Graduate students express frustration, confusion at U of T’s advisories on lab work amid COVID-19

“Non-essential” lab research to be suspended as of March 20 due to pandemic

Graduate students express frustration, confusion at U of T’s advisories on lab work amid COVID-19

On March 13, U of T announced that it would be cancelling in-person courses for undergraduate and graduate students, but that research operations would continue. “Faculty members have a responsibility to maintain the operations of laboratory and research environments,” reads the statement

Almost immediately, confusion ensued among research staff, postdoctoral fellows, visiting scientists, and graduate students across U of T.  

Days later, on March 17, U of T officials stated that lab-based research operations must be shut down by March 20 at 5:00 pm, with the exception of time-sensitive projects under the approval of the Incident Management Team, or projects related to the COVID-19 pandemic.

But before U of T made this call, research staff and graduate students were left in limbo. 

Some researchers received directions from their respective faculties, departments, or research supervisors to remain home if possible, or work in the lab during off-peak hours. In addition, several departments advised principal investigators (PIs), or heads of research groups, to move group meetings online, prepare contingency plans for experiments, and accommodate students who feel unsafe coming into work. 

Researchers at U of T-affiliated hospitals have also received additional advisories. 

On March 16, the University Health Network (UHN) suspended “non-essential on-site research activities” until April 6. The UHN noted that projects related to COVID-19, studies essential to clinical care, and those that have “significant cost- or time-related implications” will remain active, but in-person access will be limited to “essential personnel” who have been tasked with maintaining facilities, instrumentation, or looking after animal colonies.

“We all have a pile of papers to write and data to analyze,” wrote Dr. Bradly Wouters, Executive Vice-President Science and Research at UHN, in an email to PIs at UHN on March 12. “Stay home, use the time valuably and let’s all see a bump in publication productivity over the next 6 months.”

The Varsity contacted graduate students across various science departments at U of T to determine how their departments, labs, and supervisors are responding to COVID-19. 

Mixed signals: graduate students received little direction from departments, PIs

Lee*, a public health graduate student, said that their PI initially expected their team to come into the lab every day amid cancellation announcements, even though Lee’s lab does not require wet-lab or on-site experiments.  

“My PI has given us no direction on whether we’re to come in but it seems like the expectation is yes,” wrote Lee to The Varsity. Lee noted that they felt their PI’s message to lab members “seemed to downplay the situation.” 

Similarly, Alex*, a biology graduate student, wrote to The Varsity that while their PI encouraged lab members to take precautions, like washing their hands often, they still expected students to work in the lab. 

“[They want] us to do more work just in case we won’t be able to in the future. For example if we become sick and need to self-isolate,” Alex wrote. “[They think] there’s less distractions now since we don’t have as much TA work.”

“I am concerned about getting infected but since it’s worse in older people I’m more concerned about getting infected and then infecting others,” Alex noted. 

Following U of T’s announcement on March 17, both Lee and Alex’s PIs responded by either telling them to stay home, or to make preparations to work from home. 

In a comment to The Varsity, the University of Toronto Graduate Students Union (UTGSU) wrote that they have been communicating with administration regarding lab closures.

“The UTGSU Executives are disappointed that it took so long for the University to take this step, but remain advocates for safe working conditions for our members.”

Prioritizing health and safety: “It’s been instilled in the lab culture”

While some graduate students felt frustrated at a lack of response from their supervisors, several graduate students told The Varsity that their PIs have taken extra steps to support their lab members during the pandemic. 

Chemistry PhD candidate JoAnn Chen wrote to The Varsity that her PI had not explicitly said anything about COVID-19, but her lab’s culture has always made it possible for students to stay home when they are feeling sick.

“In my lab, the students have decided [that] we’ll come in when we have scheduled instrument time, but otherwise, we won’t be coming to lab,” Chen wrote on March 13. “Our supervisor has always been accommodating in terms of sick days and vacation, so we were able to decide as a group, but in other labs, the PI probably needs to say something.”

After U of T’s shutdown notice for non-essential lab work on March 17, Chen’s PI informed lab members of plans to shut down instruments. 

