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  • SA researchers introduced to the field at the National Metabolomics Platform

    14th Aug 2019

    The 2019 Introductory Metabolomics Workshop was held at the National Metabolomics Platform, based at North-West University’s (NWU) Potchefstroom Campus from 05-07th August 2019. This workshop was a collaborative effort between the African Centre for Gene Technologies (ACGT), NWU and the recently established Metabolomics South Africa (MSA).  The workshop provided a capacity building opportunity to help delegates that are in the earlier stages of the research to build a foundation with sound metabolomics techniques and tools.

    The workshop was facilitated by a panel of local metabolomics experts from several institutions from all over the country. The facilitators from North-West University were Dr Aurelia Williams, Prof Du Toit Loots, Dr Mari van Reenen, Dr Shayne Mason, Dr Zander Lindeque, Mr Emile Jansen van Rensburg and Ms Zinandre Stander. The facilitators from the University of Johannesburg included Dr Fidele Tugizimana and Mr Msizi Mhlongo. University of Pretoria was represented by Prof Duncan Cromarty and the University of Cape Town by Dr Zandile Mlamla.

    The focus on day one of the workshop was on the different metabolomics workflows, experimental design and the application of metabolomics in different disciplines and industries. On the second day of workshop the delegates were given an opportunity to participate in real wet lab experiments using NMR and Mass spectroscopy. On the final day of the workshop, the focus was mostly on data handling and interpretation. This involved normalization, quality assurance, statistics, metabolite identification and metabolomics resources.

    The participants were from multiple research institutions from all over South Africa. There were participants from the Universities of Pretoria, Johannesburg, the Witwatersrand, Council for Scientific and Industrial Research, North-West University, University of South Africa, Tshwane University of Technology, University of Cape Town, University of Limpopo and the University of KwaZulu-Natal. Below is a few takes offered by the delegates about the workshop:

    “The content of the course was well balanced to suite newbies and experienced researchers in metabolomics. It was a great mix of people at different levels of research and different themes which made it rich.” 

    “The course is very insightful to beginners, gives an idea of how to tackle metabolic profiling as well as how to analyse the data. Personally, the course has answered a lot of questions I had, and it inspired me.”

    “The statistical analysis was extensively covered and will be very useful in considering the best possible statistical tool to use on one’s data.”

    “ I enjoyed learning about the different applications of metabolomics and how various types of research questions can be answered through the platform.” 

    “The area of research is still evolving and there is the need to prepare next generation of researchers for the task ahead to apply it in various fields apart from the human area alone.”

    “I found the workshop well- structured, comprehensive and rich in content.”


    The ACGT would also like to wish all the participants of the workshops all the luck with their work and future in metabolomics. Furthermore, the ACGT sends much deserved gratitude to all the members of the organizing committee; Mr Molati Nonyane, Dr Aurelia Williams, Mrs Itseng Malao, Dr John Becker and Dr Fidele Tugizimana for all of their efforts in making this event a success. The ACGT would also like to extend their gratitude to the sponsors of this event: Shimadzu, Microsep, Separations and the Scientific Group. You are welcome to visit our facebook page for more visuals from the event.





  • Stem cell treatment – excitement is understandable but let’s tread carefully

    20th Jun 2019


    Stem cells not a panacea.

    There is no doubt that the stem cell field is generating a great deal of excitement and hope. Efforts are underway across the globe to find cures for incurable diseases. Yet despite these exciting developments, only a limited number of procedures are approved for routine therapy.

    A spinal cord injury

    Bone marrow transplantation, which has been performed for cancers and blood disorders for several decades, is one for the few universally approved and routinely practiced forms of stem cells therapy.

    On 31 May 2019, Health24 published an article stating that stem cell treatment had improved the quality of life of a rugby player who sustained a spinal cord injury. Rugby injuries are often low velocity injuries and in many cases, the injuries that are sustained are incomplete.

    The implication is that recovery is possible, to a greater or lesser degree, with follow up rehabilitation. To date, despite numerous research efforts and clinical trials, there is virtually no evidence that stem cells can cure spinal cord injury. Several factors are critical when assessing a case such as the one mentioned above. What was the origin of the cells used? How were they administered? Was the patient walking before the stem cells were administered?

    Equally important, did the administration of the stem cells comply with the laws of the country, and since this is an unproven therapy, should it have been considered as a clinical trial? In the case of the latter, a number of critical steps would have needed to be followed.

    No guarantee

    While not wanting to detract from the great joy of seeing someone recover from a debilitating injury, accurate reporting is important if one is to ensure that vulnerable patients are not emotionally and financially exploited. There is regrettably a global trend involving “stem cell clinics” that seeks to treat a range of diseases using unproven stem cell therapies. Propagating the idea that there is a direct causal relationship between the administration of stem cells and a positive outcome, without considering all of the facts, may be misleading and may prompt other vulnerable patients to undertake similar unproven therapies.

