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.
Friday, April 22, 2011
Sunday, April 17, 2011
Busy bees
The problem
THERE’S AN OLD urban myth that scientists don’t know how bees fly, that their wings can’t beat fast enough to keep the bees in the air. In reality, bees beat their wings 200–300 times a second, courtesy of the most efficient metabolic rate in nature. This ultra-efficient energy use makes them the ideal creature for studying the workhorse of biological systems: the metabolism.
This system breaks down large energy storing molecules via a series of chemical reactions, each assisted by enzymes. This creates ATP, the energy-carrying molecule that provides power to all the other functions in the body. The general pathways of this process are common to all higher organisms, so what’s true for bees is true for the animal kingdom.
The researcher
University of Ottawa professor Charles Darveau studies metabolism from a physiological and evolutionary perspective, using bees as a model organism. By comparing metabolic differences across different species of bees and weighing them with physiological differences, he can identify which changes in the series of reactions that make up bees’ metabolisms are important.
The project
Most people are familiar with the honeybee and bumblebee, but there are over 300 species of bees in Ontario alone. Darveau has a wide array of species to make comparisons. In addition to this cross-species approach, he can also look at variations within a species to examine these changes. The goal is to develop a complete characterization of the metabolic process: which enzymes make key changes, what steps bottleneck the metabolic rate, and what kind of system is most favoured evolutionarily.
The key
Darveau’s research is on the fundamentals of physiological change, but it has a number of immediate consequences. Because bees burn energy so quickly and efficiently, their wing muscles can heat up to 40°C. This allows them to flourish in environments where many other pollinators would be unable to survive, making bees an important part of northern ecosystems. Darveau’s fundamental characterization also allows other researchers to determine which species have metabolisms suited to adapting to different conditions, vital in determining the impact of climate change on fauna.
Monday, March 28, 2011
Experimenting with evolution
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.
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.
Saturday, March 12, 2011
Blowing shit up, science style
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.
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.
Monday, March 7, 2011
Beating bromine
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.
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.
Monday, February 28, 2011
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
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.
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