Difference between revisions of "Team:Waterloo/HP-Silver"

Line 77: Line 77:
 
</div></nav>
 
</div></nav>
 
<div class="content">
 
<div class="content">
−
<div class="row"><div class="col"><div class="content-main"><p>Convince the judges you have thought carefully and creatively about whether your work is safe, responsible and good for the world. You could accomplish this through engaging with your local, national and/or international communities or other approaches. write about the Human Practices topics you considered in your project, and document any special activities you did (such as visiting experts, talking to lawmakers, or doing public engagement)</p>
+
<div class="row"><div class="col"><div class="content-main"><h3 id="-project-determination-"><strong>Project Determination</strong></h3>
−
<p>In order to evaluate the project choice that Waterloo iGEM seeks to choose for the consensus of its team, proper quantitative and qualitative analysis must be done. We collected our team’s opinion and ranking of each project quantitatively, followed by consulting with our advisors to get qualitative consulting advice. </p>
+
−
<h3 id="-project-determination-"><strong>Project Determination</strong></h3>
+
 
<p>The selection process for this years project began with several of our members creating project proposals and presenting their ideas to the whole team. Each project idea went through several layers of analysis, starting with over 30 individual assessments by members from all subteams. With the diverse disciplines amongst our team, we received input from a science, mathematics, engineering and business perspective. The individual assessments were compiled, resulting in a quantitative analysis of which project the team believed was the best to pursue. The assessments were based on the set of criteria that we have carefully articulated, which is described below:</p>
 
<p>The selection process for this years project began with several of our members creating project proposals and presenting their ideas to the whole team. Each project idea went through several layers of analysis, starting with over 30 individual assessments by members from all subteams. With the diverse disciplines amongst our team, we received input from a science, mathematics, engineering and business perspective. The individual assessments were compiled, resulting in a quantitative analysis of which project the team believed was the best to pursue. The assessments were based on the set of criteria that we have carefully articulated, which is described below:</p>
 
<h3 id="-primary-criteria-evaluates-the-most-important-aspects-of-a-project-"><strong>Primary Criteria: evaluates the most important aspects of a project</strong></h3>
 
<h3 id="-primary-criteria-evaluates-the-most-important-aspects-of-a-project-"><strong>Primary Criteria: evaluates the most important aspects of a project</strong></h3>
Line 88: Line 86:
 
<h3 id="-secondary-criteria-evaluates-the-level-of-engagement-for-subteams-in-the-organisation-"><strong>Secondary Criteria: evaluates the level of engagement for subteams in the organisation.</strong></h3>
 
<h3 id="-secondary-criteria-evaluates-the-level-of-engagement-for-subteams-in-the-organisation-"><strong>Secondary Criteria: evaluates the level of engagement for subteams in the organisation.</strong></h3>
 
<h4 id="-interest-"><strong>Interest</strong></h4>
 
<h4 id="-interest-"><strong>Interest</strong></h4>
−
<p>The level of interest amongst the members in a project is valuable as a teams with a greater interest in their project are like more likely to excel and be successful </p>
+
<p>The level of interest amongst the members in a project is valuable as a teams with a greater interest in their project are like more likely to excel and be successful</p>
 
<h4 id="-applicability-of-the-team-"><strong>Applicability of the team</strong></h4>
 
<h4 id="-applicability-of-the-team-"><strong>Applicability of the team</strong></h4>
 
<p>It is important to select a project that will enable all subteams are to work on their respective aspects of the project to fulfil medal criteria</p>
 
<p>It is important to select a project that will enable all subteams are to work on their respective aspects of the project to fulfil medal criteria</p>
 
<h4 id="-usefulness-"><strong>Usefulness</strong></h4>
 
<h4 id="-usefulness-"><strong>Usefulness</strong></h4>
−
<p>The degree to which how useful the project is and how it can impact society (how stakeholders benefit and how many stakeholders are benefitted). </p>
+
<p>The degree to which how useful the project is and how it can impact society (how stakeholders benefit and how many stakeholders are benefitted).</p>
−
<p>Following the team analysis, the project proposals were presented to advisors from UW’s Faculty of Biology. Advisors from the University of Waterloo Faculty of Biology: Brian Ingalls, Trevor Charles, Barbara Moffatt, Andrew Doxey, and Forbes Burkowski. </p>
+
<p>Following the team analysis, the project proposals were presented to advisors from UW’s Faculty of Biology. Advisors from the University of Waterloo Faculty of Biology: Brian Ingalls, Trevor Charles, Barbara Moffatt, Andrew Doxey, and Forbes Burkowski.</p>
 