    It is therefore the responsibility of the person reporting the story to do so in a manner that is objective, and to avoid implicating direct causality unless this can be proven. Evidence-based and ethical marketing is also important in order to avoid misleading vulnerable patients and their families. An advertisement, currently running on one of the local radio stations, indicates that the future use of stored stem cells will “overcome my diabetes” and “treat my autism”.

    While there is ongoing research in both of these areas, and many more, there is no guarantee that stem cells will be able to be used to treat these conditions in the future. Given the extent of the emotional involvement around matters pertaining to children, potential customers might be made to believe that by banking their newborn’s stem cells, “the child you have today will be protected tomorrow”.

    Complex matter

    While there is the potential that stored stem cells might well be used in the future for bone marrow transplantation or for regenerative medicine purposes, this information should be convened objectively, which includes placing the possibility of a future cure into perspective relative to the evidence currently available. Why is it important to proceed cautiously with new treatments that have the potential to cure previously incurable diseases?

    One important reason is highlighted in a recent court decision in the US. As noted by the International Society for Cell and Gene Therapy, “this ruling an important step towards the regulation of an industry that has eluded regulatory oversight for many years, causing substantial financial, and in many cases, physical harm to patients through direct-to-consumer advertising of unproven and poorly tested “stem cell” treatments”.

    In other words, as long as a treatment that eludes regulatory oversight does no harm, financial loss will be the only issue that needs to be contended with. However, in the case mentioned above, four patients were blinded by stem cells administered directly into their eye. And there are many more examples of cases in which patients have been harmed by unproven “stem-cell” therapies. The argument is often put forward that the use of the patient’s own stem cells does not require regulatory oversight.

    Exploitation and possible harm

    This is a complex matter, particularly since the cells are often processed in one form or another before being re-administered to the patients, which would qualify them as being “minimally-manipulated”. While there is no specific legislation governing this matter in South Africa, international best practice requires regulatory oversight with the use of such a product. To conclude, evidence-based and ethical reporting and marketing are necessary if patients are to benefit from the great strides being made in the stem cell field.

    Not to do so exposes vulnerable people to exploitation and possible harm. It is critical that the South African Government provides an appropriate regulatory framework to allow patients to benefit from advances in the stem cell field while at the same time protecting them from exploitation and harm. This will also promote much needed research, investment and entrepreneurship in the stem cell field for the benefit of all of the people of our country.


    Story by: Prof Michael Pepper for Health24

    *Michael S. Pepper MBChB (Cape Town), PhD (Geneva), MD (Geneva), PD (Geneva)Professor, Dept. Immunology, Faculty of Health Sciences, University of PretoriaDirector, Institute for Cellular and Molecular Medicine, University of PretoriaDirector, SAMRC Extramural Unit for Stem Cell Research and Therapy

  • UCT, ACGT, SU and DIPLOMICS host the Trans-Proteomic Pipeline (TPP) Workshop

    14th May 2019

    The University of Cape Town, in partnership with the ACGT, DIPLOMICS and Stellenbosch University, hosted the Trans-Proteomic Pipeline (TPP) workshop which ran from the 21sttill the 22ndof March 2019.

    The workshop, which followed the HUPO-PSI meeting, held from the 18thtill the 20thof March 2019, was facilitated by Dr Eric Deutsch and Mr Luis Mendoza from the Institute of Systems Biology (Seattle-USA). Dr Deutsch is a lead designer for the Systems Biology Experimental Management System. He is the Chair of the HUPO-PSI and is one of the leaders of the TPP project- that aims to provide a free and open-source suite of tools for the processing and analysis of proteomic tandem mass spectrometry data.

    Mr Mendoza is a senior software engineer at the Institute for Systems Biology. He has been a main contributor to the development of the TPP for the past 14 years.

    The two-day workshop was attended by 35 delegates from Universities in the Western Cape region (University of Cape Town, Stellenbosch University, University of the Western Cape and Cape Peninsula University of Technology) as well as delegates from other provinces (Gauteng and KZN).

    The ACGT partnership was represented by four delegates at the workshop. The ACGT representatives hailed from the Council for Scientific and Industrial Research (Dr Previn Naiker and Dr Ireshyn Govender), the University of the Witwatersrand (Ms Genevieve Mezoh), and the University of Pretoria (Ms Denise Wilson). The delegates from the ACGT partnership are expected to transfer the knowledge gained from the TPP workshop by training their fellow unit/lab students/colleagues. A week after the workshop, Ms Denise Wilson reported that she was in the process of working with the Centre for Bioinformatics and Computational Biology (CBCB) at the University of Pretoria to install the TPP pipeline for command line execution on their Linux servers.

    The next proteomics training workshop will be in November 2019 and it will focus on the open-source software package Skyline, data analysis and SWATH. Information regarding this workshop will be disseminated at a later stage.

