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Trout ‘voracious predators’ of indigenous Redfinshttp://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8150Trout ‘voracious predators’ of indigenous RedfinsBrian van Wilgen, Centre for Invasion Biology<p></p><p><a href="https://blogs.sun.ac.za/brianvanwilgen/">Prof Brian van Wilgen</a>, emeritus professor in invasion biology, recently replied to an article published on 3 April in <em>Daily Maverick</em>'s <em>168</em> weekly newspaper by Ed Stoddard, entitled “Trout wars: In a developing country with so many challenges, the fuss looks fishy" (Online at <a href="https://www.dailymaverick.co.za/opinionista/2021-04-07-trout-wars-in-a-developing-economy-with-so-many-challenges-the-fuss-looks-fishy/">https://www.dailymaverick.co.za/opinionista/2021-04-07-trout-wars-in-a-developing-economy-with-so-many-challenges-the-fuss-looks-fishy/</a><br></p><p>His reply, titled “Contrary to Ed Stoddard's contention, trout are voracious predators and legislation has been proposed to regulate the fish, not to declare it illegal" was published in <em>DM168</em> on 6 April 2021. Read the reply below:</p><p><em>By Brian van Wilgen, emeritus professor, <a href="https://blogs.sun.ac.za/cib/">DSI/NRF Centre for Invasion Biology</a>, Stellenbosch University</em></p><p>The article by Ed Stoddard (“Spawning debate: the fuss over trout looks fishy"; Daily Maverick, 3 April 2021) is unfortunately flawed, and arguably heavily partisan because of his own admitted status as a “passionate fly-fisher". The issue of regulating trout has recently become particularly contentious. Debates like these prevail where alien species are introduced to provide some form of benefit, but then go on to become invasive, causing harm to the environment. It is important in these cases to present a balanced view, so I will address some of the points made in Mr Stoddard's article.<br></p><p>In general, Mr Stoddard's article acknowledges that invasive species can cause harm, notably on islands, but also contends that in many cases this damage is negligible. It is true that islands are more vulnerable to invasive alien species, but these impacts are now increasingly being felt on the mainland, and they certainly are not negligible. The impacts of invading alien plants in South Africa have recently been conservatively estimated at over R13 billion per year, for water resources, rangeland productivity and biodiversity only – and they are growing alarmingly. </p><p>Mr Stoddard has uncritically repeated arguments by a group within the trout industry as to why trout should not be regulated, namely that trout do minimal harm to the environment; that they have been naturalized in the country for so long (over 100 years) that they should be regarded as indigenous (rather than as alien species); and, that regulation would cause the lucrative trout industry to go “belly-up" (to use Mr Stoddard's terminology). </p><p>The contention that trout have a “fairly minimal" impact, only posing a threat to the rare redfin minnow in the Krom River in the Western Cape, is incorrect. Trout are voracious predators, and their impact is far greater than posing a mere threat to one indigenous fish species. There is now a mounting body of evidence that trout have caused the local extinction of many indigenous freshwater fish species, as well as amphibians and large invertebrates, with knock-on effects for plant life in streams. More importantly, many of the threatened fish species are found nowhere else on Earth, and South Africa is obliged to protect such species both in terms of its own laws, and in terms of the international Convention on Biodiversity. </p><p>The notion that introduced (alien) species should be granted indigenous status if they have been here for a long time is also unsound. This notion is argued in Duncan Brown's book (<em>Are trout South African?</em>), cited in Mr Stoddard's article. Any informed South African alive today would have known trout as occupants of our streams all of their lives. However, our lives are short. Indigenous fish, frogs and dragonflies have evolved over hundreds of thousands of years in environments without voracious predators. They have no instinctive means to avoid predation, and will be driven to extinction long before they are able to learn how to respond to this relatively new and deadly threat.   No “new balance" has been reached, as is often contended.  </p><p>It is also dangerous to start regarding invasive alien species as indigenous. Consider, for example, the case of mice on Marion Island, where they have been for over 200 years. They have decimated the invertebrates found (mostly) only on the island, have impacted on the indigenous plants, and now are attacking the nesting sea-birds.  Projections are that they will cause the local extinction of 18 species of birds, if left alone.</p><p>The nub of the argument though is that regulating trout will impose an unreasonable burden on the industry, requiring a permit for “every step in the trout value chain". Such a requirement would make unpermitted hatcheries, trout-fishing farms, and restaurants serving trout illegal. Further, it is contended that the government does not have the capacity to administer this, and so the industry will simply have to go out of business. However, if one reads the proposed regulations, it immediately becomes clear that many trout “value chain" activities have been exempted from requiring permits, making it perfectly legal, for example, to process, transport, consume, sell or serve trout as long as they are not alive.