Archive for the ‘Edmonton Technology’ category

New Lead on Detecting Breast Cancer

February 26, 2010

Dr. Barry Barclay

Given the current epidemic of breast cancer, wouldn’t it be great to have an early detection system?
Molecular biologist Dr. Barry Barclay, CEO of Planet Biotechnologies Inc, believes he may have stumbled upon a genetic mechanism that could lead to exactly that.
After he read an article on genetic damage related to breast cancer and a particular gene—the TYMS gene—he realized there were connections to the research he had conducted for many years on the TYMS gene. The location of interest is on Chromosome 18.
As Dr. Barclay explains, “It took me about five years to try to figure out a potential mechanism that would throw a switch that would cause a tumour. And not only does it initiate the tumour, but the structures that are generated during the episode of the switch not functioning well, themselves become tumour drivers. So once you turn the switch, it stays permanently in the position. What causes it to be dis-regulated are the factors that we know are the risk factors in breast carcinogenesis. There are environmental factors. There are nutritional factors, and there are genomic factors.”
Dr. Barclay has presented his findings at two international scientific meetings and will soon publish an article on his research. √

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More women, money & cyber ports… Less disease please

January 29, 2010

Dr. Margaret Ann Armour with Anne McLellan

Challenging the norm
For Dr. Margaret-Ann Armour, the launch of the WinSETT Centre is a dream come true.
It’s been six years in the gestation. And, true to her roots as a chemist, she birthed the new entity with a flurry of beakers and bubbling gases in front of an appreciative crowd at the Telus Centre on the University campus.
Dr. Armour has long been known for her tireless efforts to engage and promote women in the sciences and technologies. Back in the early 1980s, she was a founding member of WISEST—Women in Scholarship, Engineering, Science and Technology. The movement spread across the country.
Now, through her efforts and vision, Edmonton is home to the WinSETT Centre. An acronym for Women in Science, Engineering, Trades and Technology, this is the hub for an ambitious national effort to significantly boost the numbers of women in the workforce and change the culture of such fields as engineering and trades.
Dr. Armour points to the statistics. “Only 12 percent of engineers are women. The kind of percentages of women in construction is dismal. It’s four percent. In the sciences, it’s probably 35 percent, which is over the critical mass which makes it sustainable.”
Research shows that one major problem is that even when women do enter these fields, they tend to leave after about 10 years. The blame lies directly with an inflexible male dominated culture in the workplace.
“An awful lot of it has to do with having a family and being able work, and trying to balance the two, says Dr. Armour. “Because, if it’s a work place which is still fairly well male dominated, it has a male culture. And the male culture is, ‘you shall work 18 hours a day and always be there.’
“And women are saying, ‘I don’t want that. I don’t want that kind of lifestyle. I want a balance.’ We’re hearing that young men are saying, ‘We want a balance, too.’ So we’re hoping that things will change. But that’s been very slow.”
That theme of changing the workplace culture to retain women and improve Canadian productivity was picked by the Honourable Anne McLellan in her stunning speech at the WinSETT launch.
Among the first programs the WinSETT Centre will undertake is leadership training. According Dr. Armour, “Leaders need to appoint leaders. And, although we know it’s very important to have more women entering fields like engineering, if we don’t have women as leaders in engineering, the culture of engineering is not going to change. So when young women come into the workforce, they’re not going to stay.” √

Robin Winsor CEO of Cybera

Expanding the cyber network
The new president and CEO of Cybera is Robin Winsor. He will split his time between Edmonton and Calgary as he runs this not-for profit, university based organization set up to extend Alberta’s cyber infrastructure. His mandate is to move Cybera to the next level—into the business community.
That’s certainly a world Winsor understands. While working in the research department at Gulf, he used his knowledge of geophysics and artificial intelligence to develop the world’s first direct digital x-ray system. That was 20 years ago. He quit the day job and grew the company into a business worth hundreds of millions of dollars.
Now, as the head of Cybera, Winsor hopes to extend the services of the cyber network to Alberta’s entrepreneurs and business community. Cybera operates cyber ports at the University of Alberta. “There are similar facilities in Calgary, Lethbridge and, by extension, through networking all over the world,” he says. “We have lots of big screen TVs. We have cameras that track us and we can sit here and have a virtual meeting. You can see so much more when you are in what we would basically call a video conference. Others are giving it fancier names like tele-presence, virtual rooms, and so on, but it does add that extra measure. And this is just a small part of the services that Cybera offers.”
Winsor is particularly keen on making Alberta’s energy sector aware of the Cybera and the use it can make of the cyber facilities.
While current access to this cyber network is somewhat limited, he says Cybera’s future goal is make access as pervasive and ubiquitous as that of the telephone. Simply plug in and you’re connected.
You can learn more about Cybera’s services at www.cybera.ca

