Tag Archives: University of Toronto

University of New Brunswick (Canada), ‘sun in a can’, and buckyballs

Cutting the cost for making solar cells could be a step in the right direction for more widespread adoption. At any rate, that seems to be the motivation for Dr. Felipe Chibante of the University of New Brunswick  and his team as they’ve worked for the past three years or so on cutting production costs for fullerenes (also known as, buckminsterfullerenes, C60, and buckyballs). From a Dec. 23, 2015 article by Michael Tutton for Canadian Press,

A heating system so powerful it gave its creator a sunburn from three metres away is being developed by a New Brunswick engineering professor as a method to sharply reduce the costs of making the carbon used in some solar cells.

Felipe Chibante says his “sun in a can” method of warming carbon at more than 5,000 degrees Celsius helps create the stable carbon 60 needed in more flexible forms of photovoltaic panels.

Tutton includes some technical explanations in his article,

Chibante and senior students at the University of New Brunswick created the system to heat baseball-sized lumps of plasma — a form of matter composed of positively charged gas particles and free-floating negatively charged electrons — at his home and later in a campus lab.

According to a May 22, 2012 University of New Brunswick news release received funding of almost $1.5M from the Atlantic Canada Opportunities Agency for his work with fullerenes,

Dr. Felipe Chibante, associate professor in UNB’s department of chemical engineering, and his team at the Applied Nanotechnology Lab received nearly $1.5 million to lower the cost of fullerenes, which is the molecular form of pure carbon and is a critical ingredient for the plastic solar cell market.

Dr. Chibante and the collaborators on the project have developed fundamental synthesis methods that will be integrated in a unique plasma reactor to result in a price reduction of 50-75 per cent.

Dr. Chibante and his work were also featured in a June 10, 2013 news item on CBC (Canadian Broadcasting Corporation) news online,

Judges with the New Brunswick Innovation Fund like the idea and recently awarded Chibante $460,000 to continue his research at the university’s Fredericton campus.

Chibante has a long history of working with fullerenes — carbon molecules that can store the sun’s energy. He was part of the research team that discovered fullerenes in 1985 [the three main researchers at Rice University, Texas, received Nobel Prizes for the work].

He says they can be added to liquid, spread over plastic and shingles and marketed as a cheaper way to convert sunlight into electricity.

“What we’re trying to do in New Brunswick with the science research and innovation is we’re really trying to get the maximum bang for the buck,” said Chibante.

As it stands, fullerenes cost about $15,000 per kilogram. Chibante hopes to lower the cost by a factor of 10.

The foundation investment brings Chibante’s research funding to about $6.2 million.

Not everyone is entirely sold on this approach to encouraging solar energy adoption (from the CBC news item),

The owner of Urban Pioneer, a Fredericton [New Brunswick] company that sells alternative energy products, likes the concept, but doubts there’s much of a market in New Brunswick.

“We have conventional solar panels right now and they’re not that popular,” said Tony Craft.

“So I can’t imagine, like, when you throw something completely brand new into it, I don’t know how people are going to respond to that even, so it may be a very tough sell,” he said.

Getting back to Chibante’s breakthrough (from Tutton’s Dec. 23, 2015 article),

The 52-year-old researcher says he first set up the system to operate in his garage.

He installed optical filters to watch the melting process but said the light from the plasma was so intense that he later noticed a sunburn on his neck.

The plasma is placed inside a container that can contain and cool the extremely hot material without exposing it to the air.

The conversion technology has the advantage of not using solvents and doesn’t produce the carbon dioxide that other baking systems use, says Chibante.

He says the next stage is finding commercial partners who can help his team further develop the system, which was originally designed and patented by French researcher Laurent Fulcheri.

Chibante said he doesn’t believe the carbon-based, thin-film solar cells will displace the silicon-based cells because they capture less energy.

But he nonetheless sees a future for the more flexible sheets of solar cells.

“You can make fibres, you can make photovoltaic threads and you get into wearable, portable forms of power that makes it more ubiquitous rather than having to carry a big, rigid structure,” he said.

The researcher says the agreement earlier this month [Nov. 30 – Dec. 12, 2015] in Paris among 200 countries to begin reducing the use of fossil fuels and slow global warming may help his work.

By the way,  Chibante estimates production costs for fullerenes, when using his system, would be less that $50/kilogram for what is now the highest priced component of carbon-based solar cells.

There is another researcher in Canada who works in the field of solar energy, Dr. Ted Sargent at the University of Toronto (Ontario). He largely focuses on harvesting solar energy by using quantum dots. I last featured Sargent’s quantum dot work in a Dec. 9, 2014 posting.

Quantum teleportation

It’s been two years (my Aug. 16, 2013 posting features a German-Japanese collaboration) since the last quantum teleportation posting here. First, a little visual stimulation,

Captain James T Kirk (credit: http://www.comicvine.com/james-t-kirk/4005-20078/)

Captain James T Kirk (credit: http://www.comicvine.com/james-t-kirk/4005-20078/)

Captain Kirk, also known as William Shatner, is from Montréal, Canada and that’s not the only Canadian connection to this story which is really about some research at York University (UK). From an Oct. 1, 2015 news item on Nanotechnology Now,

Mention the word ‘teleportation’ and for many people it conjures up “Beam me up, Scottie” images of Captain James T Kirk.

But in the last two decades quantum teleportation – transferring the quantum structure of an object from one place to another without physical transmission — has moved from the realms of Star Trek fantasy to tangible reality.

A Sept. 30, 2015 York University (UK) press release, which originated the news item, describes the quantum teleportation research problem and solution,

Quantum teleportation is an important building block for quantum computing, quantum communication and quantum network and, eventually, a quantum Internet. While theoretical proposals for a quantum Internet already exist, the problem for scientists is that there is still debate over which of various technologies provides the most efficient and reliable teleportation system. This is the dilemma which an international team of researchers, led by Dr Stefano Pirandola of the Department of Computer Science at the University of York, set out to resolve.

In a paper published in Nature Photonics, the team, which included scientists from the Freie Universität Berlin and the Universities of Tokyo and Toronto [emphasis mine], reviewed the theoretical ideas around quantum teleportation focusing on the main experimental approaches and their attendant advantages and disadvantages.

None of the technologies alone provide a perfect solution, so the scientists concluded that a hybridisation of the various protocols and underlying structures would offer the most fruitful approach.

For instance, systems using photonic qubits work over distances up to 143 kilometres, but they are probabilistic in that only 50 per cent of the information can be transported. To resolve this, such photon systems may be used in conjunction with continuous variable systems, which are 100 per cent effective but currently limited to short distances.

Most importantly, teleportation-based optical communication needs an interface with suitable matter-based quantum memories where quantum information can be stored and further processed.

Dr Pirandola, who is also a member of the York Centre for Quantum Technologies, said: “We don’t have an ideal or universal technology for quantum teleportation. The field has developed a lot but we seem to need to rely on a hybrid approach to get the best from each available technology.

“The use of quantum teleportation as a building block for a quantum network depends on its integration with quantum memories. The development of good quantum memories would allow us to build quantum repeaters, therefore extending the range of teleportation. They would also give us the ability to store and process the transmitted quantum information at local quantum computers.

“This could ultimately form the backbone of a quantum Internet. The revised hybrid architecture will likely rely on teleportation-based long-distance quantum optical communication, interfaced with solid state devices for quantum information processing.”

Here’s a link to and a citation for the paper,

Advances in quantum teleportation by S. Pirandola, J. Eisert, C. Weedbrook, A. Furusawa, & S. L. Braunstein. Nature Photonics 9, 641–652 (2015) doi:10.1038/nphoton.2015.154 Published online 29 September 2015

This paper is behind a paywall.


Kavli Foundation roundtable on artificial synthesis as a means to produce clean fuel

A Sept. 9, 2015 news item on Azonano features a recent roundtable discussion about artificial photosynthesis and clean fuel held by the Kavli Foundation,

Imagine creating artificial plants that make gasoline and natural gas using only sunlight. And imagine using those fuels to heat our homes or run our cars without adding any greenhouse gases to the atmosphere. By combining nanoscience and biology, researchers led by scientists at University of California, Berkeley, have taken a big step in that direction.

