Team:British Columbia/Project Outlook

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 +
<h3>Project Achievements & Future Directions</h3>
 +
 +
<h4>Biofilm: </h4><p>
 +
We have obtained growth curves for <i>S. aureus</i> strains RN4220 and 8325-4 that demonstrate a steady growth phase followed by an oscillatory state of dynamic equilibrium. We have also optimized the existing protocol for biofilm quantification. Additionally, values derived from the biofilm experiments were integral to deriving realistic results from modeling simulations.<br/><br/>
 +
The existing curve has demonstrated that 9 hours is the optimal time point for exposure to the matrix-degrading enzyme, DspB, as well as the engineered phage construct with DspB and quorum sensing genes. Future experiments testing the biofilm response to DspB alone as well as DspB incorporated into a phage construct with the quorum sensing P2 promoter will enable the characterization of the construct’s effectiveness against the biofilms of <i>S. aureus</i> strains RN4220 and 8325-4.<br/><br/>
 +
 +
 +
<h4>Phage Standard: </h4><p>
 +
We developed a phage standard that allows for modification of any lysogenic bacteriophage as part of the Biobrick standard. The phage standard works around the problems of illegal cut sites and prohibitively large plasmids. We hope the standard will serve as a foundational advance towards phage research within the iGEM competition, the BioBrick registry and the synthetic biology community as a whole.<br/><br/>
 +
In the future we hope to continue developing this standard and optimizing the process of modifying lysogenic phage DNA.  We will strive to submit a fully functional set of parts that have been demonstrated to work following the phage standard in the lab.  Hopefully we will also be able to include lytic phages under the scope of the phage standard.  With some luck we could expand the number of chassis available to iGEM and the BioBrick registry by introducing integration site vectors for multiple species and strains.<br/><br/>
 +
 +
<h4>Quorum Sensing: </h4><p>
 +
We have made constructs to characterize the P2 promoter (BBa_I746104) of <i>S. aureus</i> via fluorescent protein production. In order to directly relate AIP to P2 promoter activity, we chose to use an agr null strain. As a next step, genes encoding AgrAC from <i>S. aureus</i> should be put on the same plasmid (the <i>S. aureus</i>/<i>E. coli</i> shuttle vector, pCN33) as the reporter constructs and transformed into agr-null <i>S. aureus</i>. This would allow proper characterization of P2 activity in the presence of AIP. Primers have already been designed and submitted to PCR the genes encoding AgrAC. Additionally, the replicon of the <i>S. aureus</i> pCN33 plasmid can be made into a BioBrick part to facilitate the expression and characterization of BioBrick parts in <i>S. aureus</i>.</p><br/>
 +
<h4>DspB: </h4><p>
 +
We have contributed to the biobrick parts registry by submitting a new part: DspB, an enzyme that degrades poly-ß-(1,6)-linked N-acetylglucosamine bonds. We have demonstrated that dspB works through a crude cell enzyme activity assay and have added this information to the Registry.<br/><br/>
 +
 +
We are currently working on obtaining data from the exposure of DspB protein on a <i>S. aureus</i> biofilm as well as isolating DspB via a histidine tag to attain further characterization data. We hope to gather this data before the presentation. If not fully completed, these components should be further explored in the future. Future directions also include testing DspB with the P2 promoter in <i>S. aureus</i> under the influence of the auto-inducing peptide (AIP) to characterize DspB under the promoter that it would be expressed in the phage. We would then incorporate DspB protein under the P2 promoter into the phage for exposure to <i>S. aureus</i> biofilms. We expect that this engineered phage will show an improvement in the elimination of the <i>S. aureus</i> biofilm with the protein incorporated into its genome.</p>
 +
<br/>
 +
 +
<h4>Modeling: </h4><p>
 +
We have developed a mathematical model that describes the dynamics of our genetically engineered phage-assisted biofilm dispersal system. Using this model, we can predict the outcome of introducing a biofilm matrix-degrading phage to a biofilm. We have demonstrated that our model can be used as a tool to help design engineered systems similar to ours and to formulate informed hypotheses for phage-biofilm experiments. We have implemented this model in an easy-to-use Java program. Future work includes the extension of this model to account for components, such as genetic elements, that may impact the system and the development of a GUI with better graphical features.
 +
</p><br/>
 +
 +
<h4>Human Practices: </h4><p>
 +
We have gathered hundreds of definitions of synthetic biology from the University of British Columbia community to construct <a href="https://2010.igem.org/Team:British_Columbia/HumanPractices">promoter maps and word clouds</a> representing the prevalent ideas in our different disciplines' awareness of synthetic biology!<br/>
 +
<br/>We have started the <a href="https://2010.igem.org/Team:British_Columbia/HP_arts">first iGEM synthetic biology art gallery</a> inviting all iGEM participants, as well as members of the public from Deviantart, IllustratedATCs and ATCsForAll to contribute.<br/><br/>We have forged the <a href="https://2010.igem.org/Team:British_Columbia/HP_nanowrimo">first NaNoWriMo-iGEM collaboration</a> to showcase novels featuring synthetic biology that are written by NaNoWriMo participants.<br/><br/>
 +
Our experience communicating with the general public and even students in the sciences and applied sciences has been an enriching one. We have gleaned a lot of insights into public perception of synthetic biology, which still remains a very new and unfamiliar field to the public despite recent press about the first synthetic cell!<br/><br/>
 +
Public opinion and risk perception appears to be more informed by controversial topics (e.g. genetically modified organisms and food) and literature featuring synthetic biology (from Frankenstein to Oryx and Crake). So outreach on the part of synthetic biologists still has quite a way to go in order to bring synthetic biology into the schools, workplaces and homes of the public. Our human practices project has generated ripples of thoughts about synthetic biology in various communities, stimulating individuals to find out more about synthetic biology and its recent developments. We hope that this will open up paths of communication between the synthetic biology research community and diverse public communities, which may lead to discussions and collaborations with the purposes of informing the public about synthetic biology and safely expanding its real world applications.<br/><br/>
 +
Some specific future directions that address this cause include: (i) Actively inviting more non-science/engineering students to participate in iGEM outreach/projects/teams/Jamboree/fundraising, (ii) Establishing an annual iGEM tradition of stimulating and showcasing works of art or literature by members of iGEM and the general public featuring synthetic biology, and (iii) Investing in other collaborative outreach activities such as elementary/secondary school educational programs and synthetic biology university courses.
 +
</p><br/>
-
<br></br>Special Prizes
 
