A self-proclaimed “military brat”, Laura was born in Calgary, Alberta but didn’t stay there long. As a kid, she lived in England, New Brunswick, and various cities in Ontario, with the longest stretch in Hawkesbury, Ontario. Continuing this nomadic pattern, Laura has worked at five different universities in her career (now six!). She did her undergrad at the University of Guelph in molecular biology and genetics, and then hopped to Dalhousie for a M.Sc. with Dr. Andrew Roger, studying deep eukaryotic evolution. After a master’s focused on single-celled eukaryotes, Laura switched gears to bacteria and archaea, working with Dr. Elizabeth Edwards at the University of Toronto on microbial systems for bioremediation. During her Ph.D., Laura was a visiting researcher with Dr. Alfred Spormann at Stanford, where she learned to program and worked on closing her first genome. Laura moved back to northern California for her post-doc, joining Jill Banfield’s group at UC Berkeley. Her postdoctoral research was on a heavy-metal impacted aquifer in Rifle, Colorado, using metagenomics and metaproteomics to characterize microbial communities. The Rifle subsurface turned out to be a trove of new organisms and interesting metabolisms, keeping Laura fascinated, and busy!
Laura’s research program in our Department at Waterloo combines techniques and tools she’s gathered during her academic travels. Laura plans to examine microbial community membership and function at contaminated sites, with an eye to identifying new lineages on the tree of life and currently unknown metabolic functions with bioremediation applications. Her particular focus is the microbial communities found in municipal landfills. Laura’s work relies on a combination of total community meta-omic analyses alongside wet-lab microbiology culture techniques. Currently you can find Laura in B1-281, writing grants, getting her lab set up, and interviewing students for the spring and fall.
At home, Laura is usually found hiking, reading, or trying out excessively complicated recipes with her partner Alexander. An avid ultimate frisbee player, you may see her on the fields around the KW area come spring!
As part of the communication component in Dr. Swanson's Advanced Aquatic Ecology Course (Biol 606), graduate students from the Department interviewed several faculty members (students choice!) about their research interests and careers. Our second guest post is by Ashley Stasko (PhD candidate) and Rachel De Jong (MSc student) - both from the Swanson Lab.
Meet Waterloo’s Resident Fish Doctor – Dr. Brian Dixon
He has travelled to more than 48 countries. He speaks four languages. He owns a lot of hats, and every one of them has a story.
Meet Dr. Brian Dixon, the Canada Research Chair in Fish and Environmental Immunology. Dr. Dixon has been a faculty member in the Biology Department at the University of Waterloo for 15 years. His research is centred around understanding the immune systems of fish, which he’ll happily tell you is slippery business!
Which came first for Dr. Dixon - a love of fish or a love of immunology? Well, not quite either. Let’s rewind a few (undisclosed) years to when Dr. Dixon was a budding scientist. He always had a keen interest in animal biology, but during his undergraduate honours project at Wilfred Laurier University he found himself working on epigenetics in flax plants. When he began his MSc at the University of Guelph, he moved away from studying plants to studying vertebrates, but his interest in molecular biology stuck with him. His MSc research investigated cell cycle regulation using mouse cell lines.
After his MSc, he claims that the most important determinant of his future – serendipity - took over. He was unsure if he wanted to begin a PhD, but he was certain that he was looking for new experiences and wanted to look beyond those available in Ontario. A few applications later, he found himself working at a molecular laboratory in Halifax where he was introduced to molecular immunology, a subject he soon fell in love with. He loved it so much, in fact, that after a year of working in the lab he agreed to stay and work longer hours for less pay. In other words, he began his PhD.
