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New framework to protect World Heritage Sites against invasive specieshttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=7689New framework to protect World Heritage Sites against invasive speciesCorporate Communication & Marketing / Korporatiewe Kommunikasie & Bemarking [Alec Basson]<p>A team of international scientists, including three researchers affiliated with the Centre of Excellence for Invasion Biology (CIB) at Stellenbosch University, came up with a new monitoring and reporting framework to help protect World Heritage Sites (WHS) from almost 300 different invasive alien species (microorganisms, animals and plants) that have been introduced to them. <br></p><p>They assessed the current status of biological invasions and their management in 241 natural and mixed WHS globally  ̶  including South Africa's Barberton Makhonjwa Mountains, Cape Floristic Region, iSimangaliso Wetland Park and Vredefort Dome  ̶  by reviewing documents collated by UNESCO and the International Union for Conservation of Nature (IUCN). The findings of their research were published in <a href="https://link.springer.com/article/10.1007/s10531-020-02026-1"><strong class="ms-rteThemeForeColor-5-0" style="">Biodiversity and Conservation</strong></a> recently.</p><p>“Our review yielded limited information on the presence, threat, and management of invasive alien species within many World Heritage Sites. Reports on the status of biological invasions were also inconsistent at times," says lead author Dr Ross Shackleton from the CIB and the Institute of Geography and Sustainability at the University of Lausanne in Switzerland.</p><p>Shackleton adds that the lack of a systematic method of reporting made it very difficult to compare information between sites to produce summaries of global trends. <br></p><p>“Detailed information on invasive alien species management undertaken in World Heritage Sites was available for fewer than half of the sites that listed them as a threat. This clearly highlights the need for a good monitoring and reporting framework for biological invasions in World Heritage Sites and other protected areas globally."<br></p><p>Shackleton says their framework proposes protocols for collecting information and reporting on (i) pathways by which alien species are introduced to WHS, (ii) current alien species that are present, (iii) their impacts and management, (iv) predicting future threat and management needs, and (v) identifying the status of knowledge and gaps. All of this information can be used to assign an overall 'threat score/level' (very high, high, moderate, low, or data deficient) to a specific site.<br></p><p>“A key facet of the new framework involves the listing all alien invasive species present. This information will allow the tracking of changes in threats and the implementation and level of success of managing these species."<br></p><p>The scientists tested their framework on seven sites across the world including the Vredefort Dome in South Africa. Shackleton says applying it to these sites has yielded more information than past monitoring initiatives.<br></p><p>“For example, the invasive alien species threat level indicated in the 2017 IUCN World Heritage Outlook for the Serengeti, Keoladeo, Donana, and the Vredefort Dome sites was 'data deficient' or 'low threat' or 'not listed', whereas all of these World Heritage Sites are now categorised as facing moderate to high threats from biological invasions based on our assessment informed by the framework." He adds that some successes in management were also uncovered where Aldabra Atoll has fewer species present due to good management. <br></p><p>Shackleton says hopefully their framework would improve the consistency, comparability and overall value of future reporting on the threats and management of invasive alien species in WHS and other protected areas.<br></p><p>“Applying this framework in World Heritage Sites and other protected areas would help facilitate comparisons and the sharing of best practices between sites and help to guide the allocation and prioritisation of funding to manage invasive alien species. It could also provide the basis for a freely available global information system with an inventory of invasive alien species threats to these areas."<br></p><p>Echoing Shackleton's sentiment regarding the importance of protecting these areas, co-author Prof Dave Richardson from the CIB says “World Heritage Sites face rapidly growing threats from a range of biological invasions which impact upon native biodiversity and the delivery of ecosystem services. Not only that, but invasive alien species are a financial burden as costs for management can be extremely high."<br></p><p>The scientists suggest that monitoring and reporting should preferably be done by local experts or managers while state authorities, in partnership with local role-players, should drive the implementation of the framework. <br></p><ul><li><strong>SOURCE</strong>: Shackleton, R.T. <em>et al</em><em>*</em>. 'Biological invasions in World Heritage Sites: current status and a proposed monitoring and reporting framework'. <em>Biodiversity and Conservation</em>. <a href="https://link.springer.com/article/10.1007/s10531-020-02026-1"><span class="ms-rteThemeForeColor-5-0" style=""><strong>DOI: 10.1007/s10531-020-02026-1</strong></span></a></li></ul><p>*Authors of this paper include Ross Shackleton (Centre of Excellence for Invasion Biology – CIB – Stellenbosch University/ Institute of Geography and Sustainability, University of Lausanne), Bastian Bertzky (Joint Research Centre, European Commission), Louisa Wood (Centre for Environment, Fisheries and Aquaculture Science, United Kingdom), Nancy Bunbury (Seychelles Islands Foundation/ Centre for Ecology and Conservation, University of Exeter), Heinke Jäger (Charles Darwin Foundation), Remco van Merm (International Union for Conservation of Nature – IUCN), Christian Sevilla (Galapagos National Park Directorate), Kevin Smith (IUCN), John Wilson (CIB/ South African National Biodiversity Institute ), Arne Witt (Centre for Agriculture and Biosciences International, Nairobi) and David Richardson (CIB).<br></p><p><strong>Photo</strong>: Vredefort World Heritage Site: <strong>Credit</strong>: Wikimedia Commons<br></p><p><strong>FOR MEDIA ENQUIRIES ONLY</strong></p><p>Dr Ross Shackleton</p><p>Centre of Excellence for Invasion Biology/ Institute of Geography and Sustainability</p><p>Stellenbosch University/ University of Lausanne</p><p>Email:<strong class="ms-rteThemeForeColor-5-0" style=""> </strong><a href="mailto:rtshackleton@gmail.com"><strong class="ms-rteThemeForeColor-5-0" style="">rtshackleton@gmail.com</strong></a> </p><p><br></p><p>Prof Dave Richardson<br></p><p>Centre of Excellence for Invasion Biology</p><p>Stellenbosch University</p><p>Email: <a href="mailto:rich@sun.ac.za"><strong class="ms-rteThemeForeColor-5-0" style="">rich@sun.ac.za</strong></a> </p><p><strong>ISSUED BY</strong></p><p>Martin Viljoen</p><p>Manager: Media</p><p>Corporate Communication and Marketing</p><p>Stellenbosch University</p><p>Email:<strong class="ms-rteThemeForeColor-5-0" style=""> </strong><a href="mailto:viljoenm@sun.ac.za"><strong class="ms-rteThemeForeColor-5-0" style="">viljoenm@sun.ac.za</strong></a> </p><p> </p><p> <br></p><p><br></p>
WWF Living Planet Report: two-thirds decline in wildlife populations on average since 1970https://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=7667WWF Living Planet Report: two-thirds decline in wildlife populations on average since 1970Media & Communication, Faculty of Science<p>​​​Prof Guy Midgley from Stellenbosch University is one of 125 specialists from around the world who have contributed to the World Wildlife Fund's (WWF) <em><a href="https://livingplanet.panda.org/">Living Planet Report 2020</a></em>, published today.</p><p>Prof Midgley, an internationally acknowledged leader in the field of biodiversity and climate change science, heads the Global Change Biology Group in the Department of Botany and Zoology at Stellenbosch University.</p><p>The <em>Living Planet Report 2020 </em>presents a comprehensive overview of the state of our natural world through the Living Planet Index. This index, provided by the Zoological Society of London, has been tracking trends in global wildlife abundance since 1970. </p><p>According to a media release issued by WWF, the Living Planet Index shows that there has been a 68% decline in global vertebrate species populations between 1970 and 2016, mainly caused by environmental destruction and the use and trade of wildlife.</p><p>In the section “Deep dive into biodiversity in a warming world" Prof Midgley writes that even with significant mitigation efforts, “up to one-fifth of wild species are at risk of extinction this century due to climate change alone". Even more concerning is the fact that recent modelling has shown that changing climate conditions could begin breaching the tolerance limits of most species in multi-species communities roughly simultaneously, causing abrupt losses of biodiversity. Midgley adds that biodiversity hotspots around the world, like the Cape Fynbos and Succulent Karoo, could be particularly vulnerable to such effects.</p><p>Reducing emissions from fossil fuel use, in particular, is essential to avoid these risks, says Midgley. “Abrupt thresholds could be reached in tropical oceans within a decade under a high-emissions scenario, spreading to tropical forests and reaching higher latitudes by mid-century. Up to 15% of ecological communities would be exposed to this threshold if global warming exceeds 4° C, but fewer than 2% if global warming is kept below 2° C," according to the work referred to in the report. Recent work by a team working on the SPARC program (http://www.sparc-website.org/), in which Midgley co-led work on modelling the vulnerability of African biodiversity to climate change, showed that increasing land available for conservation would substantially reduce climate change extinction risks, regionally and globally. </p><p>According to the <em>Living Planet Report 2020</em>, pioneering modelling shows that without further efforts to counteract habitat loss and degradation, global biodiversity will continue to decline. To turn this situation around, we need “bolder, more ambitious conservation efforts" and a transformation in how we produce and consume food". In this regard, the WWF is calling for urgent action to reverse the trend by 2030 by ending the destruction of natural habitats and reforming our food system. </p><p>In the Foreword to the report, Marco Lambertini, Director General of WWF International, writes that “a deep cultural and systemic shift is urgently needed, one that so far our civilization has failed to embrace: a transition to a society and economic system that values nature, stops taking it for granted and recognise that we depend on nature more than nature depends on us".<br></p><p><br> </p>
