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Dave Pepler talks to specialists about hallucinogens, soil microbes and ancient star galaxies Pepler talks to specialists about hallucinogens, soil microbes and ancient star galaxiesWiida Fourie-Basson (Faculty of Science)<p>​Hallucinogens, soil microbes and ancient star galaxies are some of the topics that the well-known nature lover Dave Pepler will tackle during this year's Stellenbosch Science Cafés.<br></p><p>Since Science Café Stellenbosch was presented for the first time during Woordfees in 2015, it has become a standard item on the programme. Over the years many interesting and sometimes controversial topics were covered, including climate change, why birds sing, the evolution of skin colour and artificial intelligence.<br></p><p>Science Café <span><span>Stellenbosch </span></span> is an initiative of SU's Faculty of Science to encourage conversations about scientific issues in the public sphere. This year's programme looks as follow:</p><p><em>Tuesday</em><em> 11 O</em><em>c</em><em>tober I 18:00-</em><em>19:00  I</em><em>  </em><em>Plataan</em><em> Caf</em><em>é</em> </p><p><strong>Ha</strong><strong>llucinogens for the treatment of mental health</strong> </p><p>Hallucinogens, specifically those that derive from plants, have been used for thousands of years by indigenous cultures for social and religious rituals. Dave Pepler talks to Dr Heinz Mödler, anaesthetist and author of <em>En </em><em>daar</em><em> was dagga: 'n </em><em>Biografie</em>, and clinical psychologist Louis Awerbuck, on the use of hallucinogens in the treatment of mental health issues. </p><p><em>Wednesday</em><em> 12 </em><em>O</em><em>c</em><em>tober  I</em><em>  18:00-</em><em>19:00  I</em><em>  </em><em>Plataan</em><em> Café</em> </p><p><strong>Fantastic microbes and where to find them</strong> </p><p>There are more than a billion microbes in a teaspoon of soil – that is why scientists regard soil as a living organism. Dave Pepler talks to Prof Karin Jacobs from SU's Department of Microbiology about how the soil microbiome can be revived in the spirit of regenerative agriculture.  </p><p><em>Thursday</em><em> 13 </em><em>O</em><em>c</em><em>tober  I</em><em>  18:00-</em><em>19:00  I</em><em>  </em><em>Plataan</em><em> Café</em> </p><p><strong>James Webb </strong><strong>Space Telescope: what do we see and what does it mean?</strong> </p><p>Since July this year the James Webb Space Telescope has been sending breath-taking images of antique galaxies dating back 13 billion years. Dave Pepler asks Dr Anslyn John from SU's Department of Physics what these images mean for science and humanity.  </p><p>​<a href="">Follow us on Facebook</a> or send an e-mail to <a href=""></a> to join our mailing list.  </p><p><br></p>
Dr. Adefemi Alade obtains the first position at the IAWS Doctoral Award and Medal for 2022 Adefemi Alade obtains the first position at the IAWS Doctoral Award and Medal for 2022Prof Bruce Talbot<p>​The International Academy of Wood Science (IAWS) recently announced that Dr. Adefemi Alade obtained the first position in their Doctoral Award and Medal for 2022. With this award the IAWS wishes to provide recognition to outstanding dissertation research at the PhD level by students throughout the world. Adefemi was supervised by Proff. Brand Wessels and Luvuyo Tyhoda from the Department of Forest and Wood Science, Stellenbosch University. The title of his dissertation was “An investigation into the effect of durability treatment on adhesive bonding of <em>Eucalyptus grandis </em>wood".  Dr Alade has since taken up a position as Postdoctoral fellow at the University of Idaho. Congratulations on your outstanding achievement Dr. Alade!​<br></p>
Stellenbosch theoretical physicist honoured with SAIP Gold Medal theoretical physicist honoured with SAIP Gold MedalWiida Fourie-Basson (Faculty of Science)<p>​In his career as a theoretical physicist, Prof Hendrik Geyer has always put up his hand for the big problems in physics – from developing a mathematical framework in the 1990s that has become fundamental to the building of quantum mechanical systems today, to building the field of physics in South Africa.<br></p><p>The South African Institute of Physics (SAIP) has recently awarded him with the Institute's De Beers Gold Medal, the greatest distinction that is conferred in South Africa for achievements in physics. During a special ceremony at the Stellenbosch Institute for Advanced Study (STIAS) on 13 September 2022, SAIP president Prof Makaiko Chithambo said the award recognises Prof Geyer's fundamental and novel contributions to the field of non-Hermitian quantum mechanics, his leadership in building the field of theoretical physics in South Africa, and his significant contributions to education and training of students.</p><p>“Most importantly, we want to recognise his competent leadership in the establishment of important structures such as the SAIP, the National Institute for Theoretical Physics (NITheP) and the Stellenbosch Institute for Advanced Study," he added.</p><p>Just before handing over the medal in person, the praise singer Mandlenkosi Sixolo also praised Prof Geyer for his contributions in true African style.</p><p>In his acceptance speech, Prof Geyer lifted out three take-home lessons from his own career. </p><p><strong>Firstly, never underestimate the value of dedicated teachers</strong></p><p>His formative years were spent at Templeton High School in Bedford, a small settler town 200km from Gqeberha (then Port Elizabeth). The first principal of the school in 1865 was the Scot, Reverend Templeton, who had been recruited from Lovedale College, a forerunner of the current Fort Hare University. Due to this Scottish legacy, the school maintained an ethos of dedicated teachers who knew how to teach the basics, he recalled.</p><p>He later matriculated from Afrikaanse Hoër Seunskool in Pretoria where a subject such as mechanics took the learners beyond the standard physics curriculum, focussing on Newton's Laws of Motion: a lasting impression about the implications of the third law resulted from the teacher asking questions such as: “Boys, can I pull myself up tugging on my own shoelaces", answering with an emphatic “No"."