Molly Sung, also a chemistry PhD candidate, is scheduled to defend her thesis on April 7. “I have my PhD defense coming up – the next group meeting was supposed to be my practice,” wrote Sung to The Varsity on March 15. Her PI, Professor Robert Morris, offered to meet with her one-on-one to practice her talk. 

On March 17, Sung found out that her defence will take place over a video call, but the public portion of her defence has been cancelled.

Graduate students worried about research setbacks

Even though classes and meetings shifted online this week, Kyle*, a graduate student in biology, expressed guilt about their inability to complete lab work. “It’s hard to sit at home when you know you have a growing pile of work that has to be done at the lab,” Kyle wrote to The Varsity. “This will either set you behind or create more work to do.”

Similarly, Ash*, a neuroscience graduate student who works with mice, wrote that they were worried about how a lab shutdown would impact their mouse colonies and degree progress. “I have a lot of big ideas but no concrete evidence to link everything together yet,” Ash wrote. “If research is shut down, it’s not easy to get back.”

Ash said that their PI is looking into “whether the research animals have to undergo mass euthanasia.”

“It is a huge waste of research funds if it happens and we’d like to prevent it as much as possible,” Ash wrote.

Avery*, a pharmaceutical sciences graduate student shared this sentiment. “I’m definitely worried about the impact this will have on my research.”

“The guilt I feel at the possibility of missing a few weeks in [the] lab is immense. But the guilt I feel about not doing my part to stop the spread of COVID-19 is also huge.”

*Names have been changed for privacy.

The Varsity has reached out to U of T and the UHN for comment.

How chaos theory captures the dance of planets

U of T undergraduate and Princeton fellow publish astronomy research on planetary motion

How chaos theory captures the dance of planets

You probably don’t go about your day thinking about how our solar system works and the probability of its collapse.

In fact, if you are anything like me, when you do think about our galay you likely recall pretty images of space, or astronauts from movies. However, what many people might not realize is that our solar system is borderline unstable — there is a small theoretical chance that Mercury will collide with either the Sun or Venus.

Because dynamics, which is the study of how forces influence motion, is so chaotic, astrophysicists will never be able to predict when this will happen, or even if it will happen at all.

The good news is that it could be possible to estimate the probability of distribution against all other possible outcomes in our system. This is exactly what the research paper by Naireen Hussain, a fourth-year engineering science undergraduate student majoring in robotics at the University of Toronto, and Dr. Daniel Tamayo, a Lyman Spitzer Sr. fellow and Sagan fellow at Princeton University’s Department of Astrophysical Sciences focuses on.

The paper is available on arXiv, and is pending peer review. It revolves around the relation between chaos, or unpredictable behaviour, and multi-planetary systems.

The process of discovery

Hussain and Tamayo worked together during Hussain’s second and third years of undergraduate studies, while Tamayo was at U of T’s Department of Astronomy & Astrophysics. After Tamayo left U of T, the pair worked on the project through Skype and email, and completed it over last summer.

The topic was not an easy one to research. In addition to being centred around an ambitious idea of predicting how long orbital configurations will survive, what they wanted to explore was “whether that question is even well defined in the first place,” according to Tamayo.

One of the hardest parts of the research process was actually figuring out the initial planet configuration. Another big obstacle, Hussain said to The Varsity, was finding a “substantial data set that doesn’t take too long to generate and still is able to give you valid results,” so they had to play around with various orbital configurations.

A surprise, even for the researchers

At the end of the research process, Hussain admitted, the pair was pleasantly surprised with the results. “What we went into was to see if [it] was even possible to do this, so we were quite satisfied when we realized that [it has actually] come to a consistent distribution,” she said.

She believes that this research will make an impact on other physicists studying the topic because they can now “use [their] stability analysis to strain the orbital parameters.”

Though the probability of Mercury colliding with either the Sun or Venus is less than one per cent, it is still a possibility. But since we cannot predict when the collision might happen, even with our modern-day technology and all the information available to us, the only thing we can do is look at all the possible outcomes and estimate their distribution probabilities.

The study by Hussain and Tamayo plays a significant role in this achievement by advancing research on the relationship between chaos and planetary systems.

