Institute of Biomaterials and Biomedical Engineering

Sunnybrook Health Sciences Centre

Donnelly Centre for Cellular & Biomolecular Research

Chemistry

Faculty of Arts & Science

Institute of Biomaterials and Biomedical Engineering

Mount Sinai Hospital

Researchers at the �ؿ�ζSM, in collaboration with Sunnybrook Health Sciences Centre, Public Health Ontario and Mount Sinai Hospital, have developed a COVID-19 antibody test that makes use of a smartphone camera.

The test could significantly improve the turnaround time and efficiency of infectious disease diagnosis, both for COVID-19 and beyond. The work is published in the latest issue of Nano Letters and involves U of T researchers from the Institute of Biomedical Engineering, department of chemistry in the Faculty of Arts & Science and Donnelly Centre for Cellular and Biomolecular Research.

“The goal of the study is to make COVID-19 antibody tests more accessible.” said Johnny Zhang, a PhD candidate at the Institute of Biomedical Engineering and department of chemistry who is one of the co-first authors of the publication.

“The end result is that the patients can take a self-diagnosis for COVID-19 with their phone, and that data can be immediately accessed digitally by medical professionals.”

The typical workflow for infectious disease diagnostic testing involves obtaining a sample from the patient, sending it to a laboratory for diagnostic testing and distributing the result to clinical personnel for decision making. The processes are often siloed and have a long turn-around time.

A device developed at U of T's Institute of Biomedical Engineering makes use of an ordinary smartphone camera to rapidly detect COVID-19. (Image courtesy of Matthew Osborne and Hongmin Chen)

By contrast, the U of T and hospital researchers developed a portable smartphone-based quantum barcode serological assay device for real-time surveillance of patients infected with SARS-CoV-2. They engineered quantum dot barcoded microbeads and a secondary label to search for antibodies against COVID-19 antigen in a patient’s blood. Finding the antibodies leads to a change in microbead emission colour.

The beads are then loaded into the device, activated with a laser, and the signal is imaged using a smartphone camera. An app is designed to process the image to identify the bead’s emission change. Finally, the data are interpreted and transmitted remotely across the world for data collection and decision making.

“The beauty of the system is that everything is integrated into one portable unit.” said Zhang.

This technology, by which quantum dot microbead detection can measure minuscule amounts of key biomarkers in blood, has been in development for the past 10 years.

“We really wanted to improve the performance and utility of the technology this time around,” said PhD candidate Ayden Malekjahani, the other co-first author of this study.

“Being able to detect traces of target in patients is not enough. We wanted to add more functions to the device. We designed the device to simultaneously detect multiple antibodies from different sample types, so each test run is packed with information. The results are then uploaded to an online dashboard where medical professionals and the public can see trends in real time.”

The researchers tested the device with 49 patient blood samples where varying degrees of COVID-19 infection were present, and were able to achieve 84-88 per cent sensitivity. Although this result is not as high as traditional tests, it is still approximately three times higher than lateral flow assays, which are currently the most commonly available portable antibody tests.

This result also means detecting COVID-19 antibody can now be done outside of the centralized facilities without a big drop in accuracy.

This research was a collaboration with the Public Health Ontario, Sunnybrook Hospital and Mount Sinai Hospital, where clinical samples were provided to the researchers to test and evaluate this new system.

“This device can be a game-changer in the way we monitor the spread of infectious diseases and a patient’s response to vaccines.” said Professor Warren Chan, director of the Institute of Biomedical Engineering, and the corresponding author of this research.

U of T and Hebrew University of Jerusalem launch research and innovation partnership

rahul.kalvapalle — Fri, 03 Jul 2020 19:49:59 +0000

U of T and Hebrew University of Jerusalem launch research and innovation partnership

rahul.kalvapalle Fri, 07/03/2020 - 15:49

Cutline

U of T's partnership with the Hebrew University of Jerusalem will allow faculty and students from the two institutions to combine their resources to carry out high-impact research in a variety of fields (photo by Yonit Schiller)

Rahul Kalvapalle

Topic

Global Lens

Donnelly Centre for Cellular & Biomolecular Research

Cell and Systems Biology

Faculty of Arts & Science

Institute of Biomaterials and Biomedical Engineering

Global

How did environmental conditions and climate change influence early human evolution? Can protein engineering be harnessed to block the virus that causes COVID-19? How do quantum mechanics affect biological functions, and how do our memory and learning work on a cellular level in the brain?

These are some of the big questions that will be explored by researchers at the �ؿ�ζSM and the Hebrew University of Jerusalem (HUJI) as part of a new strategic partnership that will allow faculty and students from the two institutions to combine resources to carry out high-impact research.

Each year, the �ؿ�ζSM – Hebrew University of Jerusalem Research and Innovation Alliance will select projects to receive funding of $150,000 a year for up to four years, with each research group comprising faculty drawn from both universities and covering a range of disciplines. The alliance will also occasionally provide one-time seed funding to help get promising projects off the ground.

Initially launched with endowed funding of $5.9 million from the Canadian Friends of Hebrew University and the family of Roz and Ralph Halbert, the alliance aims to raise another $14 million and eventually construct an innovation pipeline between U of T and HUJI to connect the entrepreneurship ecosystems in Toronto and Jerusalem and provide student entrepreneurs with exposure to each other’s universities and markets.

“[HUJI’s] mandate with respect to research is very closely aligned to U of T’s in terms of leading the world in a variety of areas, and that’s always the kind of partner we’re looking for,” said Alex Mihailidis, U of T’s associate vice-president of international partnerships and a professor in the Faculty of Medicine's department of occupational science and occupational therapy, as well as the Institute of Biomaterials and Biomedical Engineering.

“We both recognize that international collaborations strengthen the research within each university, and that’s why we’re excited to partner with them.”