</p><p>This exposure to Newtonian physics awakened in him an interest in nuclear physics. With a bursary of R360 a year from the Atomic Energy Corporation, he studied physics at Stellenbosch University. During holiday work at the AEC, he rubbed shoulders with senior theoretical  physicists such as Dr Chris Engelbrecht and Dr Fritz Hahne. They later became his study leaders, mentors, and lifelong friends.</p><p>At the time a new (and successful) collective model of nuclear excitations of the atomic nucleus drew on previous phenomenological descriptions, while adding a microscopic element by treating pairs of nucleons (in themselves fermions) as bosons. Since the fundamental classes of quantum particles, viz, fermions and bosons, have widely different properties, this seeming contradiction called for a systematic approach requiring a mathematical framework which allows pairs of fermions to be described in a bosonic language. This was the focus of his doctoral research for which he enrolled at SU under the leadership of Prof Engelbrecht (then at SU) and Dr Hahne. The mathematical framework resulting from the so-called boson mappings which were introduced in the thesis successfully captured the essence of introducing boson degrees of freedom to describe a quantum system comprised of fermions. It also provided a solid framework for understanding the phenomenology of the so-called interacting boson model of the nucleus.</p><p>After completion of his PhD in 1981, he took up a postdoctoral fellowship in the nuclear theory research group at the State University of New York in Stony Brook.</p><p>In the 1980s the theoretical physics group at the AEC was moved to Stellenbosch University, as part of a country-wide program to situate the fundamental sciences at universities, and the applied sciences at bodies such as the AEC and the CSIR.</p><p><strong>This is his second take-home lesson: Opportunities seldom arrive on a golden platter, so when something worthwhile comes along, grab it and do what you can with what you have</strong></p><p>For the next decade, the nuclear physics research group continued with their basic research in a house at 7 Joubert Street – currently home to the Africa Open Institute for Music, Research and Innovation at SU – just opposite the street from the Department of Physics in the Merensky Building. </p><p>“We achieved something during that time in Joubert Street. Apart from lecturing honours courses and supervising postgraduate students, we didn't bother anybody, and nobody bothered us," he recalls.</p><p>Prof Geyer continued working on quantum systems with another AEC-bursary holder, Prof Frikkie Scholtz, who joined the Pelindaba group in 1983. </p><p>By taking the non-Hermitian structures which result from a boson mapping at face value, they realised that it is often more advantageous to use variables that do not comply to the standard Hermitian point of departure. Prof Scholtz explains: “We realised that these variables still represent a consistent quantum mechanical system even if they do not comply with the standard Hermitian matrix. We then got the idea to use this as our point of departure for the construction of a quantum system".</p><p>Traditionally an observer decides which dynamical variables in a specific quantum mechanical framework are measurable (such as position and momentum) and then proceeds accordingly to introduce the Hamiltonian (or energy) from which to calculate properties of the system described in terms of these variables. The Stellenbosch group realised that by starting from the system description (or Hamiltonian, now non-Hermitian) one could systematically identify the dynamical variables in a consistent way, and thereby provide a fully self-consistent framework of quantum mechanics bases on a non-Hermitian Hamiltonian.</p><p>“People did not really know what they were doing when using a so-called variational approach to calculate the properties of a quantum system when confronted with a non-Hermitian Hamiltonian" explains Prof Geyer. “We mainly wanted to correct this at the time, but in doing so actually developed the full mathematical framework for dealing with non-Hermitian variables."</p><p>After three decades, the 1992-paper in which they published the results of this framework still receives up to two citations per week, with more than 700 citations in total.</p><p>In the world of academic publishing, this type of paper is called a “sleeping beauty", explains Prof Scholtz. In other words, nearly three decades after the publication of this fundamental work, it has literally “woken up" to find new applications, now also in the field of parity-time symmetry (PT symmetry). This includes PT symmetric optical sensors, lasers, antenna receivers and transmitters, and even invisibility cloaks.</p><p>According to Prof Mark Tame, a physicist specialising in quantum information science in SU's Department of Physics, all these physics applications are based on the novel way in which loss and gain in a physical system can be engineered to obtain a distinct advantage over conventional approaches: “Prof Geyer and his colleagues' work on PT symmetry has helped lay the mathematical foundation for these applications," he explains.  </p><p>Prof Geyer also played a pivotal role in setting up long-running programmes such as the Chris Engelbrecht Summer School, which for the past 40 years have brought together physicists from all over the world and Africa. Another major initiative was the establishment of the National Institute for Theoretical Physics (NITheP) which was established in 2008, and which has recently been renamed the National Institute for Theoretical and Computational Sciences (NITheCS). Due to his ongoing involvement with STIAS, Prof Geyer is now also part of the organising committee for the first Nobel in Africa Symposium.</p><p>“We will host a series of Nobel symposia over the next seven years, the first and only place outside Sweden to host such an event," he adds.</p><p><strong>The last life-lesson</strong> he dedicated to his wife, Jane, whom he met 50 years ago in the first-year chemistry class at SU, saying that what he achieved had all to do with her support, encouragement and love over all those years.</p><p>Several of Prof Geyer's former colleagues and students also congratulated him on this achievement, including Prof Rudolf Erasmus (SAIP council member), Prof Erich Rohwer (SU Department of Physics), Dr Hannes Kriel (former student), Prof Louise Warnich (Dean: Faculty of Science) and Dr Christine Steenkamp (SU Department of Physics). <br></p><p><em>On the photo above, from left to right, Prof Makaiko Chithambo, president of SAIP, Prof Hendrik Geyer, and the praise singer Mandlenkosi Sixolo. Photo: Wiida Fourie-Basson</em><br></p><p>​<br></p>