</p><p>The government's approach to regulating trout is carefully nuanced. The intention is to grant long-term permits that will allow for the continuation of all existing operations in demarcated areas, allowing the industry to continue to operate and to generate benefit. They have even conceded that this can continue in proclaimed protected areas. The main issue here is to prevent the spread of trout to new areas where they do not yet occur. It is well known that freshwater anglers regularly introduce new fish species into catchment areas where they do not yet occur, for the purposes of recreational fishing, and for angling competitions. To prevent the consequent harm to these ecosystems, and to the unique indigenous species that occur there, regulation is necessary. This approach should be seen as a win-win compromise, rather than a cause for prolonged and expensive litigation, which is simply unnecessary and wasteful. As Mr Stoddard points out, there are bigger fish to fry.</p><p> <strong>On the photo:</strong> Redfin minnows are one of the indigenous fish species that form the prey of trout. Streams with trout in them are simply devoid of these charming fishes. <em>Photo supplied by Brian van Wilgen​</em></p><p>​<br></p>
World Health Day: Primary health care helps combat COVID-19, lifestyle diseaseshttp://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8139World Health Day: Primary health care helps combat COVID-19, lifestyle diseasesBob Mash & Resia Pretorius<p></p><p>Wednesday (7 April) was World Health Day. In opinion pieces for the media, Profs Bob Mash (Division of Family Medicine and Primary Care) and Resia Pretorius (Department of Physiological Sciences) focus on health issues that should receive attention during and after the pandemic. Click on the links below to read the articles.</p><ul><li>​Prof Bob Mash (<a href="https://www.iol.co.za/capetimes/opinion/healthcare-adapting-to-coronavirus-pandemic-093d8d71-9475-42ef-8a7e-6e96decafa01"><strong class="ms-rteThemeForeColor-5-0" style="">Cape Times</strong></a>)<br></li><li>Prof Resia Pretorius (<a href="https://www.news24.com/health24/news/public-health/opinion-lets-manage-our-lifestyle-diseases-20210407"><strong class="ms-rteThemeForeColor-5-0" style="">Health24</strong></a>)​</li></ul><p>​<br></p>
SharkSafe BarrierTM withstands two years of testing at La Réunion Islandhttp://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8135SharkSafe BarrierTM withstands two years of testing at La Réunion IslandMedia & Communication, Faculty of Science<p style="text-align:justify;">​The SharkSafe Barrier, an eco-friendly alternative to the traditional shark-control programmes, have withstood two years of testing in Réunion's bay of St Paul. This is part of ongoing efforts by the island's shark security centre <em>Centre Sécurité Requin</em> (CSR) to find a workable and eco-friendly solution to the island's shark crisis. </p><p style="text-align:justify;">The SharkSafe Barrier<sup>TM</sup> technology, originally developed in South Africa, bio-mimicks a thick forest of kelp. Combined with shark-repellent magnets to further deter sharks, the technology has been undergoing rigorous testing in South Africa and The Bahamas since 2012, with the results of these tests published in various <a href="https://www.sharksafesolution.com/scientific-tests/">peer reviewed scientific journals</a>.</p><p style="text-align:justify;">A test barrier of 200 pipes was constructed in February 2019 to form a 10m x 10m square in order to replicate, in La Réunion waters, previously published experiments. The aim was to test the efficacy of the SharkSafe Barrier<sup>TM</sup> to exclude local bull sharks from a food source.</p><p style="text-align:justify;">According to <em>Centre Sécurité Requin</em> (CSR) Director of Operations Michael Hoarau, the barrier's efficiency to exclude bull and tiger sharks species in this instance could not be established, as the underwater cameras and the sonar did not record any bull and tiger sharks approaching the barrier during the tests. However, the developers are encouraged by the fact that the structure, which consists of vertical pipes anchored to the sea bottom, survived two seasons' winter swell, with minimum maintenance.</p><p style="text-align:justify;">“This means that the maintenance of this technology during the last two years was three times cheaper than it would have been to deploy shark exclusion nets," explain Dr Sara Andreotti, COO of SharkSafe Barrier Pty.</p><p style="text-align:justify;"><strong>Ongoing research and product development</strong></p><p style="text-align:justify;">In parallel with the St Paul experiment, differently designed units were tested in Etang-Salé, to form part of an ongoing research and development effort in the high energy zone (perpendicular to the shoreline). This research aimed to adapt the current design to enable more versatile installations across the globe. The designs were installed at different water depths and across different substrates, testing cost-effective options to provide robust solutions. The Etang-Salé experiment was sponsored entirely by the SharkSafe Barrier Pty start-up, and was conducted between January 2019 and June 2020. Three rounds of increasingly expensive and robust designs have been installed during the trials, but none proved robust enough for the Etang-Salé conditions.</p><p style="text-align:justify;">The costs associated with the experimentation in Etang Salé prompted the decision to suspend the research and development efforts in Réunion, and to continue the product development tests in South Africa. The different designs tests are being continued in Glencairn in South Africa and these are showing promising results.</p><p style="text-align:justify;"><strong>Global solution to replace current shark-control programs</strong></p><p style="text-align:justify;">According to Dr Sara Andreotti, one of the co-inventors of the SharkSafe Barrier<sup>TM</sup> technology, there is an urgent need to find an alternative to traditional shark-control programs worldwide: “The SharkSafe Barrier is currently the only available eco-friendly and shark-specific technology to reduce shark-human conflict."