As a PhD student, Dr. Dixon worked to improve the understanding of immune responses to cod worm, a parasite that had been harming the cod industry. Cod with heavy loads of this parasite were unable to be sold for human consumption; cod worm was thus a substantial economic threat. Cod worm requires seals as a host for part of its life cycle. Parasite eggs are released through seal feces, which then cycle through a number of invertebrate hosts before infecting cod. The research group that Dr. Dixon was working with targeted seals, trying to find a way to elicit an immune response that would reduce the number of parasite eggs released into the environment. The group made substantial progress, and by the time Dr. Dixon completed his PhD, cod worm was no longer an economic issue. Of course, that was because a moratorium on cod fishing closed the fishery, but the technology had been developed nonetheless and would have worked! The technology has since been applied to population control of both seals and deer, where a triggered immune response causes antibody expression on egg cells, which then are unable to implant in the womb.
After a few international post-doctoral positions, Dr. Dixon decided that fish immunology was where his greatest interests lay (not to mention, he thought it was a strategic choice considering how few fish immunologists existed in Canada). He was hired as a faculty member at the University of Windsor, and started his fish immunology research program. After two years, and with a little prodding from his wife, he decided to dust off his CV and look for a job in a more exciting city - and that’s how he came to be at the University of Waterloo.
Since beginning a research career at the University of Waterloo, Dr. Dixon has had the opportunity to work on many interesting projects that have introduced him to a wide variety of fishes, diseases, people, and countries. He has had students examine detailed protein-protein interactions in the fish immune system, the development of disease-resistant families of fish for aquaculture, and molecular markers in wild fish populations.
One of the most common research applications in the Dixon lab is improvement of fish health in aquaculture settings. Although the Dixon lab does not develop vaccines directly, research results do contribute to disease control by shedding light on the fish immune system. For instance, the lab is currently working toward a better understanding of the immunological processes involved in temperature-dependent diseases. Fish immune systems often shut down at temperatures near the lower end of their tolerance range. As a result, many cold-water specific diseases have evolved, and in a country like Canada this can have very expensive implications for sea-cage aquaculture.
Vaccines are one method for disease control in aquaculture. However, Dr. Dixon explains that vaccines often do not work well in fish because their immune systems respond differently than those of terrestrial vertebrates (for which most of the vaccine research to date has been conducted). Thus, another component of his research program involves aspects of population biology and genetics that help aquaculture facilities develop breeding stocks with higher natural disease resistance. He is currently involved in two such projects– one involving the largest Atlantic Salmon producer in the world - based in Chile - and one involving an organic Chinook Salmon farm in British Columbia.
Dr. Dixon is also hoping to advance the field of fish immunology by developing research tools that will be available to other labs. In order to study the function of cytokine (signalling) proteins in fish immune responses, cytokine-specific antibodies are needed. However, antibodies for fish cytokines are not commercially available for research. Dr. Dixon is working with Cedarlane laboratories to develop and market these antibodies so they will become available to fish immunologists worldwide.
As part of the communication component in Dr. Swanson's Advanced Aquatic Ecology Course (Biol 606), graduate students from the Department interviewed several faculty members (students choice!) about their research interests and careers. Our first guest post is by Samantha Burke, PhD student (Swanson Lab).
UWaterloo crew (Roland Hall, Nelson Zabel, Heidi Swanson), Kluane Lake, YT April 2015
Many of us had a fascination with dinosaurs as we grew up; we also made believe that we were detectives, like Sherlock Holmes or Nancy Drew. Dr. Roland Hall - a professor and palolimnologist - is able to study fossils while also acting as a sleuth.
Paleolimnologists, while not studying large dinosaur bones, do study the fossils of (sometimes ancient) creatures, and other biological and chemical evidence preserved in lake sediments. As a lake ages, it constantly fills in with sediment. Biological and chemical components are preserved as new sediment deposits over old sediment, and this creates a natural archive. Researchers can use this archive as a means to infer environmental conditions and change (e.g. temperature and lake pH) prior to the instrumental record. This is especially useful since any limnological (study of lakes) records are scarce prior to the 1960’s.