<h3 id="-criteria-weighting-out-of-5-"><strong>Criteria Weighting (out of 5)</strong></h3>
 
<h3 id="-criteria-weighting-out-of-5-"><strong>Criteria Weighting (out of 5)</strong></h3>
 
<p>Interest - /2
 
<p>Interest - /2
Line 115: Line 113:
 
<tr>
 
<tr>
 
<td><b>Feasibility </b> <br> <ul> <li> Do we have the resources? </li> <li> Do we have the experience? </li> </ul></td>
 
<td><b>Feasibility </b> <br> <ul> <li> Do we have the resources? </li> <li> Do we have the experience? </li> </ul></td>
−
<td><ul> <li> 90% feasibility 7/10 or higher </li> <li> Potential roadblock: not enough experience with yeast? </li> <li> Profs will be around to help us learn </li> <li> Last year’s project worked with prions, so we have experience with prions </li> <li> High chance of working </li> </ul> </td>
+
<td><ul> <li> 90% feasibility 7/10 or higher </li> <li> Potential roadblock: not enough experience with yeast? </li> <li> Profs will be around to help us learn </li> <li> Last year’s project worked with prions, so we have experience with prions </li> <li> High chance of working </li> </ul></td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
Line 123: Line 121:
 
<tr>
 
<tr>
 
<td><b> Novelty </b> <br> <ul> <li> Did we build on other ideas? </li> </ul></td>
 
<td><b> Novelty </b> <br> <ul> <li> Did we build on other ideas? </li> </ul></td>
−
<td><ul> <li> The idea to specifically apply prion domain to other protein is something new in our understanding </li> <li> We have previously worked with prions in 2016, but not exclusively on the prion domains </li> </ul> </td>
+
<td><ul> <li> The idea to specifically apply prion domain to other protein is something new in our understanding </li> <li> We have previously worked with prions in 2016, but not exclusively on the prion domains </li> </ul></td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
Line 157: Line 155:
 
<tr>
 
<tr>
 
<td><b> Novelty </b> <br> <ul> <li> Did we build on other ideas? </li> </ul></td>
 
<td><b> Novelty </b> <br> <ul> <li> Did we build on other ideas? </li> </ul></td>
−
<td><ul> <li>  This project was inspired by Wageningen university 2013 iGEM team </li> </ul> </td>
+
<td><ul> <li>  This project was inspired by Wageningen university 2013 iGEM team </li> </ul></td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
 
<td><b> Impact/Usefulness/Why are we doing it? </b> <br> <ul> <li> Economic </li> <li> Societal </li> <li> Environmental </li> <li> Ethical </li> <li> Material </li> <li> Emotional </li> </ul> <br> Consider both positive and negative impacts</td>
 
<td><b> Impact/Usefulness/Why are we doing it? </b> <br> <ul> <li> Economic </li> <li> Societal </li> <li> Environmental </li> <li> Ethical </li> <li> Material </li> <li> Emotional </li> </ul> <br> Consider both positive and negative impacts</td>
−
<td><ul> <li> Having to take samples and manually run tests for gene expression is a huge pain </li> <li> Last year, one of the biggest problems we had was our limited data due to this restraint </li> <li> When you don’t have enough data, it’s hard to confidently predict what is happening in your system </li> <li> This project would make it significantly easier to collect large amounts of continuous data on gene expression which would be <em>extremely</em> useful for a huge number of synbio experiments </li> </ul> </td>
+
<td><ul> <li> Having to take samples and manually run tests for gene expression is a huge pain </li> <li> Last year, one of the biggest problems we had was our limited data due to this restraint </li> <li> When you don’t have enough data, it’s hard to confidently predict what is happening in your system </li> <li> This project would make it significantly easier to collect large amounts of continuous data on gene expression which would be <em>extremely</em> useful for a huge number of synbio experiments </li> </ul></td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
 
