May 2017, Volume 11


Introducing the New BioZone Council

Hey BioZoners! Get ready to meet your new BioZone Council! While we did not receive enough applications to host an election, we are confident that this fresh Council will keep building upon the legacy left behind by the past Council. The main objectives of the BioZone Council are to maintain a collegial and collaborative atmosphere within BioZone through social events, communication, and knowledge exchange and to promote BioZone as a leading research centre to academia and industry.

Co-Presidents: Samantha Cheung & Mitchell Zak
Internal Communications Coordinators: Suzana Kraus & Kayla Nemr
External Relations Coordinator: Nadia Morson
Events Coordinators: Kylie O’Donnell & Kiki Chan
Treasurer: Spencer Imbrogno
Industrial Relations Coordinator: Scott Proulx
Executive Director of BioZone: Sean Caffrey

Active Volunteers: Mabel Wong and Peter Lee

If you have any questions, comments, or would like to volunteer please email or stop one of us in the hall!

News & Events

Battling Infectious Diseases with 3-D Structures
The BioZone Protein Structure and Function Lab contributed hundreds of purified proteins and crystals and provided expert analysis of the resulting 3-D structures. The structures provided molecular details of proteins that play roles in infectious disease, such as conferring antibiotic resistance or mediating host-pathogen interactions. Professor Alexei Savchenko, of the University of Toronto’s Department of Chemical Engineering & Applied Chemistry, directed the BioZone project. 

Click here to read the full article.
Printing 3-D Tumor Models
With support from BioZone’s Alison McGuigan, high school student Jody Mou used a bioprinter to make 3D tumor models which was recently recognized at a regional biotech science fair.
Click here to read the full article from the CBC.

Brantford Field Site Trip
On Wednesday April 26th, four BioZone students and visiting Brazilian professor, Savia Gavazza, visited a field site in Brantford, Ontario. The site was a former aerospace manufacturing facility and had been heavily contaminated with chlorinated ethenes, predominantly tetrachloroethene (PCE) and trichloroethene (TCE). When we visited, the site was being injected with ethanol to enhance anaerobic bioremediation. Additionally, the spread of contamination was controlled by phytoremediation, with hybrid poplar trees surrounding the property line. The site tour was conducted by Annie Lee, P.E. from Geosyntec, and on-site remediation was conducted by Insitu Remediation Services Ltd.

We hope to visit more field sites and industries in the future. Please keep an eye out on your emails to participate in the next visit!

10th Annual Science Rendezvous
On May 13th, the 10th annual Science Rendezvous was held all over the country. Science Rendezvous is a free event celebrating science and engineering with children and the general public. This year, BioZone, PAPTAC (Pulp and Paper Technical Association of Canada) and chemical engineer volunteers ran a booth where over 300 children made paper from pulp that contained seeds that could later be planted. Thanks again to all of the volunteers and look out for this event next year if you’re interested in participating!
Invitation to the Festa Junina!
On June 26th, we are planning a traditional Brazilian June harvest party to celebrate the past year of collaboration with visiting Brazilian professor, Savia Gavazza (Edwards Lab). Please keep June 26th from 5-8PM open in your calendars! More details to follow!

Awards & Grants

At the 10th Annual Celebrating Engineering Excellence Awards, our very own Susie was awarded the Faculty’s Quality of Student Experience Award. The award recognizes a staff member who has made significant contributions to the quality of student experience in the Faculty. Susie Susilawati is the Lab Manager for BioZone, home to approximately 80 graduate students and postdoctoral fellows. She works tirelessly to ensure that the BioZone labs run smoothly and safely so that students have an outstanding research experience, and consistently seeks student feedback on how the labs can best meet their needs. However, Susie’s contributions to the student experience go far beyond her official role – since joining BioZone in 2009 she has made it her mission to create an exceptional sense of community, making sure that every student feels welcome and connected. Susie takes the time to get to know each of BioZone’s students and ensures that they get to know each other. She is the first person students seek out when they need assistance of any kind. Susie plans and hosts community-building events such as a weekly informal social and monthly birthday celebrations, and encourages all BioZone members to get involved. Her efforts have been instrumental in creating a cohesive student community within this unique centre.

