Team:Alberta/MedalRequirements

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     <h1>Medals and Area Prize Deliverables</h1>
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     <h1>Medals and Area Prize Achievements</h1>
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<h3> Bronze: </h3>
+
<h2> Bronze </h2>
-
<p><b>Design and document Biobrick parts:</b> We’ve entered over 400 Biobrick parts in the Registry of Standard Biological Parts. See the Parts registry link the deliverables tab for a complete list. In summary, we’ve submitted: </p>
+
<p><b>Design and document BioBrick parts:</b> We’ve entered <a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=Alberta">422 BioBrick parts</a> into the Registry of Standard Biological Parts. In summary, we’ve submitted: </p>
-
<li>2 backbone plasmids</li>
+
<ul>
-
<li>12 promoters in pAB or pBA </li>
+
<li>2 <a href="https://2009.igem.org/Team:Alberta/ByteCreation">backbone plasmids</a>
-
<li>2 terminators in pAB or pBA</li>
+
<li>12 <a href="https://2009.igem.org/Team:Alberta/Project/Promoters_&_Terminators">promoters in pAB or pBA</a>
-
<li>12 reporters, selectable markers and genes in pAB or pBA </li>
+
<li>2 <a href="https://2009.igem.org/Team:Alberta/Project/Promoters_&_Terminators">transcriptional terminators in pAB or pBA</a>
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<li>5 trp synthesis genes in pSB1A3 </li>
+
<li>3 <a href="https://2009.igem.org/Team:Alberta/DNAanchor">anchor sequence components</a>
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<li>2 primers for sequencing out of pAB and pBA </li>
+
<li>3 <a href="https://2009.igem.org/Team:Alberta/DNAanchor">chain terminator components</a>
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<li>4 USER primers for the Biobyte assembly method</li>
+
<li>22 reporters, selectable markers and genes in pAB or pBA
-
<li>188 primer pairs for essential E.coli genes</li>
+
<li>2 primers for sequencing out of pAB and pBA
 +
<li>4 <a href="https://2009.igem.org/Team:Alberta/ByteCreation">USER primers for the BioByte assembly method</a>
 +
<li>2 primers for amplifying an origin with Biobyte ends
 +
<li>185 <a href="https://2009.igem.org/Team:Alberta/Project/Primer_Design">primer pairs for essential E. coli genes</a>
 +
</ul>
-
<p>All submitted parts have been verified as the correct size using test digests and gel electrophoresis, and 28 parts have been sequenced to verify correct insertion in pAB or pBA. Sequencing files are posted on the Parts Registry as advanced sequence analyses.</p>
+
 
 +
<p>All submitted parts have been verified as the correct size using test digests and gel electrophoresis. In addition, over 26 parts have been sequenced to verify correct insertion into pAB or pBA. Sequencing files are posted on the Parts Registry as advanced sequence analyses.</p>
<b>Submit DNA:</b>
<b>Submit DNA:</b>
-
<p>We’ve submitted DNA for 31 parts, including 24 parts in pAB or pBA, 5 genes in the standard biobrick plasmid pSB1A3, and both the pAB and pBA plasmids. </p>
+
<p>We’ve submitted DNA for 26 parts, including 24 parts in pAB or pBA, and both the pAB and pBA plasmids. </p>
-
<h3>Silver:</h3>
+
<h2>Silver</h2>
<b>Demonstrate that at least one new part works as expected: </b>
<b>Demonstrate that at least one new part works as expected: </b>
-
<p>All 188 pairs of primers for essential genes submitted to the parts registry have been tested in PCR and shown to give a product of the correct size. pAB/BA primers for sequencing inserts in pAB/BA also worked as intended when used to verify part insertion.   </p>
+
<p> The BioBytes rapid assembly system, consisting of the pAB and pBA plasmids and the universal uracil primers, has been demonstrated to function for rapid on-bead assembly. This is the principal achievement of the 2009 U of A team.
-
<b>Characterize the operation of at least one new biobrick part and enter this info: </b>
+
<p>In addition, all 185 pairs of primers for essential genes submitted to the Parts Registry have been tested in PCR's and shown to give a product of the correct size. The essentiality of all these genes for a minimal genome was predicted using a computer model. Also, pAB/BA primers for sequencing inserts in pAB/BA worked as intended when used to verify part insertion.   </p>
-
<p>The pAB and pBA plasmids and USER primers have been extensively tested in order to optimize the Biobytes assembly method, as documented in the DNA assembly section of this wiki.  We’ve also tested several components in pAB and pBA using the Biobytes assembly method, and verified by gel electrophoresis and sequencing that they assemble properly. Moreover, we’ve characterized the behavior of parts for Biobyte assembly in a microfluidic chip, demonstrating successful construct production on a micro-scale.</p>
+
-
<h3>Gold:</h3>  
+
<b>Characterize the operation of at least one new BioBrick part and enter this information: </b>
 +
<p>The pAB and pBA plasmids and USER primers have been extensively tested in order to optimize the BioBytes assembly method, as documented in the DNA Assembly section of this wiki.  We’ve also tested several components in pAB and pBA using the BioBytes assembly method, and verified by gel electrophoresis and sequencing that they assemble properly.  Moreover, we’ve characterized the behavior of parts for Biobyte assembly in a microfluidic chip, demonstrating successful construct production on a micro-scale.</p>
 +
 
