Don't opt out: click here to learn more about our work.

Women in STEM: Madeleine Bonsma-Fisher

PhD candidate discusses challenges faced by women in physics, and what it means to be a scientist

Women in STEM: Madeleine Bonsma-Fisher

Madeleine Bonsma-Fisher is a PhD candidate in the Department of Physics in the lab of Dr. Sidhartha Goyal, specializing in biophysics. Bonsma-Fisher’s research focuses on applying physical concepts to solve biological problems. 

Unlocking science: knowledge behind closed doors

The way bacteria defend themselves against viruses is the focus of Bonsma-Fisher’s research.

“Just like us, bacteria can get sick from viruses,” wrote Bonsma-Fisher, “except that, for bacteria (which are just single cells), this often means imminent death.”

One of the ways that bacteria fight against illness is through the CRISPR-Cas system, an adaptive immune system. 

Bonsma-Fisher tries to “understand how CRISPR-Cas immune systems change the way populations look and behave” by “using mathematical tools from physics to create models of bacteria and viruses.”

An open source project she has been working on, in collaboration with over 30 colleagues internationally, is named phageParser.

As its source code is free to use and adapt for the public, Bonsma-Fisher hopes that the project “will make it easier for people to explore and use all the available information about CRISPR immune systems in known bacteria.”

“Science is largely funded by the public and should be accessible to the public,” she noted. “The problems we need science to help us solve are becoming so large and complex that not one person or group can do it alone.”

Fostering resilience through “failure” in research

A challenge highlighted by Bonsma-Fisher was accepting the inevitable delays and setbacks that happen in a research project. 

“It’s hard to look at months of work and realize it will never see daylight,” she explained, “but I try to look at slow or ‘failed’ projects as part of the process.” 

Bonsma-Fisher has since reframed these setbacks as learning experiences. “It’s like doing a homework assignment to learn something: trying something that doesn’t work or doesn’t have an obvious point is still not a waste of time.”

“I always learn things, and I think that learning to enjoy the slow process has made me a more resilient person and a better scientist,” added Bonsma-Fisher.

Subtle pressures facing women in STEM

Another challenge she has faced has been subtle forms of prejudice due to her gender.

“I have experienced many microaggressions over the years: each one by itself is hardly worth mentioning, but some people describe it as ‘death by a thousand cuts’ — eventually the never-ending low-level discomfort wears you down.”

Microaggressions are “subtle, often unintentional, [forms] of prejudice,” according to an article from Psychology Today

Examples of what she has experienced include “overhearing people saying sexist things or making sexist jokes and not being called out, having people say or imply that I experienced some aspect of my success because I’m a woman, [and] being asked on dates by male colleagues who were older or more senior than me.”

Another experience includes her repeated encounters of people who are “completely unaware” that systemic biases exist against women.

As a result of these experiences, she has felt pressured to change the way she dresses. She avoids appearing “too feminine” to blend in better with her male colleagues. 

“The feeling of not belonging is reinforced by things [that] imply that women are newcomers and outsiders in science,” she wrote, “even though this isn’t true.” 

Women who “stick it out in the face of hostility”

As she has progressed through her academic career, Bonsma-Fisher has noticed a drop in gender diversity. 

According to Bonsma-Fisher about a third of the students in her undergraduate program was comprised of women, while her graduate program only comprises about 10 per cent. 

“In terms of other underrepresented groups of ethnic, gender, and sexual identity,” she wrote, “my experience is that physics is woefully lacking.”

The issue of diversity in physics was discussed in an article by The Varsity, which noted the number of women in physics is lower than in biology or chemistry.  

A contributor to the imbalance, wrote Bonsma-Fisher, has been “a continual stream of microaggressions,” referring to a 2016 paper in Physical Review Physics Education Research.

“In a recent study, 74% of surveyed women undergraduate physics students had experienced sexual harassment in a physics context,” she further noted. “Faced with that kind of environment, why would anyone want to stick around?”

