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The gut microbiome helps to keep us in tip-top shape https://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=9291The gut microbiome helps to keep us in tip-top shape Lauren Martin, Natasha Kitchin & Matsepo Ramaboli<p>​​​World Microbiome Day was celebrated recently (27 June). In an opinion piece for <em>Health24</em>, Lauren Martin, Natasha Kitchin & Matsepo Ramaboli from the Faculty of Medicine and Health Sciences write that the human gut microbiome — the microorganisms that live in our intestines — is crucial for our physical well-being.<br></p><ul><li>Read the article below or click <a href="https://www.news24.com/health24/medical/digestive-health/the-gut-microbiome-helps-to-keep-us-in-tip-top-shape-20220701"><strong class="ms-rteThemeForeColor-5-0">here</strong></a><strong class="ms-rteThemeForeColor-5-0"> </strong>for the piece as published.</li></ul><p><strong>Lauren Martin, Natasha Kitchin & Matsepo Ramaboli</strong><strong>*</strong><strong> </strong></p><p style="text-align:justify;"><a href="https://worldmicrobiomeday.com/"><strong class="ms-rteThemeForeColor-5-0">World Microbiome Day</strong></a> was celebrated on the 27<sup>th</sup> of June in recognition of the often-overlooked contributions that our resident microbes make to our health as well as the role that microorganisms play in maintaining healthy global ecosystems. It is, therefore, fitting that the theme for 2022 was “Celebration of The Microbial World". </p><p style="text-align:justify;">Microscopic organisms, such as bacteria, fungi, viruses, and archaea, amongst others, are everywhere. They live in and on water, soil, food, plants, animals, and humans. In fact, for every human cell, there are approximately 1.3 bacterial cells. These microorganisms cover our entire body, including our skin, eyes, genitalia, mouth and our gut. Within each of these habitats, communities of microbes called “<a href="https://www.hsph.harvard.edu/nutritionsource/microbiome/"><strong class="ms-rteThemeForeColor-5-0">microbiomes</strong></a>" are formed. Some bacteria are simply along for the ride, while others – the symbiotic bacteria – offer a mutually beneficial relationship. These symbiotic bacteria, particularly those present in the gut, play an important role in the development and maintenance of the human body.</p><p style="text-align:justify;">The human <a href="https://joinzoe.com/learn/the-gut-microbiome-and-your-health"><strong class="ms-rteThemeForeColor-5-0">gut microbiome</strong></a> — the microorganisms that live in our intestines — is one of the interesting features of our bodies. The gut microbiome plays a crucial role in early childhood-to-adult development and has a direct influence on the immune system, hence its importance in health and disease. It has a high metabolic capacity that exceeds that of the liver, and its genetic information outnumbers that of all the other cells of the human body combined. </p><p style="text-align:justify;">Although frequently debated, most researchers accept that we acquire our first microbiota (micro-organisms in or on the human body) at birth. Delivery mode (vaginal or C-section delivery) greatly influences the gut microbiome of newborns. Babies born vaginally have a gut microbiome that closely resembles their mother's vaginal microbiome, while the gut microbiome of infants delivered by C-section is more similar to their mother's skin microbiome. After birth, the choice of diet (breast milk or formula) influences the bacterial colonisation of the newborn's gut. The gut microbiome of exclusively breast-fed babies is dominated by specialised bacteria<em> </em>which break down the healthy sugars in breast milk. Following the introduction to solid food, the infant gut microbiome gradually becomes more complex — a transition that can take up to three years.</p><p style="text-align:justify;">In adults, the complexity of the gut microbiome peaks with the formation of a robust core microbiome. The microbiome helps protect us from infection, helps us digest food and medicine, and produces vitamins and hormones that are essential for our health. While the gut microbiome can buffer some changes, changes in diet, bacterial infection, antibiotic use, and stress can greatly affect it. <br></p><p style="text-align:justify;">In recent years, changes in the gut microbiome have been increasingly recognised for their contribution to disease susceptibility. The different bacteria that make up the gut microbiome work closely together to maintain the health and function of the human body and prevent disease. Disturbance of the composition of the gut microbiome (termed 'dysbiosis') promotes inflammation and disease. <a href="https://www.webmd.com/digestive-disorders/what-is-dysbiosis"><strong class="ms-rteThemeForeColor-5-0">Dysbiosis</strong></a><strong class="ms-rteThemeForeColor-5-0"> </strong>occurs because of an unhealthy diet and excessive use of antibiotics, and leads to reduced microbial diversity. In fact, decreased microbial diversity during adulthood has been associated with more than 100 diseases including obesity, type 1 and 2 diabetes, allergic conditions such as asthma, a variety of cancers as well as neuropsychiatric conditions such as depression, anxiety, and schizophrenia. </p><p style="text-align:justify;">The gut microbiome plays a key role in preventing intestinal diseases such as colon cancer and inflammatory bowel disease. The human body cannot digest dietary fibre which is found in whole-grain products, fruit, vegetables, beans, peas and other legumes as well as nuts and seeds. Thankfully the gut microbiome has the capacity to ferment fibre into readily usable short-chain fatty acids including <a href="https://insight.microba.com/blog/your-gut-bacterias-superpower-butyrate/"><strong class="ms-rteThemeForeColor-5-0">butyrate</strong></a>. Butyrate alters the immune system and protects against the development of colon cancer. A diet low in fibre contributes to dysbiosis and inflammation which, in turn, contributes to the development of certain diseases. When we eat food rich in fats, the liver digests the fat into primary bile acids which are further digested by the gut microbiome into secondary bile acids. One of these secondary bile acids – deoxycholate – promotes colon cancer. </p><p style="text-align:justify;">Recently, the gut and the brain have been found to interact with each other indirectly through what is termed the “<a href="https://encyclopedia.pub/entry/19527"><strong class="ms-rteThemeForeColor-5-0">microbiota-gut-brain axis</strong></a>". The gut microbiome plays an essential role in brain development. During critical neurodevelopmental periods such as early life, dysbiosis negatively impacts neurodevelopment and can lead to neurological and neuropsychiatric disorders later in life.</p><p style="text-align:justify;">Unlike our DNA, the microbiome is dynamic and can therefore be altered for improved health and well-being. Supplementation of the diet with prebiotics (non-digestible foods that bacteria digest), probiotics (living beneficial bacteria) or synbiotics (a combination of probiotics and prebiotics) can lessen changes in the gut microbiome associated with disease by increasing the abundance of beneficial microbes within the gut, and consequently, good health outcomes. Even in the absence of diagnosed disease, incorporating prebiotics and probiotics into your daily life, through a healthy diet and supplementation, can help feed the beneficial bacteria in your gut and can aid in boosting your immunity.  <br></p><p style="text-align:justify;">As highlighted by American board-certified gastroenterologist and member of <a href="https://joinzoe.com/"><strong class="ms-rteThemeForeColor-5-0">ZOE</strong></a>'s Scientific Advisory Board Dr Will Bulsiewicz “... what appears to be the most important thing for human health, isn't even human". No doubt, the gut microbiome is crucial for our physical well-being. We should therefore continue to build microbiome literacy and create more public awareness about the importance of microorganisms in our lives.<br></p><ul><li>Photo by Amanda Mills, USCDCP on <a href="https://pixnio.com/sport/fitness-and-jogging/happy-girl-using-light-weight-dumbbells-on-fitness"><strong class="ms-rteThemeForeColor-5-0">Pixnio</strong></a>.<br></li></ul><p style="text-align:justify;"><strong>​*</strong><strong><em>Lauren Martin and Natasha Kitchin are students within</em></strong><strong><em> the </em></strong><strong><em>Neuropsychiatric Genetics Research Group in the Faculty of Medicine and Health Sciences (FMHS) at Stellenbosch University. Dr Matsepo Ramaboli</em></strong><strong><em> is a </em></strong><strong><em>post-doctoral research fellow at the African Microbiome Institute in the FMHS.</em></strong></p><p style="text-align:justify;"> </p><p style="text-align:justify;"> </p><p style="text-align:justify;"> </p><p>​<br></p>