 +
<h2>Gold</h2>  
<p>Only one of the following criteria must be met for Gold. However, our team has met all four possible criteria:</p>
<p>Only one of the following criteria must be met for Gold. However, our team has met all four possible criteria:</p>
-
<b>Characterize or improve an existing biobrick part or device:</b>
+
<b>Characterize or improve an existing BioBrick part or device:</b>
-
<p>The GFP and RFP parts we have submitted in pAB and pBA are derived from preexisting biobrick parts. By adapting these parts to the Biobytes plasmids, we allow them to be used in the Biobytes assembly method, expanding their usefulness. </p>
+
<p>The GFP and RFP parts we have submitted in pAB and pBA are derived from preexisting Biobrick parts. By adapting these parts to the BioBytes plasmids, we allow them to be used in the BioBytes assembly method, expanding their applications. </p>
<p>Furthermore, we adapted the Anderson collection of promoters to the Biobytes method. We removed NheI and AvrII cut sites from the consensus promoter and added two nucleotides downstream of the -10 region to place an A as the +1 nucleotide. These promoters are currently being tested by cloning them upstream of a ribosome binding site-red fluorescent protein segment, and checking for red colonies. </p>
<p>Furthermore, we adapted the Anderson collection of promoters to the Biobytes method. We removed NheI and AvrII cut sites from the consensus promoter and added two nucleotides downstream of the -10 region to place an A as the +1 nucleotide. These promoters are currently being tested by cloning them upstream of a ribosome binding site-red fluorescent protein segment, and checking for red colonies. </p>
<b>Help another iGEM team: </b>
<b>Help another iGEM team: </b>
-
<p>We constructed a plasmid for the University of Lethbridge team. </p>
+
<p>We constructed an expression plasmid for MMS6 (part <a href="http://partsregistry.org/Part:BBa_K249019">K249019</a>) for the University of Lethbridge team. </p>
<b>Develop and document a new technical standard:</b>  
<b>Develop and document a new technical standard:</b>  
-
<p> We have written and submitted an RFC detailing how the biobytes assembly method can be used, and including detailed protocol for how to perform this assembly method.</p>
+
<p> We have written and submitted a new RFC, BBF RFC 47, detailing how the BioBytes assembly method can be used, and have included detailed protocol for how to perform this assembly method.  RFC #47 The BioBytes Assembly Standard can be found <a href="http://bbf.openwetware.org/RFC.html#BBF_RFC_47:_BioBytes_Assembly_Standard"> here</a>. </P>
 +
 
<b>Outline and detail a new approach to the issue of human practices:</b>
<b>Outline and detail a new approach to the issue of human practices:</b>
-
<p> As a novel approach to human practices, we worked with eight internationally competitive debaters to produce a debate about the ethical and societal implications of developing artificially engineered organisms. This debate was filmed and is posted and summarized on our wiki for the benefit of the public. The extensive experience of the debaters brings an expertise about policy issues not commonly seen among science and engineering students. The diverse background of the debaters allows a wide range of opinions to be reflected that could have been imagined by an iGEM team alone. The format of debate allows both sides of an issue equal opportunity, and requires the use of well-reasoned arguments and evidence.  Moreover, debates are fast paced and engaging, capturing an audience’s attention.  The debate is a valuable resource for educating synthetic biologists about public reactions, assessing public knowledge about genetic engineering, helping policy makers make well-reasoned decisions, and helping the public form their own opinion of synthetic biology. </p>
+
<p> As a novel approach to human practices, we worked with eight internationally competitive debaters to produce a debate about the ethical and societal implications of developing artificially engineered organisms. This debate was filmed and is posted and summarized on our wiki for the benefit of the public. The extensive experience of the debaters brings an expertise about policy issues not commonly seen among science and engineering students. The diverse background of the debaters allows a wide range of opinions to be reflected that could not have been imagined by an iGEM team alone. The format of debate allows both sides of an issue equal opportunity, and requires the use of well-reasoned arguments and evidence.  Moreover, debates are fast-paced and engaging, capturing an audience’s attention.  The debate is a valuable resource for educating synthetic biologists about public reactions, assessing public knowledge about genetic engineering, helping policy-makers make well-reasoned decisions, and helping the public form their own opinion of synthetic biology. </p>
 +
 