Peidong Yang, a professor of chemistry at Berkeley and co-director of the school’s Kavli Energy NanoSciences Institute, leads a team that has created an artificial leaf that produces methane, the primary component of natural gas, using a combination of semiconducting nanowires and bacteria. The research, detailed in the online edition of Proceedings of the National Academy of Sciences in August, builds on a similar hybrid system, also recently devised by Yang and his colleagues, that yielded butanol, a component in gasoline, and a variety of biochemical building blocks.

The research is a major advance toward synthetic photosynthesis, a type of solar power based on the ability of plants to transform sunlight, carbon dioxide and water into sugars. Instead of sugars, however, synthetic photosynthesis seeks to produce liquid fuels that can be stored for months or years and distributed through existing energy infrastructure.

In a [Kavli Foundation] roundtable discussion on his recent breakthroughs and the future of synthetic photosynthesis, Yang said his hybrid inorganic/biological systems give researchers new tools to study photosynthesis — and learn its secrets.

There is a list of the participants and an edited transcript of the roundtable, which took place sometime during summer 2015, on the Kavli Foundation’s Fueling up: How nanoscience is creating a new type of solar power webpage (Note: Links have been removed),

The participants were:

PEIDONG YANG – is professor of chemistry and Chan Distinguished Professor of Energy at University of California, Berkeley, and co-director of the Kavli Energy NanoScience Institute at Berkeley National Laboratory and UC Berkeley. He serves as director of the California Research Alliance by BASF, and was a founding member of the U.S. Department of Energy (DOE) Joint Center for Artificial Photosynthesis (JCAP).
THOMAS MOORE – is Regents’ Professor of Chemistry and Biochemistry and past director of the Center for Bioenergy & Photosynthesis at Arizona State University. He is a past president of the American Society for Photobiology, and a team leader at the Center for Bio-Inspired Solar Fuel Production.
TED SARGENT – is a University Professor of Electrical and Computer Engineering at the University of Toronto where he is vice-dean for research for the Faculty of Applied Science and Engineering. He holds the Canada Research Chair in Nanotechnology and is a founder of two companies, InVisage Technologies and Xagenic.

THE KAVLI FOUNDATION (TKF): Solar cells do a good job of converting sunlight into electricity. Converting light into fuel seems far more complicated. Why go through the bother?

THOMAS MOORE: That’s a good question. In order to create sustainable, solar-driven societies, we need a way to store solar energy. With solar cells, we can make electricity efficiently, but we cannot conveniently store that electricity to use when it is cloudy or at night. If we want to stockpile large quantities of energy, we have to store it as chemical energy, the way it is locked up in coal, oil, natural gas, hydrogen and biomass.

PEIDONG YANG: I agree. Perhaps, one day, researchers will come up with an effective battery to store photoelectric energy produced by solar cells. But photosynthesis can solve the energy conversion and storage problem in one step. It converts and stores solar energy in the chemical bonds of organic molecules.

TED SARGENT: Much of the globe’s power infrastructure, from automobiles, trucks and planes to gas-fired electrical generators, is built upon carbon-based fossil fuels. So creating a new technology that can generate liquid fuels that can use this infrastructure is a very powerful competitive advantage for a renewable energy technology.

For someone who’s interested in solar energy and fuel issues, this discussion provide a good introduction to some of what’s driving the research and, happily, none of these scientists are proselytizing.

One final comment. Ted Sargent has been mentioned here several times in connection with his work on solar cells and/or quantum dots.

Interacting photons and quantum logic gates

University of Toronto physicists have taken the first step toward ‘working with pure light’ according to an August 25, 2015 news item on Nanotechnology Now,

A team of physicists at the University of Toronto (U of T) have taken a step toward making the essential building block of quantum computers out of pure light. Their advance, described in a paper published this week in Nature Physics, has to do with a specific part of computer circuitry known as a “logic gate.”

An August 25, 2015 University of Toronto news release by Patchen Barss, which originated the news item, provides an explanation of ‘logic gates’, photons, and the impact of this advance (Note: Links have been removed),

Logic gates perform operations on input data to create new outputs. In classical computers, logic gates take the form of diodes or transistors. But quantum computer components are made from individual atoms and subatomic particles. Information processing happens when the particles interact with one another according to the strange laws of quantum physics.

Light particles — known as “photons” — have many advantages in quantum computing, but it is notoriously difficult to get them to interact with one another in useful ways. This experiment demonstrates how to create such interactions.

“We’ve seen the effect of a single particle of light on another optical beam,” said Canadian Institute for Advanced Research (CIFAR) Senior Fellow Aephraim Steinberg, one of the paper’s authors and a researcher at U of T’s Centre for Quantum Information & Quantum Computing. “Normally light beams pass through each other with no effect at all. To build technologies like optical quantum computers, you want your beams to talk to one another. That’s never been done before using a single photon.”

The interaction was a two-step process. The researchers shot a single photon at rubidium atoms that they had cooled to a millionth of a degree above absolute zero. The photons became “entangled” with the atoms, which affected the way the rubidium interacted with a separate optical beam. The photon changes the atoms’ refractive index, which caused a tiny but measurable “phase shift” in the beam.

This process could be used as an all-optical quantum logic gate, allowing for inputs, information-processing and outputs.

“Quantum logic gates are the most obvious application of this advance,” said Steinberg. “But being able to see these interactions is the starting page of an entirely new field of optics. Most of what light does is so well understood that you wouldn’t think of it as a field of modern research. But two big exceptions are, “What happens when you deal with light one particle at a time?’ and “What happens when there are media like our cold atoms that allow different light beams to interact with each other?’”

Both questions have been studied, he says, but never together until now.

Here’s a link to and citation for the paper,

Observation of the nonlinear phase shift due to single post-selected photons by Amir Feizpour, Matin Hallaji, Greg Dmochowski, & Aephraim M. Steinberg. Nature Physics (2015) doi:10.1038/nphys3433 Published online 24 August 2015

This paper is behind a paywall.

University of Toronto researchers combine 2 different materials for new hyper-efficient, light-emitting, hybrid crystal

The Sargent Group at the University of Toronto has been quite active with regard to LEDs (light-emitting diodes) and with quantum dots. Their latest work is announced in a July 16, 2015 news item on Nanotechnology Now (Note: I had to include the ‘oatmeal cookie and chocolate chips’ analogy in the first paragraph as it’s referred to subsequently),

It’s snack time: you have a plain oatmeal cookie, and a pile of chocolate chips. Both are delicious on their own, but if you can find a way to combine them smoothly, you get the best of both worlds.

Researchers in The Edward S. Rogers Sr. Department of Electrical & Computer Engineering [University of Toronto] used this insight to invent something totally new: they’ve combined two promising solar cell materials together for the first time, creating a new platform for LED technology.

The team designed a way to embed strongly luminescent nanoparticles called colloidal quantum dots (the chocolate chips) into perovskite (the oatmeal cookie). Perovskites are a family of materials that can be easily manufactured from solution, and that allow electrons to move swiftly through them with minimal loss or capture by defects.

A July 15, 2015 University of Toronto news release (also on EurekAlert), which originated the news item, reveals more about the research (Note: A link has been removed),

“It’s a pretty novel idea to blend together these two optoelectronic materials, both of which are gaining a lot of traction,” says Xiwen Gong, one of the study’s lead authors and a PhD candidate working with Professor Ted Sargent. “We wanted to take advantage of the benefits of both by combining them seamlessly in a solid-state matrix.”

The result is a black crystal that relies on the perovskite matrix to ‘funnel’ electrons into the quantum dots, which are extremely efficient at converting electricity to light. Hyper-efficient LED technologies could enable applications from the visible-light LED bulbs in every home, to new displays, to gesture recognition using near-infrared wavelengths.

“When you try to jam two different crystals together, they often form separate phases without blending smoothly into each other,” says Dr. Riccardo Comin, a post-doctoral fellow in the Sargent Group. “We had to design a new strategy to convince these two components to forget about their differences and to rather intermix into forming a unique crystalline entity.”