It’s possible to decolonise sciencehttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=7646It’s possible to decolonise scienceMargaret Blackie & Hanelie Adendorff<p>The decolonisation of science is possible, but then we must begin to recognise the influence of cultural heritage and Western modernity on the way science is being taught, write Drs Margaret Blackie (Department of Chemistry and Polymer Science) and Hanelie Adendorff (Centre for Teaching and Learning) in an opinion piece for <em>Mail & Guardian</em> (31 August).<br></p><ul><li>Read the article below or click <a href="https://mg.co.za/education/2020-08-31-it-is-possible-to-decolonise-science/"><strong class="ms-rteThemeForeColor-5-0" style="">here</strong></a> for the piece as published.</li></ul><p><strong>Margaret Blackie & Hanelie Adendorff*</strong><br></p><p>The call for decolonisation has caused much angst and much debate in academic circles in South Africa. It is important to recognise that this call is not limited to South Africa. Nonetheless, with our history and the continued economic disparity it has a particular urgency in our country. <br></p><p>Where one can see relatively easily how one might go about such a task in the humanities, the call to decolonise science was largely met with derision. For the most part, science gently ignored the call for decolonisation until the #ScienceMustFall video went viral. Tempers flared and the debate quickly shifted to two intractable positions. On the one hand a call to equate indigenous knowledge systems with science and on the other a complete lack of recognition that science is embedded in and infused with Western individualism.</p><p>Our curiosity was to find a way to facilitate a conversation between these two positions. The major challenge was that the grounds on which the debate was considered valid was itself contested because of the difference in the way in which legitimate knowledge is built in science and in the humanities. <br></p><p>In science, method is independent of the person. Once a method has been described clearly, a second person performing the same experiment can be reasonably expected to obtain the same result. This reproducibility is the deep strength of science. In the social sciences, one learns an orientation to knowledge which is built on theory, but the manner in which one interprets data will be influenced by one's own history. Part of the beauty of the social sciences is making explicit the ways in which personal experience infuse and influence one's gaze. <br></p><p>So science prides itself on being objective and frequently dismisses the relatively 'soft' approach of the social sciences. Alas in so doing scientists fail to recognise an important distinction. Scientific knowledge is objective, but scientists are not. They are also profoundly influenced by their cultural heritage. <br></p><p>There is no escaping the fact that science as we know it today has deep roots in Western Europe and much of the development of science and technology coincided with the emergence of the colonial era. The technological advances made by those societies at that time allowed for the possibility of exploration. This was inextricably linked with the development of refined measuring instruments. For example, chemistry, as a science, only really emerged once we had sufficiently accurate balances. We cannot separate the development of scientific knowledge from that history. <br></p><p>In developing a decolonised scientific curriculum, we are not going to start again. We will still teach Newton's laws, and the structure of the atom and the theory of evolution. These ideas are far too powerful as explanatory tools to lay them to one side. But what we can do is begin to recognise the practice of science by scientists has been profoundly influenced by Western modernity. The obsession with the individual is highly problematic. Is there a way in which we can begin to recognise that all knowledge is built on the work of those who have gone before and contribute not only to those who follow but to our contemporaries? Can we build a valuation system of recognition of contribution that accounts for the deep web of relationships rather than trying to carve out the individual?<br></p><p>A decolonised scientific curriculum will also have implications for teaching and learning as well as how we perceive and interact with information.  When we use an example to aid the teaching of a concept we have to ask whether that example is actually experientially accessible to everyone in the class. In other words does the example lower the barrier to learning or create yet another obstacle? <br></p><p>In a diverse science class, it is unlikely that any one example will be accessible to all, so one of the strategies we use is to offer one example, and then ask the class to discuss other possible examples in small groups. These examples can then be discussed in the large class to show which examples work and which don't and why. This way there is less bias towards just one kind of life experience – that of the academic.  </p><p>In the end our challenge is to make more visible the working of culture in academic science. To aim to help academic scientists understand that although their science may be objective, rigorous and potentially groundbreaking, they may be unconsciously perpetuating a culture which is alienating to many students. Both of these things may be simultaneously true. To ameliorate this doesn't require substituting scientific content with commentary on society, but it does require taking students seriously when they either say they feel like they do not belong or they simply vote with their feet.  <br></p><p><strong>*Dr Margaret Blackie is a senior lecturer in the Department of Chemistry and Polymer Science and Dr Hanelie Adendorff a senior advisor at the Centre for Teaching and Learning at Stellenbosch University. This article is based on their chapter in </strong><strong><em>Building knowledge in Higher Education:</em></strong><strong><em> </em></strong><strong><em>Enhancing Teaching and Learning with Legitimation Code Theory</em></strong><strong> (2020).</strong></p><p><strong> </strong></p><p> </p><p><br></p>
Top awards for SU chemistshttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=7645Top awards for SU chemistsMedia & Communication, Faculty of Science<p>​Three chemists from Stellenbosch University have been recognised by the South African Chemical Institute (SACI) for their contribution to chemistry research, teaching and learning in South Africa.<br></p><p>Prof Selwyn Mapolie was selected as a SACI Fellow, the highest category of membership of the Institute, in recognition of his sustained contribution to the chemical community in South Africa. This honour is only bestowed on a select group of members that have demonstrated excellence and leadership in the areas of the profession, education and management of chemistry and volunteer service.<br></p><p>SACI also recognised Dr Margaret Blackie's outstanding contribution to chemical education over the past five years. She is the recipient of the Institute's Chemical Education Medal, while PhD-student Jean Lombard received the SACI Postgraduate award. </p><p>Prof Peter Mallon, head of the department, said the awards are well deserved national recognition for the researchers' contribution to research and education in chemistry in South Africa. Prof Mallon is also SACI president.<br></p><p>Prof Mapolie, who's research career spans over more than 30 years, says it is a great honour to be recognised by his peers, many of whom he has admired for the significant contributions they have made to advance the discipline. He also expressed his indebtedness to the many postgraduate students he has worked with during the years: “My postgraduate students have all contributed significantly to my achievements as a scientist," he said.</p><p>Dr Blackie says she appreciates the fact that SACI recognises contributions to education in chemistry and science: “It is a tremendous privilege to be the recipient of this award. And I am deeply grateful to my mentors and collaborators. I have learnt so much along the way from working with others."</p><p>Dr Blackie recently co-authored two chapters in a book <a href="/english/Lists/news/DispForm.aspx?ID=7543"><em>Building Knowledge in Higher Education</em></a>, covering topics such as the decolonisation of the science curriculum and the gap between first year students' theoretical understanding of key concepts in chemistry and their ability to transfer that knowledge into other domains, such as medicine and engineering.</p><p>PhD-student Jean Lombard says she is grateful but surprised to receive the award, especially as the last year of her PhD was incredibly challenging and a lot of hard work. This former Tygerberg High School learner has just handed in her doctoral thesis.</p><p>“I work in the field of solid-state supramolecular chemistry. For my research, I developed new techniques to make what we call 'multicomponent materials'. We are interested in making these materials because it is a simple way of improving the physical properties of an existing material. For instance, a pharmaceutical drug molecule may not be useful because of poor solubility. With my techniques, it could be made more soluble by turning it into a multicomponent material. My focus was specifically looking at techniques which use less or no harmful solvents."</p><p>She says she is fascinated by the behaviour of molecules: “I get the feeling that there is much more going on below the surface. I am excited by every new discovery being made. It is amazing to witness the seemingly impossible for yourself!"</p><p>Jean's doctoral thesis was supervised by dr Tanya le Roex and Prof Delia Haynes.<br></p><p><em>On the photo above, from left to right, PhD student Jean Lombaard, Dr Mags Blackie and Prof Selwyn Mapolie.</em><br></p>