Police find decades-old human remains near campus

Bones were from a medical specimen used in a study

Police find decades-old human remains near campus

Around 3:00 pm on January 22, human remains were found buried beneath a home on Brunswick Street, south of Dupont Street. After consulting a forensic anthropologist, the Toronto Police Service (TPS) announced Friday afternoon that the bones were part of a specimen that had been used in a medical study.

The contractors who made the discovery were involved in renovating the private residence, and were excavating the grounds. At the time the remains were found, police were unsure whether they were the result of a crime, archaeological, or due to some kind of misfortune. An investigation was launched to “determine [the] circumstances of [the] death.”

All that was known up until recently was that the bones were decades old and buried under a property which is reportedly 140 years old. The home was cordoned off to protect the scene and two special constables were posted to guard the area.

After determining that the bones were indeed human, a forensic identification officer from TPS and a forensic anthropologist from the Office of the Chief Coroner were called in for further analysis. TPS ultimately ruled that the remains are “not associated to [a] missing person or homicide” case.

The investigation is now closed following the conclusion that the remains were part of a medical specimen dating back to the 1940s.

How to digest plastic and save the world

Toronto team wins gold standard at international synthetic biology event

How to digest plastic and save the world

Hundreds of students, from graduate to high school studies, gathered in Boston to present their research at the International Genetically Engineered Machine (iGEM) Foundation’s Giant Jamboree in early November. Over the past year, they’ve been developing projects in the emerging field of synthetic biology, which uses modern tools and biological building blocks to solve natural problems.

This year, iGEM Toronto, the University of Toronto team, returned with more than just the standard bragging rights. Rather, their project was recognized with a gold standard — the highest evaluation for a project in the iGEM competition — and they were nominated for the best manufacturing project in their competitive category.

What was the team’s project?

Over the past year, the team has conducted cutting-edge research on a possible solution to the world’s plastic waste problem. Three years ago, a team of researchers in Japan discovered a unique strain of bacteria that can break down a common type of plastic, polyethylene terephthalate — commonly called PET plastic — on a molecular level, essentially digesting it.

At the moment, plastics can only be recycled a finite number of times before they start to degrade and have to be disposed of. However, if researchers find a way to break plastics down to their molecular components, they could apply this to make a near-perfect recycling system for plastic.

Recyclers could then recreate the plastics from scratch to be as good as new, with negligible amounts of waste.

Since their conception, the iGEM Toronto team has been designing and testing ways to implement this recycling process in an industrial setting. The recently-discovered bacteria uses a particular protein, called PETase, to break down the plastics that it digests.

How the team collaborated to win gold

The team’s computational lab created the necessary tools to redesign the protein so that it could process plastics quicker, while keeping them sturdy enough to survive in an industrial setting. Building on the work of researchers like Dr. Jennifer Listgarten and David Brookes, several team members trained a neural network to search for more efficient versions of the protein.

Others used protein-modelling software to redesign PETases, giving them more useful chemical properties. Together, they modelled five alternate versions of the protein, hoping that some would be more efficient at digesting plastics than naturally-occurring PETases.

In the final analysis, all versions of the protein were successful.

The team’s biology lab then produced millions of copies of these proteins in order to test their practical efficiency. Other members of the team interviewed experts to get a better understanding of the current recycling industry, and developed preliminary models for a PETase ‘bioreactor’ that could be used in a recycling plant.

The impact of iGEM’s success

The research team considers the victory to be a huge validation. “I was able to lead a team of people who never knew each other at first, and now could come up with something that’s now on a world stage, and is worth it,” said Amy Yeung, the outgoing president of iGEM Toronto, in an interview with The Varsity.

“That sense of feeling of accomplishment, from when I’ve started to now, is the best thing I think I’ve picked up.”

What’s more, the iGEM program at U of T has the potential to set a precedent for undergraduate research. “A lot of undergrads get stuck just doing somebody’s side jobs in a lab,” said Daniel Kiss, who took over as the club’s co-president this year, to The Varsity.

iGEM Toronto’s research model is different. Although their projects are designed and run by members from a wide variety of programs — from computational biology to ethics — they’re almost entirely undergraduates.

“It’s like Lord of the Flies, but [with a] happy ending,” joked Kiss. “Let’s put all these undergrads in a room and see what happens.”