Dr. Stefan Bachu

Recognizing excellence
Just before the Alberta Research Council was merged into the new agency, Alberta Innovates-Technology Solutions, its president and CEO John McDougall honoured one of his own. He bestowed the title of Distinguished Scientist upon Dr. Stefan Bachu—the fifth ARC scientist to receive this recognition of excellence.
Dr. Bachu is world renowned for his pioneering research on carbon capture and storage technology. In 2007, he shared a Nobel Prize as lead author to the Intergovernmental Panel on Climate Change (IPCC) Special Report on CO2 Capture and Storage. That’s the same Nobel Prize Al Gore received.
Today, Dr. Bachu continues his involvement at the international level. “To start with, I represent Canada on the technical group of the Carbon Sequestration Leadership Forum, which is an organization of 24 countries major energy producers and CO2 emitters. It includes countries like United States, China, Brazil, Russia, United Kingdom, Norway, Australia, and so on. Secondly, I have been asked several times to give advice to various state or local governments in various countries. So yes, I am involved.”
As a distinguished scientist, Dr. Bachu intends to continue his research into the refinement of carbon storage technology. √

Jim Edwards

Kick-starting industry research
When it comes to funding university research, one of the main granting agencies is NSERC, the Natural Sciences and Engineering Research Council of Canada.
And now the Council is making more money available to encourage research partnerships between academia and industry.
Former Member of Parliament and long time Edmontonian, the Honourable Jim Edwards, is now chair of NSERC. He explains the particular focus on small and medium-size business.
“It’s a fact that 60 percent of the 100 largest companies in Canada use NSERC collaborations, but only seven percent of the smaller companies do… we’re seeking to fill that gap. Ultimately the goal is to improve Canada’s competitiveness. We invest more in academic-based research per capita than any other country in the G7. On the other hand, we trail very badly in terms of industry-based research. And so, we’re hoping, in a modest way, to be able to kick start that and we’re hoping to double the number of partnerships that exist within the next five years.”
To learn more about the NSERC industry program, visit www.NSERCPartnerships.ca

 
Capitalizing on datasets

Dr. Osmar Zian

With news that its funding has been renewed, the Alberta Ingenuity Centre for Machine Learning is launching into its second phase. Its scientific director, Dr. Osmar Zian, says phase two brings some new directions.
One is commercialization. The other is a major focus on biomedical applications for the machine learning and data mining technology the Centre is developing.
Says Dr. Zian, “We have applications related to cancer… It can be detecting cancer. It can be providing decision support for practitioners on the treatment or the dosage we give to patients. Predicting, for example, relapse for people. But there are other examples where we will also build data warehouses to collect data from different sources and provide decision support systems that are using machine learning and data mining techniques for decision-makers, There are techniques also that we are working on for visualization of medical images. The list goes on and on. “

Robert Murakami

For Dr Zian, turning this research into tools that can help save lives is what the new commercialization component is all about. And the man who is charged with making that a reality is Robert Murakami, the Centre’s new executive director. He’s also the president and CEO of its new commercialization arm, a company called Myriad Machine Learning. It’s his job to bring researchers and investors together to help translate the science into industrial applications.
As Murakami explains, “Machine learning is really a platform technology. It is the fundamental engine for analyzing and predicting large datasets, much like predicting new investment strategies, or new trading tools for investment management… much like predicting patient movement and predictability within a hospital environment… much like predicting whether or not the existing oil wells in this province are actually being managed efficiently. And so, because it’s such a platform technology and because we know that information technology is growing at an enormous rate—and we now have a gazillion, gazillion bits of information floating around—how does all that get analyzed and how can we actually utilize it to create something better for people?”
Through Myriad and the Alberta Ingenuity Centre for Machine Learning, Murakami is also setting the stage for the next generation of technology entrepreneurs, including a program that offers business bootcamps to university students. √