Diatoms are an often-studied taxa in Dr. Hall’s lab. Diatoms are unicellular algae that preserve well in the sediment and are very sensitive to their living conditions (having different environmental optima), thus their presence/absence and abundance can tell us a lot about past environmental conditions.
Dr. Hall did not always want to be a limnologist. During his undergrad at Queen’s University, he strived to become a molecular biologist. Although fascinated with this field, he began to grow tired of the amount of effort put forth, only to have experiments fail time after time. Nearing the end of his degree Roland needed to find a half credit in the ecological sciences, so he took limnology. It was in this class that he finally saw all of his previous classes (biology, chemistry, and physics) become integrated. Observing lakes was nothing new to Dr. Hall- his family spent summers cottaging on the Ontario/Manitoba border, where he spent a lot of time fishing, hiking, and casually observing lakes. He had always been fascinated with the mysteries held within, and now he had the tools to start investigating these. After completing a PhD at Queen’s, Dr. Hall took a Post-Doctoral position at the Dorset Environmental Science Centre, and then a Research/Assistant Professorship in Arctic Sweden (an area with no shortage of lakes). Roland came to UW in 1999, and been here ever since.
Many environmental issues have appeared and evolved during Dr. Hall’s research career. During his early career, acid rain and eutrophication were hot topics, but now climate change, energy production (oil sands), land use, and most importantly the increasing human population, are of significant concern.
Dr. Hall and his colleagues have conducted many important studies, but one recent interesting finding does stand out. There is serious concern surrounding the development of the Alberta oil sands. Dr. Hall and his colleagues recently conducted a study on the Peace-Athabasca Delta (200 km downstream of the oil sands) to determine whether they could detect an increase in the supply of contaminants (e.g. metals) since the onset of development. Overall, they found that there was no significant difference in the level of contamination pre- and post-development. This study will act as a stepping-stone, providing pre-industrial baseline metals data. Future research will be conducted further upstream closer to the oil sands.
Other than his work on the Peace-Athabasca Delta, Dr. Hall has students who conduct research in the Hudson Bay Lowlands and the Old Crow Flats; these students are investigating hydrological and ecological linkages. Recently Roland began a collaboration with the Swanson lab to study mercury dynamics through time in Kluane Lake in the Yukon. A crew including Drs. Hall and Swanson were in the Yukon in early April to collect sediment cores through the ice (apparently the trip involved a lot of laughing).
Not everyone is fortunate enough to have a job solving environmental mysteries. It is safe to say that Dr. Hall is passionate about his research, and goes the extra mile in the name of science, even if the extra mile is actually 80 meters of wading (in the buff) through subarctic waters to reach a field site.
Last Thursday night, campus was a hive of activity with the 2015 TD Walter Bean Public Lecture in Environment. Dr. Tom Stohlgren, the 2015 TD Walter Bean Visiting Professor, captivated a live and online audience with his talk, ‘Invasions from Inner Space: Species invasions and Extinction.’ His presentation attracted the largest audience ever for a TD Walter Bean lecture. (Yay, Faculty of Science!)
Tom’s talk (those of us who met Dr. Stohlgren know he does not stand on ceremony and would much rather be called Tom!) touched on many points regarding transport, establishment, and effects of invasive species, as well as possible eradication strategies. A highlight of his talk was the parachuting mice laced with acetaminophen. [Dramatic pause]
The brown tree snake (Boiga irregularis) was accidentally introduced to Guam in the mid twentieth century. The snake quickly started honing in on new and naïve prey – the native bird and lizard species that live on the island. Many native species were decimated or extirpated, but a unique management strategy is now being employed that seems to be working. Acetaminophen – the active ingredient in Tylenol – is extremely toxic to the brown tree snake. How does one deliver Acetaminophen to a wild brown tree snake? In a convenient dead mouse package. The mice are dropped from aircraft and fitted with streamers that help keep them in the tree canopy until they are eaten by a snake. Results have been very encouraging.
