Category: science

  • Panel would change Canada’s research landscape

    Panel would change Canada’s research landscape

    CanadaReportPosted on the Nature News blog on 14 October 2011. 

    In an effort to address Canada’s problem with innovation, an independent panel has recommended a radical overhaul that includes the creation of a new funding council and transforms the country’s largest research entity, the billion dollar National Research Council (NRC).

    Study after study has shown that Canada’s businesses invest less on R&D, relative to the country’s gross domestic product, than those of many other OECDcountries and, unlike others, has actually decreased its spending over the last decade. Many of these business investments include government support in the form tax credits, training programs, or grants.

    In an effort to make the best use of the government’s investments the six-member expert panel developed six broad recommendations include appointing a Minister of Innovation and creating the Industrial Research and Innovation Council (IRIC).

    According to the panel’s report, to be released on 17 October, the proposed IRIC would be an arm’s-length funding agency to help entrepreneurs bring ideas to the marketplace. Under the plan, the council would focus on business-driven support by expanding some existing programs, such as the Industrial Research Assistance Program, which offers advice and funding to support high-risk R&D, while cutting the tax credits available for business R&D. The Natural Sciences and Engineering Research Council, the granting agency that funds a large portion of Canadian scientists, but which also hosts a number of business-related support programs, would instead focus its innovation investments on projects housed within universities.

    The panel’s recommendations also include breaking up the NRC by sending those of its member institutes that are engaged in more basic research to universities where their funding would be managed by NSERC and the Canadian Institutes of Health Research. The institutes undertaking more applied, industry-oriented research would be rolled into a non-profit research organization, overseen by the IRIC. These proposed changes parallel previous reports that the NRC would focus on industry-driven research.

    When the report is released on Monday, the response is likely to be mixed. Some will favour the streamlining of multiple programs and greater direct support to R&D. Others will likely be concerned about the fate of the researchers, facilities and research at the various NRC instittutes.

    Indira Samarasekera, president of the University of Alberta, in Edmonton, says folding NRC’s basic research institutes into universities could boost output, but that it will be challenging to implement, especially if the laboratory isn’t located on campus. “It can be difficult to get independent researchers to rally around a specific scientific problem that may be industry driven,” says Samarasekera, whose university houses the NRC’s National Institute of Nanotechnology. “But this is the best of both cultures.”

    Gary Goodyear, the Minister of State for Science and Technology, would not comment on the specifics of the report, as it has not been officially released. In a statement he said the panel’s advice will help “modernize programs that support innovation” with the goal of encouraging more companies to invest in R&D.

    According to the mandate, the panel’s recommendations could not increase or reduce federal funding to R&D initiatives. “Where we have identified opportunities for savings, we expect the government to reallocate the savings to provide funds for our other recommendations,” the panel wrote.

    Canada’s innovation gap has been scrutinized before (here and here), but this time the report lays out a clear set of recommendations.

  • Are your genes your destiny? (Not if your mom has anything to say about it.)

    Are your genes your destiny? (Not if your mom has anything to say about it.)

    McGill scientists are playing a leading role in explaining how the nature vs. nurture debate is even more complicated than we thought.

    This article originally appeared in the Spring-Summer 2011 issue of the McGill News

    What if your ability to pay the rent, to buy groceries or the nature of your relationships set up your children for cardiovascular problems, diabetes or even mental health issues? Although it’s not a far-fetched idea, researchers struggled for years to find biological explanations that linked socioeconomic status or trauma to health. And then, beginning in 2004, scientists at McGill began to untangle some of those connections.

    Piece by piece, study by study, a trio of scientists, backed by a talented crew of post-doctoral fellows, graduate students and research associates, has found evidence that early life experiences can leave lasting marks on the brain. They’ve dismantled the long-standing debate over nature versus nurture, and discovered that it’s not one or the other, but both.

    Though the early 2000s were marked by gushing enthusiasm over the sequencing of the human genome and the secrets it would uncover, Michael Meaney, Moshe Szyf and Gustavo Turecki, PhD’99, targeted their study of health and heredity at another level of genetic information. They looked above the genome, at the epigenome, a code of biochemical tags, often attached to DNA, that turn genes on or off.

    Their research has run the gamut of experimental design: they’ve studied rodents to understand the impact of maternal care on stress, looked at post-mortem tissue to get at the biological effects of childhood abuse, and are currently following 500 mothers and their children to learn how maternal stress and well-being influence child development. Their group has published in the top  scientific journals and their work has been featured in media around the world, including the New York TimesBBCTime, the Economist, and, more recently, the New Yorker. Together they’ve helped usher into the spotlight this new field of epigenetics and put Montreal at its epicentre.