Honey bees can be handy pollinators of blueberries bees can be handy pollinators of blueberriesCorporate Communication & Marketing / Korporatiewe Kommunikasie & Bemarking [Alec Basson]<p>​​​Honey bees seem to be quite handy pollinators of blueberries as they help to increase fruit yield and quality, a new study at Stellenbosch University (SU) found.<br></p><p>Titled “Assessing the effectiveness of honey bee pollinators for cultivated blueberries in South Africa," the study was conducted by Keanu Martin, Bruce Anderson, Corneile Minnaar and Marinus de Jager from SU's Department of Botany and Zoology. It was published recently in the online version of the <a href=""><strong class="ms-rteThemeForeColor-5-0">South African Journal of Botany</strong></a>.</p><p>“We found that honey bees are usually extremely beneficial and can act as reliable blueberry pollinators, even in areas without access to native blueberry pollinators such bumble bees. Honey bees increase fruit production and quality, and decrease ripening times compared to when pollinators were absent," say the researchers.<br></p><p>They conducted the study to determine the effect of honey bee pollination on the fruit yield of five commercially grown blueberry varieties in South Africa, namely Emerald, Eureka, Snowchaser, Suziblue and Twilight. For each variety, they calculated 1) the benefit of the bees — a comparison of fruit yields after exposure to honey bees and fruit yields after their exclusion — and 2) the pollination deficit — the difference in yield between hand pollination (manual transfer of pollen from male blueberry anthers to the female stigma for maximum yield potential) and yields after exposure to the bees.</p><p>On a plot at a Western Cape blueberry farm, the researchers stocked honey bee hives at 15 hives per hectare, which falls within the range of commercial blueberry farm hive densities. Here they focused on fruit produced when flowers were bagged and had no access to honey bee pollination, fruit produced when flowers were open to honey bee pollination, and fruit produced through hand pollination. The researchers point out that for the approximately 280 hours they spent at the plot, honey bees were the only pollinator seen visiting blueberry flowers.<br></p><p>Following these pollination treatments, the researchers examined the development of the blueberries from pollination to harvesting to determine whether they were ready to be picked. Fruit were considered ready for picking when the entire berry had transformed to a uniform dark blue. They then harvested the blueberries and determined their weight, diameter and the period of development. <br></p><p>They also calculated the adjusted fruit mass by combining the fruit mass and percentage fruit per treatment. According to the researchers, the adjusted fruit mass is a good proxy for realised yield because blueberries are typically not thinned by farmers and so adjusted fruit mass is likely to correlate with measurements of traditional yield (e.g., total mass per 100 flowers). <br></p><p><strong>Improved yields</strong></p><p>They say their study showed that honey bees increased the set, size and mass of blueberry fruit across multiple varieties, when compared to fruits produced in the absence of pollinators. Exposure to honey bees also appeared to reduce fruit ripening time across varieties.</p><p>“Pollination by honey bees can result in very impressive yield increases for Emerald, Snowchaser, Twilight, and Ventura varieties, but for Eureka and Suziblue, honey bee exposure appeared to have relatively small effects on fruit production."<br></p><p>According to the researchers, this may occur if a variety can reproduce with itself and doesn't need any kind of stimulation to move pollen from the anthers to the stigma, or if honey bees are depositing high loads of pollen from the same variety.<br></p><p>They point out that hand pollination results in the best fruit quality as it enhances pollen deposition and crosses can be made with highly compatible varieties.<br></p><p>“The presence of the honey bees significantly increased the mass and diameter of the fruit by 30% and 13% respectively. Honey bees also significantly increased adjusted fruit mass by 62% compared to fruit produced when blueberry flowers were bagged. Hand-pollination, on the other hand, increased the adjusted fruit mass by 26%, compared to fruit produced from honey bee pollination.<br></p><p>“Honey bee pollination decreased the ripening time of blueberry fruit by a week compared to fruit produced in the absence of pollinators (bagged flowers). Additionally, hand-pollination decreased the ripening time by a further two weeks compared to fruit produced through honey bee pollination."  <br></p><p>The researchers point out that although honey bee pollination consistently resulted in improved yields, the magnitude of this improvement (i.e., the benefit of bees) was dependent on the different varieties. Similarly, the pollination deficit also varied considerably across varieties and while some varieties appeared to perform close to maximum potential, others yielded well below their maximum potential when pollinated by honey bees.<br></p><p>They add that while honey bees are useful pollinators of blueberries in areas where native blueberry pollinators are absent, it is important to select blueberry varieties that perform well with honey bees as their primary pollinator.<br></p><p>“More research is needed to identify which blueberry varieties do best under commercial honey bee pollination conditions, what makes varieties successful or unsuccessful, which varieties can be effectively pollinated by honey bees, and which varieties need other effective means to increase fruit quality.<br></p><p>“It is important to quantify the benefits of honey bees for different blueberry varieties so that objective decisions can be made about the perceived needs of importing new pollinators. This may also enable us to farm more intelligently with varieties that do better under honey bee pollination."<br></p><ul><li><strong>​Source</strong>: Martin, K; Anderson, B; Minnaar, C; & de Jager, M 2022. Assessing the effectiveness of honey bee pollinators for cultivated blueberries in South Africa. <em>South African Journal of Botany</em> 150: 113-119: <a href=""><strong class="ms-rteThemeForeColor-5-0"></strong></a>.<br></li></ul><p>​<br></p>