With this and other stories of invasions, Tom effectively conveyed to the audience what a massive problem invasive species are, and what we should be doing to mitigate the problem. The facts were sobering, but Tom capped off a particularly alarming part of his lecture with, “I’m not worried, because the NGOS’s (Next Generation of Scientists) are beginning to tackle our problem.”
Tom’s dedication to, and belief in, the talent of new researchers was evident during his visit. He visited graduate classes in Biology, met with grad students across campus, attended student mixers, and was endlessly entertaining at the Thesis Onesie event (his favourite invasive species – the wine grape!). He also engaged school-age children, and spoke with great passion about the importance of outreach and science education. Tom left a lasting impression on all those who he interacted with.
We in Biology feel very fortunate to have had a world-renowned biologist here as the 2015 TD Walter Bean Visiting Professor. His visit has spurred much interest in invasive species research in the department, and inspired students and faculty alike. Thank you, Tom, and thanks to all those who were involved in making his visit such a huge success!
Photo: Dr. Terry McMahon (Dr. Kim Cuddington on twitter in background). Credit: Chandan Vatish.
As many UW Biology folk know, the much-anticipated “Meta” table was installed in the Gleave in late December. Topics of recent hallway discussion include protecting the incredibly soft wood before the glass arrives, the amazingly warm colour(s) of the wood, and the near-miss with the Swanson lab projector (NOTE: use caution while we wait for the new/repaired projector!). Not everyone knows the full story of the Meta table, however.
In 2013, Biology lost two magnificent and much-admired trees - a Dawn Redwood, Metasequoia glyptostroboides, and a gingko tree. Both trees were harvested to make room for the new Science Teaching Complex. While the prevailing sentiment at the time was certainly excitement for the new building, certain department Loraxes wanted to ensure that the felled Metasequoia would be put to good use. Happily, the Biology Metasequoia tree now exists as a stunning pair of matching tables in the Gleave Library. The tables were designed and built from live edge planks in December 2014 by Guelph artist Erik Van Miltenburg, of Metrik Studio. You can see photos of the felled tree and the tables at http://metrikstudio.com/2014/12/06/meta-log/.
So, why all the fuss about this tree and the resulting tables? In 1948, an expedition to China identified living specimens of M.glyptostroboides, which is an ancient tree species known only from fossils that were first described in 1941. Seeds collected from the 1948 expedition were grown into trees at the Arnold Arboretum at Harvard University. Seeds from the trees grown at Harvard were then collected by Ron Eydt and brought back to the University of Waterloo. M. glyptostroboides was native to Canada during the Miocene (~ 23 – 5 MYA) and earlier, but went extinct due to climate change. Our M.glyptostroboides was planted outside Biology shortly after the completion of B2 in 1967. The species is now available from local nurseries and is an example of a "living fossil”. It is sometimes called “Dinosaur tree”.
Although we now could purchase a replacement Metasequoia, many will be pleased to know that Lynn took 63 cuttings of the original tree. One of these cuttings took and is being nurtured in the Biology greenhouse. Unfortunately, after a year of fast growth, the tree is currently looking more than a little worse for wear. Only time will tell whether the tree is a) dead, or b) in a winter dormancy period. Undeterred by minor setbacks, Lynn took yet more cuttings, and at least one of these is doing well. Hopefully, our tree will live on campus once again.
The Meta Table will be dedicated to Andrei Anghel, a third year medical student who graduated from Biomedical Sciences in 2012. He was on Malaysia Airlines Flight MH-17, which was tragically shot down en route from Amsterdam to Kuala Lumpur over Ukraine, July 17, 2014. Andrei is fondly remembered by many of his instructors. The much-used Gleave library Meta table will be a fitting way to remember him.
Mind you, it isn’t a particularly great read, by modern standards. In it you will find a classically Victorian “flair” that can be difficult to get through, and as University of Waterloo’s Prof. Emeritus Dr. John Semple suggested during this year’s ‘Darwin Day’ lecture – you should have a good deal of coffee on hand if you do sit down to read it!
