September 2017, Volume 15
  1. Pulp Mill Trip in Northern Alberta
  2. Synbiomics Annual General Meeting
  3. Elements of Bio-Mining to Turn Mine Waste into Valuable Metals
  4. Special Seminar: Dr. Morton Barlaz
  5. BioZone Mass Spec User Meeting
  6. Farewell Katrina & Welcome Back Vinthiya
  7. Congratulations to BioZone September Graduates
  8. Welcome New BioZone Students
  9. Save the Date & Call for Presenters: BioZone Fall Symposium
  10. Student Spotlight: Ruhi Choudhary
  11. BioZone Fall Retreat 2017
  12. Science Puns!
  13. Recent Publications

1. Pulp Mill Trip in Northern Alberta

"From August 20 to 23, several researchers from University of Toronto and Queen’s University, including myself, visited three of our industrial partners in Northern Alberta. These partners are supporting the new Genome Canada project 'Synbiomics', led by Prof. Emma Master. The trip led us to Innotech Alberta in Vegreville, and the two pulp mills Slave Lake Pulp (West Fraser) in Slave Lake, and Millar Western in Whitecourt. We were particularly interested in the anaerobic wastewater treatment systems operated by Millar Western and Slave Lake Pulp. The mill visits involved tours through the treatment plants, presentations and discussions about our collaborative research project."  
-Torsten Meyer, Research Associate (Edwards and Master labs)

2. Synbiomics Annual General Meeting

On Wednesday September 13 and Thursday September 14, Synbiomics held their first Annual General Meeting at St. Michael’s College. The AGM was headed by BioZone Professor Emma Master and project co-leader Harry Brumer from University of British Columbia. The AGM highlighted the direction of the Synbiomics project, the involvements of industry partners, and the research progress to date through presentations, discussions, workshops and an informative poster session. The 2-day AGM fostered many fruitful discussions with industry partners of the project and reinforced connections between students, post-docs, and research associates across the Synbiomics network.

The project entitled “Synbiomics: Functional genomics and techno-economic models for advanced biopolymer synthesis” is funded by one of 13 Genome Canada Large-Scale Applied Research Project grants of $9.5 million for four years. Synbiomics is focused on harnessing the genetic potential of microorganisms to identify and develop new biocatalysts that can be used to create materials from trees, such as resins, coatings, bioplastics and adhesives. Emma is leading a team that includes co-leader Harry Brumer from the UBC, BioZone Director Elizabeth Edwards, Adrian Tsang from Concordia University, and Steve Smith and Warren Mabee from Queen’s University.
For more information about the project, click here.

3. Elements of Bio-Mining to Turn Mine Waste into Valuable Metals

"They are invisible to the naked eye, able to withstand extreme conditions and capable of breathing rocks. They are the microbes that thrive in tailings ponds at mining sites around the world, and a team of Canadian researchers believes they are the key to transforming waste material into something much more valuable.
'There are bugs that thrive on metabolizing sulfur, others on metabolizing iron,' says Professor Vladimiros Papangelakis (ChemE). 'If we can control such biochemical reactions, we could both remediate the waste and recover valuable metals that could pay for the cost of processing.'
Papangelakis, along with Professor Elizabeth Edwards (ChemE) is leading the Elements of Bio-Mining project, a multidisciplinary collaboration between U of T Engineering (Krishna Mahadevan
, Brad Saville, Alexei Savchenko, Alexander Yakunin), Laurentian University, and the University of British Columbia (UBC), as well as a number of technology, engineering and mining companies, including Glencore, Vale, Teck, Barrick and Hatch."

Click here to continue reading the full article. To visit the Bio-Mining project website, click here.

4. Special Seminar: Dr. Morton Barlaz

On Tuesday September 12, BioZone had the pleasure of listening to Dr. Morton Barlaz present on a very important issue: heat generation and accumulation in solid waste landfills. Dr. Barlaz is a distinguished University Professor and Head of the Department of Civil, Construction and Environmental Engineering at North Caroline State University. In his talk, Dr. Barlaz discussed the reports of landfills experiencing temperatures in excess of 100°C, and how his modelling can be used to help describe the generation, consumption and release of heat from landfills.
To read his new publication about this issue, click here
5. BioZone Mass Spec User Meeting
BioZone’s Mass Spectrometry Facility is holding our annual meeting for current and future users on October 23, 2017 @ 9:00 am – 2:00 pm in Wallberg room 219 (2nd floor).

