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A Message from the McMaster Genetically Engineered Machine Team



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A YEAR IN REVIEW Our Accomplishments The iGEM Jamboree

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YOUR IMPACT Sponsor Tiers Budget Breakdown

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OUR FUTURE Investing in People Engaging the City: Hamilton Public Health Educating Beyond: McMaster and Hamilton

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ttv2018 Project Outline Investigating Protein Aggregates in Disease





MESSAGE FROM THE PRESIDENTS Aline-Claire Huynh and Audrey Jong

Dear Sponsor, As our society grapples with novel challenges in healthcare, industry, and the environment, it has become more important than ever to foster new generations of scientists, problemsolvers, and decision-makers. This goal was core to the establishment of the International Genetically Engineered Machine (iGEM) Competition for synthetic biology, and it lies at the heart of McMaster’s own iGEM team, mGEM. With 38 undergraduate members from across all disciplines this year, we at mGEM believe strongly in supporting students in their growth as both learners and leaders. Going into our fourth year of competing at iGEM, we’ve been able to empower our members to explore lab research, engage with world-gripping issues, and unpack the role of science and biotechnology in our societal systems. For our 2018 season, we are delving deeper into intersections between health and synthetic biology. This year, we are partnering with Dr. Fei Geng at the W Booth School of Engineering Practice and Technology at McMaster to develop a project using a mutational bacterial model system to investigate mechanisms of amyloid-beta aggregation in Alzheimer’s disease. Discovering factors for this disease is especially important in light of Canada’s aging population. We would be incredibly grateful for your support in realizing our research and mentorship initiatives. In coming years, we look forward to tackling new projects, catalyzing new discussions, and creating more opportunities for students to learn, grow, and boldly strive.

Co-Presidents of iGEM McMaster






Audrey Jong

Aline-Claire Huynh

2nd Year Health Sciences Student

2nd Year Health Sciences Student



Julie Robinson

Eva Liu

3rd Year Biochemistry Student


2nd Year Health Sciences Student


Rachael Gregoris

Fatima Sheikh

2nd Year Arts & Science Student

2nd Year Life Sciences Student 5

"One doesn’t often expect real, impactful research to come from freshman students... ... But we do."



One doesn’t often expect real, impactful research to come from freshman students. But we do. It is the challenge that we set for our incoming members every year, and they never fail to impress. This year, our work on DNAzyme biodetection, undertaken in collaboration with the Yingfu Li lab, led us to place with a Bronze Award at the international iGEM Giant Jamboree competition. Our experiences have made us believe more firmly than ever in the astounding scientific capabilities unlocked when passionate learners and dedicated mentors put their heads together. With your help, we’ll keep working towards our mission of nurturing, inspiring, and empowering McMaster’s undergraduate research potential.

YOUR PIVOTAL SUPPORT... • Allowed us to complete our research project on the Application of Fluorogenic DNAzymes in Bacterial Detection.

• Helped to send

11 undergraduate students to present their hard

work at the Boston iGEM Conference

• Enabled us to create incredible year-long learning experiences for:

6 new wet lab trainees

5 new policies and practices trainees 4 new dry lab trainees



OUR ACCOMPLISHMENTS mGEM’s chosen research theme this year was antimicrobial resistance. We explored the issue through multiple perspectives, taking an interdisciplinary approach that integrates wet lab research, mathematical modelling, and social-political engagement. In collaboration with the Li Lab, our wet lab team used fluorogenic DNAzymes to create a rapid bioassay which can distinguish different bacterial strains directly on an agar plate. Over the course of 6 months, we developed a functioning proof-of concept using an E.coli model, optimized it for sensitivity and specificity, and laid the groundwork for the adaptation of our system into a diagnostic tool for AMR strains of pathogenic C.difficile. Our human practices team sought to understand and highlight current challenges in the C. difficile diagnostic pipeline. We reached out to 13 experts working in research, healthcare, and policy development across Canada, including Hamilton Public Health, as well as Mayor Fred Eisenberger. We distilled their insights into a discussion paper, with the goal of situating the role of AMR research in our community’s healthcare ecosystem. Using data shared by the Li Lab, our dry lab team trained a machine learning model to predict the affinity of novel DNAzyme probes. We hope to apply this work to generating new high-affinity DNAzyme candidates that can be used to seed future research. With the support of our mentors and advisors, our trainees gained invaluable experience in lab work, scientific reasoning, and experimental design - skills which they can leverage in tackling future research challenges.




