Posts Tagged: Dunja Matic

Student team studies human genetics in microgravity

TelOmG Team Photo

The members of team TelOmG, from left to right, are Erin Richardson (EngSci Year 4), Anthony Piro, Miranda Badovinac in the top row; Taylor Peters, Dunja Matic (both EngSci Year 4), Luca Castelletto (EngSci Year 3) in the middle row; Samantha Aberdein, Emma Belhadfa (EngSci Year 3), Nicole Richardson, Krish Joshi, and MacKenzie Campbell (EngSci 2T0 + PEY, ChemE MASc candidate) in the bottom row. (Photos courtesy of team TelOmG)

 

A team of U of T students is preparing to see their research take off next week. They are among just six university teams from across Canada selected to conduct a study in a microgravity environment aboard the National Research Council Canada’s (NRC) Falcon-20 jet — the same plane used to train the Canadian Space Agency’s astronauts. 

As part of the Canadian Reduced Gravity Experiment Design Challenge (CAN-RGX), the team, called TelOmG, has spent the past year designing and building a unique experiment to examine the impact of spaceflight on astronauts’ genes. 

During the flight, scheduled for August 19, the students will investigate the effects of changes in gravity on the genetic regulation of human telomeres. Telomeres are protective caps at the ends of our chromosomes that are linked to genomic stability. Shortening of telomeres is associated with aging, while lengthening can be associated with cancer. 

The idea for the experiment came to team lead Erin Richardson (EngSci Year 4) while reading NASA’s landmark Twins Study, an investigation of spaceflight’s effects on the human body. The study examined astronaut Scott Kelly, who spent nearly a year in space, and his twin brother Mark who remained earthbound, and found Scott’s telomeres unexpectedly grew longer during his space flight. They returned to normal shortly after his return to Earth. In contrast, his twin’s telomeres remained stable during the same period.   

“Our experiment investigates whether this increase in telomere length was due to reduced gravity or some other factor, such as increased radiation or stress during the spaceflight,” says Richardson. 

Flying parabolic manoeuvres on the NRC’s Falcon 20 will allow the team to isolate microgravity from the other factors present on the International Space Station. However, while Scott Kelly spent months in space, the experiment will only undergo five periods of 20 seconds of microgravity each. 

The students had to devise a way to test whether telomeres are affected by microgravity in under 20 seconds. “Telomere length won’t change that fast,” says Richardson. “The key was to focus on the transcription of the genes that control them. Previous studies found transcriptomes changed significantly within 20 seconds of altered gravity.” 

Richardson has built her team with students from EngSci’s aerospace and biomedical systems majors and the life sciences: MacKenzie Campbell (EngSci 2T0 + PEY, ChemE MASc candidate)Dunja MaticTaylor Peters (both EngSci Year 4), Emma BelhadfaLuca Castelletto (both EngSci Year 3), physiology master’s student Anthony Piro, Year 3 life sciences student Miranda Badovinac, and Grade 12 students Samantha Aberdein, Krish Joshi, and Nicole Richardson. 

The aerospace engineering team members focused on designing and building the physical apparatus while biomedical systems and life science students designed and tested the experiment’s scientific methods. 

“The team brought together students with different areas of expertise, several age groups, and diverse mentors. One of the beautiful things that happens when you bring together people with so many different backgrounds is the ingenuity in the questions they ask each other,” says Professor Rodrigo Fernandez-Gonzalez (BME), chair of EngSci’s biomedical systems major. “Those questions often challenge dogmas and assumptions, and can ultimately lead to amazing discoveries.” 

To test their hypothesis that microgravity contributes to changes in gene transcription related to telomeres, the students will “freeze cells in time” by preserving their nucleic acids before and after each short period of microgravity. They will analyze the nucleic acids after the flight for changes in the expression levels of genes that regulate telomeres.   

The experiment’s apparatus consists of a syringe filled with a stabilization solution and connected to a series of chambers containing live cells. The electronic control system will inject the solution into the correct chamber when manually triggered by the students on board the flight just before and after each period of microgravity. Some samples are frozen before any periods of hypergravity or microgravity to control for environmental conditions on board the jet. 

TelOmG injection system

The TelOmG injection system. (Graphic courtesy of team TelOmG)

The entire experiment had to fit into a 50 cm cube and weigh no more than 45 kg, among other constraints. “Little things that you wouldn’t normally consider are much more challenging in microgravity,” says Castello, the team’s mechanical lead. “For example, we had to ensure everything is absolutely leak-proof and secured so that there’s no chance of small components or liquid floating around the plane’s cabin. Since we are dealing with cells, we had to create a sterile system while also minimizing bubbles that could interfere with our fluid pathways.” 

