Science Journalism

What’s he building in there?

The problem
WHO KNOWS WHAT other people dream of? Unless you’re a character in Inception, your dreams are for you and you alone. That’s good for you if your dreams involve your best friend’s girlfriend, but bad for scientists who want to study dreams using the scientific method.
Since dreams are not directly observable, you have to collect thousands of dream reports and depend on the reliability of the subjects’ recollection in order to systematically study their content.
To make matters worse, each of the dream reports must be analyzed. To do this, an expert judge must evaluate the content and code the accounts into a set of rankings. Say you want to study emotional content, you have to go through each report and rank how positive or negative the emotions in a dream were.
Not only can the subjects distort the research by failing to perfectly recall the dream, but human bias during coding is virtually unavoidable.

The researcher
University of Ottawa’s Joseph De Koninck studies what our minds are busy doing while we sleep. He studies the (usually more negative than positive) emotions of dreaming, and is interested in how these emotions develop throughout the dreams. As a dream psychologist, De Koninck must continually work with human error introduced during the coding process.

The project
What if researchers could eliminate the need for a human judge altogether? Computers can be taught to identify the level of emotion in a written text. This sort of Artificial Intelligence uses algorithms that can be trained from databases of reports and their corresponding rankings by human judges. The computer model uses individual words and the reoccurrence of words throughout the text to shift rankings and take into account words like “not” that flip the meaning.
Most importantly for De Koninck’s research, the computer algorithm can follow the evolution of rankings as dreams progress. By quickly ranking many accounts, it can give statistical information on the evolution of dreamers’ emotions.

The key
The computer program has the possibility to agree with the human judge 65 per cent of the time, and was hardly ever worse than a ranking from the human judge. That’s quite good considering that human judges only agree 60–80 per cent of the time. With such good agreement, these electronic judges could be used to quickly mine the huge number of dream accounts available. De Koninck wouldn’t have to rank each one individually or worry about human bias—and that sounds like a dream come true for scientists.

What’s he building in there?

The problem
THE TRANSPORT AND storage of energy is one of the main challenges of life. Creatures hunt and consume each other, stealing nutrients. Life constantly juggles energy: lifeforms evolve in order to change energy from one form to another, and store it away in their bodies. In particular, carbohydrates and fats are Mother Nature’s biological batteries.
Modern society has the same set of problems. We fight over resources; we mine fuels, like coal and petroleum; we extract energy from dams and wind farms. Then we store energy on power grids, in batteries or in the fuel tanks of our cars until we need it.
But humanity’s current sources of energy can’t sustain our needs. We need to access large amounts of energy that have been efficiently stored.

The researchers
André Tremblay and Marc Dubé are a pair of professors at the University of Ottawa whose research interests overlap when it comes to biofuels.

The project
Biodiesel is made from fatty acids produced from vegetable oils, animal fats, algae, or even waste grease. Amazingly, biodiesel can be used in current diesel engines without any modifications.
But the production of biodiesel is a remarkably difficult venture. What’s needed is a simple, single-step process that can continuously produce high-purity fuel without leaving residual gunk in the resultant.
Tremblay and Dubé have been working on a process to do just that.

The key
The reaction that turns waste grease into biodiesel is called transesterification. This reaction occurs at the surface of oil droplets mixed in alcohol. The transformation of oil into biodiesel is fast at first, when there’s very little fuel in the alcohol, but becomes less and less efficient as the alcohol becomes saturated with biodiesel.
To counter this, Tremblay and Dubé purify the results as the reaction occurs rather than after it. The oil flows through a reactor pipe. The pipe is formed by a ceramic membrane with tiny pores too small for the droplets to escape through. The biodiesel, on the other hand, can per- meate the reactor membrane easily.
What’s left? Lots of oil droplets in the reactor that are continually undergoing efficient transesterification on one side of the membrane and high purity biodiesel on the other.

What’s she building in there?

