Ecology &amp; Environmental Biology

Genetics

With CRISPR-Cas9 technology – a specific and versatile gene editing technology that can be used to modify, delete or correct precise regions of DNA – humans can now rapidly change the evolutionary course of animals or plants by inserting genes that can easily spread through entire populations.

In an opinion paper published recently in the journal Trends in Genetics, ��߲ݴ�ý evolutionary geneticist Asher Cutter says we must scientifically and ethically scrutinize the potential consequences of this “genetic welding” before we put it into practice.

Asher Cutter

“The capability to do genetic welding has only taken off in the last few years, and much of the thinking about it has focused on what can happen in the near term,” says Cutter, a professor in the department of ecology and evolutionary biology in the Faculty of Arts & Science.

“Ethically, before humans apply this to natural populations, we need to start thinking about what the longer-term consequences might be on a time scale of hundreds or thousands of generations.”

In classical Mendelian genetics, genes have a 50-50 chance of getting passed from parent to offspring – but this isn’t always the case. In a natural phenomenon known as “genetic drive,” some genes are able to bias their own transmission so that they are much more likely to be inherited.

Genetic welding is the human-mediated version of this: introducing genes that have an unfair advantage when it comes to heritability in natural populations. Because these genes spread easily and rapidly through populations, they result in much faster evolutionary change than the usual slow plod that we see from natural and artificial selection.

In contrast to natural selection, genetic drives and genetic welding can perpetuate genes that don’t necessarily benefit the organisms that carry them – making them an attractive potential method to control problematic and invasive disease-bearing species.

For example, genetic welding has been proposed as a tool to control disease-bearing mosquito populations and invasive species. It could also be used to genetically engineer endangered species to be resistant to infectious pathogens that threaten them with extinction.

“It raises the question of how much should humans intervene into processes that are normally beyond our control,” Cutter says.

“If ethicists, medical practitioners and politicians decide that it is acceptable in some cases to edit the ‘germline’ of humans – the population of cells that pass on their genetic material to offspring – then that would open the possibility that genetic welding could be used as a tool in that regard. This would open a much bigger can of worms by virtue of the fact that genetic welding could change the entirety of a population or species – not just a few individuals that elected to have a procedure.”

Though it might be difficult to experimentally assess the long-term implications of genetic welding, Cutter says that thought experiments, mathematical theory, computer simulations and conversations with bioethicists could all play important roles, as could experiments in organisms with short lifespans and rapid reproduction.

Cutter’s research is supported by the Natural Sciences and Engineering Research Council of Canada.

With files from Cell Press

U of T Trash Team finds masses of plastic, 'fatbergs' and other waste in Toronto’s harbour: Toronto Star

Christopher.Sorensen — Thu, 09 Feb 2023 22:23:06 +0000

U of T Trash Team finds masses of plastic, 'fatbergs' and other waste in Toronto’s harbour: Toronto Star

Christopher.Sorensen Thu, 02/09/2023 - 17:23

Cutline

(Photo supplied)

Topic

Sustainability

New findings by the ��߲ݴ�ý Trash Team and PortsToronto are raising awareness about Toronto harbour’s pollution problem, according to the Toronto Star.

Over a four-month period, specially engineered seabins – think floating trash collectors – removed 100 kilograms of plastic waste, or almost 100,000 pieces of plastic from Lake Ontario.

Chelsea Rochman, assistant professor in the department of ecology and evolutionary biology in the Faculty of Arts & Science and head of operations at the U of T Trash Team, told the Star that 2022 was a “big year” for pollution.

“Our trash trapping season included the highest number of trash traps yet,” said Rochman.

The report also noted the collection of several “fatbergs,” which are masses of household grease, baby wipes and toilet paper.

With this discovery, the U of T Trash Team is reminding everyone to, “only flush the three Ps! (pee, poop and paper).”

U of T students return to the field for 2022 Research Excursion Program

Christopher.Sorensen — Wed, 14 Sep 2022 13:22:07 +0000

U of T students return to the field for 2022 Research Excursion Program

Christopher.Sorensen Wed, 09/14/2022 - 09:22

Cutline

Abigail Wagner and Lily Peters at the Koffler Scientific Reserve north of Toronto where they spent the summer conducting research on the parasitic goldenrod gall fly (photo by Kemeisha McDonald)

Chris Sasaki

Topic

Student Experience

st. michael's

Undergraduate Students

Victoria College

When the pandemic halted in-person instruction at the ��߲ݴ�ý in the spring of 2020, it also paused valuable experiential learning opportunities like the Faculty of Arts & Science’s Research Excursions Program (REP).

But with pandemic restrictions now easing and students back in the classroom, the program is once again providing undergraduates with a chance to take part in a faculty member’s research project off campus.

Lily Peters and Abigail Wagner spent the summer taking part in a study of the parasitic goldenrod gall fly and the common goldenrod plant at U of T’s Koffler Scientific Reserve at Joker’s Hill (KSR), located north of Toronto in a region of the province known as the Oak Ridges Moraine. The site comprises 350 hectares of wetlands, pastures and forests – and the wildlife that calls those habitats home – and is used by the university for research, training and public outreach.

A member of Victoria College, Peters is entering her second year in an ecology and evolutionary biology specialist program with a genome biology major. Wagner, meanwhile, is entering her fourth year in a genome biology and physiology program and is a member of St. Michael’s College.

“This has been my first real experience doing research,” says Peters. “I'm planning to do a master’s degree or PhD, so I wanted to see if research was for me and see what type of research I liked. I wanted to get a feel for how this type of research is done.”