</p><p style="text-align:justify;">“In the case of Réunion, for example, a non-invasive shark barrier will have a positive impact on the local ecology by protecting top-predators and their key role in the marine ecosystem. It will also positively impact on the local economy, by protecting beach-goers and thereby promote potential tourism revenue. Lastly, it can help the community to better cope with the historical trauma associated with a number of shark accidents since 2011.</p><p style="text-align:justify;">“Irresponsible and unsustainable fishery practices are still undoubtedly the biggest global threat to sharks. The socio economic and ecological impact of a solution such as the SharkSafe Barrier<sup>TM</sup>, is a step in the right direction. For Blue Economy inspired countries such as France, it could prove key to ensuring long term and peaceful coexistence between humans and sharks, while promoting ocean sustainability and coastal eco-tourism," she concludes.</p><p style="text-align:justify;"><strong>For the editors</strong></p><ul><li>Developed in South Africa the <a href="http://www.sharksafesolution.com/">SharkSafe Barrier<sup>TM</sup></a> is the only eco-friendly shark management method in the world combining biomimicry and magnetism to reduce shark-human conflict, by keeping sharks and surfers physically separated from each other. Distributed by SharkSafe Barrier Pty Ltd, a start-up spin-off company of Stellenbosch University, the <a href="http://www.sharksafesolution.com/">SharkSafe Barrier<sup>TM</sup></a> is designed to be a visual shark-deterrent by mimicking a thick forest of kelp composing of vertical recycled plastic pipes, coupled to a strong magnetic field, also tested and proven to affect the swimming behaviour of large sharks.</li><li>Réunion's <em>Centre Sécurité Requin</em> (CSR) and SharkSafe Barrier Pty Ltd respectively contributed 66% and 34% towards the construction and installation of the test barrier at St Paul. The pipes were constructed in South Africa, and shipped to Réunion at the end of 2018. The construction of 40 meters of barrier at St Paul took nine days, and was performed in collaboration with local subcontractors TSMOI, as well as a crane boat and four divers.</li><li>To collect data on the bull sharks' behaviour the CSR operators deployed underwater cameras and sonar, with a canister of fish positioned in the middle of the exclusion square. This activity was performed sixty three times over the two year period. Unfortunately, no bull and tiger sharks were recorded during the data collection, despite adjacent acoustic tags indicating the sporadic presence of bull sharks in the bay. This resulted in the experiment being inconclusive.</li><li>The CSR's research permit conditions require that the installation in St Paul must now be removed from the bay.</li><li>The SharkSafe Barrier<sup>TM</sup> was also labelled as a Solar Impulse Efficient Solution in 2020, completed the <a href="http://www.oceanhub.africa/">Oceanhub Africa business accelerator program</a>, was the recipient of the prestigious NSTF-Lewis Foundation Green Economy Award at the <a href="/english/Lists/news/DispForm.aspx?ID=7542">National Science and Technology Forum</a> and was one of the finalists in the Smart-Eco-responsible Tourism category of the France <a href="https://www.tech4islands.com/tributech4islands/">Tech4Island Award</a>. More recently the company was recognised by the <a href="https://www.weforum.org/agenda/2021/01/meet-the-latest-innovations-protecting-life-below-water-and-above-it/">World Economic Forum</a>'s digital platform UpLink as one of its top ocean innovators.</li></ul><p style="text-align:justify;"><strong>ENDS</strong></p><p style="text-align:justify;"><strong><em>Contact details</em></strong></p><p style="text-align:justify;">Dr Sara Andreotti</p><p style="text-align:justify;">E-mail: andreottisara@gmail.com</p><p style="text-align:justify;">Mobile: 072 3219198</p><p style="text-align:justify;"><strong><em>Website and Social Media links:</em></strong></p><ul><li>OIO LinkedIn: https://www.linkedin.com/company/oceanimpactorg</li><li>OIO Facebook: https://www.facebook.com/oceanimpactorg</li><li>OIO Instagram: https://www.instagram.com/oceanimpactorg/ (@oceanimpactorg)</li><li>OIO Twitter: https://twitter.com/oceanimpactorg (@oceanimpactorg)</li><li>SSB Website: <a href="http://www.sharksafesolution.com/">www.sharksafesolution.com</a></li><li>SSB Facebook: <a href="https://www.facebook.com/Sharksafebarrier/">https://www.facebook.com/Sharksafebarrier/</a></li><li>SSB LinkedIN: <a href="https://www.linkedin.com/company/sharksafe-barriers-rf-">https://www.linkedin.com/company/sharksafe-barriers-rf-</a></li><li>SSB Instagram: <a href="https://www.instagram.com/sharksafebarrier/">https://www.instagram.com/sharksafebarrier/</a></li><li>SSB Twitter: <a href="https://twitter.com/SharksafeB">https://twitter.com/SharksafeB</a><br></li></ul><p>​<br></p>
Accurate quantification of cell dynamics possible with new software toolhttp://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8126Accurate quantification of cell dynamics possible with new software toolWiida Fourie-Basson<p>​Engineers and scientists from Stellenbosch University have developed a visualisation tool that can automatically localise and quantify specific cellular processes such as mitochondrial fission and fusion – and that in three-dimensional space and time.<br></p><p>Mitochondria are organelles that generate most of the chemical energy needed to power the cell's biochemical reactions. Mitochondrial processes, such as fission and fusion, therefore play a central role in the balance, function and viability of cells. When things go wrong, it is often a sign of the onset of neurodegenerative diseases such as Parkinson's and Alzheimer's disease.</p><p>To date, however, the accurate quantification of these cell dynamics has been a challenge, with most of the work being done manually.