Pioneering study of TB in rhinos aids Kruger Park’s conservation effortshttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=9231Pioneering study of TB in rhinos aids Kruger Park’s conservation effortsFMHS Marketing & Communications / FGGW Bemarking & Kommunikasie – Ilse Bigalke<p>​​​The largest study ever to be conducted on a free-ranging population of rhinoceros, revealed that about one in every seven rhinos in the Kruger National Park (KNP) had evidence that they had been infected with <em>Mycobacterium bovis (M. bovis)</em> – the pathogen that causes bovine tuberculosis (bTB).<br></p><p>The study, conducted by Stellenbosch University's (SU) Animal Tuberculosis Research Group, South African National Parks (SANParks), and the San Diego Zoo Wildlife Alliance, USA, tested samples of 437 rhinoceros collected from 2016 to 2020 in KNP. It revealed an estimated prevalence of <em>M. bovis</em> infection of 15,4% in black and white rhino populations in the park.</p><p>While the research results are worrying, the evidence provided by the study is crucial to the effective conservation of the already vulnerable rhino population. Added to this, scientists with the Animal TB Research Group, situated within SU's Faculty of Medicine and Health Sciences, developed a novel diagnostic test to detect <em>M. bovis</em> in rhinos, which will greatly aid conservation efforts.</p><p><strong>Infected, but asymptomatic</strong></p><p>The researchers emphasise that the presence of infection does not mean that the animals are diseased or dying. Prof Michele Miller, who leads the Animal TB Research Group and is the National Research Foundation (NRF) South African Research Chair in Animal TB, says their research shows that most of the rhinos can contain the infection if they are otherwise healthy.<strong> </strong></p><p>“It can be compared to humans who are infected with Covid-19 or have latent TB but are asymptomatic. The infected rhinos are harbouring the bacteria, but their immune system is keeping it in check. They are not losing weight or coughing, and if you looked at a group of 400 rhinos, you wouldn't be able to pick out those that are infected. They can potentially live for years with infection if it is contained."</p><p>Dr Peter Buss, Veterinary Senior Manager in KNP's Veterinary Wildlife Services, adds that there is no evidence at this point to suggest that TB will have any impact on the rhino population. “The rhinos are being exposed to the organism, they are mounting an immune response, but they are not getting sick and dying from it.<strong> </strong>The same applies to other species.<strong> </strong>For example, we know that we get TB in our lions and that individuals will die of the disease. But if you look at the population level of the disease, lions seem to be doing fine and their numbers have remained fairly static."</p><p>The authors further emphasise that the findings don't really come as a surprise since TB is prevalent in at least 15 other species in KNP, but that their research has significant positive implications for SANParks' rhino conservation and management strategy. </p><p>“While this pathogen may not appear to drastically impact the health of rhinoceros individuals, the research has significant implications for conservation management decisions. For example, tuberculosis testing in KNP rhinoceros that are earmarked for translocation for conservation reasons can increase confidence of minimal risk to other susceptible individuals at their destinations," explains Rebecca Dwyer, lead author of the study and a PhD candidate in the Animal TB research team.  </p><p><strong>Risk factors</strong></p><p>The study, which was published in the prestigious American scientific journal <em>PNAS</em> (<em>Proceedings of the National Academy of Sciences</em>) this week, identified proximity to buffalo herds (white rhinos) and sampling year (black rhinos) – which coincided with periods of drought – as risk factors for <em>M. bovis</em> infection. </p><p>A significant cluster of cases was detected near KNP's south-western border, although infection was widely distributed. The identified cluster is close to the KNP border with the surrounding Mpumalanga province, consisting primarily of farmland with livestock herds that have historically been implicated in spill-over of <em>M. bovis</em> to wildlife in KNP, especially to buffaloes. </p><p><strong>Significance</strong></p><p>“With South African rhinos being threatened by poaching, habitat loss and drought, it is key to be able to translocate them to strongholds where they can be kept safe and to preserve their genetic diversity," says Miller. “But TB is a controlled veterinary disease, so once our research group, in partnership with SANParks, found TB in Kruger rhinos in 2016, the Department of Agriculture, Land Reform, and Rural Development (DALRRD) imposed movement restrictions to prevent spreading the infection to other populations." </p><p>These restrictions created a barrier to the movement of rhinos to other national or private reserves and has a significant impact on the conservation of the species, as KNP has historically been an important population source of rhinoceros for other conservation strongholds in South Africa and other African countries. </p><p>The solution was to come up with a test to identify infected animals before they were moved to prevent disease transmission. According to Dr Wynand Goosen, Wellcome International Training Fellow in the Animal TB Research Group, the screening test that was used in their KNP study was validated by the Animal TB Research Group in 2019 and was recently approved by DALRRD for use in KNP rhinos (see info box below).<strong> </strong></p><p>A management strategy involving a quarantine protocol and testing schedule was devised in collaboration with SANParks and has been approved. “Should we now wish to start moving rhinos out of Kruger, we have that option to quarantine them and test them, and then send them out," says Buss.</p><p>Dwyer adds: “The findings of this study are significantly important for wildlife conservation, not just of rhinoceros, but of many other species in this context. It demonstrates that the spread of pathogens in multi-host systems has important consequences for the conservation of different species and of the ecosystem as a whole."   </p><p><strong>The way forward</strong></p><p>Dr Carmel Witte, a quantitative epidemiologist with the San Diego Zoo Wildlife Alliance and senior author of the study, emphasises that the eventual population-level health effects of bTB are currently unknown. “Tuberculosis tends to be a disease that manifests over long periods of time and when you compound an infectious disease with stochastic events such as climate change and unprecedented mortality due to poaching of endangered animals, it is cause for concern. </p><p>“Continued surveillance of rhinoceros as well as other animals can help us understand the long-term impact of this disease in wildlife and prevent catastrophic population losses and further disease spread."</p><p>Goosen highlights the importance of the further development of diagnostic tools and of a 'Tuberculosis One Health' approach. “Even though our research is very important from an animal conservation perspective, it is just as important from a human health-risk perspective. To avoid the next pandemic in people, livestock and wildlife will have to be actively monitored for various infectious pathogens with zoonotic potential. This requires appropriate diagnostic tools that are rapid and accurate. To develop these tools research in all susceptible species is of the utmost importance."</p><p> </p><p><strong>ADDITIONAL INFORMATION:</strong></p><p><strong>More about the diagnostic test used in the bTB study</strong></p><ul><li>It was developed based on a blood test used for TB detection in humans. </li><li>It is an improvement on traditional diagnostic methods using culture because it is based on the immune response.</li><li>The entire system is a modified commercial test which ensures standardisation.</li><li>It is simple for in-field use and reproducible.</li></ul><p>The Animal TB Research Group has developed tests that can be used for African wildlife species over many years of research. Improved tests are in demand by veterinarians throughout the world since there are currently limited tests for diagnosing TB in wildlife. To name a few species: African buffaloes, warthogs, African elephants, African lions, cheetahs, leopards, wild dogs, hippos, baboons, and meerkats.