British Ecological Society award for SA climate change researcherhttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=7641British Ecological Society award for SA climate change researcherWiida Fourie-Basson<p>​The British Ecological Society's <a href="https://www.britishecologicalsociety.org/membership-community/honours-awards-and-prizes/">Marsh award for climate change research</a> has been awarded to Professor Wendy Foden, a world-leading researcher in climate change vulnerability assessments of threatened species.</p><p>According to a media release issued by the British Ecological Society (BES), Prof Foden is recognised for the global reach of her work with the International Union for the Conservation of Nature (IUCN) and the Red List of Threatened Species, as well as for her interest in translating science for practical conservation use, and in fostering conservation leadership. The award, provided by the Marsh Christian Trust and administered by the British Ecological Society, will be handed over in 2021.</p><p>Prof Foden is currently based at South African National Parks' Cape Research Centre, where she leads a team carrying out applied research in and around the region's national parks. She is also associated with the Universities of Stellenbosch and Cape Town as associate professor, and has chaired the Climate Change Specialist Group of the International Union for the Conservation of Nature's (IUCN) Species Survival Commission since 2014.</p><p>Prof Foden says a non-linear career path, which has left her with one foot in research and the other in applied conservation, has enabled her to spot gaps and opportunities for trans-disciplinary collaboration: “Most of my research has been highly collaborative, so the award recognises the work of a community of very dedicated researchers. I'm simply fortunate to be in a position to gather key people together to create really useful products while we have a good laugh. I'm glad that such 'soft skills' are increasingly recognised in science."</p><p>From 2007 to 2013,  she led IUCN's development of a method for assessing species' vulnerability to climate change, drawing on a wide range of experts' field knowledge and research findings to produce an assessment that could be used alongside the IUCN Red List of Threatened Species: “We applied the method to the world's birds, amphibians, corals and the study became the first to tackle entire species groups across the world. The approach has been widely adopted and is now used by researchers and conservationists around the world," she explains.</p><p>From 2014 to 2016 she continued this work to establish global best-practice guidelines for assessing species' vulnerability to climate change, again bringing together a diverse group of researchers and practitioners from around the globe: “Since our field is new it meant arduously wading through a great many dark and tangled uncertainties. Ultimately we managed to draw together practical guidance for conservation practitioners and we're currently working with IUCN to include these as part of IUCN Red List training."  </p><p>“The guidelines also highlight a number of important research needs and gaps. I think that the messiest and most uncertain areas of science are the most exciting and provide the greatest opportunity to do meaningful and innovative work. I may have a lot more grey hair and stronger reading glasses than when I began this work, but I've never been bored and it's very satisfying to see it being used," she adds.</p><p>For this work, she recently received the IUCN's George Rabb award for her “innovative, dynamic and thoughtful leadership of SSC's work on climate change". </p><p>Professor Jane Memmott, President of the British Ecological Society, said every year the prizes recognise and celebrate the exceptional contributions of individuals to advancing ecology and communicating its importance for society: “I am delighted to offer my congratulations to the winners of this year's BES awards for their exceptional contributions to ecology."</p><p> Prof Foden said she was surprised by the award, but extremely proud to represent Africa's woman scientists: “I hope that the award inspires other women scientists, particularly from developing countries, to step up to conservation and climate change challenges," she concludes. </p><p><strong>More about the British Ecological Society</strong> <br> Founded in 1913, the British Ecological Society (BES) is the oldest ecological society in the world. The BES promotes the study of ecology through its six academic journals, conferences, grants, education initiatives and policy work. The society has 6,000 members from more than 120 different countries. <a href="http://www.britishecologicalsociety.org/">www.britishecologicalsociety.org</a>  <br></p><p><br></p>
EM contributes to local production of PPEhttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=7637EM contributes to local production of PPEJurgen Kriel<div style="text-align:justify;"> ​​One of the main reasons for the strict lockdown regulations in South Africa during COVID-19, was to prevent overcrowding of hospitals and provide them with precious time to prepare for the expected influx of patients as transmissions peaked. Over time, it became apparent that this preparation mainly centred around one critical element – the procurement of personal protective equipment (PPE). In light of these events, the Electron Microscopy (EM) Unit is currently providing critical EM analytical support to the Stellenbosch Nanofiber Company (SNC), which is in the process of manufacturing reusable filters for face masks.  <br></div><div> <br> </div><div><table class="ms-rteTable-default" width="100%" cellspacing="0" style="height:137px;"><tbody><tr class="ms-rteTableEvenRow-default"><td class="ms-rteTableEvenCol-default" style="width:50%;"> <img src="/english/faculty/science/CAF/Documents/20200630_170213-em1.jpg" alt="" style="margin:5px;width:413px;height:240px;" />​​​​<br></td><td class="ms-rteTableOddCol-default" style="width:50%;"> <img src="/english/faculty/science/CAF/Documents/20200525_NEV01_box8_14_9000x_02_ap_em2.jpg" alt="" style="margin:5px;width:312px;height:240px;" /> <br> </td></tr><tr class="ms-rteTableFooterRow-default"><td class="ms-rteTableFooterEvenCol-default" rowspan="1" style="width:50%;">​<em>One of the filter layers (which is part of medical-grade face masks) before the SEM analysis.​​</em><br></td><td class="ms-rteTableFooterOddCol-default" rowspan="1" style="width:50%;">​<em>An image of a SEM analysis of the filter.</em>​<br></td></tr></tbody></table> <br></div><div style="text-align:justify;">Continuous provision of PPE to health care workers (HCWs) is of paramount importance in the fight against the COVID-19 pandemic. PPE constitutes a range of products including gloves, face shields, surgical gowns and face masks. HCWs come into contact with multiple patients per day and therefore require certified equipment to serve as an effective barrier between them and their patients. Therefore, PPE can be regarded as the barrier that not only prevents HCWs from becoming carriers of the novel coronavirus but also prevents hospitals themselves from becoming transmission ‘hotspots’, which can result in the closing of hospitals. Sadly, as a result of increased global demand, many countries are struggling to provide frontline HCWs with adequate PPE and South Africa is no exception. <br></div><div style="text-align:justify;"> <br> </div><div style="text-align:justify;">In response to these shortages, many local manufacturers have repurposed their production lines to manufacture various forms of PPE for general public use. The difficulty with mass producing medical-grade PPE is that manufacturers must adhere to the strict International Organization for Standardization guidelines as well as be certified by government to produce medical equipment. <br></div><div style="text-align:justify;"> <br> </div><div style="text-align:justify;">SNC is a prime example of a company specialising in the commercial-scale manufacturing of advanced biomedical nanofiber materials. Nanofiber materials have extremely versatile biomedical applications, encompassing wound dressing, drug release materials and cell culture scaffolds. In response to the growing demand for PPE, SNC is currently working on the production of the most important part of medical-grade face masks, namely the filter layer.  