<td><b> Alternative </b> <br> <ul> <li> Is there another more efficient/better way to go about solving the problem? </li> </ul></td>
 
<td><b> Alternative </b> <br> <ul> <li> Is there another more efficient/better way to go about solving the problem? </li> </ul></td>
−
<td><ul> <li> Measurement of LuxI - how does one know what the protein of interest is doing? (either fuse our protein of interest to LuxI or get the same promoter to control LuxI expression and the expression of protein of interest, but in the latter case we don’t know about protein degradation of our protein of interest, and the former is harder to do) </li> </ul> </td>
+
<td><ul> <li> Measurement of LuxI - how does one know what the protein of interest is doing? (either fuse our protein of interest to LuxI or get the same promoter to control LuxI expression and the expression of protein of interest, but in the latter case we don’t know about protein degradation of our protein of interest, and the former is harder to do) </li> </ul></td>
 
</tr>
 
</tr>
 
</tbody>
 
</tbody>
Line 173: Line 171:
 
<tr>
 
<tr>
 
<th>Criteria</th>
 
<th>Criteria</th>
−
<th>Magnetic Bacteria </th>
+
<th>Magnetic Bacteria</th>
 
</tr>
 
</tr>
 
</thead>
 
</thead>
Line 179: Line 177:
 
<tr>
 
<tr>
 
<td><b> Description of Project </b> <br> <ul> <li> What kind of problem are we solving? </li> <li>How are we doing it? </li> </ul></td>
 
<td><b> Description of Project </b> <br> <ul> <li> What kind of problem are we solving? </li> <li>How are we doing it? </li> </ul></td>
−
<td><ul> <li> Ability for the bacteria to move throughout the body (flagella) </li> <li> Ability to externally control the movement of bacteria </li> <li> Specific apoptosis targeting of cancerous cells only </li> <li> Ability to detect the bacteria </li> <li> How to do this? Use mgFRN as a transcription factor to express a gene of interest </li> <li> Cytotic gene only turned on during low oxygen levels </li> <li> As tumor shrinks, levels of O2 increase turning off our system </li> </ul> </td>
+
<td><ul> <li> Ability for the bacteria to move throughout the body (flagella) </li> <li> Ability to externally control the movement of bacteria </li> <li> Specific apoptosis targeting of cancerous cells only </li> <li> Ability to detect the bacteria </li> <li> How to do this? Use mgFRN as a transcription factor to express a gene of interest </li> <li> Cytotic gene only turned on during low oxygen levels </li> <li> As tumor shrinks, levels of O2 increase turning off our system </li> </ul></td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
Line 195: Line 193:
 
<tr>
 
<tr>
 
<td><b> Impact/Usefulness/Why are we doing it? </b> <br> <ul> <li> Economic </li> <li> Societal </li> <li> Environmental </li> <li> Ethical </li> <li> Material </li> <li> Emotional </li> </ul> <br> Consider both positive and negative impacts</td>
 
<td><b> Impact/Usefulness/Why are we doing it? </b> <br> <ul> <li> Economic </li> <li> Societal </li> <li> Environmental </li> <li> Ethical </li> <li> Material </li> <li> Emotional </li> </ul> <br> Consider both positive and negative impacts</td>
−
<td><ul> <li> The magnetic properties could be utilized to improve targeted delivery of drugs </li> <li> This will be promising in the treatment of on-site diseases such as cancer, infection </li> </ul> </td>
+
<td><ul> <li> The magnetic properties could be utilized to improve targeted delivery of drugs </li> <li> This will be promising in the treatment of on-site diseases such as cancer, infection </li> </ul></td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
 
<td><b> Alternative </b> <br> <ul> <li> Is there another more efficient/better way to go about solving the problem? </li> </ul></td>
 
<td><b> Alternative </b> <br> <ul> <li> Is there another more efficient/better way to go about solving the problem? </li> </ul></td>
−
<td><ul> <li> No viable alternatives discussed </li> </ul> </td>
+
<td><ul> <li> No viable alternatives discussed </li> </ul></td>
 
