Membrane madness

What’s he building in there?

The problem
ONE IMPORTANT STEP in water treatment is filtration. Nobody wants little gritty pieces of dreg or oily bits of gunk in their drinking water. River water is passed through membranes in water treatment plants which block oversized contaminants from going any farther. Making membranes with large surface areas, but with small enough pores (micro- or nanofiltration), is possible by casting polymers into a film. These films are either hydrophilic (water-loving) or hydrophobic (water-hating).
It turns out that most contaminants are oily, hydrophobic gook, and since “the enemy of my enemy is my friend” the contaminants are very likely to bury themselves in the hydrophobic membrane to hide from the water. They can’t get through at first, but eventually contamination degradates the membrane’s performance.
On the other hand, hydrophilic membranes have their own set of problems. The contaminants don’t like the membrane, don’t bury themselves in it, and so degradation is slower. But hydrophilic membranes tend to be significantly weaker than hydrophobic ones, and so will often break during water treatment.

The researcher
Takeshi Matsuura is a chemical engineer at the University of Ottawa who develops modified membranes that can improve the distillation and filtration processes. In particular, he is interested in modifying surfaces using large macromolecules that can be attached to membranes.

The project
Filtration science would really benefit from filters that are strong, and that do not rapidly degrade. Hydrophobic and hydrophilic membranes each have their drawbacks, but by combining them, Matsuura hopes that he can get the best of both worlds.

The key
While other scientists cast a strong hydrophobic membrane, and later modify it by grafting hydrophilic polymers on top to make a protective coating, Matsuura thinks this is too slow (and costly). He mixes the hydrophilic and hydrophobic polymers together in solution and then casts them. As the water evaporates, the polymers naturally separate. Matsuura is left with a single membrane with a strong bottom layer and protective coating on top. In just one step, he gets a surface modified film that has the strength of a hydrophobic filter, but degrades slowly like a hydrophilic filter. That really is the best of both worlds.

Experimenting with evolution

What’s he building in there?

The problem
LOOK AROUND YOU. The world is brimming with the diversity of life. The great assortment of species is so much a part of our world that we take it for granted. It’s easy to say that diversity results from the theory of evolution and be done with it. But why is there such a wide gamut of life and how does diversification actually unfold? The question isn’t ‘Does evolution happen?’ but rather ‘How does evolution happen?’
When we look back in time we see that evolution has been punctuated by bursts of spectacularly rapid diversification during which many new species suddenly appeared. This process (called adaptive radiation) is very fast compared to the usually steady march of evolution, but it’s still too slow for scientific study.

The researcher
Rees Kassen is the University of Ottawa’s Research Chair in Experimental Evolution. When it comes down to it, Kassen wants to know the answer to a straightforward question: Why are there so many different kinds of living things in the world?

The project
To study the process of biodiversity, Kassen needs to watch evolution take place in his laboratory. He can do this by studying microbes. Since microbes live for only a short time, Kassen can observe changes that occur over generations in only a matter of days. This makes microbes an ideal model for studying adaptive evolution.

The key
When Kassen places colonies of microbes in a beaker of nutrient-rich broth, the colonies choose to live at the centre where there’s the most food. Early on the colony is smooth and round. After a while, resources become scarcer and competition becomes more fierce. Some of the colonies realize that if they stop fighting for control of the centre and move to the fringes they will have an ecological niche all to themselves. And so some colonies fall to the bottom of the beaker where they evolve into brush-shaped colonies. Others rise to the top where they change into very wrinkly colonies.
The new ecosystem offers the microbes opportunities to specialize and to a certain extent determines the form of the diversity. On the other hand, it is competition for resources that drives the specialization. Kassen suspects that these two factors cause adaptive radiation to occur quickly and helps explain why diversification happens in bursts.

Blowing shit up, science style

What’s she building in there?

The problem
RECENT IMPROVEMENTS IN technology have allowed scientists to accelerate electrons in ways that create high-energy, extremely bright, and short laser pulses. Before the invention of these lasers, scientists could not study how high-intensity ultraviolet and X-ray light interacts with matter. Now that such lasers exist, everybody’s dying to know what happens when you blast stuff with short, high-intensity, high-energy laser beams.
The obvious answer is that you blow shit up, and that’s cool and all, but the potential applications of these beams are much greater than that. High-intensity ultraviolet and X-ray lasers might be able to image materials that are currently challenging to study. But before scientists can use these lasers, they have to understand this completely unexplored area of light-matter interaction.