</p><p>Prof Ben Loos, a physiologist in the Department of Physiological Sciences, says they are very excited about this work: “We believe it moves the field forward on many fronts, from life sciences dealing with mitochondria and microscopy, to the fields of image analysis and object recognition, computation and machine learning, data handling and analysis, and 3D visualisation.</p><p>Since 2015, he has been working with Prof Thomas Niesler from the Department of Electronic and Electrical Engineering on improving 3D visualisation tools associated with microscopy. The current tool, called the Mitochondrial Event Localiser (MEL), was developed by Dr Rensu Theart as part of his PhD research into the virtual reality visualisation and analysis of microscopy data. </p><p>Prof Loos says image analysis of biological data is often so time consuming that only few research groups embrace such a task: “With MEL, we are able to quantify the structures and the interaction (fission and fusion) between the structures in the cell, as well as pin-pointing where these are occurring.</p><p>“This is incredibly exciting, to locate where in the cell fission, fusion and depolarisation occurs, and to quantitatively describe their magnitude of occurrence".</p><p>Why is this so important? </p><p>He says researchers struggle to interpret the morphology of the mitochondrial network: “Some say that a highly networked mitochondrial structure indicates improved cellular health, other evidence suggests that it is the beginning of a stress response. The same for a fragmented mitochondrial picture, some scientists advocate that fragmentation equals stress and detriment, while other evidence indicates it as adaptive mechanism to enable mitochondrial quality control.</p><p>“This really bothered us. Especially since this plays such an important role in neurodegenerative disease, we wished to come up with a tool that could describe the mitochondrial network dynamically, meaning to work with real-time data sets. In doing so, a completely new data set is generated, which allows to showcase the state of equilibrium of mitochondria between a fission and a fusion state." </p><p>They believe this software tool will be of major benefit to the research community dealing with mitochondrial dysfunction. Especially those laboratories focussing on Alzheimer's disease and Parkinson's disease.</p><p>“It could also become part of a diagnostic tool, if integrated into so called high throughput imaging platforms. And because mitochondrial depolarisation is a critical part in the beginning of cell death, there may be an even wider application base," he concludes. </p><p><strong>Information box: How does MEL work?</strong></p><ol><li>First, a time-lapse sequence of a cell, labelled for mitochondria, is acquired in 3D with confocal microscopy.</li></ol><ol start="2" style="list-style-type:decimal;"><li>This time-lapse sequence is then pre-processed to ensure the best image quality and consistency between the frames in the sequence.</li><li>Two consecutive frames are then chosen, and binarized. From this the separate mitochondrial structures can be extracted.</li><li>Through various mathematical steps, including a new algorithm called “back-and-forth structure matching", the presence and location of the mitochondrial events can be determined.</li><li>These locations are then overlaid as different colours on the original mitochondrial image.</li><li>This process is then repeated for all consecutive image pairs in the time-lapse sequence, thereby allowing a quantitative evaluation of how the mitochondrial events vary over time. </li></ol><ul><li>Compiled by <em>Dr Rensu Theart</em></li></ul><p>The article “Mitochondrial event localiser (MEL) to quantitatively described fission, fusion and depolarisation in the three dimensional space" was published in the journal <em>Plos One</em> recently and is available online at <a href="https://doi.org/10.1371/journal.pone.0229634">https://doi.org/10.1371/journal.pone.0229634</a></p><p>The code that implements MEL is available for download at <a href="https://github.com/rensutheart/MEL">https://github.com/rensutheart/MEL</a></p><p><strong><img src="/english/PublishingImages/Lists/dualnews/My%20Items%20View/MEL%20event_Image%20credit%20Renso%20Theart_small.png" alt="MEL event_Image credit Renso Theart_small.png" style="margin:5px;" /></strong> </p><p>This is the result produced by the Mitochondrial Event Localiser (MEL) when applied to an image showing only the mitochondrial network of a cell acquired by confocal microscopy. The different colours indicate the location of where the mitochondrial fission, fusion, and depolarisation events were detected. <em>Image: Rensu Theart</em></p><p><strong>Contact details</strong></p><table cellspacing="0" width="100%" class="ms-rteTable-default"><tbody><tr><td class="ms-rteTable-default" style="width:33.3333%;"><p>Prof Ben Loos</p><p>E-mail: bloos@sun.ac.za</p><p> </p></td><td class="ms-rteTable-default" style="width:33.3333%;"><p>Dr Rensu Theart</p><p>E-mail: rptheart@sun.ac.za</p><p> </p></td><td class="ms-rteTable-default" style="width:33.3333%;"><p>Prof Thomas Niesler</p><p>E-mail: trn@sun.ac.za​ </p></td></tr></tbody></table><p><em><br></em></p><p>​<br></p>