</tr>
 
</tr>
 
</tbody>
 
</tbody>
Line 207: Line 205:
 
<tr>
 
<tr>
 
<th>Criteria</th>
 
<th>Criteria</th>
−
<th>Zika </th>
+
<th>Zika</th>
 
</tr>
 
</tr>
 
</thead>
 
</thead>
Line 221: Line 219:
 
<tr>
 
<tr>
 
<td><b>Interest/Applicability to Subteam </b> <br> <ul> <li> Personal opinions </li> </ul></td>
 
<td><b>Interest/Applicability to Subteam </b> <br> <ul> <li> Personal opinions </li> </ul></td>
−
<td><ul> <li> 83.4% interest 7/10 or more </li> <li> 73.4% applicable to subteam 7/10 or more </li> </ul> </td>
+
<td><ul> <li> 83.4% interest 7/10 or more </li> <li> 73.4% applicable to subteam 7/10 or more </li> </ul></td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
Line 229: Line 227:
 
<tr>
 
<tr>
 
<td><b> Impact/Usefulness/Why are we doing it? </b> <br> <ul> <li> Economic </li> <li> Societal </li> <li> Environmental </li> <li> Ethical </li> <li> Material </li> <li> Emotional </li> </ul> <br> Consider both positive and negative impacts</td>
 
<td><b> Impact/Usefulness/Why are we doing it? </b> <br> <ul> <li> Economic </li> <li> Societal </li> <li> Environmental </li> <li> Ethical </li> <li> Material </li> <li> Emotional </li> </ul> <br> Consider both positive and negative impacts</td>
−
<td><ul> <li> Protect people in Latin American countries from being infected with zika virus without harming the mosquito population and surrounding ecosystem </li> <li> Deployment is intuitive and fast to implement with closed off bodies of water and pellets of yeast thrown into </li> </ul> </td>
+
<td><ul> <li> Protect people in Latin American countries from being infected with zika virus without harming the mosquito population and surrounding ecosystem </li> <li> Deployment is intuitive and fast to implement with closed off bodies of water and pellets of yeast thrown into </li> </ul></td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
Line 238: Line 236:
 
</table>
 
</table>
 
<h3 id="-conclusion-"><strong>Conclusion:</strong></h3>
 
<h3 id="-conclusion-"><strong>Conclusion:</strong></h3>
−
<p>In conclusion, the Waterloo iGEM 2017 team has decided to select the engineered prion project for this year. </p>
+
<p>In conclusion, the Waterloo iGEM 2017 team has decided to select the engineered prion project for this year.</p>
 
</div></div></div>
 
</div></div></div>
 
</div>
 
</div>

Revision as of 21:55, 29 October 2017

Project Determination

The selection process for this years project began with several of our members creating project proposals and presenting their ideas to the whole team. Each project idea went through several layers of analysis, starting with over 30 individual assessments by members from all subteams. With the diverse disciplines amongst our team, we received input from a science, mathematics, engineering and business perspective. The individual assessments were compiled, resulting in a quantitative analysis of which project the team believed was the best to pursue. The assessments were based on the set of criteria that we have carefully articulated, which is described below:

Primary Criteria: evaluates the most important aspects of a project

Novelty

This year, each of the project proposals fell under the Foundational Advance track. The basis of this track is to develop novel solutions to technical problems, thus the novelty of the project was one of the priorities.

Feasibility

When developing project ideas, teams must also consider the amount of resources available to them. It is important to be able to achieve their goals with what they have to produce a complete project

Secondary Criteria: evaluates the level of engagement for subteams in the organisation.

Interest

The level of interest amongst the members in a project is valuable as a teams with a greater interest in their project are like more likely to excel and be successful

Applicability of the team

It is important to select a project that will enable all subteams are to work on their respective aspects of the project to fulfil medal criteria

Usefulness

The degree to which how useful the project is and how it can impact society (how stakeholders benefit and how many stakeholders are benefitted).