-
<br></br>
 
-
<br></br>Best Human Practices Advance
 
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<br></br>Issues? We've got issues! How will you sell your project if you have to give away the parts? What does your family think about your genetic engineering dreams? Will the world be a safe place if we make biology easy to engineer? How do the lessons of the past inform everybody's discussion going forward? Find a new way to help human civilization consider, guide, and address the impacts of ongoing advances in biotechnology.
 
-
<br></br>
 
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<br></br>Best Experimental Measurement
 
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<br></br>There are a lot of exciting Parts in the Registry, but most of the Parts have never been characterized. Can you make a great measurement for one new Parts? Or, can you develop and implement a new method for characterizing thousands of parts? Go for it!
 
-
<br></br>
 
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<br></br>Best Model
 
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<br></br>Parts and Devices have a lot of details, too many to think about all the time, in fact. Models provide a great way to describe the functioning and operation of Parts and Devices. Show everybody what you can do!
 
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<br></br>
 
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<br></br>Best Software Tool
 
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<br></br>Computers have been around for a long time. How come we don't have more, great software tools for helping everything engineering synthetic biological systems based on standard biological parts? Cadence, Synopsis, Microsoft, Google, will these names mean anything to the future of synthetic biology? Or, will you add a new name at the top of the heap? It's up to you.
 
-
<br></br>
 
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<br></br>Best New Standard
 
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<br></br>There's so much work to do in making biology easy to engineer. If we could easily share and build on each other's work, then we could all do so much more. Standards help to make sharing easier. For example, the BioBrick standard for physical assembly of BioBrick parts makes it easier to design and construct parts that can be readily assembled with the parts that everybody else is making. What other sorts of standards do we need? How about standards for measurements? How about standards for different types of parts (for example, what about a standard BioBrick promoter, with a fixed transcription start site? Or, how about a standard phosphorylation motif, for post-translational devices? Or, how about a standard signal carrier for biosynthetic devices? Or, how about a standard model for a class of BioBrick Devices? Or, how about a standard for sharing information about parts across computer networks?). You get the idea.
 
-
<br></br>
 
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<br></br>Best Wiki
 
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<br></br>The project Descriptions on the iGEM website provide a great resource for future iGEM students and teams, as well as the rest of the world, so that everybody can see what iGEM is about. For example, check out this Description from the 2007 UC Berkeley iGEM team, Bactoblood. Wow! Can you do better?
 
-
<br></br>
 
-
<br></br>Best Poster
 
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<br></br>Posters are a great way to concisely present your team's work. You can bring your poster to the Jamboree, but also to other meetings and conferences as well. Print out a second copy and post it at your home school so that everybody in your department or school can learn about your team. Show us what you've got.
 