He added that the timing of the partnership speaks to U of T’s commitment to forge ahead with research partnerships despite the challenges of working and collaborating amid the pandemic.

“From an international partnerships perspective, it’s business as usual,” said Mihailidis, who is also cross-appointed to the department of computer science in the Faculty of Arts & Science. “We’ve not shut anything down and we’ve not stopped collaborations. We’re going full-speed ahead – it’s looking a bit different, but we are still moving ahead both with existing and new partners.”

The funding will enable Professor Michael Chazan of U of T’s department of anthropology in the Faculty of Arts & Science to work closely with geologist Ari Matmon at HUJI’s Institute of Earth Sciences to build a more comprehensive picture of how climate affected the evolution of early humans in the Kalahari Basin. The basin covers more than 2.5 million square kilometres across South Africa, Botswana and Namibia.

Both researchers developed an interest in the Kalahari – Chazan as an archeologist analyzing early evidence of human activity and Matmon as a geologist carrying out dating techniques to study the evolution of the landscape – and they’re now looking to combine their perspectives.

“The next phase of work with this funding is to expand Ari’s geological work, particularly looking for evidence of wet environments, so we can try and understand when there was a shift to modern arid conditions,” said Chazan. “At the same time, I’ll be working in the town of Kathu in South Africa, which is a major mining area today, and we’re looking at some very large sites and trying to understand what the conditions were when this place supported large groups of people.

“So it’s a really new area of study that combines geological perspectives on how the landscape and hydrology evolved with an archeological perspective which is asking – in more narrowly focused locations – what the human behaviour was and what was drawing people to these sites.”

Oron Shagrir, vice-president for international affairs at HUJI, said the partnership brings together “the two leading universities in Israel and Canada,” and that the call for research proposals resulted in several exciting submissions.

“In these challenging and unprecedented times for societies and universities alike, international partnerships are an invaluable source of support and inspiration,” said Shagrir, a professor of philosophy and cognitive science. “They are not only an important asset and tool in advancing universities on all levels, but also serve as a valuable platform to promote and support collaborative research projects.”

Chazan points to his project as an example of how the two universities can combine their respective strengths.

“At U of T, we’re strong in terms of field archeology and geophysics,” he said. “Hebrew University is particularly strong in looking at the evolution of landforms over the period of the last two to five million years ... [and] that requires some very specialized labs.”

Among the labs that Chazan and his students will have access to is a high-tech facility that “blocks out any modern magnetic signals” to precisely study fluctuations in the earth’s magnetic field. “Having access to that is a major asset for the project and for our students, who get to learn how to operate in that kind of system,” said Chazan.

Meanwhile, Sachdev Sidhu, a professor appointed to U of T’s Donnelly Centre for Cellular and Biomolecular Research, the department of molecular genetics and the Institute of Biomaterials and Biomedical Engineering, will be working with Professor Julia Shifman of HUJI’s Alexander Silberman Institute of Life Science to study how the fast-growing fields of protein engineering and design can be leveraged to develop treatments for diseases, including COVID-19.

Their project will use insights gained from past outbreaks of coronaviruses to understand the functions of the proteins that power SARS-CoV-2 – the virus that causes COVID-19 – and to develop molecules with the potential to disarm the virus and pave the way to a potential cure.

Additionally, the U of T – HUJI Research and Innovation Alliance is providing $5,000 in seed funding to two projects.

The first will see Professor Dvira Segal of U of T’s departments of chemistry and physics and Professor Roi Baer of HUJI’s Fritz Haber Research Center for Molecular Dynamics and Institute of Chemistry explore the role of quantum processes in natural and engineered quantum systems.

The second aims to better understand how the brain acquires and stores information in order to help prevent and treat debilitating memory and learning disorders. The principal investigators are Associate Professors Sheena Josselyn and Paul Frankland of the department of physiology in U of T’s Faculty of Medicine, Professor Melanie Woodin of the department of cell and systems biology and HUJI scholars Adi Mizrahi, Ami Citri and Inbal Goshen.

Ronald Appleby, a U of T alumnus and campaign chair for the partnership, said the research efforts made possible by the partnership speak to the two universities’ “shared commitment to advancing interdisciplinary teams of researchers and students working on translational research, bolstered by mutual respect and friendship.

“The attention paid to research in engineering and medicine, the sciences, the social sciences, humanities, and law reflects our mutual interest in creating novel solutions for some of the most pressing current issues,” Appleby said.

With international partner, U of T launches research centre focused on robotics and elder care

Christopher.Sorensen — Thu, 04 Jun 2020 16:38:55 +0000

With international partner, U of T launches research centre focused on robotics and elder care

Christopher.Sorensen Thu, 06/04/2020 - 12:38

Cutline

Alex Mihailidis, U of T's associate vice-president, international partnerships, says the partnership with China's Huazhong University of Science and Technology will speed up development of new technologies (photo by Nick Iwanyshyn)

Liz Do

Topic

Global Lens

China

Institute of Biomaterials and Biomedical Engineering

Global

Occupational Therapy

Robotics

Seniors

The �ؿ�ζSM’s Faculty of Applied Science & Engineering and the AGE-WELL Network of Centres of Excellence has partnered with the Huazhong University of Science and Technology (HUST) in China to launch a centre dedicated to researching and commercializing robotics for elder care. The centre will be virtually housed within the U of T Robotics Institute.

“We’re really excited to form this international partnership, which will allow us to speed up the development of better technologies and make an impact from both sides of the world,” says Professor Alex Mihailidis, associate vice-president, international partnerships, at U of T and a leading researcher in intelligent health systems for older adults.

Mihailidis is leading efforts alongside Professor Yan Fu at HUST. The joint centre has already gained an industry partner, robotics company UBTECH, which will provide support on various research projects, as well as commercialization.