The researcher
Lora Ramunno studies computational photonics at the University of Ottawa. Using her parallel supercomputer (equivalent to about 600 desktops), Ramunno studies nonlinear optical imaging and the interaction between matter and intense laser beams.

The project
Ramunno decided to look at how tiny clusters of matter interact with a high-intensity laser pulse by simulating each and every one of the atoms. When atoms are hit by a photon of light there is some probability that they will absorb the photon and eject one of their electrons. This leaves the atom as a positively charged ion. At every step of her simulation, Ramunno’s computer program must stop and evaluate the quantum probabilities that give these rates before it can move on to the next step.

The key
Before the laser blows up the cluster of atoms, electrons escape from their atomic orbitals and the cluster becomes a plasma. The first few electrons that are ejected simply fly away and leave behind a charged cluster of ions. However, the electrons emitted later find themselves in this charged environment that they can’t escape from.
These electrons are free to zip around, but can’t leave the cluster, and from time to time they collide with unionized atoms. They usually don’t have enough energy to free an orbiting electron from the atom they collided with, but they can excite one of the atom’s electrons up to higher energy. Ramunno found that if a second free electron collides with the same atom that had been energized by an earlier collision, it has a better chance of releasing the orbiting electron. When pairs of free electrons work together like this the cluster charges more quickly than if the laser didn’t have any help and so the cluster explodes in a shorter period of time. Ramunno calls this process Augmented Collision Ionization.

Beating bromine

What’s he building in there?

The problem
THE QUANTUM WORLD works quite contrary to our own concrete and everyday existence. When we are first taught about atoms, we are shown a solar system-like model with electrons orbiting the nucleus like planets orbit the sun. But physicists have known for nearly a hundred years that this picture is too simple.
Electrons are both a particle and a wave at the same time. So electrons shouldn’t just be thought of like planets, but also like a vibrating guitar string. These so-called wavefunctions can be experimentally probed and scientists understand them very well. But for more complicated molecules—combinations of more than just one atom—it becomes very difficult to directly see that theory and reality are the same.

The researcher
On top of being a professor in the physics department at the University of Ottawa, Paul Corkum heads the Attosecond Science Laboratory at the National Research Council. He is renowned for using a laser pulse to accelerate an electron out of its atom, turn the electron around, and drive it back into its orbital. When the electron recollides with the atom, short bursts of light are given off that tells Corkum about the environment in which the electron settles.
Using very short laser pulses, Corkum was able to take a high definition snap shot of the quantum cloud that defines where the electrons are around the atom.

The project
Taking high-resolution pictures of quantum orbitals is one thing, but filming a movie of the wavefunctions during a chemical reaction is another altogether. And yet, this is exactly the challenge Corkum set for his lab. Using the same technology he invented for imaging orbitals, Corkum wanted to watch a single molecule of bromine disassociate into two separate bromine atoms.

The key
Corkum blasted bromine gas with blue light. Blue is exactly the right colour to excite bromine molecules. Immediately after the blue light excites the bromine, the short laser pulse that knocks an electron out and drives it back in is shot at the gas.
Corkum saw that the blue light had not excited all the bromine molecules. This turned out to be an advantage since the resulting bursts of light from the recollision of the excited and the non-excited molecules mixed into beats.
The non-excited bromine acted exactly like a tuning fork: Corkum could use the beating between the bursts of light from molecules of bromine and from excited, separate atoms to see the difference between the two.

Mighty mice meet their match

The problem
IT’S AN EVOLUTIONARY arms race out there. Viruses that infect organisms evolve to evade the immune systems of their hosts. Every time that happens, host animals like us must create strategies to battle the infections and diseases they cause.
For example, retroviruses are a family of viruses that have an RNA genome. While it’s often said that the fundamental building block of life is DNA, the genetic material of these viruses is RNA. Retroviruses produce DNA from their RNA and insert it into a host’s genome, changing the host forever. From then on, the virus replicates with the host cell’s DNA.
Our immune system protects us against most retroviruses. Only the human immunodeficiency virus (HIV) and the human T-lymphotropic virus (HTVL) have been shown to cause diseases in humans. Both have evolved ways to get around our immune defences.

The researcher
Marc-Andre Langlois does his research for the Faculty of Medicine at Roger Guindon Hall on the General Hospital Campus. He studies how retroviruses replicate and infect cells—specifically how cells are able to protect themselves against retroviruses.