Early detection of increased risk for colorectal cancer http://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8128Early detection of increased risk for colorectal cancer Wiida Fourie-Basson<p></p><p>A PhD student from Stellenbosch University has established that the early detection of colorectal cancer risk would be greatly enhanced by a holistic approach that takes into account the complex interplay between chronic inflammation, abnormal blood clotting and the involvement of a bacterial presence. </p><p>Colorectal cancer, also known as colon cancer, is currently the third most diagnosed cancer in the world. When diagnosed early, about 90% of the patients will have a five-year life expectancy. It reduces to 13% with a late or delayed diagnosis.</p><p><a href="https://www.researchgate.net/profile/Greta-De-Waal-2">Dr Greta de Waal</a>, who received her doctoral degree during the Faculty of Science's SU's graduation ceremony on 1 April 2021, emphasises that colorectal cancer is a multifactorial and heterogeneous cancer, with various contributors and drivers involved in its pathogenesis: “Most cases of colorectal cancer encompass a variety of contributing risk factors, in addition to genetic features. Because of the heterogeneity of the disease, it is crucial to employ holistic approaches to determine how all the different factors involved in the carcinogenic process are linked to (and may fuel) each other," she explains.</p><p>In her research, she analysed and described both the systemic environment and local tumour environment of patients with colorectal cancer. She developed and optimised a novel fluorescence antibody-based technique to detect the bacterial inflammagen, lipopolysaccharide (LPS), in blood. She was then able to show that the circulating levels of this bacterial wall component are significantly elevated in patients with colorectal cancer, compared to healthy individuals. In addition, she also demonstrated an intratumour bacterial presence in these patients. She thus found that the presence of a bacterial component forms a key part of the overall profile of patients with colorectal cancer, with systemic inflammation and increased hypercoagulability also being central.</p><p>Dr De Waal says there is an intricate relationship between a dysfunctional gut microbiome and a pro-inflammatory profile in these patients: “Alterations in the composition of the gut microbiota can contribute to the development of a dysfunctional gut barrier, thereby facilitating the translocation of bacteria and their inflammagenic molecules. Such leaky gut conditions can promote systemic inflammation, of which a hallmark is abnormal blood clotting".</p><p>Chronic inflammation and hypercoagulation are both implicated in the formation of tumours. The researchers believe these conditions – elevated presence of certain circulating bacterial and other inflammatory markers, and the incidence of abnormal blood clotting – could be used as biomarkers in blood-based screening tools when screening patients for colorectal cancer risk.</p><p>“All of this information can be obtained by taking a simple blood sample, and then knowing what to look for," adds <a href="http://www.resiapretorius.net/">Prof Resia Pretorius</a>, her supervisor and a physiologist in the <a href="http://www0.sun.ac.za/physiologicalsci/eng/index.php">Department of Physiological Sciences</a> at SU.</p><p>Prof Pretorius says the work is the result of a fruitful collaboration between herself and clinicians from SU's Faculty of Medicine and Health Sciences at Tygerberg, with the SU rector Prof Wim de Villiers, who is a gastroenterologist himself, acting as co-supervisor.</p><p>“While we benefited from Prof De Villiers' expertise of the clinical side of colorectal cancer and its treatment, we could add our expertise of what is happening at the molecular level," she explains.</p><p><strong>Media enquiries</strong></p><p>Prof Resia Pretorius</p><p>Head: Department of Physiological Sciences, SU</p><p>E-mail: <a href="mailto:resiap@sun.ac.za">resiap@sun.ac.za</a></p><p>​Dr Greta de Waal<br></p><p>Postdoctoral Fellow, Department of Physiological Sciences, SU</p><p>E-mail: 18340164@sun.ac.za<br></p><p>On the photo, Dr Greta de Waal (middle), together with her study leaders Prof Resia Pretorius and Prof Wim de Villiers, after the 1 April 2021 graduation ceremony. <em>Photo: Stefan Els</em><br></p><p>​<br></p>
Why tree diversity in the tropic mattershttp://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8129Why tree diversity in the tropic mattersWiida Fourie-Basson<p></p><p>What can the decomposed leaf litter from 40 streams on six continents tell us about the impact of biodiversity loss on global carbon fluxes?</p><p>According to a study published in <em>Science Advances </em>today (26 March 2021), there is reason to be concerned, especially at low latitudes where the rate of deforestation and conversion of forest to monoculture, plantations and agricultural land are already high. </p><p>The decomposition of plant litter in streams is a fundamental ecosystem service, as it mainly serves as a sink for carbon, thereby keeping the global carbon budget in balance. When the optimal functioning of that ecosystem service is disturbed, some of the world's rivers could become a source rather than a sink for carbon, creating potential feedbacks on climate.</p><p>Prof Cang Hui, a bio-mathematician from Stellenbosch University and a co-author of the article, says some broad-scale roles of biodiversity and the impacts of climate change only emerge and become detectable at the global scale. In this study, for example, the latitudinal gradient of instream decomposition only became clear over more than 100° of latitude, roughly around 10 000 km.</p><p>To conduct this global experiment, scientists from 67 institutions across six continents joined forces to coordinate the sampling of the rivers. From 2017 to 2019, they placed a total of 2 580 leave litter bags in 40 streams. Four rivers from Africa were sampled: the Lourens River near Somerset West in South Africa, the Njoro and the Ngetunyek rivers in Kenya and the Djigbè River in Guinea. </p><p>The bags were retrieved after 23 to 46 days, depending on the water temperature in each stream, put in individual ziplock bags and transported on ice to various laboratories. The aim of the study was to assess how the decomposition rates in streams vary from the lower to the higher latitudes, from which we can infer how biodiversity loss and climate change affect this ecosystem service.