Mercer at the bat

Rick Mercer visits McMaster University, stabs a man in the neck with a pen and is attacked by a bat.

Happy Hallowe’en from Research Matters.

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Helping infertile men avoid ...

Sharon Oosthoek | May 26, 2016

Infertile men who want children face the prospect of painful and expensive testicular biopsies with no guarantee it will result in their partner's pregnancy. But thanks to the collaborative work of University of Toronto scientists, there is now another way. Stephen Scherer, a geneticist and director of the Centre for Applied Genomics, and laboratory geneticist Elena Kolomietz at Mount Sinai Hospital, have come up with a non-invasive test that lets men know whether a biopsy has a chance of leading to fatherhood. Testicular biopsies are designed to retrieve sperm from men whose ejaculate contains none. The problem is that men with certain types of genetic mutation don't have any sperm in their testes to retrieve. The new  test makes it easier to diagnose these mutations and to find other genetic abnormalities that have yet to be linked to male infertility. "It's extremely important to know the genetic cause of a disease. It's important for the patient to know for closure," says Kolomietz. "Infertility is unfortunately considered a social issue and not a disease. But it is a disease." Fifteen per cent of couples trying to conceive run into fertility problems, with men and women equally likely to be infertile. Among men, the most common culprit is missing genes on the Y chromosome. These genes contain instructions that tell sperm how to develop. When a sperm cell is created, the chromosomes duplicate, rearrange and sometimes misalign, leading to dropped genes called microdeletions. Men with these microdeletions produce few sperm, and some produce none at all, depending on the type of microdeletion. The traditional test designed to diagnose which type of microdeletion is at play can analyze only five regions of the genome at a time. "To investigate more regions, you have to run several experiments, so it's labour-intensive and costly," says Kolomietz. Plus, the traditional test picks up only those genetic abnormalities which it has been programmed to seek, ruling out unknown mutations. A better way Kolomietz and Scherer’s test, on the other hand, uses microarray technology to analyze the entire Y chromosome at once. A microarray, also known as a DNA chip or biochip, is a collection of microscopic DNA spots attached to a solid surface. Researchers place biological samples — in this case, blood — on the surface. The DNA spots then act as a sort of lure, capturing genes in the blood cells that contain the same DNA sequence. Their microarray can quickly pick out not only the known microdeletions linked to infertility, but also other mutations that can then be tested for possible links to infertility. That’s because the DNA spots on Kolomietz’s microarray are designed to detect either extra or missing genetic material on a patient’s Y chromosome. It does this by comparing it to DNA from a healthy person. Kolomietz's microarray test has been available since 2014. She hopes it will not only save men unnecessary pain and suffering, but let them realistically assess options for treatment and consider other possibilities such as donor sperm or adoption. “Once you know what you’re facing, you can make informed decisions,” she says.

Outrunning the fat gene

Pippa Wysong | May 17, 2016

Moderate physical activity blunts the effects of a key gene known to cause obesity, according to recent research out of McMaster University. This is good news for people who are prone to being overweight because it runs in the family. It shows your genes are not your destiny, says McMaster human geneticist David Meyre,  and that often their effects can be modulated by lifestyle choices. Meyre and his team published a study this year showing just how much of an effect varying levels of exercise have on the activity of several obesity genes. To do this, he and his colleagues looked at the genetics and exercise history of 17,400 people from six ethnic groups from 17 countries. The researchers used data from EpiDREAM, a large international study designed to investigate the interplay of environment (such as lifestyle choices) and genetics on people at risk for developing diabetes. It was launched by researchers at McMaster in 2006. Meyre's team focused on the participants’ self-reported activity levels, genetic predisposition to obesity, body mass index (BMI) and body adiposity index (BAI). The BAI is a relatively new measure used to determine the amount of body fat a person has. Not surprisingly, those who were more physically active had, in general, lower BMI and BAI readings, both at the start of the study and three years later. The researchers also analyzed the mutated form of 14 different genes known to play a role in obesity, and how each was related to participants' obesity and exercise. Of the genes analyzed, they found that people with any of four particular genes (FTO, CDKAL1, TNN13K and GIPR) were more likely to be obese. But what was intriguing was that people who had one particular gene, FTO, had a bigger response to exercise. In fact physical activity decreased the impact of the mutated FTO gene on BMI and BAI by up to 70 per cent —  a much stronger effect than exercise had on people who had any of the other genes studied. The study shows that physical activity can combat genetic risks. Gene linked to appetite The mutated FTO gene was discovered in 2007 and is known to be associated with early-onset and severe obesity. This gene occurs in about 22 per cent of people who are prone to obesity and is believed to have a role in modulating appetite. People with one mutated form of FTO are generally about 1.5 kg heavier than their counterparts with normal versions of the gene. But if they have two of the genes, they are about 3 kg heavier. The take-home message from Meyre's study is simple: “Exercise is good for everybody, but it is even more beneficial for this particular subgroup – people with the mutated FTO gene. They lose more weight from physical activity than those whose obesity was associated with other genes,” he says. How much exercise? “Even with one hour a week of something like jogging, these people get a benefit,” he says. Meyre argues that people would benefit from knowing whether or not they have specific genes predisposing them to obesity. If people know how much exercise they need to do, they would be more likely to stick with it, he says. Even better, they could use exercise to prevent packing on the pounds in the first place. Once a person puts on extra weight, “the body works to try to replace those cells, to restore equilibrium,” says Meyre. This is why keeping weight off is so difficult. “The best way to eradicate obesity is to prevent it,” he says.  