Wagner, for her part, says she is interested in genomics and wants to pursue a career in genetic counseling. “Our project is related to uncovering how different characteristics correlate with different gene variations and how common these variations are in a population – so it was just what I was looking for,” she says.

The students’ REP supervisor is Arthur Weis, a professor in the Faculty of Arts & Science’s department of ecology and evolutionary biology. Weis studies natural selection – one of the mechanisms by which species evolve – in particular, when evolution occurs over a short period of time.

Abigail Wagner “bags” a gall to protect it from parasitic wasps (photo by Kemeisha McDonald)

The goldenrod fly is a parasite that lays its eggs on goldenrod plants. After about 10 days, a larva emerges from the egg and burrows into the plant’s stem, triggering the growth of a gall – a round, tumour-like sphere measuring a half-inch to an inch in diameter. The larva survives the winter inside the gall and in the spring, the adult fly emerges, ready to start the cycle over.

Peters and Wagner are helping Weis in his research into the genetic connection between individual flies and the size of the galls their larvae produce.

Gall size is important. Larvae in small galls are vulnerable to parasitic wasps that lay eggs in galls which then hatch into larvae that prey on the fly larvae. Larger galls offer protection from wasps but larger galls are preyed upon by woodpeckers for the larvae within. The researchers’ goal is to shed light on the natural selection forces that favour a gall that is neither too small nor too large – and the genes that may be the basis for determining size.

The students began by finding goldenrod plants with galls. Their next step was to protect the fly larvae from wasps by wrapping the galls in mesh. Over the summer, Peters and Wagner “bagged” over 700 galls.

The students then collected galls and sorted them by size.

The students collected goldenrod flies that have emerged from galls (photo by Kemeisha McDonald)

“Next, we’ll sequence all the flies to figure out whether all the big-gall flies have a similar section of their genome,” says Wagner. “Then, we’ll look to see if some of the genes in this section play a role in causing a specific size of gall.”

For Weis, the program is rewarding as both an instructor and a scientist.

“This is what it's all about – working with students in the lab or in the field,” he says. “Students who are curious, enthusiastic and want to learn. And in the process, it extends my own research and helps me answer the questions I'm curious about.”

For Wagner and Peters, the experience has provided them with much more than an opportunity to do research.

“It’s really added context for me for when I’m reading a research paper,” says Wagner. “Because now, I've experienced the entire research process, hands-on.”

Peters, meanwhile, says she’s planning to pursue a PhD, “so, it's been cool seeing and talking with other researchers up here and learning about what they're doing for their masters and PhDs.

“And working outside in the field all day has been amazing. I’ve seen so many things – like my first porcupine! It’s been a really great experience that’s shown me how amazing field work is. It’s really solidified in my mind that this is what I want to do for the rest of my life.”

Massive new animal species discovered in half-billion-year-old Burgess Shale

Christopher.Sorensen — Wed, 29 Sep 2021 19:22:51 +0000

Massive new animal species discovered in half-billion-year-old Burgess Shale

Christopher.Sorensen Wed, 09/29/2021 - 15:22

Cutline

Titanokorys gainesi was a giant compared to most animals that lived in the seas during the Cambrian period, most of which barely reached the size of a pinky finger (illustration by Lars Fields/Royal Ontario Museum)

ROM/A&S News Staff

Topic

Breaking Research

Earth Sciences

Graduate Students

Royal Ontario Museum

��߲ݴ�ý palaeontologists based at the Royal Ontario Museum (ROM) have uncovered the remains of a huge new fossil species belonging to an extinct animal group in half-a-billion-year-old Cambrian rocks from Kootenay National Park in the Canadian Rockies.

Named Titanokorys gainesi and described in a study published in Royal Society Open Science earlier this month, the new species is remarkable for its size. With an estimated total length of half a metre, Titanokorys was a giant compared to most animals that lived in the seas at that time – most of which barely reached the size of a pinky finger.

Jean-Bernard Caron sits above a fossil of Titanokorys gainesi at the quarry site located in Kootenay National Park (ohoto by Joe Moysiuk)

“The sheer size of this animal is absolutely mind-boggling – this is one of the biggest animals from the Cambrian period ever found,” says Jean-Bernard Caron, an associate professor in the departments of Earth sciences and ecology and evolutionary biology (EEB) in the Faculty of Arts & Science at U of T and the Richard M. Ivey Curator of Invertebrate Palaeontology at the ROM.

Evolutionarily speaking, Titanokorys belongs to a group of primitive arthropods called radiodonts. The most iconic representative of this group is the streamlined predator Anomalocaris, which may itself have approached a metre in length. Like all radiodonts, Titanokorys had multifaceted eyes, a pineapple slice-shaped, tooth-lined mouth, a pair of spiny claws below its head to capture prey and a body with a series of flaps for swimming. Within this group, some species also possessed large, conspicuous head carapaces, with Titanokorys being one of the largest ever known.

“Titanokorys is part of a subgroup of radiodonts, called hurdiids, characterized by an incredibly long head covered by a three-part carapace that took on myriad shapes. The head is so long relative to the body that these animals are really little more than swimming heads,” added Joe Moysiuk, co-author of the study, and a PhD student in EEB based at the ROM.

Jean-Bernard Caron and Joe Moysiuk in the ROM palaeontogy lab room examining Titanokorys gainesi and Cambroraster falcatus (photo by Andrew Gregg/© Red Trillium)

Why some radiodonts evolved such a bewildering array of head carapace shapes and sizes is still poorly understood and was likely driven by a variety of factors, but the broad flattened carapace form in Titanokorys suggests this species was adapted to life near the seafloor.