    Workshop programme: View here

    Story by: The ACGT team, 14 May 2019

  • ‘The next Einstein could be African’ – newly elected UP head of Next Einstein Forum’s Community of Scientists

    'The next Einstein could be African’ – newly elected UP head of Next Einstein Forum’s Community of Scientists
    16th Apr 2019

    Sanushka Naidoo, associate professor in the Department of Biochemistry, Genetics and Microbiology at the University of Pretoria (UP), was recently elected chairperson of the Next Einstein Forum’s (NEF) Community of Scientists programme. The NEF is a joint initiative of the Robert Bosch Stiftung Foundation and the African Institute for Mathematical Sciences (AIMS), which has centres in South Africa, Ghana, Senegal, Cameroon and Tanzania.

    Prof S. Naidoo

    “The next Einstein could be African,” Prof Naidoo said. “It is up to us to find and nurture such upcoming generations of Einsteins. I am looking forward to presenting our NEF Community of Scientists vision and progress at the next World Economic Forum.”

    The NEF provides opportunities for some of the brightest minds in Africa to look at the most persistent problems experienced on the continent and apply technology, engineering and mathematics as well as the social sciences to come up with possible solutions.

    “I am honoured and humbled to be elected by such accomplished young scientists,” Prof Naidoo added. “I feel inspired and motivated to lead the community of scientists one step closer to achieving our vision.”

    The KwaZulu-Natal-born professor’s vast experience in the field of plant biotechnology will stand her in good stead in her new position. She heads the Eucalyptus and Pine Pathogen Interactions group and works closely with the Forest Molecular Genetics Programme, part of the world-renowned Forestry and Agricultural Biotechnology Institute (FABI) at UP. She is also a committee member of Future Africa at the University of Pretoria.

    She has also published more than 30 papers in international peer-reviewed journals, was awarded a Y-rating by the South African National Research Foundation (2015-2020), a Mellon Foundation Mentoring scholarship for her doctoral studies in plant biotechnology, and serves as president of the South African Genetics Society (2017-2020).

    The professor’s research interests include genetics, plant biotechnology as well as cell and environmental biology, and she currently teaches molecular genetics at UP. She is the main supervisor to two postdoctoral researchers (Dr Caryn Oates and Dr Erik Visser), two PhD students (Ms Lorraine Mhoswa and Mr Demissew Teshome), one MSc student (Ms Shannon Flemington) and two honours students (Shae Swanepoel and Kgopotso Pakwako).

    Prof Naidoo first became involved with the NEF when she was awarded an NEF Fellowship (2017-2019), a programme that recognises the contribution of top young scientists and emerging leaders in Africa, and gives them the opportunity to grow their careers and present their work at the global NEF Spotlight Sessions. As part of the programme, fellows are expected to participate in national and continental policy formulation, cross-cutting research and innovation activities, lead public engagement around science and technology in Africa, and provide mentorship to early-career scientists and students.

    During her tenure at the NEF, Prof Naidoo plans to focus on breaking down some of the barriers young African scientists face, such as lack of infrastructure, collaborative networks and resources. She says it’s important for people in leadership positions to remain positive and persevere despite challenges. Over the next two years, the NEF aims to strengthen ties with the community of scientists in order to offer them a strong support network that enables them to achieve their goals. The organisation also intends to build capacity and empower African scientists so they’re able to make use of international opportunities.

    Prof Naidoo’s love affair with nature started at a young age. Her parents – both teachers – have always encouraged her to ask questions about the world around her. Her interest in plant science was piqued by a science teacher who encouraged learners to establish a nature club at school.

    “We built a pond on the school premises and we watched a whole ecosystem develop over time. This became a teaching tool for our biology classes, and we were fascinated with how organisms depend on each other for survival.”

    After matriculating, she enrolled for a degree in Cell and Environmental Biology at the University of KwaZulu-Natal (UKZN), and became interested in plant genetics. She completed her honours at UKZN before obtaining an MSc degree in plant biotechnology at the University of Stellenbosch, and her PhD at UP.

    Her current research focuses on mechanisms that can confer broad-spectrum, long-lasting resistance by dissecting gene families and responses to pests and pathogens. With the development of new technologies, novel genetically modified crops are poised to increase yield and protect against pests and pathogens under harsh African climates.

    When she’s not among the trees or in the lab, she loves spending time with her husband Tyrrell, her three children Tristan (15), Sunera (8) and Telana (7), and Dakota Rouge, whom she describes as “a beautiful King Charles Cavalier spaniel”. She also enjoys writing poetry and reading motivational books on leadership.

    About 40% of the NEF fellows are women, and Prof Naidoo is quick to remind anyone that women have been integral to important scientific discoveries over the ages.

    “I think of physicist Marie Curie, cytogeneticist Barbara McClintock and biochemist Jennifer Doudna as exemplars of women who have made impactful scientific breakthroughs. There are other types of contributions by women scientists that deserve attention too, such as Kenyan scientist Wangari Muta Maathai, who was the first African woman to win a Nobel Peace Prize for her efforts to combat deforestation. I believe that women will continue to break through glass ceilings and shape the future because of their passion and commitment to changing lives for the better.”