Dr. Norm Neumann

Zoning in with ozone
When it comes to prion research, decontamination is a huge issue. The misfolded prions that cause mad cow and chronic wasting disease are almost indestructible by traditional means.
But, according to Dr. Norm Neumann of the School of Public Health at the University of Alberta, experiments with advanced oxidation and ozone treatment may hold some promise. “The pathological disease, as we know it, is caused by a misfolded protein causing another normal protein to misfold. And so there’s this chain reaction that goes on. Some of the work that we’re doing demonstrates that ozone can actually destroy that protein enough to inactivate the templating properties or the pathological process that we see.
“We’ve seen that in a test tube—and the big question for us now is can we begin to understand this and model it in an engineering context and understand complete destruction of this? Then we must cross validate that information in animal infectivity models.”
Dr. Neumann suggests that, if the advanced ozone treatment works, we may one day be able to dispose of prion infected material through something as simple as composting. √

How clean are your keys? Think infection

January 29, 2010

Randy Marsden

“The assistive technology provided is amazing in its ability to erase the boundaries of disability.”
That was what (the late) Christopher Reeve said about the OnScreen keyboard in Microsoft Windows. He and Muhammad Ali are among millions who have benefited from products developed by Randy Marsden of Edmonton.
For more than two decades, Marsden has concentrated on creating specialized computer technologies for people with physical disabilities: quadriplegia, cerebral palsy, multiple sclerosis, ALS and muscular dystrophy. His career took direction with a third-year electrical engineering university project when he and another student developed a communications device for his friend, Si Peterson, a quadriplegic since a gymnastics accident in high school. Upon graduation, with funding from the National Research Council’s IRAP program and the Alberta Heritage Foundation for Medical Research, they started Madentec Limited.
Over the years, numerous communications products (Tracker and Discover lines) emerged that have made an enormous difference to disabled people around the world—allowing them to operate computers with blinks, tooth picks, puffs or touching of lips. Spin-off technology includes various applications for cell phones and computers. In fact, Marsden is the co-founder of Swype, the cutting edge text input software used in Samsung smart phones.
But, when a dentist from France purchased his TrackerPro, it led to major changes in focus. TrackerPro is a wireless device—a small dot of reflective tape worn on the forehead, hat brim or glasses—that replaces a mouse for users with limited or no hand movement. Curious about why someone who obviously is able to use his hands would need a product designed for head movement, Marsden called the dentist.
It turned out it was actually the time-savings that motivated the dentist, who explained that he needed to view digital x-rays on computers, right in treatment rooms. Marden learned that, “Treatment rooms have strong infection control requirements and if devices were not sterilized, the dentist would have to take his gloves off to use a mouse, and de-glove and re-glove each time.”
Forming a focus group of four veteran dentists to get their perspectives, he discovered that anything within two metres/six feet of a patient’s mouth needed to be wiped down between patients. “That includes almost the entire room.”
But while TrackerPro might be a solution to the mouse problem, the ultimate challenge was really the keyboard.
“You can’t (properly) wipe down a keyboard. And, those that did use a keyboard, had them wrapped in Saran Wrap.” It had to be changed frequently, and looked unprofessional.
“Keyboards are the number one cause of bacterial infections and are more germ-infested than public toilet seats.”
Marsden points to studies that indicate hospital keyboards are known to spread infection more than any other surface—and more than 100,00 people died last year from hospital acquired infections (in North America). Patients entered with a broken leg but caught pneumonia and died because they caught a bug.
So Marsden marshaled his team. “We’re ‘input guys’… We can do this.”
They created a proof-of-concept USB keyboard: slightly smaller than a typical keyboard (15” versus 18-20”) to save cubicle space, with a completely smooth glass top with the lettering on the underside of the glass. With no nooks or crannies, it was quick and easy to wipe down and disinfect. Adjustable touch capacitive circuitry allowed it to be sensitive to the touch even when wearing gloves, and it made a clicking sound when a key was hit. Despite its smaller footprint, it housed both a numeric keypad and an integrated oval touch pad, so no was mouse needed. The bottom was constructed from machined Corian (counter-top material). It weighed a hefty 3.2 lbs./1.48kg.
