Kurt Kleiner

Regent Park redevelopment reinforces need for public housing funding: Researchers

Christopher.Sorensen — Thu, 17 Aug 2023 14:13:49 +0000

Regent Park redevelopment reinforces need for public housing funding: Researchers

Christopher.Sorensen Thu, 08/17/2023 - 10:13

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The redevelopment of Regent Park in downtown Toronto aimed to create a mixed-income, amenity-rich neighbourhood with a strong sense of community (Richard Lautens/Toronto Star via Getty Images)

Kurt Kleiner

Topic

Breaking Research

Cities

Regent Park

Research & Innovation

��˾��ֱ�� Mississauga

The redevelopment of Toronto’s downtown Regent Park neighbourhood has won praise from some observers for taking a neglected housing project and turning it into a successful mixed-income area with impressive public amenities.

But the ongoing $1.5-billion redevelopment has also disrupted lives, suffered major financial and political difficulties and now faces mixed reviews from the very residents it was designed to help.

“There continues to be contention around whether or not this redevelopment was better or worse for the community,” says Shauna Brail, an associate professor and the director of the Institute for Management & Innovation at the University of Toronto Mississauga.

“I am on the side that says that Regent Park today is an improved neighbourhood beyond what it was in 1999, or in 2006,” she says.

Yet, she acknowledges the project has faced a host of problems since it was first proposed and agrees it hasn’t done everything it set out to do.

Brail is an economic geographer and urban planner interested in how economic, social and cultural change transforms cities. She’s been studying the Regent Park redevelopment since the project broke ground in 2006.

Along with Toronto journalist and ��˾��ֱ�� alumnus John Lorinc, she recently published an examination of the project in the Journal of Planning Education and Research.

Regent Park was originally built as a public housing in the late 1940s, with 2,083 subsidized units on 69 acres. By the 1990s, the housing was in poor repair and the neighbourhood was experiencing problems with crime and stigma. At the same time, the federal government had decreased the funding available for social housing.

Land values, though, had gone up. The Toronto Community Housing Corp. (TCHC) decided to pay for redevelopment through “financialization” – building and selling some housing at market prices and using the profits to finance new subsidized housing.

The vision was to create a mixed-income neighbourhood with a strong sense of community and amenities shared by everyone. Existing tenants were relocated during reconstruction, but were offered a right to return – and so far about half have come back.

One of the things Brail was interested in was how low-income community residents would be able to influence the redevelopment process. She says they empowered themselves, giving input on planning and insisting that money and resources be dedicated to the community for things like parks, social centres, jobs and training.

But the community is also divided on the outcomes so far, she says.

“There are some who say, without a doubt, this is better,” Brail says. “On the other side is the narrative of destruction of community – the sense that this is a very patronizing kind of approach to redeveloping public housing.”

In their paper, Brail and Lorinc outline the political, financial and social complications of the nearly 20-year-long project, which has been delayed by a number of factors, including the election of the late mayor Rob Ford and his promise to slash spending. Redevelopment is now five to eight years behind schedule, with two of five phases unfinished.

Brail says she’s interested in how the rising value of downtown real estate changed how planners thought about public housing: Rather than relying on public funding, the projects could finance themselves. Financialization, however, didn’t cover the full cost of Regent Park’s redevelopment. The three levels of government have collectively kicked in about $500 million so far.

One of the major lessons of the project is that redevelopment doesn’t come free, Brail says.

“The financialized model on its own is not sufficient. Governments still need to continue to think through just how to fund public housing, and they need to continue to be pushed to do that.”

'We're learning more every day': How ��˾��ֱ�� is leading efforts to understand – and respond to – COVID-19

Christopher.Sorensen — Tue, 10 Mar 2020 23:25:17 +0000

'We're learning more every day': How ��˾��ֱ�� is leading efforts to understand – and respond to – COVID-19

Christopher.Sorensen Tue, 03/10/2020 - 19:25

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From tracking its spread to developing new diagnostic tools and educating the public, ��˾��ֱ�� experts have been on the front lines of the battle to understand and ultimately respond to COVID-19 and the novel coronavirus behind it.

Topic

Dalla Lana School of Public Health

Disease

Factor-Inwentash Faculty of Social Work

Faculty of Medicine

Faculty of Arts & Science

Global

Laboratory Medicine and Pathobiology

Political Science

Research & Innovation

Startups

Sunnybrook Hospital

��˾��ֱ�� Scarborough

University Health Network

As the world watches the spread of the COVID-19 virus, researchers from the University of Toronto are at the forefront of monitoring, predicting, and managing the disease – from creating mathematical models that help predict its spread to working on rapid diagnostics and potential treatments.

They are also providing critical advice to world leaders – and the rest of us via numerous appearances on TV, radio and online news sources – on the best ways to respond to an outbreak that has so far sickened more than 114,000 on every continent except Antarctica and is responsible for more than 4,000 deaths.