“These kinds of systemic biases are almost invisible to any individual woman in, say, a physics undergraduate program,” wrote Bonsma-Fisher, “but it can be very sobering (and it was for me) to learn that the system is subtly stacked against you, mostly in ways that will never be obvious to you.” 

Advice for students pursuing a career in STEM

When asked for advice for other students pursuing a career in STEM, she wrote that it’s difficult to give general guidance, as “what helps one person is often specific to their situation and might not help another.”

“But I think some things apply in general: the system does suck in a lot of ways, but there’s no one right way to do science and be successful.”

Rather than feeling out of place, she encourages students to remind themselves that “[their] perspective and unique experience is important and makes science better, and it’s okay to be yourself AND be a scientist.”

“I wish I knew then that there is no one kind of person who is meant to be a scientist, and also that “academic success” isn’t the only, or even best way to contribute to science.”

“I saw only a narrow path forward at that time that was basically just get good grades, go to a prestigious grad school, and write good papers. I would tell a younger me, ‘you belong in science,’” wrote Bonsma-Fisher.

Undergraduate students take on Ecology & Evolutionary Biology Research Fair

More than 30 students presented their research to peers and faculty

Undergraduate students take on Ecology & Evolutionary Biology Research Fair

Undergraduate students from the Department of Ecology & Evolutionary Biology presented their research on an array of topics, from biodiversity to gene-environment interactions, on April 5 at the Ecology & Evolutionary Biology Undergraduate Research Fair.

Judges selected four winners for a cash prize: Natasha Klasios for research in gene-environment interactions, Elenore Breslow for research in biodiversity & morphology, Joshua Craig for research in mutualism & parasitism, and Edita Folfas for the category of life history ecology & evolution.

Highlights from microplastics research

Klasios, supervised by Dr. Chelsea Rochman, investigated whether wildlife in the San Francisco Bay were absorbing microplastics. Microplastics are tiny pieces of plastic less than five millimetres in diameter which can potentially harm wildlife.

In an interview with The Varsity, Klasios explained that her experiment’s design was to compare the absorbance of microplastics in mussels residing in the bay, to those taken from a marine reserve and left in the Bay for 90 days. Unexpectedly, she found that the transplanted mussels absorbed a greater number of microplastics per individual on average versus the resident species.

Closer analysis revealed that the data was skewed due to specific sites of the Bay having higher concentrations of microplastics, particularly in the central and lower south regions.

Describing the applications, Klasios explained that since her research shows site-specific differences in microplastic absorption by mussels, officials could potentially take samples of mussels from bodies of water over time to monitor microplastic concentrations, and identify “hotspots of pollution” for clean-up.

Jacqueline Bikker, also supervised by Rochman, explained how she analyzed the distribution density and composition of microplastics in the Chesapeake Bay.

Using spectroscopic analysis of surface water samples, she found that the most common type of microplastic pollution consisted of the polymers polyethylene and polypropylene. She also discovered that pollution in the Bay was highest downstream of Baltimore and Washington, D.C.

Highlights from botanical research

Miguel Eduardo Felismino, supervised by Dr. John Stinchcombe, explained how his research found a correlation between the flower size of the ivy-leaved morning glory and a measure called “stomatal conductance.” This is the rate at which carbon dioxide enters and water vapour exits a plant, through small holes in the leaves called stomata.

The findings provided evidence of an abiotic factor that could affect flower size. It does not involve other creatures, unlike known biotic factors that affect flower size, such as the population of local pollinators and the reproductive strategies of nearby plants.

Also supervised by Stinchcombe, Matthew Coffey investigated whether a population of Queen Anne’s lace, or wild carrot, could evolve to develop frost tolerance over time.

While he did not find evidence of evolutionary change over the relatively short six-year timeframe of the study, his investigation showed that developing a seedbank over time through a “resurrection study” design could be a viable way to conduct evolutionary studies.

Julia Boyle, supervised by Dr. Megan Frederickson, investigated whether there are “priority effects” in mutually beneficial relationships between plants and microbes. In other words, she studied whether the order in which microorganisms were introduced to a legume affected the plant’s growth.