In memoriam: Dr Rehana Malgas-Enus memoriam: Dr Rehana Malgas-EnusFaculty of Science (media)<p>It is with great sadness that the Stellenbosch University community has learned of the sudden passing earlier this week of Dr Rehana Malgas-Enus, a senior lecturer in the Department of Chemistry and Polymer Science. She was in Germany where she was an Eleanor Trefftz Fellow at the Dresden University of Technology.<br></p><p>In a tribute, Prof Peter Mallon, head of the Department of Chemistry and Polymer Science, said since Rehana joined the Department in 2013, she has made a significant impact in all areas of service to Stellenbosch University and the broader chemistry community. She was an outstanding and passionate teacher and was recently recognised as such by being nominated by the best first year student in the Faculty of Science in 2021 as the lecturer who contributed most to their academic achievement. </p><p>Rehana established and led the nanotechnology research group in the Department of Chemistry and Polymer Science and made a significant contribution to both postgraduate student training and research publication outputs.<br></p><p>Rehana will be remembered for her passion and efforts in promoting interest in chemistry especially with less privileged learners. She established and has driven the Stellenbosch University Chemistry Outreach Initiatives (SUNCOI) in which many thousands of learners and teachers have participated. Since its establishment in 2013, this programme has grown nationally and the most recent event took place at Nelson Mandela University earlier this month. </p><p>Prof Mallon said they are truly thankful for Rehana's many contributions: “With Rehana's passing, we have lost a colleague whose passion, commitment and drive has impacted many people. In the time she was with us she achieved so much, often against the odds, and we lament the fact that with her passing we have lost someone who no doubt would have continued to make a major impact and contribution". </p><p>Prof Louise Warnich, Dean of the Faculty of Science, said Rehana's passion and commitment inspired everyone who came into contact with her: “She had a passion for students, and a passion to create opportunities for less privileged learners. Nothing was too much for her, and all her projects and initiatives were planned to the finest detail. She leaves a lasting legacy in all the lives she touched."</p><p>Prof Jacqueline du Toit, on behalf of the fellows of the Future Professors Programme, also expressed their deepest sympathy: “Rehana was a wonderful teacher, a committed scholar and an inspiring human being." </p><p>In a tribute to his former student and colleague for over twenty years, Prof Selwyn Mapolie from the Department of Chemistry and Polymer Science, said he first encountered Rehana in his second-year chemistry class at the University of the Western Cape: “She was one of the strongest role models I have ever encountered for those students who came from single parent households or impoverished backgrounds. On the whole she was a true champion for the marginalised."</p><p>He recounted how she recently took a struggling PhD-student from Atlantis into her home for eight weeks to enable him to do the final write-up for his PhD. He is now a postdoctoral fellow at the University of Johannesburg. A few years ago, one of her postgraduate students was diagnosed with cancer shortly before submitting his thesis. After his death, she made sure the thesis was examined and for the degree to be awarded posthumously. She also fought hard to enable a technical officer in the department to complete an MSc at the Cape Peninsula University of Technology – he is now submitting a proposal for his PhD studies at SU.</p><p>He is also proud of how his former PhD student has established her own research group and niche research area: “She has finally established herself to such an extent in the field of nanotechnology for her research career to finally take off. Her passing is going to leave a huge gap in our department," he said. </p><p>Dr Malgas-Enus served on the editorial board of Springer Nature Applied Sciences, and was a member of the executive of the Catalysis Society of South Africa (CATSA) and Western Cape Chapter of the South African Chemical Institute (SACI). She was also the current treasurer of the Royal Society of South Africa. In 2021, she was selected to participate in the Department of Higher Education and Training's Future Professors Programme. For her ongoing outreach work, she was awarded the NRF Excellence in Science Engagement Award in 2018. </p><p>Mr Jabu Lukhele, principal technical officer in the department and co-manager of the SUNCOI initiative, said she was his friend, mentor, supervisor and colleague: “We have taken chemistry to places in South Africa where no one was willing to go or could imagine going. She is one of the most driven people I've ever met. I've learned so much from her. I promise to make her proud of me one day."</p><p>Messages of condolences were also received from Prof Sibusiso Moyo, Vice-Rector: Research, Innovation and Postgraduate Studies at SU, Prof Jonathan Jansen, project leader of the Futures Professors Programme and distinguished professor at SU, and Mr Ronald Engelbrecht. FET Curriculum Coordinator for the Metro South Education District in the Western Cape Education Department.<br></p><p>​​<br></p>