The main challenge was making the orientation of the two crystal structures line up, called heteroexpitaxy. To achieve heteroepitaxy, Gong, Comin and their team engineered a way to connect the atomic ‘ends’ of the two crystalline structures so that they aligned smoothly, without defects forming at the seams. “We started by building a nano-scale scaffolding ‘shell’ around the quantum dots in solution, then grew the perovskite crystal around that shell so the two faces aligned,” explained coauthor Dr. Zhijun Ning, who contributed to the work while a post-doctoral fellow at UofT and is now a faculty member at ShanghaiTech.

The resulting heterogeneous material is the basis for a new family of highly energy-efficient near-infrared LEDs. Infrared LEDs can be harnessed for improved night-vision technology, to better biomedical imaging, to high-speed telecommunications.

Combining the two materials in this way also solves the problem of self-absorption, which occurs when a substance partly re-absorbs the same spectrum of energy that it emits, with a net efficiency loss. “These dots in perovskite don’t suffer reabsorption, because the emission of the dots doesn’t overlap with the absorption spectrum of the perovskite,” explains Comin.

Gong, Comin and the team deliberately designed their material to be compatible with solution-processing, so it could be readily integrated with the most inexpensive and commercially practical ways of manufacturing solar film and devices. Their next step is to build and test the hardware to capitalize on the concept they have proven with this work.

“We’re going to build the LED device and try to beat the record power efficiency reported in the literature,” says Gong.

I see that Sargent’s work is still associated with and supported by Saudi Arabia, from the news release,

This work was supported by the Ontario Research Fund Research Excellence Program, the Natural Sciences and Engineering Research Council of Canada (NSERC), and the King Abdullah University of Science & Technology (KAUST).

Here’s a link to and a citation for the paper,

Quantum-dot-in-perovskite solids by Zhijun Ning, Xiwen Gong, Riccardo Comin, Grant Walters, Fengjia Fan, Oleksandr Voznyy, Emre Yassitepe, Andrei Buin, Sjoerd Hoogland, & Edward H. Sargent. Nature 523, 324–328 (16 July 2015) doi:10.1038/nature14563 Published online 15 July 2015

This paper is behind a paywall.

Finally, the researchers have made a .gif of their hybrid crystal available.

A glowing quantum dot seamlessly integrated into a perovskite crystal matrix (Image: Ella Marushchenko). Courtesy: University of Toronto

A glowing quantum dot seamlessly integrated into a perovskite crystal matrix (Image: Ella Marushchenko). Courtesy: University of Toronto

ETA July 17, 2015:

Dexter Johnson provides some additional insight into the work in his July 16, 2015 posting on the Nanoclast blog (on the Institute for Electrical and Electronics Engineers website), Note:  Links have been removed,

Ted Sargent at the University of Toronto has built a reputation over the years as being a prominent advocate for the use of quantum dots in photovoltaics. Sargent has even penned a piece for IEEE Spectrum covering the topic, and this blog has covered his record breaking efforts at boosting the conversion efficiency of quantum dot-based photovoltaics a few times.

Earlier this year, however, Sargent started to take an interest in the hot material that has the photovoltaics community buzzing: perovskite. …

Brain data (neuroscience) crowdsourced at Toronto’s (Canada) 2013 Nuit Blanche event

The brain data was crowdsourced in 2013 in Toronto but only recently published according to a July 8, 2015 Baycrest Centre for Geriatric Care news release (also on EurekAlert),

Neuroscientists in Toronto have shown that crowdsourcing brain data with hundreds of adults in a short period of time could be a new frontier in neuroscience and lead to new insights about the brain.

More than 500 adults aged 18 and older participated in the experiment at the 2013 Scotiabank Nuit Blanche arts event in Toronto. Baycrest, in partnership with the University of Toronto and industry partners, created a large-scale art-science installation called My Virtual Dream. Festival-goers were invited to wear a Muse™ wireless electroencephalography (EEG) headband and participate in a brief collective neurofeedback experience in groups of 20 inside a 60-foot geodesic dome. The group’s collective EEG signals triggered a specific catalogue of artistic imagery displayed on the dome’s 360-degree interior, along with spontaneous musical interpretation by live musicians on stage.

The installation was one of the most popular at Nuit Blanche, with an average lineup wait time of two hours.

Studying brains in a social and multi-sensory environment is closer to real life and may help scientists to approach questions of complex real-life social cognition that otherwise are not accessible in traditional labs that study one person’s cognitive functions at a time.

“In traditional lab settings, the environment is so controlled that you can lose some of the fine points of real-time brain activity that occur in a social life setting,” said Dr. Kovacevic, creative producer of My Virtual Dream and program manager of the Centre for Integrative Brain Dynamics at Baycrest’s Rotman Research Institute.

“What we’ve done is taken the lab to the public. We collaborated with multi-media artists, made this experiment incredibly engaging, attracted highly motivated subjects which is not easy to do in the traditional lab setting, and collected useful scientific data from their experience.”

Results from the experiment not only demonstrated the scientific viability of collective neurofeedback as a potential new avenue of neuroscience research that takes into account individuality, complexity and sociability of the human mind, but yielded new evidence that neurofeedback learning can have an effect on the brain almost immediately.

Neurofeedback learning supports mindful awareness and joins a growing market for wearable biofeedback devices. The device used in this study, Muse™, is a clinical-grade EEG brain computer interface (BCI) headband that helps individuals to be more aware of their brain states (relaxed versus focused versus distracted) and learn self-regulation of brain function to fit their personal goals.

A total of 523 adults (209 males, 314 females), ranging in age from 18 to 89, with an average age of 31, contributed their EEG brain data for the study. Each session involved 20 participants being seated in a semicircle in front of a stage and divided into four groups (“pods”) of five. They played a collective neurofeedback computer game where they were required to manipulate their mental states of relaxation and concentration. The neurofeedback training lasted 6.5 minutes, which is much shorter than typical neurofeedback training experiments.

The massive amount of EEG data collected in one night yielded an interesting and statistically relevant finding – that subtle brain activity changes were taking place within approximately one minute of the neurofeedback learning exercise – unprecedented speed of learning changes that have not been demonstrated before.

“These results really open up a whole new domain of neuroscience study that actively engages the public to advance our understanding of the brain,” said Dr. Randy McIntosh, director of the Rotman Research Institute and vice-president of Research at Baycrest. He is a senior author on the paper.

The idea for the Nuit Blanche art -science experiment was inspired by Baycrest’s ongoing international project to build the world’s first functional, virtual brain – a research and diagnostic tool that could one day revolutionize brain healthcare.

Baycrest cognitive neuroscientists collaborated with artists and gaming and wearable technology industry partners for over a year to create the My Virtual Dream installation. Partners included the University of Toronto, Scotiabank Nuit Blanche, Muse™ and Uken Games.

Here’s a link to and a citation for the paper,

‘My Virtual Dream’: Collective Neurofeedback in an Immersive Art Environment by Natasha Kovacevic, Petra Ritter, William Tays, Sylvain Moreno, and Anthony Randal McIntosh. DOI: 10.1371/journal.pone.0130129 PLOS Published: July 8, 2015

This is an open access paper.

A few final words, I last wrote about MUSE (a Canadian technology company) in a March 6, 2015 posting. Uken Games , also a Canadian company, is new to this blog.

Testing for antibiotic resistance in one hour

University of Toronto researchers have devised a test for antibiotic resistance which cuts down the time from up to three days to one hour. From a May 27, 2015 news item on Azonano,

We live in fear of ‘superbugs’: infectious bacteria that don’t respond to treatment by antibiotics, and can turn a routine hospital stay into a nightmare. A 2015 Health Canada report estimates that superbugs have already cost Canadians $1 billion, and are a “serious and growing issue.” Each year two million people in the U.S. contract antibiotic-resistant infections, and at least 23,000 people die as a direct result.

But tests for antibiotic resistance can take up to three days to come back from the lab, hindering doctors’ ability to treat bacterial infections quickly. Now Ph.D. researcher Justin Besant and his team at the University of Toronto have designed a small and simple chip to test for antibiotic resistance in just one hour, giving doctors a shot at picking the most effective antibiotic to treat potentially deadly infections. Their work was published this week in the international journal Lab on a Chip.

