Team:Waterloo

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Idea

Due to its nature as an information-encoding molecule, the use of DNA as an intercellular messaging molecule would enable more information-rich communication between populations of cells than traditional AHL-based messaging. The first demonstration of DNA messaging was published by the Endy group at Stanford University in late 2012, wherein DNA encoding instructions for expression of fluorescence and antibiotic resistance were transmitted from one bacterial population to another, carried by M13 bacteriophage particles.

Incorporation of well-established in vivo DNA modification techniques into DNA messaging will diversify and extend potential intercellular communication programs, and will enable the integration of recent developments in DNA digital logic with DNA messaging.

The goal of our project is to place on a DNA message a switch that can be flipped in receiver cells under inducible conditions, and whose state determines whether or not the DNA message is retransmitted from receiver cells to a population of secondary receiver cells. The switch consists of a promoter that can be inverted using a serine integrase, leading to transcription of different genes. It is directly inspired by the recombinase addressable data (RAD) module published by the Endy group in early 2012.

We have synthesized four such DNA switches and will soon test the ability of PhiC31 and Bxb1 serine integrases, along with the respective recombination directionality factors (RDFs), to control their states. We have also produced constructs that we will use to attempt to control the production of M13 viral particles containing a DNA message and we will test these soon. We will integrate these efforts to demonstrate our goal of incorporating digital DNA logic into DNA messaging. Through this work, we will broaden the horizons of engineered intercellular communication.

Videos

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Results

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Conclusions

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BioBricks

Ottawa's Collaboration

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Notebook

Switch Modelling

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Population & Infection Modelling

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Phage Particle Production Modelling

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The University of Waterloo’s iGEM – Human Practices team is a diverse team whose goal is to raise awareness on issues regarding synthetic biology. In addition, the team also provides the student community information about the latest in the research area of synthetic biology to help the community make informed, accurate and fact-based opinions. Our goal is to strengthen the bridge between the community and their knowledge of synthetic biology along with eliminating misconceptions regarding synthetic biology.

In the past year, this team gained valuable experience and information through the projects they worked on. Each project provided more insight on how informed the student community is on the topic of synthetic biology. This further helped us plan out activities that help us achieve our goal.

One of the main purposes behind the projects this year to enrich, educate and empower the student community. To achieve this goal, various activities were planned to inform the student community about the field of synthetic biology, it’s potentials and how it affects the world around us. These activities provide fundamental knowledge of synthetic biology and it’s uses, allowing the participants and the viewers to form an informed, accurate and fact-based opinion about the topic.

Intent to Invent

Intent to Invent was hosted on March 07, 2013 at the University of Waterloo’s Quantum Nano Center. The purpose of the event was to:

1. Connect the students to experts in 3 key industries that use synthetic biology in their processes: Agriculture, Health and Pharmaceuticals.

2. Bridge the level of discomfort a scientist has in regards to business.

3. To encourage entrepreneurship within the scientific community by delivering resourceful content from industry experts.

The event promoted open panel discussions of emerging technologies in biotechnology and other advanced biological fields within the 3 industries. Students got a chance to see how synthetic biology is the connected to entrepreneurship, innovation and commercialization. They learned about the industry perspectives and barriers faced by biological companies at different stages in their business model. This talk also encouraged entrepreneurship within the scientific community by delivering resourceful content form industry experts. Each speaker gave a 20-minute mini lecture on topics including: Clinical Trial Drug Development, Commercialization of Biomass and Energy Products and Entrepreneurial Barriers for Biotechnology Companies.

Steve jobs once said, “I think the biggest innovation of 21st century will be the intersection of biology and technology. A new era is beginning, just like the digital one…”. Through sessions such as Intent to Invent, Waterloo iGEM hopes to enrich the experience of science enthusiasts as well as those just curious about synthetic biology and it’s potential. By connecting these students to industry experts, we were able to gage their interests in an innovative and entrepreneurial aspect of science. Many students showed interest in learning more about the bridge between science and business in the future. iGEM received good feedback regarding Intent to Invent, as many students felt that the information they learned was very valuable. Waterloo iGEM provided many students the appropriate connection and information they need to start connecting the scientist in them with the businessman/businesswoman in them.

T.I.L.

iGEM is a community of people passionate about synthetic biology –how can we best convey this while reaching out to the public? Sometimes reading papers and textbooks doesn't quite do it for understanding an idea. As students, we know it can be difficult to grasp some concepts we’re not familiar with. So what’s a better way to communicate an idea? Could social media be the answer? That was the idea behind the VLOG series TIL: Syn Bio. Social media is a powerful tool to reach out to the World Wide Web –this could be a great means to quickly and effectively convey the ideas and the passion we share!

The series begins with the basic question of “What is synthetic biology?”, explaining the basis of synthetic biology in an animated style. Next, the “Fundamental Advances” explain the mechanism behind the ‘magic’ of synthetic biology. With this foundation, the next episode explains how we apply synthetic biology to Waterloo iGEM's project for 2013. This phase of the series is important to orient the viewers and provide some background information. During the second part of the series, the team takes a fun twist. Using the TIL: Synthetic Biology outreach event footage to compare the viewpoints of students and professors on various topics relating to synthetic biology. The footage from this event is used for addressing the stigma associated with modifying organisms in the video “Stigma”. Students and professors also recognize the potential in the area of synthetic biology in the video “Future”. With all the potential this area holds, it is important to know who’s allowed to do what. This is addressed in the video “Regulations”. Students and professors address the impact of laws, policy, social effects and the role of the media as it applies to the advancement of synthetic biology.