“These enigmatic animals certainly had a big impact on Cambrian seafloor ecosystems. Their limbs at the front looked like multiple stacked rakes and would have been very efficient at bringing anything they captured in their tiny spines towards the mouth. The huge dorsal carapace might have functioned like a plough,” added Caron, who is Moysiuk’s PhD adviser.

All fossils in the study were collected around Marble Canyon in northern Kootenay National Park by successive ROM expeditions. Discovered less than a decade ago, this area has yielded a great variety of Burgess Shale animals dating back to the Cambrian period, including a smaller, more abundant relative of Titanokorys named Cambroraster falcatus in reference to its Millennium Falcon-shaped head carapace. According to the authors, the two species might have competed for similar bottom-dwelling prey.

These and other Burgess Shale specimens will be showcased in a new gallery at the ROM, the Willner Madge Gallery, Dawn of Life, opening in December 2021.

The Burgess Shale fossil sites are located within Yoho National Park and Kootenay National Park and are managed by Parks Canada. Parks Canada works with leading scientific researchers to expand knowledge and understanding of this key period of earth history and to share these sites with the world through award-winning guided hikes. The Burgess Shale was designated a UNESCO World Heritage Site in 1980 due to its outstanding universal value and is now part of the larger Canadian Rocky Mountain Parks World Heritage Site.

Support for the research came from a Natural Sciences and Engineering Research Council of Canada Discovery Grant to Caron and a Vanier Canada Graduate Scholarship to Moysiuk. Additional support for the research and fieldwork came from the Polk Milstein Family, the ROM, the National Geographic Society, the Swedish Research Council, the National Science Foundation and Pomona College.

Studying guppies, researchers find ADHD drugs can affect later generations

Christopher.Sorensen — Thu, 03 Jun 2021 16:12:45 +0000

Studying guppies, researchers find ADHD drugs can affect later generations

Christopher.Sorensen Thu, 06/03/2021 - 12:12

Cutline

U of T PhD candidate Alex De Serrano is the lead author of a study that found the effects of drugs such as Ritalin and Concerta could be detected in multiple generations of guppies, including those with no direct exposure (photo by Helen Rodd)

Sean Bettam

Topic

Breaking Research

Drugs

Graduate Students

By studying guppies, scientists at the ��߲ݴ�ý and Florida State University found that behaviours affected by methylphenidate hydrochloride (MPH) – the active ingredient in stimulants such as Ritalin and Concerta used to treat ADHD – can be passed along to several generations of descendants.

“We exposed male and female Trinidadian guppies to a low, steady dose of MPH and saw that it affected the anxiety and stress-related behaviour of males, but not females,” said Alex De Serrano, a PhD candidate in the department of ecology and evolutionary biology (EEB) in the Faculty of Arts & Science and lead author of a study published recently in Scientific Reports.

“Because of this male-specific effect, we investigated the effects of MPH through the paternal line and observed the same behaviours in several generations of their descendants not directly administered the drug.”

The findings add to growing knowledge about paternal effects on offspring, as well as the capacity for those effects to span multiple generations – of which even less is known.

From one month of age and through adolescence and into adulthood, first-generation guppies were exposed to MPH via the water in which they lived. The researchers then compared their behaviour against a control population exposed to non-treated water and observed that the males exposed to Ritalin were less cautious when placed in a new environment, compared to those not treated with the drug.

“The Ritalin-treated males showed less inhibition than expected when moved to a new environment,” said De Serrano. “Under natural conditions, guppies would be expected to freeze if they found themselves in such a situation, as this allows them to assess their new surroundings for predators and other threats.”

De Serrano then produced three generations of offspring from these individuals to see if the behaviour of their descendants differed from descendants of those not exposed to the drug and observed behaviours similar to those of first-generation males exposed to the drug.

“It suggests that Ritalin has the potential to cause changes that persist across several generations,” De Serrano said.

The study’s findings contribute to a growing understanding of paternal effects on offspring, as well as the capacity for those effects to span multiple generations (photo by Alex De Serrano)

The researchers say the paternal effect of behavioural change may be transmitted to descendants via non-genetic modifications to the sperm of male ancestors exposed to Ritalin. Such molecular changes that don’t affect DNA are a potential mechanism for males to transmit information about their environment – including exposure to drugs or pollutants – to future offspring.

“In many species, including guppies, males do not interact with offspring beyond contributing sperm, so it was traditionally thought that paternal effects would be limited to species where fathers provide some type of care to offspring or other resources to mothers,” said Helen Rodd, a professor in the department of ecology and evolutionary biology who is De Serrano’s supervisor.

“As of now, most known examples in animals of paternal effects and transgenerational effects – effects that span several generations – come from rodents, so our findings add to the handful of studies that have found paternal, transgenerational effects in other species, though the actual mechanism remains unclear.”

It has been suggested that Ritalin could cause transgenerational effects because MPH has been shown to affect the sperm cells of male rodents. Further, paternal effects have been observed in descendants of rats exposed to drugs with a similar mode of action. Despite these concerns, the transgenerational effects of paternal exposure to MPH in humans are unknown.

“I was surprised to learn that no studies had investigated whether a drug so commonly prescribed to adolescent boys to treat ADHD affects the behaviour of their offspring,” said De Serrano. “Because reduced caution in new situations has been associated with increased drug-seeking behaviour in rodents and humans, our results suggest that long-term exposure to Ritalin could increase the propensity for drug abuse and other affective disorders in males and their descendants.”