</p><p><strong>TB in other KNP species </strong></p><p>According to the researchers, the distribution of <em>M. bovis</em> infection in KNP rhinoceros is similar to that reported for other species in the park. For example, a 1991-'92 survey of buffaloes showed widespread bTB in the central and southern regions of the park, with individual herd prevalence of up to 67%. A later study (2012/'13) showed an overall infection prevalence of 44% in lions in the same areas. Such extensive infection is increasingly observed in species like warthogs, wild dogs and elephants, with cases identified in more than 15 species to date. Taken together, these findings suggest that spill-over of bTB is not a new occurrence and support the need for ongoing bTB surveillance across species to continuously assess disease risk and conservation impact.</p><p><strong>Why rhinos are translocated</strong></p><p>KNP<strong> </strong>has been a source of rhinos for other locations starting new populations or for genetic diversity reasons – a strategy that has been adopted because rhinos were doing so well in the Park until the onset of poaching, explains Miller. “If a disaster affects an isolated population of an endangered species, that species could be lost. To avoid that risk, you don't want all the animals in one location, and they are moved to multiple places. One of those risks is poaching. It is often easier to manage the security of rhinos in smaller reserves than in a huge, complex park. Moving animals to other locations will ensure that there are future breeding populations even if the threat of poaching continues in Kruger."</p><p><strong>Is bTB a threat to humans? </strong></p><p>Although people can become infected with bTB, it usually only happens when they regularly handle infected (uncooked) animal organs or drink unpasteurised milk. Unlike diseases such as Covid-19, people need close prolonged contact to get TB and won't contract it from visiting KNP, stresses Miller.<strong> </strong></p><p>Witte adds that although most humans are not interacting with wild rhinoceros in a way that would put them at risk for acquiring <em>M. bovis</em>, the study highlights the ongoing potential for pathogen spill-over from animals to people (and people to animals!) at the human-domestic animal-wildlife interface.</p><p>According to Goosen TB has similar consequences for humans and a broad range of animal species, yet cases in humans and animals are commonly treated as separate problems.<strong> </strong>A TB One Health approach is therefore warranted<strong> </strong>by improving the surveillance of zoonotic mycobacteria in humans, livestock, wildlife and their environment throughout South Africa using various novel technologies.<strong> </strong></p><p><strong>Ongoing work in KNP</strong></p><p>According to Buss a lot of work still remains to be done on TB, especially the epidemiology, and particularly at a population level. “Although it has been around for maybe 60-70 years in Kruger, it would still be considered a relatively new disease. Because TB manifests itself so slowly, we would imagine that the disease is still expressing itself at a population level, and we still need to reach some sort of equilibrium with the disease – and we just don't know exactly where that is.</p><p>“Although we might not see much happening at the moment, it is very difficult to predict the future. It would really be helpful to have some idea of the potential impact of this disease, particularly in advance, should we be required to manage this. And that's in all animals, not only rhinos."</p><p><strong>Prevalence in other parks and reserves? </strong></p><p>According to Buss, KNP is currently the only national park where TB has been diagnosed in rhinos. “The problem is currently contained to the Kruger, thank goodness. But we would certainly want to keep it that way for other national parks."</p><ul><li><em>Follow this link to read the full article in </em><em>PNAS</em><em>: </em><a href="https://eur03.safelinks.protection.outlook.com/?url=https://www.pnas.org/doi/pdf/10.1073/pnas.2120656119&data=05%7c01%7c%7c930756f67b4a4c24532f08da47fee015%7ca6fa3b030a3c42588433a120dffcd348%7c0%7c0%7c637901458321087234%7cUnknown%7cTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7c3000%7c%7c%7c&sdata=TXjfMKSZqKu/5skGwHdq2CH5pRMXnQ6foIGlPjlLnQ8%3D&reserved=0">https://www.pnas.org/doi/pdf/10.1073/pnas.2120656119</a> <br></li></ul><p>​<br></p><p><em><span style="font-size:11pt;line-height:107%;font-family:calibri, sans-serif;">Photo caption: Prof Michele Miller (second from right) collects blood samples from a white rhino in the Kruger National Park. </span></em><br></p>
SU researchers compete for National Science Awardshttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=9198SU researchers compete for National Science AwardsCorporate Communication & Marketing / Korporatiewe Kommunikasie & Bemarking [Alec Basson]<p>​​​Five eminent researchers from Stellenbosch University will represent the institution at the annual <a href="https://nstf.org.za/about-the-nstf-awards/"><strong class="ms-rteThemeForeColor-5-0">National Science and Technology Forum (NSTF)/South32Awards</strong></a>. They will be competing as finalists for the 2021/2022 NSTF/South32 Awards at South Africa's “Science Oscars" on Thursday 21 July 2022.</p><p>The NSTF Awards Gala Event will take place as a hybrid event to be broadcast from two cities – Johannesburg and Cape Town. This means the usual Gala Dinner will be reintroduced with the addition of a celebration in Cape Town and broadcasting from both cities to an online audience via the NSTF YouTube channel. The patron of the Awards, the Minister of Higher Education, Science and Innovation, Dr Blade Nzimande, has been invited to preside over the presentation of the awards.</p><p>Regarded as the most sought-after national accolades of their kind in the country, the NSTF/South32 Awards recognise, celebrate and reward the outstanding contributions of individuals, teams and organisations to science, engineering and technology (SET) in the country. Among the competitors are experienced scientists, engineers, innovators, science communicators, engineering capacity builders, organisational managers and leaders, as well as data and research managers.</p><p>The SU finalists (with department or environment) and the categories in which they will compete are as follows:</p><p><strong><em>Lifetime award</em></strong></p><ul><li>Profs Gerhard Walzl (Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences) & Guy Midgley (Department of Botany and Zoology/School for Climate Studies). Midgley is also a finalist in the <strong><em>Green Economy Award</em></strong> category.</li></ul><p><strong><em>Communication Award</em></strong></p><ul><li>Prof Nox Makunga (Department of Botany and Zoology)</li></ul><p><strong><em>TW Kambule-NSTF Award: Emerging Researcher</em></strong></p><ul><li>Dr Wynand Goosen (Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences)</li></ul><p><strong><em>Engineering Research Capacity Development and Special Annual Theme Awards</em></strong></p><ul><li>Prof Oluwole Makinde (Department of Mathematics, Faculty of Military Science)</li></ul><p><strong>Photo</strong>: Profs Gerhard Walzl, Oluwole Makinde, Guy Midgley, Nox Makunga, and Dr Wynand Goosen.<br></p><p>​<br></p>
Two FMHS scientists join ranks of A1-rated researchershttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=9060Two FMHS scientists join ranks of A1-rated researchersFMHS Marketing & Communications / FGGW Bemarking & Kommunikasie<p>​Two eminent researchers at Stellenbosch University's (SU) Faculty of Medicine and Health Sciences (FMHS) were recently added to the National Research Foundation's (NRF) prestigious list of A1-rated scientists. <br></p><p>Profs Mark Cotton (Department of Paediatrics and Child Health) and Robin Warren (Division of Molecular Biology and Human Genetics) obtained A1-ratings during the latest round of NRF-ratings. Warren, who previously had a B2-rating, joins Cotton (who previously had an A2-rating) and Profs Elmi Muller (FMHS Dean) and Simon Schaaf (Department of Paediatrics and Child Health) on the list of A-rated researchers at the FMHS. </p><p>A-rated researchers are unequivocally recognised by their peers as leading international scholars in their respective fields for the high quality and impact of recent research outputs.</p><p>Along with Cotton and Warren, a further 15 FMHS researchers were rerated or received new NRF ratings, bringing the FMHS' total number of rated scientists to 97.</p><p>The NRF's rating system is a benchmarking system whereby individuals who exemplify the highest standards of research, as well as those demonstrating strong potential as researchers, are identified by an extensive network of South African and international peer reviewers. Ratings are based on the quality and impact of recent research outputs (over and eight-year period).</p><p>Five researchers were also given a B-rating in the latest round of ratings, bringing the tally of B-rated scientists at the FMHS to 13. B-rated researchers enjoy considerable international recognition by their peers for the high quality and impact of their recent research outputs. The newly selected B-rated scientists at the FMHS are Profs Wayne Derman (Institute of Sport and Exercise Medicine), Quinette Louw (Department of Health and Rehabilitation Sciences), Susan van Schalkwyk (Centre for Health Professions Education), Adrie Bekker (Department of Paediatrics and Child Health), and Novel Chegou (Department of Biomedical Sciences).