“Both HUST and U of T are leaders in robotics research, so the marriage of the two promises to produce outstanding results,” says Fu. “With an increasingly aging population in China, and fewer younger family members to take care of them, robotics is going to play a vital role down the road.”

By 2030, Canadians over the age of 65 will make up 23 per cent of the population. And in China, seniors will make up 28 per cent of the population by 2040. Though these are future scenarios, the health-care challenges around aging populations can be felt today. One instance is the recent dispatch released by the Canadian military on living and working conditions of residents and health workers at long-term care homes in Ontario.

“This revelation underscores the kinds of critical gaps we see in elder care,” says Mihailidis, who envisions the centre helping to address these gaps by leveraging and catalyzing research already taking place at the two partner institutions.

Developed in Mihailidis’ lab, ‘Ed,’ the robot, helps guide seniors with dementia through everyday tasks (photo courtesy of the Intelligent Assistive Technology and Systems Lab)

At U of T Engineering, robotics research in elder care is led by faculty such as Mihailidis, whose team develops smart-home robotics for older adults, and Professor Goldie Nejat, who designs socially assistive robots that cognitively stimulate and promote social interaction in long-term care homes.

“We can take these projects, put them on the UBTECH robotic platform, work with our counterparts in China to do the same thing, test robots in our respective countries, and work towards making commercially viable products,” Mihailidis says.

Over the next year, Mihailidis hopes to expand the centre’s research cohort. And, once travelling restrictions are lifted due to the COVID-19 pandemic, he sees vast opportunities for student and faculty research exchanges.

“The possibility to work with HUST and with UBTECH – we have the opportunity to see some real-world impact,” says Mihailidis. “And if this partnership model is successful, it presents a novel approach for collaboration going forward at the university.”

Overcoming prejudice and poverty: Meet U of T grad and 'doctor of the future' Amanda Khan

rahul.kalvapalle — Fri, 29 May 2020 19:08:32 +0000

Overcoming prejudice and poverty: Meet U of T grad and 'doctor of the future' Amanda Khan

rahul.kalvapalle Fri, 05/29/2020 - 15:08

Cutline

Amanda Khan, who received scholarship support from U of T and is now graduating with an MD and PhD, says she is the first in her extended family to receive an advanced degree (photo by Johnny Guatto)

Rahul Kalvapalle

Topic

Convocation 2020

Diversity and Inclusion

Graduate Stories

Institute of Biomaterials and Biomedical Engineering

St. Michael's Hospital

Amanda Khan’s graduation from the �ؿ�ζSM’s MD/PhD program marks a giant step toward her goal of becoming a surgeon-scientist. But more than anything, she’s looking forward to becoming the kind of mentor and role model that she didn’t have growing up.

Born and raised in Trinidad and Tobago, Khan moved to Canada with her family and grew up in Toronto’s Rexdale neighbourhood.

She always wanted to be a doctor and a scientist, but says she had no one to look up to.

“It’s hard when you don’t have examples of people from your community going to medical school, because no one I knew from my neighbourhood went to university or did an advanced degree,” Khan says. “None of us has ever done this level of education. There’s no one in my family or extended family who’s a physician or went to grad school.”

But what Khan lacked in role models or financial backing she more than made up for with determination, force of will and the encouragement of her loved ones. She is now graduating with a Doctor of Medicine (MD) from the Faculty of Medicine and a PhD from the Institute of Biomaterials and Biomedical Engineering (IBBME) in the Faculty of Applied Science & Engineering.

Along the way, she has racked up numerous awards, including a Canadian Medical Hall of Fame award, a Vanier Canada Graduate Scholarship and being named one of Canada’s 100 most powerful women by the Women’s Executive Network. She’s now set to begin a five-year residency in radiation oncology in Calgary.

It’s been a long road for Khan, who recounts the abject state of her bank balance when she was applying to MD/PhD programs across Canada and the U.S.

“I literally had $200 remaining in my bank account,” Khan says. “I wouldn’t have been able to pay rent that month if I didn’t get into MD/PhD because I put every dollar I had into trying to get into this program.”

Khan, who did her undergraduate and graduate degrees at Western University, says she was drawn to U of T because it’s a world-class research institution with top-notch hospital affiliations and a generous financial support program.

“U of T gave me the most money in scholarship support – and that was very important for me because I had so much debt from my undergrad and master’s. I’m from a poor family so I needed financial assistance and U of T was brilliant in financially supporting me through these eight years,” Khan says.

“U of T also has the biggest MD/PhD program in the country and you’re learning at world-class institutions like IBBME, IMS [the Institute of Medical Science], [the department of] medical biophysics – and with the kind of clinical research I wanted to do, obviously the hospital connections U of T has are the best.”

It was one of those hospital connections that gave Khan the inspiration for her PhD research. In her first year, Khan took part in Day of the Doctor, an initiative where medical students shadow a physician for a day.

Khan was paired with a general surgeon at St. Michael’s Hospital who was performing laparoscopy – a type of surgery where small incisions are made in the abdomen using elongated tools, with the aid of a camera.

One of the challenges with laparoscopic surgery is that surgeons don’t have the tactile feedback that they would have during a conventional surgery, so it’s not uncommon for them to inadvertently tear tissue by grasping it too hard or applying too much force. This can lead to internal bleeding, infection and even death.

Watching the surgeon go about his surgeries, Khan wondered out loud how the amount of force applied by laparoscopic tools could be measured to stay within a safe range.

“I asked, ‘How do we know how much force we should be applying with these laparoscopic tools? How do you even prove such a thing and how do you make the tools smarter so that they will automatically make surgeons not go into the dangerous force zone?’ So the doctor was joking with me and said, ‘Maybe you should do your PhD on it’ – and so I did.”

It’s a field of research that involves a heavy emphasis on engineering, which isn’t Khan’s background. She credits her husband, who graduated from U of T with a degree in mechanical engineering, for playing a key role in her PhD.