    Getting a good licking

    Michael Meaney is a neurobiologist and clinical psychologist who splits his time between the Douglas Mental Health University Institute at McGill and the Singapore Institute for Clinical Science. In his lab, there are two kinds of rat mothers: those that lick and groom their pups and those that don’t. He and his team have found that the well-licked pups are even-tempered critters that produce less of the stress hormone cortisol when faced with a pressure-filled situation. These cool-headed traits persist into adulthood. But Meaney wanted to understand how an environmental signal, such as the nuzzles and caresses of a nurturing mother, could reshape the genome and change the rat’s response to stress.

    At a research meeting in Madrid, Meaney encountered Szyf, a molecular biologist and a fellow McGill scientist. The two hadn’t really known each other in Montreal, but as they sipped beer together in a Spanish bar, they launched into an animated discussion about how experiences could leave a lasting mark on the genome and a new research partnership was soon forged.

    Szyf, the University’s James McGill professor of pharmacology and therapeutics, has long studied epigenetics in tumour cells—the dynamic modification of the genome through a process called methylation. The pair thought methylation, which alters how genes function, might be the mechanism they were looking for.

    Switching the signals

    The genetic code is written in letters, each one representing a different chemical: guanine (G), cytosine (C), adenine (A) and thymine (T). Three billion of these letters are strung end to end like patio lanterns, coiled and wrapped around proteins and packed into each cell. The genome is the ultimate insider’s guidebook to the human: it contains all the information a cell needs to produce a neuron, an acid-producing cell in the stomach, or any of the other 200 different cell types crowded into the human body.

    But it is the epigenome that provides the directions, revealing which genes should be expressed by adding or removing chemical tags composed of carbon and hydrogen from the genome. A tag planted near a gene will shut it down.

    When the researchers looked at the epigenomes of the rats, they found that when a mother licks her pups, she switches on a gene that dials down the amount of stress hormones that get released in times of duress. Meaney and Szyf had found a mechanism to link environmental cues and gene expression.

    It was an unconventional conclusion. Though scientists have known about these tags for some time, many thought their role was restricted to cell differentiation, the process that ensures that, for example, a heart cell remains a heart cell when it divides by expressing only the genes a heart cell requires. Instead, Meaney and Szyf, working with graduate student Ian Weaver, PhD’06, and their team, found evidence that life experiences alter DNA by painting it with chemical tags and altering nearby gene expression.

    They also showed that they could remove the stress-related methylation by putting unlicked pups with nurturing foster-mothers, or by injecting a drug called trichostatin A into the brains of adult rats—in effect erasing the negative effects of early life experiences.

    They submitted the study to Nature and Science and elsewhere. “We got mixed responses. Some were really excited, others were really skeptical,” says Szyf. The reviewers took issue with the idea that such epigenetic changes could occur after birth. How could a complex system that made sure your eye was always an eye also be manipulated by motherly love? Szyf speculates that the system has a highly organized component that is very strict, “and can’t be messed up,” and a responsive component that allows the system to adapt. The study was finally published in Nature Neuroscience in 2004, and it made a huge splash.

    Traumatized brains

    One of the scientists who took note was Gustavo Turecki. “The nature vs. nurture debate has been very divisive and created very strong rivalries between the different factions, dividing psychiatry departments,” he says.

    A psychiatrist and the director of the McGill Group for Suicide Studies, Turecki approached Meaney after hearing him speak about his research at a scientific meeting. Turecki, who is also the director of the Réseau Québécois de recherche sur le suicide, had access to the Quebec Suicide Brain Bank, an almost unique resource for scientists keen on understanding the neurobiology of suicide.

    In 2005, Patrick McGowan joined Meaney’s lab as a postdoctoral fellow after finishing his PhD at Duke University. He’d jumped at the chance to come back to Montreal (he’d obtained his undergraduate degree from Concordia) and to work with Meaney in the field of epigenetics. “I was interested in the epigenetics story from the beginning. It had always been an interesting question: Why do these effects of early life experiences persist? And why do [traumatic experiences] lead to an increased risk for mental disorders? There hadn’t really been a good explanation, but epigenetics offered the first clues as to how that can happen,” says McGowan.

    McGowan thought that when he joined Meaney’s lab he’d be working with animals, where his background lay. Instead, because of Turecki’s involvement, McGowan found himself examining human tissue. “Humans are so variable. A lot of people asked, ‘How could you possibly pull out the effects of early life experiences?’” he says. “We had to find the right population, the right cohort, and with Gustavo Turecki’s subjects, we had that. These people had committed suicide. [We] also had the life histories of these individuals and [we knew] they’d suffered terrible, terrible experiences.”