</p><p>The FMHS also boasts 59 C-rated scientists, of which 10 are newly selected. C-rated scientists are established researchers with a sustained recent record of productivity in their respective fields, who are recognised by their peers as having (1) produced a body of quality work, the core of which has coherence and attests to ongoing engagement with the field; and (2) demonstrated the ability to conceptualise problems and apply research methods to investigate them. </p><p>The FMHS researchers who joined the ranks of C-rated scientists are Profs Andre van der Merwe (Division of Urology), Rajiv Erasmus (Department of Pathology), Susan Hanekom (Division of Physiotherapy), Franclo Henning (Division of Neurology), Xikombiso Mbhenyane (Division of Human Nutrition), Lana van Niekerk (Department of Health and Rehabilitation Sciences), Annie Zemlin (Division of Chemical Pathology), and Ekkehard Zöllner (Department of Paediatrics and Child Health), as well as Drs Yolandi Brink (Division of Physiotherapy) and Sharain Suliman (Department of Psychiatry).</p><p>In addition to the FMHS' A, B and C-rated scientists, the Faculty also boasts with 18 Y-rated scientists. These are young researchers (40 years or younger), who have held a doctorate or equivalent qualification for less than five years at the time of application, and are recognised as having the potential to establish themselves as researchers within a five-year period after evaluation, based on their performance and productivity of quality research outputs during their doctoral studies and/or early postdoctoral careers. </p><p>“We are tremendously proud of our researchers and their achievements, including the large number of newly rated scientists in the Faculty, which includes two new A1-rated researchers. This achievement attests to the world-class research performed at the FMHS. The number of NRF-rated researchers has more than doubled since 2014 (when there were only 37 rated researchers), which is an indication of the significant growth in the research enterprise of the FMHS over the last number of years, and our ability to draw the best scientists in South Africa and the world," said Prof Nico Gey van Pittius, Vice Dean: Research and Internationalisation.</p><p>Commenting on the latest results, Dr Therina Theron, Senior Director for Research and Innovation at SU, said the NRF's rating process remains a very important indicator of the international recognition of SU's researchers. “With more in the pipeline, our increasing pool of A-rated researchers attest to the enormous contribution our researchers are making to SU's vision of being Africa's leading research-intensive university. We salute and celebrate them!"<br></p><p><br></p><p><img src="/english/faculty/healthsciences/PublishingImages/NewsCarousel/Nuus2020/RatingsGraph_ENG.JPG" class="ms-rtePosition-4" alt="" style="margin:5px;width:750px;height:387px;" /><br></p><p><br></p><p><em>Caption: (Top left to right) Professors Quinette Louw, Mark Cotton and Rob Warren. (Bottom left to right) Professors Adrie Bekker, Wayne Derman, Susan van Schalkwyk and Novel Chegou.</em><br><br></p>
PhD maps genome of critical endangered African wild dog https://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=9028PhD maps genome of critical endangered African wild dog Faculty of Medicine and Health Sciences (Sue Segar)<p>​​​When Christina Meiring graduates with a PhD in Molecular Biology today (5 April) it will mark the completion of the first large-scale investigation of the genetic diversity in the African wild dog population of the Kruger National Park (KNP).<br></p><p>Meiring has been working within the Animal TB Research Group at Stellenbosch University's Faculty of Medicine and Health Sciences. Her study of the critically endangered African wild dog provides a foundation for future genomic testing to inform conservation management.</p><p>The largest self-sustaining population of African wild dogs in South Africa is in the KNP. Remaining populations are fragmented and only survive due to human intervention.</p><p>In an interview, Meiring (26), said she would be continuing her research as a postdoctoral fellow in the Animal TB Research Group and the TB Host Genetic Research Group.</p><p>“I thoroughly enjoyed my project, which started in 2018, and I love what I do," she said, adding that she will be expanding her research into different African wild dog populations in South Africa and Zimbabwe.</p><p>During her project, she visited the KNP twice where she saw how wild dogs are sampled. </p><p>“I love these creatures. I love watching their behaviour," she said of the enigmatic wild dogs. “They are fascinating, unique and charismatic. They are caring, beautiful animals and so loving to their pups. If one wild dog is injured, they will do all they can to help it survive. They are not like other carnivores who kick out a weak member. Their unique coat patterns, the sounds they make and their hunting success is amazing."</p><p>Meiring was born in Gqeberha (formerly Port Elizabeth) and raised in Kirkwood in the Eastern Cape on a citrus farm. Her parents loved nature and the family spent a lot of time in the Addo Elephant National Park during her childhood. “I inherited my father's love for the outdoors and was always interested in the sciences, biology and wildlife."</p><p>She completed a BSc in human life sciences, followed by honours in genetics before “realizing I was more interested in animals than humans. For my Masters, I looked at animal research, particularly genetics as, while doing my undergraduate studies, I realized I was interested in genetics.</p><p>“I have a twin sister, Elizabeth (Libby) who did an MSc in embryology and who works at a fertility clinic in the Netherlands. Being a twin has made me even more interested in genetics."</p><p>According to Meiring, the survival of African wild dogs (<em>Lycaon pictus</em>) has been impacted by human and other conflict, as well as habitat loss and disease.</p><p>“The result is a limited number of individual wild dogs that can maintain the genetic pool. These small populations lose genetic diversity and individuals are more likely to breed with close relatives (inbreeding), leading to decreased fitness and limiting their ability to adapt to challenges, such as environmental changes or disease.</p><p>“Recently, the infectious disease bovine tuberculosis, caused by <em>Mycobacterium bovis</em>, has caused mortality in wild dogs across South Africa and little is known about how this disease affects this species. Additionally, the assessment of genetic diversity in this species, a crucial component required to support the planning of conservation strategies, has not been done."</p><p>“A full picture of the genetic makeup of individuals of a population is important, since that would most likely provide the means to conserve the genetic diversity to increase their fitness and adaptability."</p><p>A technique called whole-genome sequencing was used to get the entire genetic code of 71 wild dogs (from blood samples) from the KNP, which allowed for the comparison between individuals.</p><p>“We hope this study will provide the foundation to develop genomic profiles which can be used for strategic population management."</p><p>Meiring's research found that African wild dogs are mostly likely to get infected with bovine TB via ingestion of infected prey.</p><p>The findings are important, she said, because “the consequences of an emerging infectious disease on a population with low levels of genome variation may threaten the long-term viability of African wild dogs. This is critical information to consider when planning future conservation actions for this species."</p><p>Meiring's parents will be cheering her on at her graduation. “They've played a major role in my success and have been so supportive and interested in my research. For the past two years during lockdown, I've been writing up my PhD on the farm, an ideal setting.</p><p>She paid warm tribute to her “most amazing supervisors" – Prof Michele Miller and Prof Marlo Moller and her “mentor and friend" Prof Paul van Helden for his major role in her project.</p><p>“I'm so happy to have finished my PhD. It has been a very long and pleasant journey. It will be wonderful to graduate in person."</p><ul><li><em>This article by Sue Segar on behalf of the Faculty of Medicine and Health Sciences</em></li></ul><p><strong>Photo </strong>by <a href="https://unsplash.com/%40lebalu?utm_source=unsplash&utm_medium=referral&utm_content=creditCopyText">Leon Pauleikhoff</a> on <a href="https://unsplash.com/?utm_source=unsplash&utm_medium=referral&utm_content=creditCopyText">Unsplash</a></p><p>​<br></p>