The story of “Charles Darwin, Facts and Fictions,” as told by Dr. Semple, was of a Charles Darwin that many may not have known. A Charles Darwin that was largely disinterested in over-achieving in his studies, rather preferring to collect beetles found in the English countryside, and fascinated by the deeper understanding of geology that was changing how the age of the Earth was understood. This was a portrait of a brilliant thinker, capable companion to the captain of the H.M.S. Beagle (though, not the primary naturalist during the five year voyage), and a quiet family man.
Dr. Semple could also be caught spending time collecting specimens in the countryside during his tenure in the University of Waterloo’s biology department – though few would ever accuse him of being the quiet type. Over a 40 year career, which officially was complete upon his retirement in 2012, John described the cytology, morphology, phylogeny, and taxonomy of asters, goldenasters, and goldenrods of Canada and the United States. With plenty of extra time since retiring, John continues to publish his work at a steady pace (his latest being published February 12, 2015). As the marquee speaker at this year’s Darwin Day celebration, John spoke on Darwin’s time in the field from the perspective of someone who has spent a career in the same vein, personally seeing natural selection in action as he traversed an estimated 500,000 km collecting specimens for his own work. John spoke to the audience with the enthusiasm and care that On the Origin of Species deserves.
The book’s greatness goes beyond its word count. Charles Darwin presented voluminous descriptions of facts supporting evolution by natural selection. Its proponents argued the case for this work only briefly and it was just a short time before any form of debate had evaporated. It stands as one of the most broad theories of biology – as Dr. Semple put it, Natural Selection is a theory, which is a scientist’s word for true. The book set the science of Biology on a course that would revolutionize how we think about the natural world. Evolution by natural selection is a lens through which we can understand our natural world, and on February 12, 2015 the Biology Department was pleased to celebrate the 206 birthday of Charles Darwin, the author of Biology’s truly great book.
For more on the career of Dr. John Semple, a fantastic interview was posted on the UW website just prior to his retirement.
In the future, when borrowing the overhead projector and filling out the form (attached), please check the “RETURNED” box so everyone knows that it has been replaced. We will also be talking with students of Drs. Kendrick, Kovac, Mayfield, and others, to correct this pervasive issue.
The Historical Management Branch of the Biology Outreach Team
Because I am leaving for sabbatical, this blog post marks the end of my tenure as chair of the Biology Outreach Team. I want to thank the team (currently: Trevor Charles, Heidi Swanson, Vivian Dayeh, Rebecca Rooney, Mark Servos, Sue Whyte, Maya D’Alessio, Heather Neufeld) for their dedication to telling our Department’s story in so many ways. The activities we have helped organize, facilitate, and promote include public lectures, Department branding, open houses, twitter (@WaterlooBio), newsletter, blog (you’re here!), updating our building space, and more.
And, as I say goodbye, I am glad to report that our Department Photo Boards have been updated (see above). It is such a relief to have this yearly-ish labour of love behind us. Hopefully future updates will be smooth and timely with Creative Services offering their services to us without charge under their new model.
Importantly, Heidi Swanson will be taking the reigns of the Outreach Team from January onwards. Thanks Heidi!
Heading into 2015, please help the Outreach Team continue to do their job well by letting anyone on the team know when awards are won, key article are published, or other noteworthy stories arise from our day-to-day activities.
Every year in the biology department, the BGSA hosts a holiday door decorating contest. This year the competition was steep, with six labs throwing their hat in the ring to take home the bragging rights that come with having the best door.
The judges roamed the halls of B1, B2 and ESC yesterday morning, deliberating over who brought the goods this year. After an intense debate and much discussion, the winners were announced.
The first place prize basket was awarded to the “12 Days of Fish-mas” door created by the Swanson lab (above). This marks the second win in a row for the Swanson lab, so next year the rest of the department needs to step it up to de-throne the reigning champions.