Following the team analysis, the project proposals were presented to advisors from UW’s Faculty of Biology. Advisors from the University of Waterloo Faculty of Biology: Brian Ingalls, Trevor Charles, Barbara Moffatt, Andrew Doxey, and Forbes Burkowski.

Criteria Weighting (out of 5)

Interest - /2 Application to Subteam - /3 Novelty - /5 *For Foundational Advancements only Usefulness - /2 Impact - /2 Feasibility - / 5

Criteria Functional Prion Project
Description of Project
  • What kind of problem are we solving?
  • How are we doing it?
  • It is observed that fusing proteins together typically reduces function, although it is possible to engineer the prions such that the function increases
  • Reconstruct DNA such that it creates a prion domain in a new protein, allowing it to aggregate with other prion proteins
Feasibility
  • Do we have the resources?
  • Do we have the experience?
  • 90% feasibility 7/10 or higher
  • Potential roadblock: not enough experience with yeast?
  • Profs will be around to help us learn
  • Last year’s project worked with prions, so we have experience with prions
  • High chance of working
Interest/Applicability to Subteam
  • Personal opinions
  • 63.4% interested 7/10 or more
  • 76.6% applicable to subteam 7/10 or more
Novelty
  • Did we build on other ideas?
  • The idea to specifically apply prion domain to other protein is something new in our understanding
  • We have previously worked with prions in 2016, but not exclusively on the prion domains
Impact/Usefulness/Why are we doing it?
  • Economic
  • Societal
  • Environmental
  • Ethical
  • Material
  • Emotional

Consider both positive and negative impacts
  • Understanding the aggregation mechanisms of prion could contribute in the discovery of new treatment against it
  • The aggregation of enzyme with prion domain could help increasing the speed and efficiency of biochemical reactions
  • The aggregate structure could be used to construct new biomaterial with additional durability, etc.
Alternative
  • Is there another more efficient/better way to go about solving the problem?
  • No viable alternatives discussed
Criteria Oscillational Fluorescence for Measurement
Description of Project
  • What kind of problem are we solving?
  • How are we doing it?
  • Fusing Green Fluorescent Protein (GFP) to a protein of interest is a common way to detect the expression of that protein
  • The idea is that when you shine a certain frequency of light on your sample, if you see that it’s glowing green, you know that the GFP is being expressed and so the protein it’s fused to is also being expressed
  • Problem: The problem is that if you want to measure how much a given protein is being expressed, you have to measure how much it is fluorescing, which is appreciably harder to do
  • Solution: Fluorescence is hard to measure whereas time is easy to measure.
  • If we can create a system where we see fluctuations in time rather than fluorescence, we can make a much easier technique for continuously collecting data on the level of expression of a protein over time
Feasibility
  • Do we have the resources?
  • Do we have the experience?
  • 86.6% feasibility 7/10 or higher
  • System involves many parts, chance that lab will have troubles with manipulating concentrations of components
  • Only working with E.Coli, no other organisms
  • Flow cytometry is widely used
  • General agreement that it’s feasible
Interest/Applicability to Subteam
  • Personal opinions
  • 56.7% interest 7/10 or more
  • 66.6% applicable to subteam 7/10 or more
Novelty
  • Did we build on other ideas?
  • This project was inspired by Wageningen university 2013 iGEM team
Impact/Usefulness/Why are we doing it?
  • Economic
  • Societal
  • Environmental
  • Ethical
  • Material
  • Emotional