In the pilot study, 12 keys on three keyboards—silicone, glass and standard plastic—were infected. After wiping with a Cavi-Wipe (disposable disinfecting towelette), they discovered no significant difference with the amount of remaining bacteria between the plastic and silicone keyboards. However, the glass keyboard was “100 times less infected” than the other two.
“We wanted market feedback… Although we had no (actual) product to sell, we booked a booth at the American Dental Association Trade Show in Las Vegas—at the last minute in January 2008.”
Unbeknownst to Marsden, his “Cleankeys” keyboard joined 27 other innovations in the new product showcase, which featured major players like Proctor & Gamble, Oral-B and Colgate. “We shared our showcase with Crest. We won Best of Show for best new product. Even better, we won by a wide margin.”
Marsden would win other awards: The 2008 ASTech Award for Societal Impact (his second win); the 2009 University of Alberta Alumni Honour Award, and the Innovation Awards from the Canadian Manufacturing and Exporters Association in 2009 and the National Research Council in January.
Cleankeys was a hit, but it was not meant to be a mass produced device. Nevertheless, orders rolled in—selling 4,500 units in 18 months. That number may not sound significant when you consider how many dentists there are around the world. Or, not a lot compared to the over one billion on-screen keyboards shipped with every copy of Windows since 1998 that bears Madentec’s copyright credits. But, it was significant enough to see the demand.
Marsden realized that the need for a cleanable keyboard went way beyond the dentist’s office. “Most keyboards aren’t used by just one person. Think clinics, schools and airport check-ins and food services—any place people share computers.” For example, automated plants like Lucerne Ice Cream were using his product.
“You can share this keyboard without sharing your germs.” It also hits closer to the Marsden home. “We have a family computer in the house and have five kids—the keyboard is disgusting.”
The need became even more apparent with infection control and H1N1 very much in the public eye, and hand sanitizers being found almost everywhere.
So, with a broader demand, updating more suitable for a wider audience became necessary. It also prompted the change of the company name to Cleankeys Inc., with Marsden as the CEO, to reflect the primary focus on keyboard design and production.
The forthcoming second-generation glass keyboard will be a wireless USB model that’s lighter and improves performance. In addition, another wireless model, made from high-grade acrylic with molded keywells with slight indentations, will be introduced.
“Some prefer glass, because it’s inert and smoother and perceived quality, but (as an alternative), acrylic is ideal—it’s harder and less susceptible to breaking. If it’s flat, they can’t feel the keys—it’s not good for touch-typists.” They need a place to rest their fingers, a challenge with his touch sensitive keyboard. So Marsden’s acrylic model incorporates an accelerometer, an electromechanical device that measures acceleration forces like the one found in Apple’s iPhone. “It’s also like the vibration sensors in a Wii remote.”
The keyboard sells for $400—high compared to typical models—but Marsden says it’s more costly to produce, and it’s niche-market justifiable. (Although we may see a consumer model down the road)
“Look at the time it saves dentists—no wrap, no gloves on and off pays off in a month or two. In hospitals, if it cuts down days not have to be spent in hospitals—that costs $5 billion a year in the U.S., not to mention the suffering and fatalities caused.” Liability is also being transferred to hospitals. “As of October 2008, U.S. insurance companies stopped reimbursing hospitals for treatment for their insured patients, if the infection was acquired in the hospital.”
While Cleankeys is primarily sold in Europe, it will be launched worldwide this month. “It’s a world market we’re taking this product to from Edmonton and we’re making it here in Edmonton.”
Logican, a boutique electronics service manufacturing company specializing in medical, military and industrial products in Edmonton Research Park, is building them. President Harvey Sheydwasser travels the world and sees the extent of the problem He believes Marsden’s technology will be widely adopted. “We’ve worked with Randy before and are happy to be part of the solution.”
Marsden, 46, hopes to help fight infection and save lives… one keyboard at a time. √

