January 2018, Volume 18

  1. Introducing the New Biozone Council!
  2. Welcome New BioZone Members!
  3. Student Spotlight - Sofia Lemak
  4. iGEM in Biozone
  5. Holiday Party Recap
  6. Recent Publications

1. Introducing the New BioZone Council!

2. Welcome New BioZone Members!

Top row left to right:
Suly Rambinaising (Visiting PhD) - Prof. Edwards
Benjamin Pichette (Research Technician) - Prof. McGuigan
Dr. Christine Romano (Research Associate) - Prof. Edwards 
Dr. Courtney Toth (PDF) -  Prof. Edwards.

Bottom Row left to right:
Dr. Jolanda Van Munster (PDF) -  Prof. Masters
Dr. Olanrewaju Raji (PDF) - Prof. Masters
 Jose Cadavid Cardenas (PhD) - Prof. McGuigan

We wish you all a brilliant journey during your time at BioZone and we put ourselves available for anything that you might need help with!

3. Student Spotlight - Sofia Lemak

This month’s Student Spotlight is on Sofia Lemak, a PhD candidate in the Yakunin lab.



The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immunity system has generated massive interest in academia and industry for its potential as a powerful synthetic biology tool. The CRISPR-associated complex for antiviral defense (Cascade) from the Type I-E system of Escherichia coli has been shown to be a versatile tool for bacteria to protect themselves against invading generic elements during CRISPR immunity. While the structure of the E.coli Cascade has been solved, the precise mechanism of action is not completely understood. Working both in the Interference and Adaptation stages of immunity, the role of Cascade has been shown to vary, and the specifics of the interactions between protein, RNA and DNA have not been described.
In order to better understand the Cascade complex, Sofia's project goal is to characterize the E.coli Cascade with respect to assembly and function. Understanding the mechanism of the Cascade complex could lead to CRISPR gene editing tools with different gene targeting characteristics than existing CRISPR-Cas9 systems. This could significantly widen the applications of current CRISPR based systems in medicine, synthetic biology, and industry.

Can you tell me a bit about your research?
I am characterizing and engineering cascade complex from E.coli, which is RNA guided, DNA targeting complex. I am working on creating a gene-editing tool. I plan to stay in academia; I am flexible in terms of which sector to work in.

What drew you to Prof Yakunin’s lab?
I worked here as a summer student in undergrad. I really enjoyed the characterization, enzymology and discovery process. This is a great environment to work in!

What do you like to do in your free time?
Oh I am pretty outdoorsy. Whenever I get time from research I like to go horseback riding. I enjoy long hikes and some reading too.

What’s your worst fear?
I don’t really have any major fears but if I have to choose I’ll say spiders. And heights.

In some parallel universe, what would you be?
Oh! I’d love to be a pet aesthetician. That would involve massage therapy and spa treatments for small animals!

What advice would you give to new grad students?
Be patient with your project. Try to stay focused because 4 years feels like a long time but it goes by very fast. It’s crazy!

What do you like the most about BioZone?
It is a very collaborative environment. You meet a lot of different kinds of people from different walks of life. I really enjoy working and socializing with such a diverse group of people. Definitely, a good representation of the academic world.

If you were the Empress of BioZone, what would be the new thing you introduce?
I would move all lab spaces outdoors in the summer months…introduce lab patios. In the winter, they could get converted to solariums. (Maybe change the building…)

4. iGEM in Biozone

UofT iGEM is a synthetic biology undergraduate team that tackles a new project each year. BioZone's support has opened opportunities for them to begin recruiting engineering students. Given BioZone's heavy focus on environmental issues, the iGEM team this year is seeking graduate students who would be open to elaborating on environmental issues that they're addressing with their graduate research. The iGEM R&D team will be reaching out to specific BioZone graduate students, but if you're particularly open to this or want more information, please e-mail Patrick:

5. Holiday Party Recap

It was smiles all around on December 8th for the 2017 BioZone Holiday Party. The potluck competition was fierce once again this year so congrats to our winners and everyone else who brought in a dish:

Best Appetizer: Scott Proulx

Best Veggie Entrée: Peter Lee

Best Meat Entrée: Patrick Diep

Best Dessert: Rachel Kwan

Besides the great food there were also plenty of fun and games, with a costume contest and a trivia game hosted by Kiki and Scott. Congratulations to Kylie O’Donnell whose costume and BioZone knowledge led her to victory in both events. Finally, who can forget the highlight of the night when our very own Scott and Spencer led us through a rousing rendition of 12 Years of Grad School. Thanks to everyone who attended and I hope you’re all looking forward to next year!