The aims of this meeting are:
  1. to provide users with information on the latest techniques and methods the facility is capable of performing,
  2. and to determine what sample prep techniques and analysis tools our users are interested in having access to.
Planned presentations:
  1. Keynote Address: Metabolomics for enzyme discovery – Dr. Amy Caudy, University of Toronto
  2. Differential analysis of mass spectrometry data for metabolomics and small molecule approaches – Robert Flick, BioZone MS Metabolomics Specialist
  3. What are you missing in your metabolome…the orbitrap MS perspective – Amanda Souza, Thermofisher
  4. Success stories – Short presentations from HQP on successful projects using the MS facility
The meeting will conclude with a User Forum to discuss emerging trends, new technologies, and new protocol development, followed by a tour of the BioZone Mass Spectrometry Facility.

Students will also have a Q&A session with our experts to find out how the facility can help their projects.

Find out more about the BioZone Mass Spec facility here.

6. Farewell Katrina & Welcome Back Vinthiya

The bittersweet Tea Time: Hello new students but farewell Katrina
On Tuesday September 19, we held an EXTRA SPECIAL two-part Tea Time. The first part welcomed some of the new students to BioZone: Ileana, Nila, Ruhi, Michael, Lais, and Ainsley. The second part was a surprise potluck for Katrina Chu who left BioZone at the end of the month. Aside from the mountains of food that were brought, a gift was presented to Katrina on behalf of all of BioZone, Prof. Mahadevan personally thanked her for all of her help specifically in organizing our stipends (we thank her too), and tears were held back as Katrina expressed how grateful she was to work in BioZone with us. Thank you Katrina for everything you have done for BioZone, we truly appreciate it and will miss you! But don’t worry, she hasn’t gone too far; if you want to go visit, she will be at the Public Health and Preventative Medicine Residency Program with the School of Public Health at 155 College, across the street! Word is she will also have a candy bowl at her desk for any visitors...

Vinthiya returns from maternity leave!
Welcome back Vinthiya Param! She left BioZone in October 2016 for maternity leave, and has returned with a healthy baby boy at home. She will be back as the Research Grant and Project Administrator in WB314 so please stop by and welcome her back in her office or at the next Tea Time!

7. Congratulations to BioZone September Graduates

Congratulations to our September graduates:
Nigel Guilford (Ph.D. - Edwards)
Mahbod Hajighasemi (Ph.D. - Yakunin and Edwards)
Zheng Lu (M.Eng. - Allen)
Elisa McGee (Ph.D. - Diosady)
Elisse Magnuson (M.A.Sc. - Edwards)
Roman Malekzai (M.A.Sc. - Master)
Vik Aditya Pandit (Ph.D. - Mahadevan)
Zi (Johnny) Xiao (M.A.Sc. - Edwards)

8. Welcome New BioZone Students

The 2017 Fall semester has just started and the new BioZone members have already arrived!
We wish you all a brilliant journey during your studies and we are available for anything that you might need help with!
Thank you for coming to the Orientation Day, where we could share a lot of useful information for our daily activities in BioZone!

9. BioZone Fall Symposium

Reminder to save the date in your agenda: Friday November 10th, 2017 from 1PM - 5PM.
BioZone needs presenters in the following categories:
  1. 15-minute Presentation
  2. 3-minute Thesis Competition
  3. Poster Presentation
There will be prizes to be won for each category!!!!!
We are also looking for recommendations for external speakers. If you have any UofT Professors in mind, please email us!

10. Student Spotlight: Ruhi Choudhary

This month’s Student Spotlight is on Ruhi Choudhary, a M.A.Sc. student in the Mahadevan lab. See the abstract below for details on Ruhi’s research during her time here in BioZone.