NRF honours SU ecologist with Lifetime Achievement Award honours SU ecologist with Lifetime Achievement AwardFaculty of Science<p>​The National Research Foundation (NRF) honoured Emeritus Professor Brian van Wilgen with the <a href="">Lifetime Achievement Award</a>, the highest honour that is bestowed by the NRF for a deserving South African for their outstanding contribution to the development of science in and for South Africa, what they stand for as a South African, and for the extent to which their work has positively touched and shaped the lives of many South Africans.<br></p><p>Spanning ​a research career of more than four decades, Prof van Wilgen's work on alien plants and water resources has helped place South Africa at the forefront of managing biological invasions. He is mostly recognised for his work in 1995 on developing models of water use by alien trees, while working with a team at the CSIR. This work led to the establishment of the Working-for-Water programme – an innovative project to not only clear the country of invasive plants, but to simultaneously provide employment opportunities to thousands of South African, particularly women, the youth and the disabled. </p><p>By 2020 the Working for Water programme, now administered by the Department of Forestry, Fisheries and the Environment, had invested an average of R355 million per year (expressed in 2020 rand values) over 25 years and created more than 8 300 full-time jobs annually.</p><p>“Few people realise," he says, “that pines, for example, are not indigenous to South Africa. They are highly invasive, and threaten to obliterate our natural heritage, like fynbos, with its over 6000 plant species found nowhere else on earth, or that they could potentially reduce Cape Town's water supplies by 30%".</p><p>His practical approach to tackling these problems is based on over four decades of research, first conducted as a researcher in the Department of Forestry at Jonkershoek and the CSIR in the 1990s, and later as a core team member of the DSI/NRF Centre of Excellence for Invasion Biology at Stellenbosch University, where he remains actively involved in his capacity as an emeritus professor at the age of 70.</p><p>Prof. van Wilgen received the award during a special awards function on 1 September – <a href="">watch video here</a>.</p><p>Several of his colleagues congratulated him for this achievement:</p><ul><li><strong>Prof Richard Cowling from Nelson Mandela University:</strong> “Brian van Wilgen is internationally recognised for his substantive contribution to the fields of invasive plant ecology and fire ecology. But more importantly he is recognised for framing his research in such a way that it leads seamlessly to implementation. In fact I would say that it puts Brian in a very small group of scientists globally – his ability to bridge the gap between research and management."</li><li><strong>Dr Tineke Kraaij, Nelson Mandela University: </strong>“Overall, Brian's example shaped my own research career in many ways and even my own fields of interest. Brian uses sensible and simple methods, rather than to baffle and impress with complicated and expensive materials and methods. Brian laid the foundation in the fields of fire ecology and invasion biology in both fynbos and savanna ecosystems. I have huge respect for Brian as a colleague and a scientist. It was a privilege to work with him and I think his research work will have a significant impact on conservation today and into the future."   </li><li><strong>Prof Dave Richardson, former director of the DSI/NRF Centre of Excellence for Invasion Biology at SU</strong>: “Brian's research on the role of fire in Mediterranean type of ecosystems and savannas have been highly influential. His work on how fire interacts with invasive plants and how this influences the options for management has been highly cited. He has published important papers on the impacts of invasive species on biodiversity and ecosystem services and on optimising strategies for their management. Brian's research over more than 40 years has had a huge influence on ecosystem management in South Africa and has also inspired a new generation of researchers."</li><li><strong>Dr Guy Preston, former Deputy Director-General in the Department of Environment, Forestry and Fisheries</strong>: “I have known Brian van Wilgen since the 1980s when we developed the concept of the Working for Water programme. He was very much one of the key thinkers behind the idea. He is a systematic thinker and played an enormously important role in the beginning years of the programme, and later as scientific adviser. What I admire most was his ability to provide outcome-orientated and practical solutions, as well as his willingness to speak out on issues."<br></li></ul><p>​<br></p>
African scientists show with genomics surveillance how COVID-19 variants reached and spread across Africa scientists show with genomics surveillance how COVID-19 variants reached and spread across AfricaCorporate Communication and Marketing / Korporatiewe Kommunikasie en Bemarking<p>​​​A scientific report featured in the respected global journal <a href="">Science</a>, revealed that a large consortium of African scientists and public health institutions illustrated how the SARS-CoV-2 variants reached and spread across the African continent. The study shows that most of the introductions of variants in Africa were from abroad and not from Africa. Yet, Africa was the most discriminated against and penalized continent in the world with travel bans. The consortium found that the initial waves of infections in Africa were primarily seeded by multiple introductions of viral lineages from abroad (mainly Europe).<br></p><p>The scientific report shows how the rapid expansion of genomics surveillance in Africa allowed the continent’s scientific community to describe the introduction and spread of the SARS-CoV-2 variants in African countries in real-time during the COVID-19 pandemic. This is a feather in the cap of African science and the restoration of incorrect perceptions based on unscientific and inappropriate reactions in the international community. </p><p><span style="font-size:10pt;font-family:helvetica, sans-serif;color:#4d5356;"><span style="font-size:10pt;font-family:helvetica, sans-serif;color:#4d5356;"></span></span></p><p>READ THE COMPLETE OFFICIAL MEDIA STATEMENT BELOW<br></p><p><strong>Addis Ababa, Durban, Brazzaville and Stellenbosch, 15 September 2022.</strong> A major scientific report from Africa is featured in the journal <a href="">Science</a> today. This scientific report shows how the rapid expansion of genomics surveillance in Africa allowed the continent to describe the introduction and spread of the SARS-CoV-2 variants in African countries in real time during the Covid-19 pandemic.