What is unique about SNC’s filter layers is that they physically entrap and immobilise viral particles as opposed to conventional melt-blown polypropylene layers that electrostatically trap particles. This might seem like a small difference, but it allows for the nanofiber-based filters to be washed and reused, whereas the electrostatic properties of the polypropylene-based filters diminish with each wash. </div><div style="text-align:justify;"> <br> </div><div style="text-align:justify;">In order to confirm whether these filter layers are capable of entrapping nanoscale particulates and to assess how robust these nanofibers are, scanning electron microscopy (SEM) analysis is required to measure the distance between fibres as well as the fibre size. This makes SEM analysis integral to the production of nanofiber-based filter layers. </div><div style="text-align:justify;"> <br> </div><div style="text-align:justify;">The ThermoFischer Apreo VolumeScope scanning electron microscope is the newest addition to the CAF Electron Microscopy Unit and has been instrumental in assisting SNC to perform this much-required analysis. Although the main purpose of the Apreo is to function as a serial block-face microscope, capable of acquiring 3D volumetric EM datasets, it is also a very capable scanning electron microscope for general image acquisition, which makes it an extremely versatile tool. </div><div style="text-align:justify;"> <br> </div><div style="text-align:justify;">The procurement of the Apreo was accompanied by the appointment of a new CAF staff member, Mr Jurgen Kriel. Currently finishing his PhD in Physiological Sciences at Stellenbosch University, Kriel was appointed in March 2020 to provide SEM analytical services to medical researchers on Tygerberg Campus. Although the national lockdown has put a hold on many research projects, the Apreo continued running to provide industry clients such as SNC with essential analytical services. However, these services are not provided without risk. Being near Tygerberg Hospital has its inherent dangers in a time when Tygerberg has the highest number of confirmed COVID-19 cases in the Western Cape (at the time of writing this article). </div><div style="text-align:justify;"> <br> </div><div style="text-align:justify;">Safety guidelines are of paramount importance, not only for the safety of employees but also for that of their families. “It was quite a difficult decision to go back to work. Right before the Level 5 lockdown was imposed, my mother started with chemotherapy. As much as I wanted to help SNC, I also did not want to place my family in harm’s way. My manager, Ms Madelaine Frazenburg, was very understanding and left the decision up to me. Having a vulnerable family member really puts the importance of adhering to the safety guidelines into perspective. After I decided to help SNC, I was very relieved to see how well everyone on Tygerberg Campus adhered to these guidelines” Kriel said.</div><div style="text-align:justify;"> <br> </div><div style="text-align:justify;">Until a vaccine is developed, the demand for appropriate PPE will remain high. Being able to reuse medical-grade face masks will alleviate the financial burden on hospitals significantly. “Various tests are ongoing to demonstrate the robustness of the filters, but initial tests have already shown that we maintain filtration efficiency even after 10 cycles of submersion in boiling water for 10 minutes and air drying”  Dr Megan Coates, Research and Development Manager at SNC said.  SNC is currently in the process of building partnerships for further production of face masks once testing on the filters has been completed. </div><div> <br> </div><div> <br>(As published in the <a href="/english/faculty/science/CAF/Documents/CAF%202020%20Annual%20Report_FINAL_29%20July%202020.pdf">CAF Annual Report</a>)<br></div><p>​<br></p>
Individual dolphin calls used to estimate population size and movement in the wildhttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=7633Individual dolphin calls used to estimate population size and movement in the wildMedia & Communication, Faculty of Science<p>An international team of scientists has succeeded in using the signature whistles of individual bottlenose dolphins off the coast of Namibia to estimate the size of the population and track their movement.<br></p><p>The research, led by Stellenbosch University and the University of Plymouth, marks the first time that acoustic monitoring has been used in place of photographs to generate abundance estimates of dolphin populations. </p><p>Writing in the <a href="https://academic.oup.com/jmammal/advance-article/doi/10.1093/jmammal/gyaa081/5893454?guestAccessKey=af719cb6-c7ca-4463-9e1f-453768da4f6a"><em>Journal of Mammalogy</em></a>, researchers say they are excited by the positive results yielded by the method, as the number of dolphins estimated was almost exactly the same as estimated through the more traditional photographic mark-recapture method.</p><p>They are now working to refine the technique, in the hope it can be used to track other species – with a current focus on endangered species such as humpback dolphins.</p><p>Quicker information processing and advances in statistical analysis mean in the future that automated detection of individually distinctive calls could be possible. This can generate important information on individual animals and would be particularly useful for small, threatened populations where every individual counts.</p><p><em>“The capture-recapture of individually distinctive signature whistles has not been attempted before,"</em> says the paper's senior author Dr Tess Gridley, Co-Director of <a href="http://seasearch.co.za/about/">Sea Search</a> and the <a href="http://www.namibiandolphinproject.org/">Namibian Dolphin Project</a> and a postdoctoral fellow in the <a href="/english/faculty/science/botany-zoology/Pages/default.aspx">Department of Botany and Zoology at SU</a>. <em>“The dolphins use these sounds throughout life and each has its own unique whistle. Therefore, by recording signature whistles over time and in different places we can calculate where animals are moving to and how many animals there are in a population."</em></p><div class="ms-rtestate-read ms-rte-embedcode ms-rte-embedil ms-rtestate-notify"><iframe width="540" height="303" src="/english/faculty/science/_layouts/15/videoembedplayer.aspx?site=fd815503b3e242dba5d4c9d4c07b52b0&web=d93d49112e8c49ef86c9bfe52409f593&list=d248721804dd440b8d88638cc1fd8f1e&item=166&" data-duration="0"></iframe> </div><p><em>Supplied by the Namibian Dolphin Project</em><br></p><p>Working with Dr Simon Elwen of Stellenbosch University, the Namibian Dolphin Project has been researching Namibia's resident bottlenose dolphins for the past 12 years, and built up a catalogue of more than 55 signature whistles dating back to 2009.<br></p><p>This particular study was led by Emma Longden, who began the project during her BSc (Hons) Marine Biology degree at the <a href="http://www.plymouth.ac.uk/">University of Plymouth</a>. As an undergraduate, Emma completed an internship with the Namibia Dolphin Project for a month in 2016, and returned again in 2018 to complete work on the mark-recapture project.</p><p>She analysed more than 4000 hours of acoustic data from four hydrophones positioned along the coast south and north of Walvis Bay, Namibia, during the first six months of 2016.</p><p>All in all, they identified 204 acoustic encounters, 50 of which contained signature whistle types. From these encounters, 53 signature whistle types were identified; 40 were in an existing catalogue developed in 2014 for the Walvis Bay bottlenose dolphin population, and 13 were newly identified. </p><p>Of the 53 signature whistle types identified, 43% were captured only once, whereas the majority (57%) were recaptured twice or more.</p><p><em>“One of the great things about bioacoustics is that you can leave a hydrophone in the water for weeks at a time and collect so much data without interfering with the lives of the animals you are studying,"</em> says Emma, whose work on the project was also supervised by Dr Clare Embling, Associate Professor of Marine Ecology at the University of Plymouth.</p><p>Future research includes the work undertaken by PhD student Sasha Dines from Stellenbosch University to further refine the technique to better understand the population of endangered humpback dolphins in South Africa. Another PhD student, Jack Fearey from the University of Cape Town, is continuing to conduct research along the Namibian Coast.<br></p><ul><li>The research article was authored by Emma G. Longden, Simon H. Elwen, Barry McGovern, Bridget S. James, Clare B Embling and Tess Gridley and is available online at <a href="https://academic.oup.com/jmammal/advance-article/doi/10.1093/jmammal/gyaa081/5893454?guestAccessKey=af719cb6-c7ca-4463-9e1f-453768da4f6a">https://academic.oup.com/jmammal/advance-article/doi/10.1093/jmammal/gyaa081/5893454?guestAccessKey=af719cb6-c7ca-4463-9e1f-453768da4f6a</a></li></ul><p><strong>More about bottlenose dolphins' use of sound</strong></p><p>From the day they are born, bottlenose dolphins produce high frequency whistles. During learning and practice in the first year of life, these whistles develop into individually distinct signature whistles and each animal has its own unique call throughout life. Once learned, signature whistles act like a name and are used to help animals stay in contact and to address each other when communicating under the water.</p><p>These signature whistles help animals keep in contact if they become separated, they are exchanged before groups meet (as a kind of greeting) and they can copy each other's whistles to address each other (in the same way humans use names). They are therefore friendly sounds and used between animals that are well acquainted – such as group members and mothers to their calves.</p><p><strong>More about the Namibia Dolphin Project</strong></p><p>The <a href="http://www.namibiandolphinproject.org/">Namibia Dolphin Project</a> is a research and conservation project operating in Walvis Bay and Luderitz in Namibia. It is managed as part of the Sea Search Research and Conservation non-profit group and involves scientists and specialists from various South African and international universities and institutes. Interested students can intern with the Namibian Dolphin Project and Sea Search to gain important fieldwork skills. <br></p><p><strong>Media interviews</strong></p><p>Dr Tess Gridley</p><p>Co-Director of the Namibia Dolphin Project/Sea Search and postdoctoral fellow, Department of Botany and Zoology, Stellenbosch University. Founder : African Bioacoustics Community. </p><p>E-mail: nam.dolphin.project@gmail.com</p><p>Mobile: +27(0)794292702</p><p>Land Line : +27 (0) 21 788 1206</p><p> </p><p>Dr Simon Elwen</p><p>Co-Director of the Namibia Dolphin Project/Sea Search and research associate, Department of Botany and Zoology, Stellenbosch University</p><p>E-mail: nam.dolphin.project@gmail.com</p><p>Mobile: +27(0)711395951<br></p><p>Land Line : +27 (0) 21 788 1206<br></p><p><br></p><p>Ms Emma Longden</p><p>BSc-graduate and main author, University of Plymouth</p><p>E-mail: <a href="mailto:emmaglongden@gmail.com">emmaglongden@gmail.com</a></p><p>Mobile: +44 7931 448886<br></p><p><em>​On the photo above, a common bottlenose dolphin off the coast of Namibia. Image: Tess Gridley</em></p><p style="text-align:center;"><em>Media release issued by the Faculty of Science, S​tellenbosch University, science@sun.ac.za</em></p>