The series begins with these six videos, leaving the rest of the series to be shaped by viewers. Ultimately, viewers engage with the team about what they want to see in future videos, ask questions they want answered and connect with information from a variety of sources. The internet connects us according to one's interest. It is becoming easier and easier to find content users are interested in (especially on Youtube). This is why a video medium was chosen to connect with viewers.

The team encountered some challenges engaging professors to take part of the video series because of spring/summer holidays. This encouraged the diversification of professor background -looking to professors with different academic disciplines In this way, a broader view of synthetic biology is captured by looking at individuals studying synthetic biology along with those from other backgrounds.

The TIL: Synthetic Biology outreach event (used as part of the video series) was well-received. The team came prepared with questions to ask passing students. Students were also given 4-5 days notice via Facebook. The idea behind this aspect of the video was to have it be a surprise. Questions like "do you support GMOs?", "would you eat modified fruit/meat?", "who should be able to practice synthetic biology/should it be opensourced?" and many more were asked. The team was in for some surprises with the diversity of knowledge on campus! We hope incorporating the footage into our series will give participants a fun look into their experience, which they can easily share with their friends and family.

Overall, we hope that the team's work will inspire more leaders to take part and contribute to the advances in synthetic biology, regardless of their academic or professional background.

Special Project

Laboratory

Intent to Invent

Safety

All experiments are carried out in a BL2 certified lab. Researcher safety when using E. coli, would not be compromised in safety issues due to use of M13. It poses no threat at all to humans. While, the E. coli strain used was relatively harmless, treatment of possible infections may potentially be affected by the antibiotic resistance. Furthermore, spontaneous mutations which result in increased infectivity may result. However, measures and precautions suggested by the Canadian biosafety guidelines were taken to minimize even the slight chance of infection. Additionally, the working conditions of the lab is already above the recommended safety level of BL1 for usage of M13 viruses. Every member of the team has been trained with safety modules and went through a week of lab training and continuous oversight from the Advisors and his graduate students in the lab. All lab members, including graduate students or other students that were working in the lab, wore appropriate PPEs and disposed all consumable in appropriate biological waste boxes. All surfaces were wiped down with ethanol after use and all glassware was washed immediately after their usage.

The design of the project does not call for release into the public. Additionally, the project design does not produce any harmful products. Through it is possible that the construct could get released to the general public accidentally. But, the product of the constructs only produce fluorescent proteins and it can only be used in a controlled setting with a certain type of chemical present in the environment, thus making it ineffective when released to the public. Because safety of the public and the lab members is our utmost concern, we have ensured that all wastes are thrown out appropriately and autoclaved so that accidentally release would never occur.

There are no additional risks posed by our projects compared to other general BL1 lab concerns. Our bacteria are not pathogenic and are unable to survive outside of the lab environment, because they are unable to effectively compete with other organisms in nature. As stated above, all wastes are discarded according to the Waterloo standards and autoclaved.

There is no potential for harm to human health through use of our constructs, as described above. There is therefore no risk of malicious use.

Our constructs pose no threats to human health, as described above, and scaling up would not change this. Our project is a "fundamental advance" that contributes to the coordination of population-level cellular behavior by allowing messages to be sent between populations of E. coli cells. However, many additional layers of complexity in engineering would be required to use our method to enable pathogenic or otherwise dangerous behaviors in populations of cells.

The cell to cell communication project does include packaging viral particles. Although there are only some proteins of the M13 virus that are packaged and are therefore not a safety risk. M13 is not a safety risk even if its whole genome is packaged. Our project poses no threat to safety and thus we haven't implemented any of these mechanisms.

All the lab and design team members successfully passed the following safety training: Employee Orientation Training Session: https://info.uwaterloo.ca/infohs/hse/online_training/employee-orientation/Staff%20Orientation.swf Workplace Violence and Harassment Training: https://info.uwaterloo.ca/infohs/hse/online_training/workplace_violence/workplace_violence.html General Laboratory Safety: https://info.uwaterloo.ca/infohs/hse/online_training/lab_safety/lab_safety_course.html WHMIS: http://www.safetyoffice.uwaterloo.ca/hse/lab_safety/index.html Laboratory BioSafety Training: https://info.uwaterloo.ca/infohs/hse/online_training/biosafety/biosafety.swf

The BioSafety Guidelines followed by uWaterloo iGEM team can be found here: http://www.safetyoffice.uwaterloo.ca/hse/bio_safety/legislation.html

University of Waterloo has a Biosafety Committee and can be found here: http://www.safetyoffice.uwaterloo.ca/hse/bio_safety/bsc.html. Although the project has not been discussed with the Biosafety Committee, it has been discussed with several faculty members and has been found to have no risks. Furthermore, the laboratories operating at the University of Waterloo have obtained permits from the Bio-Safety Committee in order to perform intended research. Since the Waterloo iGEM team performs all laboratory work in a parent lab under the guidance of the Masters and PhD students of that lab, the permits obtained by the parent lab cover the projects carried out in the lab.

Canada has very well established biosafety regulations and guidelines which can be found here: http://www.phac-aspc.gc.ca/lab-bio/

The laboratory we work on cell to cell communication project is rated level 1.

E.coli strains that Waterloo iGEM team works with falls within the risk level 1. Additionally the laboratory we operate in is certified for work with the above listed risk group of the E.coli.

Sponsors

Administrators

Lab & Design

M13 Group

BxB1 Group

Φ C31 Group

Mathematical Modelling

Human Practices

Advisors

Graduate Student Advisors

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