A May 26, 2015 University of Toronto news release (also on EurekAlert), which originated the news item, provides more details about current testing regimes and about the new technique,

Resistant bacteria arise in part because of imprecise use of antibiotics—when a patient comes down with an infection, the doctor wants to treat it as quickly as possible. Samples of the infectious bacteria are sent to the lab for testing, but results can take two to three days. In the meantime, the doctor prescribes her patient a broad-spectrum antibiotic. Sometimes the one-size-fits-all antibiotic works and sometimes it doesn’t, and when the tests come back days later, the doctor can prescribe a specific antibiotic more likely to kill the bacteria.

“Guessing can lead to resistance to these broad-spectrum antibiotics, and in the case of serious infections, to much worse outcomes for the patient,” says Besant. “We wanted to determine whether bacteria are susceptible to a particular antibiotic, on a timescale of hours, not days.”

The problem with most current tests is the time it takes for bacteria to reproduce to detectable levels. Besant and his team, including his supervisor Professor Shana Kelley of the Institute for Biomaterials & Biomedical Engineering and the Faculties of Pharmacy and Medicine, and Professor Ted Sargent of The Edward S. Rogers Sr. Department of Electrical & Computer Engineering, drew on their collective expertise in electrical and biomedical engineering to design a chip that concentrates bacteria in a miniscule space—just two nanolitres in volume—in order to increase the effective concentration of the starting sample.

They achieve this high concentration by ‘flowing’ the sample, containing the bacteria to be tested, through microfluidic wells patterned onto a glass chip. At the bottom of each well a filter, composed of a lattice of tiny microbeads, catches bacteria as the sample flows through. The bacteria accumulate in the nano-sized well, where they’re trapped with the antibiotic and a signal molecule called resazurin.

Living bacteria metabolize resazurin into a form called resorufin, changing its electrochemical signature. If the bacteria are effectively killed by the antibiotic, they stop metabolizing resazurin and the electrochemical signature in the sample stays the same. If they are antibiotic-resistant, they continue to metabolize resazurin into resorufin, altering its electrochemical signature. Electrodes built directly into the chip detect the change in current as resazurin changes to resorufin.

“This gives us two advantages,” says Besant. “One, we have a lot of bacteria in a very small space, so our effective starting concentration is much higher. And two, as the bacteria multiply and convert the resazurin molecule, it’s effectively stuck in this nanolitre droplet—it can’t diffuse away into the solution, so it can accumulate more rapidly to detectable levels.”

“Our approach is the first to combine this method of increasing sample concentration with a straightforward electrochemical readout,” says Professor Sargent. “We see this as an effective tool for faster diagnosis and treatment of commonplace bacterial infections.”

Rapid alternatives to existing antibiotic resistance tests rely on fluorescence detection, requiring expensive and bulky fluorescence microscopes to see the result.

“The electronics for our electrochemical readout can easily fit in a very small benchtop instrument, and this is something you could see in a doctor’s office, for example,” says Besant. “The next step would be to create a device that would allow you to test many different antibiotics at many different concentrations, but we’re not there yet.”

Here’s a link to and a citation for the paper,

Rapid electrochemical phenotypic profiling of antibiotic-resistant bacteria by Justin D. Besant, Edward H. Sargent, and Shana O. Kelley. Lab Chip, 2015, Advance Article DOI: 10.1039/C5LC00375J First published online 13 May 2015

This paper is behind a paywall.

It was surprising to see Ted (Edward) Sargent mentioned with regard to a lab-on-a-chip project. I have featured research from him and from his laboratory many times here and, as I recall, it’s always been focused on solar cells. This Dec. 9, 2014 post features the latest research solar cell research that I’ve stumbled across from Sargent and the University of Toronto.

Synthetic Aesthetics update and an informal Canadian synthetic biology roundup

Amanda Ruggeri has written a very good introduction to synthetic biology for nonexperts in her May 20, 2015 Globe and Mail article about ‘Designing for the Sixth Extinction’, an exhibit showcasing designs and thought experiments focused on synthetic biology ,

In a corner of Istanbul’s Design Biennial late last year [2014], photographs of bizarre creatures sat alongside more conventional displays of product design and typefaces. Diaphanous globes, like transparent balloons, clung to the mossy trunk of an oak tree. Rust-coloured patterns ran across green leaves, as if the foliage had been decorated with henna. On the forest floor, a slug-like creature slithered, its back dotted with gold markings; in another photograph, what looked like a porcupine without a head crawled over the dirt, its quills tipped blood-red.

But as strange as the creatures looked, what they actually are is even stranger. Not quite living things, not quite machines, these imagined prototypes inhabit a dystopic, future world – a world in which they had been created to solve the problems of the living. The porcupine, for example, is an Autonomous Seed Disperser, described as a device that would collect and disperse seeds to increase biodiversity. The slug would be programmed to seek out acidic soils and neutralize them by dispersing an alkali hygroscopic fluid.

They are the designs – and thought experiments – of London-based Alexandra Daisy Ginsberg, designer, artist and lead author of the book Synthetic Aesthetics: Investigating Synthetic Biology’s Designs on Nature. In her project Designing for the Sixth Extinction, which after Istanbul is now on display at the Design Museum in London, Ginsberg imagines what a synthetic biology-designed world would look like – and whether it’s desirable. “

I have a couple of comments. First, the ‘Synthetic Aesthetics: Investigating Synthetic Biology’s Designs on Nature’ book launch last year was covered here in a May 5, 2014 post. where you’ll notice a number of the academics included in Ruggeri’s article are contributors to the book (but not mentioned as such). Second, I cannot find ‘Design for the Sixth Extinction’ listed as an exhibition on London’s Design Museum website.

Getting back to the matter at hand, not all of the projects mentioned in Ruggeri’s article are ‘art’ projects, there is also this rather practical and controversial initiative,

Designing even more complex organisms is the inevitable, and controversial, next step. And those designs have already begun. The British company Oxitec has designed a sterile male mosquito. When the bugs are released into nature and mate, no offspring result, reducing the population or eliminating it altogether. This could be a solution to dengue fever, a mosquito-carried disease that infects more than 50 million people each year: In field trials in Cayman, Panama and Brazil, the wild population of the dengue-carrying mosquito species was reduced by 90 per cent. Yet, as a genetically engineered solution, it also makes some skittish. The consequences of such manipulations remain unforeseen, they say. Proponents counter that the solution is more elegant, and safer, than the current practice of spraying chemicals.

Even so, the engineered mosquito leads to overarching questions: What are the dangers of tinkering with life? Could this cause a slide toward eugenics? Currently, the field doesn’t have an established ethics oversight process, something some critics are pushing to change.

It’s a surprising piece for the Globe and Mail newspaper to run since it doesn’t have a Canadian angle to it and the Globe and Mail doesn’t specialize in science (not withstanding Ivan Semeniuk’s science articles) or art/science or synthetic biology writing, for that matter. Perhaps it bodes an interest and more pieces on emerging science and technology and on art/science projects?

In any event, it seems like a good time to review some of the synthetic biology work or the centres of activity in Canada.  I believe the last time I tackled this particular topic was in a May 24, 2010 post titled, Canada and synthetic biology in the wake of the first ‘synthetic’ bacteria.

After a brief search, I found three centres for research:

Concordia [University] Centre for Applied Synthetic Biology (CASB)

[University of Toronto] The Synthetic Biology and Cellular Control Lab

[University of British Columbia] Centre for High-Throughput Biology (CHiBi)

Following an Oct. 27 – 28, 2014 UK-Canada Synthetic Biology Workshop held at Concordia University, Rémi Quirion, Vincent Martin, Pierre Meulien and Marc LePage co-wrote a Nov. 4, 2014 Concordia University post titled, How Canada is poised to revolutionize synthetic biology,

Rémi Quirion is the Chief Scientist of Québec, Fonds de recherche du Québec. Vincent Martin is Canada Research Chair in Microbial Genomics and Engineering and a professor in the Department of Biology at Concordia University in Montreal. Pierre Meulien is President and CEO of Genome Canada. Marc LePage is the President and CEO of Génome Québec.

Canada’s research and business communities have an opportunity to become world leaders in a burgeoning field that is fast shaping how we deal with everything from climate change to global food security and the production of lifesaving medications. The science of synthetic biology has the transformative capacity to equip us with novel technology tools and products to build a more sustainable society, while creating new business and employment opportunities for the economy of tomorrow.