    Story by: ©University of Pretoria, News. April 12, 2019

  • ACGT’s Liaison Scientist Attends a Multi-Stakeholder Partnership Facilitation Course in the Netherlands

    29th Jan 2019

    Wageningen University and Research (WUR) is a higher institute of learning based in the Netherlands that specialises in the areas of food and food production, living environment, and health, lifestyle and livelihood. WUR opens its doors to the international community and offers short courses in the areas that the institution specialises in. One such course came to ACGT’s attention as it related closely to what the ACGT as an organization is mandated to achieve and the projects that the ACGT is involved in.

    The institution offers a short course (three weeks) called “Facilitating Multi-Stakeholder Partnerships to Foster Sustainable Food Systems”. This course was deemed quite applicable for ACGT staff as the Centre is itself a multiple stakeholder partnership mandated to build capacity in the area of advanced biotechnology for five institutions (three universities and two science councils).

    The ACGT found it necessary to send one of its staff members, Mr Thabo Khoza – Liaison Scientist at ACGT, to the Netherlands to attend this three-week course in order to enable ACGT staff to be better multi-stakeholder facilitators. The course ran from the 22nd of October 2018 till the 9th of November 2018.

    The course took the participants on a journey of (1) establishing what sort of a multiple stakeholder partnerships (MSPs) are required for different projects and needs, (2) who to involve in such MSPs, (3) how to design the required MSP, and (4) how to facilitate the MSP to yield desired outcomes. While all four mentioned steps are crucial in ending up with an MSP that works, step 4 would require the most effort and resources from the MSP facilitator. This effort is especially highlighted when dealing with different stakeholders who have different interests and varying levels of influence. The course gave the participants a number of tools to use in the facilitation process to make sure that the MSP is a success. Each tool would be chosen based on the stakeholders involved as well as on the type of MSP that has been created.

    The course had theory and practical components to it. The participants were divided into groups at the beginning of the course and they were tasked to come up with a problem (project) that would require an intervention of an MSP. Throughout the course, the participants would then have to apply what they were learning in their project. At different levels of formulating their MSPs, the participants would give presentations on how they applied what they have learned during their projects.

    The participants were also given a real life problem to design an MSP on. This scenario took the participants to Friesland where they had to design a pathway of creating a cooperative that would address the biodiversity problems that are faced in the Friesland region. The participants had to interview farmers, government officials, business owners, nature reserve experts, activists and civil society. The participants then, based on the interviews and what they had been learning at Wageningen, created a roadmap for establishing this cooperative. This roadmap was presented to the community of Friesland where all the stakeholders were invited. The presentation took about two hours with Mr Khoza being the master of ceremonies, together with a fellow participant from Indonesia. The MSP design suggested by the course participants was well received with the project lead promising to use the suggested roadmap.

    The course came to an end with participants giving presentations based on their individual MSP that they want to set up when returning to their home countries. The course facilitators as well as the course participants gave suggestions at the end of each presentation.

    The course was also a great platform for networking as it was attended by individuals from 14 different countries representing different sectors and expertise such as government and policy makers, scientists and NGOs. The participants have an active network and are actively looking for opportunities for collaboration.

    The ACGT hopes that Mr Khoza will put into practice the knowledge he acquired at Wageningen University and Research especially in creating new initiatives for the ACGT community, such as the Proteomics Society for South Africa.

    Story by: ACGT Team, January 2018

  • Plant-Pathogen Systems Under The Spotlight At Regional Forum

    20th Dec 2018

    The second Regional Plant Biotechnology Forum for 2018, co-hosted by the ACGT and the University of Johannesburg, centered around plant-pathogen interactions; a particular area of interest for numerous researchers in the partnership and beyond. As is appropriate in the “-omics” and systems biology era, the theme for the forum was “Advances in Plant Defense Responses: Towards Plant-Pathogen System Perspectives”. The topic was deliberately chosen to provide a platform for those who aim to unravel such responses from a wider systems perspective.

    The wide variety of presentations, most with a focus on genome-wide approaches to deciphering plant defence systems, managed to attract in excess of 60 delegates from a range of universities, science councils (the majority being from ACGT partner institutions) as well as funders. The keynote speaker for the event was Dr Naadirah Moola, a researcher associated with both the University of Cape Town and the University of Ghent, Belgium. The title of her address was “A cereal killer’s killer: chitosan and plant defence”. Her address was followed by ten additional presentations, mostly from researchers associated with the Universities of Johannesburg and Pretoria. The presentations included studies utilizing technologies including transcriptomics, proteomics, multi-platform metabolomics, as well as combinations of the above. In addition, classical biochemical approaches were also utilised in addressing the research questions at hand.

    The forum provided an excellent networking opportunity for researchers active in this field and exposed them to different approaches to elucidating plant-pathogen interactions in different systems.

    The ACGT would like to sincerely thank the organizing team at ACGT (Thabo Khoza, Molati Nonyane and Itseng Malao), as well as UJ (Dr Farhahna Allie, Dr Ian Dubery and Dr Fidele Tugizimana).

