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Since late June, staff and students have been returning to BioZone labs. In light of the new normal under which these re-opening procedures are taking place, here are a few important things we all need to keep in mind:
- Do NOT come to Wallberg if you feel unwell.
- Make sure to fill in the calendar(s) in advance: Department Calendar (mandatory at every visit), Lab schedule calendar, Equipment Calendar, and Visitor Calendar (if you need one).
- Always wear a mask inside Wallberg. Both cloth and disposable masks are available for everyone's use.
- Always record your name on the lab door when entering some lab room(s), and erase the name when exiting.
- Make sure to fill in the BZ Online Ordering Sheet if lab consumables are running short!
- Phil, Rodney, and Alex Dean are available until 3 pm on work days. If you need help with gas cylinders, shipments, etc. make sure to find them in advance.
- Office access: respect the occupancy limit of your office. Do not enter the room in case of maximum occupancy. Time in the office should be minimized and computer work should take place off site.
- Lunch room access: maximum occupancy is 3. Make sure to clean the area before leaving!
- Washroom access: A yellow cone is used to indicate whether or not the room is occupied. Use the cone to block the door when you enter the room; and when you leave, move the cone aside using your foot. Make sure to respect maximum occupancy in washrooms at all times.
You can find more details in the SOP brochure on the BZ Portal (find it under: Useful Documents/BzLab_Re-opening_Entry/Bz Lab Space Info & SOP) and Hosting Guidelines.
Once again, stay safe, keep physical distance, wear a mask, and wash your hands (you can find hand soaps of the best quality in all BZ labs!) .
Thank you to all the BZ support staff who have contributed so much in this process of re-opening! |
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With the lab reopening well underway and a new academic year beginning, BioZone would like to welcome and rewelcome all new and returning BZ students, staff, and faculty for the fall semester!
In light of the limited opportunities for connection available to our BZ community, we will be replacing the traditional BZ Orientation for new students with a BZ Welcome Event for all BZers. The welcome event will be held virtually on Monday September 14th, from 10 am-12 pm. Stay tuned for an email invite!
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REMEMBER -- this event is for everyone at BZ! See you all there!
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A number of staff and students have recently moved on from BioZone (or will be leaving very soon) who, due to COVID restrictions, have not received the recognition they deserve!
We would like to extend our best wishes to the following BZers as they move on to their next chapter in life:
- Peter Lee (Edwards lab)
- Scott Proulx (Mahadevan lab)
- Esmond Tang (Allen lab)
- Amir Meysami Fard (McGuigan lab)
- Dylan Mendonca (McGuigan lab)
- Ehssan H. Koupaie (Allen lab)
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A special congratulations to Ehssan H. Koupaie and BZ alumnus Tommy (Po-Hsiang) Wang, who have recently been appointed to faculty positions!
Ehssan is now an Assistant Professor in the Department of Chemical Engineering at Queen's University, while Tommy has recently become an Assistant Professor at the Institute of Environmental Engineering in the National Central University of Taiwan.
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We would also like to wish our cohort of undergraduate students from this summer the very best in the year ahead:
- Diosady lab: Diana Teichman, Ugo Ndem-Chijioke, Anais Hourau, Amelie Housiaux, and Willa Wei
- Edwards lab: Jeremy Rau, Joe Zhang, Dylan S. Perera, and Daniel Kiss
- Yakunin lab: Yao Sheng Chai
- Mahadevan lab: Austin Zheng, Sartaaj Khan, and Anaqi Muhamad Efendi
- McGuigan lab: Kirtana Devaraj, Subaita Rahman, Saif Rjaibi, Eryn Bugbee, Divy Raval, and Ziting Xia
- Passeport lab: Ami Zeng
- Master lab: Kirsten Hart, Liwah Keller, and Sung An
- iGEM: Cathy Wang, Gamen Liu, Sydney Tsuyuki, Rose Talebi, Sarit Radak, Shea Garcia, Corinne Bernett, Jenny Zhang, Jingxiu Ji, Raghav Sharma, Adnan Sharif, Joseph Bellissimo, and Victoria Sajtovich
Finally, thank you to everyone who came to last week's Farewell Teatime and had a chance to say goodbye personally!