</p><p>The results demonstrated that plant diversity has a major impact on litter decomposition. The experiment was able to show that plant litter high in diversity (e.g., in toughness, nutrient content, presence of toxins) stimulates decomposition more at low latitudes than in cooler climates. This suggests that stream ecosystem functioning could be particularly vulnerable to forest practices that are detrimental to native tropical forests.</p><p>In other words, biodiversity loss in the lower latitudes will negatively affect tropical detritivores, as they require a diet high in diversity. If their ability to break down leaf litter is diminished, it will enhance the relative contribution of microbial decomposition in rivers to carbon fluxes.</p><p>Prof Hui, the only South African scientist to participate in the study, holds a <a href="https://math.sun.ac.za/hui/">South African Research Chair on mathematical biosciences</a> in the Department of Mathematical Sciences at SU, and has been collaborating with the lead author of the study, Prof Luz Boyero from the University of the Basque Country in Spain, for the past ten years. She is also the coordinator of the <a href="https://www.globenetwork.es/">GLoBe network</a>, an international network of freshwater ecologists.</p><p>“For me, biodiversity is the most striking reality and puzzle of our biosphere. How biodiversity structures and functions across spatial and temporal scales is the focus of our research," he explains.</p><p>He believes we cannot enter an era of global change with the traditional view of a stable ecosystem: “Such novel ecosystems, constantly challenged by human activities and issues such as biological invasions and climate change, are in persistent transition. We are yet to develop a new set of theoretical frameworks to study such systems."</p><p>“Biomathematics, with its reaches into data science and informatics, provides a powerful set of tools from different areas of mathematics to (re)invent this theoretical framework for open adaptive systems. This era is not only an opportunity for global change biology, but also a chance for mathematics and physics to create new pathways," he concludes.</p><p>The article, “Latitude dictates plant diversity effects on instream decomposition" was published in <em>Science Advances</em> on 26 March 2021.</p><p><strong>Media enquiries</strong></p><p>Prof Cang Hui</p><p><a href="https://math.sun.ac.za/hui/">South African Research Chair in Mathematical Biosciences</a>, Department of Mathematical Sciences, Stellenbosch University, South Africa</p><p>E-mail: <a href="mailto:chui@sun.ac.za">chui@sun.ac.za</a></p><p>Tel: +27 _21 808 3853<br></p><p>​<br></p>
Young PhD-graduate in physiological sciences already has 15 publicationshttp://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8120Young PhD-graduate in physiological sciences already has 15 publicationsMedia & Communication, Faculty of Science<p><br><br></p><p>With 250 citations from 15 research papers published in peer reviewed journals, Dr Martin Page has certainly earned the honour of walking over the stage when he receives his doctoral degree in Physiological Sciences from Stellenbosch University on 1 April 2021.</p><p>Dr Page started with a BScHons-degree in 2017 under the guidance of Prof Resia Pretorius, a physiologist and distinguished professor in the Department of Physiological Sciences. He continued with postgraduate studies and at the end of 2019 his MSc was upgraded to a PhD. That means he managed to graduate with a PhD only three years after finishing his BScHons-degree.</p><p>Dr Page says while a doctoral thesis is tough, he chose to focus on his research and the impact it could have for biomedicine: “I work in the field of inflammation and blood clotting. Inflammation is the centrepiece of many diseases. It is the body's normal response to injury and infection, but especially in patients with non-communicable diseases such as type 2 diabetes, Parkinson's disease, and rheumatoid arthritis, the inflammatory response is persistent and dysregulated. This has various harmful consequence, one of which is abnormal blood clotting," he explains.</p><p>His research focused on the characterisation of clotting mechanics and the underlying structural changes of blood from patients with inflammatory conditions. He also tested the effects of individual inflammatory mediators on healthy blood to dissect the complex interplay of the inflammatory environment on blood clotting.</p><p style="text-align:justify;">His findings demonstrate that disturbances in the blood can signify broader dysfunction in the body: “This means that the blood is a trove of biological signatures that can warn of possible pathology in other areas of the body. It also means that pathological clotting is a general fear with chronic inflammatory conditions, and it needs to be targeted to prevent worsened pathology".</p><p>During his postgraduate studies, he has visited the Manchester Institute of Biotechnology at the University of Manchester in the United Kingdom, and the Medical University of Vienna in Austria to work with some of Prof Pretorius' international collaborators.</p><p style="text-align:justify;">About his 250 citations on Google Scholar from 15 publications, some of them as first author and others co-authored,  he says the purpose of science is to communicate one's work to move the field forward: “I am glad that our research has been well-received by the scientific community and this exemplifies the impact of our work. Publishing is also a great learning experience and it teaches you to think critically about your findings."</p><p style="text-align:justify;">His studies have been supported by the Skye Foundation and the Harry Crossley Foundation. In 2020 he was selected as one of ten young scientists from South Africa to attend the 70th Lindau Nobel Laureate Meeting, postponed to 2021 because of the pandemic.</p><p style="text-align:justify;">Dr Page is now participating in Stellenbosch University's Consolidoc programme to finalise the last publications from his doctoral research. He is also provisionally accepted for a Commonwealth Scholarship in the UK to study a one-year Master's degree in data science and machine learning. </p><p style="text-align:justify;"><img src="/english/PublishingImages/Lists/dualnews/My%20Items%20View/RBC%20figure.jpg" alt="RBC figure.jpg" style="margin:5px;width:607px;" /><br></p><p style="text-align:justify;">On the photo above, a scanning electron microscopy image of red blood cells exposed to serum amyloid A, an inflammatory molecule produced in the liver. When blood cells clump together like this, it is called agglutination. <em>Image: Martin Page</em></p><p>​<br></p>