The problem
NORTHERN MAP TURTLES (that’s Glyptemys geographica for those of you who like Latin) are found in northern states and southern Ontario and Quebec. They hibernate through the coldest parts of the year in communal groups on the floor of lakes and rivers. They don’t come up to breathe for the entire hibernation. Since they spend a lot of time in the sun during the summer, Map Turtles like areas that have fallen trees or other objects to bask on near large bodies of water. Basking sets their body temperature, but the more important question is just how energetically vital is sun-basking to these northern turtles?

The researcher
University of Ottawa professor Gabriel Blouin-Demers studies the physiological ecology of reptiles. He integrates laboratory experiments with field observations to better understand how phenotypes or biological traits—especially behavioural—are set by reptiles’ physiologies.
Blouin-Demers hopes that the research coming out of his laboratory can contribute to reptile conservation. Reptiles are in fact the most threatened vertebrates in Canada.

The project
The northern Map Turtles that Blouin-Demers studied were from Lake Opinicon (100 km south of Ottawa). He implanted thermometers into the abdomen of juvenile turtles to continuously monitor their body temperature for two years. Using their body temperature, Blouin-Demers can calculate the turtles’ metabolic rates to estimate how important thermoregulation is to the energy available for growth and reproduction.

The key
Blouin-Demers determined that basking has a huge impact on the energy budgets of northern Map Turtles. The turtles spend three-quarters of their day basking in the sun.
More importantly, he found that if northern Map Turtles don’t bask, their metabolic rate slows by as much as a third. This amounts to a huge loss in available energy for growth, reproduction, and everyday turtlely business. Despite the clear importance of basking, Blouin-Demers discovered that the turtles bask a little less than the theoretically expected optimal amount. Blouin-Demers speculates that this is because basking is a mutually exclusive behaviour: Turtles can’t multi-task while basking. They bask on land but do all their other important activities (like foraging and mating) in the water, so they must compromise.

What’s she building in there?

The problem
OIL IS EVIL. Humanity go green now. Solar panels suck. Apocalypse therefore inevitable.

The researcher
Karin Hinzer is the Canada Research Chair in Photonic Nanostructures and Integrated Devices. In 2007, Hinzer founded SunLab at the University of Ottawa, and since then has collaborated with many industrial partners. Just this year, a collaborative effort earned SunLab the 2010 Canadian Innovation Award.

The project
One such joint project is the Advancing Photovoltaics for Economical Concentrator Systems (APECS). APECS is a project that demonstrates the use of innovative technology in a practical setting. In January, Hinzer will install experimental solar panels on the roof of the Sports Complex parkade here at the University of Ottawa and at a sister site in northern California.

The key
Hinzer will use efficient gallium/arsenide(Ga/As) based multi-junction solar cells in the APECS project. Traditional silicon solar cells only absorb a small range of photons efficiently, while multi-junction cells absorb over a broader spectrum and so increase the efficiency. However, these solar cells are not cheap. APECS seeks to bring the cost down in a couple of ways.
First, Ga/As cells are usually grown on expensive germanium sheets, but Hinzer is testing Ga/As cells grown on much cheaper silicon sheets. Secondly, Hinzer is reducing the cost by getting more light to a smaller area. The way Hinzer does this is analogous to a kid using a magnifying glass to turn a normal sunbeam into a highly focused death ray for burning ants. But instead of using normal lenses, Hinzer uses waveguides that have been tested in SunLab under an artificial sun. Since the waveguides are much lighter than traditional lens systems, it won’t need the same kind of heavy-duty foundation that other big solar panels require. Therefore, it can be set on rooftops.
But having an efficient solar cell is only half the battle. If there’s only a little light shining on the solar panels, they won’t produce much electricity, no matter how efficient they are. To get around this, the modules will automatically track the motion of the sun to maximize their efficiency throughout the day. Solar panels work best when the sun’s rays are perpendicular to their surface. This is why APECS will have one station here in Ontario and a second one in California. Each panel will have an associated weather station, which Hinzer will use to compare any differences in efficiency to differences in latitude and weather.

What’s he building in there?