However, the researchers note that, as with all comparative studies, their results only hint at general processes that might be occurring in humans and are not directly translatable to human populations.

“More research is required to determine the mechanism that caused this altered behaviour to persist across generations,” said De Serrano. “And in order to extend these results to humans, longitudinal studies following individuals taking Ritalin and their offspring are needed.”

Support for the research was provided by the Natural Sciences and Engineering Research Council of Canada.

Six ways U of T researchers – and the Royal Society of Canada – are working to make our lives better

Christopher.Sorensen — Thu, 19 Nov 2020 17:22:31 +0000

Six ways U of T researchers – and the Royal Society of Canada – are working to make our lives better

Christopher.Sorensen Thu, 11/19/2020 - 12:22

Cutline

Clockwise from top left: Aimy Bazylak, Chelsea Rochman, Kelly O’Brien, Kevin Lewis O’Neill, Marc Cadotte and Diana Fu

Rahul Kalvapalle

Topic

Temerty Faculty of Medicine

Earth Sciences

Faculty of Applied Science & Engineering

Political Science

Religion

Royal Society of Canada

Ted Sargent

U of T Scarborough

From clean energy and water to urban biodiversity, disability in HIV patients and labour activism in China, the next generation of researchers at the ��߲ݴ�ý is engaged in tackling some of the most difficult – and pressing – questions of our time.

Six of those researchers were recently recognized for their leadership, talent and the transformative potential of their research by being elected to the Royal Society of Canada (RSC)’s College of New Scholars, Artists and Scientists.

Their appointment makes them members of an exclusive group who have demonstrated excellence and extraordinary productivity at an early stage in their career, and whose perspectives and expertise will strengthen the College of New Scholars, Artists and Scientists’ mission of harnessing interdisciplinary approaches to generate ideas and solutions.

“Our researchers’ strength across the full breadth of areas of scholarship fuels an extraordinary range of cross-disciplinary collaborations – work that is vital to developing creative and sustainable solutions for the challenges facing Canada and the world,” says University Professor Ted Sargent, U of T’s vice-president, research and innovation, and strategic initiatives.

The new members of the college will be honoured at the Royal Society of Canada’s 2020 Celebration of Excellence and Engagement, a week-long exploration of scholarly, scientific and artistic topics. They will be recognized alongside 12 leading U of T researchers, across a diverse array of disciplines, who were named fellows of the society this year, as well two faculty members who won Royal Society of Canada medals: Barbara Sherwood Lollar of the department of Earth sciences and Marla Sokolowski of the department of ecology and evolutionary biology – both in the Faculty of Arts & Science.

U of T is a presenting sponsor of the event, which runs from Nov. 23 to Nov. 29 and includes a virtual symposium examining the impact and legacy of the discovery of insulin by U of T scientists 100 years ago.

U of T experts receive $9.5 million in funding for research infrastructure

rahul.kalvapalle — Wed, 26 Aug 2020 16:52:29 +0000

U of T experts receive $9.5 million in funding for research infrastructure

rahul.kalvapalle Wed, 08/26/2020 - 12:52

Cutline

(photo by Ken Jones)

Rahul Kalvapalle

Topic

Institute of Biomedical Engineering

Electrical & Computer Engineering

Faculty of Applied Science & Engineering

Hospital for Sick Children

Faculty of Dentistry

Faculty of Information

Faculty of Medicine

Immunology

Laboratory Medicine and Pathobiology

Leslie Dan Faculty of Pharmacy

Mechanical & Industrial Engineering

Ontario Institute for Studies in Education

Physics

Psychology

St. Michael's Hospital

University Health Network

UTIAS

Thirty-three research projects at the ��߲ݴ�ý, spanning fields from artificial intelligence and smart manufacturing to cancer detection and neurodegeneration, are set to benefit from more than $9.5 million in federal funding that will support research infrastructure needs and expenses.

The grants, which range in amount from more than $76,000 to $800,000, are being awarded by the Canada Foundation for Innovation’s John R. Evans Leaders Fund. Named for the late U of T President Emeritus John R. Evans, the fund aims to empower researchers with the equipment and technology they need to move their projects forward and maximize their impact.

The funding also helps universities remain competitive in global research and technology development by helping to attract top researchers in their fields.

“The crucial support provided by the Canada Foundation for Innovation underpins the important research that takes places every day across our three campuses,” said Ted Sargent, U of T’s vice-president, research and innovation, and strategic initiatives.

“Researchers at U of T are addressing some of the most complex and interesting challenges of our time, in fields ranging from the humanities and social sciences to medicine and engineering, and they depend on facilities, equipment and technology to help realize their discoveries.”

The largest award destined for U of T – $800,000 – goes to an active learning research lab project being led by James Slotta, professor and President's Chair in Knowledge Technologies at the Ontario Institute for Studies in Education.

Goldie Nejat, professor in the department of mechanical and industrial engineering in the Faculty of Applied Science & Engineering, will receive $440,474 for her work on robotics infrastructure for smart manufacturing.

Bianca Schroeder, an associate professor in U of T Scarborough’s department of computer and mathematical sciences, will use her $120,000 award for her work in the area of computer systems support for machine learning and artificial intelligence.

Other funded projects at U of T include the Sleep and Human Evolution Lab led by Assistant Professor David Samson of the department of anthropology at U of T Mississauga, which will receive $151,714 in support.

In total, CFI awarded more than $96 million in funding to 377 research infrastructure projects at 55 institutions across Canada. That includes more than $22 million under CFI’s Infrastructure Operating Fund, which helps pay for the incremental operating and maintenance costs of new infrastructure.