SU honours globally renowned mathematicianhttp://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8122SU honours globally renowned mathematicianCorporate Communication & Marketing / Korporatiewe Kommunikasie & Bemarking [Alec Basson]<p>​<br><br></p><p>Stellenbosch University (SU) bestowed an honorary doctorate on globally renowned mathematician Professor Batmanathan Dayanand Reddy on Thursday (1 April 2021) at SU's March graduation. Reddy received the degree Doctor of Science (DSc), honoris causa, at a small physical graduation ceremony for doctoral graduates from the Faculty of Science held at the Endler Hall in the Konservatorium (Conservatoire) on the Stellenbosch campus. </p><p>He was honoured for his research leadership and scientific breakthroughs; for his exceptional contribution in strengthening and advancing science at a national and international level; and for his generosity in sharing his knowledge and expertise to develop students in the field of computational and applied mechanics.<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/sAzZh9KP3iA" title="YouTube video player" frameborder="0"></iframe> </div><p><br></p><ul><li>Cellphone users click <a href="https://www.youtube.com/watch?v=sAzZh9KP3iA"><strong class="ms-rteThemeForeColor-5-0" style="">here </strong></a>for video.<br></li></ul><p>​In his acceptance speech, Reddy said SU has done him a great honour by awarding him the degree. “It is doubly an honour being conferred by an institution of undoubted stature in the world of scholarship and beyond."<br></p><p>Speaking on the importance of science, Reddy said it has to be an integral part of our efforts to address the social and environmental challenges of our time. <br></p><p>“Science is absolutely essential to addressing the existential challenges posed by the COVID pandemic. We are witnessing roles played by not only health scientists, but also mathematicians, statisticians, demographers, chemists, social scientists and psychologists working across disciplines.<br></p><p>The scientific community has been exemplary in its cooperative approach and has set an example to governments and other sectors, an example which will be pivotal in determining the success of our efforts in building a sustainable and resilient future."<br></p><p>Reddy said scientists should do their work ethically and with integrity so that people can have trust in science, especially in the face of misinformation and pseudoscience which pose a real threat to the value of science.<br></p><p>He encouraged the doctoral graduates to be vigilant and to advocate strongly and publically for scientific values and methods.<br></p><p><strong>MORE ABOUT PROFESSOR BATMANATHAN DAYANAND REDDY</strong></p><p>Reddy has a notable record of sustained activity in strengthening the scientific enterprise. An A-rated National Research Foundation scientist, Reddy's journey into science began back in 1973, when he completed a BSc in Civil Engineering at the University of Cape Town (UCT), followed by a PhD at the University of Cambridge in the United Kingdom. </p><p>He has made major contributions to the analysis of problems in solid mechanics, most notably plasticity, and to the development and analysis of mixed and related finite element methods.  Beyond these major areas of expertise, he has also made significant contributions to aspects of biomedical mechanics.  <br></p><p>Reddy is a founding member of the African Institute for Mathematical Sciences, chaired a steering group of academics who established the South African Centre for High Performance Computing, and is a founding fellow of the Academy of Engineering and Technology of the Developing World.<br></p><p>He served a seven-year term as Dean of the Faculty of Science at UCT, where he also held the South African Research Chair in Computational Mechanics in the Department of Mathematics and Applied Mathematics. He retired from UCT at the end of the end 2020. <br></p><ul><li><strong>​Photo</strong>: Prof Batmanathan Dayanand Reddy at the graduation ceremony. <strong>Photographer</strong>: Stefan Els.</li></ul><p>​<br></p>
From Namibia and Tanzania to Ghana – discovering Africa as an economic geologisthttp://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8114From Namibia and Tanzania to Ghana – discovering Africa as an economic geologistMedia & Communication, Faculty of Science<p>​With a doctoral degree in <a href="/english/faculty/science/earthsciences/research/economic-geology">economic geology</a> from Stellenbosch University in his pocket, Dr Stephan Dunn has already travelled far and wide on the African continent – first for his research on gold mineralisation processes in Tanzania, and now as project geologist for the company Remote Exploration Services (RES).</p><p>Stephan will be receiving his PhD-degree together with 20 other PhD-graduates during the Faculty of Science's graduation ceremony on 1 April 2021.</p><p><strong>Where did you matriculate and when?</strong></p><p>I matriculated from Vredenburg High School in 2013.