Team TelOmG presented their proposal at the Johnson Space Centre Astronomical Society in June and has been invited to share their findings at the International Aeronautical Congress in Dubai in October. 

 Working in the midst of a pandemic presented additional challenges. Access to wet labs and lab safety training was restricted. “We’ve been blown away by the support we received from professors, researchers and private companies during this time,” says Belhadfa. “They helped us to get what we needed when public health restrictions created obstacles.”  

Team members also had to work on components in isolation for many months. “Normally when we work in a team and something goes wrong during equipment testing, we have a good laugh together,” says Castelletto. “It’s a lot less funny when you’re all alone in your house.” 

Planning and testing a complex experiment from start to finish has been an eye-opening journey for the team. “From our experiences in design courses like Praxis, we knew to expect things not to go as planned,” says Campbell. “We really learned to take a wide view of the project and lean on our project management skills.” 

Team members Piro and Richardson will take part in the flight next week. 

This article originally appeared in the U of T Engineering News.


What undergraduate summer research looks like in the time of COVID-19

By Tyler Irving

KMUTT virtual research meeting

 

Lauren Streitmatter (Year 2 EngSci) thought she’d be heading to Imperial College London this summer, but the pandemic had other plans.

“I was really looking forward to the hands-on experience working in a research lab, as well as going to Europe for the first time,” she says. “After that fell through, I didn’t have many ideas for a new summer position.”

But a few days after the cancellation, Streitmatter got an email about a new research opportunity, this one at Carnegie Mellon University. The project involved pandemic modelling, so it could be completed remotely, and the supervisor was U of T Engineering alumnus Professor Peter Zhang (EngSci 1T1, MIE MASc 1T3).

“I thought it looked really interesting,” says Streitmatter. “I got an interview and was accepted in early May to start the remote placement. We hope to uncover fundamental physical laws of epidemic processes by designing novel Explainable AI (XAI) methods.”

Lauren Streitmatter

Lauren Streitmatter is completing her summer research project remotely with Peter Zhang (EngSci 1T1, MIE MASc 1T3), a professor at Carnegie Mellon University. (Photo courtesy Lauren Streitmatter)

Streitmatter is one of dozens of U of T Engineering students who are forging ahead with summer research placements, despite the physical distancing restrictions in place throughout much of the world.

More than 50 of these projects are supported through the Engineering Science Research Opportunities Program (ESROP), which provides fellowships that are matched by project supervisors. ESROP is made possible by philanthropic donations from many benefactors, including Engineering Science alumni and industry partners.

“We’ve had an absolutely tremendous response from our partners both here at U of T and abroad, many of whom are our alumni,” says Scott Sleeth, Curriculum Officer in the Division of Engineering Science, who coordinates summer research placements.

“Summer is a perfect time to explore and learn in these open-ended projects,” says Zhang. “My mentors — including Dean Emerita Cristina Amon (MIE), David Romero, professors Chris Beck (MIE), Tim Chan (MIE), and Yu-Ling Cheng (ChemE) — lit the entrance for me, and I hope I can do something similar for future generations of students.”

All of the placements are being completed online. Many of them focus on topics such as data science, artificial intelligence, or bioinformatics, which naturally lend themselves to remote collaboration.

Like Streitmatter, some of the students have shifted their placements from one supervisor to another, including many within U of T. But others are going ahead with their original placements abroad, albeit virtually.

These include eight students studying with Professor Jonathan Chan (EngSci 8T4, ChemE MASc 8T7, PhD 9T5) another EngSci alumnus who is now a professor at King Mongkut’s University of Technology Thonburi.

“We all have biweekly meetings with Professor Chan and each other to keep updated on relevant online events, such as seminars and conferences, and to check-in on the progress everyone is making,” says Dunja Matic (Year 3 EngSci).

Matic is working on two projects: one which uses physiological data from EEGs or ECGs to train algorithms to classify emotions, and another that uses deep learning (a form of artificial intelligence) to predict the effects of genetic variations.

“I am being challenged to learn about topics that are out of my comfort zone, such as artificial intelligence,” says Matic. “The new plan for this placement is still very exciting, despite not being able to work in person.”

“Everything is going as expected,” says Chan. “There are ups-and-downs as usual and the team is learning to work with one another and their mentors and research collaborators. In some ways, I’d say this batch of students is able to produce even more as they able to focus on the projects that they selected. But we may distract them with some other events so they do not overexert themselves.”

The high number of placements is another example of the way that U of T Engineering is adapting to the new normal.

“I’m quite pleased with how this all turned out,” says Sleeth. “It’s been rewarding to see the lengths to which professors are willing to go to ensure that these students can still have meaningful research experiences, and to support them in their professional development.”


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