Stellenbosch University’s cohort of A-rated researchers increaseshttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=9011Stellenbosch University’s cohort of A-rated researchers increasesCorporate Communication & Marketing / Korporatiewe Kommunikasie & Bemarking; Research Development / Navorsingsontwikkeling <p>​​The National Research Foundation (NRF) is in the process of releasing the outcome of the latest round of NRF ratings. Although we are still awaiting more results, Stellenbosch University (SU) would like to acknowledge that so far, we have received a record number of newly rated A-rated researchers. <br></p><p>The following researchers received an A-rating: Profs Sandy Liebenberg (Department of Public Law & HF Oppenheimer Chair in Human Rights Law); Andre Weideman (Division of Applied Mathematics; Department of Mathematical Sciences); Johan Cilliers (Department of Practical Theology and Missiology); Len Barbour (Department of Chemistry & Polymer Science); Willem Visser (Division of Computer Science; Department of Mathematical Sciences), Robin Warren (Molecular Biology and Human Genetics) and Mark Cotton (Department of Paediatrics & Child Health). Liebenberg, Weideman, Warren, and Cilliers received their first A-rating, Visser and Cotton their second, and Barbour his fourth. </p><p>A-rated researchers are unequivocally recognised by their peers as leading international scholars in their respective fields for the high quality and impact of recent research outputs.</p><p>The NRF rating system is a benchmarking system whereby individuals who exemplify the highest standards of research, as well as those demonstrating strong potential as researchers, are identified by an extensive network of South African and international peer reviewers. Ratings are based on the quality and impact of recent research outputs (over an eight-year period).</p><p>Commenting on the latest results, Dr Therina Theron, Senior Director for Research & Innovation at SU, said the NRF-ratings process remains a very important indicator of the international recognition of SU's researchers. “With more in the pipeline, our increasing pool of A-rated researchers attests to the enormous contribution our researchers are making to SU's vision of being Africa's leading research-intensive university. We salute and celebrate them!"</p><p>SU currently has 477 NRF-rated researchers, of which 16 are A-rated. </p><ul><li>Click <a href="https://bit.ly/3711FBM"><strong class="ms-rteThemeForeColor-5-0">here</strong></a><strong class="ms-rteThemeForeColor-5-0"> </strong>for a list of SU NRF-rated researchers.​<br></li></ul><p><br></p>
Top FMHS scientists on the red carpethttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8998Top FMHS scientists on the red carpetFMHS Marketing & Communications / FGGW Bemarking & Kommunikasie – Ilse Bigalke<p>​​​Four leading scientists of Stellenbosch University's (SU) Faculty of Medicine and Health Sciences (FMHS) were recently awarded prestigious accolades in recognition of the profound impact that their research has had on the health and lives of South Africans.<br></p><p>The South African Medical Research Council (SAMRC) honoured Prof Marlo Möller (silver award), Profs Tulio de Oliveira and Grant Theron (gold awards), as well as Prof Andre Kengne, extraordinary FMHS professor (platinum award), at its <a href="https://youtu.be/43pLSnx9YIY">8th Scientific Merit Awards</a> ceremony held at its head office in Cape Town on 10 March. </p><p>SAMRC President and CEO, Prof Glenda Gray, told the mainly virtual audience that scientific research remains fundamental to reduce South Africa's burden of disease and preventing mortality. “The knowledge produced by these exceptional scientists will carry our country's legacy of science forward and continue to improve the lives of citizens, as is evident with Covid-19." </p><p>She added that their work is testimony to the country's ingenuity, saying that “it was scientists in South Africa who first discovered and sounded the alarm on Omicron, which rapidly became the dominant variant of concern".</p><p>SAMRC awardees in all categories were identified last year through an open public nomination process and adjudicated by the SAMRC Awards Nominations Committee. </p><p><strong>Prof Marlo Möller (silver medal)</strong></p><p>In her acceptance speech, Möller, head of the TB Host Genetics Research Group within the Division of Molecular Biology and Human Genetics of the FMHS, thanked her team. “Research is very much a team effort, and I am so privileged to accept this award on behalf of the TB Host genetics research group."</p><p>She also emphasised the importance of resources in the fight against TB and highlighted the celebration of World TB Day on 24 March with the theme “Invest in TB and save lives". “We have to invest resources to ramp up the fight against this terrible disease to achieve the commitments that global leaders make to end this pandemic," she told the audience.  </p><p>The SAMRC's silver medal is awarded to emerging scientists and those committed to capacity development. Criteria include research contributions that impact on health, especially in developing countries.</p><p>Möller's primary research focus is on finding the human genetic underpinnings of infectious diseases, especially TB. Major research topics include common genetic variants that predispose the general population to pulmonary TB, as well as individuals that display extreme forms of TB resistance and susceptibility.</p><p>Möller is a National Research Foundation (NRF) C3-rated researcher who has won several awards, including the NRF Research Career Award and the SU Rector's award for general performance. Her qualifications include a PhD in medical biochemistry. She is also a member of the SAMRC Centre for Tuberculosis Research.</p><p><em>Watch a YouTube video of Möller's research and nomination </em><a href="https://youtu.be/kVspDlUyeQI"><em>here</em></a><em>.</em></p><p><strong> </strong></p><p><strong>Prof Tulio de Oliveira (gold medal)</strong></p><p>“This is just the beginning. I think South Africa is really going to lead the world in infectious diseases," the world-renowned bioinformatics scientist predicted after having accepted a medal in the gold category, which is bestowed on established senior scientists who have made substantial and influential contributions.</p><p>The criteria for this award include a recent exceptional accomplishment, breakthrough, or contribution to research which is acknowledged at an international level. This contribution must have clearly enhanced the prestige of South African medical research and extended medical knowledge.</p><p>According to the SAMRC an attempt in 2022 to describe De Oliveira in one sentence would probably read something like “the man who facilitated the identification of the SARS-CoV-2 variants of concern Beta and Omicron in South Africa … but this description does not even begin to scratch the surface to capture his journey".</p><p>Most recently De Oliveira, who has worked with viral outbreaks throughout his career, has cemented his place as one of the top scientists in the forefront of South Africa's fight against Covid-19. He collaborated with leading research organisations to create the Network for Genomic Surveillance in South Africa (NGS-SA), which started producing genomes as early as March 2020 and sequenced the first Covid-19 case in South Africa.  </p><p>He wears different leadership hats, including as professor of bioinformatics, School for Data Science and Computational Thinking at the FMHS, and as Director of the FMHS' proposed Centre for Epidemic Response and Innovation. </p><p>In his acceptance speech, De Oliveira stressed the efforts in collaboration with the SAMRC to create a Centre for Epidemic Response and Innovation that can challenge the status quo and really make South Africa and Africa a leader in science. </p><p>“The last two years were extremely busy, but it was very exciting to see how South Africa really came together to almost lead the world in scientific research," he said.</p><p><em>Watch a YouTube video of De Oliveira's research and nomination </em><a href="https://youtu.be/-rQWIPDPdU4"><em>here</em></a><em>.</em> </p><p><strong>Prof Grant Theron (gold medal)</strong></p><p>Theron, a professor of molecular biology and human genetics in the FMHS' Division of Molecular Biology and Human Genetics, is also a member of the DST/NRF Centre for Excellence in Tuberculosis Research and the SAMRC's Centre for Tuberculosis Research, both of which are embedded within the FMHS.