</p><p><strong>When did you decide to study earth sciences and why?</strong></p><p>I've always had a fascination with nature and how natural processes operate to shape our world, and I guess that curiosity drove me into this field.</p><p><strong>It is not very often that geologists continue up to PhD level. What made you continue with the postgraduate study path? And your interest specifically in economic geology?</strong></p><p>Of all the various fields within geology, I believe that research related to economic geology has the greatest impact on the exploration and mining industry. So, when the opportunity arose to pursue a research project related to gold mineralization in Tanzania with <a href="/english/faculty/science/earthsciences/staff-and-postgrads/academic-staff/dr-bjorn-von-der-heyden">Dr Bjorn von der Heyden</a>, I knew that I had to take it. </p><p>I think the reason for continuing up to PhD level can be attributed to two factors; firstly, the opportunity to conduct research under the incredible guidance and mentorship of Dr Von der Heyden; and secondly, my passion for geology and always discovering new things.</p><p><strong>Where are you working now, and how did you get there?</strong></p><p>I joined the company, <a href="https://www.res.co.za/">Remote Exploration Services</a> (RES), as a Project Geologist at the start of 2021. In every aspect I am still a junior employee, but my experience to date with them has been amazing. I am currently working on an exciting orogenic gold exploration project in the magnificent Erongo Region of Namibia.</p><p><strong>A typical day in your life?</strong></p><p>Our fieldwork days start quite early in the morning and we are normally in the field by 7am until 5pm in the afternoon. Not one day is ever the same, but usually it involves geological mapping, core logging, report writing and data capture. It is certainly not the most glamorous lifestyle, but very rewarding if you have an appetite for discovery and exploration.</p><p><strong>What are some of the remotest places you have been to?</strong></p><p>My research and work as a geologist have allowed me to explore some very cool parts of Africa, the highlight of which has to be <a href="https://en.unesco.org/biosphere/africa/lake-bosomtwe">Lake Bosomtwe in Ghana</a>, one of six meteoritic lakes in the world.</p><p><strong>Any advice for undergraduate students? Or those starting to prepare for a career?</strong></p><p>Mental resilience, perseverance and passion – if you have that, you are already halfway there.<br></p><p>​<br></p>
Exciting capabilities of X-ray tomography at CT Scanner highlighted in Nature Reviewshttp://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=8110Exciting capabilities of X-ray tomography at CT Scanner highlighted in Nature ReviewsE Els<h4>​X-ray computed tomography (CT) can reveal the internal details of objects in three dimensions non-destructively. This non-destructive imaging modality is well known in its medical form, but it is also very useful for imaging materials and structures of non-medical nature. <br></h4><p style="text-align:justify;"><br></p><p style="text-align:justify;">The non-destructive nature of the method allows examining delicate samples that can't be easily sectioned, like priceless museum artefacts, unique biological specimens, brittle engineering materials, even such things as frozen ice cream. It is also of advantage on samples where the structural integrity of an engineering component must be assured before it is deployed, like a turbine blade. It can also be used to evaluate wear and tear on in-service parts, among many other uses.​<br><br></p><p style="text-align:justify;">In an article published in <em>Nature Reviews Methods Primers</em>, scientists outlined the basic principles of CT and described the ways in which a CT scan can be acquired using X-ray tubes and synchrotron sources, including the different possible contrast modes that can be exploited. They explained the process of computationally reconstructing three-dimensional (3D) images from 2D radiographs and how to segment the 3D images for subsequent visualization and quantification.  The field of X-ray CT is expanding rapidly both in terms of the range of applications and with regard to the development of new imaging modalities. Many applications now popular are explained in the paper, highlighting the potential and capabilities for new users of the technique in particular.<br><br></p><p style="text-align:justify;">CT is widely used in medical and heavy industrial contexts at relatively low resolutions, but in this article, scientists focused on the application of higher resolution X-ray CT across science and engineering. They considered the application of X-ray CT to study subjects across the materials, metrology and manufacturing, engineering, food, biological, geological and palaeontological sciences. They also examined how CT can be used to follow the structural evolution of materials in three dimensions in real-time or in a time-lapse manner, for example, to follow materials manufacturing or the in-service behaviour and degradation of manufactured components. Finally, they considered the potential for radiation damage and common sources of imaging artefacts, discuss reproducibility issues and consider future advances and opportunities.<br></p><ul style="list-style-type:disc;"><li>The article  'X-ray computed tomography' was published in <em>Nature Reviews (</em>18: 2021) and is available online at  <a href="https://www.nature.com/articles/s43586-021-00015-4">https://www.nature.com/articles/s43586-021-00015-4</a><br><br></li></ul><p style="text-align:justify;"><strong>Media requests:​</strong></p><p style="text-align:justify;">Prof Anton du Plessis</p><p style="text-align:justify;">E-mail: <span style="text-decoration:underline;"><a href="mailto:anton2@sun.ac.za">anton2@sun.ac.za</a></span></p><p style="text-align:justify;"><br></p>