While Canada has so far escaped the worst of the growing health crisis, with just 65 confirmed cases, Isaac Bogoch (left), a specialist in epidemiology and infectious diseases, says it’s only a matter of time before the novel coronavirus makes its presence felt here in a much larger way.

“In Canada, we're certainly not immune to this, and we will very likely see more and more imported cases into Canada as we see more cases throughout the world,” says Bogoch, who is an associate professor of medicine in the Faculty of Medicine and a clinician investigator at the Toronto General Hospital Research Institute, part of the University Health Network (UHN).

Understanding the virus and tracking its spread

In addition to making regular appearances in the media to help inform and educate a nervous public, Bogoch is one of a number of ��˾��ֱ�� researchers who is tracking the disease using official reports and computer models in an attempt to predict how bad the outbreak is likely to get. In January, he was first author on a study in the Journal of Travel Medicine that predicted the likely spread of the disease based on analyzing flights originating in or passing through Wuhan, China, which would later emerge as the epicentre of the outbreak, but at the time had only a few confirmed cases. The paper correctly predicted that the disease would soon spread to Bangkok, Hong Kong, Tokyo and Taipei.

BlueDot Health, founded by the Dalla Lana School of Public Health’s Kamran Khan, alerted its clients to the outbreak of an infectious illness in China about one week earlier than the World Health Organization (photo by TK)

Bogoch's co-authors on the paper included Kamran Khan, an associate professor at the Dalla Lana School of Public Health. Khan is the founder of a company called BlueDot that uses data analytics to track and predict infectious disease risk – essentially an automated global surveillance system that can peer into the future. The power of the technology was underscored when the company alerted its clients to the unusual outbreak of illness in China about a week before the World Health Organization alerted the world to the emergence of the novel coronavirus.

On Feb. 5, epidemiologists Ashleigh Tuite and David Fisman (both at left), both of the Dalla Lana School of Public Health, published a paper in the Annals of Internal Medicine that looked at data on the spread of the disease and concluded that it must have originated in November, a month earlier than previously thought. They also published an online model that allows researchers to test different assumptions about the novel coronavirus such as how infectious it is and how well control efforts are working.

“Modelling allows us to move from data to understanding,” says Fisman, who has also been a fixture on TV, radio and online publications in recent weeks. “You can easily do interventions or experiments on the population on your computer. And that can give you ideas, for example, about how you might slow this epidemic – what might be the impact of flattening the epidemic curve, for instance, so the epidemic is less fierce at any given point of time, but lasts longer?”

More recently, Bogoch, Khan, Fisman and Tuite wrote a paper to predict the size of the COVID-19 outbreak in Iran. At the time they wrote the paper, Iran had confirmed only 43 cases of the disease. But three international cases had also been traced back to Iran. Based on that number and an analysis of travel patterns, they calculated that Iran likely had 18,300 active cases. Since then, Iran has identified thousands of confirmed cases.

Despite successes like these, Bogoch points out that a lot is still unknown about the disease. For instance, although the mortality rate is reported at two to three per cent, the rate could go down as we discover that more people than we thought had mild cases of the disease and recovered without anyone knowing.

It's also difficult to say how widespread the disease will eventually become, or how it will compare in severity to other diseases such as SARS or the seasonal flu.

“I think we have to be careful and humble in our approach to this infection. We're learning more and more every day, and we don't have all the answers,” he says.

New tools to combat COVID-19

Robert Kozak and Samira Mubareka, both in ��˾��ֱ��’s department of laboratory medicine and pathobiology and at Sunnybrook Health Sciences Centre, are working on new tools to help hospitals diagnose the virus more quickly (photo by Nick Iwanyshyn)

Beyond understanding the spread of COVID-19, there are several ��˾��ֱ�� researchers who are racing to develop new tools for physicians to combat the virus both here in Canada and around the world.

Samira Mubareka and her colleague Robert Kozak, both in ��˾��ֱ��’s department of laboratory medicine and pathobiology in the Faculty of Medicine and at Sunnybrook Health Sciences Centre, are using the latest in whole-genome sequencing technology to help hospitals characterize the virus more quickly. The research also promises to help track the virus’s evolution and spread.

“If the virus’s genome was a book, we’re going to figure out its entire story,” Kozak told ��˾��ֱ�� News in late February.

At the same time, a ��˾��ֱ�� startup company that was co-founded by former PhD student Ali Punjani played a key role in helping researchers create the first 3D, atomic scale map of the part of the virus that attaches to and infects human cells – a key step toward developing a vaccine that some described as a “critical breakthrough.”

There will likely be more discoveries to come. Late last week, the federal government announced it was investing $27 million in coronavirus-related research, nearly $6 million of which is going to ��˾��ֱ�� and affiliated institutions.

