of DNA. In one final step, the single stranded DNA is released from the biotin and recircularized with the end of the final brick. This is illustrated in Figure 2 (See below). The Life Bytes chromosome assembly system requires ~15 minutes per gene addition cycle, a marked improvement over the current three day methods.</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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Figure 1: A means for linking consecutive genes using the Life Bytes chromosome assembly system.
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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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Figure 2: A means for recircularizing the artificially constructed chromosome once all the desired bricks have been sequentially added.
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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>The Minimal Genome Project</h2>
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     <h2>Team Achievements</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% its original size shows a great simplification of this model organism.</P>
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<font size="2"><P> Through our efforts we have made the following accomplishments:</p>
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To create such an organism, we plan on building an artificial <i>E. coli</i> chromosome using the Life Bytes 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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<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
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<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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