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🚨 S A V E T H E D A T E 🚨
Thursday September 24th 2020
5-7 PM
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Kickoff the Fall 2020 semester with new friends at the BioZone Virtual Welcome Mixer!
Join us and get to know your fellow students, staff, and faculty across BZ. Make connections before the semester gets busy and get a chance to ask questions about opportunities available to you within and outside of BZ and the Department (e.g. mentorship programs, upcoming events, etc.).
Stay tuned for an email invite to this event!
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Open science presentations
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The global pandemic has underscored the value of collaborative and open practices in science to solve our largest problems and renewed discussion and support for Open Science.
But how do we quantify or measure the impact and importance of research in the context of Open Science? How can we incentivize and attribute value to the practice of Open Science? What exactly does “Open Science” mean? What are BioZoners’ conceptions and misconceptions of Open Science? How can the practices of Open Science help a student entrepreneur transform their research project into a commercialized product?
Please join our esteemed CREATE for BZ summer law students Kirsten Hart, Sung An, and Liwah Keller, on Friday August 28th, from 2-4 pm, to engage in an open forum on the topic of Open Science.
A Zoom link has been sent out by Robert Lam via email!
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The CREATE for BioZone program connects bioscience and bioengineering researchers with experts in leadership, entrepreneurship, law, and open science to establish a training hub producing graduates with alternative perspectives and dynamic, adaptable skills needed to grow Canada's share of the global circular bioeconomy. The CREATE program will provide students with the skills needed to lead Canada's transition to a sustainable circular bioeconomy. Learning experiences include annual workshops in:
- Accelerating innovation through open science and novel business models
- Improving data fluency through programming and using, sharing, and visualizing large omics datasets
- Evaluation of biotechnologies using TEA and LCA methodologies
- Science communication and leadership training
CREATE for BZ students are also eligible to access funds for international research exchanges and funds to support company creation.
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On July 30th it was announced that our very own Professor Emma Master has been appointed Associate Chair of the Department of Chemical Engineering & Applied Chemistry, taking over for Prof. Milica Radisic.
Prof. Master was selected in part by an Advisory Committee composed of Profs. Kortschot, Papangelakis and Bender as well as graduate students Sam Cheung (Allen Lab) and Folake Oyewole (Diosady Lab).
Congratulations Emma!
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Graduate Super Women Engineers (GradSWE) would like to welcome all new and returning graduate students to the University of Toronto for the 2020-2021 academic year!
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It has a been a roller coaster of a year and we are here to make your graduate engineering experience at UofT amazing and meaningful. Please join us for our online information sessions led by a dedicated team of graduate student volunteers from different engineering programs at UofT.
We are happy to answer any questions you might have about navigating school, UofT life and advancing women and minorities in engineering. Volunteers will provide information about our student group, events planned for the year and opportunities to get involved and develop leadership skills.
Please see our Eventbrite page for more details on how to register and receive Zoom meeting details. |
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GradSWE is led in part by Anupama Sharan, a fellow BioZoner and PhD student co-supervised by Profs. Emma Master and Elizabeth Edwards.
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Despite the many changes brought on by the pandemic we are experiencing, BioZone still hosted a cohort of undergraduate students this summer.
Judy Xia and Saif Rjaibi were part of this group of students. They spent their summer working as part of the McGuigan research group.
We asked them about how COVID has affected their research plans, how they have dealt with the current circumstances, and what they cherish the most from their time at BZ. See our interviews with Judy and Saif below:
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Q: What does your project consist of?
A: My current project involves optimizing the culture media and digestion protocol for tumour-macrophage co-culture on TRACER for improved downstream analysis.
TRACER (Tissue Roll for Analysis of Cellular Environment and Response) is a 3D engineered tumour model developed by the McGuigan lab that recapitulates the hypoxic tumor micro-environment.
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The project my supervisor is working on entails probing interactions between pancreatic adenocarcinoma (PDAC) and tumour-associated macrophages (TAM) and discovering potential therapeutic targets through establishing a co-culture on TRACER.