Unlocking the heart’s ...

Laura Eggertson | May 13, 2016

Whenever she hears about the sudden death of a young athlete who has collapsed with heart failure on a hockey rink, soccer field or basketball court, Mona Nemer is painfully reminded of the importance of her work. The University of Ottawa biochemist and molecular cardiologist's pioneering work involves discovering genes critical for normal heart development – genes that, if mutated or absent, lead to birth defects or heart disease. One of those genes, which Nemer and her team identified, is GATA4. The nondescript name does not do justice to the gene’s vital function: if defective, GATA4 can cause a condition called atrial septal defect, a tiny hole between the two chambers of the heart. This hole is so small it may remain undetected. But an atrial septal defect can disrupt the heart’s blood flow, oxygenation and pressure. It is often the cause of the sudden, and sometimes fatal, collapse of otherwise healthy young athletes who no one knew had the problem. “Every year, we hear about a player who collapses during a game and, inevitably, they later diagnose a congenital heart defect,” says Nemer. Ultimate goal: preventing disease Identifying the gene responsible is the first step in diagnosing and, one day, preventing the cardiac disease that people born with these defects may experience. And identification alone isn’t enough, Nemer points out, because not everyone with the genetic mutation will have the same structural heart defect. Additional genetic and environmental factors can change the outcome, even for siblings, she says. “The new frontier is to understand what the modifiers are that will actually cause the same change (in a gene) to be linked to a defect in one person, but not to cause any defect in another person,” she says. Although Nemer’s research involves studying the biochemistry of animal models, she collaborates with researchers at the University of Ottawa Heart Institute and networks in Montreal, England and Australia to investigate how her findings translate into human genomics. “The ultimate goal is to prevent these birth defects, and I think we will likely be able to prevent some, but not all of them,” Nemer says. In the meantime, knowing that someone carries a mutated copy of the gene, and thus faces a higher risk of cardiac disease, could lead to better screening and follow-up, as well as lifestyle interventions aimed at prevention. Second gene identified  In addition to GATA4, Nemer and her colleagues have also identified GATA5, another cardiac gene they have linked to two critical issues: blood pressure regulation and bicuspid aortic valve defect. This is another common heart defect that results in babies being born with two rather than three leaflets (branches) on the aortic valve. The researchers now know that GATA5 interferes with blood pressure regulation by causing defects in small blood vessels. Those defects increase blood pressure and can eventually lead to heart attacks. The gene also interferes with the normal functioning of heart valves and can disrupt the heart’s normal rhythm. It is the main reason why some people under 60 require valve replacements. Nemer hopes her research to identify the genes and proteins that drive the normal formation of the heart will also advance regenerative medicine. In the next decade, she believes that researchers will be able to grow cardiac cells outside the body that will, once they are grafted onto the heart, help repair damaged tissue. Although researchers have begun that process, they haven’t yet captured all the “ingredients” – the different genes – that could help repair specific areas of the heart, such as valves. Nemer’s discovery of the important roles played by GATA4 and GATA5 may lead to the development of more targeted, regenerative heart cells. “This is the kind of incremental knowledge that we are collecting. Once you have a key, you can unlock other things,” says Nemer. "We are extremely well placed to continue making discoveries, but just as importantly, to translate them into better patient care.”   This story was originally published by the University of Ottawa. It has been edited for brevity and is republished here with permission. 

Ancient Black Death DNA ...