Getting our act together

Ross Upshur, a researcher and bioethicist, says some of the responses to COVID-19 from governments have been questionable (photo courtesy of Dalla Lana School of Public Health)

Ross Upshur is a researcher and bioethicist with the Dalla Lana School of Public Health. He is especially interested in the ethics of responses to infectious disease outbreaks, and is chairing a World Health Organization working group on the topic.

Upshur says that the ethics of responses to emergencies like COVID-19 have been laid out in a number of recommendations and enjoy a general consensus. But he says that, with each new outbreak, there’s a tendency for governments tend to forget lessons of the past.

“Most outbreaks start out interesting, then they become weird, then they become weirder, but structurally the same sorts of issues arise again and again and again. That's the thing I find fascinating. When are we going to get our act together on this?”

Even though there are well-established ethical guidelines about the best ways to respond to disease outbreaks, Upshur says that governments never seem to remember those lessons from one outbreak to another.

For instance, measures to control the outbreak have been more restrictive than usual, and look more like security responses than public health measures. And Upshur thinks at least some of the measures are questionable. For instance, Japan quarantined 3,711 passengers and crew on the Diamond Princess cruise ship, and 705 eventually became sick. Upshur says an alternative would have been to send everyone home with thermometers and to check in with them daily. Such a measure was effective in dealing with a similar incident during an Ebola outbreak, he says.

Zoonotic disease

An assistant professor in the Faculty of Medicine, Kerry Bowman points to the widespread trade of wild animals as a contributor to a number of diseases, including SARS, Ebola, and now COVID-19 (photo by Jacklyn Atlas)

Kerry Bowman is an assistant professor of medicine and a bioethicist with an interest in the effects of environmental degradation and wild animal consumption on the spread of disease. Several years ago, he visited the market in Wuhan that is the epicentre of the disease and saw first-hand the wild animals for sale there.

He counted 56 species of animals for sale, wild and domestic, crowded together in stacked cages. Not only were the animals suffering, but the conditions were perfect for the spread of disease, he says.

Bowman acknowledged that there are cultural sensitivities around consumption of wild animals, and that it occurs in many countries, including eating of deer and other game animals in Canada. But he says the widespread trade of wild animals has contributed to a number of diseases, including SARS, Ebola, and now COVID-19. In each case, the disease seems to have originated in a wild animal being used for food.

“Unless we collectively begin to deal with the commodification of wildlife and the consumption of wildlife we are not going to get on top of this,” he says.

Politics and xenophobia

An associate professor of political science, Lynette Ong says China's government didn't respond well during the outbreak’s early days (photo by Riley Stewart)

Lynette Ong has been watching the effect of the outbreak on the Chinese government and its relationship with its citizens and other countries. The associate professor of political science says that China's centralized, authoritarian government did not initially respond well in the course of the outbreak.

“Because of the authoritarian nature of the political system, people are afraid to report bad news, even if it's the truth. People try to avoid responsibility,” she says. On the other hand, once the government is convinced there is a problem, it does have the ability to take strong measures.

She also thinks the outbreak has made Chinese citizens more interested in holding their government accountable. “This is an awakening moment in China for people as they become aware that information is controlled tightly. People are realizing that the information being controlled can affect them,” she says.

Almost as soon as people became aware of the outbreak in China, xenophobic and racist comments began circulating in Canada and elsewhere. Carmen Logie (left), an associate professor in the ��˾��ֱ��'s Factor-Inwentash Faculty of Social Work, told ��˾��ֱ�� News that fear of infection during disease outbreaks can amplify existing prejudices and intensify discriminatory behaviours

That was particulary the case during the initial days of the COVID-19 outbreak, when it was largely confined to Asia, and Chinese-Canadians were being unfairly targeted.

“We need a multi-pronged approach,” Logie says in the interview. “Yes, we need the information, but we also need to share how this is connected to our biases towards, say, Chinese people in Canada, as well as the negative impacts it's currently having on communities."

Bowman, who worked as a doctor during the SARS outbreak, says that racism was a factor then, too, and it is important to address it quickly.

"An outbreak is not just a biological event,” he says. “It's a political and sociological event as well, and an economic one. And sometimes the economic and social and political can be as powerful or even more destructive than the physical threat, and ‘us against them’ is something that sets in very quickly under this kind of pressure.”

Although he says he has seen racism emerge in similar ways to the SARS outbreak, he thinks that there was more and quicker pushback against it in the media and elsewhere. He also thinks that as the virus spreads to more countries, it will no longer be associated in people's minds solely with China.

Lessons from SARS?

Passengers on the deck of the Diamond Princess cruise ship, which recorded 705 infections and raised serious questions about Japan’s decision to quarantine thousands of people aboard the vessel (photo by Kyodo News via Getty Images)

Canada, not surprisingly, has tended to look at the COVID-19 outbreak through the lens of the 2003 SARS epidemic. But Bogoch points out that they are actually very different diseases. SARS tended to cause severe illness, and had a death rate of around 10 per cent. Coronavirus, on the other hand, usually comes with milder symptoms and a lower rate of death.