BioZone Insider 

The BioZone Insider section of the BioZone Newsletter is a new section that we hope will update BioZoners on news, events, and more! Stay tuned for this section in upcoming newsletters!
Student Spotlight: Elisse Magnuson
See abstract below for more information on Elisse’s research.
Elisse was brought to Toronto in 2011 when she started her undergraduate degree in biochemistry at the University of Toronto. Throughout her undergraduate degree, she worked in numerous research labs as an undergraduate assistant, which transferred remarkably well when she decided to pursue a master’s degree in the department of chemical engineering. Elisse’s decision to work in the field of bioremediation stems both from the skills obtained from her undergraduate degree and her keen interest in protecting the environment. Her work in the Edwards lab involves studying bacterial cultures capable of benzene degradation. As soon as Elisse wraps up her master’s degree at the University of Toronto, she will be starting her PhD at McGill University to study bacterial populations in the Arctic to understand the boundary conditions to support life.

An avid reader, when Elisse is not reading academic journals and papers, she enjoys reading a wide variety of genres and is always working her way through a non-fiction book as well as a novel at the same time. Elisse also enjoys cooking but humbly insists that she is a mediocre cook compared to those around her. This would fit well with her dream job as a food critic as Elisse likes to learn about the history and origins of the food she eats.

Benzene is a simple hydrocarbon that occurs naturally in crude oils and refined fuels, and is used as a precursor in industrial processes. It is a common contaminant in fuel storage and industrial sites. Benzene is highly toxic and carcinogenic, and therefore its removal from sites near human habitation is a priority in contaminated site cleanup. Many common remediation methods, including soil removal and pumping out groundwater (“pump and treat”), are environmentally invasive and risk worker exposure. Bioremediation, or degradation of contaminants by bacteria, is increasingly used as a strategy to supplement or supplant other benzene removal methods. Benzene biodegradation can occur under a variety of environmental conditions, including aerobic and anaerobic. Aerobic benzene degradation occurs quickly and is fully characterized, but few contaminated sites are aerobic beyond the surface layer. Anaerobic benzene degradation occurs slowly and is a relatively uncharacterized process, and therefore needs further study. The Edwards lab has cultivated enriched benzene-degrading cultures from a variety of contaminated sites over fifteen years. I study the bacterial community and degradation in some of these cultures in order to elucidate the mechanism of degradation and, ultimately, improve the options for bioremediation of benzene.
Window Renovation Update
As we are all aware, funding from the federal government has allowed the department to replace the old windows in Wallberg. Renovations have already begun on the northwest to southwest walls, where new window panes and poly sheeting can be seen. The work is currently on-schedule, and is slated for completion by the end of August. For those who are looking for a different place to work during the renovations, WB242 has been booked for the summer. At press time, the windows seem to be pleased with their makeovers. Remember that renovations take time!
BioZone Baby Watch
We are populating BioZone with new babies!
Sean’s baby boy, Ethan Caffrey, is about one month old and already has professional pictures!
The next baby is yet to be born, and his name will be Hayden Yang. Look how beautiful mom, Ivy, is!
IT Safety with Dean
Have you ever thought about what you would do if one day your computer failed to turn on, and some IT person told you your hard drive had failed.  Well you should! And, you should give it some serious thought about what your “critical data” really is.  This will vary from person to person, but what should be the same for everyone is that you backup your “critical data”, and most importantly you verify that the backup is working as intended.

Within BioZone, there is an OwnCloud ( service available to everyone that provides an easy-to-use mechanism to keep local folders in-sync with the OwnCloud server.  You can also contact me ( with any questions you may have.  There many different backup solutions besides OwnCloud as well, but step one is still identifying “critical data” and going from there.

Recent Publications

Klamt, S., Regensburger, G., Gerstl, M. P., Jungreuthmayer, C., Schuster, S., Mahadevan, R., Zanghellini, J. & Müller, S. From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. PLoS Comput. Biol. 13, (2017).

Pandit, A. V., Srinivasan, S. & Mahadevan, R. Orthogonal design of metabolic pathways. Proceedings in 11th Metabolic Engineering Conference.  p. 474-475. (2016) (Conference Proceedings)

Kalami, S., Arefmanesh, M., Master, E. & Nejad, M. Replacing 100% of phenol in phenolic adhesive formulations with lignin. Journal of Applied Polymer Science, doi:10.1002/app.45124 (2017).

Mai-Gisondi, G. & Master, E. R. Colrimetric detection of acetyl xylan esterase activities in Methods in Molecular Biology Vol. 1588. p. 45-57 (2017).

Pereira, L. G., Maclean, H. L. & Saville, B. A. Financial analyses of potential biojet fuel production technologies. Biofuel Bioprod. Biorefining, doi:10.1002/bbb.1775 (2017).

Please email us if you have something to add to the next edition of the BioZone Newsletter
Copyright © 2017 Biozone Centre for Applied Bioscience and Bioengineering, All rights reserved.

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