Women in STEM: Shoshanna Saxe

Civil engineering professor discusses the importance of infrastructure investment, finding mentors

Women in STEM: Shoshanna Saxe

Dr. Shoshanna Saxe is an Assistant Professor at the Department of Civil & Mineral Engineering. Her research focuses on how the infrastructure we build shapes the society that we live in: everything from how we work, to the ways in which we consume and travel. 

She is particularly interested in the relationship between infrastructure and environmental sustainability.

How infrastructure affects our environment and lifestyle

Saxe recently wrote an opinion piece in The New York Times, in which she described the role of an infrastructure engineer as someone who “[seeks] the simplest effective solution to a problem with a minimum of negative consequences.” 

“Infrastructure [serves as] the skeletal structure of society, [and] everything relies on infrastructure,” wrote Saxe to The Varsity. “If we can get the infrastructure part right, we have the potential to have a more sustainable society.”

Infrastructure touches almost any urban design we can think of: sidewalks, roads, public transportation systems — even sports facilities and public parks are deliberately shaped by infrastructure engineers.

Saxe’s research has examined both the impact of Toronto’s Sheppard subway line on greenhouse gas emissions and the influence that airport infrastructure has on the reliability of flight arrivals in remote North Canadian communities.

Overall, Saxe noted that her research focuses on finding “levers that would allow us to better align our infrastructure delivery and societal scale goals.”

She described her path to becoming an infrastructure engineer as a winding one, having accumulated research experience in wind energy, geothermal heat storage, and subway design, among other areas. 

Facing exclusion in academia 

Despite the barriers she has faced, Saxe noted that she has found supportive colleagues. 

“The most painful challenges have been when I have been excluded from events based on my gender or religion,” noted Saxe, singling out a golf event in a workplace outside of U of T, where no women were invited.

While instances of clear differential treatment like these are extremely difficult to handle, Saxe also highlighted that there are other times where exclusion may be more subtle. 

Saxe wrote that she has worked through these challenges in two ways. The first, she wrote, is by “continuing to work and not letting any of these occasional events make me feel like I don’t belong in engineering.”

The second is remembering that “many people stood up in harder situations before me making it possible for me to be where I am today.”

Reflection has encouraged her to “stand up for what I think is important even if it feels like it would be better for me (on a personal career level) to be silent.” 

Her advice for those in academia navigating sexism is to “focus on the big challenges,” find mentors and allies, and ask for help. 

Celebrating mentorship

Saxe explained that mentorship has provided her with “access to wisdom from experience I don’t have yet, perspective from the other side of the hurdle.”

She expressed that one of the benefits of having a woman mentor is “the shared experience.”

At each stage of Saxe’s career, her women peers have been some of her greatest mentors. One of which is her sister, Dr. Rebecca Saxe, a neuroscience professor at the Massachusetts Institute of Technology, who Saxe lists as her biggest mentor. “Talking to her about my work always makes it better,” wrote Saxe. 

Advice for undergraduate and graduate students 

Saxe’s main advice for undergraduate students interested in research is to stay well-informed. 

“This involves researching the current ongoing research at U of T in the area you are interested in,” wrote Saxe. She recommends that before contacting a professor, students should read their recent publications and draft an email that explains their specific interests in the professor’s work. 

Her advice for graduate students is a little different. “Don’t forget to have fun,” she explained, noting they should “take some advantage of the flexibility being a grad student offers.”

In her experience, wrote Saxe, she has seen an increase in diversity in her field since she began her career. Her advice for women in STEM is to “work hard [and] speak up.”

Young long-term cannabis users may have higher levels of chronic stress biomarker

CAMH study links cannabis usage with biomarker, but not with symptoms of stress

Young long-term cannabis users may have higher levels of chronic stress biomarker

A landmark study conducted by researchers at the Centre for Addiction and Mental Health (CAMH) found elevated levels of a brain protein associated with chronic stress and anxiety in the brains of young long-term cannabis users.

Published on September 18 in the JAMA Psychiatry medical journal, this study was one of the first to use the Positron Emission Tomography (PET), an imaging technique, to study the association between cannabis and the neuro-immune function in the brain.

The brain protein that was studied is called a translocator protein, or TSPO. It is involved in immune functions and is associated with levels of stress and anxiety.