THE iGEM JAMBOREE In November 2017, we presented our poster and project at the iGEM Giant Jamboree in Boston, Massachusetts. With over three hundred international teams gathering, collaborating, and competing at the Jamboree, the opportunity to learn from this host of interdisciplinary synthetic biology projects is immense. After long nights of practicing, our final presentation was well-received by both judges and other teams. We were later challenged to defend our project’s method, efficacy, and global relevance during poster Q&A sessions. Interacting with the judges prompted us to reflect on our strengths and consider further perspectives. In addition to our presentations, we attended a variety of thought-provoking panels led by industry experts, such as talks on biosecurity and dual-use by FBI representative and synthetic biology challenges testing our abilities for quick-thinking and creativity. Collaborations for the 2018 season and friendships with other universities were also established, especially with the Ontarian teams of the University of Ottawa and the University of Waterloo. As a culmination of our overall efforts, mGEM is excited to have brought home a bronze medal! Our scores from the judges reflect the high levels of dedication from all of our members this last year, and their feedback will facilitate improvement in our research. The opportunities to integrate what we have learned from the conference into our future projects drive us to work even harder for 2018.




Welcome aboard. You are helping us get off the ground and your support will go a long way in allowing us to purchase the materials we need to execute our project. We would offer you the following perks: xxxx • Logo & link to your website on our iGEM website • Logo & link to your website on our iGEM wiki

DNA Tier: $501-$2000

At this level, you are making a significant contribution to our progress and success as a team - we really appreciate your support! We would offer you the following perks: • Promoter Tier Benefits • Mention on social media • Logo on all promotional posters • Medium-sized logo on our iGEM T-shirts

mRNA Tier: $2001-$6000

We could not do it without you. You are allowing us to expand the scope and reach of our project and make more impactful discoveries and developments in synthetic biology. We would offer you the following perks: • DNA-tier benefits, except with a large-sized logo on our iGEM T-shirts • Mention during community and high school outreach events • Invitation to have a tour of our lab and get to know the team and our project

Protein Tier: $6001-$10,000

You’re as much a part of the team as we are. At this level, you’re enabling us to make huge strides forward in our project and dramatically increasing the resources we have to complete our work. We would offer you the following perks: • Promoter Tier benefits, plus • Mention on social media • Representation on the front of our t-shirts with a large company logo • Mention during community and high school outreach events • Logo on all promotional materials (including posters, stickers, decals, etc.) • Representation on our research posters with your logo at all research presentations • Invitation to have a tour of our lab and get to know the team and our project We’d love to work with you to customize any of the sponsorship tiers above or develop a custom package that best suits your needs, including in-kind sponsorships. Please don’t hesitate to ask our team about any perks or sponsorship arrangements that you would like to pursue!





Department Donations Biochemistry Chemical Engineering Oï¬&#x192;ce of the President Faculty of Health Sciences Alumni Association BHSc Program

Subtotal (Incl. taxes, conversion costs, etc.) (CAD) 500.00 100.00 2,000.00 4,000.00 250.00 2,500.00

Corporate Sponsorships Hamilton Health Sciences SickKids

6,682.00 750.00



Revenue from 2016 MSU Club Reimbursement Funds

9,192.96 87.00

Total Revenue

Expenses Research Team Registration Fees Lab Supplies DNA Order (Chart Field from Li Lab) Lab Reimbursement to Li Lab Jamboree Jamboree Reimbursements Lodging Transportation


Expenses Subtotal (Incl. taxes, conversion costs, etc.) (CAD) 5,979.00 122.88 12.41 2,000.00 7,535.00 996.00 2,750.00