    For any queries about future Plant Biotechnology fora or suggestions for topics related to forums or workshops in this field, kindly contact Mr Thabo Khoza, ACGT Liaison Scientist, az.ca1569080615.pu@a1569080615zohk.1569080615obaht1569080615.


  • UP receives boost in NRF ratings

    UP receives boost in NRF ratings
    18th Dec 2018

    Two University of Pretoria (UP) academics have received prestigious A1 ratings by the National Research Foundation (NRF) for 2018, bringing the number of UP scientists rated in the A category to 14.

    Prof. Don Cowan, Director of the Centre for Microbial Ecology and Genomics, has received an A1 rating, up from his previous A2 rating, while Prof. Mike Wingfield, founding director of UP’s Forestry And Biotechnology Institute (FABI), had his A1 rating renewed.

    An NRF rating is a measure of the quality of a researcher, based on peer reviews of their publication performance and impact, including international recognition. A researcher in the A-rated category is recognised by all reviewers as a leading scholar in his/her field internationally for the high quality and wide impact – beyond a narrow field of specialisation  – of his/her recent research outputs.

    Prof. Cowan established the Centre for Microbial Ecology and Genomics in 2013. The Centre works on various aspects of soil microbial ecology, with a particular focus on hot and cold desert ecosystems. The team uses the latest metagenomic and bioinformatics methods to investigate the structure, function, adaptation and resilience of soil microbial communities, to further understanding of their roles in soil health, plant productivity and the provision of genetic resources. “I am absolutely delighted with the NRF rating result,” Prof. Cowan says. “One of the wonderful elements of academia is that it is possible to be rewarded for working on something about which one is passionate. But this is not a solo effort: I must also gratefully acknowledge and sincerely thank all those who have played their part, whether big or small, in this wonderful result: my research collaborators, my postdocs and students, my friends and my colleagues, and my wife.”

    Prof. Wingfield’s research interests are focused on the broad area of forest health, particularly those caused by insect pests and pathogens of trees, and their patterns of global movement. Together with his colleagues and collaborators, the research team applies a wide range of biotechnology tools in order to better understand the biology and epidemiology of tree pests, and reduce the dramatic impact they are having globally. Asked about once again receiving an A1 NRF rating, Prof. Wingfield said, “This award belongs as much to me as it does to the amazing FABI team, including a wonderful group of colleagues, students and collaborators globally. I hope they will enjoy the fruits of the award with me and, more importantly, continue to have fun doing impactful research in the interests of forests and forestry globally.”

    Meanwhile, Dr Eshchar Mizrachi, a senior lecturer at FABI, is one of four scientists in South Africa to be awarded a highly prestigious P rating for research on understanding the molecular biology of polysaccharide metabolism, especially cellulose and xylan, during wood formation in Eucalyptus trees. This rating is assigned to researchers normally under 35 years of age who have held a doctorate or equivalent qualification for less than five years at the time of application. His research primarily focuses on constructing a model of the regulatory network (genes, proteins and pathways) that play a role in influencing the partitioning of carbon and the deposition of cellulose and xylan in wood, and identifying candidate pathways or processes for biotechnological improvement of trees (applied via breeding using molecular selection tools, or genetic modification).

    Prof. Slippers, Director of FABI, said, “These recent ratings show that we do not only compete locally in terms of excellence, but also with the best in the world. It is exciting to have both established world leaders and upcoming young and leading scientists in FABI. That is good for the future of the institute and University, and shows that we have a vibrant academic environment.”

    All three scientists are academically linked to the Department of Biochemistry, Genetics and Microbiology. Head of Department Prof. Paulette Bloomer said, “It is a true privilege to be the academic home of these world-leading scientists, to share their passion for discovering the fundamental basis of biology, and to do research that is locally and internationally relevant.”

    In addition to these A and P ratings, so far in the current round of awards and renewals of NRF ratings, UP academics have received a total of no less than 30 new ratings, and 49  renewed ratings, of which 2 are A ratings, 20 are in the B category, with 43 C and 9 Y ratings. The University of Pretoria now hosts 507 rated researchers, representing about 12% of the total number of rated researchers in South Africa.

    Prof. Stephanie Burton, UP Vice-Principal for Research and Postgraduate Education, said the University is proud of the achievements of all these academic colleagues. “We are one of the biggest producers of university research in the country and Africa, and we produce research that is relevant and which matters.”

    NRF A1 rated UP academics Prof Don Cowan (left) and Prof Mike Wingfield

    Story by: Buyisiwe Nkonyane, University of Pretoria

  • ACGT life scientists trained in Linux use for data analysis

    ACGT life scientists trained in Linux use for data analysis
    9th Oct 2018

    The Centre for Bioinformatics and Computational Biology

    Capacity building is one of the objectives of the African Centre for Gene Technologies (ACGT) as a means to improve the skills level of South African scientists, especially in the field of bioinformatics data analysis. For African scientists to continue to produce quality work that is internationally recognized and competitive, there has to be continuous efforts to equip the scientists with the most relevant and applicable skills available. Advancements in sequencing platforms and the amount of data generated require specialized skills and programs that generally require some knowledge of command-line. Linux is one such useful alternative operating system for data analysis and visualization. For this reason, the ACGT organized a Linux course to benefit life scientists and introduce them to basic Linux concepts. The Linux course ran from the 25th to 28th September 2018 at the University of Pretoria, Hatfield campus at the Centre for Bioinformatics and Computational Biology (CBCB).