“For me to learn all the engineering stuff during my PhD was really challenging – really hard. Electrical engineering, mechanical engineering – he was absolutely instrumental in showing me how to do all those things. I dedicated my PhD to him,” Khan says.

In addition to the challenge of navigating complex engineering terrain, Khan says it was difficult to progress through two different programs and cohorts.

“It’s hard because you start medical school with a medical school class, and then you have to withdraw to your PhD while your friends from your original class go on and become physicians and residents while you’re doing your PhD,” she says.

“Then when you come back to medicine, you’re in a different class. It’s hard because you see your friends who are already physicians and practising after four years.”

The program’s workload meant Khan had to make plenty of sacrifices.

“There were friends’ weddings I couldn’t go to, family events I couldn’t go to, parties that I can’t go to because I’m on call or I’m studying or defending my thesis,” she says. “There are all these things you miss out on. You have to be willing to make sacrifices.”

Khan says what kept her going was keeping her an eye on the ultimate prize “of being a physician who does translational research that directly benefits my patients.”

A champion of diversity and representation in the STEM fields, Khan set up the Research Application Support Initiative, a U of T Community of Support program that connects students to research positions and mentors to guide them on their journey to get accepted into medical school and other graduate programs.

“I’ve had a lot of success with people whom I’ve mentored getting into medical school and who are now lifting their families out of poverty, says Khan. “I think that’s a big deal and I’m really glad U of T supports that.”

However, Khan says there’s a long way to go when it comes to diversity.

“As a brown woman, I’m often discounted. I’ve had physicians tell me it’s a shame I’m not my husband – who’s a white man – because my research would’ve been taken more seriously,” she says.

“You face racism even in Toronto, even from physicians, even from engineers. You face sexism as well, especially in surgery. It’s still an old boys’ club and I’ve had a few surgeons tell me that surgery is for men, not for women.”

Indeed, one of Khan’s missions as she heads to Calgary is to expand the Communities of Support program and make a contribution toward making the fields of medicine and engineering more diverse and welcoming to people of all backgrounds.

“I want medicine to be very diverse,” she says. “I want there to be representation from everybody. If we’re supposed to be treating society – which is made up of hundreds of different backgrounds, cultures, religions, sexual orientations – these are the people who should be in medical school and should be the doctors of the future.”

U of T Engineering set to host first-ever virtual research conference

Christopher.Sorensen — Mon, 25 May 2020 20:05:46 +0000

U of T Engineering set to host first-ever virtual research conference

Christopher.Sorensen Mon, 05/25/2020 - 16:05

Cutline

U of T Engineering’s first-ever faculty-wide research conference is organized by members of the Graduate Engineering Council of Students as well as faculty (Photo courtesy of Samantha Cheung)

Topic

Institute of Biomaterials and Biomedical Engineering

Graduate Students

Undergraduate Students

Brandon Rufino’s preparation for his big presentation is a bit different today: He’s testing out his laptop mic and finding a spot in his apartment with the most light and least clutter.

Rufino, a student in the �ؿ�ζSM’s Faculty of Applied Science & Engineering, is among nearly 100 undergraduate and graduate students taking part in the inaugural U of T Engineering Research Conference (UTERC) on June 9 and 10. Due to COVID-19 restrictions, the event will be broadcast digitally, with students presenting their research as poster presentations via Twitter or through non-technical lightning lectures on Zoom.

The conference will feature the latest in undergraduate and graduate research in six key areas: advanced manufacturing; data analytics and artificial intelligence; human health; robotics; sustainability; and water. Industry partners and alumni are also invited to connect with students and discuss the work.

Rufino, who is pursuing a master’s degree in health science at the Institute of Biomaterials and Biomedical Engineering (IBBME), will be presenting in the human health category as a lightning lecture speaker. Under the supervision of Assistant Professor Elaine Biddiss, he and his fellow grad students develop and evaluate technologies to allow young people with disabilities to participate more meaningfully in arts, music, physical activities and therapies.

“I’ve yet to attend a fully digital conference,” says Rufino. “I’m excited about this format, which really lends itself to being easily accessible and shareable.”

The idea to host a virtual conference was hatched after the university shutdown in March. With no access to labs, many students’ experimental work has been put on pause. U of T Engineering’s Graduate Engineering Council of Students (GECoS) began brainstorming.

“I thought a virtual conference would be useful for those looking for ways to progress their academic and professional development during this time when many conferences have been cancelled and some of us have less work to do,” says Samantha Cheung, a chemical engineering PhD candidate, UTERC organizer and president of GECoS mental wellness commission.

“When Sam approached us with this idea, we fully supported the initiative,” says Chaim Katz, a PhD candidate at IBBME and chair of GECoS. “We’ve been supporting the conference team’s efforts ever since and are looking forward to what will be an excellent opportunity to showcase research going on at U of T Engineering.”

After receiving positive feedback from students, faculty and staff, Cheung immediately created a committee made up of faculty and graduate students to plan a conference to be held within two months.

“I’m most excited to see people from various backgrounds connecting and engaging with each other through these online platforms,” says Cheung. “I think the best part about hosting this virtual conference is the ability for people from all over the world to participate.”

The organizers have even considered another important aspect of most academic conferences: networking. In addition to participants asking questions during posters and talks, UTERC will also facilitate networking with breakout sessions and through Slack.

Cheung hopes the success of the faculty’s first-ever virtual conference serves as a framework for future events at U of T Engineering, and for other institutions that want to engage their research community.

“Right now, we are all adjusting to new living circumstances and ways to socialize,” says Cheung. “UTERC is a reminder that the U of T Engineering community is here to support our students even if we aren’t physically together.”