The problem
HAS IT EVER amazed you how quickly children seem to recover from injuries? Tumbles and falls are just part of everyday play. But that’s not what it’s like for adults—or grandparents, for that matter. Falling or breaking a bone can be a dangerous event, because injuries are not easily healed.

Why is that?
The foundation of the muscles’ repair system is a particular group of stem cells called satellite cells. Unlike most cells in the body, stem cells don’t have a unique type. Instead, they have the ability to transform into any specialized cell that is required by the body. This talent allows them to regenerate injured tissue by replenishing the old and damaged cells.
But satellite cells aren’t as industrious in adults as they are in children. In fact, their activity diminishes as we age. They’re still in the body, but if modern medicine wants to harness them for directed muscle repair, the stem cells will require stimulation.

The researcher
Dr. Michael Rudnicki is the director of the Regenerative Medicine Program and the Sprott Centre for Stem Cell Research at the Ottawa Hospital Research Institute. His laboratory researches the molecular mechanisms that control stem cells during tissue regeneration.

The project
One of Rudnicki’s special interests is the function of stem cells in adult skeletal muscle—the muscle attached to bones by fibrous tendons.
Satellite cells may be the foundation of the muscles’ repair system, but they certainly don’t work alone. Ridnicki’s work stresses that myogenesis, the formation of muscle tissue, requires coordination between many different cells.

The key
A key player in myogenesis is a group of cells called fibro/adipogenic progenitors (FAPs). Rudnicki found that in healthy muscle, FAPs are dormant, but, in the event of acute muscle damage, they rapidly multiply.
That’s because FAPs are the distress beacon that signal the satellite cells. Rudnicki’s research shows that FAPs encourage the satellite cells to get active and to fuse with damaged muscle fibres or produce new fibres entirely. FAPs do this by establishing a specialized environment in the damaged muscle that facilitates the satellite cells. In myogenesis, FAPs stimulate satellite cells to regenerate muscle. In children, FAPs stimulate satellite cells and then are free to leave once myogenesis is complete; however, in elderly muscle, FAPs become firmly engrafted to the damaged site, and can no longer move on to the next injury.

What’s she building in there?

The problem
IMAGINE YOU’RE AN anaerobic bacteria. You’ve swam around eating up nutrients, but you can hear that biological clock ticking. It’s time to have your very own bouncing baby bacteria. But how do you guarantee that you and your daughter turnout exactly the same? Of course, your DNA will be unchanged, but what about everything else? What molecular interactions ensure that your daughter is exactly the same size as you—that you divide symmetrically at the midpoint?

The researcher
Natalie Goto, an associate professor at the University of Ottawa’s Chemistry Department, sees protein as the machinery of life. Proteins bind molecules together in very specific ways and their interactions act as a clock, telling cells what phase of life they are in. Goto is interested in how the shapes of proteins mediate the interactions between them.

The project
In order to divide symmetrically, rod-shaped cells must construct a new wall at their exact midpoint. In bacteria, this process is controlled by the Min family of proteins.
The protein called MinC inhibits wall formation, but only when it is binded with its sister protein, MinD. MinD likes to moor on the cell wall. MinC and MinD have an affinity for each other.—whenever MinC floats by a MinD, it cuddles up and forms a complex that stops the cell from growing a dividing wall.
But there’s one last member of the Min family: MinE. MinE continually pushes its sister proteins around. MinE shoulders its way between MinC and MinD, displacing MinC. Afterward, MinE leaves MinD, forcing it to dissociate from the wall and driving it from the middle toward the pole of the cell. With no MinC and MinD left at the centre to stop the formation of a new wall, the cell divides.

The key
MinE has a special site in the cell that it uses to breakup MinC and MinD and push them from the centre. Goto found that MinE folds to keep this binding site wrapped inside itself. Only when MinE opens itself up can the site disunite the other pair of proteins. Goto suspects that by keeping the binding site inaccessible, MinE can specifically focus on chasing its sister proteins from the centre. By pushing MinC and MinD duos from the centre and into the poles, MinE frees the cell to form a new wall and divide symmetrically.

What’s he building in there?