“Support from the Canada Foundation for Innovation ensures researchers are equipped for success at every stage of their career,” Roseann O’Reilly Runte, president and CEO of the Canada Foundation for Innovation, said in a statement.

“The John R. Evans Leaders Fund helps Canadian universities, institutes and research hospitals create the conditions necessary for their talented researchers to excel.”

The following 33 U of T researchers and projects received funding through the John R. Evans Leaders Fund:

Christine Allen, Leslie Dan Faculty of Pharmacy: Next generation polymeric microparticles for the treatment of osteoarthritis

Alán Aspuru-Guzik, departments of chemistry and computer science in the Faculty of Arts & Science: Chemspeed automated chemical synthesis system

Michael Best, department of psychology at U of T Scarborough: Psychosis research lab – assessment of biological, psychological, and behavioural factors associated with psychosis

Matthew Buechler, department of immunology in the Faculty of Medicine: A research program to study the role of fibroblasts in the pathogenesis of idiopathic pulmonary fibrosis

Jessica Burgner-Kahrs, department of mathematical and computational sciences at the U of T Mississauga: Immersive interaction and morphological control for continuum robot systems

Jean Chen, department of medical biophysics in the Faculty of Medicine and Baycrest Centre: Linking neural and vascular aging in the brain: from biophysics to cognition

Leo Chou, Institute of Biomedical Engineering in the Faculty of Applied Science & Engineering: DNA nanotechnology for spatially programmed immune receptor activation

Xu Chu, department of Earth sciences in the Faculty of Arts & Science: Mass transport in Earth’s lithosphere revealed by in-situ LA-ICP-MS micro-analyses

Miriam Diamond, department of physics in the Faculty of Arts & Science: Detector prototype units for long-lived particle searches

Peter Dirks, department of surgery in the Faculty of Medicine and the Hospital for Sick Children: A non-invasive approach to visualizing tumour growth in vivo through space and time

Claudia dos Santos, department of medicine in the Faculty of Medicine and Unity Health: A shift in paradigm – a novel stratification system for critical illness

Siew-Ging Gong, Faculty of Dentistry: Infrastructure for Canadian National Caries Network

Björn Herrmann, department of psychology in the Faculty of Arts & Science and Baycrest Centre: Sensory-cognitive listening assessment to transform hearing loss outcomes

Jane Howe, department of materials science and engineering in the Faculty of Applied Science & Engineering: Advanced scanning electron microscope for in situ and liquid-phase electron microscopy studies

Nikolina Ilic, department of physics in the Faculty of Arts and Science: Readout the answers

Rutsuko Ito, department of psychology at U of T Scarborough: Neural circuit changes in decision-making across the lifespan – relevance to mental health disorders

Gabor Kovacs, department of laboratory medicine and pathobiology in the Faculty of Medicine and University Health Network: Tracking down neurodegeneration in the human brain – from functional systems to the subcellular level

Cara Krmpotich, Faculty of Information: Recovery and recuperation – mobilizing the next generation of GRASAC

Hon Sing Leong, department of medical biophysics in the Faculty of Medicine and Sunnybrook Research Institute: Extracellular vesicle and patient avatar technology cores for translational and clinical research

Goldie Nejat, department of mechanical and industrial engineering in the Faculty of Applied Science & Engineering: Robotics infrastructure for smart manufacturing (RISM)

Nicolas Papernot, department of electrical and computer engineering in the Faculty of Applied Science & Engineering: Trustworthy machine learning

Tomas Paus, department of psychology in the Faculty of Arts & Science and Holland Bloorview Kids Rehabilitation Hospital: Charting diversity in brain maturation

Trevor Pugh, department of medical biophysics in the Faculty of Medicine and University Health Network: Defining cancer and immune landscapes in multiple myeloma using single cell transcriptomics and ultra-deep DNA sequencing

Chelsea Rochman, department of ecology and evolutionary biology in the Faculty of Arts & Science: Microplastic sources, fate and effects research laboratory

David Samson, department of anthropology at U of T Mississauga: Sleep and Human Evolution Lab (SHEL) – testing evolutionary hypotheses in a clinical, controlled space

Bianca Schroeder, department of computer and mathematical sciences at U of T Scarborough: Computer systems support for machine learning and artificial intelligence

Florian Shkurti, department of mathematics in the Faculty of Arts & Science: Autonomous mobile manipulation in human environments – learning algorithms and robot systems

John Sled, department of medical biophysics in the Faculty of Medicine and the Hospital for Sick Children: Advanced imaging of mouse development – early adversity and brain health

James Slotta, Ontario Institute for Studies in Education: Active learning research labs

Hoon-Ki Sung, department of laboratory medicine and pathobiology in the Faculty of Medicine and the Hospital for Sick Children: In-depth 2D and whole tissue 3D detection of tissue fibro-inflammation in metabolic diseases

Jacqueline Sztepanacz, department of ecology and evolutionary biology in the Faculty of Arts & Science: Mapping genotypes to phenotypes and phenotypes to fitness

Sara Vasconcelos, department of laboratory medicine and pathobiology in the Faculty of Medicine and University Health Network: Cardiac regeneration and in vitro disease modeling

Steven Waslander, U of T Institute for Aerospace Studies in the Faculty of Applied Science & Engineering: Autonomous docking and active perception for unmanned aerial vehicles

Microplastic pollution is everywhere, but scientists are still learning how it harms wildlife: U of T experts

Christopher.Sorensen — Tue, 28 Jan 2020 19:57:51 +0000

Microplastic pollution is everywhere, but scientists are still learning how it harms wildlife: U of T experts

Christopher.Sorensen Tue, 01/28/2020 - 14:57

Cutline

Large plastics break up into tiny particles called microplastics that can persist in the environment for hundreds of years (photo via Shutterstock)

Chelsea Rochman

Kennedy Bucci

Topic

Plastic pollution is a growing global concern. Large pieces of plastic have been found almost everywhere on Earth, from the most visited beaches to remote, uninhabited islands. Because wildlife are regularly exposed to plastic pollution, we often ask what effects plastics have on the animals.

