Team:Alberta/Achievements

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Latest revision as of 02:07, 28 October 2010

TEAM ALBERTA

Gold Medal

Design and Document BioBrick Parts and DNA submission

We characterized and uploaded 31 new parts to the Registry of Parts. These were:

11 Plasmids
15 ORFs
4 Linkers

All submitted parts have been verified as the correct size using test digests and gel electrophoresis. Sequencing files are posted on the Parts Registry as advanced sequence analysis.

Beyond our additions to the Registry of Parts, we also have parts that will work with GENOMIKON that could not be uploaded to the registry because they are created from oligonucleotides.

BioBytes 2.0 Assembly Method

The BioBytes 2.0 assembly method was engineered to allow for the fast and efficient assembly of BioBytes into larger constructs. This method was demonstrated successfully in multiple on-bead assemblies, which included the construction of a 12kBp long octamer and construction of multiple plasmids that were effectively transformed into E. coli. The successful construction and transformation of E. coli with the plasmids created using the BioBytes 2.0 method was a major accomplishment of this year's project. All of our parts have been tested in PCRs and shown to produce a product of the correct size.

Demonstration of New Parts

All of the 31 parts uploaded to the Registry of Parts are new and conform to the BioBrick standard. All of our RFP plasmids work as we designed them to and can be used to rapidly create BioByte 2.0 parts. These BioBytes can subsequently be used to assemble DNA constructs.

Characterization of New Parts

All of the 31 new parts that were uploaded to the Parts Registry were tested extensively, as this was required for their operation in the BioBytes 2.0 system as documented. All the parts were checked using PCR and gel electrophoresis to ensure proper size. The untransformed constructs that were made, including the octamer, were shown using gel electrophoresis to be of expected length. All of the parts that worked in the transformation experiments have been shown to work in vivo. This also shows that they all work within the BioBytes 2.0 assembly standard.

Helping Other iGEM Teams

Many of our team members completed many of the online questionnaire that were distributed by the other iGEM teams. In addition to this, we sent in our funny pictures to the Cuckoo Clock competition.

We had a two day conference, aGEM, with the University of Calgary and the University of Lethbridge. At aGEM, we constructively criticized the other teams' projects and provided helpful insights into the respective strengths of each teams' projects. We also met with a variety of professionals involved in the synthetic biology sector and conversed with them regarding their thoughts on synthetic biology and our project.

Development of The BioBytes 2.0 Standard

The BioBytes 2.0 standard was designed and developed by our team for this year's competition. It allows for the rapid assembly of BioBytes into larger constructs. BioBytes 2.0 does not require the production of a new BBF standard, as BioBytes 2.0 parts are BioBrick compliant. For more information on the BioBytes 2.0 standard, see our BioBytes 2.0 page.

GENOMIKON: The Educational Toolkit

The major focus of our project was to create an inexpensive synthetic biology tool-kit that could effectively be used in a high school setting. We have tested our BioBytes 2.0 Assembly Method with a group of high school students. In the course of an afternoon, they were able to successfully construct a 4-Byte plasmid, which was transformed into E. coli. This represents a huge innovation beyond the current capacities of high school labs and is sure to garner a wave of excitement in not only synthetic biology, but in subsequent student generations.

Special Prizes

Best Human Practices Advance

Our project culminated in the idea of GENOMIKON, an educational toolkit that allows high school students to construct their own plasmids. In supplement of the physical kit, we created [http://www.genomikon.ca GENOMIKON.ca], which contains an online lab manual, glossary, encyclopaedia articles, and protocol generator. One of our goals is to challenge common misconceptions surrounding E. coli, such as the belief that all E. coli is harmful. GENOMIKON will educate not only students, but parent and teachers alike. Our kit will expose society's up and coming scientists to a field of unlimited potential: synthetic biology. Aymen Saidane, one of the high school students who used the kit, described GENOMIKON as the "application of what [he] learned in high school". Although this innovation is a huge step, it will not change the future of education if it cannot get into the hands of students, so our team also created a hypothetical product distribution plan, outlining the entry of GENOMIKON into the market. For more details, please visit the distribution analysis and human practices pages.