    The course was facilitated by Mr Shaheem Sadien from the Cisco Networking Academy from Cape Town. Mr Sadien is a renowned lecturer and skilled technician with a wealth of over 12 years of experience and knowledge on networking, operating systems and applications. The lectures were kept as relaxed as possible with open discussions and computer-based practical sessions. The topics outlined below were covered during the course:

    The ACGT and capacity building
    • The shell,
    • the file system,
    • files and directories,
    • permissions,
    • finding files,
    • basic system commands,
    • redirection with command and file pipes,
    • basic grep, sed and awk,
    • processes,
    • environment variables, and
    • basic shell scripts.

    The sessions were kept as interactive as possible to create a relaxed environment where the participants could ask questions and get the most out of the four days. The 25 delegates were from different research backgrounds and hailed mostly from the ACGT partner institutions; the Universities of Pretoria and the Witwatersrand, the Agricultural Research Council and Council for Scientific and Industrial Research.

    The Delegates during the interactive sessions

    Following conclusion of the workshop, there has been very positive feedback from the participants of the course. There was a general sense from the course evaluations that the course was informative, practical and interesting. Moving forward, there are plans to adjust some aspects of the course such as content and more bioinformatics-specific approaches. Keep an eye on the ACGT website and e-mail alerts for news of future iterations of the Linux workshop.

    The ACGT and all of its partners would like to extend enormous gratitude to Mr Shaheem Sadien and Professor Fourie Joubert for running the course smoothly and successfully. The ACGT would also like to thank all the behind-the-scenes people that had a hand in putting this course together: Itseng Malao, Johann Swart and Vaughan Beckerling. The ACGT wishes all the participants good luck with their future work. Due to limited space, not all of the applicant could be hosted but the ACGT encourages those that were not placed this year to keep an eye out for future courses.

    For any other capacity building and networking queries, kindly contact Mr Molati Nonyane, ACGT Liaison Scientist (az.ca1569080615.pu@e1569080615nayno1569080615n.ita1569080615lom1569080615, 012 420 6139).


  • ACGT and Wits host national week of proteomics activities

    ACGT and Wits host national week of proteomics activities
    13th Sep 2018

    The proteomics community of South African came together for a week of proteomics events in the month of August 2018. In this week, two events organised by the ACGT, CSIR, DILPOMICS and the Universities of Cape Town and the Witwatersrand took place. The Advanced Proteomics Workshop was facilitated between the 20th and 22nd of August 2018; which was followed by the South African Proteomics Symposium a day later. Both these events were hosted at the Wits Parktown Health Sciences Campus.

    The proteomics week kicked off with the Advanced Proteomics Workshop, which was facilitated by three world experts in the field. Each facilitator gave a series of lectures and hands-on exercises in the field which were highly respected for. In the three days dedicated to the workshop, the delegates were taught different aspect of Spatial Proteomics, Clinical Proteomics and Quality Control.  The workshop began with Prof Kathryn Lilley (Research Group Head and Director, Cambridge Centre for Proteomics, University of Cambridge) taking the delegates through a series of lectures on Quantitative Proteomics and Spatial Proteomics. Included in Prof Lilley’s sessions were tutorials on Experimental Design, which enabled the delegates work on different scenarios to design effective experiments. These tutorials allowed the delegates to think outside the box and helped them think through their own experiments and how they would design them in the future.
    Prof Stephen Pennington, a professor of Proteomics and Senior Fellow at the Conway Institute of Biomolecular and Biomedical Research at the University of College Dublin, took over from Prof Lilley and facilitated the Clinical Proteomics section of the workshop.
    The last section of the workshop, Quality Control, was presented by Prof David Tabb. David Tabb is a Professor in the Division of Molecular Biology and Human Genetics at the Faculty of Medicine and Health Science at Stellenbosch University. Prof Tabb combined his lectures with tutorials and assisted the delegates to work with real proteomics data.

    The workshop was attended by delegates from the following national institutions:

    African Health Research Institute
    Cape Peninsula University of Technology
    Centre for Proteomic and Genomic Research
    Council for Scientific and Industrial Research
    Fort Hare University
    The National Health Laboratory Services
    The National Institute for Communicable Diseases
    Rhodes University
    Stellenbosch University
    University of Cape Town
    University of Johannesburg
    University of Pretoria
    University of the Western Cape
    University of the Witwatersrand


    The second part of the proteomics week saw seventy-two delegates gather at the Adler Museum of Medicine (Wits Parktown Health Sciences Campus) to attend the South African Proteomics Symposium.