    McGowan identified 36 brain tissue samples for the study. They came from men who had been abused as children and who had later committed suicide, and men who had committed suicide, but had no history of abuse. The last group came from otherwise healthy men and made up the control group.

    The researchers chose to focus on the stress response genes that are expressed in the hippocampus, one of the brain structures involved in anxiety, depression, placing events in place and time, and storing long-term memories. The researchers discovered something consistent among the suicide victims who had troubled pasts. They found methyl groups fixed to the genes that control the production of stress hormone receptors in the brain, making these individuals far more biologically sensitive to stress.

    “What we did was pretty cool. It might take us somewhere that lets us understand why the genome operates differently in one individual versus another, and why environmental events might explain that,” says Meaney.

    In 2003, Meaney and other investigators began recruiting pregnant women to participate in the Maternal Adversity, Vulnerability and Neurodevelopment (MAVAN) project. They enrolled 500 women, some of whom suffered from depression or lived in poverty. They visited the mothers to evaluate the type of stressors they faced: Did they have enough money to pay for rent, or buy food for the family? Were they in a violent relationship? What sort of social support did they have? And they followed the children from birth, checking in at three, six, 12, 18 and 24 months, and every year after until they turned eight. The researchers did a battery of tests, measuring cognitive and physical development, attention, food preferences and mother-child interaction. They measured hormone levels and collected DNA.

    “MAVAN is unique in Canada,” says Hélène Gaudreau, MAVAN’s study coordinator.

    A question of confidence

    The study is ongoing, so few of the results have been published. Part of the project measures the kids’ confidence and compares it to their genetic backgrounds and upbringing. Generally, a child’s confidence level drops following the experiencing of a failure. But what Meaney and Gaudreau have found is that genetics and maternal care combine to determine whether confidence plummets or only dips following failure.

    The serotonin transporter is one of the proteins associated with emotion. Individuals who possess a shorter version of the gene are at a greater risk of developing depression. But genetics alone can’t predict which children will be most upset when they fail a test. It also depends on the child’s attachment to his mother, they discovered. The study found that those with the shorter gene avoided the emotional crash if they were cuddled and cooed over, and formed a strong bond with their mothers.

    “There are two points to this: one is the interdependence of genes and environment, and the other is that your genes don’t make you sick. They make us more or less susceptible to environmental influences. It’s a much more sophisticated way of thinking about what genes do,” says Meaney.

    “Hopefully, we’ll be able to see which children are more sensitive to developing vulnerabilities, and we can find a way to help those families,” says Gaudreau. “A lot of people talk about maternal stress and its impact on the baby. But it’s not fixed—you can reverse some of those effects and that is good news.”

    Over the last decade, Montreal has become an epigenetics hotspot. In addition to the MAVAN study, Meaney continues to study rodents, taking a broader look at the genome to understand whether particular types of genes are more vulnerable to the maternal influence than others. Szyf recently received funding through a European neurosciences and mental illness research network to study the effects of prenatal, perinatal and postnatal stress and its epigenetic impacts on depression. McGowan, who is now an assistant professor in biological science at University of Toronto Scarborough, is collaborating with Szyf and researchers at Université de Montréal and Université Laval on a study of twins that will examine such things as parenting behaviour and family functioning. The study could help explain how environmental factors affect early mental health development. McGowan is also preparing to teach a university-level course in epigenetics, introducing the next generation of scientists to a field he helped pioneer.

  • Canadian research shift makes waves

    Canadian research shift makes waves

    McDougallNRC

    Agency’s focus on industry-driven projects raises concerns that basic science will suffer.

    Published in Nature, 19 April 2011.

    Canada’s largest research entity has a new focus — and some disaffected scientists. On 1 April, the National Research Council (NRC), made up of more than 20 institutes and programmes with a total annual budget larger than Can$1 billion (US$1 billion), switched to a funding strategy that downplays basic research in favour of programmes designed to attract industry partners and generate revenue. Some researchers suggest that the shift is politically driven, because it brings the agency into philosophical alignment with the governing Conservative Party of Canada, which is in the middle of an election campaign.

    The change was announced in a memo from NRC president John McDougall on 2 March, and involves the transfer of authority over 20% of the agency’s research funds and the entire Can$60-million budget for large equipment and building costs to the NRC’s senior executive committee, which will direct it towards research with a focus on economic development, rather than pure science. Until now, individual institutes have had authority over research spending. McDougall wrote that in future, 80% of the research budget will be centralized, with “curiosity and exploratory activities” to be funded by the remaining 20%.