Building long-term immunity against COVID-19https://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=7622Building long-term immunity against COVID-19Prof Dirk Bellstedt<p>​<span style="text-align:center;">We simply know too little about how the immune system counterattacks COVID-19 infections. Upon careful interpretation of the picture that is emerging, emeritus professor Dirk Bellstedt believes there are reasons for optimism for bringing the disease under control. During a recent online Science Café Stellenbosch talk, he explained how complex our immune system is, and that antibodies are only the first line of defence. In the article below he gives an overview of the functioning of the immune system and how it will builld long-term immunity against the SARS-CoV-2 virus.</span></p><p><em>Prof Dirk U. Bellstedt is emeritus professor of biochemistry at Stellenbosch University. </em></p><p><em></em></p><div class="ms-rtestate-read ms-rte-embedcode ms-rte-embedil ms-rtestate-notify"><iframe src="https://www.facebook.com/plugins/video.php?href=https://www.facebook.com/ScienceCafeStellenbosch/videos/316253976246198/&show_text=false&width=734&height=411&appId" width="734" height="411" frameborder="0" style="border:none;overflow:hidden;"></iframe> </div><p><em><br></em></p><h3>What do we know about the human immu​​ne system?<br></h3><p>Our immune system is incredibly complex. In the fight against the SARS-CoV-2 virus, all aspects of immunity need to be taken into account, not just the antibody response. </p><p>Many sub-systems of immunity work together to give total immunity. If plan A does not work, then it's plan B and if that does not work, plan C and so on. Different parts of the immune system work together to eliminate diseases. There is cross talk between these mechanisms, making it even more complex. Different types of disease-forming organisms activate different parts of the immune system, and general comparisons from one type to another cannot be made.</p><p>The body can recognize about 10 million different shapes and, depending on certain conditions, will make antibodies that recognize the shape of a corona virus or influenza virus or specific bacteria. In immunology all disease-forming organisms are collectively called an antigen. </p><p>​We now know that the immune system has two basic branches, namely innate immunity and adaptive immunity. Our innate immunity consists of a set of systems which will fight any foreign organism when it enters the body for the first time. Pathogenic organisms want to use the resources of the body, in other words the building blocks and the energy reserves of the body, to multiply themselves. But in the process they damage the body's tissues. Obviously the body does not want to allow this to continue and fights back. It does so by different mechanisms which are collectively called <strong>innate immunity</strong>. This includes the mechanism of phagocytosis: when big cells gobble up bacteria to kill them inside the white blood cells (phagocytic macrophages and polymorphonuclear cells are white blood cells); another mechanism consists of a system of proteins which drill holes into organisms thereby causing them to burst (the complement system); then there are also natural killer cells that kill virus-infected cells; and lastly there are mechanisms whereby infected cells give signals to cells next to them to warn them of the threat that they may be infected soon (signalling molecules which are proteins called cytokines). </p><p>The <strong>second</strong> branch of the immune system, called <strong>adaptive immunity,</strong> leads to a specific acquired immune response and can be sub-divided into so-called <strong>cell-mediated immunity</strong> and <strong>humoral immunity</strong>. Let's first look at the innate immune response. </p><h3>The innate immune resp​​onse</h3><p>In the case of a first-time infection with COVID-19, the body tries to use innate immunity to stop it. This innate immunity is what could be referred to as an “emergency response" as it takes place without any previous contact with the disease. Because it is easier to measure dissolved substances such as cytokines and antibodies, most published research thus far has focused on this first response mechanism of the immune system. Research on the immune system's response on a cellular level is much more complex and requires specialised equipment and technical expertise. For this reason, the first results have been published on dissolved substances such as cytokines and antibodies and not on cells such as natural killer cells, B cells and T cells.</p><p>From other respiratory virus infections such as influenza, we would expect that cytokines and natural killer cells would be the counterattack by innate immunity against an initial COVID-19 infection. Cytokines, which are dissolved proteins, are produced by cells infected with COVID-19. There are many types of cytokines that can be released by infected cells, but in viral infections, the most important are the interferons. The name interferon derives from “interfering with viral replication". Interferons are released by an infected cell and serve as a warning signal to healthy cells to prepare themselves against viral infection. This allows healthy cells to stop getting infected, which is very important in controlling a viral infection. </p><p>Simultaneously other cytokines are released which cause inflammation, resulting in swelling to enable dissolved substances and cells to get to the site of infection, in the case of a COVID-19 sufferer, to the lungs and likely to other organs as well. This inflammatory response, the so-called “cytokine storm", is a double-edged sword: if the inflammation is too severe, it blocks the functions of the lung cells in COVID-19 infections, which means that oxygen can no longer be absorbed into the blood, which can be fatal. It is this almost overreaction of the immune system that many COVID-19 infected patients have died from.</p><p>Researchers have thus far established that some patients who had severe disease symptoms produced less interferon in comparison to inflammatory cytokines (Hadjadj et al., 2020, Terrier Nature, <a href="https://www.nature.com/articles/d41586-020-00502-w">https://www.nature.com/articles/d41586-020-00502-w</a>). This finding has had important implications: COVID-19 patients showing severe symptoms of respiratory distress are now treated with drugs such as dexamethasone that reduce inflammation, and others that increase interferon production, which significantly improves treatment.</p><h3>Adaptive im​​munity</h3><p>The <strong>second</strong> branch of the immune system, called <strong>adaptive immunity,</strong> leads to a specific acquired immune response and can be sub-divided into so-called <strong>cell mediated immunity</strong> and <strong>humoral immunity</strong>. Humoral immunity involves the production of antibodies which are proteins, by so-called B-cells that are found in the red-bone marrow at the tips of the sponge-looking long bones, the breast-bone and other areas. These antibodies are then moved throughout the body by the blood stream, also to between the cells into the tissues, but not into cells. </p><p>Antibody-based immunity is called humoral immunity, because “humoral" refers to the blood where they are found. B-cells are like factories making antibodies: some factories produce antibodies against a strain of influenza virus that you got last winter; others make antibodies against a tummy bug that you had two months ago; and if you got COVID-19 and recovered from it, you would have factories making antibodies against COVID-19! </p><p>These antibodies move through the body by means of the blood circulation in veins and arteries. If we view the cells of the body as houses, and the blood circulation as a set of roads, this would be a good comparison. The antibodies move out of the arteries and veins to move between the cells of the body, in other words they get off the roads and move between the houses. If a virus enters the body, whether in the blood circulation or between the cells, antibodies will bind to the virus particles, tagging them for destruction. Antibodies therefore play a very important role in pointing out the virus and marking it for destruction.