-
<br></br>
 
-
<br></br>Best Presentation
 
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<br></br>At the end of the day, many people learn best by watching and listening. Online video also provides a wonderful legacy to help others, from students, to teachers, to the general publics. Giving a great presentation is a challenge, and benefits greatly from practice and study.
 
-
<br></br>
 
-
<br></br>Area Prizes
 
-
<br></br>
 
-
<br></br>Best Health or Medicine Project
 
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<br></br>Many health and medical problems might best be addressed by improved biological technologies. What can synthetic biology do?
 
-
<br></br>
 
-
<br></br>Software Tools
 
-
<br></br>
 
-
<br></br>Bronze Mousepad:
 
-
<br></br>Register the team, have a great summer, and have fun attending the Jamboree.
 
-
<br></br>Create and share a Description of the team's project via the iGEM wiki.
 
-
<br></br>Present a Poster and Talk at the iGEM Jamboree.
 
-
<br></br>Develop and make available via the Registry an open source software tool that supports synthetic biology based on BioBrick standard biological parts (remember, the iGEM judges will be looking for substantial team-based software projects).
 
-
<br></br>
 
-
<br></br>Silver Mousepad:
 
-
<br></br>Provide a detailed, draft specification for the next version of your software tool, or a second, distinct software tools project.
 
-
<br></br>
 
-
<br></br>Gold Mousepad:
 
-
<br></br>Help another iGEM team by, for example, analyzing a Part, debugging a Device, or modeling or simulating a System.
 
-
<br></br>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 of BioBrick Parts or <br></br>Devices, either via physical DNA or as information via the internet.
 
-
<br></br>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.
 
</div> <!-- end SubWrapper -->
</div> <!-- end SubWrapper -->
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<div id="news" style="height:700px;">  
+
<div id="news" style="height:2500px;">  
 +
<br/>
 +
 
 +
<center><h3>Quick Links</h3>
 +
<a href="https://igem.org/Judging_Form.cgi?id=391">See our Judging Form</a>
 +
<br></br><a href="https://2010.igem.org/Team:British_Columbia/Parts">See our characterized Biobrick Parts</a>
 +
<br></br><a href="https://2010.igem.org/Team:British_Columbia/Project_Phage">See our new Phage Standard</a>
 +
<br></br><a href="https://2010.igem.org/Team:British_Columbia/HumanPractices">See our Human Practices Project</a>
 +
 
<br></br>
<br></br>
-
<ul>
+
<br></br><h3>Consideration for Special Awards</h3>
-
</ul>
+
<p>Besides striving for a Gold Medal and a place as one of the finalists, our team would also like to be considered for the following special awards:</p>
 +
<a href="https://2010.igem.org/Team:British_Columbia/HumanPractices"><img src="https://static.igem.org/mediawiki/2010/f/fa/Bhpa.jpg"></a>
 +
<p><b>"What a society deems important is enshrined in its art." -Harry Broudy</b></p>
 +
<p>Our <a href="https://2010.igem.org/Team:British_Columbia/HumanPractices">human practices project</a> presents the <b>first iGEM art gallery</b> dedicated to synthetic biology and all its diverse aspects. Sometimes art answers our deepest questions. Sometimes art only deepens the mystery. And sometimes a picture is just worth a thousand words. This is our way of helping human civilization consider, guide and address the impacts of ongoing advances in synthetic biology. Not limited to conventional artwork, our gallery also features synthetic biology <b>promoter maps</b> and poems. We also proudly present the <b>first iGEM collaboration with NaNoWriMo</b> to showcase 50,000 word novels featuring synthetic biology, written from scratch during the month of November!</p>
 +
<a href="https://2010.igem.org/Team:British_Columbia/modeling_description"><img src="https://static.igem.org/mediawiki/2010/1/17/Bm.jpg"></a>
 +
<p><b>"One of the most insidious and nefarious properties of scientific models is their tendency to take over, and sometimes supplant, reality." -Erwin Chargaff</b></p>
 +
<p>Right before your eyes, watch how the population dynamics of a biofilm is affected by the introduction of bacteriophage and a biofilm matrix-degrading enzyme. Using our <a href="https://2010.igem.org/Team:British_Columbia/modeling_description">model</a>, we are able to run simulations that predict outcomes of the system and construct informed hypotheses to test in reality.</p>
 +
 
 +
<a href="https://2010.igem.org/Team:British_Columbia/Project_Phage"><img src="https://static.igem.org/mediawiki/2010/7/7f/Bs.jpg"></a>
 +
<p><b>"Acceptance of prevailing standards often means we have no standards of our own." -Jean Toomer
 +
</b></p>
 +
<p>There are standards for prokaryotes and standards for eukaryotes. But what about standards for the living dead? Our new <a href="https://2010.igem.org/Team:British_Columbia/Project_Phage">Phage standard</a> lays down a foundation for future work involving viruses and integrating Biobrick parts into their genome. Prepare to be infected!!!</p>
 +
 