Over time, macroplastics (plastic debris larger than five millimetres in size) break up into tiny particles called microplastics (smaller than five millimetres), which can persist in the environment for hundreds of years.

Macroplastics are known to cause detrimental effects for wildlife. Individual animals can ingest large pieces or become entangled in plastic items, such as fishing gear, and suffocate or starve to death. Although there is no question that macroplastics are harmful to wildlife, the effects of microplastics are not as straightforward.

While many studies find microplastics can affect the gene expression, growth, reproduction or survival of an animal, others conclude that microplastics have no negative effects. The lack of clear consensus makes it more difficult for decision-makers to enact effective policies to mitigate plastic pollution.

Not all plastics are the same

We recently took a deep dive into the research that has looked at how plastic pollution affects aquatic and terrestrial wildlife.

We found that while macroplastics continue to cause detrimental effects to individual animals, they are also causing larger-scale changes to populations of animals, communities and ecosystems. For example, plastic pollution can introduce invasive species to new habitats by transporting organisms hundreds of kilometres from their native range, changing the composition of species in a community.

The effects of microplastics, however, are much more complicated. Of the studies we included in our review, nearly half (45 per cent) found that microplastics caused an effect. Some studies saw that microplastics caused animals to have shorter lives, eat less or swim slower, and others saw changes in the number of offspring produced, and changes in the genes being expressed. Yet, 55 per cent of the studies didn’t detect any effects.

Why do some studies detect effects while others do not? There are several possibilities. For one, the researchers used different experimental designs in their lab experiments.

There’s also the issue of using the term microplastics, which refers to a complex mixture of plastics that vary in material (such as polyethylene, polystyrene or polyvinyl chloride), the chemicals associated with them (including additives, fillers and dyes), as well as their size and shape. Each of these characteristics, along with how much plastic the animal is exposed to in the experiment, could affect their potential to detect an effect.

Microfibres and microbeads

For example, we saw that when studies exposed crustaceans to polystyrene, a type of plastic used to make disposable containers, lids and cutlery, the crustaceans generally produced more offspring. But when they were exposed to polyethylene or polyethylene terephthalate, which is used to make plastic bags and beverage bottles, the crustaceans produced fewer offspring.

We also found that studies using smaller particles are more likely to detect an effect. This may be because smaller particles are more easily consumed by small organisms, or because they can move across the cell membrane and cause harmful effects such as inflammation.

Microbeads are found in exfoliating products such as face cleansers and toothpaste. Several countries have banned their production and sale (photo by Shutterstock)

When it came to the shape of the plastic, microfibres (from clothing or rope) and fragments were more likely to have a negative effect on the organism compared to spheres (from facial cleansing products). For example, one study found that microfibres were more toxic to a species of marine shrimp than microplastic fragments or spheres.

Finally, one might expect animals to be more harmed when they are exposed to higher concentrations of microplastics. While it’s true that crustaceans were more likely to die when exposed to increasing doses of microplastics, the effect on reproduction was more complex. The number of offspring increased with extremely high doses, but decreased at lower doses, similar to what is seen in the environment.

Many types, many outcomes

Based on our review, we believe future research needs to recognize the complexity of microplastics and scientists need to design their tests strategically so that we can really understand how the different types, sizes, shapes, doses and the duration of exposure to microplastics affect wildlife.

Several countries, including Canada, the United Kingdom and United States have recently banned plastic microbeads – the spherical beads and fragments in face wash, body scrubs and toothpaste – because they were contaminating the environment and could cause negative effects in aquatic animals. Although this legislation reduces one type of microplastic in the environment, it is irrelevant to countless others.

Only if we have a better understanding of how the different types, shapes and concentrations of microplastics affect wildlife can we make better policy decisions. If, for example, microfibres are indeed found to be more harmful than spheres, we could focus our attention on keeping these fibres from entering our waterways from known sources, such as from washing machines.

Chelsea Rochman is an assistant professor of ecology and evolutionary biology at the ��߲ݴ�ý. Kennedy Bucci is a PhD student in the department of ecology and evolutionary biology at the ��߲ݴ�ý.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

U of T students who crushed it in 2019

geoff.vendeville — Tue, 17 Dec 2019 15:12:56 +0000

U of T students who crushed it in 2019

geoff.vendeville Tue, 12/17/2019 - 10:12

Cutline

Diagnosed with cystic fibrosis as a baby, Elspeth Arbow graduated with a degree in cinema studies in June after overcoming a double-lung transplant – the second time she had undergone the procedure (photo by Lisa Lightbourn)

Geoffrey Vendeville

Topic

Munk School of Global Affairs & Public Policy

Student Experience

Accessibility

Dalla Lana School of Public Health

Factor-Inwentash Faculty of Social Work

Entrepreneneurship

Entrepreneurship

Faculty of Applied Science & Engineering

Faculty of Kinesiology & Physical Education

Near and Middle Eastern Civilizations

Undergraduate Students

University College

Victoria College

Woodsworth College

Convocation season is a time when many students at the ��߲ݴ�ý reflect on their accomplishments. But U of T students are doing and achieving things on a daily basis that make the university an outstanding place.