The problem
INDUSTRIAL NATIONS EMIT countless millions of tons of carbon dioxide (CO2) into the atmosphere every year. Coal combustion produces approximately a third of all that pollution and there is an immediate need to reduce emissions. One controversial idea is to bury the emissions deep in the ground before the CO2 can escape into the atmosphere and contribute to the greenhouse effect.
But you can’t just bury gas. You have to capture it first. Unfortunately, current methods of scrubbing CO2 out of a coal plant’s exhaust would require at least a quarter of all the energy produced by the power plant. It’s a prohibitively expensive procedure.

The researcher
Tom Woo is a researcher in the the Department of Chemistry and Centre for Catalysis Research and Innovation at the University of Ottawa. Woo specializes in molecular simulations and uses computer algorithms to model chemical systems at the molecular level. His simulations give fellow chemists insight into their experimental results and point them toward potential new designs for engineering materials.

The project
Compounds called metal-organic frameworks are special crystals of metal ions linked together by organic molecules. They are special because they can form very porous structures. In fact, these nanoporous materials can selectively capture CO2 molecules in their pores and hold the greenhouse gas trapped there. The rest of the combustion exhaust would float by and the CO2 would be left, filtered out of the gas.
But there’s one problem: the energy binding the CO2 to the pore is a little too weak. The material currently captures water vapour better than CO2. If the interaction trapping gas can be increased and the material made to not bind water, then nanoporous materials could be the short term solution to reducing carbon emissions.

The key
In order to design nanoporous material that better imprisons CO2, chemists must first understand the forces that hold the pollutant gas in the pore cavity. Woo’s simulations show that the forces responsible for keeping the CO2 captured are almost entirely made up of dispersion forces—a type of force that is weaker than most chemical bonds.
Woo believes that future materials can be designed to replace dispersion forces with stronger electrostatic forces. Using a stronger force ensures that the CO2 stays securely imprisoned while discouraging the seizure of water. Nanoporous materials engineered to use electrostatic interactions to selectively bind CO2 to their cavities would be an important step forward in carbon capture technology.

What’s he building in there?

The problem
HEART DISEASE IS a blanket term for any illness that causes the cardiac muscles to lack circulation (coronary heart disease) or to weaken (cardiomyopathy). Traditional medicine can only help patients cope with a weakened heart. However, techniques in cell therapy may one day allow doctors to direct special cells to regenerate tissue and repair heart damage through stem cell transplantation.
Unfortunately, stems cells are hard to come by and their use in clinics is strictly regulated. To make matters worse, cells taken from patients with cardiovascular disease are often dysfunctional. There is a desperate need for alternative cell therapies for tissue regeneration.

The researcher
Erik Suuronen is the director of the Cardiovascular Tissue Engineering Lab at the University of Ottawa Heart Institute. Suuronen wants to use stems cells and tissue engineering to treat heart disease. He hopes that one day these cell therapies will allow patients to regenerate new muscle and blood vessels rather than live their lives with chronic disease.

The project
Therapeutic cells already exist in the body, called progenitor cells. Rather than transplanting cells to the weakened muscle, Suuronen’s research aims to attract the body’s own progenitor cells to perform the repair and cause tissue regeneration. Normally, only a small number of these cells reach the damaged tissue, but if the target site could be encouraged to attract more of them then the progenitor cells would mobilize to repair and regenerate damaged tissue.

The key
Suuronen has developed a matrix of collagen (collagen is a common extracellular protein) and a complex sugar called sialyl LewisX. Sialyl LewisX instructs the progenitor cells to attract more therapeutic cells and regenerate the damaged tissue while the collagen acts as a “smart” scaffold that supports them during the repair.
Suuronen injected the enhanced matrix into the thigh muscles of rats with damaged blood vessels and dying muscles. The enhanced matrix recruited progenitor cells from the rats’ bone marrow into the bloodstream, leading them to the damaged site. The recruited cells then grew into new blood vessels and galvanized muscle regeneration. By successfully stimulating new muscle growth to replace lost tissue, this research suggests that heart damage could one day be repaired through cellular therapy.