Michelle Donovan | May 9, 2016

An international team of researchers, including McMaster University's Hendrik Poinar, has uncovered new information about the Black Death in Europe and its descendants, suggesting it persisted on the continent over four centuries, re-emerging to kill hundreds of thousands in Europe in separate, devastating waves. The findings address the longstanding debate among scientists about whether or not the bacterium Yersinia pestis — responsible for the Black Death — remained within Europe for hundreds of years and was the principal cause of some of the worst re-emergences and subsequent plague epidemics in human history. Until now, some researchers believed repeated outbreaks were the result of the bacterium being re-introduced through major trade with China, a widely-known reservoir of the plague. Instead, it turns out the plague may never have left. “The more plague genomes we have from these disparate time periods, the better we are able to reconstruct the evolutionary history of this pathogen” says Poinar, an evolutionary geneticist. Poinar collaborated with researchers at the University of Sydney, the École Pratique des Hautes Études in France, the University of Tubingen, and others, to map the complete genomes of Y.pestis, which was harvested from five adult male victims of the 1722 Plague of Provence. To do so, they analyzed the dental pulp taken from the five bodies, originally buried in Marseille, France. Researchers were able to extract, purify and enrich specifically for the pathogen’s DNA, and then compare the samples with over 150 plague genomes representing a world wide distribution as well as from other points in time, both modern and ancient. By comparing and contrasting the samples, researchers determined the Marseille strain is a direct descendant of the Black Death that devastated Europe nearly 400 years earlier and not a divergent strain that came, like the previous pandemic strains Justinian and Black Death, from separate emergences originating in Asia. More extensive sampling of modern rodent populations, in addition to ancient human and rodent remains from various regions in Asia, the Caucasus and Europe, may yield additional clues about past ecological niches for plague. Rodents and their fleas are carriers of the plague. “There are many unresolved questions that need to be answered: why did the plague erupt in these devastating waves and then lay dormant? Did it linger in the soil or did it re-emerge in rats? And ultimately why did it suddenly disappear and never come back? Sadly, we don’t have the answer to this yet,” says Poinar. “Understanding the evolution of the plague will be critically important as antibiotic resistance becomes a greater threat, particularly since we treat modern-day plague with standard antibiotics. Without methods of treatment, easily treatable infections can become devastating again,” he says. This story was originally published by McMaster University. It has been edited for brevity and is republished here with permission.
genetic barcodes

Barcoding life, one species ...

Sharon Oosthoek | May 2, 2016

Nobody knows for sure how many species exist. But scientists are certain we have identified only a fraction of the plants, animals and fungi on the planet — roughly 1.7 million species out of an estimated 10 to 20 million. "Most of the yet-to-be-identified species will be tinier life forms, but the numbers could even be larger," says University of Guelph biologist Paul Hebert. "That's just a best guess." Making an inventory of all life then would seem a Sisyphean task. But back in 2003, Hebert and his research team proposed a DNA tool for doing exactly that. At the same time, they made a convincing case for why we might want such an inventory: our species is accelerating the extinction rate of other species, and as Hebert puts it, "people take action when they know what is happening to life." Their argument was convincing enough to lead to the creation in 2010 of the International Barcode of Life (iBOL) project, an alliance representing 26 countries and headquartered at the University of Guelph.  Since then, affiliated researchers have collected from all over the world biological samples such as feathers, fur, blood and tiny bits of tissue. In 2015, they reached their goal inventorying half a million species. They have now set a ambitious target of identifying all species on the planet by 2040. As Hebert and his team originally envisioned, the tool the researchers are using to identify species is a short section of DNA from a standardized region of the genome, found in all living things. The sequence of the molecules that make up that chunk of DNA can be used to identify different species, in the same way a supermarket scanner uses the black stripes of the UPC barcode to identify purchases. As an added bonus, the DNA section is short enough to be sequenced quickly and cheaply, yet long enough to discriminate species. Fish out of water The tool has already been used to identify invasive species and the illegal sale of mislabelled endangered fish. While Hebert and his team are certainly on board with that, their ultimate vision has always been much loftier. "Each species is a book of life that describes how to reconstruct a robin or a blue jay or a monarch butterfly," says Hebert. "It's possible that by the end of the century, one-sixth of those books of life will not longer be with us. One of the objects of our work is to register all the species on the planet before they disappear." But this isn't just about creating an inventory. Rather it's about creating a digital Noah's ark. Along with the identifying section of DNA, the barcode project saves each species' entire genome — in other words, its complete set of DNA, representing instructions for building each species. That means the chemical pathways responsible for producing yet-to-be-discovered life-saving drugs will be preserved. "It's even possible that we might be able to reconstruct species," says Hebert. "Maybe humanity will decide it's sad living on a planet with few other species on it. It would be completely impossible to restore lost species if we don't have their DNA. "        
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