U of T researchers aim to make testing for COVID-19 'simpler and more streamlined'

Christopher.Sorensen — Wed, 13 May 2020 18:47:25 +0000

U of T researchers aim to make testing for COVID-19 'simpler and more streamlined'

Christopher.Sorensen Wed, 05/13/2020 - 14:47

Cutline

Leo Chou, of the Institute of Biomaterials and Biomedical Engineering, says his non-traditional approach to testing for the novel coronavirus could help avoid the bottlenecks that have emerged with established methods (photo by Qin Dai)

Tyler Irving

Topic

Institute of Biomaterials and Biomedical Engineering

Testing for viruses is not a new science, but the COVID-19 pandemic has exposed the bottlenecks in established methods. Now, a team led by Leo Chou of the �ؿ�ζSM’s Institute of Biomaterials and Biomedical Engineering is pursuing a non-traditional approach that, if successful, could lead to simpler, faster tests.

“What we are finding out in this pandemic is that surges in global demand can cause every step in the process to break down due to supply chain shortage,” says Chou, an assistant professor who joined U of T’s Faculty of Applied Science & Engineering as a faculty member in January 2019. “There are opportunities to make these tests simpler and more streamlined.”

While the project is in its early stages, the team hopes to overcome the limitations of traditional testing methods by pursuing a strategy based on short, synthetic strands of DNA. These strands can be customized to react in certain ways in the presence of genes from the virus that causes COVID-19.

Currently, most tests begin with a nasal swab to extract virus particles from the body. These particles are then shipped to a testing lab, where heat, detergents and enzymes are used to open them up and expose the viral RNA – the genes that the virus uses to replicate itself.

The RNA is then subjected to the “gold standard” technique known as real-time polymerase chain reaction (RT-PCR). Using specialized enzymes and a device called a thermocycler, RT-PCR amplifies targeted RNA sequences – such as those known to code for viral genes – to determine whether they are present in the sample.

In theory, RT-PCR can provide results in a matter of hours, but the need for specialized infrastructure has been a key limitation of testing around the world.

“Because samples collected at the point of care must be shipped to a central lab for testing, logistics become a key issue,” says Chou. “For one single sample to get tested, you are usually talking about a turnaround time of two or three days.”

In contrast, the new approach could lead to a one-step test. The team aims to design customized DNA sequences that are capable of self-assembling into a larger structure, but which are missing a key catalyst to bring them all together: an RNA sequence specific to the COVID-19 virus.

“The best analogy I can think of is growing rock candy,” says Chou. “You start with a saturated solution of sugar molecules in water, but they don’t do anything because they don’t have anything to crystallize around. When you introduce a stick into the solution, the crystals form rapidly around it.”

In this analogy, the short DNA sequences made by Chou and his team are the sugar, and the viral RNA serves as the stick. By design, only the correct RNA sequence would work – genes from other viruses or contaminating organisms would not trigger the same reaction.

If the virus is present, its RNA would quickly cause the DNA strands to self-assemble. The team could easily attach pigments or light-emitting molecules to the DNA strands, resulting in a solution that changes colour in the presence of viral genes.

Chou says that the technology already exists to manufacture the short DNA sequences quickly and inexpensively, and that these molecules are stable, meaning they can be stored wet or dry at room temperature for months or years.

Because it wouldn’t require complex materials or equipment such as enzymes or thermocyclers, the new test could be done in one step at the point of care, eliminating logistical bottlenecks that are currently hampering global testing efforts.

While he believes that the new approach is promising, Chou cautions that it will take many months before a prototype can be developed, and many more to determine whether the test is anywhere near as reliable as RT-PCR.

“All the tests that are being used right now took years to develop and clinically validate,” he says. “This is no different, but the strategy we’re proposing is unlike anything that is already being used.

“We aim to have proof-of-concept done within a year. If it works, it could have some very exciting advantages.”

U of T researchers use diphtheria toxin to target genes in cancer cells

Christopher.Sorensen — Wed, 06 May 2020 17:08:52 +0000

U of T researchers use diphtheria toxin to target genes in cancer cells

Christopher.Sorensen Wed, 05/06/2020 - 13:08

Cutline

Modified diphtheria toxin used to reduce the activity of genes connected to the propagation of glioblastoma, a type of brain cancer.

Topic

Hospital for Sick Children

Graduate Students

Institute of Biomaterials and Biomedical Engineering

Donnelly Centre for Cellular & Biomolecular Research

A group of researchers from the �ؿ�ζSM and the Hospital for Sick Children have developed a new way to deliver molecules that target specific genes within cells. The platform, which uses a modified form of diphtheria toxin, has been shown to “downregulate” critical genes in cancer cells, and could be used for other genetic diseases as well.

The team, led by University Professor Molly Shoichet of the Faculty of Applied Science & Engineering and Roman Melnyk, an associate professor the department of biochemistry in the Faculty of Medicine and a senior scientist at SickKids, found inspiration from an unexpected source: diphtheria toxin.

The research was published recently in the journal Science Advances.

“A major challenge in the field of drug delivery is most therapeutic vehicles cannot escape the acid environment of the endosome once they get into the cell,” says Shoichet, the corresponding author of the research. “The diphtheria toxin platform as a delivery vehicle effectively solves that.”

Scientists looking to place molecules inside cells have a number of existing tools to choose from, but most suffer from the same drawback: while the molecule gets inside the cell, it remains trapped in a kind of bubble called an endosome. If the goal is to deliver therapeutics that will interact with the cell’s DNA, breaking out of the endosome is critical.

As a natural defence mechanism, bacteria such as Corynebacterium diphtheriae produce a protein-based toxin that enters surrounding cells, eventually killing them. Critically, this toxin is known to be capable of escaping from endosomes, which led to the idea of re-engineering it as a delivery platform.