    The symposium was opened by Dr John Becker (ACGT – Centre manager) and Prof Michele Ramsay (Champion: Molecular Biosciences Research Thrust, University of the Witwatersrand). Prof Kathryn Lilley and Prof Stephen Pennington each gave a keynote address followed by presentations from top proteomics researchers in South Africa. These South African researchers represented the following institutions: African Health Research Institute, CSIR, CPGR, Fort Hare University, North West University, Stellenbosch University, University of Cape Town, University of the Western Cape as well as the University of the Witwatersrand. The following event sponsors also gave talks at the symposium: Microsep, Anatech Instruments and Separations. Click here to view the symposium booklet that contains the full programme as well poster abstracts for posters that were displayed at the symposium.

    Both the workshop and symposium gave the delegates the platform to interact with world class proteomics researchers and to explore opportunities (postdoctoral fellowships, collaborative opportunities, etc.) that may arise from the proteomics week. This week also provided the delegates with a platform to network with each other for possible future collaborative opportunities- as well as to informally have discussions around the formation of a Proteomics Society of South Africa.  The ACGT has made itself available to assist in the establishment of this society. This process will be guided by the proteomics community of South Africa that the society will serve.

    The ACGT would like to thank the following sponsors for financial assistance to make the workshop and symposium possible: Anatech, CPGR, DIPLOMICS, inqaba biotec, Microsep, Separations and The Scientific Group.


    Story by: The ACGT team, September 2018

    For more photos from these events, please visit our Facebook page: ACGT Facebook page

    Poster session
    Symposium booklet
    Workshop group session
    Workshop facilitators
    (from left: Prof D. Tabb, Prof K. Lilley and Prof S. Pennington)
    Symposium delegates
















    Prof Michele Ramsay
  • New draft White Paper on Science, Technology and Innovation

    New draft White Paper on Science, Technology and Innovation
    10th Sep 2018

    Science, technology and innovation enabling sustainable and inclusive development in a changing world

    Twenty years after the adoption of the first White Paper on Science and Technology (DST) in 1996, the Department of Science and Technology began developing a new draft White Paper on Science, Technology and Innovation (STI), which was approved by Cabinet last week. The new document will ensure a growing role for STI in building a more prosperous and inclusive society.  It focuses on using STI to accelerate inclusive economic growth, make the economy more competitive and improve people’s everyday lives.

    The review of the 1996 White Paper, which included broad consultation within the national system of innovation, showed that, while there has been good progress in the implementation of this document, South Africa has not yet fully benefited from the potential of STI to advance the objectives of the National Development Plan.  The STI institutional landscape is a case in point.  It has been expanded and there has been a threefold increase in publications, significant growth in the participation of black people and women in the research and development workforce, and a rise in doctoral graduation rates.  However, challenges remain, and the national system of innovation is still not fully inclusive.

    Since the adoption of the 1996 White Paper, the world has changed. The Fourth Industrial Revolution, which is rapidly transforming the way people interact, transact and learn is already well advanced in the developing world.  To enable South Africa’s effective participation in this new world order, which is bringing increasing automation and digitisation, the Department of Science and Technology has developed a new policy document.

    The new draft policy focuses on two main goals, namely, to ensure that South Africa benefits from STI for economic growth, social development and transformation, and to respond to the risks and opportunities brought by rapid global technological advancement and other global changes.

    With rapid change comes increasing uncertainty about the future, particularly for emerging markets like South Africa’s. The new draft White Paper has considered a number of megatrends spanning the geopolitical, economic, social, technological and environmental spheres.

    These megatrends include a growing population, increased consumption driven by an expanding middle class in emerging economies, the rise of China and India, and the impact on the natural environment.  The degree to which countries prepare for these changes will determine whether they thrive.

    Some of the megatrends are creating market opportunities. For example, the growth of a middle class in emerging economies, and the high proportion of young people in the total population in Africa – the so-called “youth bulge” – are stimulating manufacturing, widening markets for mobile telephones and creating job opportunities for ICT-enabled young entrepreneurs in the services sector.  South Africa can benefit from these opportunities by using technology to modernise sectors such as agriculture and mining and increase exports to growing markets.  Innovation is required to address needs arising from these megatrends, such as protecting the environment and improving service delivery.

    Rapid technological change is driving some of these megatrends to shape a world that will soon look very different.  The lines between physical, digital and biological systems are becoming blurred, and governments around the world are planning for the impact of the Fourth Industrial Revolution.  In particular, it is necessary to prepare for the ways in which artificial intelligence and advances in ICT will change the way society and the economy function.

    Already, traditional jobs are being lost due to automation and traditional commerce is being disrupted by the move to online, just-in-time personalised services and products. The role of cryptocurrencies in the digital economy is uncertain.  The possibilities are exciting and the implications vast.

    STI lies at the heart of the preparation for this emerging future, and South Africa therefore needs to build on progress in areas such as biotechnology, nanotechnology, advanced manufacturing, and ICT research and innovation. This White Paper proposes policy interventions to accelerate skills development, leverage ICT, commit to openness, and support inter- and transdisciplinary research.  It also puts in place mechanisms to institutionalise foresight capacity to assist collaborative planning across government for STI.