We can now decipher the code of life for any organism faster and less expensively than ever before. Canadian scientists are producing anti-malarial drugs from organic materials that increase the availability and decrease the cost of lifesaving medicines. They are also developing energy efficient biofuels to dramatically reduce environmental and manufacturing costs, helping Canadian industry to thrive in the global marketplace.

The groundwork has also been laid for a Canadian revolution in the field. Canada’s scientific community is internationally recognized for its leadership in genomics research and strong partnerships with key industries. Since 2000, Genome Canada and partners have invested more than $2.3 billion in deciphering the genomes of economically important plants, animals and microbes in order to understand how they function. A significant proportion of these funds has been invested in building the technological toolkits that can be applied to synthetic biology.

But science cannot do it alone. Innovation on this scale requires multiple forms of expertise in order to be successful. Research in law, business, social sciences and humanities is vital to addressing questions of ethics, supply chain management, social innovation and cultural adaptation to new technologies. Industry knowledge and investments, as well as the capacity to incentivize entrepreneurship, are key to devising business models that will enable new products to thrive. Governments and funding agencies also need to do their part by supporting multidisciplinary research, training and infrastructure.

It’s a bit ‘hype happy’ for my taste but it does provide some fascinating insight in what seems to be a male activity in Canada.

Counterbalancing that impression is an Oct. 6, 2013 article by Ivan Semeniuk for the Globe and Mail about a University of Lethbridge team winning the top prize in a synthetic biology contest,

If you want to succeed in the scientific revolution of the future, it helps to think about life as a computer program.

That strategy helped University of Lethbridge students walk away with the top prize in a synthetic biology competition Sunday. Often touted as the genetic equivalent of the personal computer revolution, synthetic biology involves thinking about cells as programmable machines that can be designed and built to suit a particular need – whether it’s mass producing a vaccine or breaking down a hazardous chemical in the environment.

The five member Lethbridge team came up with a way to modify how cells translate genetic information into proteins. Rather than one bit of DNA carrying the information to make one protein – the usual way cells go about their business – the method involves inserting a genetic command that jiggles a cell’s translational machinery while it’s in mid-operation, coaxing it to produce two proteins out of the same DNA input.

“We started off with a computer analogy – kind of like zipping your files together – so you’d zip two protein sequences together and therefore save space,” said Jenna Friedt, a graduate student in biochemistry at Lethbridge. [emphasis mine]

There are concerns other than gender issues, chief amongst them, ethics. The Canadian Biotechnology Action Network maintains an information page on Synthetic Biology which boasts this as its latest update,

October 2014: In a unanimous decision of 194 countries, the United Nation’s Convention on Biological Diversity formally urged countries to regulate synthetic biology, a new extreme form of genetic engineering. The landmark decision follows ten days of hard-fought negotiations between developing countries and a small group of wealthy biotech-friendly economies. Until now, synthetic organisms have been developed and commercialized without international regulations. …

Finally, there’s a June 2014 synthetic biology timeline from the University of Ottawa’s Institute for Science, Society, and Policy (ISSP) which contextualizes Canadian research, policy and regulation with Australia, the European Union, the UK, and the US.

(On a closely related note, there’s my May 14, 2015 post about genetic engineering and newly raised concerns.)

Research2Reality: a science media engagement experience dedicated to Canadian science

As of May 11, 2015, Canadians will be getting an addition to their science media environment (from the May 4, 2015 news release),

Research2Reality to celebrate Canadian research stars

Social media initiative to popularize scientific innovation

May 4, 2015, TORONTO – On Monday, May 11, Research2Reality.com goes live and launches a social media initiative that will make the scientist a star. Following in the footsteps of popular sites like IFLScience and How Stuff Works, Research2Reality uses a video series and website to engage the community in the forefront of scientific discoveries made here in Canada.

The interviews feature some of Canada’s leading researchers such as Dick Peltier – director of the Centre for Global Change Science at the University of Toronto, Sally Aitken – director of the Centre for Forest Conservation Genetics at the University of British Columbia and Raymond Laflamme – executive director of the Institute for Quantum Computing at the University of Waterloo.

“Right now many Canadians don’t understand the scope of cutting-edge work being done in our backyards,” says Research2Reality co-founder and award-winning professor Molly Shoichet. “This initiative will bridge that gap between researchers and the public.”

Also launching Monday, May 11, courtesy of Research2Reality’s official media partner, Discovery Science, is a complementary website www.sciencechannel.ca/Shows/Research2Reality. The new website will feature the exclusive premieres of a collection of interview sessions. In addition, Discovery Science and Discovery will broadcast an imaginative series of public service announcements through the end of the year, while social media accounts will promote Research2Reality, including Discovery’s flagship science and technology program DAILY PLANET.

About Research2Reality:
Research2Reality is a social media initiative designed to popularize the latest Canadian research. It was founded by Molly Shoichet, Professor of Chemical Engineering & Applied Chemistry and Canada Research Chair in Tissue Engineering at the University of Toronto, and Mike MacMillan, founder and producer of Lithium Studios Productions. Research2Reality’s founding partners are leading research-intensive universities – the University of Alberta, the University of British Columbia, McMaster University, the University of Toronto, the University of Waterloo, and Western University – along with the Ontario Government and Discovery Networks. Discovery Science is the official media partner. Research2Reality is also supported by The Globe and Mail.

Research2Reality details

A Valentine of sorts to Canadian science researchers from Molly Shoichet (pronounced shoy [and] quette as in David Arquette)  and her producing partner Mike MacMillan of Lithium Studios, Research2Reality gives Canadians an opportunity to discover online some of the extraordinary work done by scientists of all stripes, including (unusually) social scientists, in this country. The top tier in this effort is the interview video series ‘The Orange Chair Sessions‘  which can be found and shared across

Shoichet and MacMillan are convinced there’s an appetite for more comprehensive science information. Supporting The Orange Chair Sessions is a complementary website operated by Discovery Channel where there are

  • more interviews
  • backgrounders,
  • biographies,
  • blogs, and
  • links to other resources

Discovery Channel is also going to be airing special one minute  public service announcements (PSA) on topics like water, quantum computing, and cancer. Here’s one of the first of those PSAs,

“I’m very excited about this and really hope that other people will be too,” says Shoichet. The audience for the Research2Reality endeavour is for people who like to know more and have questions when they see news items about science discoveries that can’t be answered by investigating mainstream media programmes or trying to read complex research papers.

This is a big undertaking. ” Mike and I thought about this for about two years.” Building on the support they received from the University of Toronto, “We reached out to the vice-presidents of research at the top fifteen universities in the country.” In the end, six universities accepted the invitation to invest in this project,

  • the University of British Columbia,
  • the University of Alberta,
  • Western University (formerly the University of Western Ontario),
  • McMaster University,
  • Waterloo University, and, of course,
  • the University of Toronto

(Unfortunately, Shoichet was not able to answer a question about the cost for an individual episode but perhaps when there’s time that detail and more about the financing will be made available. [ETA May 11, 2015 1625 PDT: Ivan Semeniuk notes this is a $400,000 project in his Globe and Mail May 11, 2015 article.]) As part of their involvement, the universities decide which of their researchers/projects should be profiled then Research2Reality swings into action. “We shoot our own video, that is, we (Mike and I) come out and conduct interviews that take approximately fifteen minutes. We also shoot a b-roll, that is, footage of the laboratories and other relevant sites so it’s not all ‘talking heads’.” Shoichet and MacMillan are interested in the answer to two questions, “What are you doing? and Why do we care?” Neither interviewer/producer is seen or heard on camera as they wanted to keep the focus on the researcher.

Three videos are being released initially with another 67 in the pipeline for a total of 70.  The focus is on research of an international calibre and one of the first interviews to be released (Shoichet’s will be release later) is Raymond Laflamme’s (he’s also featured in the ‘quantum PSA’.

Raymond Laflamme

Who convinces a genius that he’s gotten an important cosmological concept wrong or ignored it? Alongside Don Page, Laflamme accomplished that feat as one of Stephen Hawking’s PhD students at the University of Cambridge. Today (May 11, 2015), Laflamme is (from his Wikipedia entry)

… co-founder and current director of the Institute for Quantum Computing at the University of Waterloo. He is also a professor in the Department of Physics and Astronomy at the University of Waterloo and an associate faculty member at Perimeter Institute for Theoretical Physics. Laflamme is currently a Canada Research Chair in Quantum Information.