Best New Standard

The BioBytes 2.0 standard is an innovation in the way DNA pieces are assembled into multi-piece constructs. With the BioBytes 2.0 system, all the parts that are created still fit the BioBrick standard and, as such, offer maximum utility to users of the Parts Registry. The BioByte 2.0 method is:

Fast - The addition of a piece to a growing construct takes 7 minutes.
Efficient - The BioBytes 2.0 Assembly Method was modeled as 95% efficient and has produced plasmids that have been successfully transformed into E. coli.
Modular - The BioBytes 2.0 system allows for the production of your own BioBytes by PCR, which can be cloned into our RFP plasmids or used directly in the assembly of a DNA construct.
Sequential - The BioBytes 2.0 system's sequential addition of parts and anchoring to an iron micro bead allows for complete control over the construction of your DNA assembly.
In Vitro - BioBytes 2.0 is an in vitro system, allowing it to be specific and fast. The parts that can be made allow for the in vitro production of plasmids that can be cloned into an organism to interface our in vitro system to living systems.

The BioBytes 2.0 assembly method is simple to understand. We have shown that even high school students, with limited molecular biology backgrounds, can construct and transform a plasmid in one afternoon. Beyond its educational purposes, BioBytes 2.0 can also be used in both fundamental and application-based research. Visit BioBytes 2.0 for more details.

Best Foundational Advance

The innovation that is inherent in the BioByte 2.0 standard represents a foundational advance above and beyond any current method to rapidly create parts and then use those parts in the assembly of DNA constructs. It is a faster and more efficient way to assemble DNA constructs and allows for the sequential and controlled addition of parts. For an in-depth look at the engineering of the BioByte 2.0 system, head over to BioBytes 2.0.