Consider both positive and negative impacts
  • Having to take samples and manually run tests for gene expression is a huge pain
  • Last year, one of the biggest problems we had was our limited data due to this restraint
  • When you don’t have enough data, it’s hard to confidently predict what is happening in your system
  • This project would make it significantly easier to collect large amounts of continuous data on gene expression which would be extremely useful for a huge number of synbio experiments
Alternative
  • Is there another more efficient/better way to go about solving the problem?
  • Measurement of LuxI - how does one know what the protein of interest is doing? (either fuse our protein of interest to LuxI or get the same promoter to control LuxI expression and the expression of protein of interest, but in the latter case we don’t know about protein degradation of our protein of interest, and the former is harder to do)
Criteria Magnetic Bacteria
Description of Project
  • What kind of problem are we solving?
  • How are we doing it?
  • Ability for the bacteria to move throughout the body (flagella)
  • Ability to externally control the movement of bacteria
  • Specific apoptosis targeting of cancerous cells only
  • Ability to detect the bacteria
  • How to do this? Use mgFRN as a transcription factor to express a gene of interest
  • Cytotic gene only turned on during low oxygen levels
  • As tumor shrinks, levels of O2 increase turning off our system
Feasibility
  • Do we have the resources?
  • Do we have the experience?
  • 13.3% feasibility 7/10 or higher
  • Lack of time to complete this, slow growth rate of bacteria
  • Lack of resources, no access to mice
  • Lack of experience, would need more time to learn how to perform this in lab
  • Low feasibility in performing this with non-model organism
  • General agreement of low feasibility
Interest/Applicability to Subteam
  • Personal opinions
  • 80% interested 7/10 or more
  • 76.7% applicable to subteam 7/10 or more
Novelty
  • Did we build on other ideas?
  • We have rarely observed any project that have focused on magnetic bacteria
  • We believe that the idea of use magnetism as a guiding mechanism is relatively new and minimally developed
Impact/Usefulness/Why are we doing it?
  • Economic
  • Societal
  • Environmental
  • Ethical
  • Material
  • Emotional

Consider both positive and negative impacts
  • The magnetic properties could be utilized to improve targeted delivery of drugs
  • This will be promising in the treatment of on-site diseases such as cancer, infection
Alternative
  • Is there another more efficient/better way to go about solving the problem?
  • No viable alternatives discussed
Criteria Zika
Description of Project
  • What kind of problem are we solving?
  • How are we doing it?
  • Our proposal aims to provide a novel method for controlling the prevalence of Zika virus (ZIKV) in Aedes mosquito populations through the use of genetically engineered Pichia, a yeast endosymbiont of Aedes
  • This measure utilizes two components: the expression of AXL, a tyrosine-protein kinase receptor thought to be required for ZIKV internalization; and a CRISPR/FnCas9 system, equipped with a guide RNA (gRNA) to target the RNA-dependent RNA polymerase (RdRP) encoding region of the ZIKV ssRNA genome
  • These constructs will be integrated into the Pichia genome, allowing the yeast to sequester ZIKV intracellularly and destroy the viral particles, effectively decreasing the risk of transmission from Aedes to humans
  • Since Pichia are naturally part of the Aedes gut microbiome, this process should not change the competitiveness of Aedes, resulting in minimal ecological consequences
Feasibility
  • Do we have the resources?
  • Do we have the experience?
  • 49.9% feasibility 7/10 or higher
  • No access to Zika or mosquitoes, our lab team would be performing very different experiments than what we actually want
  • Working with non-model organisms
  • The resources needed to develop this include different strains of yeast, dry pellets, CRISPR, zika like strands of RNA to implement as a proof of concept
  • Most certainly not enough experiment to implement this far reaching proof of concept design not yet tested
Interest/Applicability to Subteam
  • Personal opinions
  • 83.4% interest 7/10 or more
  • 73.4% applicable to subteam 7/10 or more
Novelty
  • Did we build on other ideas?
  • The idea of using a yeast species employed with CRISPR is an interesting and novel idea, albeit it is inspired by research papers
  • However, we would be really excited with the opportunity to work with these
Impact/Usefulness/Why are we doing it?
  • Economic
  • Societal
  • Environmental
  • Ethical
  • Material
  • Emotional

Consider both positive and negative impacts
  • Protect people in Latin American countries from being infected with zika virus without harming the mosquito population and surrounding ecosystem
  • Deployment is intuitive and fast to implement with closed off bodies of water and pellets of yeast thrown into
Alternative
  • Is there another more efficient/better way to go about solving the problem?
  • Wolbachia bacteria have been used similar studies, but have not implemented CRISPR, nor would this experiment work to use a human AXL receptor inside a prokaryote cell

Conclusion:

In conclusion, the Waterloo iGEM 2017 team has decided to select the engineered prion project for this year.

Waterloo iGEM 2017

© 2017 Waterloo iGEM