Melnyk’s lab specializes in bacterial toxins and invented a non-toxic version of the diphtheria toxin, known as attenuated diphtheria toxin. This new molecule has the capacity to enter the cell and efficiently escape the endosome – and thus excels as a delivery vehicle without any of the toxic effects of diphtheria toxin.

To prove that the concept would work, the researchers used the system to deliver molecules that they believed would be effective against glioblastoma, a form of brain cancer.

“Glioblastoma is a highly invasive disease and patients have a very short life expectancy after initial diagnosis,” says Shoichet. “We want to change this and have thus pursued the delivery of gene therapeutics to treat glioblastoma.”

The group first targeted glioblastoma neural stem cells, which are thought to be resistant to chemotherapeutics. Specifically, the researchers focused on delivering silencing RNA (siRNA) against two genes: integrin beta 1 (ITGB1), which is associated with the highly invasive nature of glioblastoma (and other cancers), and eukaryotic translation initiation factor 3 sub-unit b (eIF-3b), which is an essential survival gene. By eliminating this invasive trait, the researchers could potentially limit progression in diseases like cancer.

“ITGB1 is involved in cancer cell migration, which contributes to glioblastoma’s invasion into healthy brain tissues,” says Laura Smith, a senior PhD student on the publication. “We used an innovative three-dimensional culture system to significantly reduce cell invasion after treatment with our siRNA-attenuated diphtheria toxin system, which suggests that it may be effective in slowing disease progression.”

To demonstrate the breadth of this platform, the researchers also delivered a different nucleic sequence that knocks down eIF-3b, which participates in the “survival pathway” of cancer cells.

“We treated the cells with the attenuated diphtheria toxin-siRNA against eIF-3b and observed downregulation at genetic and phenotypic levels,” says Amy E. Arnold, a recent PhD graduate from the Shoichet lab and first author on the paper.

The group is planning on using this delivery vehicle to treat other diseases in the future.

“We recognize the strength of this platform strategy and are actively testing it for the delivery of RNA and other cargoes,” Shoichet says.

The research received support from the Canadian Institutes of Health Research and the Natural Sciences and Engineering Research Council of Canada, among others.

U of T to support high-impact coronavirus research projects through Toronto COVID-19 Action Fund

rahul.kalvapalle — Mon, 20 Apr 2020 20:34:01 +0000

U of T to support high-impact coronavirus research projects through Toronto COVID-19 Action Fund

rahul.kalvapalle Mon, 04/20/2020 - 16:34

Cutline

(photos by Steve Russell/Toronto Star via Getty Images, Christopher Morris/Corbis/Getty Images, Nick Iwanyshyn)

Topic

Institute of Health Policy Management and Evaluation

Biochemistry

Chemistry

Dalla Lana School of Public Health

Faculty of Arts & Science

Faculty of Information

Hospital for Sick Children

Global

Institute of Biomaterials and Biomedical Engineering

Laboratory Medicine and Pathobiology

Lawrence S. Bloomberg Faculty of Nursing

University Health Network

Sociology

St. Michael's Hospital

Sunnybrook Hospital

U of T Mississauga

U of T Scarborough

Vivek Goel

The �ؿ�ζSM will support more than 30 research projects through the nearly $9-million Toronto COVID-19 Action Fund – set up less than a month ago to support high-impact research by U of T and its hospital partners that contributes to the global fight against the novel coronavirus.

The projects, which range from medical interventions to measures aimed at supporting the economy and vulnerable populations, were chosen on the basis of their potential to have a positive impact on individuals, communities and public health systems within a timeframe of a year or less.

They were selected from among 338 applicants via a fast-tracked, peer-reviewed competition. Less than 30 days elapsed between the creation of the fund and the winning projects being announced.

“The Toronto COVID-19 Action Fund is a testament to the �ؿ�ζSM’s unique ability to quickly mobilize its resources, engage the creativity and ingenuity of its researchers and draw on the strength of its partnerships with partner hospitals to respond to the most urgent public health, economic and societal challenge of our time,” said Vivek Goel, U of T’s vice-president, research and innovation, and strategic initiatives.

“COVID-19 presents an array of unprecedented global problems that require urgent attention and expertise from experts in a wide variety of disciplines – from medical specialists and public health researchers to economists, social scientists and mathematicians.

“We are confident these projects will each, in their own way, make important contributions to the global fight against this pandemic.”

The projects include an initiative to research the effects of the COVID-19 pandemic response on marginalized people, led by Ahmed Bayoumi, a professor in the department of medicine in the Faculty of Medicine and a scientist at the Li Ka Shing Knowledge Institute of St. Michael’s Hospital, part of Unity Health Toronto.

In the realm of medical interventions, Jordan Feld, associate professor in U of T’s department of medicine in the Faculty of Medicine and a senior scientist at the Toronto General Hospital Research Institute at the University Health Network, plans to carry out a phase two drug trial for the treatment of COVID-19.

Also funded were research projects by Sunnybrook Health Sciences Centre's Samira Mubareka and Robert Kozak, both of the department of laboratory medicine and pathobiology at U of T’s Faculty of Medicine, that could pave the way to better understanding and treatment of the novel coronavirus, also known as SARS-CoV-2.

The role of genetics in the pandemic response will be explored by Aled Edwards, professor at the Donnelly Centre for Molecular and Biomolecular Research and director of the Structural Genomics Consortium. He will lead work on the Toronto Open Access COVID-19 Protein Manufacturing Centre.

Other research projects will address social, economic and public policy issues.

Janet Smylie is a professor at the Dalla Lana School of Public Health, director of Well Living House at St. Michael’s Hospital and an expert in public health in the context of Indigenous populations. She will use an action fund grant to support the rapid implementation of a shared COVID-19 tracking and response platform for First Nations, Inuit and Métis populations.

U of T Mississauga anthropologist and lecturer Madeleine Mant will receive support for her project titled, “Going viral: COVID-19 and risk in young adult health behaviour models.”