Nevertheless, the experience of SARS seems to have taught Canada important lessons that will help it control COVID-19.

“Our systems are so much more robust than they were in the time of SARS, just in terms of the coordination and communication between the various levels of public health and clinical medicine,” he says. “And the infection prevention and control initiatives in hospitals are much more robust now than they were.”

Upshur isn't so sure. He acknowledges that Canada has invested a great deal in public health since SARS, including creating the Public Health Agency of Canada and the position of chief public health officer. On the other hand, the Government of Ontario has proposed cutting funding for public health service.

“Public health is always the first to go because you don't notice it when it's working,” he says. “But woe on you when you start to mess with it. Because you pay the price every time.”

In the meantime, ��˾��ֱ�� experts will continue to be on the front lines of the current outbreak. That includes experts like Seema Yasmin, a former epidemic intelligence officer at the U.S. Centers for Disease Control and Prevention and global journalism fellow at ��˾��ֱ��’s Munk School of Global Affairs & Public Policy, who has been a frequent commentator on U.S. media like CNN and Wired magazine.

It also includes Abdu Sharkawy, an assistant professor in the Faculty of Medicine and infectious disease specialist at Toronto Western Hospital, part of UHN, who recently penned a viral Facebook post that, if nothing else, is helping to keep the wall-to-wall coverage of the COVID-19 crisis in perspective.

Sharkawy argued that while the illness does indeed pose a danger, the panic surrounding it could ultimately do more damage. His prescription? “Facts not fear. Clean hands. Open hearts. Our children will thank us for it.”

Pumped up: These 3D printers create perfect models of life-sized human hearts, spines and other body parts

noreen.rasbach — Mon, 28 Oct 2019 13:59:56 +0000

Pumped up: These 3D printers create perfect models of life-sized human hearts, spines and other body parts

noreen.rasbach Mon, 10/28/2019 - 09:59

Cutline

A 3D printed model of a heart (photos by Hamin Lee)

Topic

Faculty of Information

Faculty of Medicine

Research & Innovation

In a small, windowless room at Toronto General Hospital, a bank of seven 3D printers runs day and night, patiently laying down layer after layer of coloured plastic. When the printing is done, the pieces are trimmed and fitted together into perfect models of human hearts, life-sized and correct down to the smallest detail.

The 3D printers are part of the Lynn & Arnold Irwin Advanced Perioperative Imaging Lab at the University Health Network’s Peter Munk Cardiac Centre. Combined with advances in medical imaging and computer modelling, they are allowing doctors to get a better look at heart defects before they go in to repair them, as well as providing better training methods.

The models of the hearts use extremely detailed data from MRIs, CT scans, ultrasounds or other imaging techniques. Normally, doctors are working with two-dimensional images on a printout or a flat screen. As anyone who has ever tried to see their baby on a prenatal ultrasound can appreciate, this isn’t always easy. By turning the data from those images into three-dimensional computer models, and using those models to make solid printed hearts, the lab gives the doctor something that can be held in the hand and examined in detail.

With the printers whirring away in the background, Josh Qua Hiansen, the biomedical industrial designer at the lab, shows how the model will be used by doctors. This particular patient has a malformation of a part of the heart called the superior vena cava, which is allowing blood to mix with blood from pulmonary veins. Doctors want to fit an implant to close the malformed area, and they will use the model to make sure the implant is sized and positioned appropriately to close the area.

The lab was created in collaboration with Matt Ratto, a University of Toronto associate professor in the Faculty of Information and the head of the university’s Critical Making Lab. Co-founders are Dr. Massimiliano Meineri, a ��˾��ֱ�� professor of anesthesia, and Dr. Azad Mashari, an anesthesiologist at Toronto General Hospital and a ��˾��ֱ�� lecturer who heads the imaging lab. The mandate is to evaluate, refine and translate 3D imaging, modelling and micromanufacturing techniques into clinical and educational practice.

Mashari says that the new techniques provide an inexpensive and flexible way to create all sorts of learning aids. These include medical “phantoms” – printed hearts, spines and other body parts. For instance, heart phantoms are used to train ultrasound technicians. And a phantom spine in flesh-like gel can be used to instruct on how to give spinal injections.

With the capability provided by in-house 3D printing, along with 3D computer models and even virtual reality, Mashari thinks that training and medical visualization will continue to become less expensive and more effective.

Close-up picture of a model of a human heart created with a 3D printer, with numbers 1-5 associated with various parts of the model

1. Left atrium and aorta. 2. Superior vena cava and right atrium. 3. Artifical conduit connecting the right ventricle to the pulmonary arteries (also green). 4. Pulmonic ventricle. 5. Systemic ventricle.

The 3D printed model of the heart above is taken from the scan of a patient with dextrocardia and transposition of the great arteries. The patient has had many surgeries in order to create a normal circulation.