<br>  <br> The scientific report includes over 300 authors from Africa and abroad who worked together to describe and analyse over 100 000 genomes and characterise SARS-CoV-2 variants in real time. This was the largest consortium of African scientists and public health institutions ever to work together to support data-driven Covid-19 response in Africa.<br>  <br> This report shows how the large investment, collaboration and capacity building in genomic surveillance on the African continent enabled real-time public health response. Particularly it describes the setting up of the Africa Centres for Disease Control (CDC) - Africa Pathogen Genomics Initiative (Africa PGI) and the continental network by the Africa CDC and World Health Organisation (WHO) Regional Office for Africa (WHO AFRO) to expand access to sequencing and cover surveillance blind spots, in parallel with the growth of the number of countries that are able to sequence SARS-CoV-2 within their own country.<br>  <br> “The publication highlights that sustained investment for diagnostics and genomic surveillance in Africa was needed to not only combat SARS-CoV-2 on the continent, but establish a platform to address the emerging, re-emerging, endemic infectious disease threats, such as Ebola, HIV/AIDS, TB and Malaria. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century," said Dr. Yenew Kebede, Head Division of Laboratory Systems and Acting Head: Surveillance and Disease Intelligence at the Africa CDC. </p><p>This study was led by two labs that setup the network for genomics surveillance in South Africa – the <a href="">Centre for Epidemic Response and Innovation</a> (CERI) at <a href="">Stellenbosch University</a> and the <a href="">KwaZulu Natal Research and Innovation Sequencing Platform</a> (KRISP) at the University of KwaZulu-Natal, in close coordination with the Africa CDC, WHO AFRO and 300 other institutions across the continent.<br>  <br> “The enormous leap Africa made in genomic surveillance during the past two years is the silver lining in the Covid-19 pandemic," said Dr Matshidiso Moeti, WHO Regional Director for Africa. “The continent is now better prepared to face down both old and emerging pathogens. This is a model of how when Africans are in the driving seat we can come up with lasting change and stay a step ahead of dangerous diseases."<br>  <br> “It has been an inspiring experience to continuously share knowledge, support and learn from colleagues all over the continent during the pandemic. We witnessed small countries with no previous genomics experience become empowered in sequencing and bioinformatics methods, and how they started to actively participate in regular pathogen genomic surveillance for SARS-CoV-2. I think it will be a real model of how scientists and public health officials across countries can form a unified front against infectious diseases in the future," says Houriiyah Tegally, Bioinformatician at KRISP and CERI and first author on this report.<br>  <br> The results also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most relevant being the detection of the Beta and various Omicron subvariants. The report highlights that most SARS-CoV-2 variants, which caused  an epidemic in Africa, were introduced from abroad. </p><p>​The scientists proceeded carefully in analysing genomic and epidemiological data collected in over 50 countries that experienced quite heterogenous epidemics in order to reconstruct transmission dynamics of the virus in the most accurate way. “The phylogeographic methods that we employ to investigate the movement of the SARS-CoV-2 virus and its variants into, out of, and within the African continent account for uneven testing and sampling proportions across countries, arising from the realities of doing genomic sequencing in the middle of a pandemic, often in low resourced settings," explains Dr Eduan Wilkinson, head of bioinformatics at CERI at Stellenbosch University and senior author on this report.<br>  <br> The initial waves of infections in Africa were primarily seeded by multiple introductions of viral lineages from abroad (mainly Europe). The Alpha variant that emerged in Europe at the end of 2020, was responsible for infections in 43 countries with evidence of community transmission in Ghana, Nigeria, Kenya, Gabon and Angola. For the Delta variant, the bulk of introductions were attributed to India (~72%), mainland Europe (~8%), the UK (~5%), and the US (~2.5%). Viral introductions of Delta also occurred between African countries in 7% of inferred introduction. For Omicron, the scientific results indicate more reintroductions of the variant back into Africa, with at least 69 (95% CI: 60 - 78) from Europe and 102 (95% CI: 92 - 112) from North America than from other African countries. This was amplified for Omicron BA.2; the results suggest at least 99 separate introduction or reintroduction events of BA.2 into African countries, ~65% of which are from Europe and ~30% from Asia.<br>  <br> “The ironical part of these results is that most of the introductions of variants in Africa were from abroad, but Africa was the most discriminated and penalized continent in the world with travel bans imposed. Instead of unscientific and inappropriate reactions, we should be building on the infrastructure established in Africa so that the continent can rapidly pivot to other epidemics without the fear of being punished," says Prof Tulio de Oliveira, director of CERI and KRISP, which lead the consortium analysis with the Africa CDC and WHO AFRO.<br>  <br> “This study is a testament of the Africa CDC – Africa PGI efforts to expand access to sequencing to member states and create a platform of coordination and collaboration among institutions within and outside of the continent," said Dr. Ahmed Ogwell, Acting Director of the Africa CDC.<br></p><p>Photo: <span style="font-size:10pt;font-family:"trebuchet ms", sans-serif;color:#4d5356;"><em>African Scientists receiving training in genomics surveillance at the Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa</em></span><br></p><p><span style="font-size:10pt;font-family:helvetica, sans-serif;color:#4d5356;">  </span>​<br></p>