The second place prize basket was awarded to the Rooney lab’s door (below).
The ecologists really brought the bacon this year, sweeping the coveted top two spots in the competition.
Honourable mentions go to the Rose lab (above) and the Marsden lab (below)!
The van der Meer lab also made an appearance (below), re-using their lobster from last year's contest. Santa is actually a lobster, who flies on a sleigh pulled by mice.
Guest post by Suzie Alexander (Team Director, Waterloo iGEM)
40 students. 8 months. 1 project.
It all starts with an idea.
Picture this: Undergraduate students gathered in various classrooms around the University of Waterloo campus brainstorming. The purpose? To design a novel synthetic biology system that would make a difference. Students bounced ideas around the room, with possibilities including radiation cleanup solutions, bioenergy production, and cystic fibrosis treatments. Ultimately, the Waterloo iGEM team decided on a project born out of Biol 349, a synthetic biology design course offered in the Winter term at UWaterloo. The team took the project, proposed by a Waterloo Biology student, Cody Shirriff, and hit the ground running.
The problem: Antibiotic resistance in MRSA or methicillin-resistant Staphylococcus aureus, a bacterium responsible for difficult-to-treat infections.
The solution: Staphylocide, a mechanism of delivering antibiotic resistance gene silencing.
There are three phases to their design. Deliver, silence, and translate.
The first challenge for the team was to test different silencing mechanisms that would inhibit the expression of the resistance gene in MRSA. The team used mathematical models to compare their data sets and determine the most efficient silencing system. Next, the team looked into ways to deliver the silencing system into a population of MRSA. Bacterial conjugation dynamics were analyzed using two different mathematical models that provided information on the behaviour of the cells over time. Finally, to translate the project into an idea for the marketplace, the team proposed developing an antibiotic resistance ointment that patients could use on their skin to treat MRSA infections.
Putting the idea to the test
With a plan in mind, the team got to work designing constructs (above), running simulations and beginning experimentation. Students were in the lab during the summer and fall months to check their plates and run their gels (below). Did my ligation work? Did my DNA transform into the cell? Maybe I should run one more control…
While completing their project, the team also submitted and characterized many BioBrick parts. BioBricks are standardized DNA pieces and are a result of contributions from the iGEM community.
Fast forward to October and the team gets closer to the infamous Wiki Freeze, the deadline to create a wiki-media website containing the entire project. This required a team effort. Students crowded into the team office (above), which was generously provided by the Department of Biology and Faculty of Science, for a few nights of coding. Keyboards ticked and computer mice clicked as the team worked into the night. The clock struck twelve on Friday October 17th, just in time to put the finishing touches on the Wiki.
On October 30th, around 5 AM, the team gathered in front of EIT (above) to begin their journey to the competition. With their scientific poster in one hand and passport in the other, the team piled into minivans and drove to Boston, MA to present their project at the International Genetically Engineered Machine (iGEM) competition.
With approximately 225 distinguished teams from around the globe set to attend, the Waterloo team was excited! Teams worked on projects to create stable circularized proteins, a bacterial cellulose filter capable of filtering water, and a pheromone-based insect trap. Many more interesting projects were presented! All team projects can be found here.
The team saw great innovation and dedication to the fundamental sciences involved in creating exceptional synthetic biology projects. The Waterloo team achieved Gold Standing for the quality of their project. Ninety of the 225 teams received Gold Standing, three of which were Canadian teams. Where Waterloo dominated the competition was the mathematics.
The team won the special award Best Model for the simulation of their system.
All in all, the competition was an excellent opportunity for students to take ownership of a research project research project and see it through from beginning to end.
The future of the team
So what’s next for the team? A new competition year means a new project and team. Got a great idea? Waterloo iGEM wants you! The team is currently recruiting Senior Leaders and will also be recruiting in January 2015. Keep an eye on our website for all openings! You can also find them on Facebook and Twitter.