</p><p>Cell-mediated immunity is mediated by cells that attack the disease-forming organism. These cells also come from the bone marrow, but are transported to the thymus where they mature to become T cells (T for the thymus gland next to your thyroid gland just under your oesophagus). There are two types of T cells: T-cytotoxic cells and T-helper cells. They are abbreviated as T<sub>c</sub> and T<sub>h</sub>. Corona viruses attack the lung cells, penetrates them and hijack the cells from the inside. Instead of the cell performing its normal functions, it changes into a virus-producing factory, thereby exhausting the cell completely. When all the virus particles are assembled inside the cell, it kills the cell, breaks its cell membrane and the virus particles are released allowing them to spread throughout the body to infect new cells. </p><p>While the virus is outside of the cells, antibodies can bind to the virus tagging it for destruction, but once inside the cells the virus can escape the antibodies. The T<sub>c</sub> cells of cellular immunity can then recognise virus-infected cells and kill them. The body has a reserve of T<sub>c</sub> cells that can recognize about ten million different viruses or intracellular organisms, such as many other viruses and tuberculosis bacteria. </p><p>When a lung cell becomes infected with the corona virus, T<sub>c</sub> immunity against the virus will be induced. Just as each person's immune system has developed B cells to recognize a vast array of different disease-forming organisms, so also has a vast array of T<sub>c</sub> cells been developed, which literally sit and wait for an infection to appear to which they can react. Upon infection with SARS-CoV-2, specific T<sub>c</sub> cells are activated and multiplied. These T<sub>c</sub> cells will destroy the SARS-CoV-2 infected cells before the virus can start to replicate and infect even more cells. T<sub>c</sub> cells are like a “bomb squad" that go in and blow up the cells that have been hijacked to become virus-producing factories. Any virus particles that are still outside the cells will be targeted by the antibodies and destroyed. These two branches of the immune system work together to eliminate the virus. However, this results in severe damage to the infected lungs – the tissue then needs to recover and new cells have to be produced in order for the lungs to be able to absorb sufficient oxygen again.</p><p>In all infections T<sub>h</sub> cells assist the T<sub>c</sub> cells and the B-cells that make antibodies to perform their functions better: they are the support team for the immune system's special forces and bomb squad. The T<sub>h</sub> cells also produce cytokines, such as interferon, which assists with the recovery of virus-infected cells. When infected by a virus such as SARS CoV-2, T<sub>h</sub> and T<sub>c</sub> cells could be expected to play a very important role in combatting infections.</p><p>However, when these systems have been successfully employed in combating the virus (or any other infective organism for that matter), the body stops producing antibodies, and by implication also the T<sub>h</sub> and T<sub>c</sub> cells, as it would cost the body far too much energy and foodstuff to continue producing them. However, the factories and the bomb squads are not destroyed - those remain as memory B-cells,T<sub>h</sub> and T<sub>c</sub> cells . When a SARS-CoV-2 re-infection occurs, the large numbers of memory B cells,T<sub>h</sub> and T<sub>c</sub> cells can be reactivated, rapidly producing massive amounts of antibodies and more T<sub>h</sub> and T<sub>c</sub> cells. The re-infection can then be overcome far more quickly and efficiently than after the first infection. This is why vaccinations are given to people. A primary immune response follows after vaccination so that a large reserve of memory B cells and T<sub>h</sub> and T<sub>c</sub> cells is built up, and upon infection by the real disease-forming organism, the secondary immune response can kick in much faster and more efficiently overcome the disease.</p><p>Recent reports have suggested that immunity does not last against COVID-19. The drop in antibody levels following COVID-19 infection is being interpreted to mean that immunity against COVID-19 is not long lasting (<a href="https://theconversation.com/immunity-to-covid-19-may-not-last-this-threatens-a-vaccine-and-herd-immunity-142556">https://theconversation.com/immunity-to-covid-19-may-not-last-this-threatens-a-vaccine-and-herd-immunity-142556</a>). In a recent article, the incidence of anti-COVID-19 antibodies in Spain was determined to be around 5% of the population (<a href="https://www.sciencedirect.com/science/article/pii/S0140673620314835#%21">Pollán</a> et al., 2020). This was interpreted to mean that immunity to COVID-19 was low and makes only brief mention that cellular immunity may give protection against COVID-19 infection. This may be because the study was specifically aimed at the determination of antibody levels only, but in an overview by Africa's Medical Digest, Medical Brief (<a href="https://www.medicalbrief.co.za/archives/covid-19-herd-immunity-may-be-unachievable-spanish-study-of-61000-people/">https://www.medicalbrief.co.za/archives/covid-19-herd-immunity-may-be-unachievable-spanish-study-of-61000-people/</a>), this was interpreted as “strengthening evidence that a so-called herd immunity to COVID-19 is “unachievable"". Although it is not written as such, by stating that the immunity against COVID-19 is not long lasting it implies that cell mediated immunity by T<sub>h</sub> and T<sub>c</sub> cells also does not last for long. In the Medical Brief article, the cautionary statement made by Pollan et al. (2020) and I quote “However, cellular immunity, which was not evaluated here, might also play a role in protecting against SARS-CoV-2 reinfection." was not considered and shows how quickly misinterpretations can be made. If cell mediated immunity mediated by T<sub>h</sub> and T<sub>c</sub> cells would not last for long, then you could theoretically get a new infection, just as bad as the first, a short while after the first. </p><p>In my opinion, when getting re-infected with SARS-CoV-2 or any other disease forming organism for that matter, the memory B-cells and the memory T<sub>h</sub> and T<sub>c</sub> cells should then be re-activated and the levels of antibodies and T<sub>h</sub> and T<sub>c</sub> cells should go up rapidly again. Due to the fact that there are the B cell antibody factories and reserve T<sub>h</sub> and T<sub>c</sub> cells that are ready and waiting, they kick in very quickly, and the fight back against the SARS-CoV-2 or any other disease forming organisms, is very, very rapid and is stronger than the response after the first infection. </p><p>In my opinion, the interpretation that the drop in antibody levels following COVID-19 infections means that the total immunity against COVID-19 is not long lasting, is therefore not justified. Such statements are misleading both for doctors and for the general public. Antibody levels drop after any infection once the disease-forming organism has been combatted and killed successfully, in some infections more rapidly than in others, but the memory B-cells and the memory T<sub>h</sub> and T<sub>c</sub> cells are present as in an infection with any other disease-forming organism, and can be activated rapidly again. </p><h3>Recent research findi​​ngs on cellular immunity</h3><p>In recent weeks, results about cellular immunity have finally appeared in the scientific press. Grifoni et al. (2020) compared the cellular immunity against SARS-CoV-2 of 20 recovered patients that had been infected 20 to 35 days before in comparison to 20 uninfected individuals (samples collected between 2015 and 2018). Most of the recovered patients possessed antibodies against parts of the SARS CoV-2 virus in comparison to negative controls. Cellular immunity assessments of the recovered patients showed a high level of responses of T<sub>h</sub> and T<sub>c</sub> cells against SARS-CoV-2. What was interesting was that a certain percentage of the uninfected individuals also showed cellular immunity against SARS-CoV-2. This was interpreted to mean that they possessed immunity possibly as a result of previous infections by mild strains of corona viruses.</p><p>In a study by Le Bert et al. (2020) both T<sub>h</sub> and T<sub>c</sub> cellular immunity was assessed. In 36 people that had recently recovered from COVID-19 they could show that T<sub>h</sub> and T<sub>c</sub> cellular immunity, that recognized the virus, was significantly raised. This would limit spread and multiplication of the virus after infection. They then analysed patients that had survived the first SARS CoV-1 outbreak in 2003 and determined that even 17 years later they still possessed T<sub>h</sub> and T<sub>c</sub> cells that recognized SARS CoV-2. The researchers interpreted this to mean that long lasting immunity against corona viruses therefore certainly can be achieved. </p><p>Finally, the researchers assessed the cellular immunity of individuals that were not infected with SARS CoV-1 or SARS CoV-2 and found that over 50% possessed cellular immunity against both of these variants of corona virus as well as corona virus types that produce common cold symptoms. Both studies show firstly that cellular immunity is definitely induced by infection, the second study showed that the cellular immunity is long lasting and both studies showed that a percentage of the population (in Singapore in this instance) possesses immunity to SARS CoV-2. This would explain why some individuals only get very mild infections without symptoms. These individuals already have memory cells that will overcome infections very rapidly. These studies present conclusive evidence that SARS CoV-2 induces cellular immunity in infected patients.</p><p>It therefore appears that the majority of individuals will be perfectly capable of giving a good adaptive immune response in the form of antibodies and T<sub>h </sub>and T<sub>c</sub> cells after a SARS-CoV-2infection including a secondary immune response following a re-infection. If the immune system was not able to build up adaptive immunity with memory, there would be no recoveries from the disease. However, we see that there are many recoveries now, so the bulk of the human population must be capable of developing adaptive immunity against SARS-CoV-2. </p><p>This is how the immune system has protected all vertebrates over millions of years, from fishes to mammals, and being infected with this virus is just another disease-forming organism once again. However, this does not mean COVID-19 is not a severe disease. COVID-19 has a distinctly higher mortality rate than flu, and the damage caused by a COVID-19 infection appears to be severe. Only time will tell whether individuals that have been infected will suffer from long-term effects. Why there is perhaps not fast and full recovery and fatigue after infection is because of the damage the virus infection has caused, not because of a lack of adaptive immunity. Many of the body's own cells would have been killed in the lungs and other tissues and they have to regenerate and this costs the body a lot of energy and foodstuffs, including proteins and vitamins. It appears that the damage caused by a COVID-19 infection is far greater than say that caused by a normal flu infection. Not only are lung cells injured and killed but also cells of the nervous system and other organs are, so recovery from a COVID-19 infection may take much longer.  </p><h3>Finding a v​​accine</h3><p>A vaccine will contain "parts" of the virus and not the whole virus because if it was introduced as a vaccine it would cause infection and disease. The disease-forming ability of the virus needs to be removed, but a vaccine must still induce adaptive immunity that specifically identifies COVID-19 and induce the formation of antibodies and activate T<sub>h</sub> and T<sub>c</sub> cells. This is not so easy to achieve.</p><p>Often a vaccine therefore consists of non-infective “parts" of the virus. The "parts" of the virus can be its proteins, but if those were injected, only antibodies would be made against them, because the immune system does not recognize those free proteins as occurring inside cells and the T<sub>c</sub> cells are not activated to multiply. Such a vaccine would also be ineffective because this would not stop the virus from getting into the cells and using the cells as virus-producing factories. This is where DNA vaccines, about which a lot is currently written in the press, can be valuable. After being injected with a DNA vaccine, the vaccine DNA penetrates the cells and temporarily causes those cells to produce virus proteins. The T<sub>h</sub> and T<sub>c</sub> cells then recognize these cells as though they were virally infected cells and the body starts multiplying the T<sub>h</sub> and T<sub>c</sub> cells that can recognize virally infected cells. If a SARS-CoV-2infection would occur after this, they would immediately kill the first SARS-CoV-2 infected cell and stop the viral multiplication. </p><p>A vaccine that results in antibody production by B cells and activation of T<sub>h</sub> and T<sub>c</sub> cells would therefore be an effective vaccine. The vaccines that are currently being developed are aimed at inducing both. Thus, the vaccine would mimic a natural infection, and induce antibody production and production of T<sub>h</sub> and T<sub>c</sub> cells, but not cause disease. This is precisely the objective of any vaccine, to give long-lasting protection, but does not induce disease.</p><p>Adaptive immunity against a vaccine could be very effective and long lasting. It is not the SARS-CoV-2 virus which decides whether a vaccine would work well, it is the actual design of the vaccine, and whether it activates both B cells and T<sub>c</sub> cells, which will determine how effective it will be. It is refreshing to see that journalists are now gaining insights into the complexities of the immune system (<a href="https://elemental.medium.com/what-to-make-of-research-suggesting-immunity-to-covid-19-is-short-lived-8f0a92ecce51">https://elemental.medium.com/what-to-make-of-research-suggesting-immunity-to-covid-19-is-short-lived-8f0a92ecce51</a>) and are now writing, and I quote: “Over the course of the pandemic, many science experts and communicators (myself included) have written about immunity solely as it relates to antibodies, but the reality is actually much more complex than that". In the title of that article the author warns “Be careful not to jump to conclusions" and it is precisely that which is needed at the moment, not articles that induce fear and anxiety in readers who are already stressed by the pandemic and lockdowns.</p><h3>In conclus​ion</h3><p>This is very complex because of the complexity of the immune system, but it is this complexity that has saved all vertebrates over millions of years. The induction of adaptive immunity either follows a natural infection of SARS-CoV-2 or can be induced by a vaccine. It is the adaptive immune response that gives long-lasting immunity, and if we refer to this in the context of the human population, it gives herd immunity. The term "herd immunity" is used to describe which percentage of the population possesses immunity, in other words has shown this secondary adaptive immune response, and typically, the disease will not spread once levels of 80% herd immunity have been reached. The chain of infection is broken when there are literally too many people that have adaptive immunity, and therefore can no longer be infected, for the disease to be able to jump from one person to the next. At present, limiting the spread is only a temporary measure, it is this control through vaccination which will result in herd immunity that is required to finally bring the disease under control. </p><p>The recently acquired knowledge that both arms of the adaptive immune response, antibody formation and cellular immunity in the form of T<sub>h</sub> and T<sub>c</sub> cells, can be induced by natural infection and by vaccination, gives us hope that this is achievable.</p><p><strong>References</strong></p><p>Andersen, G. A., A. Rambaut, W.A. Lipkin, E.C. Holmes & R.F. Garry (2020) The proximal origin of SARS CoV-2. Nature Medicine 26, 450–452.</p><p><a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Grifoni</a>, A., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Weiskopf</a>, D., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Ramirez</a>, S.I., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Mateus</a>, J., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Dan</a>, J.M., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Rydyznski Moderbacher</a>, C., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Rawlings</a>, S.A., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Sutherland</a>, A., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Premkumar</a>, L., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Jadi</a>, R.S., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Marrama</a>, D., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">de Silva</a>, A.M., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Frazier</a>, A., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Carlin</a>, A.F., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Greenbaum</a>, J.A., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Peters</a>, B., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Krammer</a>, F., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Smith</a>, D.M., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Crotty</a>, S., <a href="https://www.cell.com/cell/fulltext/S0092-8674%2820%2930610-3?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S0092867420306103?showall%3Dtrue">Sette</a>, A. (2020) Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell 181, 1489–1501. DOI:<a href="https://doi.org/10.1016/j.cell.2020.05.015">https://doi.org/10.1016/j.cell.2020.05.015</a></p><p>Hadjadj, F., Yatim, N., Barnabei, L., Corneau, A. , Boussier, J., Smith, N., Péré, H., Charbit, B., Bondet, V., Chenevier-Gobeaux, C., Breillat, P., Carlier, N., Gauzit, R., Morbieu, C., Pène, F., Marin, N., Roche, N., Szwebel, T.-A., Merkling, S.H., Treluyer, J.-M., Veyer, D., Mouthon, L., Blanc, C., Tharaux, P. -L., Rozenberg, F., Fischer, A., Duffy, D., Rieux-Laucat, F., Kernéis, S., Terrier, B. (2020) Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients. 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Cape fur seals can nurse their pups well into adulthoodhttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=7575Cape fur seals can nurse their pups well into adulthoodMedia & Communication, Faculty of Science<p>​Some Cape fur seal (<em>Arctocephalus pusillus pusillus</em>) mothers may nurse their young for several years longer than previously thought, thereby potentially improving their offspring's chances of survival.</p><p>The observations of this unusual behaviour has now been published in the journal <em>African Zoology</em> in an article entitled “<a href="https://www.tandfonline.com/doi/abs/10.1080/15627020.2020.1768144">Prolonged nursing in Cape fur seals (<em>arctocephalus pusillus pusillus</em>) at Cape Cross colony, Namibia</a>". </p><p>Researchers from the <a href="http://www.namibiandolphinproject.org/">Namibian Dolphin Project</a>, a research project run by <a href="http://seasearch.co.za/">Sea Search Africa</a>, made the observation at the Cape Cross colony in Namibia. Cape Cross is one of the world's largest breeding colonies of Cape fur seals, hosting up to 210 000 animals. While adult males are only present during the breeding season, females stay at Cape Cross all year long with their offspring, hunting in the nearby waters.</p><p>Dr Anna Osiecka, lead author, says Cape fur seals normally wean their young within a year: “It appears that some may choose to keep the bond with their pups or even feed unrelated pups. As seal milk is very rich in fat and protein, this extra 'free' food can give their offspring an upper hand by allowing the young to grow larger and improve their chances of survival. </p><p>“For male pups, this can translate into better chances to defend a harem and father offspring when they grow up, as larger males tend to be more successful," she explains.</p><p><strong>What we know about maternal care in Cape fur seals</strong></p><p>Cape fur seals are the only seals which breed in southern Africa, with a range from southern Angola to the Port Elizabeth, in South Africa. “These animals were hunted to the brink of extinction in the last century, but with appropriate protection measures they have recovered and became numerous throughout their range", says Dr Simon Elwen, a marine mammal expert and director of Sea Search.