The project
One of the best armaments our cells have is a family of proteins called APOBEC3. It’s still a mystery how they do it, but APOBEC3 proteins can completely deactivate all retroviral invaders by mutating the attacking DNA before it can be inserted into the host’s genome. The exceptions are HIV and HTVL. Those two have out evolved our protein parapets.
While primates have seven APOBEC3 proteins, mice have only one. This really interests Langlois. The mice APOBEC3 protein is more general than any of our seven. However, even mice can be infected by retroviruses. One of their versions of HIV is called AKV.

The key
Langlois was able to observe the arms race between AKV and the mouse APOBEC3 protein. Mice with diverse abundances of APOBEC3 were better at restricting AKV than mice with any specific form of APOBEC3. They can mutate (and so deactivate) more variations of the retrovirus. Langlois concludes that, since APOBEC3 stops infections by mutating the attackers, it pressures AKV to evolve. Because the mice’s own weapons against AKV cause it to mutate at an exaggerated rate, a broad set of deterrents provides for the best defense against such a varied viral foe.

Miniscule monsters

What’s he building in there?

The problem
Genomicists have a serious bias toward “model” organisms. Model organisms are species that have historically been well studied. Fruit flies, yeast, zebrafish, and mice are examples of model organisms. So are humans.
But these model organisms are each just some leaf on a random twig of the tree of life. Scientists are only beginning to realize the true extent of biodiversity and the staggering variety of differing genes and structures that make up genomes.

The researcher
Nicolas Corradi studies comparative genomics, which means that he sequences organisms’ genomes and then compares their genes and structure to those of other species. Corradi’s lab in the biology department at the University of Ottawa focuses on unicellular eukaryotes, single-celled micro-organisms that harbour curious genomes in their nuclei.

The project
Corradi’s favourite eukaryotes are microsporidia, parasitic unicellular fungi. These little monsters are highly adapted for infecting host cells. They are opportunistic bugs that steal everything they need to survive from their host. In fact, the only time microsporidia spend outside of a host cell is as spores, scouring to invade other cells.

The key
Corradi sequenced the genome of the microsporidia Encephalitozoon intestinalis. This particular microsporidia has the smallest nuclear genome of any known organism. It is made of only 1,800 genes (1,500 times smaller than the human genome and 20 per cent smaller than the next smallest genome ever sequenced).
Why do they have such small genomes? Because these microsporidia are marauding picaroons. They don’t do anything they don’t have to. They steal so much from their hosts that they have shed every gene but the bare minimum needed to function.
Evolutionarily speaking, it is easier to lose genes than to gain them, so these microsporidia are extremely adapted for their parasitic lifestyle. Their genome is so compact that Corradi believes it may represent the limit for a fully functional genome.

Digital drugs

What’s he building in there?

The problem
IT IS POSSIBLE to cure certain cancers by surgically removing the tumors, but this requires that every single cancer cell is extracted. If any cancer cells remain, or if they spread to further, undetected sites, only remission has been achieved—not a complete cure.
Therefore, tracking surviving cancer cells is vitally important. Given the opportunity, they will grow into deadly new tumors. Unfortunately, treatments that can deal with remaining cells, like radiation or chemotherapy, indiscriminately kill cancer cells and healthy cells alike, making the treatments brutal on the body. Targeted therapies are at the forefront of cancer treatment.

The researcher
In the Department of Chemistry, professor Maxim Berezovski has a laboratory that is, in many ways, obsessed with selectivity. In one project, Berezovski studies separation techniques that can teach him about biochemical reaction rates. In another, he isolates biomarkers from cells. In yet another, he marks cells of one type without marking any of the others. The flags he uses to mark cells are called aptamers.

The project
Aptamers are short polymers of nucleic acids that bind to specifically targeted molecules. In many ways, researchers can use them as synthetic artificial antibodies. Berezovski builds them from little chunks of DNA to target the surface of different cells, in particular cancer cells. The selectivity of aptamers makes them perfect for marking or attacking cancer cells while ignoring the healthy ones.

The key
Berezovski proposes that once a tumor is surgically removed, a cocktail of aptamers can be specifically designed for those individual tumor cells. Tumors that reappear are actually clones of the original tumor. This means that the personal recipe of aptamers for the original tumor could be kept as a digital record in case of recurrence. Since there is no need to keep the actual aptamers, Berezovski refers to this record as a digital drug.
The digital drug could be used to produce a personalized mixture of aptamers that will target clones of the original tumor. Doctors could then attach labels to the aptamers to track cancer cells that escaped surgical removal or to identify new tumors. The selectivity of aptamers could even direct the delivery of toxins or medicine specifically to the tumor, allowing for a more finite cancer survival rate.

Do academics dream of electric sheep?

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.

Energy enthusiasts

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.

Tanning turtles

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.