This picture shows the top of the heart, so it is as if you were looking down at it from above the person’s head.

The model shows the spaces inside – as if the walls of the chambers, arteries and veins had been removed, and only the blood they contain was visible. This allows doctors to get a good look at the connections between the chambers of the heart.

To make the heart, images from CT scans were converted into 3D computer models, and then rendered into thousands of “slices.” The printer used these image slices to build up the pieces one layer at a time.

The models are fairly cheap to make, but they do take time. It took a technician about three hours to convert the CT scan for this one into a computer model. Total printer time was 30 to 40 hours.

This story first appeared in the University of Toronto Magazine. Read the most recent issue

The deadly global fungus: Leah Cowen’s lab aims to understand how C. auris works and how to stop it

noreen.rasbach — Tue, 22 Oct 2019 21:55:02 +0000

The deadly global fungus: Leah Cowen’s lab aims to understand how C. auris works and how to stop it

noreen.rasbach Tue, 10/22/2019 - 17:55

Cutline

(Illustration by Adam Hale, The Daily Splice)

Topic

Research & Innovation

In 2009, medical researchers in Japan examined the infected ear of a 70-year-old woman and found a curious new pathogen – a drug-resistant fungus that no one had ever identified. The researchers christened it Candida auris (auris is Latin for “ear”) and published a paper about it.

Ten years later, C. auris has spread to six continents and more than 30 countries, including Canada. It is hard to diagnose with standard lab tests, and difficult to treat because it has developed a resistance to antifungal drugs. C. auris spreads easily through touch and can survive on surfaces for weeks. It kills between 30 and 60 per cent of people it infects, most of whom are hospital patients.

Although C. auris is recognized as a serious emerging global health problem, its origins remain mysterious, how it functions isn’t well understood and treatment options are limited. For Professor Leah Cowen, all of these unknowns made it an intriguing organism to research. Cowen is chair of ��˾��ֱ��’s department of molecular genetics, and holds the Canada Research Chair in Microbial Genomics and Infectious Disease. Her lab aims to understand how C. auris works, and hopes to develop new drugs that will be effective against it and other fungal pathogens in humans and crops.

“We’ve been very busy trying to understand what genes are responsible for drug resistance in this organism, and what genes are important for its ability to cause disease,” Cowen says. In fact, she and her research team have identified a molecule in the fungus that is a promising target for what could eventually be a new class of antifungal drugs.

Professor Leah Cowen (centre), working with students in her lab (photo by Steve Southon)

At Cowen’s lab in the MaRS Centre, the interdisciplinary group of 26 researchers includes structural biologists, geneticists and chemists. They work on understanding the different genes that affect the behaviour of disease-causing fungi, including the genes that make them drug resistant and give them the ability to harm humans. The team also exposes the fungi to different substances, hoping to find something that causes them to weaken or die and could therefore be used to develop new drugs.

The fungi kingdom includes a broad range of organisms such as mushrooms, as well as yeasts, mildews and moulds. In healthy people, fungal pathogens tend to be an annoyance – a case of athlete’s foot, for instance, or a yeast infection. Most fungi prefer temperatures cooler than the human body temperature and so don’t infect people as easily as, say, bacteria.

Even so, around the world, fungi kill 1.6 million people a year – nearly four times more than malaria. Often, the victims are people with weakened immune systems, such as those with HIV-AIDS, those who are undergoing chemotherapy or those who are on immunosuppressant therapy following an organ transplant.

Other types of disease-causing fungi are far more common, but cases of C. auris are on the rise. In the U.S., about 700 people have been found to be infected with the fungus, and screening has found another 1,300 people carrying the fungus but not made ill by it. Canada has had 20 cases of C. auris, with no attributed deaths.

Fungal infections are notoriously difficult to treat. That’s partly because human beings are much more closely related to fungi than most other pathogens, including bacteria and viruses. This makes it harder to come up with drugs that will harm the fungus but not the patient. Fungi also have cell walls that drugs have difficulty penetrating, and excel at pumping harmful substances out of their cells.

Although there are well over a dozen classes of drugs to treat bacterial infections, there are only three main classes of antifungal drugs. As the use of drugs in humans, plants and animals increases, pathogens of all sorts, including fungi, are developing resistance. And because there are only three classes of antifungals, doctors quickly run out of options.

It’s not yet clear where C. auris came from, but its high tolerance to salt suggests it evolved in brackish, marshy areas. Researchers can’t find any trace of it before 1996, and the best guess is that until then the yeast lived unnoticed in the environment, and only recently became dangerous to humans.

One theory is that as temperatures have risen due to global warming, C. auris has evolved a tolerance to heat. At the same time, it was exposed to residues of the antifungals used on crops, which led it to develop resistance to antifungal medications. Heat tolerance and drug resistance combined to make it dangerous to humans.