Laflamme changed his focus from quantum cosmology to quantum information while at Los Alamos, “To me, it seemed natural. Not much of a change.” It is the difference between being a theoretician and an experimentalist and anyone who’s watched The Big Bang Theory (US television programme) knows that Laflamme made a big leap.

One of his major research interests is quantum cryptography, a means of passing messages you can ensure are private. Laflamme’s team and a team in Vienna (Austria) have enabled two quantum communication systems, one purely terrestrial version, which can exchange messages with another such system up to 100 km. away. There are some problems yet to be solved with terrestrial quantum communication. First, buildings, trees, and other structures provide interference as does the curvature of the earth. Second, fibre optic cables absorb some of the photons en route.

Satellite quantum communication seems more promising as these problems are avoided altogether. The joint Waterloo/Vienna team of researchers has  conducted successful satellite experiments in quantum communication in the Canary Islands.

While there don’t seem to be any practical, commercial quantum applications, Laflamme says that isn’t strictly speaking the truth, “In the last 10  to 15 years many ideas have been realized.” The talk turns to quantum sensing and Laflamme mentions two startups and notes he can’t talk about them yet. But there is Universal Quantum Devices (UQD), a company that produces parts for quantum sensors. It is Laflamme’s startup, one he co-founded with two partners. (For anyone unfamiliar with the Canadian academic scene, Laflamme’s home institution, the University of Waterloo, is one of the most actively ‘innovative’ and business-oriented universities in Canada.)

LaFlamme’s interests extend beyond laboratory work and business. He’s an active science communicator as can be seen in this 2010 TEDxWaterloo presentation where he takes his audience from the discovery of fire to quantum physics concepts such as a ‘quantum superposition’ and the ‘observer effect’ to the question, ‘What is reality?’ in approximately 18 mins.

For anyone who needs a little more information, a quantum superposition is a term referring the ability of a quantum object to inhabit two states simultaneously, e.g., on/off. yes/no, alive/dead, as in Schrödinger’s cat. (You can find out more about quantum superpositions in this Wikipedia essay and about Schrodinger’s cat in this Wikipedia essay.) The observer effect is a phenomenon whereby the observer of a quantum experiment affects that experiment by the act of observing it. (You can find out more about the observer effect in this Wikipedia essay.)

The topic of reality is much trickier to explain. No one has yet been able to offer a viable theory for why the world at the macro scale behaves one way (classical physics) and the world at the quantum scale behaves another way (quantum physics). As Laflamme notes, “There is no such thing as a superposition in classical physics but we can prove in the laboratory that it exists in quantum physics.” He goes on to suggest that children, raised in an environment where quantum physics and its applications are commonplace, will have an utterly different notion as to what constitutes reality.

Laflamme is also interested in music and consulted on a ‘quantum symphony’. He has this to say about it in an Sept. 20, 2012 piece on the University of Waterlo website,

Science and art share a common goal — to help us understand our universe and ourselves.  Research at IQC [Institute for Quantum Computing] aims to provide important new understanding of nature’s building blocks, and devise methods to turn that understanding into technologies beneficial for society.Since founding IQC a decade ago, I have sought ways to bridge science and the arts, with the belief that scientific discovery itself is a source of beauty and inspiration.  Our collaboration with the Kitchener-Waterloo Symphony was an example — one of many yet to come — of how science and the arts provide different but complementary insights into our universe and ourselves.

I wrote about the IQC and the symphony which debuted at the IQC’s opening in a Sept. 25, 2012 posting.

Music is not the only art which has attracted Laflamme’s talents. He consulted on a documentary, The Quantum Tamers: Revealing our weird and wired future, a co-production between Canada’s Perimeter Institute and Title Entertainment,

From deep inside the sewers of Vienna, site of groundbreaking quantum teleportation experiments, to cutting-edge quantum computing labs, to voyages into the minds of the world’s brightest thinkers, including renowned British scientist Stephen Hawking, this documentary explores the coming quantum technological revolution.

All of this suggests an interest in science not seen since the 19th century when scientists could fill theatres for their lectures. Even Hollywood is capitalizing on this interest. Laflamme, who saw ‘Interstellar’, ‘The Imitation Game’ (Alan Turing), and ‘The Theory of Everything’ (Stephen Hawking) in fall 2014 comments, “I was surprised by how much science there was in The Imitation Game and Interstellar.” As for the Theory of Everything, “I was apprehensive since I know Stephen well. But, the actor, Eddie Redmayne, and the movie surprised me. There were times when he moved his head or did something in a particular way—he was Stephen. Also, most people don’t realize what an incredible sense of humour Stephen has and the movie captured that well.” Laflamme also observed that it was a movie about a relationship and not really concerned with science and its impacts (good and ill) or scientific accomplishments.  Although he allows, “It could have had more science.”

Research2Reality producers

Molly Shoichet

Co-producer Shoichet has sterling scientific credentials of her own. In addition to this science communication project, she runs the Shoichet Lab at the University of Toronto (from the Dr. Molly Shoichet bio page),

Dr. Molly Shoichet holds the Tier 1 Canada Research Chair in Tissue Engineering and is University Professor of Chemical Engineering & Applied Chemistry, Chemistry and Biomaterials & Biomedical Engineering at the University of Toronto. She is an expert in the study of Polymers for Drug Delivery & Regeneration which are materials that promote healing in the body.

Dr. Shoichet has published over to 480 papers, patents and abstracts and has given over 310 lectures worldwide.  She currently leads a laboratory of 25 researchers and has graduated 134 researchers over the past 20 years.  She founded two spin-off companies from research in her laboratory.

Dr. Shoichet is the recipient of many prestigious distinctions and the only person to be a Fellow of Canada’s 3 National Academies: Canadian Academy of Sciences of the Royal Society of Canada, Canadian Academy of Engineering, and Canadian Academy of Health Sciences. Dr. Shoichet holds the Order of Ontario, Ontario’s highest honour and is a Fellow of the American Association for the Advancement of Science. In 2013, her contributions to Canada’s innovation agenda and the advancement of knowledge were recognized with the QEII Diamond Jubilee Award. In 2014, she was given the University of Toronto’s highest distinction, University Professor, a distinction held by less than 2% of the faculty.

Mike MacMillan

MacMIllan’s biography (from the Lithium Studios website About section hints this is his first science-oriented series (Note: Links have been removed),

Founder of Lithium Studios Productions
University of Toronto (‘02)
UCLA’s Professional Producing Program (‘11)

His first feature, the dark comedy / thriller I Put a Hit on You (2014, Telefilm Canada supported), premiered at this year’s Slamdance Film Festival in Park City. Guidance (2014, Telefilm Canada supported, with super producer Alyson Richards over at Edyson), a dark comedy/coming of age story is currently in post-production, expected to join the festival circuit in September 2014.

Mike has produced a dozen short films with Toronto talents Dane Clark and Linsey Stewart (CAN – Long Branch, Margo Lily), Samuel Fluckiger (SWISS – Terminal, Nightlight) and Darragh McDonald (CAN – Love. Marriage. Miscarriage.). They’ve played at the top film fests around the world and won a bunch of awards.

Special skills include kickass hat collection and whiskey. Bam.

Final comments

It’s nice to see the Canadian scene expanding; I’m particularly pleased to learn social scientists will be included.Too often researchers from the physical sciences or natural sciences and researchers from the social sciences remain aloof from each other. In April 2013, I attended a talk by Evelyn Fox Keller, physicist, feminist, and philosopher, who read from a paper she’d written based on a then relatively recent experience in South Africa where researchers had aligned themselves in two different groups and refused to speak to each other. They were all anthropologists but the sticking point was the type of science they practiced. One group were physical anthropologists and the other were cultural anthropologists. That’s an extreme example unfortunately symptomatic of a great divide. Bravo to Research2Reality for bringing the two groups together.