The impact of COVID-19 on the economy is another area of significant concern, with Professor Scott Schieman, chair of the department of sociology in the Faculty of Arts & Science, leading a project to explore the impacts of COVID-19 on the quality of work and economic life in Canada.

The funding for these and other projects was drawn from U of T and other university sources, including the McLaughlin Centre, Medicine by Design, partner hospitals and philanthropic donors. Successful applicants are also eligible for additional support for a trainee through a generous agreement with MITACS.

“We would like to extend our thanks to all the scholars who submitted proposals to the Toronto COVID-19 Action Fund, and we will continue to work hard to find ways to support our researchers in their efforts to devise solutions to this crisis,” said Goel. “I would also like to thank the reviewers that provided assessment in a short period of time and our staff that worked diligently and around the clock to complete this record-setting peer review process.”

“U of T takes very seriously its public responsibility to make key contributions to the response to COVID-19, and I would like to congratulate everybody involved in the rapid creation and execution of the action fund for their tireless efforts.”

Goel noted that additional projects may be funded through the action fund as funds continue to be raised and additional partners contribute. All those that were not selected are being directed to other funding sources, including those listed on the Centre for Research and Innovation Support’s COVID-19 research website.

Here are the researchers being supported by the Toronto COVID-19 Action Fund:

Note: this list was updated with additional projects on May 8, 2020

Upton Allen of the department of paediatrics in the Faculty of Medicine, Institute of Health Policy, Management and Evaluation and the Hospital for Sick Children – Immune responses to COVID-19: Correlates across the age spectrum

Robert Batey of the department of chemistry in the Faculty of Arts & Science – Synthetic chemistry as a core technology platform for the response to the COVID-19 pandemic: chemistry COVID-19 core facility

Ahmed Bayoumi of the department of medicine in the Faculty of Medicine and Unity Health Toronto –The effects of the COVID-19 pandemic response for people who are marginalized

Laurent Brochard of the department of medicine in the Faculty of Medicine and Unity Health Toronto – Careful ventilation in patients with ARDS induced by COVID-19

Jeannie Callum of the department of laboratory medicine and pathobiology in the Faculty of Medicine and Sunnybrook Health Sciences Centre – Convalescent plasma for COVID-19 research trial

Warren Chan of the Institute of Biomaterials and Biomedical Engineering in the Faculty of Applied Science & Engineering – A quantum dot portable diagnostic device for COVID-19

Angela Cheung of the department of medicine in the Faculty of Medicine and Institute of Health Policy, Management and Evaluation and the University Health Network – The Ontario COVID-19 prospective cohort study

Leo Chou of the Institute of Biomaterials & Biomedical Engineering in the Faculty of Applied Science & Engineering – Enzyme-free, one-step nucleic-acid detection for point-of-care COVID-19 diagnostic screening

Gerald Chaim Cupchik of the department of psychology at U of T Scarborough – Managing coping strategies and avoiding anxiety during the COVID-19 pandemic: A multilevel analysis from epidemiology to psychology and education

Paul Dorian of the department of medicine in the Faculty of Medicine and Unity Health Toronto – Evaluation of a small gas-powered and patient-responsive automated resuscitation/ventilation

Aled Edwards of the Donnelly Centre for Molecular and Biomolecular Research – Toronto Open Access COVID-19 Protein Manufacturing Centre

Jordan Feld of the department of medicine in the Faculty of Medicine and the University Health Network – Interferon lambda for immediate antiviral therapy at diagnosis: a phase II randomized, open-label, multicentre trial to evaluate the effect of peginterferon lambda for the treatment of COVID-19

Jessica Fields of the Interdisciplinary Centre for Health & Society at U of T Scarborough – Impact of COVID-19 on the mental health and vulnerability of sexual and gender minorities living in Toronto

Benjamin Fine of the department of medical imaging in the Faculty of Medicine and Trillium Health Partners – Building a real-time health system COVID collaborative data and analytics hub in Ontario

Joseph Hermer of the department of sociology at U of T Scarborough – Pandemic policing of the homeless: from crime control to public health strategy

Shana Kelley of the Leslie Dan Faculty of Pharmacy – Accelerated, centralized development of diagnostics and therapeutics to combat the COVID-19 pandemic

Robert Kozak of the department of laboratory medicine and pathobiology in the Faculty of Medicine and Sunnybrook Health Sciences Centre – Development of models of pathogenesis and vaccines for SARS-CoV-2

Madeleine Mant of the department of anthropology of U of T Mississauga – Going viral: COVID-19 and risk in young adult health behaviour models.

Rhonda McEwen of the Institute of Communication, Culture, Information and Technology at U of T Mississauga – Digital technologies and Chinese interpersonal communication on the mainland and in the diaspora: the case of COVID-19

Allison McGeer of the department of laboratory medicine and pathobiology in the Faculty of Medicine, Dalla Lana School of Public Health and Mount Sinai Hospital – Working on control of COVID-19 outbreaks in long-term care

Andrew Miles of the department of sociology at U of T Mississauga – Using pro-social behaviour to safeguard mental health and foster emotional well-being

Jason Moffat of the Donnelly Centre for Molecular and Biomolecular Research – Identification of host dependency factors for SARS-CoV-2 infection and replication to accelerate drug repurposing efforts

Samira Mubareka of the department of laboratory medicine and pathobiology in the Faculty of Medicine and Sunnybrook Health Sciences Centre – Just-in-time pathogenomics for SARS-CoV-2, data for immediate action

Elizabeth Peter of the Lawrence S. Bloomberg Faculty of Nursing – Reducing the moral distress of nurses during the COVID-19 pandemic

Blake Poland of the Dalla Lana School of Public Health – Connected communities in a time of physical distancing: community-led responses to the COVID-19 pandemic in City of Toronto