One of the Cowen lab’s most promising treatment approaches involves a protein in the fungus called heat shock protein 90 (Hsp90). This “chaperone protein” helps other important proteins do their jobs. Hsp90 also helps cells adapt to stressful environments. This includes damage caused by exposure to toxins. Work at the Cowen lab shows that Hsp90 plays an important role in C. auris’s resistance to drugs.

Earlier this year, Cowen’s team published a paper that describes their work using a strain of C. auris they engineered so they can easily turn down the gene responsible for Hsp90. Without a fully functioning Hsp90 protein, C. auris has a much harder time surviving, and is much more susceptible to antifungal drugs.

The research opens up a hopeful treatment option. Cowen and her team want to find a molecule that will penetrate the cell wall of the fungus, then bind to and disable Hsp90, weakening the yeast and making it more vulnerable to existing antifungal drugs.

“We’re uncovering fundamental biology. How do these organisms become drug resistant? How do they cause disease? What kind of molecules can we use to perturb those processes? Do these molecules and their targets in fungal cells influence interactions with host cells? We’re interested in going all the way to translate those discoveries into new therapeutic strategies,” says Cowen, a co-founder of Bright Angel Therapeutics, which develops treatments for drug-resistant fungal infections.

One potential problem with targeting Hsp90 is that the protein is also present in human cells, and fulfils similar important functions there. A useful drug will have to target the fungal version of Hsp90 while mostly leaving the human version alone. Work in Cowen’s lab has shown this is possible. The researchers have found that although the human and fungal versions of Hsp90 look similar, the fungal version is somehow more flexible – the protein “stretches,” making room for the potential drug molecules to interact with the target. By taking advantage of the difference, Cowen and her team hope to develop a drug that kills the pathogen, and leaves human cells alone.

“We think in the next few years we’re going to see at least a couple of new classes of antifungals come on board,” Cowen says.

“We’d like one of those to have come from our lab.”

This story first appeared in the University of Toronto Magazine. Read the most recent issue

What's going on beneath the planet's surface

sgupta — Tue, 02 Jul 2013 09:24:31 +0000

What's going on beneath the planet's surface sgupta Tue, 07/02/2013 - 05:24

Cutline

Associate Professor Julian Lowman of the Department of Physical and Environmental Sciences at UTSC is cross-appointed to the Department of Earth Sciences, Department of Physics and Department of Astronomy & Astrophysics (photo by Ken Jones)

Kurt Kleiner

Author legacy

Kurt Kleiner

Topic

Faculty of Arts & Science

Features

Subheadline

Understanding Earth and super-Earths

Julian Lowman is a physicist with the University of Toronto Scarborough who studies the internal dynamics of the Earth and of terrestrial planets beyond our solar system, especially the many large ‘super-Earths’ which have recently been discovered around other stars.

Using the Canadian SciNet supercomputer network Lowman runs complex mathematical models simulating what's going on beneath the surface of our world. Among other things, his work might help predict whether the conditions needed for the development of terrestrial life might exist on other planets.

Can you tell us a bit about your work?
Our area of interest is the evolution of planets. A planet in the most rudimentary terms has a hard outer crust, a rocky mantle underneath that, and a dense metallic core. It’s the evolution of the mantle and how it rids itself of heat that determines the evolution of the entire planet. In the Earth's case mantle convection is manifested by plate tectonics, and plate tectonics is responsible for continental drift. And continental drift plays into all of these areas of science, everything from biological evolution to the storing of carbon dioxide that affects climate of the planet over a long-term scale. It affects the rotation rate of the planet, it affects the gravity field of the planet and it is likely very important in the generation of the magnetic field.

You name it, plate tectonics probably affects it.

What questions are you trying to answer?
I suppose the one most interesting to most people is whether other planets have mobile surfaces, and why the Earth’s surface is mobile. This is one of the reasons plate tectonics is so interesting now that we’re starting to discover all of these exoplanets. We've come to understand the importance of plate tectonics in the evolution of the Earth and the fact that without plate tectonics we might not have terrestrial life. If it wasn't for plate tectonics there wouldn't be any human beings.

Why wouldn't terrestrial life have developed?
Because we wouldn't have continents. You've got essentially a battle between continents being pushed above sea level and erosion wanting to wash them down below sea level. Given the 4.6 billion year lifetime of the Earth, erosion would have washed all the land above sea level into the oceans by now. So all the land we have is a result of mantle convection pushing around the surface. In fact, as time goes on we're gaining continental surface area.

How do you do your research?
It would be impossible to do this work without a facility like SciNet. We do 3D computational fluid dynamics. The mantle's very interesting. On very short time scales mantle rocks act like a solid so they do things like transmit seismic waves. But over long geologic time scales they flow by what’s called creep mechanisms. So they're able to behave like a fluid but the evolution takes place very slowly, on the order of centimeters per year. Mantle rocks move at the rate your fingernails grow.