Public Relations Misc. Social/Internal Club Expenditures Website & Email

133.00 134.89

Community Outreach Discovery Day Costs


Total Expenses

Net Revenue





OUR FUTURE McMaster iGEM has developed a number of strong relationships to prepare our group for continued growth in the upcoming years. This year has involved a great deal of foundational effort in building a framework for (1) a robust mentorship program & curriculum within the club, (2) engagement with Hamilton Public Health, and (3) engagement with the broader McMaster and Hamilton student public. As a student group with access to lab space and highly skilled mentorship, one of our core focuses as an iGEM team is the professional development of our team members, and the development of our community. Beyond our team, we look to marry our interests in basic science towards practical applications for public health concerns in the broader city of Hamilton- building a bridge between discovery and purpose. We furthermore look to apply our depth of mentorship and relationships with the city to facilitate a broader educational outreach strategy, that skillfully leverages our role as students to serve as peer educators in the broader McMaster and Hamilton community. We see these three regions as areas of growth in our expansion and professionalization as a student group.

INVESTING IN PEOPLE Nurturing mentorship and Developing a Curriculum

The access to high-quality expertise across the sciences, humanities, and business have supported the growth of a strong culture of mentorship in McMaster’s iGEM. Consistent with the aims of McMaster University as an institution for higher learning that appreciates both peer-based, inquiry-driven, and student-centred learning, our team has modelled many such approaches towards the cultivation of an edifying student educational experience. The growing interest in iGEM at McMaster is a clear indication of the desirability of the iGEM experience. With over 120 applications across McMaster for 10-15 spots on our team, we are attracting some of the strongest student talent at McMaster. Feedback from this year’s team members suggest that the open-endedness, student-driven aspect of the iGEM experience 14

offers students a greater sense of ownership over the research. This sense of ownership and commitment to the iGEM cause has been critical in shaping our strategy of mentorship and curriculum development. This year, iGEM took strides to introduce two types of team positions: a mentor role, and a junior team member role. This change was welcomed by returning members of the team, as it highlighted the additional effort put forth by mentors to train mentees across sub-teams, such as the wet lab, dry lab, and human practices. Wet lab mentors primarily trained junior team members in basic lab skills, and served as a reliable support to brainstorm and troubleshoot lab concerns. In the dry lab, mentors were helpful in pair programming, debugging, and serving as a point contact for students to develop stronger programming skills. In the human practices team, mentors were capable of serving as project managers, and trainers for professional skills development when interacting with external stakeholders.


Moving forward, iGEM McMaster looks to develop a more formalized mentorship structure, where more experienced student mentors can support mentees outside of the iGEM relationship. We look to develop a broader ecosystem, where mentors can support mentees in pursuing professional pathways along their respective disciplines (graduate school, industry, or work in related non-profits), and serve as supports throughout the year. Developing cross-disciplinary mentorship relationships will also serve as a focus in the upcoming year, to support in the development of a rich interdisciplinary educational experience.

Building upon our objectives to deliver an interdisciplinary experience, moving forward, McMaster iGEM is looking to develop an internal curriculum for staďŹ&#x20AC; members across the respective sub-teams to familiarize themselves with their other team memberâ&#x20AC;&#x2122;s principal tools and techniques. While relationships across subteams have been a strong focus this year, we hope to develop cross-disciplinary workshops, where wetlab team members may engage in a workshop, or data management workshop by human practices and dry lab respectively. These experiences reinforce our objective in nurturing a robust educational experience for team members, with the hopes to sustainably train and retain such expertise within our organization.