Q: How did COVID disrupt your research? What steps helped you mitigate said disruption?
A: My original summer research plan was to work on optimizing a digestion protocol. I was also hoping to learn more wet-lab techniques. However, due to COVID and the quarantine, I started my summer research remotely.
Fortunately, Prof. McGuigan and Ileana made some modifications to my project to ensure that my summer could be as productive as planned. For instance, a bioinformatics component was added, and I was given tutorials on R to learn about analyzing scRNA data using various packages and workflows as well as data visualization. A second component, culture media optimization, was also added to my summer project as a learning opportunity for me to use ImageJ to analyze and quantify cancer cell maturation markers imaged by fluorescent confocal microscopy.
Being at home, I also had more time to review a wide scope of resources in the literature ranging from topics specific to my own project to new findings relevant to my supervisor’s study. I also had ample time to discuss them during our weekly meetings.
Q: What did you enjoy most about your time at BZ? Is there anything in particular you learned or any valued skills you gained?
A: The supportive atmosphere and readily available mentorships at the McGuigan Lab are definitely what I enjoyed the most throughout the summer. Our lab has weekly alternating subgroup meetings (cancer subgroup and imaging subgroup) run in journal-club style where graduate students present a paper they find relevant to the work our lab does. This has been an extremely beneficial learning experience for undergraduates in the lab as we are not only exposed to the different techniques used in research, but also are able to learn how to analyze and present papers in the future.
Personally, the silver lining of this pandemic was realizing the multifaceted nature of research and the enormous potential that one should explore. Back in January, when I was applying for a research position at the McGuigan lab, I was convinced to seek only wet-lab experience as I am not an avid coder. But due to the pandemic, most of my work have been centered around dry-lab skills such as creating image analysis workflow, data visualization in R, as well as being introduced to bioinformatics. By the end of the summer, I have grown more and more passionate about learning dry-lab techniques and gained more confidence in setting foot in this area.
The takeaway for me from my summer research experience is always be fearless when embracing new areas of research and keep an open mindset to the skills entailed, because chances are, you will end up enjoying it.
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Saif Rjaibi (Chem Eng 2T1)
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Q: What does your project consist of?
A: We are developing an image analysis workflow to quantitatively validate our 3D in vitro obesity model through assessing the hallmark of adipocyte (fat cell) hypertrophy in obesity.
Once validated, our model will serve as a foundation for investigating future therapies to prevent obesity-associated disease.
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Q: How did COVID disrupt your research? What steps helped you mitigate said disruption?
A: It would have been great to be in Wallberg to connect with fellow undergraduate and graduate students and develop my hands-on laboratory skills. However, due to COVID-19 closures, I completed my project entirely remotely.
We organized weekly meetings amongst the McGuigan lab students. This served as a platform to keep connected and provide feedback on our projects. I also had the opportunity to interact with the greater BioZone community through BioZone Council's online social events!
Q: What did you enjoy most about your time at BZ? Is there anything in particular you learned or any valued skills you gained?
A: Summer research at BioZone was an excellent learning experience and allowed me to broaden my skillsets and network. For instance, despite having little prior experience in image analysis, I was able to develop this skill, complete a project, and present my findings at the Undergraduate Engineering Research Day Conference.
Overall, the student community has been very supportive in the midst of these challenging times.
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Thank you both for your sharing your experiences!
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Working from home can be challenging for many of us, especially when we're expected to keep productivity up in the long term, that is for weeks and months at a time.
For those seeking advice and/or resources regarding how to best adjust to the new normal of performing research-related activities at home, check out this guide compiled by some of our peers and professors at our Department!
Another very real challenge many of us face is pandemic fatigue. For tips on how to deal with fatigue and how to keep well, check out the infographic below: |
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There have been some requests for a place within Microsoft Teams to discuss issues in your research related to bioinformatics and coding as well as to encourage some inter-lab problem-solving.
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We can now use the BioZone_IT_bioinformatics channel for these discussions when anyone needs advice or a second pair of eyes on a computational problem they're experiencing!
If you DO NOT HAVE ACCESS to the BioZone Teams, please contact the BZ council for access, as we will be using Teams for most communication within BZ moving forward.