Boyle found evidence that the first microbial strain introduced to the plant affected it the most, compared to a subsequently introduced strain. She found that initially introducing a parasitic microbe led to stunted above-ground plant growth, compared to the introduction of a mutualistic microbe.

Even if both strains were ultimately introduced to the plant in identical amounts, Boyle’s observations showed that the order of introduction would significantly affect the plant’s growth.

Highlights from animal research

Cole Brookson, under the supervision of Dr. Martin Krkosek, investigated how two species of sea lice could affect populations of three different species of wild pacific salmon – chum, pink, and sockeye.

L. salmonis is a specialist species of lice that only affects salmon, while C. clemensi is a generalist species that affects all fish. From examining how they affect the salmon species as they swim from the British Columbian coast, he found that the pink salmon species was the most susceptible to both species of lice.

He further found that L. salmonis was more prevalent in the southern Discovery Islands, while C. clemensi was more prevalent around the northern Johnstone Strait. These findings could help guide local communities to manage parasite populations.

Vicki Zhang, supervised by Dr. Locke Rowe, investigated how environmental factors are projected to affect the populations of two ambush bug species in Southern Ontario.

Zhang used Maxent — a machine learning species distribution model — to visualize data. From this data, Zhang created presence-absence maps and discovered that bug population ranges may be contracted in specific areas due to climate change. These maps could help guide future field work on the Phymata americana and Phymata pennsylvanica bug species.

Under the supervision of Sebastian Kvist, Sophia Samuelsson created a “Hitchhiker’s Guide to the Leeches of Canada.” In doing so, she created the first meta-analysis of natural history information for Canadian leech species since the 1970s.

To collect findings, Samuelsson combed through a variety of studies, from how leeches affect turtles, to how leeches carry disease between hosts and respond to lake acidity. She hopes the reference resource may be useful for leech biologists, scientists who study species affected by leeches, and researchers in environmental health.

U of T team wins silver at international synthetic biology competition

Students developed alternative wastewater cleaning system using genetically engineered bacteria

U of T team wins silver at international synthetic biology competition

A U of T team took home a silver medal at this year’s International Genetically Engineered Machine (iGEM) Giant Jamboree competition for their project on an “environmentally friendly and economically feasible” way to clean wastewater using genetically engineered bacteria.

The competition, held on October 24–28 in Boston, Massachusetts, brought together more than 6,000 students and professionals of all levels and countries to showcase achievements in synthetic biology.

In trying to find an alternative wastewater cleaning solution, the U of T team used biomass flotation for bioremediation processes.

“We hypothesized that one could genetically engineer E. coli to bind to waste particles, and then float to the surface of the reactor, allowing for easy E. coli removal,” wrote the team in their drylab model.

“We have engineered bacteria to float by producing gas vesicles, and now we are trying to get these bacteria to bind pollutants so that they can float up with them and separate them from wastewater,” wrote Vice-President Internal Jack Castelli to The Varsity. The team has also mathematically modelled a bioreactor platform that makes use of their system.

According to President Amy Yeung, the group came up with the idea by talking to graduate students at their lab and reading scientific literature, and then searching for novel tools to find solutions to the problems they encountered.

“Coming across the use of gas vesicle in ultrasound imaging we also thought that it could be expressed in bacteria and used as a novel wastewater cleaning solution. So naturally, we decided to combine the two,” wrote Yeung.

When asked about any challenges they faced during their project, Lab Manager Tashi Rastogi said that the group had problems troubleshooting their genetically engineered constructs in the lab.

“With time we realised the importance of exercising reflexivity in our scientific process,” wrote Rastogi.

She also credited advice from graduate mentors in helping the group understand “both the biological systems [they] worked to engineer and the needs of the industrial systems [they] were designing [their] solution for.”

“The overarching goal of our project is to construct an efficient and inexpensive bio-remediation system, capable of separating pollutants from wastewater using bacteria,” wrote Castelli, who added that current processes are very costly and not environmentally friendly.