 +
<p align=right><a href="https://2009.igem.org/Team:Alberta/Project/UofADebate">See U of A Debate</a>
 +
</p>
 +
<p>Moreover, we reached out to high schools, summer camps, libraries and colleges, doing demonstration debates about ethics and presentations on the science of synthetic biology. We’ve reached over 230 students already and are scheduled to reach over 400 students by January. We’ve developed and posted resources for teaching synthetic biology to a wide range of age groups. From the feedback we’ve collected and analyzed, students almost unanimously feel learning about synthetic biology is valuable.  </p>
 +
 
 +
<p align=right><a href="https://2009.igem.org/Team:Alberta/Project/Presentations">See Presentations</a>
 +
</p>
 +
<h2> Special Prizes</h2>
 +
 
 +
<h3> Best Model:</h3>
 +
<p>We’ve developed a novel system for comprehensively analyzing the entirety of the known metabolic network of E. coli. Through this system, one can assess the net biomass production of an E. coli in which any combination of metabolic gene are present, and thus assess which combination of pathways are necessary for cell survival. We used this model to predict the minimal set of metabolic genes required for E.coli survival, towards the goal of producing a minimal E. coli genome. This minimal gene list included 117 essential genes never previously identified as essential for a minimal genome. Moreover, a graphical user interface has been developed for exploring the results of our minimal metabolism modeling. </p>
 +
 
 +
 
 +
<p align=right><a href="https://2009.igem.org/Team:Alberta/Project/Modeling">See Modeling</a>
 +
</p>
 +
 
-
<p>Moreover, we reached out to high school, summer camps, libraries and colleges, doing demonstration debates about ethics and presentations on the science of synthetic biology. We’ve reached over 230 students already and are scheduled to reach over 400 students by January. We’ve developed and posted resources for teaching synthetic biology to a wide range of age groups. From the feedback we’ve collected and analyzed students almost unanimously feel learning about synthetic biology is valuable.  </p>
 
-
<h3> Special Prizes:</h3>
+
<h3> Best New Standard and Best Foundational Advance: </h3>
 +
<p>  The BioBytes RFC (BBF RFC 47) outlines what is currently the only method for DNA assembly that is fast, modular, sequential and in vitro.  </p>
-
<p> <b> Best Model:</b> We’ve developed a novel system for comprehensively analyzing the entirety of the known metabolic network of E. coli. Through this system, one can assess the net biomass production of an E. coli in which any combination of metabolic gene are present, and thus assess which combinations of pathways are necessary for cell survival. We used this model to predict the minimal set of metabolic genes required for E.coli survival, towards the goal of producing a minimal E. coli genome. This minimal gene list included 117 essential genes never previously identified as essential for a minimal genome. Moreover, a graphical user interface has been developed for exploring the results of our minimal metabolism modeling. </p>
+
<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>
-
<p> <b>Best New Standard and Best Foundational Advance:  </b> The Biobytes RFC outlines what is currently the only method for DNA assembly that is fast, modular, sequential and in vitro.  </p>
+
<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>
 +
<P>
 +
<b>BioBytes is the only method that is fast, modular, sequential and in vitro:</b></P>
 +
<ul>
 +
<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>
 +
<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>
 +
<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>
 +
<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>
 +
</ul>
 +
<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>
 +
<p align=right><a href="https://2009.igem.org/Team:Alberta/Project/assemblyoverview">See DNA Assembly</a>
 +
</p>
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Latest revision as of 03:43, 22 October 2009

University of Alberta - BioBytes










































































































Medals and Area Prize Achievements

Bronze

Design and document BioBrick parts: We’ve entered 422 BioBrick parts into the Registry of Standard Biological Parts. In summary, we’ve submitted:

All submitted parts have been verified as the correct size using test digests and gel electrophoresis. In addition, over 26 parts have been sequenced to verify correct insertion into pAB or pBA. Sequencing files are posted on the Parts Registry as advanced sequence analyses.