This year alone, students have gone to Ottawa to advocate a better, co-ordinated strategy to prevent concussions. They have researched news ways to fight dangerous, antibiotic-resistant superbugs. They have saved lives amid an opioid epidemic and used library books to pinpoint the identity of a lost Mesopotamian queen – all while overcoming the many challenges, big and small, that life threw at them along the way.

And that's just the start.

Here's U of T News's annual – if far from exhaustive – list of students who crushed it in 2019:

The first-year student who served as head dancer at U of T’s powwow

(photo by Nick Iwanyshyn)

Although she was only in her first year at U of T, Miyopin Cheechoo was asked to take on a big responsibility: being the head dancer at the U of T powwow.

The Cree student from Moosonee rose to the occasion. Wearing red polka dot print and an eagle feather, she danced her heart out and got a large section of the crowd in the Goldring Centre up on its feet.

The PhD student who located an ancient queen’s remains using only books

(photo by Perry King)

Tracy Spurrier, a PhD student in the department of Near and Middle Eastern Civilizations, helped track down the remains of a long-lost Mesopotamian queen – all without lifting a shovel or brush.

Queen Hama is said to have lived 3,000 years ago in Assyria. But the whereabouts of her body were a mystery until Spurrier, using a paleopathology report and book in her department’s rare book collection, managed to pin down the identity of her remains.

The twin sisters who went from lab to legislature in a campaign against concussions

(photo by Geoffrey Vendeville)

Sandhya Mylabathula, a PhD student, and her twin sister Swapna, doing a MD-PhD, have been interested in concussions since their undergraduate years. They spoke to legislators on Parliament Hill about the need for a culture shift within sport and offered other recommendations to reduce concussions.

The Indigenous twins in law and medicine who called for greater diversity in their fields

(photo by Geoffrey Vendeville)

No, you’re not seeing double. Brothers Patrick and Curtis Sobchak are another set of twins who crushed it this year. Patrick, who studied law, and Curtis, in medicine, were among the few Indigenous students in their classrooms.

Before graduating in June, they both took steps to call for greater representation of Indigenous Peoples in their respective fields.

Patrick championed the inclusion of Indigenous values and law in the curriculum, while Curtis wrote about the lack of diversity in medicine on the Canadian Medical Association Journal’s blog.

The theatre and drama major who amped up the conversation about diversity and disability on TV

(photo by Nick Iwanyshyn)

George Alevizos had no lines in his debut on Star Trek: Discovery as a Starfleet engineer, but his appearance was widely acclaimed for an important reason: Alevizos, who uses a wheelchair, was one of the few actors on the show – indeed television – with a visible disability.

He graduated from a U of T Mississauga-Sheridan College joint program in June and hopes to continue pressuring his industry to show greater diversity on the stage and screen.

The Syrian activist and master’s student who wouldn’t give up

(photo by Lisa Lightbourn)

Noura Al-Jizawi, a Syrian activist who was detained and tortured in her home country, came to U of T through the Scholars at Risk program. She was seven months pregnant when she started a master’s degree in global affairs, also known as an MGA, at the Munk School of Global Affairs & Public Policy.

It was her first time taking lessons in English rather than Arabic.

In the summer, she completed her studies and celebrated her convocation with her daughter, whom her classmates call the “MGA baby.”

“I imagine the moment I hold my diploma,” Al-Jizawi said before graduating. “It’s going to be the moment I defeat the dictators in Syria because it’s going to send the message: ‘You cannot defeat me.’”

The student who was ‘too stubborn to stop’

(photo by Lisa Lightbourn)

Elspeth Arbow, diagnosed with cystic fibrosis as a baby, kept up with her studies for a full nine months as her health spiralled and she waited for an organ donor. She then spent 2018 recovering from a double-lung transplant – the second time in her young life that she had undergone the procedure.

Her gutsy resolve paid off: She graduated from Innis College with a degree in cinema studies in June and landed a job at the Toronto International Film Festival.

“It’s this huge sense of accomplishment because I wanted to give up all the time,” she said.

The student whose award-winning startup empowers people in Nigeria

(photo by Rahul Kalvapalle)

Olugbenga Olubanjo, a master's degree student in engineering, often called his friends and family back home in Nigeria – only to have his conversations be interrupted by frequent power outages. So he decided to help his fellow Nigerians – some 70 million of whom live without electricity – gain access to a stable and safe power source.

Enter Reeddi, a startup Olubanjo runs with two fellow U of T students, Osarieme Osakue and Joshua Dzakah. The company provides portable, clean-energy capsules that are charged at solar-powered stations in local communities. It was a big year for Reeddi, which won a US$10,000 award and secured a provisional patent.

The Indigenous student whose grandfather inspired her to act

(photo by Tina Adamopoulos)

Diane Hill's grandfather – or laksotha, as he was known to his grandkids – was forbidden from speaking his native Oneida language in school during his childhood.

That injustice is one of the reasons Hill came to U of T Scarborough to study health policy and socio-cultural anthropology, with the long-term goal of supporting her community through education.

In her undergraduate years, she served as president of the Indigenous Students Association and as Indigenous program developer in the campus’s department of student life. She also traveled to New Zealand for an internship and received a Gordon Cressy Student Leadership Award.

Hill graduated in June and isn't losing any time in pursuit of her dream. She returned to U of T this fall to begin a master’s degree in social justice education at the Ontario Institute for Studies in Education.