“If you have a substrate of interest that cells can bind or uptake, say heavy metals, and that’s present in a liquid medium, say mining effluent, then you could adapt the system to bind to or uptake the substrate and remove it from the medium,” he continued.

“This same logic can then be applied to microplastics, hormones, pharmaceuticals and other molecules of interest in other industries.”

The team included over 30 U of T students from across the Faculty of Arts & Science and the Faculty of Applied Science & Engineering. This is the third medal that U of T has won since the club was founded in 2007.

The competition is run by the iGEM Foundation, which has its roots in an independent study course at the Massachusetts Institute of Technology. Since its founding in 2003, it has grown into the non-profit organization that runs this international competition.

For dance flies, size does matter

UTM study shines light on sexual differences in animal mating behaviour

For dance flies, size does matter

For female North American dance flies, size definitely matters.

A recent UTM study discovered that, for North American male dance flies, sexual attraction is highest when female mates display large inflatable abdominal sacs. 

The study was published in Proceedings of the Royal Society B by UTM postdoctoral fellow Rosalind Murray, UTM biology professor Darryl Gwynne, U of T biology lecturer Jill Wheeler, and University of Stirling biologist Luc Bussiere.

To attract male dance flies for fertilization, the researchers found that female flies display signs of sexual ornamentation. The female flies use valuable energy reservoirs to expand their abdominal sacs, which is appealing to their male counterparts. 

In cases where female dance flies have smaller abdominal sacs, they attract males flies through larger leg scales.  

When discussing the reasoning behind her study, Murray said she “wanted to do an experiment to see if these ornaments were actually attracting the males and if they were working in the same way we typically see male ornaments — so, bigger is better.”

Why are the female flies using large amounts of energy to attract their male counterparts? 

According to Murray, the male flies provide them with a “food gift,” because the female flies have lost their ability to hunt, “so the males go hunting and they bring, usually another fly or insect. They kill it and they present it to the female in exchange for mating.”

The research took place over a 10-day period on an island in Credit River last June. North American dance flies are peculiar creatures that only appear for one hour at dawn and another hour at dusk.

As such, to complete the field research, Murray would wake up before sunrise to study the flies for an hour when they came out.  

During the day, Murray would analyze the data collected from the morning, and then she would venture out again at 8:30 pm to study the flies until sundown.

To test her theory, Murray created models that imitate female shapes and examined the impact of the two ornament types.

The research is particularly significant because it demonstrates a stark shift in our understanding of the animal kingdom. 

Typically, research has suggested that male animals use their energy to attract female counterparts. Much of Charles Darwin’s research, for example, focused on this phenomenon of sexual selection between mates.

However, Murray and Gwynne’s research turns this idea on its head.

“There are certain ways across animal kingdoms that males and females behave… It’s rare that you do find the vice versa, whereas in these flies, the subject of the paper, females are displaying very male-like traits,” Gwynne said. “They have reversed roles.”

Within the field of evolutionary biology, Murray’s study is the first that demonstrates this kind of female sexual ornamentation. “It’s such a bizarre system,” Murray said. 

“We’re looking at similar questions among many species of dance flies, thinking about how different species have evolved these ornaments.” 

With files from Srivindhya Kolluru

Researchers identify a Neanderthal-Denisovan hybrid

The discovery sheds light on our human ancestors

Researchers identify a Neanderthal-Denisovan hybrid

A single bone fragment can reveal thousands of years of human history.

In a study published in Nature, a team of researchers, including U of T Professor Bence Viola, identified a hybrid between two extinct lineages of hominids — Neanderthals and Denisovans — in a bone fragment.

Neanderthals lived on earth about 40,000 years ago, and, along with modern humans, they evolved from Homo erectus. Denisovans diverged from Neanderthals, but little is known about them other than bits of information recovered from bone fragments of their extremities, found in a Denisova Cave in Siberia’s Altai Mountains.

This is why, when researchers found a bone fragment in the Denisova Cave in 2012, they didn’t give much thought to the finding; it looked like all the others, an ordinary and tiny piece of what was thought to be part of a bear or lion.

After all, when a site is being excavated, many items are found, including pieces from animals and insects.