Monitoring Alberta’s biodiversity…from mites to moose

January 4, 2010

Jim Herbers

In her famous song, Joni Mitchell sang, “You don’t know what you’ve got til it’s gone.”
When it comes to Alberta’s biodiversity, let’s hope we never get to that point.
That’s why the scientists behind the Alberta Biodiversity Monitoring Institute have developed a reporting system that tells us just where we sit on that spectrum between paradise and a parking lot.
They run a program that monitors the health of Alberta’s wildlife and ecosystems across the province.
As director of information for the ABMI, it is Jim Herbers’ job to communicate to the public, government, industry and the scientific community just where we are at in terms of protecting or destroying our natural world.
“In a nutshell, you manage what you measure,” he says, pointing to the scale of many of the new development policies in Alberta. There’s the Land Use Framework, the Energy Strategy, and there’s heightened interest in the cumulative effects of human activity on the landscape.
Herbers explains, “We traditionally have very little in terms of knowledge that operates at that scale. So being able to report on Alberta’s regions, parklands, prairies, municipalities even, certainly the new Land Use Framework regions, our program fills a gap in that information.”
Getting that information is truly a magnificent feat.
The ABMI scientists have mapped the province into a systematic grid of data collection points. In total there are 1656 points, each placed 20 kilometres apart. When the program is running at full capacity, each point will be visited on a five-year rotation.
About 30 percent of the sites are on private land, so the ABMI consults with ranchers and landowners to obtain permission to monitor biodiversity on their properties. The grid also covers the national parks, military lands, crown land, and municipalities like Edmonton and Calgary.
“When we go to a site,” says Herbers, “we collect information on the understorey vegetation, the overstorey vegetation, trees, the bird community, moss community, lichen community, fungi and invertebrates in the soil. We’ve also got an aquatic component that is coupled with that information about the state of Alberta’s aquatic resources.”
The sites are surveyed the same way on each five-year visit. “We can look at how they’ve change through time and relate that to how Alberta is managing the resources out there on the land base.”
Conducting the surveys is a demanding job for the young and the fit—those rare souls who can handle the rugged outdoors and all it offers in terms of weather and bugs.
A crew of two people will survey a site in the spring, collecting data on birds, trees, habitat and deadwood. A month later the crew returns to survey the plants. They also take note of bugs in the soil, moss, lichens and other features.
In the summer, a different crew visits a wetland near the grid point. “They will put a boat in the water and float out there with their hip waders. They take samples of the water to look at the habitat quality and bugs that are living in the water as well as the plants that are living on the shores of those wetland systems. And then finally some poor, unfortunate soul has to go out in January, February or March, and do a survey for winter tracks. So they are looking for moose, deer, coyotes, lynx, fox… those kind of mammals that are active in the winter are also surveyed.”
Samples of plants and organisms are sent to the Royal Alberta Museum for identification.
This has led to some exciting discoveries. Take the lowly mite, for example. Smaller than the head of a pin, these spider-like organisms play an important role in maintaining soil vitality. “We’re very proud to report that there’s well over a hundred new species to Canada that we’ve identified and well over thirty new species to the world.”
Once all is said and done, the field biologists are collecting data on two to three thousand species. While this may seem an extraordinary number, it is just a smidgeon of what’s out there.
“There are more than 80,000 species that we know of, and that number is probably twice as high living in Alberta,” Herbers points out.
Rather than simply focusing on rare and endangered species, the ABMI scientists chose to report on a variety of species that would give an indication of the overall health of Alberta’s biodiversity.
But what happens with this massive collection of data?