Also, let’s not forget about the recipients of the 2017 BioZone recognition awards. Thanks for all your hard work and let’s be sure to keep it up for 2018!

Technical Excellence: Line Lomheim

Community Service: Nadia Morson

Innovation: Sean Caffrey

5. Recent Publications

December 2017

1. Gaskell, J., Kersten, P., Larrondo, L.F., Canessa, P., Martinez, D., Hibbett, D., Schmoll, M., Kubicek, C.P., Martinez, A.T., Yadav, J. and Master, E. Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12. Genomics Data. 14,21-23. doi: 10.1016/j.gdata.2017.08.003. (2017)

2. Kolliopoulos, G., Holland, A.M. and Papangelakis, V.G., Modeling of density and electrical conductivity of aqueous carbonated trimethylamine (TMA–CO2–H2O) solutions at 20° C. Monatshefte für Chemie-Chemical Monthly 1-8. doi: 10.1007/s00706-017-2091-9 [Article in Press]. (2017)

3. Wong, M.T., Wang, W., Couturier, M., Razeq, F.M., Lombard, V., Lapebie, P., Edwards, E.A., Terrapon, N., Henrissat, B. and Master, E. Comparative metagenomics of cellulose-and poplar hydrolysate-degrading microbial enrichments from gut microflora of the Canadian beaver (Castor canadensis) and North American moose (Alces americanus) after long term enrichment. Frontiers in Microbiology. 8, 2504. doi: 10.3389/fmicb.2017.02504. (2017)

4. Javaherian, S., D’Arcangelo, E., Slater, B., Londono, C., Xu, B. and McGuigan, A.P., 2017. Modulation of cellular polarization and migration by ephrin/Eph signal-mediated boundary formation. Integrative Biology. 9, 12, 934-946. doi: 10.1039/c7ib00176b. (2017)

January 2018

1. Wang, W., Andric, N., Sarch, C., Silva, B.T., Tenkanen, M. and Master, E.R., Constructing arabinofuranosidases for dual arabinoxylan debranching activity. Biotechnology and Bioengineering. 115,1:41-49. Doi:10.1002/bit.26445. (2018)

2. Bonilla, S., Choolaei, Z., Meyer, T., Edwards, E.A., Yakunin, A.F. and Allen, D.G., Evaluating the Effect of Enzymatic Pretreatment on the Anaerobic Digestibility of Pulp and Paper Biosludge. Biotechnology Reports. 17,77-85. Doi: 10.1016/j.btre.2017.12.009. (2018)

3. McGee, E.J.T. and Diosady, L.L.. Prevention of iron-polyphenol complex formation by chelation in black tea. LWT-Food Science and Technology. 89,756-762 DOI: 10.1016/j.lwt.2017.11.041. (2018)

4. Rodenhizer, D., Dean, T., D'Arcangelo, E. and McGuigan, A.P. The Current Landscape of 3D In Vitro Tumor Models: What Cancer Hallmarks Are Accessible for Drug Discovery? Advanced healthcare materials. DOI: 10.1002/adhm.201701174. [Article in Press].(2018)

5. Coscolín, C., Martínez-Martínez, M., Chow, J., Bargiela, R., García-Moyano, A., Bjerga, G.E., Bollinger, A., Stokke, R., Steen, I.H., Golyshina, O.V. and Yakimov, M.M. Relationships between Substrate Promiscuity and Chiral Selectivity of Esterases from Phylogenetically and Environmentally Diverse Microorganisms. Catalysts. 8 (1): 10. (2018)

6. Telling, J., Voglesonger, K., Sutcliffe, C., Lacrampe-Couloume, G., Edwards, E. and Lollar, B.S. Bioenergetic constraints on microbial hydrogen utilization in Precambrian deep crustal fracture fluids. Geomicrobiology Journal. doi: 10.1080/01490451.2017.1333176. (2018).

Please email us if you have something to add to the next edition of the BioZone Newsletter
Copyright © 2018 Biozone Centre for Applied Bioscience and Bioengineering, All rights reserved.

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