    In Canada, most funding for academic researchers flows through agencies other than the NRC. However, with 4,700 scientists, guest researchers, technologists and support staff pursuing specialities from astrophysics to plant biotechnology at its institutes, the NRC plays a vital part in the nation’s scientific community, as a generator of original research and a service provider to government and industry. The shift away from basic science “weakens” the NRC’s labs, because they “are required to bridge two cultures — the basic and applied”, says John Polanyi, a Nobel laureate and a chemist at the University of Toronto.

    But in a follow-up memo on 24 March, McDougall said “most ‘researcher directed’ and basic work is now carried out in academic institutions. Duplicating the efforts of universities at NRC doesn’t make much sense.”

    Four proposed ‘flagship programmes’ described in the original memo, each with a marketable outcome, provide a glimpse at the direction the agency has in mind. They include developing a strain of wheat resilient to environmental stress; improving the manufacture of printable electronics; increasing domestic production of bio composite materials; and using algae to soak up carbon dioxide emissions from industry. NRC researchers have expressed concern that jobs and programmes that do not fit with the new agenda are at risk. The agency declined to comment.

    Tom Brzustowski, who studies commercialization of innovation at the University of Ottawa, says that the adjustment to the NRC’s focus will support areas that have been weak. “By focusing on the flagship programmes there is still room to do the whole spectrum of research. It’s a good strategic move,” he says.

    But the news has rekindled anxiety over how Canada’s government has been directing science funding — criticisms that have grown sharper as the federal election on 2 May approaches.

    On 22 March, the government presented its 2011 budget, which offered modest increases to the federal research councils, but did not make up for cuts in 2009 (see Nature 457, 646; 2009). The budget also included multi million-dollar investments in neuroscience and physics. Few question the quality of work that such investments would produce, but critics say that the government is exerting too much control over the country’s research, rather than allowing peer review to guide funding.

    “It’s risky to divert funds away from the granting councils, but the government does it because it looks politically better for them,” says Robert Dunn, associate director of scientific affairs at the Montreal Neurological Institute. “Peer review is the very best mechanism to ensure that the limited research resources we have are allocated to the best researchers and projects.”

    Photo: NRC Canada

  • Banking on biodiversity

    Banking on biodiversity

    The diversity of life on Earth gives ecosystems the resilience they need to thrive. Yet every day scores of plants and animals go extinct, victims of activities we humans undertake to feed, clothe, house and trans­port ourselves. How can we meet our own needs without destroying that which sustains us?

    The west coast of Vancouver Island in British Columbia, Canada, has a rugged, involuted shoreline, etched by fjords, sand dunes and shel­tered coves. It is sandwiched between two biospheres, the dark swelling sea and the emerald temperate rain forest, and it attracts all sorts—from salmon to surfers.

    As idyllic as it seems, the island is under pressure. Wild salmon populations seem to ebb and flow unpredictably, and logging, transporta­tion and aquaculture—activities that promise economic prosperity for the people who live here—are chipping away at the natural coastal ecosystem and the species it contains.

    The tug-of-war between opposing priorities—the conservation of natural assets and de­velopment—poses a challenge for West Coast Aquatic, the public-private partnership in charge of creating a marine spatial plan for the 285-mile-long shoreline. How to lay out a plan that allows the area to develop while preserving its natural resources, ecosystems and habitat?

    This balance of development and conservation is a challenge wherever people are found. At its core is the ability to understand and factor in the true impact—economic and otherwise—of human activity, whether it’s shipping, aquaculture or recreation, on the environment. Would con­struction of an offshore wave energy installation cut into revenues brought in by recreation? If so, by how much? Is it worth it? What effect would expansion of aquaculture have on native finfish and shellfish? At what price to ecosystem (and economic) integrity?

    For West Coast Aquatic, the answers may come from “SimCity”-like software that can illustrate the impacts of different scenarios on human well-being and biodiversity.

    Called Marine InVEST, the software considers a region’s underwater topography, native habitats, species distribution, fishing practices, aquaculture sites, coastline features (such as dunes and sea grasses), wave height and periodicity, and recreational activities. Once those data have been collected, Marine InVEST can calculate the outcomes of a variety of scenarios, such as establishing a protective area or shellfish aquaculture sites.

    “The tool is flexible in terms of outputs, whether it’s in meters of shoreline not eroded or pounds or number of fish—or dollars,” says Anne Guerry, lead scientist for the project’s marine initiative.

    The west coast of Vancouver Island is the first demonstration site of Marine InVEST by the Natural Capital Project, a partnership among Stanford University, The Nature Conservancy, World Wildlife Fund, and the University of Minnesota’s Institute on the Environment.