As for the science appetite Shoichet and MacMillan see in Canada, this is not the only country experiencing a resurgence of interest; they’ve been experiencing a science media expansion in the US.  Neil deGrasse Tyson’s Star Talk television talk show, which also exists as a radio podcast, debuted on April 19, 2015 (Yahoo article by Calla Cofield); Public Radio Exchange’s (PRX) Transistor; a STEM (science, technology, engineering, and mathematics) audio project debuted in Feb. 2015; and video podcast Science Goes to the Movies also debuted in Feb. 2015 (more about the last two initiatives in my March 6, 2015 posting [scroll down about 40% of the way]). Finally (for the burgeoning US science media scene) and neither least nor new, David Bruggeman has a series of posts titled, Science and Technology Guests on Late Night, Week of …, on his Pasco Phronesis blog which has been running for many years. Bruggeman’s series is being included here because most people don’t realize that US late night talk shows have jumped into the science scene. You can check  David’s site here as he posts this series on Mondays and this is Monday, May 11, 2015.

It’s early days for Research2Reality and it doesn’t yet have the depth one might wish. The videos are short (the one featured on the Discovery Channel’s complementary website is less than 2 mins. and prepare yourself for ads). They may not be satisfying from an information perspective but what makes The Orange Chair Series fascinating is the peek into the Canadian research scene. Welcome to Research2Reality and I hope to hear more about you in the coming months.

[ETA May 11, 2015 at 1625 PDT: Semeniuk’s May 11, 2015 article mentions a few other efforts to publicize Canadian research (Note: Links have been removed),

For example, Research Matters, a promotional effort by the Council of Ontario Universities, has built up a large bank of short articles on its website that highlight researchers across the province. Similarly, the Canada Foundation for Innovation, which channels federal dollars toward research infrastructure and projects, produces features stories with embedded videos about the scientists who are enabled by their investments.

What makes Research2Reality different, said Dr. Shoichet, is an approach that doesn’t speak for one region, field of research of  [sic] funding stream.

One other aspect which distinguishes Research2Reality from the other science promotion efforts is the attempt to reach out to the audience. The Canada Foundation for Innovation and Council for Ontario Universities are not known for reaching out directly to the general public.]

Frogs: monitoring them, finding new species, and research about the golden ones in Panama

I have three frog-oriented items and while they’re not strictly speaking in my usual range of topics, given this blog’s name and the fact I haven’t posted a frog piece in quite a while, it seems this is a good moment to address that lack.

Monitoring frogs and amphibians at Trent University (Ontario, Canada)

From a March 23, 2015 Trent University news release,

With the decline of amphibian populations around the world, a team of researchers led by Trent University’s Dr. Dennis Murray will seek to establish environmental DNA (eDNA) monitoring of amphibian occupancy and aquatic ecosystem risk assessment with the help of a significant grant of over $596,000 from the Natural Sciences and Engineering Research Council of Canada (NSERC).

Awarded to Professor Murray, a Canada research chair in integrative wildlife conservation, bioinformatics, and ecological modelling and professor at Trent University along with colleagues Dr. Craig Brunetti of the Biology department, and Dr. Chris Kyle of the Forensic Science program, and partners at Laurentian University, University of Toronto, McGill University, Ontario Ministry of Natural Resources and Forestry and Environment Canada, the grant will support the development of tools that will promote a cleaner aquatic environment.

The project will use amphibian DNA found in natural breeding habitats to determine the presence and abundance of amphibians as well as their pathogens. This new technology capitalizes on Trent University’s expertise and infrastructure in the areas of wildlife DNA and water quality.

“We’re honoured to have received the grant to help us drive the project forward,” said Prof. Murray. “Our plan is to place Canada, and Trent, in a leadership position with respect to aquatic wildlife monitoring and amphibian conservation.”

Amphibian populations are declining worldwide, yet in Canada, amphibian numbers are not monitored closely, meaning changes in their distribution or abundance may be unnoticeable. Amphibian monitoring in Canada is conducted by citizen scientists who record frog breeding calls when visiting bodies of water during the spring. However, the lack of formalized amphibian surveys leaves Canada in a vulnerable position regarding the status of its diverse amphibian community.

Prof. Murray believes that the protocols developed from this project could revolutionize how amphibian populations are monitored in Canada and in turn lead to new insights regarding the population trends for several amphibian species across the country.

Here’s more about NSERC and Trent University from the news release,


NSERC is a federal agency that helps make Canada a country of discoverers and innovators. The agency supports almost 30,000 post-secondary students and postdoctoral fellows in their advanced studies. NSERC promotes discovery by funding approximately 12,000 professors every year and fosters innovation by encouraging over 2,400 Canadian companies to participate and invest in post-secondary research projects.

The NSERC Strategic Project Grants aim to increase research and training in areas that could strongly influence Canada’s economy, society or environment in the next 10 years in four target areas: environmental science and technologies; information and communications technologies; manufacturing; and natural resources and energy.

About Trent University

One of Canada’s top universities, Trent University was founded on the ideal of interactive learning that’s personal, purposeful and transformative. Consistently recognized nationally for leadership in teaching, research and student satisfaction, Trent attracts excellent students from across the country and around the world. Here, undergraduate and graduate students connect and collaborate with faculty, staff and their peers through diverse communities that span residential colleges, classrooms, disciplines, hands-on research, co-curricular and community-based activities. Across all disciplines, Trent brings critical, integrative thinking to life every day. As the University celebrates its 50th anniversary in 2014/15, Trent’s unique approach to personal development through supportive, collaborative community engagement is in more demand than ever. Students lead the way by co-creating experiences rooted in dialogue, diverse perspectives and collaboration. In a learning environment that builds life-long passion for inclusion, leadership and social change, Trent’s students, alumni, faculty and staff are engaged global citizens who are catalysts in developing sustainable solutions to complex issues. Trent’s Peterborough campus boasts award-winning architecture in a breathtaking natural setting on the banks of the Otonabee River, just 90 minutes from downtown Toronto, while Trent University Durham delivers a distinct mix of programming in the GTA.

Trent University’s expertise in water quality could be traced to its proximity to Canada’s Experimental Lakes Area (ELA), a much beleaguered research environment due to federal political imperatives. You can read more about the area and the politics in this Wikipedia entry. BTW, I am delighted to learn that it still exists under the auspices of the International Institute for Sustainable Development (IISD),

Taking this post into nanotechnology territory while mentioning the ELA, Trent University published a Dec. 8, 2014 news release about research into silver nanoparticles,

For several years, Trent University’s Dr. Chris Metcalfe and Dr. Maggie Xenopoulos have dedicated countless hours to the study of aquatic contaminants and the threat they pose to our environment.

Now, through the efforts of the International Institute for Sustainable Development (IISD), their research is reaching a wider audience thanks to a new video (Note: A link has been removed).

The video is one of a five-part series being released by the IISD that looks into environmental issues in Canada. The video entitled “Distilling Science at the Experimental Lakes Area: Nanosilver” and featuring Professors Metcalfe and Xenopoulos profiles their research around nanomaterials at the Experimental Lakes Area.

Prof. Xenopolous’ involvement in the project falls in line with other environmental issues she has tackled. In the past, her research has examined how human activities – including climate change, eutrophication and land use – affect ecosystem structure and function in lakes and rivers. She has also taken an interest in how land use affects the material exported and processed in aquatic ecosystems.

Prof. Metcalfe’s ongoing research on the fate and distribution of pharmaceutical and personal care products in the environment has generated considerable attention both nationally and internationally.

Together, their research into nanomaterials is getting some attention. Nanomaterials are submicroscopic particles whose physical and chemical properties make them useful for a variety of everyday applications. They can be found in certain pieces of clothing, home appliances, paint, and kitchenware. Initial laboratory research conducted at Trent University showed that nanosilver could strongly affect aquatic organisms at the bottom of the food chain, such as bacteria, algae and zooplankton.

To further examine these effects in a real ecosystem, a team of researchers from Trent University, Fisheries and Oceans Canada and Environment Canada has been conducting studies at undisclosed lakes in northwestern Ontario. The Lake Ecosystem Nanosilver (LENS) project has been monitoring changes in the lakes’ ecosystem that occur after the addition of nanosilver.

“In our particular case, we will be able to study and understand the effects of only nanosilver because that is the only variable that is going to change,” says Prof. Xenopoulos. “It’s really the only place in the world where we can do that.”