@@ Line 4: / Line 4: @@
 {{Team:Alberta/beginLeftSideBar}}
 {{Team:Alberta/endLeftSideBar}}
 {{Team:Alberta/beginRightSideBar}}
-== WWW.GENOMIKON.CA ==
+[[Image:Alberta gold.jpg|240px|center]]
-This is the online lab manual and educational resource for the Genomikon Kit
 {{Team:Alberta/endRightSideBar}}
 {{Team:Alberta/beginMainContent}}
+==Gold Medal==
-==BRONZE MEDAL==
+<div id="horiz-line"></div>
-----------------------------------------------------
 '''Design and Document BioBrick Parts and DNA submission''' <p>
 We characterized and uploaded 31 new parts to the Registry of Parts.
@@ Line 22: / Line 21: @@
 *15 ORFs
 *4 Linkers
-All submitted parts have been verified as the correct size using test digests and gel electrophoresis.  Sequencing files are posted on the Parts Registry as advanced sequence analyses.
+All submitted parts have been verified as the correct size using test digests and gel electrophoresis.  Sequencing files are posted on the Parts Registry as advanced sequence analysis.</p>
+<p>
-Beyond our additions to the Registry of Parts we also have parts that will work with Genomikon that could not be uploaded to the registry because they are created from oligonucleotides. <\p>
+Beyond our additions to the Registry of Parts, we also have parts that will work with GENOMIKON that could not be uploaded to the registry because they are created from oligonucleotides. </p>
-==SILVER MEDAL==
+'''BioBytes 2.0 Assembly Method'''<p>
-----------------------------------------------------
+The BioBytes 2.0 assembly method was engineered to allow for the fast and efficient assembly of BioBytes into larger constructs.
-'''BioByte 2.0 Method'''<p>
+This method was demonstrated successfully in multiple on-bead assemblies, which included the construction of a 12kBp long octamer and construction of multiple plasmids that were effectively transformed into ''E. coli''.  The successful construction and transformation of ''E. coli'' with the plasmids created using the BioBytes 2.0 method was a major accomplishment of this year's project.
-The BioByte 2.0 system was engineered to allow for the fast and efficient assembly of BioBytes into large constructs.
-This was shown to work in multiple on-bead assemblies which included the construction of a 12kBp long octamer and construction of multiple plasmids that were successfully transformed into ''E. coli''.  The successful construction and transformation of ''E. coli'' with plasmids created using the BioByte 2.0 method was a major accomplishment of this years project.
-All of our parts have been tested in PCR's and shown to give a product of the correct size
+All of our parts have been tested in PCRs and shown to produce a product of the correct size.</p>
 '''Demonstration of New Parts'''<p>
 All of the 31 parts uploaded to the Registry of Parts are new and conform to the BioBrick standard.
-All of our RFP plasmids work as we designed them to and can be used to rapidly create BioByte 2.0 parts. These BioBytes can subsequently be used to assemble DNA constructs.
+All of our RFP plasmids work as we designed them to and can be used to rapidly create BioByte 2.0 parts. These BioBytes can subsequently be used to assemble DNA constructs.</p>
 '''Characterization of New Parts'''<p>
-All of the 31 new parts that were uploaded to the Registry of Parts were tested extensively as this was required for their operation in the BioByte 2.0 system as documented. All the parts were checked using PCR and gel electrophoresis to ensure proper size. The untransformed constructs that were made, including the octamer, were shown using gel electrophoresis to be of expected length.  All of the parts that worked in the transformation experiments have been shown to work in vivo. This also shows that they all work within the BioByte 2.0 assembly standard.
+All of the 31 new parts that were uploaded to the Parts Registry were tested extensively, as this was required for their operation in the BioBytes 2.0 system as documented. All the parts were checked using PCR and gel electrophoresis to ensure proper size. The untransformed constructs that were made, including the octamer, were shown using gel electrophoresis to be of expected length.  All of the parts that worked in the transformation experiments have been shown to work in vivo. This also shows that they all work within the BioBytes 2.0 assembly standard.</p>
-Listing out how this fufills the judging criteria?
-(going by last year's example? [https://2009.igem.org/Team:Alberta/MedalRequirements])
-Plus the special/area prizes
-----------------------------------------------------
-The requirements to earn a Gold are:
+'''Helping Other iGEM Teams'''<p>
+Many of our team members completed many of the online questionnaire that were distributed by the other iGEM teams. In addition to this, we sent in our funny pictures to the Cuckoo Clock competition.</p>
+<p>We had a two day conference, aGEM, with the University of Calgary and the University of Lethbridge. At [[Team:Alberta/human_practices#Social_Aspect|aGEM]], we constructively criticized the other teams' projects and provided helpful insights into the respective strengths of each teams' projects. We also met with a variety of professionals involved in the synthetic biology sector and conversed with them regarding their thoughts on synthetic biology and our project.</p>
-#Register the team, have a great summer, and have fun attending the Jamboree.
+'''Development of The BioBytes 2.0 Standard'''<p>
-#Successfully complete and submit a Project Summary form.
+The BioBytes 2.0 standard was designed and developed by our team for this year's competition. It allows for the rapid assembly of BioBytes into larger constructs. BioBytes 2.0 does not require the production of a new BBF standard, as BioBytes 2.0 parts are BioBrick compliant. For more information on the BioBytes 2.0 standard, see our [[Team:Alberta/biobyte2| BioBytes 2.0]] page.