    “In the past, we didn’t think too much about the spatial overlap of marine activities. We tended to think of them in silos,” says Guerry. “A tool like Marine InVEST allows us to make clear connections between different activities, so we can understand and value each one and how emphasizing one can come at the cost of another.”

    The group plans to use Marine InVEST in other demonstration sites around the world, including Belize, Puget Sound, Chesapeake Bay and Galveston Bay.

    Already, governments, nongovernmental organizations and scientists at universities and institutes in Indonesia, Hawaii, Tanzania, Colom­bia, Ecuador and China are adopting InVEST, the Natural Capital Project’s land-focused companion to Marine InVEST, in their decision making. In the East Cauca Valley, Colombia, The Nature Conservancy and ASOCAÑA, an association of sugarcane producers, formed a water fund called Fondo de Agua por la Vida y la Sostenibilidad (Water Fund for Life and Sustainability) to invest in key areas to keep the water sediment-free and available. The group then used InVEST to map carbon storage, habitat quality and soil stabiliza­tion within the region—showing, for example, where the group should invest in reforestation or in fencing off an area, while taking into account the communities that live within the watersheds.

    “Spatial mapping [like InVEST] lets us map out impacts, letting stakeholders better view and understand impacts and trade-offs,” says Ken Bag­stad, a postdoctoral associate at the University of Vermont. Bagstad is applying InVEST models for water, carbon, biodiversity and cultural services to the exceptionally biodiverse San Pedro River watershed in southeastern Arizona. Home to one of the last free-flowing rivers in the Southwest and a key bird migration corridor, the region is struggling to balance the water needs of the com­munity with the riverbank ecosystem. Bagstad is using InVEST and another mapping tool, ARIES, to test several scenarios, including an option that would restore an invasive mesquite shrubland to native grasslands. The main challenge of using such tools, says Bagstad, is that they are still in their infancy and require some more work before they can be considered a generalized global tool.

    The Planet’s Heartbeat

    Biodiversity is the measure of the variety of life. It is the seed from which all ecosystems spring. It is the foundation of the wetlands that purify water and offer protection against floods, the forests that capture carbon dioxide from the atmosphere and store it in biomass, and the coral reefs that offer breeding grounds for fish. Biodiversity provides societies with goods—food, fuel, fiber and medicinal plants—and services—erosion control, hydropower, cultural significance, recreation, carbon sequestration. Clean air, Vermont maple syrup, opportunities to ice fish, plant-sustaining soil and much more all trace back to thriving living things. Each species is like a spot of paint in one of Seurat’s pointillist masterpieces—an element of the whole picture.

    Environmentalists Tina Fujikawa and Joseph Dougherty recently wrote, “Monitoring trends in biodiversity is like listening to the heartbeat of the planet.” If so, the planet’s pulse is weak and sluggish. Many of Earth’s mammal, bird and amphibian species—10 to 30 percent—are threatened with extinction due to human activities. Some, like corals, which have long been identified as extinction risks, are moving closer to extinction, and ecosystems continue to deteriorate and be splintered apart. Scientists say that if current trends endure, societies could suffer heavy consequences.

    In a 2009 article in Nature, an international group of scientists and economists led by Johan Rockström of the Stockholm Resilience Centre at Stockholm University identified and quantified nine planetary boundaries—from climate change and ocean acidification to global fresh water use and biodiversity loss. These boundaries map out humanity’s safe operating space on Earth. Species loss, the group acknowledged, was a natural process, albeit one that has acceler­ated under human influence. If the extinction rate could be kept at or below 10 species per million species per year, they reasoned, the Earth’s ecosystems might survive. Alas, the current rate is 10 times the goal. For biodiversity loss, the planetary boundary has been exceeded.

    Continue reading the article in Momentum, the magazine of the University of Minnesota’s Institute on the Environment.

  • Cold cash for cold science

    Cold cash for cold science

    The recent funding wrap-up from the international polar year (IPY) has left many Canadian researchers scratching their heads, trying to find a way to continue their arctic science projects. A new grant from the Natural Sciences and Engineering Research Council of Canada may help close that research-funding gap.

    In its announcement yesterday, NSERC opened a competition to fund large-scale research with a focus—for this round of funding—on northern earth systems. The Discovery Frontiers initiative will heft Can$4 million over five years on the successful research team to study the physical, chemical, biological and social factors that affect the North and its inhabitants—and to come up with solutions. Fresh water, sea level, permafrost, weather patterns, biodiversity or climate change adaptation could be part of the successful pitch. The northern community will help define the projects and their goals.

    The story continues at Nature’s blog The Great Beyond.