</p><p>He holds a P-rating from the NRF (the highest rating available to researchers younger than 35). </p><p>His core research interests are the design and field evaluation of improved diagnostics for tuberculosis and drug resistance, the transmission and aerobiology of tuberculosis, including drug-resistant tuberculosis, and most recently the microbiome in the context of tuberculosis. </p><p>He has led several projects on tuberculosis diagnostics, which have measured their impact on long-term patient outcomes. He has also held several fellowships. In a relatively short period, he has published approximately 60 papers in international peer-reviewed journals and has registered one patent. </p><p>Named one of the Top 200 Young South Africans by the <em>Mail & Guardian</em> in 2014, his sterling work has attracted international recognition including the Gertrud Meisner Award by the European Society of Mycobacteriology; the TW Kambule Emerging Researcher Award by the NSTF-BHP Billiton; and the Meiring Naudé medal in recognition of outstanding early career contributions to the furtherance of science by the Royal Society of South Africa.</p><p>Theron is a member of various local and international organisations, including the American Society of Microbiology and the European Society for Mycobacteriology. </p><p>Accepting his gold medal, Theron thanked all the awardees, “since it's been a really hard couple of years to be a scientist, especially if your research is Covid adjacent and not on Covid itself". </p><p><em>Watch a YouTube video of Theron's research and nomination </em><a href="https://youtu.be/id2HdS4qhq0"><em>here</em></a><em>.</em><br></p><p><strong>Prof Andre Pascal Kengne (Platinum medal)</strong></p><p>The SAMRC's platinum medal was awarded to Kengne, an internationally renowned non-communicable diseases epidemiologist. </p><p>Kengne holds a PhD in medicine from the Sydney University, Australia. His major focus is on cardiovascular disease, diabetes, metabolic disease and chronic kidney disease. He is the current Director of the SAMRC's Non-Communicable Diseases Research Unit and holds conjoint appointments as professor of medicine at the University of Cape Town, as well as extraordinary professor of Global Health at SU's FMHS. </p><p>Platinum medals are awarded to accomplished South African scientists for outstanding lifetime scientific achievements in the field of health, who have raised the profile of South African science and helped build the foundations of health research in the country for future generations. </p><p>Over the course of Kengne's journey, he has co-authored numerous peer-reviewed articles, book chapters and monographs on chronic diseases in Africa and at a global level.</p><p>Kengne's immense contribution to research has earned him multiple awards and recognition from local and international bodies, including the Sir Alberti Award for excellence in research on diabetes in Africa, the SAMRC Gold Award for Scientific Excellence, and the International Society of Hypertension Research Scholar Award.</p><p>In his acceptance speech, Kengne paid tribute to everyone who supported him on his scientific journey, including his family, friends, and colleagues all over the world.</p><p><em>Watch a YouTube video of Kengne's research and nomination </em><a href="https://youtu.be/CoVA6mjRBtc"><em>here</em></a><em>.</em></p><p> </p><p>Additional source: SAMRC</p><p> </p><p><em>Caption: Profs Grant Theron, Marlo Moller, Andre Kengne and Tulio de Oliveira receiving their respective awards at the SAMRC's 8</em><em><sup>th</sup></em><em> Scientific Merit Award Ceremony.</em></p>
South Africans with rare diseases still being left behindhttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8930South Africans with rare diseases still being left behindShahida Moosa<p>​February is Rare Disease Month with Rare Disease Day being observed on 28 February. In an opinion piece for <em>Health24</em>, Prof Shahida Moosa (Division of Molecular Biology and Human Genetics / Rare Disease Genomics in South Africa Group) calls for an increase in awareness and advocacy for better access to healthcare, testing, services, resources, support and acceptance for families with rare diseases.</p><ul><li>Read the article below or click <a href="https://www.news24.com/health24/News/Public-Health/opinion-south-africans-with-rare-diseases-still-being-left-behind-20220228"><strong class="ms-rteThemeForeColor-5-0">here</strong></a><strong class="ms-rteThemeForeColor-5-0"> </strong>for the piece as published.<br></li></ul><p><strong>Shahida Moosa*</strong></p><p style="text-align:justify;">The United Nations <a href="https://sdgs.un.org/goals"><strong class="ms-rteThemeForeColor-5-0">Sustainable Development Goals</strong></a> (UN-SDGs) aim to achieve a world in which “no one is left behind". Among those furthest behind are people affected by Rare Diseases (RDs), as undeniably, they have been disproportionately deprived in terms of research, diagnosis and treatment, especially in Africa. </p><p style="text-align:justify;">Although individually “rare", these diseases collectively affect a large proportion of the population; yet, there has been too little in terms of their prioritisation from governments and stakeholders in Africa, including South Africa. Over 72% of rare diseases are genetic in origin, collectively estimated to affect <a href="https://www.rarediseases.co.za/"><strong class="ms-rteThemeForeColor-5-0">up to four million South Africans</strong></a>. Most of these conditions, also called “orphan diseases", have their onset in childhood (often recognised at birth), continue for life, and are chronic and disabling. Much focus is put on the considerable health burden posed by these conditions; yet, additional burdens including stigma and alienation from the community, lack of access to resources, and lack of accurate diagnoses remain foremost in the day-to-day experiences of affected families. In South Africa, the majority of RD families, numbering in the hundreds of thousands, remain undiagnosed due to lack of access to the genomic technology needed to provide a definitive diagnosis. Our RD population is thus understudied and under-represented globally. </p><p style="text-align:justify;">This is one of the reasons why our <a href="/english/faculty/healthsciences/Molecular_Biology_Human_Genetics/rare-disease_genomics/Pages/default.aspx"><strong class="ms-rteThemeForeColor-5-0">Rare Disease Genomics in South Africa</strong></a> research group, based at Stellenbosch University's Faculty of Medicine and Health Sciences and Tygerberg Hospital, hosts a social media campaign every February to enhance awareness of RDs. February was chosen as Rare Disease Month, due to it having a “rare" number of days. Activities during February culminate in the international celebration of <a href="https://www.rarediseaseday.org/"><strong class="ms-rteThemeForeColor-5-0">Rare Disease Day</strong></a> on the last day of the month. For our 2022 Rare Diseases in South Africa Awareness initiative <a href="https://www.facebook.com/SuMBHG/">(<strong class="ms-rteThemeForeColor-5-0">#28DaysOfRare campaig</strong><strong class="ms-rteThemeForeColor-5-0">n</strong></a>), we interviewed families affected by RDs to explore what their daily challenges are, what their unmet needs are, what impact a diagnosis through our Undiagnosed Disease Programme has had, and what messages they wanted to share with other families, their communities and government. </p><p style="text-align:justify;">The campaign has provided these families with a voice beyond the confines of the genetic clinic. It was important to include patient voices from a state-run facility like Tygerberg Hospital, as they are traditionally not the ones represented when RDs are discussed in the South African media. Families with RDs live in Sandton and Constantia, but they also live in Khayelitsha, Soweto and Delft. This campaign has allowed us all to get a more accurate picture of what life is like for them. We have realised throughout the campaign that they face numerous challenges. These include, among others, getting help for their complex constellation of symptoms, accessing appropriate and timely testing, accessing therapies and proper management, gaining access to resources needed outside the hospital setting, finding appropriate schooling, accessing local support groups and dealing with issues around stigma and acceptance in the extended family and community.  <br></p><p style="text-align:justify;">One of our research studies is the Undiagnosed Disease Programme, the first programme of its kind in sub-Saharan Africa. The aim of the programme is to use the latest genomic sequencing technology to provide families with RDs with a definitive diagnosis. The impact of the diagnosis, especially for those families who have been on their “diagnostic odyssey" for many years, has come with feelings of relief and eased long-standing feelings of guilt. Having an answer for why their child is different to other children has facilitated acceptance. For some, we have been able to change their medication based on their genetic test result and improve their quality of life. For all, the information came with more accurate recurrence risks and prognoses. From the responses of these families, it became clear that the diagnosis has had a physical and emotional impact beyond what could have been expected.