In an interview with The Varsity, Dr. Romina Mizrahi, the lead author of the study and Senior Scientist at the CAMH Research Imaging Centre, talked about the motivation behind the research.

“Young people use cannabis a lot and they usually think or perceive cannabis as harmless,” she said.

“I, as a scientist, I know that the brain develops and is still developing until the age of 25, so I wanted to understand how cannabis affects the developing brain.”

The study’s design and results

Mizrahi and her co-authors conducted the study in Toronto. The participants included 24 long-term cannabis users, who met the criteria for Cannabis Use Disorder (CUD).

The study also consisted of 27 non-cannabis users, who acted as the control group to compare the protein levels in the brain.

Each participant underwent a scan with the PET imaging technique, which the researchers used to measure the subjects’ levels of TSPO.

The study found that long-term cannabis users had significantly higher levels of the biomarker associated with stress and anxiety compared to the non-users.

Limitations of the study

Mizrahi warns readers, however, that this experiment only studied the relationship between cannabis use and the biomarker associated with stress.

While she and her co-authors studied the biomarker’s levels, they did not examine the impact of its elevated levels on the subjects’ behaviour. The study therefore does not provide a direct link between long-term cannabis use and the symptoms of stress and anxiety.

“We cannot say that cannabis causes this increase in this protein or that it causes stress and anxiety,” said Mizrahi. “We know they are related, but we don’t know which comes first.”

However, Mizrahi spoke about the potential future research that aims to study causation. Such studies could also examine whether the biomarker’s levels would normalize after a period of abstinence for long-term cannabis users.

These findings could refine research and have major future implications regarding attitudes toward the consumption of cannabis for adolescents.

Effects of cannabis on the developing brain still unknown

Mizrahi still added that she would caution adolescents against using cannabis due to their developing brains.

“What I would tell them is that they should be careful when using cannabis because their brains are still developing until the age of 25,” she said. “Whether [the effects are] long-term or short-term, we need to study this moving forward.”

“But I would still caution them not to use cannabis. To use or to not use cannabis while the brain is developing… is an important decision [that adolescents] have to make.”

Remembering Dr. Jay Keystone

U of T professor’s life profoundly impacted residents, colleagues through quality education and influential research

Remembering Dr. Jay Keystone

Dr. Jay Stephen Keystone, a travel and tropical medicine specialist at the Toronto General Hospital and a professor of medicine at U of T, passed away from cancer while surrounded by family on September 3. He was 76 years old.

He is remembered fondly for his empathy and frequent use of humour as he trained residents, treated patients, and worked with colleagues through difficult days in the hospital.

“When people found out he had passed away, there was an outpouring of love and support from people all over the country and even worldwide,” said Dr. Isaac Bogoch, a close friend and colleague of Keystone, to The Varsity.

Bogoch recalled that Keystone fostered a working environment “where you don’t really recognize that it’s work, because you’re enjoying yourself too much.”

“He’d always be smiling and enjoying life along the way,” even on days with heavy workloads, said Bogoch. “That’s one thing I certainly picked up from him.”

Keystone’s empathy in medical education

Dr. Sumontra Chakrabarti, who is now an infectious disease specialist at Trillium Health Partners, recalled his time working with Keystone as a resident for three years. He recounts those years as some of the “most enriching” of his career.

He wrote to The Varsity that Keystone was a “very outgoing, friendly and warm individual” with a “larger than life presence.” He attributed Keystone’s personality in large part to his “amazing sense of humour, that made everyone around him smile.”

“From a resident’s standpoint,” continued Chakrabarti, “any room Dr. Keystone was in, was one guaranteed to be relaxed, jovial, and a place where you would leave knowing much more than when you walked in.”

“It was because of him [that] I have pursued my special interest of tropical infections within my infectious diseases practice,” wrote Chakrabarti. “The type of clinician I am today is in large part my efforts to emulate the type of physician he was.”

Dr. Christopher David Naylor, the former president of U of T, also commented on the empathy of Keystone’s mentorship style, which sharply contrasted the approach that other medical educators used at the time.

“What stood out is that he was humble and kind to his students and residents at a time when, frankly, some of the older clinical teachers were into ritualized humiliation as a mode of instruction,” wrote Naylor.