“It comes here to the University of Alberta. All of the data goes through quality control with our partners at the Alberta Research Council as well as at the Royal Alberta Museum. They send that information here to the U of A where we store and manage that data.”
The public, industry and government can access the raw data from the ABMI website for use in their own monitoring or modeling programs.
As well, through detailed analysis, the ABMI scientists distill all the information down to one number that indicates the state of biodiversity in a region.
According to Herbers, “We use a scale of zero to 100 where 100 represents a pristine habitat, a wilderness area where there’s very little human footprint, and zero represents a parking lot, [or] an area where there is a gravel pit, for example, with no biodiversity living there.”
Last February the ABMI issued a report for the lower Athabasca Planning region. This covers a vast area from the Northwest Territories down to Cold Lake and Lac La Biche. “The current human footprint in that area is seven percent. That’s roads, energy activity, forestry activity, urban activity, and in the south, agriculture. And our data are showing that the intactness for that entire region is 94 percent intact today.”
Herbers goes on to predict that as more oil sands mines and energy projects come on line, biodiversity in the region will decline.
This first report from the ABMI focused on birds and vascular plants in northeastern Alberta. Despite the relatively high level of intactness, the survey indicates that some non-native species are moving into the boreal region.
These include, says Herbers, “the American crow, the common dandelion, some of the European or non-native clovers seem to be expanding and aggressively starting to colonize the northeastern part of the province. On the flip side of that, when we are talking about species declining or becoming much rarer, in the species that we looked at, there’s no strong evidence that many of the species are declining today.”
But that can change over time, a state which future surveys will reveal.
“This whole program really comes down to sustainability and informed understanding about what the outcome of our activities are on Alberta’s landscape. Our industry partners, the companies that are operating on Alberta’s landscape, are interested in making sure they are operating in a way that is sustainable.”
It’s a decade now since a handful of concerned biologists and forest ecologists sat down to discuss over a few beers the need to systematically document change in Alberta’s biodiversity. It took five years to develop the scientific protocols to conduct the surveys. Today, the ABMI initiative has evolved into a world class monitoring program. And industry benefits from the consistent, harmonized approach to the collection of data which they can then use in their own research initiatives.
The ABMI offers a program that is designed to monitor the state of biodiversity across Alberta in perpetuity. But keeping the money in place to carry out the program is an ongoing endeavour. To run the program at full capacity would cost $12 million a year but that goal is still some distance away.
Funding partners include forest and energy companies, the federal and provincial governments, as well as the University of Alberta, Alberta Research Council, Royal Alberta Museum, and the Alberta Conservation Association.
With the economic downtown, the provincial government put the squeeze on the ABMI early in 2009. “We were asked to scale back our operations to the tune of $2.1 million. And we made some pretty tough decisions about being able to provide relevant information at appropriate scales,” says Herbers. As a result, the ABMI has concentrated all of its efforts in two of the seven provincial regions, the Lower Athabasca Planning and the South Saskatchewan Planning Region. “It takes a big commitment to get out there to measure each one of these sites.”
The ABMI is still working its way through its first rotation in order to establish a baseline of those 1656 points on the grid. Herbers reports, “We’ve visited about 350 sites and the majority of them are north of Edmonton to Fort McMurray and then across to Grande Prairie. We’ve started to do quite a bit of work around Calgary right down to the U.S. border, and then east-west to the Saskatchewan and BC borders.”
You can see for yourself what has been documented on the Alberta Biodiversity Monitoring Institute website at http://www.abmi.ca