“There are 100,000 bone fragments found at a time and this particular one had a length of only 2.5 centimetres long, roughly the size of a toe bone,” said Viola.

A few years following the discovery, the fragments were analyzed for collagen. Finding a long bone fragment gave researchers an advantage for conducting DNA extraction techniques because of its morphology; it preserves better and allows for further manipulation.

“The bone was also discovered to have an acid coating which suggested it was digested by hyenas,” added Viola. The fact that DNA evidence survived this process makes this discovery even more extraordinary.

The bone was determined to belong to a female around age 13. This teenager died 90,000 years ago and was the offspring of a Neanderthal mother and Denisovan father.

Viola couldn’t believe it.

Based on previous studies, it was assumed that Neanderthals and Denisovans occasionally interacted, but interbreeding between the two hominins was thought to be rare.

This breakthrough informs researchers that interbreeding could have contributed to the gene flow, or transfer of genetic information, and it is now evident in the bone fragment.

The fragment is also evidence that the two species were in the same region at the same time.

Interbreeding is a result of various factors, such as an attempt to colonize certain areas. The discovery could help shape our understanding of hominin interactions and forms the basis to determine further benefits to interbreeding.

As such, this finding allows researchers to try and understand the lives of our closest ancient human relatives.

Dude, what’s that smell?

U of T study explains link between smell and memory

Dude, what’s that smell?

I am sitting at my maternal grandmother’s house in New Delhi, India. Masi, my aunt, has prepared a dish for me that she promises I will love. I don’t particularly like surprises, but I wait outside the kitchen.

I catch a whiff of something sweet. I can’t place it but it’s familiar. I close my eyes and I know it’s a smell from my childhood. Then it hits me. My Masi is making an Indian confection called almond halwa using my grandmother’s recipe.

This connection that I made — that we all make — between odour and memories, is explained in a study published in Nature Communications. The study, led by Afif J. Aqrabawi, a PhD candidate in the Department of Cell & Systems Biology at U of T, sheds light on this connection and how it could help develop new diagnostic tests for Alzheimer’s disease.

The hippocampus (HPC) is essential to episodic memory. It organizes memories of sensory events, including smell, in terms of space and time. The HPC stores the condition of the brain when said events take place, and then retrieves and recreates cerebral cortex activity of the original memory’s context when we encounter the sensation again.

The anterior olfactory nucleus (AON) is the largest source of feedback projections in the olfactory cortex, and the anatomical junction where the connection between olfactory and contextual information is made. HPC projections into the AON can alter the way smells are perceived and what behaviours are associated with specific odours.

Aqrabawi and Department of Psychology Professor Jun Chul Kim had determined that inputs from the HPC to the AON are necessary for the retrieval of odour memory based on spatial and temporal contexts. They knew the AON played a role in connecting spatial and olfactory events, but they did not know the exact function of the AON-HPC junction.

Thereafter, Aqrabawi and Kim found a neural pathway between the HPC and AON and they were able to define its role in memory retrieval. This pathway is responsible for contextual retrieval of odours and is affected in patients with Alzheimer’s.

In the study, mice whose AON-HPC junction was blocked kept returning to investigate the same scent even after being exposed to it several times prior. This was an indication that the AON plays a significant role in memory retrieval.

On the other hand, mice whose junctions were left to function normally spent less time smelling familiar odours because of the episodic memories associated with them. Inhibition of the HPC-AON pathway results in a loss of the odour memory linked to a given context in space and time.

This is the first study that demonstrates that inputs from the HPC to the olfactory cortex are necessary for forming and retrieving episodic odour memories. Findings from the study also show that the anatomical location of AON behind the olfactory bulb is an ideal bridge between olfactory and contextual information.

Multiple studies have reported a loss of olfactory function in Alzheimer’s patients. In fact, diagnostic smell tests are currently used to detect the earliest symptoms of the disease. This olfactory dysfunction is due to the neurodegeneration of the AON, which stores episodic odour engrams, during the early stages of Alzheimer’s disease.