To model the evolution of a material that flows so slowly you can speed up that entire process on a computer. But the biggest problem we have is it’s very computationally intensive. You need very high resolution and you're doing things in 3D and you have to step things forward in time to simulate hundreds of millions to billions of years. They are very large computational problems. And the bigger the planet the more computationally intensive the problem becomes.

Are you trying to model Earth-like planets?
We’re looking at terrestrial planets, that is, rocky planets. Venus and Mars don’t have plate tectonics. There are no other bodies in the solar system that have plate tectonics. The oceans may play a very important role in creating plate tectonics. What you can get is something called stagnant lid convection, where the convection goes on underneath the surface, but the surface is so rigid that what's going on in the interior can't actually get enough traction on the base of the plates to get the base to move. You can only get the surface to move if you've got some weak points on the surface, which on Earth are the oceanic ridges and the subduction zones.

I've been looking at what allows mantle convection to be expressed as plate tectonics and whether this is more likely on super-Earths. Is a super-Earth going to be big enough that it doesn’t get to that decoupled stage like Venus and Mars, so that plate tectonics is therefore bound to appear? Or does plate tectonics need water? Is that the key?

Kurt Kleiner is a writer with the University of Toronto Scarborough.

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Darwin was right: productivity increases with species diversity

sgupta — Thu, 23 May 2013 11:37:20 +0000

Darwin was right: productivity increases with species diversity sgupta Thu, 05/23/2013 - 07:37

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Plant species with the greatest evolutionary distance from each other have the greatest productivity gains, says Marc Cadotte (photo by Ken Jones)

Kurt Kleiner

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Environments containing species that are distantly related to one another are more productive than those containing closely related species, research from the University of Toronto Scarborough (UTSC) shows.

The experimental result from Assistant Professor Marc William Cadotte confirms a prediction made by Charles Darwin in On the Origin of Species, first published in 1859. Darwin had said that a plot of land growing distantly related grasses would be more productive than a plot with a single species of grass.

Since then, many experiments have shown that multi-species plots are more productive. Cadotte’s experiment showed for the first time that species with the greatest evolutionary distance from one another have the greatest productivity gains.

“If you have two species that can access different resources or do things in different ways, then having those two species together can enhance species function. What I’ve done is account for those differences by accounting for their evolutionary history,” Cadotte says.

Cadotte grew 17 different plants in various combinations of one, two, or four species per plot. As in previous experiments, he found that multi-species plots produced more plant material. But when he analyzed the results he also found that combinations of plants that were distantly related to one another were more productive than combinations of plants that were closely related. For instance, a plot planted with goldenrod and the closely related black-eyed susan wasn’t as productive as a plot with goldenrod and the more distantly related bluestem grass.

What’s going on isn’t mysterious, Cadotte says. Distantly related plants are more likely to require different resources and to fill different environmental niches – one might need more nitrogen, the other more phosphorus; one might have shallow roots, the other deep roots. So rather than competing with one another they complement one another.

What’s interesting about his result, says Cadotte, is that evolutionary distance is all you need to know to predict productivity.

The result suggests that, as plant species disappear, the Earth will become less productive and plants will draw even less carbon from the atmosphere, possibly increasing the rate of global warming.

On the other hand, the results could give a valuable tool to conservation efforts. Environmentalists trying to restore damaged habitats could use the information to help them pick which combinations of species to introduce.

Kurt Kleiner is a writer with the University of Toronto Scarborough.

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Pioneering the psychology of mindfulness

sgupta — Tue, 14 May 2013 12:06:54 +0000

Pioneering the psychology of mindfulness sgupta Tue, 05/14/2013 - 08:06

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Professor Zindel Segal talks to a subject wearing electrodes during a mindfulness exercise (photo by Ken Jones)

Kurt Kleiner

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UTSC

Psychology

Zindel Segal is a pioneer in the emerging field of mindfulness-based psychotherapy.

For more than 20 years, Segal has studied and promoted mindfulness as a way to prevent relapse in people who have suffered depression.

Using techniques such as meditation and yoga, patients learn to pay attention to their experiences, thoughts, and feelings as a way of heading off a depressive spiral.

Segal is currently the Cameron Wilson Chair in Depression Studies in the Department of Psychiatry at the University of Toronto and is also head of the Cognitive Behaviour Therapy Clinic at the Centre for Addiction and Mental Health.

But he's set to take on a new role as the director of training in UTSC’s new Graduate Department in Psychological Clinical Science this fall.

Segal spoke with writer Kurt Kleiner about his upcoming move.

What’s attractive about this position?
This program in psychological clinical science is a tremendous opportunity to build something from the ground up with a talented and committed core group of faculty. It also allows us to provide graduate training that integrates the scientific foundations of clinical psychology with the acquisition of assessment and treatment skills that are evidence based.