-#Create and share a Description of the team's project via the iGEM wiki (see [https://2008.igem.org/Team:TUDelft TUDelft 2008] for a great example).
+</p>
-#Present a Poster and Talk at the iGEM Jamboree (watch the [https://2008.igem.org/files/video/Heidelberg.mp4 Heidelberg 2008 video] for a great example).
-#Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Parts
-#Submit DNA for at least one new BioBrick Part or Device to the Registry of Parts.
-#Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected.
-#Characterize the operation of at least one new BioBrick Part or Device and enter this information on the Parts or Device page via the Registry of Parts (see [http://parts.mit.edu/registry/index.php/Part:BBa_F2620 BBa_F2620] for an exemplar).
-#*------------------------------------
-#*****Plus:
-#*------------------------------------
-#Characterize or improve an existing BioBrick Part or Device and enter this information back on the Registry.
-#**AND/OR
-#Help another iGEM team by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.
-#**AND/OR
-#Develop and document a new technical standard that supports the (i) design of BioBrick Parts or Devices, or (ii) construction of BioBrick Parts or Devices, or (iii) characterization of BioBrick Parts or Devices, or (iv) analysis, modeling, and simulation of BioBrick Parts or Devices, or (v) sharing BioBrick Parts or Devices, either via physical DNA or as information via the internet.
-#**AND/OR
-#Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.
+'''GENOMIKON: The Educational Toolkit'''<p>
+The major focus of our project was to create an inexpensive synthetic biology tool-kit that could effectively be used in a high school setting. We have tested our BioBytes 2.0 Assembly Method with a group of high school students. In the course of an afternoon, they were able to successfully construct a 4-Byte plasmid, which was transformed into ''E. coli''. This represents a huge innovation beyond the current capacities of high school labs and is sure to garner a wave of excitement in not only synthetic biology, but in subsequent student generations.
+</p>
-== Team Alberta in the Media ==
+==Special Prizes==
-----------------------------------------------------
+<div id="horiz-line"></div>
+'''Best Human Practices Advance'''<p>
+Our project culminated in the idea of GENOMIKON, an educational toolkit that allows high school students to construct their own plasmids.  In supplement of the physical kit, we created  [http://www.genomikon.ca GENOMIKON.ca], which contains an online lab manual, glossary, encyclopaedia articles, and protocol generator.  One of our goals is to challenge common misconceptions surrounding <em>E. coli</em>, such as the belief that all <em>E. coli</em> is harmful.  GENOMIKON will educate not only students, but parent and teachers alike.  Our kit will expose society's up and coming scientists to a field of unlimited potential: synthetic biology.  Aymen Saidane, one of the high school students who used the kit, described GENOMIKON as the "application of what [he] learned in high school". Although this innovation is a huge step, it will not change the future of education if it cannot get into the hands of students, so our team also created a hypothetical product distribution plan, outlining the entry of GENOMIKON into the market. For more details, please visit the [[Team:Alberta/human_practices/distribution_analysis|distribution analysis]] and [[Team:Alberta/human practices|human practices]] pages.
+</p>
+'''Best New Standard'''<p>
+The BioBytes 2.0 standard is an innovation in the way DNA pieces are assembled into multi-piece constructs. With the BioBytes 2.0 system, all the parts that are created still fit the BioBrick standard and, as such, offer maximum utility to users of the Parts Registry. The BioByte 2.0 method is:
+*'''Fast''' - The addition of a piece to a growing construct takes 7 minutes.
+*'''Efficient''' - The BioBytes 2.0 Assembly Method was modeled as 95% efficient and has produced plasmids that have been successfully transformed into ''E. coli''.
+*'''Modular''' - The BioBytes 2.0 system allows for the production of your own BioBytes by PCR, which can be cloned into our RFP plasmids or used directly in the assembly of a DNA construct.
+*'''Sequential''' - The BioBytes 2.0 system's sequential addition of parts and anchoring to an iron micro bead allows for complete control over the construction of your DNA assembly.
+*'''In Vitro''' - BioBytes 2.0 is an in vitro system, allowing it to be specific and fast. The parts that can be made allow for the in vitro production of plasmids that can be cloned into an organism to interface our in vitro system to living systems. </p>
+<p>The BioBytes 2.0 assembly method is simple to understand. We have shown that even high school students, with limited molecular biology backgrounds, can construct and transform a plasmid in one afternoon.  Beyond its educational purposes, BioBytes 2.0 can also be used in both fundamental and application-based research.
+Visit [[Team:Alberta/biobyte2| BioBytes 2.0]] for more details.
+</p>
-*Edmonton Sun - October 25, 2010
+==Best Foundational Advance==
-**http://www.edmontonsun.com/news/edmonton/2010/10/24/15813611.html
+<div id="horiz-line"></div>
+<p>
+The innovation that is inherent in the BioByte 2.0 standard represents a foundational advance above and beyond any current method to rapidly create parts and then use those parts in the assembly of DNA constructs. It is a faster and more efficient way to assemble DNA constructs and allows for the sequential and controlled addition of parts. For an in-depth look at the engineering of the BioByte 2.0 system, head over to [[Team:Alberta/biobyte2|BioBytes 2.0]].
+</p>
 {{Team:Alberta/endMainContent}}