Submit DNA:

We’ve submitted DNA for 26 parts, including 24 parts in pAB or pBA, and both the pAB and pBA plasmids.

Silver

Demonstrate that at least one new part works as expected:

The BioBytes rapid assembly system, consisting of the pAB and pBA plasmids and the universal uracil primers, has been demonstrated to function for rapid on-bead assembly. This is the principal achievement of the 2009 U of A team.

In addition, all 185 pairs of primers for essential genes submitted to the Parts Registry have been tested in PCR's and shown to give a product of the correct size. The essentiality of all these genes for a minimal genome was predicted using a computer model. Also, pAB/BA primers for sequencing inserts in pAB/BA worked as intended when used to verify part insertion.

Characterize the operation of at least one new BioBrick part and enter this information:

The pAB and pBA plasmids and USER primers have been extensively tested in order to optimize the BioBytes assembly method, as documented in the DNA Assembly section of this wiki. We’ve also tested several components in pAB and pBA using the BioBytes assembly method, and verified by gel electrophoresis and sequencing that they assemble properly. Moreover, we’ve characterized the behavior of parts for Biobyte assembly in a microfluidic chip, demonstrating successful construct production on a micro-scale.

Gold

Only one of the following criteria must be met for Gold. However, our team has met all four possible criteria:

Characterize or improve an existing BioBrick part or device:

The GFP and RFP parts we have submitted in pAB and pBA are derived from preexisting Biobrick parts. By adapting these parts to the BioBytes plasmids, we allow them to be used in the BioBytes assembly method, expanding their applications.

Furthermore, we adapted the Anderson collection of promoters to the Biobytes method. We removed NheI and AvrII cut sites from the consensus promoter and added two nucleotides downstream of the -10 region to place an A as the +1 nucleotide. These promoters are currently being tested by cloning them upstream of a ribosome binding site-red fluorescent protein segment, and checking for red colonies.

Help another iGEM team:

We constructed an expression plasmid for MMS6 (part K249019) for the University of Lethbridge team.

Develop and document a new technical standard:

We have written and submitted a new RFC, BBF RFC 47, detailing how the BioBytes assembly method can be used, and have included detailed protocol for how to perform this assembly method. RFC #47 The BioBytes Assembly Standard can be found here.

Outline and detail a new approach to the issue of human practices:

As a novel approach to human practices, we worked with eight internationally competitive debaters to produce a debate about the ethical and societal implications of developing artificially engineered organisms. This debate was filmed and is posted and summarized on our wiki for the benefit of the public. The extensive experience of the debaters brings an expertise about policy issues not commonly seen among science and engineering students. The diverse background of the debaters allows a wide range of opinions to be reflected that could not have been imagined by an iGEM team alone. The format of debate allows both sides of an issue equal opportunity, and requires the use of well-reasoned arguments and evidence. Moreover, debates are fast-paced and engaging, capturing an audience’s attention. The debate is a valuable resource for educating synthetic biologists about public reactions, assessing public knowledge about genetic engineering, helping policy-makers make well-reasoned decisions, and helping the public form their own opinion of synthetic biology.

See U of A Debate

Moreover, we reached out to high schools, summer camps, libraries and colleges, doing demonstration debates about ethics and presentations on the science of synthetic biology. We’ve reached over 230 students already and are scheduled to reach over 400 students by January. We’ve developed and posted resources for teaching synthetic biology to a wide range of age groups. From the feedback we’ve collected and analyzed, students almost unanimously feel learning about synthetic biology is valuable.

See Presentations

Special Prizes

Best Model:

We’ve developed a novel system for comprehensively analyzing the entirety of the known metabolic network of E. coli. Through this system, one can assess the net biomass production of an E. coli in which any combination of metabolic gene are present, and thus assess which combination of pathways are necessary for cell survival. We used this model to predict the minimal set of metabolic genes required for E.coli survival, towards the goal of producing a minimal E. coli genome. This minimal gene list included 117 essential genes never previously identified as essential for a minimal genome. Moreover, a graphical user interface has been developed for exploring the results of our minimal metabolism modeling.

See Modeling

Best New Standard and Best Foundational Advance:

The BioBytes RFC (BBF RFC 47) outlines what is currently the only method for DNA assembly that is fast, modular, sequential and in vitro.

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?

See DNA Assembly