What drew you to Chemical Engineering?
When I started my undergraduate studies I was in Engineering Science, but I decided to switch to Chemical Engineering when I learned about the diverse bio-related research projects that the professors worked on. I was interested in eventually pursuing research in the biotechnology field.
Why Biotech in particular?
My cousin introduced me to biotech. He’s a PhD student now, and when I was younger he would teach me biology. He was the first person to explain to me what DNA is and how it is the building block of genes. It’s just so interesting – he’s a very good teacher and he made it sound so cool! My high school also offered an advanced course in biotech in which I isolated DNA. When I saw that I thought it was the coolest thing in the world!
So I guess that your passion for biotechnology is what led you to Professor Mahadevan’s lab then?
Yes! Honestly, this lab is the only lab that does the research I’ve always wanted to get into. I always wanted to manipulate microbes to produce chemicals but also incorporate that in the context of human health. This is also one of the only labs that deals with not only understanding metabolism, but engineering that metabolism, which I found intriguing.
Can you tell me a bit about your research?
I genetically modify probiotic strains of bacteria so that they produce therapeutic molecules that help in the treatment of Crohn’s disease. It’s really thrilling because I’m using engineering in a health context.
Are you trying to lead yourself into the health sector then?
I do want to get into the health care industry – that is my dream! And if I’m not going to be a doctor this is how I can contribute. When I work on this project, it’s because it’s so closely related to medicine that I feel that I’m making a real difference in the world. I think medicine is very important and I feel that what I am doing is important.
Okay time for some fun ones… What do you like to do in your free time?
I like to read. All kinds of books. I have many favourite authors – Harper Lee, Jane Austin, Charlotte Bronte, Stephen King…
What’s your worst fear?
Reptiles. Any kind of reptile… lizards in particular.
There are a lot of ups and downs in grad school. What gets you through the down parts?
It’s very easy for me to lose interest – I get bored very easily. So it’s always been kind of hard for me to see something through. But for the first time, I’ve finally found something that’s kept my interest long enough that I want to see it through… I NEED to! Basically, I think if you’re passionate enough in the topic, then that should get you through the lows.
What advice would you give to new grad students or just new researchers in general?
I guess my advice would be to have a balance – do other things as well as research. It’s very easy to be completely consumed by your research. You never know… you may get inspired if you look away from a problem!
Crohn’s disease is one of the most common chronic inflammatory diseases of the small and large intestine. The symptoms include diarrhea, fatigue, weight loss and abdominal pain due to inflammation of the lining of the digestive tract. Currently, there is no known cure for the disease. The symptoms can be managed using medication but not the underlying cause. The gut microbiome consists of trillions of microbes that have huge potential to impact our physiology by contributing to metabolic functions, regulation of immune system and resistance to pathogens. The interaction between microbes and gut cells is an important one as it can trigger immune response to dysbiosis. Probiotics are living medicine, which help the gut stay healthy by maintaining a good balance between the ‘good’ and ‘bad’ microbes. The gut microbiome of a Crohn’s disease patient differs from that of a healthy patient in terms of microbial composition and mutations in epithelial gut cells. My goal is to genetically engineer probiotic strains to produce therapeutic molecules and assess the effect on the gut cells to help treat Crohn’s disease.

11. BioZone Fall Retreat 2017

On Saturday September 30, we had the annual BioZone Retreat where we headed out to the Hamilton Waterfalls. We successfully walked all 6.2 km of the King’s Forest Walk and saw the beautiful Albion Falls. We followed this up with an impromptu stop at the Stoney Creek Apple Festival, where everyone got to enjoy some delicious apple cider. Finally, we finished up the day with even more tasty food and drinks, followed by some shuffleboard at Pogue Mahone’s. We had a fantastic time and are looking forward to next year’s retreat!

12. Science Puns!

The BioZone Council is excited to announce a new column in the BioZone Insider section of the monthly newsletter. We will be posting science jokes and puns you just can't stop laughing at! Here's two more we enjoyed, but from now on you can submit your favourite science jokes and puns to to see them in the next BioZone Newsletter!
Submitted by: Nadia Morson (Edwards lab)
Submitted by: Spencer Imbrogno (Master lab)

13. Recent Publications

Azimi, Y., Liu, Y., Tan, T. C., Allen, D. G. & Farnood, R. R. The tail of two models: Impact of circularity and biomass non-homogeneity on UV disinfection of wastewater flocs. Water Res. 126, 70-78, doi:10.1016/j.watres.2017.09.011 (2017).

Sarv, V., Trass, O. & Diosady, L. L. Preparation and Characterization of Camelina sativa Protein Isolates and Mucilage. JAOCS J Am Oil Chem Soc, 1-7, doi:10.1007/s11746-017-3031-x (2017).

Woolman, M., Tata, A., Dara, D., Meens, J., D'Arcangelo, E., Perez, C. J., Saiyara Prova, S., Bluemke, E., Ginsberg, H. J., Ifa, D., McGuigan, A., Ailles, L. & Zarrine-Afsar, A. Rapid determination of the tumour stroma ratio in squamous cell carcinomas with desorption electrospray ionization mass spectrometry (DESI-MS): A proof-of-concept demonstration. Analyst 142, 3250-3260, doi:10.1039/c7an00830a (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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