Click here to put Eskom’s loadshedding schedule directly into your electronic calendar here to put Eskom’s loadshedding schedule directly into your electronic calendar Wiida Fourie-Basson, Faculty of Science (media)<p>A super frustrated computer science student at Stellenbosch University developed an open source software project tracking the latest loadshedding timetables and tweets from Eskom so that it can be added directly into your calendar. <br></p><p>Boyd Kane says he wanted the very latest loadshedding schedules to show “right there where I can see it – on my electronic calendar". </p><p>“It's not nice working the whole day and then getting home at eight, ready to start dinner, and then the lights go out," he says. So out of pure frustration he decided to put his skills to work in developing a project that could provide him with the very latest information on Eskom's loadshedding timetable. </p><p>Anyone can now put the loadshedding schedule directly into their electronic calendar by clicking on this <a href=""><strong class="ms-rteForeColor-1">open source link</strong></a><strong class="ms-rteForeColor-1">. </strong></p><p>He started working on the technical details in July 2022, and then had to go through the tedious process of cleaning up the raw data. For those areas receiving their electricity directly from Eskom, it was easy. But in other instances he had to find the timetables from the municipalities. All these timetables were in different formats, so it took some time to figure out how to clean the raw data into a useable format. The project also scrapes off information from Eskom's official Twitter account, to make provision for those sudden surprises when the country moves from stage one to stage six loadshedding, or anything in between. </p><p>“I first tested the project on Cape Town, because I lived there and I had friends who could confirm whether the alerts from the project corresponded with their reality," he explains. </p><p>Now there are over 500 municipal areas supported by the project – from Stellenbosch to Matatiele in the Eastern Cape. </p><p>The project is also open source, which means that other developers can jump in and make suggestions on how to improve it, or use the loadshedding schedules for their own ideas. </p><p>For now, a reliable way of publishing the calendars is more important to him than having a good-looking user-interface or website. He is also not interested in turning this into a business venture: “I learned to code from open source and free software on the internet and besides, the internet itself would not have existed if it wasn't for free software. So now it is my turn to give back". </p><p>Boyd is specifically interested in data science and probability theory and plans to continue with his MSc in Computer Science next year. <br></p><p>​<br></p>
Prof Ben Loos wants to help improve treatment of Alzheimer’s disease, cancer Ben Loos wants to help improve treatment of Alzheimer’s disease, cancerCorporate Communication & Marketing / Korporatiewe Kommunikasie & Bemarking<p>Prof Ben Loos from the <span style="font-size:11pt;font-family:calibri, sans-serif;">Department of Physiological Sciences </span>at Stellenbosch University recently delivered his professorial inaugural lecture, titled 'On the role of autophagy and cell death control in neurodegeneration and gliomas'. He spoke to the Corporate Communication and Marketing Division about how his work on cell death offers hope for the improved treatment of neurodegenerative diseases such as Alzheimer's disease and certain resistant cancers. <br></p><p><strong>Tell us more about your research and why you became interested in this specific field.</strong></p><p>In my research, I study the susceptibility of cells to undergo cell death and the molecular mechanisms that govern such a cellular response. Specifically, I am interested in a fundamental cellular stress response, termed autophagy (from Greek 'self-eating'). It describes a process by which cells degrade long-lived proteins and damaged organelles. This process, when dysfunctional, leads to early cell death (such as observed in neurodegenerative diseases, including Alzheimer's disease or Parkinson's disease), but can also assist the cell not to die (such as in most cancers). I have been interested in cell death for a long time and am captivated by the fundamental role of autophagy in this context. Seeing and measuring the processes involved is captivating and makes the research very real. </p><p><strong>How would you describe the relevance of your work?</strong></p><p>There is substantial application to exploit autophagy clinically, not only in neurodegeneration and cancers, but also in the aging process. On the one hand, enhanced autophagy, such as brought about through fasting or exercise, has a tremendous impact on a person's health and lifespan. On the other hand, dysfunctional autophagy increases the risk for the development of diseases associated with aging, which includes heart disease and diabetes. Hence, our work may have broader application. It is relevant to clinicians and the public, and for new therapeutic interventions. </p><p><strong>Can you tell us more about the impact of your research?</strong></p><p>We provide evidence that the control and increase of autophagy can indeed help the cell to remove toxic, aggregated material and proteins, and can thereby impact the onset of nerve cell death.  This offers new hope in highlighting druggable targets (i.e., targets that can be therapeutically modulated by medicines) that are associated with the molecular defect. Likewise, in cancer we have shown that by adjusting autophagy in the presence of a chemotherapeutic drug, we can overcome, to some degree, the cell's ability to resist death. This also provides new hope in the treatment of resistant, poorly treated cancers, such as gliomas (tumours in the brain and spinal cord). The fact that we are using either FDA (Food and Drug Administration) approved drugs or physiological interventions, impacts the therapeutic value of our research because it enhances the potential of this work being used in the treatment of cancer. We do this purposefully to shorten the time it takes for our work to be translated into products that have therapeutic value.</p><p><strong>Which aspects of your work do you enjoy the most?