The undergraduates who helped to preserve endangered languages in Brazil

(photo courtesy of uoftbrazil.blog)

Three undergraduate students travelled to Boa Vista, a city in the northwestern Brazilian state of Roraima, last spring to document and help preserve some of the region’s Indigenous languages: Macuxi, Ye’kwana and Taurepang.

The students – Octavia Andrade-Dixon, Guilherme Teruya and Gregory Antono – and their faculty supervisor Suzi Lima, in the department of Spanish and Portguese, met with native speakers to study the languages by translating simple nouns and discussing more complex linguistic concepts.

The PhD student who is fighting to prevent overdose deaths

(photo by Nick Iwanyshyn)

By some estimates, the opioid crisis in Canada has claimed more than 9,000 lives in just three years. Gillian Kolla, a PhD student at

the Dalla Lana School of Public Health, is a fierce advocate for street-involved drug users and has worked with other volunteers to establish supervised injection sites.

Stocked with naloxone kits, oxygen tanks and sterile injection equipment, they have saved 251 lives.

The student researching how to fight antibiotic-resistant superbugs

(photo by Perry King)

Chidozie Ojobor, who grew up in Nigeria, lost his older sister Ginika to typhoid fever 20 years ago.

Her death prompted him to study microbiology at the University of Nigeria in order to understand the mechanisms of disease and develop treatments. As a PhD student at U of T, he has identified novel bacteria-killing entities known as tailocins that have been shown to kill antibiotic-resistant superbugs in the laboratory.

Ojobor’s research received support from MPower Financing, a Washington, D.C.-based fintech company that provides loans to international students. He is the first university student in Canada to win an MPower Global Citizen scholarship worth US$5,000.

The swimmer who’s still on top of the world

(photo by Nick Iwanyshyn)

Kylie Masse, a star of U of T’s varsity swim team and Olympic bronze medalist in Rio, defended her world title in the 100-metre backstroke last summer at the world aquatic championships in South Korea.

It was a bold statement by the 23-year-old kinesiology student ahead of the 2020 Olympic Games in Tokyo.

Masse appeared to have a point to prove after another swimmer previously beat her world-record time in the 100-metre backstroke.

“Obviously I was a bit disappointed,” she recalled after her record was broken. “But I think it just gave me more motivation and lit a fire under me, like, ‘I want it back.’”

The PhD student who was part of team who discovered a prehistoric species

(photo courtesy of Joe Moysiuk)

More than a billion years ago, Cambroraster falcatus must have been a fearsome predator, with its rake-like claws and pineapple slice-shaped mouth. It reached up to a foot in length when most other animals in the Cambrian Period were smaller than your little finger.

PhD student Joe Moysiuk, in the department of ecology and evolutionary biology, was the lead author of a study documenting the newly discovered species based on fossils uncovered in the Burgess Shale in B.C.

The student who will pursue her research on housing inequality with a full Cambridge scholarship

(photo by Romi Levine)

Hafsah Siddiqui, a geography and planning master’s degree student, landed a full scholarship to study at Cambridge University.

The Gates Cambridge Scholarship recognizes students with leadership potential, outstanding intellectual ability and a commitment to improving the lives of others.
She planned to continue focusing on housing inequality as a PhD student across the pond.

Her research focuses on Pakistan and the informal settlement communities in Islamabad known as katchi abadis, which are home to many refugees and other marginalized people.

The first-year student who wants to use her education to help her c ommunity

(photo by Lisa Lightbourn)

Symone Pelletier made her dreams of studying psychology at U of T come true. She came to campus from Manitoulin Island, a six-hour drive from Toronto, where she was top of her high school class. “I chose psychology,” she said, “because I’m coming from an Indigenous community and a single-parent family.”

“We have experienced a lot more unfortunate situations than most people have.”

After graduation, she has set her sights on eventually returning home to work with the Wiikwemkoong First Nation community.

The students who screened 8,000 U of T courses for sustainability-related content

(photo by Geoffrey Vendeville)

Climate change represents arguably the single greatest challenge of our times. It's a problem of such magnitude that students who want to make a difference may wonder where to start.

Five undergraduates took the guesswork out of the equation by screening about 8,000 courses for sustainability-related content and creating an inventory of those courses for current and future students. They also catalogued sustainability campus groups, projects and initiatives. They published their work in an open-access journal so that other universities and large organizations can learn from their approach.

The mature student who made her mark on the univesity

(photo by Nick Iwanyshyn)

Julie Blair went out on a limb when she decided to return to university after a 20-year hiatus to take Indigenous studies. Blair, who is of Anishinaabe and Dutch ancestry and a member of the Serpent River First Nation, said she wasn’t part of the Indigenous community in Toronto until she learned more about her culture and roots in university.

She graduated with a master’s degree in social work this fall. She not only excelled in her studies, but also became a pillar of the community. In 2017, she was part of the team that organized the first campus powwow in two decades, an event that has since become a fixture on the U of T calendar.

Three U of T faculty appointed members of the Royal Society of Canada’s college for new scholars

perry.king — Tue, 10 Sep 2019 16:31:36 +0000

Three U of T faculty appointed members of the Royal Society of Canada’s college for new scholars

perry.king Tue, 09/10/2019 - 12:31

Cutline

From left to right: U of T researchers Jean-Philippe Julien, David Evans and Daniel De Carvalho are being recognized for demonstrating a high level of achievement in their careers to date (all photos by Perry King)

Topic

Hospital for Sick Children

Faculty of Medicine

Immunology

Princess Margaret Hospital