The knowledge gained from the study will help policy-makers make decisions about whether nanomaterials can be a threat to aquatic ecosystems and whether regulatory action is required to control their release into the environment.

You can find the 13 mins. video here: https://www.youtube.com/watch?v=_nJai_B4YH0#action=share

Shapeshifting frogs, a new species in Ecuador

Caption: This image shows skin texture variation in one individual frog (Pristimantis mutabilis) from Reserva Las Gralarias. Note how skin texture shifts from highly tubercular to almost smooth; also note the relative size of the tubercles on the eyelid, lower lip, dorsum and limbs. Credit: Zoological Journal of the Linnean Society

Caption: This image shows skin texture variation in one individual frog (Pristimantis mutabilis) from Reserva Las Gralarias. Note how skin texture shifts from highly tubercular to almost smooth; also note the relative size of the tubercles on the eyelid, lower lip, dorsum and limbs.
Credit: Zoological Journal of the Linnean Society

Here’s more about the shapeshifting and how the scientists figured out what the frogs were doing (from a March 23, 2015 Case Western Research University news release on EurekAlert; Note: A link has been removed),

A frog in Ecuador’s western Andean cloud forest changes skin texture in minutes, appearing to mimic the texture it sits on.

Originally discovered by a Case Western Reserve University PhD student and her husband, a projects manager at Cleveland Metroparks’ Natural Resources Division, the amphibian is believed to be the first known to have this shape-shifting capability.

But the new species, called Pristimantis mutabilis, or mutable rainfrog, has company. Colleagues working with the couple recently found that a known relative of the frog shares the same texture-changing quality–but it was never reported before.

The frogs are found at Reserva Las Gralarias, a nature reserve originally created to protect endangered birds in the Parish of Mindo, in north-central Ecuador.

The researchers, Katherine and Tim Krynak, and colleagues from Universidad Indoamérica and Tropical Herping (Ecuador) co-authored a manuscript describing the new animal and skin texture plasticity in the Zoological Journal of the Linnean Society this week. They believe their findings have broad implications for how species are and have been identified. The process may now require photographs and longer observations in the field to ensure the one species is not mistakenly perceived as two because at least two species of rain frogs can change their appearance.

Katherine Krynak believes the ability to change skin texture to reflect its surroundings may enable P. mutabilis to help camouflage itself from birds and other predators.

The Krynaks originally spotted the small, spiny frog, nearly the width of a marble, sitting on a moss-covered leaf about a yard off the ground on a misty July night in 2009. The Krynaks had never seen this animal before, though Tim had surveyed animals on annual trips to Las Gralarias since 2001, and Katherine since 2005.

They captured the little frog and tucked it into a cup with a lid before resuming their nightly search for wildlife. They nicknamed it “punk rocker” because of the thorn-like spines covering its body.

The next day, Katherine Krynak pulled the frog from the cup and set it on a smooth white sheet of plastic for Tim to photograph. It wasn’t “punk “–it was smooth-skinned. They assumed that, much to her dismay, she must have picked up the wrong frog.

“I then put the frog back in the cup and added some moss,” she said. “The spines came back… we simply couldn’t believe our eyes, our frog changed skin texture!

“I put the frog back on the smooth white background. Its skin became smooth.”

“The spines and coloration help them blend into mossy habitats, making it hard for us to see them,” she said. “But whether the texture really helps them elude predators still needs to be tested.”

During the next three years, a team of fellow biologists studied the frogs. They found the animals shift skin texture in a little more than three minutes.

Juan M. Guayasamin, from Universidad Tecnológica Indoamérica, Ecuador, the manuscript’s first author, performed morphological and genetic analyses showing that P. mutabilis was a unique and undescribed species. Carl R. Hutter, from the University of Kansas, studied the frog’s calls, finding three songs the species uses, which differentiate them from relatives. The fifth author of the paper, Jamie Culebras, assisted with fieldwork and was able to locate a second population of the species. Culebras is a member of Tropical Herping, an organization committed to discovering, and studying reptiles and amphibians.

Guayasamin and Hutter discovered that Prismantis sobetes, a relative with similar markings but about twice the size of P. mutabilis, has the same trait when they placed a spiny specimen on a sheet and watched its skin turn smooth. P. sobetes is the only relative that has been tested so far.

Because the appearance of animals has long been one of the keys to identifying them as a certain species, the researchers believe their find challenges the system, particularly for species identified by one or just a few preserved specimens. With those, there was and is no way to know if the appearance is changeable.

The Krynaks, who helped form Las Gralarias Foundation to support the conservation efforts of the reserve, plan to return to continue surveying for mutable rain frogs and to work with fellow researchers to further document their behaviors, lifecycle and texture shifting, and estimate their population, all in effort to improve our knowledge and subsequent ability to conserve this paradigm shifting species.

Further, they hope to discern whether more relatives have the ability to shift skin texture and if that trait comes from a common ancestor. If P. mutabilis and P. sobetes are the only species within this branch of Pristimantis frogs to have this capability, they hope to learn whether they retained it from an ancestor while relatives did not, or whether the trait evolved independently in each species.

Golden frog of Panama and its skin microbiome

Caption: Researchers studied microbial communities on the skin of Panamanian golden frogs to learn more about amphibian disease resistance. Panamanian golden frogs live only in captivity. Continued studies may help restore them back to the wild. Credit: B. Gratwicke/Smithsonian Conservation Biology Institute

Caption: Researchers studied microbial communities on the skin of Panamanian golden frogs to learn more about amphibian disease resistance. Panamanian golden frogs live only in captivity. Continued studies may help restore them back to the wild.
Credit: B. Gratwicke/Smithsonian Conservation Biology Institute

Among many of the pressures on frog populations, there’s a lethal fungus which has affected some 200 species of frogs. A March 23, 2015 news item on ScienceDaily describes some recent research into the bacterial communities present on frog skin,

A team of scientists including Virginia Tech researchers is one step closer to understanding how bacteria on a frog’s skin affects its likelihood of contracting disease.

A frog-killing fungus known as Batrachochytrium dendrobatidis, or Bd, has already led to the decline of more than 200 amphibian species including the now extinct-in-the-wild Panamanian golden frog.

In a recent study, the research team attempted to apply beneficial bacteria found on the skin of various Bd-resistant wild Panamanian frog species to Panamanian golden frogs in captivity, to see if this would stimulate a defense against the disease.

A March 23, 2015 Virginia Tech University news release on EurekAlert, which originated the news item, provides a twist and a turn in the story (Note: Links have been removed),

They found that while the treatment with beneficial bacteria was not successful due to its inability to stick to the skin, there were some frogs that survived exposure to the fungus.

These survivors actually had unique bacterial communities on their skin before the experiments started.

The next step is to explore these new bacterial communities.

“We were disappointed that the treatment didn’t work, but glad to have discovered new information about the relationship between these symbiotic microbial communities and amphibian disease resistance,” said Lisa Belden, an associate professor of biological sciences in the College of Science, a Fralin Life Science Institute affiliate, and a faculty member with the new Global Change Center at Virginia Tech. “Every bit of information gets us closer to getting these frogs back into nature.”

Studying the microbial communities of Panamanian golden frogs was the dissertation focus of Belden’s former graduate student Matthew Becker, who graduated with a Ph.D. in biological sciences from Virginia Tech in 2014 and is now a fellow at the Smithsonian Conservation Biology Institute.

“Anything that can help us predict resistance to this disease is very useful because the ultimate goal of this research is to establish healthy populations of golden frogs in their native habitat,” Becker told Smithsonian Science News. “I think identifying alternative probiotic treatment methods that optimize dosages and exposure times will be key for moving forward with the use of probiotics to mitigate chytridiomycosis.”

Here’s a link to and a citation for the paper,

Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus by Matthew H. Becker , Jenifer B. Walke , Shawna Cikanek , Anna E. Savage , Nichole Mattheus , Celina N. Santiago , Kevin P. C. Minbiole , Reid N. Harris , Lisa K. Belden , Brian Gratwicke. April 2015 Volume: 282 Issue: 1805 DOI: 10.1098/rspb.2014.2881 Published 18 March 2015

This is an open access paper.

For anyone curious about the article in the Smithsonian mentioned in the news release, you can find it here.