CWD Impacts Hunting Revenue

January 4, 2010

Dr. Vic Adamowicz

Chronic Wasting Disease is a prion folding disease that attacks deer. It is similar to bovine spongiform encephalopathy that riddles the brains of cattle and kills them.
Dr. Vic Adamowicz is a rural economist at the University of Alberta. With funding from the Alberta Prion Research Institute, he is studying the social and economic impacts of CWD on hunting, agriculture and aboriginal people.
Resident hunting, for example, is worth $50 million a year to the Alberta economy.
According to Dr. Adamowicz, “…avoiding the spread of chronic wasting disease to the extent that it may occur if we can’t slow it down, we’re looking about a half a million dollars a year in losses to hunters in this worse case scenario. That doesn’t sound like a lot, but that half million dollars a year would occur every year if we can’t stop CWD. If we could invest in a program that in two years reduces CWD at a cost less than a $2 to $4 million, it’s worth it just from the hunting perspective.”
Dr. Adamowicz is quick to point out that there is no documented case of humans catching Chronic Wasting Disease from infected deer. His research shows that hunters are split on their perception of health risks, and that about one third of hunters feel comfortable eating deer meat before it is tested for CWD. √

Unfolding the mystery of misfolding PRIONS

November 27, 2009
Just mention the term prion and you’ll draw a blank look from most people. But say mad cow, and you’ll get a reaction.
Mad cows have spongy brains. They fall over. And, if you eat their parts, you might get the disease, too. That’s what most people remember of the mad cow crisis that swept Britain in the late 1980s. Thousands of cattle were destroyed before the epidemic was contained.
The culprit turned out to be cattle feed which contained ground up sheep offal contaminated with scrapies, a neurodegenerative disease of sheep. Scientists eventually figured out misfolded prions were behind the infection that had crossed the species barrier from sheep to cows and, sadly, to humans. In humans, it is called Variant Creutzfeldt-Jakob Disease.
In May 2003, Canada’s first official case of mad cow or BSE (bovine spongiform encephalopathy) popped up on a farm in Alberta. Overnight trade borders closed, stifling a $4.1 billion dollar a year beef export business. While barely a dozen mad cows have appeared in the ensuing years, the BSE crisis here cost billions in lost trade and lost jobs.
The Alberta government responded with a $35 million fund to support research into BSE and prion related diseases through Alberta Ingenuity and the Alberta Prion Research Institute. The federal government poured support into PRIONet, a member of the Network of Centres of Excellence. The University of Alberta set up the Centre for Prions and Protein Folding Diseases.
Over the past few years, the scientists involved with these groups have collaborated on some of the most important prion research in the world.
This year, I have had the opportunity to interview some of these scientists, thanks to a journalism award from the Canadian Institutes for Health Research.
What I find remarkable is the breadth of their research projects and the advancements they are making here. What started with one mad cow in Alberta has evolved into an intriguing investigation of a host of neurodegenerative diseases that impact all of us.
Two of the many talented researchers working in this area are Dr. David Westaway and Dr. David Wishart. Both are professors at the University of Alberta, although Dr. Westaway arrived from Britain via the University of Toronto. He is director of the Centre for Prions and Protein Folding Diseases.

Dr. David Wisehart

Dr. Wishart is a bio-informatics specialist and he was the lead scientist on the Human Metabolome Project. He describes prions as “small proteins that we all have. They’re in every living organism as far as we can tell, from yeast all the way to humans.”
The exact purpose of prions is not known, although they are thought to play a protective role. The normal or cellular prion protein is harmless. But sometimes things go wrong.
“Occasionally, if the protein has been mutated or if some external agent modifies the prion protein, it changes shape. Once it changes shape, it starts doing something bad. It actually starts self-assembling into what are called fibrils. And these fibrils start filling up brain cells, leading to brain cell death,” explains Dr. Wishart.
His most recent work uses a variety of techniques, including nuclear magnetic resonance spectroscopy, mass spectronomy and circular dichroism, to observe the prion protein at an atomic scale. The point is to observe the folding process in real time and hopefully find a way to stop it.
“Prions are naturally helical, meaning they look like a bunch of springs stuck together. But, when they misfold,” Dr. Wishart says, “they turn from a helical protein to something that’s called a beta strand or a sheet. And the beta sheet is in a sense a bunch of ribbons. And, in fact, silk is an example of a fibre that is made up almost exclusively of beta sheets. So when prions go from the helical to a beta sheet, they say that they convert or they misfold. This is something that proteins will often do. Normally, the body gets rid of them but, in the case of prions, when they misfold, they aggregate and they actually become toxic.”
It’s this aggregation the gives rise to the term “infectious”. A chain reaction starts and cannot be stopped.