<br></p><p style="text-align:justify;">“The community told me my child is like this because of the tight jeans I wore during pregnancy. I believed them and felt very guilty until I was told that this is a genetic condition. It was not my fault", said Okwenam's<strong>*</strong> mother. </p><p style="text-align:justify;">“We live in a shack. When it rains, the rain comes in. When the wind blows, it comes in. This affects my child's breathing. We have such big rats which are eating the grownups, imagine how they bite the small ones", said Anothando's mother. The need for improved housing for their children with RDs, also affectionately called #RareWarriors, was something voiced by many mothers interviewed. Having a diagnosis and being able to anticipate future needs for little Anothando, has meant that the family will receive one of the first units in the new housing project for people with special needs. For her mother, this “is a dream come true!"<br></p><p>For other families, their struggle to find appropriate schooling for their children, despite having a diagnosis, continues. Felicia, the only girl currently diagnosed with her condition in Africa, is six years old but not yet toilet-trained; MJ has a rare form of genetic epilepsy, which is associated with hyperactivity and behavioural issues; and Iviwe is profoundly intellectually disabled needing constant supervision. Not having access to a school means that these children need to be cared for at home, requiring one or both their parents to give up jobs and educational opportunities. “The challenges? There have been millions!" said Felicia's father. <br></p><p>If this is the case for families who already have a diagnosis, we cannot begin to estimate the impact of being undiagnosed. One of the reasons that genomic technology is not more widely accessible in South Africa, is that there is a basic lack of support from all stakeholders necessary to roll out genomics and genomic testing. Rare diseases in other parts of the world are receiving much more attention, funding and support. We see stakeholder buy-in even in other low- and middle-income countries like Brazil and India. Unfortunately, change has been very slow in sub-Saharan Africa, despite the UN General Assembly's recent adoption of a resolution on “<a href="file:///C:/Users/alecbas/Downloads/A_RES_76_132-EN.pdf"><strong class="ms-rteThemeForeColor-5-0">Addressing the Challenges of Persons Living with a Rare Disease and their Families</strong></a>". </p><p>Patients with RDs in South Africa are low priority because government cannot quantify the burden of RDs accurately – we do not have nationwide registries, there is no access to necessary testing across the country, seven of the nine provinces do not have Genetic Services, there is a lack of trained personnel (clinical, laboratory and bioinformatics), and a lack of funded posts to train and retain skilled personnel, to name only a few. While we can more accurately quantify the number of patients admitted to hospital with COVID-19, HIV or TB, the footprint of RDs is less visible. <br></p><p style="text-align:justify;">South Africa cannot decrease infant and under-5 mortality rates, nor can we achieve the SDGs without focussing more on RDs – specifically SDG 3 (improving health outcomes), SDG 10 (reduced inequalities) and SDG 17 (increased partnerships across stakeholders) are impossible without taking RDs into account. <br></p><p style="text-align:justify;">The #28DaysOfRare campaign is one step of many to increase awareness and advocacy for better access to healthcare, testing, services, resources, support and acceptance for families with RDs, to increase adoption of policies to benefit them and to enlarge the footprint of RDs in South Africa.<br></p><p style="text-align:justify;"><strong><em>*</em></strong><em>The names of children used in this article are real. Stellenbosch University's Health Research Ethics Committee</em><em> (</em><em>HREC ref N21/09/098) approved this initiative and the parents signed informed consent to use videos, pictures and names.</em></p><p style="text-align:justify;">*<strong>Prof Shahida Moosa is a Senior Specialist in Medical Genetics at Tygerberg Hospital and Associate Professor of Medical Genetics in the Division of Molecular Biology and Human Genetics at Stellenbosch University. She directs the research programme on Rare Disease Genomics in South Africa.</strong></p><p style="text-align:justify;"><strong> </strong></p><p>​<br></p>
Researchers harness artificial intelligence for rare disease diagnosishttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8922Researchers harness artificial intelligence for rare disease diagnosisFMHS Marketing & Communications / FGGW Bemarking & Kommunikasie – Sue Segar<p>​​The families of patients with rare genetic diseases have, historically, struggled for years – or even for entire lifetimes – to get a correct diagnosis for their disease. But these often gruelling “diagnostic odysseys" might soon be a thing of the past, now that researchers are using artificial intelligence (AI) to accurately detect rare diseases through facial feature recognition.<br></p><p>A global research team which includes Shahida Moosa, Associate Professor of Medical Genetics in the Division of Molecular Biology and Human Genetics at Stellenbosch University, has come up with a new tool that can help clinicians and researchers diagnose a rare disease far more quickly than in the past, based on an AI-driven analysis of facial features.<br></p><p>The tool, known as GestaltMatcher, is featured in a paper which was recently published in the prestigious <em>Nature Genetics</em> journal. The tool was developed by a team of researchers from the University of Bonn, in Germany, and other institutions, with Moosa's team being the only group contributing from Africa.</p><p>Moosa, who is second author of the paper and whose student, Kimberly Coetzer, is a co-author of the paper, said the GestaltMatcher is an exciting new tool.<br></p><p>“It is going to change the way we practice medical genetics, as well as how we do research," she said in an interview.<br></p><p>Moosa, also a senior consultant in medical genetics at Tygerberg Hospital, directs the new research programme on Rare Disease Genomics in South Africa. Through this programme, which falls under the Faculty of Medicine and Health Sciences' new Biomedical Research Institute, she aims to change the lack of focus on rare diseases, particularly in Africa, where many patients pass away without ever hearing a name for their condition because rare diseases are “complex" and “under-studied" in Africa.<br></p><p>Interviewed about her role in the paper on GestaltMatcher, Moosa said that most rare diseases are genetic in origin and many of those have associated distinctive facial features, or a so-called facial gestalt.<br></p><p>“It is often with the facial features where we start in trying to find a diagnosis but it is not always easy.<br></p><p>“For instance, we have seen hundreds of thousands of people with Down Syndrome, so it is not difficult to make a spot diagnosis – even in a shopping centre or in the streets. However, there are many much rarer diseases, even so-called ultra-rare diseases, which even an experienced dysmorphologist may never have encountered in his or her clinic. It is for this reason that we are increasingly relying on help in the form of AI.<br></p><p>“GestaltMatcher is what we call next generation phenotyping, which means that the AI is not only able to 'look' at clinical features on the face and come up with a differential diagnosis for the patient's condition, but it is able to 'match' the facial gestalt of two unrelated undiagnosed patients. The ability to make these matches based solely on the facial gestalt is unique."<br></p><p>Moosa said a big benefit of the GestaltMatcher tool is that “it doesn't rely on being trained on dozens of patients in order to make a diagnosis or a match. It is able to see a patient's features once and then match it to the very next patient it sees with similar facial features. That is beyond what the human experts can do."<br></p><p>She said most syndromes which present with unique facial features would be amenable to diagnosis using GestaltMatcher. “We already have web-based and app-based tools, which help us in the clinic every day, but GestaltMatcher takes this to the next level, because, without much training, it can match those who are still undiagnosed. For example where a syndrome hasn't been seen before or is undiagnosed, GestaltMatcher can match two patients with similar features. A match in this scenario points us towards a common diagnosis for these patients. Novel syndromes can be delineated using GestaltMatcher.