Mohammad Qadura of the department of surgery in the Faculty of Medicine and Unity Health Toronto – Keeping everyone safe: Using contactless transdermal optical imaging to obtain patient vitals and symptom report in the time of COVID-19

Matt Ratto of the Faculty of Information – Toronto Emergency Device Accelerator

Scott Schieman of the department of sociology in the Faculty of Arts & Science – COVID-19 impacts on the quality of work and economic life in Canada

Michelle Science of the department of paediatrics in the Faculty of Medicine and the Hospital for Sick Children – Health-care worker seroprevalence of anti-SARS-CoV-2 antibodies

James Scott of the Dalla Lana School of Public Health – Improving and evaluating aerosol PPE and containment devices for the COVID-19 virus

Jayeeta Sharma of the department of historical and cultural studies at U of T Scarborough – Feeding our city, pandemic and beyond: documenting food system experiences, community challenges and local resilience, lessons for sustainable food solutions

Janet Smylie of the Dalla Lana School of Public Health and Unity Health Toronto – Rapid implementation of a shared COVID-19 tracking and response platform for First Nations, Inuit and Metis populations in Canada

Igor Stagljar of the department of biochemistry in the Faculty of Medicine – Immunotyping of COVID-19 Patient Sera Using Novel Protein Complementation-Based Assays

Rima Styra of the department of psychiatry in the Faculty of Medicine and the University Health Network – Mental health outcomes in health-care workers during COVID-19

Jeff Wrana of the department of molecular genetics in the Faculty of Medicine and Mount Sinai Hospital – A massively parallel, ultra-high throughput next-generation sequencing platform for widespread screening of COVID-19 and associated risk factors

William Yun Yu of the department of computer and mathematical sciences at U of T Scarborough – Privacy-preserving contact tracing app

U of T researchers use mini-computer to remotely monitor COVID-19 patients' blood oxygen

Christopher.Sorensen — Fri, 17 Apr 2020 14:26:45 +0000

U of T researchers use mini-computer to remotely monitor COVID-19 patients' blood oxygen

Christopher.Sorensen Fri, 04/17/2020 - 10:26

Cutline

Researchers at U of T's Faculty of Applied Science & Engineering used a mini-computer to continuously read data from a COVID-19 patient's fingertip probe so health-care workers don't need to physically check the device (photo via Unsplash)

Jessica MacInnis

Topic

Electrical & Computer Engineering

Institute of Biomaterials and Biomedical Engineering

Graduate Students

Mount Sinai Hospital

University Health Network

A team from the �ؿ�ζSM’s Faculty of Applied Science & Engineering has created a simple, scalable solution to remotely monitor the vital signs of COVID-19 patients, while preserving vital personal protective equipment (PPE) for health-care workers.

Currently, hospitals use a fingertip probe to monitor the respiratory status of COVID-19 patients. These probes monitor blood oxygen saturation and send the data to bedside monitors that must be read by nursing staff roughly every four hours.

But some patients experience a rapid deterioration in respiratory status that requires even more frequent monitoring, putting additional pressure on staff.

“Because health-care workers need to put on and remove PPE before interacting with patients, this requires considerable time and use of resources,” says Associate Professor Willy Wong in the Edward S. Rogers Sr. department of electrical and computer engineering and the Institute of Biomaterials and Biomedical Engineering, who led the project.

Two weeks ago, clinicians from Mount Sinai Hospital in Toronto reached out to U of T Engineering to see if researchers could come up with a solution – quickly – that would help clinicians monitor respiratory probes both continuously and remotely.

In just three days Wong and PhD candidates Bill Shi, Yan Li and Brian Wang put together a proof-of-concept using a Raspberry Pi, a simple and affordable single-board computer. Just a few days later, they were ready to deploy their prototype in a hospital setting.

“The challenge was to find something that was small, affordable and that we could put together very quickly,” says Wong. “I don’t have specific expertise in the area, but as a researcher working in the biomedical engineering group here in ECE, I have experience in the development of medical devices and thought I might be able to help.”

Raspberry Pi is a mini-computer about the size of a credit card. When attached to the fingertip probe, it can continuously read data and communicate via WiFi to a server that Wong’s team deployed.

“The most challenging part has been decoding the data the monitors provide because there are a number of different manufacturers of these probes and each one has its own format,” says Wong. “The students were working day and night to decode the data outputted from these devices.”

One key aspect is the portability of the solution that Wong and his students came up with. “In a hospital setting, we don’t really have the luxury of putting a laptop with wires going everywhere next to each patient,” says Wong. “The Raspberry Pi is something that our undergraduates use a lot in their fourth-year design projects – it just connects by cable to the oxygen saturation probe and then another cable to an outlet in the wall for power. That’s it.”

The new setup enables doctors and nurses to read a patient’s oxygen saturation levels every few minutes or less from a nursing station. The team is working with Mount Sinai and Toronto General Hospital to determine the feasibility and demand for these devices. Their solution is rapidly deployable and scalable to other venues, including emergency hospitals.

“When you put together a solution quickly, there are a few things you need to be mindful of, including concerns like patient privacy and data security, as well as usability of equipment by the front-line medical staff,” says Wong.

Wong adds that it has been a valuable experience for his students.

“This was a quintessentially electrical and computer engineering problem,” says Wong. “I saw the opportunity to help and this group of really smart and hard-working students rose to the challenge.”

U of T startup’s "buddy badge" encourages handwashing in hospitals, could help stem COVID-19 spread

Christopher.Sorensen — Mon, 13 Apr 2020 19:14:25 +0000

U of T startup’s "buddy badge" encourages handwashing in hospitals, could help stem COVID-19 spread

Christopher.Sorensen Mon, 04/13/2020 - 15:14

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(photo by Christine Sandu via Unsplash)

Qin Dai

Topic

Institute of Biomaterials and Biomedical Engineering