 +
<a href="https://2010.igem.org/Team:British_Columbia"><img src="https://static.igem.org/mediawiki/2010/3/31/Bw.jpg"></a>
 +
<p>We've worked really hard on our wiki to make it accessible, fun and interactive! So we hope that future iGEM teams, students worldwide, and even the general public will visit us here and see what iGEM and synthetic biology is about!</p>
 +
 
 +
<img src="https://static.igem.org/mediawiki/2010/5/59/Bpbp.jpg">
 +
<p>Come and see our poster and team presentation! It will be a great opportunity to meet our team and learn more about our project. A soft copy of our poster and video of our presentation will be linked here during the Jamboree.</p>
 +
 
 +
<a href="https://2010.igem.org/Team:British_Columbia"><img src="https://static.igem.org/mediawiki/2010/6/68/Bhmp.jpg"></a>
 +
<p>Several diseases and medical conditions are known to be caused by biofilm infections. Pathogens existing in biofilms survive under harsher conditions and are much more difficult to eliminate than free-floating pathogens. Our project aims to engineer a bacteriophage equipped with a biofilm matrix-degrading enzyme to eradicate pathogenic Staphylococcus aureus biofilms. Door knob, we shall fear thee no longer.</p>
 +
</center>
 +
 
</div>  <!-- end news -->
</div>  <!-- end news -->

Latest revision as of 02:05, 28 October 2010


Project Achievements & Future Directions

Biofilm:

We have obtained growth curves for S. aureus strains RN4220 and 8325-4 that demonstrate a steady growth phase followed by an oscillatory state of dynamic equilibrium. We have also optimized the existing protocol for biofilm quantification. Additionally, values derived from the biofilm experiments were integral to deriving realistic results from modeling simulations.

The existing curve has demonstrated that 9 hours is the optimal time point for exposure to the matrix-degrading enzyme, DspB, as well as the engineered phage construct with DspB and quorum sensing genes. Future experiments testing the biofilm response to DspB alone as well as DspB incorporated into a phage construct with the quorum sensing P2 promoter will enable the characterization of the construct’s effectiveness against the biofilms of S. aureus strains RN4220 and 8325-4.

Phage Standard:

We developed a phage standard that allows for modification of any lysogenic bacteriophage as part of the Biobrick standard. The phage standard works around the problems of illegal cut sites and prohibitively large plasmids. We hope the standard will serve as a foundational advance towards phage research within the iGEM competition, the BioBrick registry and the synthetic biology community as a whole.

In the future we hope to continue developing this standard and optimizing the process of modifying lysogenic phage DNA. We will strive to submit a fully functional set of parts that have been demonstrated to work following the phage standard in the lab. Hopefully we will also be able to include lytic phages under the scope of the phage standard. With some luck we could expand the number of chassis available to iGEM and the BioBrick registry by introducing integration site vectors for multiple species and strains.

Quorum Sensing:

We have made constructs to characterize the P2 promoter (BBa_I746104) of S. aureus via fluorescent protein production. In order to directly relate AIP to P2 promoter activity, we chose to use an agr null strain. As a next step, genes encoding AgrAC from S. aureus should be put on the same plasmid (the S. aureus/E. coli shuttle vector, pCN33) as the reporter constructs and transformed into agr-null S. aureus. This would allow proper characterization of P2 activity in the presence of AIP. Primers have already been designed and submitted to PCR the genes encoding AgrAC. Additionally, the replicon of the S. aureus pCN33 plasmid can be made into a BioBrick part to facilitate the expression and characterization of BioBrick parts in S. aureus.


DspB:

We have contributed to the biobrick parts registry by submitting a new part: DspB, an enzyme that degrades poly-ß-(1,6)-linked N-acetylglucosamine bonds. We have demonstrated that dspB works through a crude cell enzyme activity assay and have added this information to the Registry.

We are currently working on obtaining data from the exposure of DspB protein on a S. aureus biofilm as well as isolating DspB via a histidine tag to attain further characterization data. We hope to gather this data before the presentation. If not fully completed, these components should be further explored in the future. Future directions also include testing DspB with the P2 promoter in S. aureus under the influence of the auto-inducing peptide (AIP) to characterize DspB under the promoter that it would be expressed in the phage. We would then incorporate DspB protein under the P2 promoter into the phage for exposure to S. aureus biofilms. We expect that this engineered phage will show an improvement in the elimination of the S. aureus biofilm with the protein incorporated into its genome.