<br></p><p>“It can also group patients according to how closely their facial features resemble those of identified syndromes. This helps us to look at genomic sequencing data and to see if the patient for whom we seek a diagnosis has a variant in the same pathway as the genes responsible for the known syndrome, thereby cutting down the search space for the underlying genes considerably."<br></p><p>Moosa said the new tool is going to “change the way we practice medical genetics in a big way.<br></p><p>“With the growing number of syndromes and ultra-rare syndromes, it is impossible for human experts to be an expert in every one of those syndromes, so we will rely on tools like GestaltMatcher in the future to be able to get to a diagnosis earlier.<br></p><p>“GestaltMatcher is one of the pieces in the puzzle to drive the mission to get a diagnosis as soon as possible. It is also a tool we will use for novel syndrome discovery and novel gene discovery. This is especially exciting for us in Africa, as our patients have not been sufficiently represented in other tools.<br></p><p>“This is one of the tools we will increasingly use to shorten the long, sometimes painful, odyssey that patients go on to get a diagnosis for their rare diseases."<br></p><p>Moosa, who has been involved with the team of researchers for some time, said she is pleased the paper is finally out.<br></p><p>“The best thing about the GestaltMatcher is that it's not behind a paywall. We've given all the data to a non-profit organisation (Association for Genomic Diagnostics) and made it available for clinicians and researchers to use to drive the field forward.<br></p><p>“I'm so excited about that aspect because, using the tool and the data collected, opens up a whole new avenue for us to be able to help our patients in the clinic and for data scientists and researchers to use it and make better tools of it."<br></p><p>​<br></p><p><em>Caption: Professor Shahida Moosa with her colleague Kimberly Coetzer, a co-author of the paper. </em><em>The image on the right shows matches, an allusion to matching facial features and diseases. A gene sequence is also burned onto the matches. This encryption contains the title and the authors of the study. The blue match heads symbolize rare diseases. Image: Jean Tori Pantel</em><br></p>
WHO: SU plays key role in SA’s mRNA vaccine hubhttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8910WHO: SU plays key role in SA’s mRNA vaccine hubFMHS Marketing & Communications / FGGW Bemarking & Kommunikasie – Ilse Bigalke<p>​The presence of Stellenbosch University's (SU) world-class Biomedical Research Institute (BMRI) and Centre for Epidemic Response and Innovation (CERI) at SU's Faculty of Medicine and Health Sciences (FMHS), was one of the main reasons why the World Health Organisation (WHO) chose South Africa to host Africa's first mRNA vaccine manufacturing hub.<br></p><p>During a media briefing after a tour by a high-level international delegation of these facilities on 11 February 2022, WHO Director-General Dr Tedros Adhanom Ghebreyesus explained that it is this kind of capacity in South Africa that will make the project successful.<br></p><p>“And success is the only option," he added.<br></p><p>The delegation included South African Minister of Health, Dr Joe Phaahla, South African Deputy Minister of Higher Education, Science and Innovation, Buti Manamela, Belgian Minister of Development Cooperation, Meryame Kitir, and other national and international stakeholders.<br></p><p>CERI, which is at the heart of South Africa's world-class viral genomics surveillance programme, is a partner-member of SAMVAC, the South African vaccine consortium selected to become the first Covid mRNA vaccine technology transfer hub in Africa.<br></p><p>The purpose of the hub is to develop a training facility where mRNA technology is developed to the scale required for mass production of vaccines and then for that technology to be transferrable to multiple recipients in low- and middle-income countries.<br></p><p>At the media briefing held at SU's Tygerberg Campus, Ghebreyesus said the “extraordinary scientific triumph" of the development and approval of several Covid-19 vaccines in record time that have saved countless lives and are now giving many countries the confidence to relax restrictions, has been marred by vast inequities in access.<br></p><p>“More than half of the world's population is now fully vaccinated, but 84% of the African population is yet to receive a single dose. Much of this inequity is due to the concentration of vaccine production in a few mostly high-income countries."<br></p><p>He added that one of the pandemic's most obvious lessons is the urgent need to increase local production of vaccines, especially in low- and middle-income countries. That is why the WHO invited applications for the establishment of a technology transfer hub for mRNA vaccines and eventually chose South Africa from the many applications.<br></p><p>The hub is already producing results, with Afrigen Biologics' recent announcement that it has produced its own mRNA vaccine. Clinical trials are expected to start in the fourth quarter of this year, with approval expected in 2024, Ghebreyesus said.<br></p><p>“And the mRNA technology is not just for Covid. It will be for malaria, TB and HIV – it will be a game changer. We expect this vaccine to be more suited to the contexts in which it will be used, with fewer storage constraints and at a lower price."<br></p><p>Asked when the “acute phase" of the pandemic could end, Ghebreyesus said this could happen by the end of 2022 if 70% of the world's population is vaccinated by July. “It's not a matter of chance; it's a matter of choice. If the world wants to end it, it has the means to end it."<br></p><p>Responding to a question about future pandemics, the WHO chief said an underinvestment in public health hampers the world's preparedness to prevent or deal with pandemics. “The world has really progressed a lot in terms of innovation for high-tech medicine, medical interventions, robotics, and so on, while investment in very simple public health is lacking. There are simple things that should be done, starting with surveillance, preparedness, early detection, and response."<br></p><p>Kitir said international recovery depends largely on the world's ability to effectively fight the pandemic together, and that is exactly what the hub project is all about: to bring structural solutions to local needs in worldwide efforts.<br></p><p>“This initiative is showing the world how you solve the fight against inequality. The project is not only a solution for South Africa, but for the whole continent."<br></p><p>Phaahla thanked the WHO for championing vaccine equity. He added that South Africa had not even administered a single vaccine dose a year ago. “Since then, we have come a long way and we have already administered more than 30 million doses. This delegation is the maturation of a very long struggle to access vaccines."<br></p><p>Manamela acknowledged the “tremendous" work scientists have been doing at South African institutions of higher learning to really understand the virus and to contribute to the body of world knowledge. “The capacity of these institutions put us way ahead of many other countries who wanted to host this vaccine hub."<br></p><p>Prof Wim de Villiers, SU Rector and Vice Chancellor, described the hosting of the world's top health officials at a crucial time for the globe as a “proud moment". <br></p><p>“We are in the middle of a pandemic, but thankfully we are making remarkable progress in fighting it. The facilities and initiatives that are helping us fight it, are being highlighted today and are part of that success story."<br></p><p>FMHS Dean Prof Elmi Muller said the Faculty is committed to find practical and impactful solutions to the health challenges faced by the people of South Africa and the African continent. “We are proud to help close the vaccine gap for low- and middle-income countries, by pairing our scientific expertise with our new cutting-edge technology available in the BMRI.<br></p><p>“Today we celebrate the important opportunity to be a part of what we can call a scientific breakthrough – developing an mRNA vaccine in record time," Muller added.<br></p><p><br></p><div class="ms-rtestate-read ms-rte-embedcode ms-rte-embedil ms-rtestate-notify"><iframe width="560" height="315" src="https://www.youtube.com/embed/0mu_x5vnKC0" title="YouTube video player" frameborder="0"></iframe> </div><p><br></p><p><em>Photo caption: Profs Gerhard Walzl (second from right) and Tulio de Oliveira (far right) takes the WHO's Director General,</em><em> dr Tedros Adhanom Ghebreyesus and other high-level delegates on a tour through SU's Biomedical Research Institute.</em></p><p><em>Photo credit: Nardus Engelbrecht</em></p><p><br></p><p>​<br></p>