You can download MS Teams or access it directly on your browser by logging into your university Office 365 account. |
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- Batyrova, K.A., Khusnutdinova, A.N., Wang, P.H., Di Leo, R., Flick, R., Edwards, E.A., Savchenko, A. and Yakunin, A.F. (2020). Biocatalytic in vitro and in vivo FMN prenylation and (de)carboxylase activation. ACS Chemical Biology. 15(7):1874-1882.
- Chen, Z., Tang, X., Qiao, W., Jácome, L.A.P., Edwards, E.A., He, Y. and Xu, J. (2020). Nanoscale zero-valent iron reduction coupled with anaerobic dechlorination to degrade hexachlorocyclohexane isomers in historically contaminated soil. Journal of Hazardous Materials. 400:123298.
- Dean, T., Li, N.T., Cadavid, J.L., Ailles, L. and McGuigan, A.P. (2020). A TRACER culture invasion assay to probe the impact of cancer associated fibroblasts on head and neck squamous cell carcinoma cell invasiveness. Biomaterials Science. 8(11):3078-3094.
- Chan, Y.K., Gurumeenakshi, G., Varadharaju, N., Cheng, Y.L. and Diosady, L.L.(2020). Debittering Moringa oleifera (Lam.) Leaves in Fortified South Indian Instant Soup. Chemosensory Perception. [Article in Press].
- Soleas, J.P., D'Arcangelo, E., Huang, L., Karoubi, G., Nostro, M.C., McGuigan, A.P. and Waddell, T.K. (2020). Assembly of lung progenitors into developmentally-inspired geometry drives differentiation via cellular tension. Biomaterials. 254:120128.
- Milovanoff, A., Posen, I.D., Saville, B.A. and MacLean, H.L. (2020). Well-to-wheel greenhouse gas implications of mid-level ethanol blend deployment in Canada's light-duty fleet. Renewable and Sustainable Energy Reviews. 131:110012.
- Yang, M.I., Previdsa, M., Edwards, E.A. and Sleep, B.E. (2020). Using cell yields and qPCR to estimate biotic contribution to 1,1,1-trichloroethane dechlorination at a field site treated with granular zero valent iron and guar gum. Water Research. 186:116310.
- Paquette, A.J., Sharp, C.E., Schnurr, P.J., Allen, D.G., Short, S.M. and Espie, G.S. (2020). Dynamic changes in community composition of Scenedesmus-seeded artificial, engineered microalgal biofilms. Algal Research. 46:101805.
- Raj, K., Venayak, N. and Mahadevan, R. (2020). Novel two-stage processes for optimal chemical production in microbes. BioRxiv. 803023.
- Liu, Y., Chen, J., Khusnutdinova, A.N., Correia, K., Diep, P., Batyrova, K.A., Nemr, K., Flick, R., Stogios, P., Yakunin, A.F. and Mahadevan, R. (2020). A novel C-terminal degron identified in bacterial aldehyde decarbonylases using directed evolution. Biotechnology for biofuels. 13(1):1-11.
- Choudhary, R. and Mahadevan, R. (2020). Toward a systematic design of smart probiotics. Current Opinion in Biotechnology. 64:199-209.
- Diep, P., Mahadevan, R. and Yakunin, A.F. (2020). A microplate screen to estimate metal-binding affinities of metalloproteins. Analytical Biochemistry. 113836. [In Press]
- Liu, Y., Chen, J., Crisante, D., Lopez, J.M.J. and Mahadevan, R. (2020). Dynamic Cell Programming with Quorum Sensing-Controlled CRISPRi Circuit. ACS Synthetic Biology. 9(6):1284-1291.
- Al-Fahad, A.J., Al-Fageeh, M.B., Kharbatia, N.M., Sioud, S. and Mahadevan, R. (2020). Metabolically engineered recombinant Saccharomyces cerevisiae for the production of 2-Deoxy-scyllo-inosose (2-DOI). Metabolic Engineering Communications. 11:e00134.
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Please email us if you have something to add to the next edition of the BioZone Newsletter
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