</p><p>When they reach maturity, Cape fur seal females give birth to a single pup annually. Pups are weaned at 10-12 months and getting separated from their mother earlier often results in death. To sustain this long period of nursing, mothers spend about half of the time out at sea feeding, leaving their young alone onshore in big nursery groups. </p><p>According to Dr Tess Gridley, a postdoctoral fellow at Stellenbosch University's Department of Botany and Zoology, Cape fur seals are a fascinating species. She is leading the research project on their biology and behaviour in South Africa and Namibia.</p><p>Dr Osiecka says the observations prove that mother-and-pup relations are not as simple as previously thought. “Mothers can continue nursing their older offspring if the year's pup dies or is lost as a still birth. This is a great advantage to the older pups: they can grow larger faster, and this will ultimately increase their chances of survival and reproduction when they grow up." </p><p>This also implies that seals can recognise their family members over many years and maintain their bonds.</p><p>While physically costly, prolonged nursing may also benefit the mother. Removing excess milk helps to prevent mastitis, and in some cases it may be simply be more efficient to support older, healthy offspring, e.g. if the new pup is very sickly or lost.</p><p>“In some species nursing inhibits future pregnancies – we don't know yet if this is the case with Cape fur seals, but if so, prolonged nursing could also provide a year without a pregnancy, allowing the mother to recover her physical condition," says Osiecka. </p><p>Prolonged suckling has been observed in other fur seals, though it is often attributed to milk theft or mistaken identity with females nursing an unrelated pup. </p><p>“This is not the case in our observations. In all of the cases, the females were aware and allowing of the situation, and sniffed the sucklers. This is how these animals recognise each other, and it implies that the females know and accept the sucklers."</p><p>However, Dr Osiecka points out that there is still much to learn. “Our observations, and in fact all descriptions of unusual nursing in fur seals, are based on opportunistic sightings. We are still not sure how females decide on whether to extend nursing their young, or whether adoption takes place in this species. Longer, dedicated studies are needed to better understand the social dynamics of these animals." <br></p><p><strong>On the photos above:</strong> A Cape fur seal mother nurses a year's pup (right) and a two-year-old juvenile simultaneously.<em>  </em>The Cape Cross colony in Namibia hosts up to 210 000 seals. <em>Photo: ©Anna N Osiecka/Sea Search</em><br></p><blockquote style="margin:0px 0px 0px 40px;padding:0px;border:medium;"><p>​​Full report: Osiecka, A. N., Fearey, J., Elwen, S., & Gridley, T. (2020). Prolonged nursing in Cape fur seals (Arctocephalus pusillus pusillus) at Cape Cross colony, Namibia. <em>African Zoology</em>, 1-7. <a href="https://doi.org/10.1080/15627020.2020.1768144">https://doi.org/10.1080/15627020.2020.1768144</a></p></blockquote><p><strong>Media interviews only</strong></p><p>Dr Anna Osiecka - ​E-mail: <a href="mailto:ann.osiecka@gmail.com">ann.osiecka@gmail.com</a></p><p>Dr Tess Gridley - <a href="mailto:nam.dolphin.project@gmail.com">nam.dolphin.project@gmail.com</a><br></p><p><br> </p>
SU researchers discover new species of lice, chigger miteshttps://www.sun.ac.za/english/Lists/news/DispForm.aspx?ID=7563SU researchers discover new species of lice, chigger mitesEngela Duvenage<p>Two new lice species and six new chigger mite species, collected by a postgraduate student and a researcher from Stellenbosch University (SU) respectively, have been named and their discovery announced. It just goes to show how rich the diversity of parasites in South Africa are, and how many are still waiting to be discovered, says Prof Sonja Matthee of the SU Faculty of AgriSciences' Department of Conservation Ecology and Entomology, who collected and named the chigger mites.<br></p><p>The two new lice species were discovered by JC Bothma from Bellville, during his MSc studies in Zoology. At the time, he was researching the evolutionary relationship between parasites and their hosts in terms of the lice found on four South African mouse species. Bothma, who obtained his degree cum laude last year, sampled mice and lice from more than twenty localities in the country and discovered the two new species in the Fraserburg area.<br></p><p>News about the new lice species recently appeared in the <em>Journal of Parasitology</em>. Lice expert Prof Lance Durden from Georgia Southern University in the USA conducted the technical investigations and description of the new species. </p><p>He has been working regularly with Prof Sonja Matthee on various projects since 2003. He was visiting Stellenbosch University in 2018 to present a lice identification course for her students when Bothma showed him some of the lice he found during a fieldtrip in the Karoo. <br></p><p>Among them were two unknown species, barely larger than 1 mm each, which Bothma had removed from a pair of Grant's rock mice (<em>Micaelamys granti</em>). At this stage, the Stellenbosch team already knew that the lice were genetically distinct from any other known louse species found on rodents in South Africa. Durden took them back to the USA, where he went through the step-by-step process of analysing and describing the new species. </p><p>The species are named <em>Hoplopleura granti</em> and <em>Polyplax megacephalus</em>. The two blood-sucking parasites spend their whole lifecycle - from the egg stage to adulthood - only on the body of a Grant's rock mouse.</p><p><em>Hoplopleura granti</em> is so named because of its host, Grant's rock mice. <em>Polyplax megacephalus</em> was named for its fairly large ("mega" in Latin) head ("cephalus"), compared to most of the other 550 lice species found worldwide.</p><p>Bothma conducted his studies under the guidance of molecular ecologist Prof Conrad Matthee from the Department of Botany and Zoology in the SU Faculty of Science, and Prof Sonja Matthee of the SU Faculty of AgriSciences.<br></p><p>Prof Sonja Matthee also recently collaborated with a Russian colleague, Prof Alexandr Stekolnikov of the Zoological Institute of the Russian Academy of Sciences, to identify six new chigger mite species. She found the mites on field mice near Hoedspruit in Mpumalanga. The announcement about the new species was made in the journal <em>Systematic and Applied Acarology</em>.</p><p>Chigger mites are at less than a millimetre by no means easy to spot or to identify. They fall into the larger Arachnida class to which spiders, ticks and scorpions also belong.<br></p><p>Chigger mites are to be found on hosts during their larval stage, and then fall off the host to continue developing through their different live stages in the vegetation. Larvae that feed on hosts such as humans, livestock and pets can cause irritating, itchy bites.<br></p><p>Most of the 80 South African chigger mite species described (there are 440 known species worldwide) are to be found in KwaZulu-Natal, but few surveys elsewhere in the country have been done. <br></p><p>Two of Prof Matthee's mentors were honoured in the naming of the new species, <em>Ascoschoengastia ueckermanni</em> and <em>Schoutedenichia horaki</em>. They are the South African acarologists (mite and tick experts) Prof Eddie Ueckermann from North-West University and Professor Ivan Horak from the University of Pretoria. Both have been retired for several years (currently Ueckermann is 69 years old and Horak 86) but are still engaged in research in their respective fields. A third species, <em>Trombicula walkerae</em>, was named after the late Dr Jane Walker, who was an expert on Africa's tick species, and among others helped write guides on tick species to be found in Botswana and Kenya.</p><p>Fleas, lice, mites and ticks are all external parasites that occur on the bodies of host animals and feed on their blood at some point during their life cycle. Internal parasites include tapeworms, flatworms and roundworms. For every animal species, there is usually a specific set of parasites that are very unique to them.<br></p><p>Prof Matthee believes more effort should be made with surveys on the distribution of parasite species and their description, as each plays a unique role in ecosystems. Further, parasites make up a significant part of biodiversity on earth as more that 50% of all animal species are either parasites or exhibit some form of parasitism as part of their lifecycle. Because some can also transmit diseases to humans and animals, it is therefore necessary to know where in the country different species occur.<br></p><p>"Parasite research is a very neglected field of study in South Africa," says Prof Matthee, who has been involved in such work for the past two decades. "There is a shortage of local experts and that is why we regularly use overseas colleagues to help us describe new species."<br></p><p>One of Prof Matthee's former doctoral students, Dr Andrea Spickett of the Agricultural Research Council's Onderstepoort Veterinary Institute, surveyed the internal parasites found in 13 mice species across South Africa as part of her studies. In the process she found at least 13 unknown species of worms. These must first be formally studied to confirm whether they are perhaps new species. <br></p><p><strong>Photo</strong>:<br></p><p>Prof Sonja Matthee from Stellenbosch University collected six new species of chigger mites and helped name them. JC Bothma, who discovered two new lice species near Fraserburg. <em>Polyplax megacephalus </em>is one of the new lice species that were discovered by JC Bothma. <br></p><p> </p><p><br></p><p><br></p>