Modeling:

We have developed a mathematical model that describes the dynamics of our genetically engineered phage-assisted biofilm dispersal system. Using this model, we can predict the outcome of introducing a biofilm matrix-degrading phage to a biofilm. We have demonstrated that our model can be used as a tool to help design engineered systems similar to ours and to formulate informed hypotheses for phage-biofilm experiments. We have implemented this model in an easy-to-use Java program. Future work includes the extension of this model to account for components, such as genetic elements, that may impact the system and the development of a GUI with better graphical features.


Human Practices:

We have gathered hundreds of definitions of synthetic biology from the University of British Columbia community to construct promoter maps and word clouds representing the prevalent ideas in our different disciplines' awareness of synthetic biology!

We have started the first iGEM synthetic biology art gallery inviting all iGEM participants, as well as members of the public from Deviantart, IllustratedATCs and ATCsForAll to contribute.

We have forged the first NaNoWriMo-iGEM collaboration to showcase novels featuring synthetic biology that are written by NaNoWriMo participants.

Our experience communicating with the general public and even students in the sciences and applied sciences has been an enriching one. We have gleaned a lot of insights into public perception of synthetic biology, which still remains a very new and unfamiliar field to the public despite recent press about the first synthetic cell!

Public opinion and risk perception appears to be more informed by controversial topics (e.g. genetically modified organisms and food) and literature featuring synthetic biology (from Frankenstein to Oryx and Crake). So outreach on the part of synthetic biologists still has quite a way to go in order to bring synthetic biology into the schools, workplaces and homes of the public. Our human practices project has generated ripples of thoughts about synthetic biology in various communities, stimulating individuals to find out more about synthetic biology and its recent developments. We hope that this will open up paths of communication between the synthetic biology research community and diverse public communities, which may lead to discussions and collaborations with the purposes of informing the public about synthetic biology and safely expanding its real world applications.

Some specific future directions that address this cause include: (i) Actively inviting more non-science/engineering students to participate in iGEM outreach/projects/teams/Jamboree/fundraising, (ii) Establishing an annual iGEM tradition of stimulating and showcasing works of art or literature by members of iGEM and the general public featuring synthetic biology, and (iii) Investing in other collaborative outreach activities such as elementary/secondary school educational programs and synthetic biology university courses.



Quick Links

See our Judging Form

See our characterized Biobrick Parts

See our new Phage Standard

See our Human Practices Project



Consideration for Special Awards

Besides striving for a Gold Medal and a place as one of the finalists, our team would also like to be considered for the following special awards:

"What a society deems important is enshrined in its art." -Harry Broudy

Our human practices project presents the first iGEM art gallery dedicated to synthetic biology and all its diverse aspects. Sometimes art answers our deepest questions. Sometimes art only deepens the mystery. And sometimes a picture is just worth a thousand words. This is our way of helping human civilization consider, guide and address the impacts of ongoing advances in synthetic biology. Not limited to conventional artwork, our gallery also features synthetic biology promoter maps and poems. We also proudly present the first iGEM collaboration with NaNoWriMo to showcase 50,000 word novels featuring synthetic biology, written from scratch during the month of November!

"One of the most insidious and nefarious properties of scientific models is their tendency to take over, and sometimes supplant, reality." -Erwin Chargaff

Right before your eyes, watch how the population dynamics of a biofilm is affected by the introduction of bacteriophage and a biofilm matrix-degrading enzyme. Using our model, we are able to run simulations that predict outcomes of the system and construct informed hypotheses to test in reality.

"Acceptance of prevailing standards often means we have no standards of our own." -Jean Toomer

There are standards for prokaryotes and standards for eukaryotes. But what about standards for the living dead? Our new Phage standard lays down a foundation for future work involving viruses and integrating Biobrick parts into their genome. Prepare to be infected!!!

We've worked really hard on our wiki to make it accessible, fun and interactive! So we hope that future iGEM teams, students worldwide, and even the general public will visit us here and see what iGEM and synthetic biology is about!

Come and see our poster and team presentation! It will be a great opportunity to meet our team and learn more about our project. A soft copy of our poster and video of our presentation will be linked here during the Jamboree.

Several diseases and medical conditions are known to be caused by biofilm infections. Pathogens existing in biofilms survive under harsher conditions and are much more difficult to eliminate than free-floating pathogens. Our project aims to engineer a bacteriophage equipped with a biofilm matrix-degrading enzyme to eradicate pathogenic Staphylococcus aureus biofilms. Door knob, we shall fear thee no longer.