How did you become interested in mindfulness?
My own trajectory is a wonderful example how innovative treatments can be developed by drawing on basic research in cognitive and affective science. For example, work on mood-dependent cognitive processing has shown that for people with a history of depression, experiencing mild dysphoric moods can retrigger depressive thinking styles.

The risk here is that when setbacks occur, as they do to all of us, some folks may fall back into ways of looking at themselves that make them more prone to depression returning. If people could learn skills to stop these processing styles from dominating the mind, then the setbacks could be contained as temporary and not snowball into full-blown clinical relapses.

One of the key skills we found to be helpful was teaching people to attend to their thoughts and emotions in a non-judgmental and curious manner. Doing so encourages active approach and curiosity of negative experiences, activates regulatory neural networks and provides people with greater choice in what do next. Most importantly, it provides an alternative to habits of suppression or distraction for getting rid of negative feelings. The beauty of it all is that regular practice of mindfulness meditation helps to train up all of these skills.

Do you expect the graduate program here to become a centre of mindfulness therapy?
Not really. I think that our blueprint for our program achieving a standard of excellence is having our graduates be proficient in a broad range of evidence-based psychological treatments. In the practice of mindfulness, there is less of a premium placed on talking and analyzing client narratives. In more traditional psychotherapy people do need to talk and process their experiences. Our graduates will have exposure to these and other approaches.

Having said that, I do plan to continue my research program, which is centered on investigating the psychological and neural mechanisms of mindfulness practice. Who knows, if our work as a collective draws sufficient notice, an initiative such as an interdisciplinary centre for mindfulness studies may be warranted. Right now, though, I am focused on more proximal targets, such as getting our program ready for accreditation and enhancing its North American profile.

Do you have your own mindfulness practice?
Yes. I meditate for 40 minutes in the morning. Not every single day, but the intention is nevertheless there. I also go to a yoga class once a week if I can manage it.

Kurt Kleiner is a writer at UTSC.

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Stressed mother squirrels make faster-growing babies

sgupta — Wed, 24 Apr 2013 11:36:18 +0000

Stressed mother squirrels make faster-growing babies sgupta Wed, 04/24/2013 - 07:36

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Bigger squirrels live shorter lives but are more likely to survive to the next spring in crowded conditions, says Professor Boonstra

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Breaking Research

How DNA barcoding could help endangered fish

sgupta — Wed, 24 Apr 2013 10:42:51 +0000

How DNA barcoding could help endangered fish sgupta Wed, 04/24/2013 - 06:42

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Megan McCusker examined DNA from a thousand fish caught by commercial and research vessels (photo by Ken Jones)

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Breaking Research

Largest undergrad finance lab in Canada open for business

sgupta — Mon, 15 Apr 2013 10:27:07 +0000

Largest undergrad finance lab in Canada open for business sgupta Mon, 04/15/2013 - 06:27

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Finance librarian Stephanie Perpick helps students learn to use the tools of a job in finance (photo by Ken Jones)

Kurt Kleiner

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Squint a little, and you might imagine you’re on the floor of a Bay Street financial firm. A stock ticker on the wall displays real-time information on hundreds of publicly traded companies, while 60 dual-screen computers flash results from professional-grade financial programs.

The only giveaway that you’re at a university campus is that the computers are being used by students in jeans and t-shirts, their backpacks tossed down at their feet. That and the lectern in the corner.

The new finance lab in the Instructional Centre will give University of Toronto Scarborough management students a leg-up in the work world, allowing them to learn using state-of-the-art software.

“These computers are equipped with the databases and analysis tools that you would find in the big Bay Street financial firms,” says Stephanie Perpick, the new finance librarian. “Students get to practice using tools that they’ll use for the rest of their careers.”

Every computer is loaded with market data and analysis programs including FactSet and Capital IQ, and the lab also boasts four Bloomberg terminals.

Students take finance courses in the lab, and also use the facility to complete assignments. Other software allows professors to run simulations that can compress six months of trading data into a 10-minute session, simulating the pressure of the fast-paced world of trading.

“Nowadays technical skills are important for any finance-related profession,” says Amad Qureshi, a fourth-year co-op management student and member of the Investment Society. “We all know the theories. But the real thing is how we apply those concepts.

"When we leave from this campus having learned all these technical skills, in the workplace we will definitely be able to make ourselves stand out from the rest of the candidates.”

Perpick was hired in January to direct the lab. She comes fresh from a job at BMO Capital Markets as a research consultant to the investment and corporate banking group, where she worked for six years. Before that she earned a master’s degree in library and information science at the University of Western Ontario

“For me it was an opportunity to come back to my roots. I’m a librarian and I wanted to be in a traditional library setting. It was a great way for me to get back to that goal, but still be engaged in the world of finance. It was a perfect fit,” Perpick says.

For students, it’s a chance to get training in the tools from a hands-on professional, as well as first-hand career advice.

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