ENGAGING THE CITY Hamilton Public Health

This year, the topic of the iGEM project was on developing rapid diagnostics for C. difficile, a wellknown antibiotic resistant bacteria commonly acquired through hospital outbreaks in the broader Ontario region. While socially relevant to the broader McMaster, Hamilton, and Ontario regions, this topic selection was not deliberate. However, moving along the year, we recognized the importance of focusing our research efforts towards a scientific issue with strong social relevance. As such, the iGEM Human Practices and Public Engagement teams met with the Mr. Fred Eisenberger, the Mayor of the City of Hamilton, to discuss the importance of student engagement in antimicrobial resistance, and C. difficile. Building upon conversations with the mayor, our iGEM teams had met with Hamilton’s Medical Officer of Health, Dr. Elizabeth Richardson, as well as members of the Hamilton Infection Control Unit. This rapport with Hamilton Public Health has led McMaster iGEM to pursue future


research programs in area of public health relevance for the broader Hamilton community. Through this strategic alignment, we hope to pursue issues relevant to our local community and engage with stakeholders at the vanguard of these concerns. We see this reflexivity of conducting basic scientific research on a core public health problem as a strength of future iGEM teams, and we are delighted to see how this will move forward.


EDUCATING BEYOND McMaster and Hamilton

Another core relationship built this year was through facilitation of the annual Discovery Day, a day-long enrichment program for local high school students hosted by Hamilton Health Sciences and the Canadian Medical Hall of Fame. Part of our mGEM goal is to prepare future researchers for the growing field of synthetic biology and develop our membersâ&#x20AC;&#x2122; mentorships skills. Together, the Wet lab and Community Outreach Team led two unique workshops, Gel Electrophoresis and Analysis & Bacterial Gram Staining respectively. Each workshop emphasized the skills needed to master the techniques as well as possible real world applications.

In total, we presented our workshops to 73 people (8 teachers and 65 students) from secondary schools all across Ontario. We connected with both students and teachers, both of whom emphasized the need for more hands on learning in order to help students learn about the applications of concepts learned in class. Through this event, we were able to successfully showcase value and applications of synthetic biology, taught practical lab skills to students who otherwise would lack access to equipment and training, and inspired students to explore diďŹ&#x20AC;erent paths in science. We look forward to implementing workshops and other events in our community to help students bridge the gap between knowledge learned in the classroom and the practical applications of this knowledge.



2018 PROJECT OUTLINE PROTEIN AGGREGATES IN DISEASE Our proposed project seeks to investigate amyloid-beta aggregopathy in Alzheimer's disease (AD) through an E.coli model system. We will generate a mutational library of the Amyloid Beta 1-42 (Aβ1-42) gene, to be recombinantly expressed in E.coli as part of a drop-out screen. Given that Aβ1-42 spontaneously aggregates into toxic plaques, we expect the dropout cultures to become enriched over time for Aβ1-42 gene variants correlated with a reduced capacity for aggregation. We will used the recovered information to develop a model identifying key regions of the Aβ1-42 sequence crucial to plaque formation. This can potentially inform future research by revealing plaque-inhibiting Aβ mutations.

Background A characteristic feature of AD pathology is the development of extracellular amyloid plaques consisting of Aβ protein. While the role of Aβ in AD pathogenesis is unknown, it has been significantly implicated in neurotoxicity over the course of disease development. The two major species involved in plaque formation are Aβ1-40 and Aβ1-42, where the latter is believed to be the more toxic species. The toxicity of Aβ1-42 when recombinantly expressed in E.coli suggests that its plaque forming properties may be maintained in bacteria, and that bacterial systems may be useful in modelling some aspects of Aβ aggregation.

Methods Initial Validation

We will assess the capability for an E.coli system to capture variation in Aβ aggregation by generating growth curves for cultures expressing wild-type Aβ1-42, as well as those expressing high-aggregation mutations such as D7H. We will assess through co-culture experiments whether WT expressers can outcompete those expressing the D7H mutation in culture.

Drop-out Screen

We will use error-prone PCR to generate a mutational library of the Aβ1-42 gene, which will be transformed into E.coli under the control of an inducible promoter. Upon induction we will longitudinally sample the culture over several generations and conduct targeted NGS or Sanger sequencing to track the prevalence of different mutants as the culture progresses.

Data Analysis

We will generate a probabilistic model identifying key regions of the Aβ1-42 sequence involved in aggregation/toxicity. We will use 3D structural prediction to suggest how the identified mutations may impact aggregation on a molecular level.




CONNECT WITH US AT /igemmcmaster @igemmcmaster

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iGEM McMaster Sponsor Package  
iGEM McMaster Sponsor Package