Dr. David Westaway

According to Dr. Westaway, a normal prion or protein is a solo operator. As such, the outside of the molecule is covered with chemical charges that like water.
“The positive and negative charges interact with the water molecule and the protein molecule stays under control. It’s basically dissolved in water and everything is fine and dandy. But, in the context of disease, the proteins start to assemble into aggregates and very often this aggregation property is somehow linked to the fact that the non-water loving part of the molecule gets turned inside out. So, in chemical jargon, the hydrophobic parts of the molecule, instead of being hidden inside, come to the outside. The hydrophobic parts of a molecule like to interact with the hydrophobic parts of other molecules. So you start to get an assembly where the contact between the molecules is a bit more like an oily interface that pushes water out of the way.”
This initiates a domino effect where the proteins build up on one another.
In his lab, Dr. Wishart has been exploring how the prion converts or misfolds and has identified that the tail end of the molecule seems to be the part that gets disrupted or unfolded first.
“It aggregates first in what we call dimers or pairs, then in tetramers or sets of four and then, ultimately, in octamers, or groups of eight molecules. These aggregates are all hung together near the back end from last to about 70 residues. So they produce this insoluable, tightly massed core that can’t be cut… that can’t be broken down. Then these octamers eventually start forming fibrils or threads.”
Dr. Wishart goes on to say that it appears the tetramer and octamer, the groups of four and eight proteins, become highly toxic and form the principle seed that leads to infection.
It’s an exciting discovery that opens up the door to developing a means of stopping the misfolding process.
Dr. Westaway suggests that once you define the misfolding process in molecular terms, “then you can create an anti-molecule to stop it from happening. It’s what is called smart therapy.”
Over in his lab at the Centre for Prions and Protein Folding Diseases, Dr. Westaway has uncovered at least two important pieces to the prion puzzle. These are chaperone and shadoo proteins.
Chaperones are helper molecules. Sometimes when proteins start folding into the right shape, they get stuck, so along comes a chaperone to smooth it out so it goes into the right shape. This is well known in the science of cell biology for proteins inside the cell.
Says Westaway, “The field of chaperones is well known in the science of cell biology for proteins inside the cell. But prion disease is a bit more cutting edge because it seems there may well be chaperone-type activity involved in the wrong way, in helping a good protein go bad. Some of the crucial events of refolding or misfolding may not be going on inside the cell. In fact, they may be going on outside the cell. This is an important frontier that will bear close scrutiny in the coming years.”
A student in Westaway’s lab, Joe Watts, confirmed that this protein exists. It is quite abundant in the brain and has a lot of features similar to normal prion proteins.
“We think that shadoo may be part of a family of a molecules on the surface of brain cells that help brain cells deal with damage,” Dr. Westaway explains. “We have looked at what happens to the shadoo protein in an animal that has a prion disease and we were very surprised to get a very simple answer: that the shadoo protein starts to disappear when animals are replicating prions. It is what we call a tracer. We didn’t expect to make this discovery but, somehow when the protein is disappearing, it’s telling you that prions are replicating.”
He goes on to speculate that in a disease state, the shadoo proteins are being cannibalized by what he calls chopping proteins known as proteases. These get rid of proteins that are no longer needed by the body. What triggers the sudden attack warrants further investigation.
So what is it that brings home all this talk about how prions fold?
Catching Variant Creutzfeldt-Jakob Disease from a mad cow is still a very rare event. The odds in Canada are one in a million. However, there are other protein folding diseases that are all too common: Alzheimer’s, Parkinson’s and Lou Gehrig’s Disease.
The research of Westaway and Wishart goes a long way toward informing discovery on this front.
A provocative article, published in the journal Nature in early 2009, suggests that normal prion proteins, thought to be the protectors of nerve cells, are involved in the killing of brain cells. It appears the misfolded protein aggregates that cause Alzheimer’s bind to the normal prion proteins to initiate the killing.
Dr. Westaway is adamant. “We’ll check that out, and other labs will check that and very likely some important new knowledge will come out of looking at those ideas with a fine tooth comb.” √

New Mite Species Discovered— Grizzly Bears of the Soil World

November 27, 2009

Jim Herbers

The Alberta Biodiversity Monitoring Institute has laid out a grid of 1656 points across the entire province, with each point 20 kilometres apart. The data collected from these sites gives scientists a measure of the changing state of biodiversity in Alberta.
When ABMI researchers collect samples from these sites, they check for various kinds of flora and fauna in the water, in the trees, on the ground, and in the soil. And it’s not uncommon to discover new species.
Of particular interest are mites, tiny invertebrates that play a big role in maintaining the health of our soils.
Jim Herbers, director for information for the ABMI, says,“We’re very proud to report that there are well over 100 new species to Canada that we’ve identified and well over 30 new species to the world.”
These mites are microscopic, but don’t let their diminutive size fool you. Herbers explains, “Some of them are like the grizzly bears of the soil world. They go around and they’re predators. Many of them are frugivores. Many of them eat fungus and mushrooms. And then there are a number of other species that live in the soil that break down the soil organic matter, making sure that it’s turned over and that the nutrients are available for plants to use.”
These new species of mites were identified for the ABMI when scientists at the Royal Alberta Museum analyzed soil samples collected from the grid points