Naylor also recalled one incident from Keystone’s education that he would never forget.

It involved Keystone teaching medical students that Ascaris lumbricoides infections could be almost asymptomatic. This means that, in Keystone’s words, on many occasions the only “presenting symptom of the patient [would] be horror.’’

“Why?” Keystone would ask rhetorically, “Well, how would you feel if you defecated and found a large worm wriggling in the toilet bowl?”

Keystone’s impact on clinical research

Reflecting on Keystone’s research, Naylor highlighted how he brought the Canadian medical community’s attention to the implications of globalization on the spread of infectious diseases at a time when its impact was not widely recognized.

Keystone graduated as a gold medallist in the U of T Medical School’s class of 1969, and conducted postgraduate work and fieldwork on multiple continents. He returned to Toronto in 1977 to found and lead the Tropical Medicine Unit at the Toronto General Hospital.

His legacy includes more than 200 scientific papers and textbook chapters that he co-authored, a premier travel medicine textbook he wrote as a senior author, and the organizations he was a part of, including the International Society of Travel Medicine where he served as president.

In 2015, he received the Order of Canada for his contributions to tropical and travel medicine.

But despite Keystone’s stature, wrote Naylor, “Jay himself often said that his greatest professional accomplishment was to teach himself out of a job.”

In an article published in May, co-authored with twin brother and rheumatologist Dr. Edward Keystone, Dr. Jay Keystone encouraged those reading “to think about the people who made an impact or provided you with mentorship, and how you can pay it forward to others.”

This fits with Dr. Jay Keystone’s approach to education. In Naylor’s words, Keystone was “involved in inspiring, recruiting, and educating literally hundreds of postgraduate medical trainees.”

“Those individuals, practising all across the country and all over the world, along with his beloved family, are Jay’s living legacy and most important gift to the world.”

The race of the male black widow spider to find mates

Male spiders follow trails of competitors, according to recent UTSC study

The race of the male black widow spider to find mates

How do male black widow spiders find potential mates? According to a recent UTSC-affiliated study, they follow the silk trails left by their competitors.

In a majority of mate-seeking insect species, the males follow pheromones — chemicals released by an individual of the same species — in order to find available mates. Traditional thinking would suggest that males follow pheromones from female spiders, while avoiding those released by males, to prevent any vicious competition during courtship.

However, according to the study’s results, the male black widow spider instead leverages the scent and the silk trails released by other males to efficiently find potential mates.

The motivation for the adaptation

The reproductive success of the black male widow spider hinges on its ability to locate a potential mate as quickly as possible, due to the low number of available female black widow spiders and lengthy courtship behaviour.

“On any given night, there are only a handful of sexually receptive females. Hence competition is inevitable,” explained Catherine Scott, the study’s author and a PhD candidate at UTSC, to The Varsity.

“Furthermore, courtship can last hours. So, even if a male is not the first to arrive and if he gets to the female quickly enough, he might just be able to win the competition and be the first one to mate.”

Given the intense competition male black widow spiders face in courtship, it is best for them to follow the trails of other males rather than completely lose the chance to mate.

However, these are not the only hurdles that male black widow spiders face. Even after successful mating, the male spider is sometimes cannibalized by its partner, as the females are much larger than the males of the species.

The study’s design and results

To conduct the study, the researchers set up a series of races to track the spiders’ behaviour on the sand dunes of Vancouver Island.

Before the races, each male was weighed on a scale. The length of his legs were then measured, and his body was painted with unique racing stripes for identification. The race’s finish line was set up with cages containing the pheromone-releasing females.

Due to the nocturnal behaviour of black widow spiders, the males were released at sunset in 10-metre intervals from the finish line. The shortest race was 10 metres away from the finish line, while the longest was a length of 60 metres.

The great “Black Widow Races of 2016 and 2017,” as Scott nicknamed them, enabled the researchers to determine the speed taken by each male to find the cages.

Unexpectedly, they found that the males were able to locate the females faster if they also had access to the pheromones of other males.

While further research needs to be done, Scott hypothesizes that the study’s results could be generalized to other species of spiders.

“In other spider species where there is a similarly high level of competition over access to receptive females, and where the last male to mate has an advantage, I would expect that males may use similar tactics,” wrote Scott.