</strong></p><p>What I enjoy most, is to look with my postgraduate students through the confocal/super-resolution microscope, capturing data and sharing in this exciting moment of what the cells reveal. I also enjoy stitching together the pieces of our results like a puzzle that forms a clearer picture and a potential storyline. It is most exciting to brainstorm with my students about that, and about where the data and results are leading us. I also enjoy watching the students becoming independent and passionate about implementing and expanding on what they have learnt. Similarly, I enjoy undergraduate teaching, to link the textbook knowledge to our societal challenges and the problems whose solutions require young scientists with fresh ideas and approaches. It is a wonderful process to witness. In every undergraduate student's ideas and passion for potential postgraduate studies we can find a key approach or answer that we have not thought of. It's an exciting process to be part of. </p><p><strong>The pandemic has changed the way we work and live. What has kept you motivated during these times?</strong></p><p>The research work had to go on, hence I was motivated to help our postgraduate students return to the lab safely as early as possible. It was important to keep the work going and shift to theoretical approaches and articles to help students stay focused and to encourage them. I felt for undergraduate students and thought about how hard this online class experience must have been for them. Therefore, I made every effort to at least keep my presentations, albeit recorded, as personal and entertaining as possible. I am glad we are back, hands-on. Science is hands-on and real-life engagement with the team is critical. </p><p><strong>Tell us something exciting about yourself that people would not expect.</strong></p><p>Before the pandemic, I was on par to train for the Comrades Marathon. Now I have to start from scratch. I love these kinds of challenges, to witness my own limits and (hopefully) overcome them. I love music, opera, the arts, black and white portraits and concerts.  </p><p><strong>How do you spend your free time away from lectures and research?</strong></p><p>I spend my free time with my wife and two boys. My boys (seven and 11) are now at the age where they are often invited to their classmates' birthday parties.  Off late, I have also been spending time and taking joy in training our family dog, a young Hungarian Vizsla, who has now achieved the advanced training level 'In control'. It seems that he is indeed that. <br></p><p>​<br></p>
“I didn’t know one can do so many things with a BSc-degree!”“I didn’t know one can do so many things with a BSc-degree!”Media & Communication, Faculty of Science<p>While it is not always clear where a BSc-degree in the biological, mathematical or physical sciences can take you while you are still studying, it does open the door to a wide range of career opportunities – from the monitoring and management of groundwater sources to the development of green technologies for major companies such as <a href="">SASOL</a>.<br></p><p>This was the main message from a range of industry representatives during the Faculty of Science's Science Careers Fair in August 2022. During this week BSc-students were exposed to presentations from and discussion with companies such as GEOSS South Africa, SASOL, Reutech, Distell, Inizio Medical, Axiology Labs, Carl Zeiss Pty Ltd, the <a href="">South African National Biodiversity Institute</a> and the <a href="">South African Police Services' Forensic Science Laboratory</a>.</p><p>Riyaadh Adams, a software developer, explained how he as a mathematics graduate plays an important role at an engineering company such as <a href="">Reutech</a>. He is part of the data-processing team, where they make sense of the digitized data from tracking and search radar systems.</p><p>From SAPS, Lieutenant Colonel Johan Kock explained how science students majoring in microbiology, biochemistry, genetics, botany, human physiology and even entomology can apply their knowledge in fields such as forensic anthropology, forensic entomology, DNA analysis and the newly established Disaster Victim Identification Centre.</p><p>In all instances, he said, at least a BScHonours and an advanced degree in any of the specialised fields are required. </p><p>And who would have guessed that in 2018, there were 418 000 biodiversity-related jobs in the world. At SANBI, science graduates follow careers such as a climate change adaptation officer or a biodiversity information and policy advisor. SANBI's Biosystematics and Collections Division, for example, employs taxonomists and geneticists.</p><p>At <a href="">Distell</a>, there is scope for BSc-graduates with majors in analytical chemistry, microbiology, biochemistry and horticulture. According to Mare-Loe Prinsloo and Marelize Scheepers, some of the extra-curricular skills companies such as Distell are looking for include technical knowledge, communication skills, self-awareness, the ability to collaborate, strong networking skills, the ability to organise, prioritise and make decisions, flexibility, and a commitment to your work. Most importantly, critical and independent thinking and a willingness to learn and grow, they concluded.</p><p>Gideon Burger, the CEO of <a href="">Axiology Labs</a>, says he became a serial entrepreneur after completing a three-year BSc-degree, followed by an MBA. Over the last three years he has established five new companies – all in the field of microbiology and laboratory equipment. His advice for those students with the entrepreneurial spirit was to jump in and create jobs instead of looking for one: “Science never stops, because the world will always need unique solutions," he added.</p><p>Dr Ascentia Seboko from <a href="">Inizio Medical</a> talked about the growing field of medical communication, especially for those scientists who want to leave the bench, while Ania Henning from Zeiss talked about the company's plans to develop microscopy in Africa.</p><p>Ms Maambele Khosa, recruitment officer for the Faculty of Science and host of the event, said students can now rest assured that there are a range of career options in science.</p><p>As one BSc-student remarked: “I didn't know one can do so many things with a BSc-degree!"<br></p><p>​<br></p>