Future research involving these findings will likely aim to better understand the connection between smell and memory, and particularly the neural circuits involved in this association.

Blind as a bat

Visual constraints were necessary for the evolution of echolocation in bats

Blind as a bat

 

Believe it or not, Batman was not the first winged creature to use echolocation to hunt down his prey — ancestors of the modern bat began using echolocation, the process in which objects are located by reflected sound, between 65 million and 85 million years ago.

John Ratcliffe, an Assistant Professor of Biology at UTM, and his team used molecular phylogeny techniques to decode the evolution of echolocation in bats, reconstructing our perspective on how and why these creatures came to be sonar crusaders of the night.

Their study, recently published in Nature Communications, has built on an existing phylogenetic study to reveal that bats evolved advanced biosonar capabilities through ancient tradeoffs between vision and echolocation.

Bats are the second largest order of mammals in the world, with more than 1,300 species. The bulk of these species are carnivorous and nocturnal, hunting small insects in the night using echolocation.

The researchers used phylogenetic comparative methods to understand evolutionary relationships between sensory systems, neuroanatomy, and morphology in bats. The results of the study indicate that ancestral bats possessed insufficient visual capabilities to hunt small prey at night but had the neuroanatomical potential to echolocate. This proved that there was a pre-existing opportunity for echolocation to flourish into an advanced sensory system in future descendants.

Evolutionarily, bats have continuously exhibited processes of behavioural tradeoff: species with poor echolocation abilities tend to have better visual resolution, and vice versa.

They further found that modern bats that use echolocation of the weakest frequency had the best vision out of those in all other sensory frequency groups, demonstrating that this tradeoff can function in either direction. The non-echolocating pteropodid is an example of a family with this tradeoff.

Surprisingly, the pteropodids have auditory brain regions the same size as echolocators. This vestige confirmed that bats from this family were once capable of echolocating but have since lost the trait. This is in contrast to the alternative scenario that proposes they evolved independently of echolocators — instead they are descendants of the same group.

This study not only answers questions about the evolution of a key trait of one of the most diverse mammals in the world, but it also cements the importance of phylogenetic research.

“It’s like replaying the video of evolution under different scenarios,” said Jeneni Thiagavel, the primary author of the paper, who has been working in this area of research for the past four years. “That essentially gives users [of these comparative methods] the power to reconstruct what that was like.”

Love makes scents

UTSC professor’s study finds ring-tail lemurs use ‘stink-flirting’ to attract mates

Love makes scents

If you think the smell of Axe is bad, be glad you’re not a lemur. In a study led by Amber D. Walker-Bolton, a UTSC professor in the Department of Anthropology, researchers found that male ring-tailed lemurs use their ‘stink’ to impress potential mates.

This unique behaviour allows lemurs to display their rank among other males and attract suitable mates, albeit at a cost.

Lemurs belong to the Strepsirrhine sub order and live in male groups that have a core female lineage. Each of these groups have dominant central males and periphery males, where rank is correlated with age.

‘Stink-flirting’ refers to male display of tail anointing and wafting, which is considered “a submissive display prior to a close approach.” The study found these displays are associated with male dominance and that they are reciprocated by females. Females preferred the exaggerated displays and are said to set the male apart from the rest of the population.

Additionally, the study found females showed a preference for dominant resident males as opposed to lower-ranking immigrant males. Immigrants are rarely found mating with females of the group.

Surprisingly, male lemurs are more frequently faced with aggression from both females and other males when they perform stink-flirting displays compared to other mating rituals. Only when females in estrus were receiving the olfactory display would they then mate.

Some of the females are also mate-guarded by a male. These guarded females were found to receive a higher rate of displays than non-guarded females. Although mate-guarding doesn’t completely eliminate displays from other males, it hinders approach to guarded females.

While the majority of females chose the most dominant mate, the opposite was not the case. According to the study, male ring-tailed lemurs did not “preferentially target high-ranked females for olfactory displays.”

In the future, Walker-Bolton’s team hopes to study the correlation between ‘stink-flirting’ and reproductive success.