    Overview of the new draft White Paper

    The new draft White Paper focuses on the following:

    • Raising the profile of STI in South Africa by instilling an innovation culture in South African society and integrating STI into cross-cutting government planning at the highest levels.
    • Strengthening partnerships between business, government, academia and civil society, creating a more enabling environment for STI.
    • Focusing on innovation for social benefit and for fundamental economic transformation.
    • Expanding and transforming the human resource base of the national system of innovation.
    • Increasing investment, both public and private, in STI.

    Raising the profile of STI in South Africa

    • South Africa needs to set its innovation agenda at the highest level of government and business so that all actors pursue the same objectives and pool resources where possible.  The Presidency will therefore chair an STI Plenary meeting, involving business leaders, academic experts in the field of STI, government departments that have a focus on STI, and leaders from civil society.  Among other matters, the STI Plenary will discuss STI priorities.
    • To ensure that STI is integrated into the planning of relevant government departments and that the STI programmes have sufficient funding, an Interministerial Committee on STI, chaired by the Minister of Science and Technology, will be formed.
    • To provide the necessary data on and analysis of STI progress and enablers, the National Advisory Council on Innovation will be strengthened.

    Strengthening partnerships among business, government, academia and civil society

    While government has an important role to play in enabling and stimulating STI, it cannot do it alone.

    The White Paper therefore has a strong focus on including business in STI planning (at the level of the STI Plenary, but also at the level of, for example, the mining or agricultural sector level) and on support measures for business, for instance, by means of incentives for small and medium enterprises and the direct funding of research and development through Sector Innovation Funds.

    • The White Paper also draws civil society formally into STI planning and aims to empower civil society to distribute the benefits of technology to communities, as well as to help identify and support grassroots innovators.

    Creating a more enabling environment for STI

    • All government departments working in areas that affect STI will embrace a national innovation compact to ensure that there is policy coherence across the national innovation system, and that immigration, education, trade, competition and procurement policies, to name a few, support innovation.
    • The various incentives offered by government for STI will be aligned to ensure synergy rather than duplication in using the available funding, and their administration will be improved to ensure effectiveness.
    • Government procurement will support locally developed technologies.
    • Local innovation systems will be stimulated by, for example, walk-in innovation centres for communities and more incubators, and encouraging the involvement of local universities.
    • Measures to create greater access to STI information such as solutions developed at universities will be created through an open science approach.

    Focusing on innovation for social benefit and for fundamental economic transformation

    • Civil society will be involved in high-level government planning for STI programmes and will be supported through training, funding and networks to play a stronger role.
    • Support for grassroots and social innovation, when linked to provincial and local development strategies, will have significant transformative results.
    • The intellectual property regime for publicly funded research and development (R&D) will be reviewed to expand South Africa’s patenting.  Intellectual property generated from publicly funded R&D will be used to help increase black and female ownership of new technology-based companies.
    • Government itself will become more innovative in using digital information and innovative technologies for service delivery.  This will involve accelerated digitisation, establishing innovation units in STI-intensive departments, and increasing the movement of human resources between government, science councils and business, among other things.

    Expanding and transforming the science and human resource base of the national system of innovation

    • A policy nexus will be developed to achieve collaboration, increased funding, and policy coherence to improve educational outcomes from early childhood and school level (to increase the number of Grade 12 university exemption passes with Science and Mathematics – the pipeline) and higher education (to further increase the number of PhDs produced, and improve the representation of blacks and women).
    • Internships and training opportunities abroad are to be expanded.
    • The untapped potential of historically disadvantaged universities and universities of technology will be used.
    • There will be increased support for research, both basic and transdisciplinary.

    Increasing investment, both public and private, in STI

    South Africa’s gross expenditure on research and development as a percentage of GDP, which is currently about 0,76%, needs to be increased to 1,5% over the next decade.  This will be done through improved incentives for business R&D, contributions to public STI by provincial governments, and expanding measures to attract foreign funding for South African STI.

    An annual STI investment framework, linked to the national STI agenda, will be developed to direct the allocation of public funding to priority STI programmes.

    Implementing the White Paper

    The White Paper sets the high-level, long-term policy direction for the next five to 15 years.  It will be implemented through regularly updated decadal plans, which will be based on performance evaluation and foresight, as well as collaborative planning with relevant business sectors and government departments.  The decadal plans will detail the deliverables, partnerships and funding required, as well as the indicators that will be used to measure progress.  To this end, the National Advisory Council on Innovation is currently undertaking a foresight exercise for South Africa.

    The truest test of this White Paper will be the impact that it has in realising the potential of STI to support the achievement of the National Development Plan and to help change the reality of South African’s lives over time.

    The next steps

    This is a draft White Paper released for public consultation.  Members of the public have 30 days to make inputs.  After the comments have been integrated, we intend to have a summit on 9 November 2018 to engage various stakeholders on the White Paper before taking the final document to Cabinet for approval.

    For the full document visit

    For more information

    Veronica Mohapeloa (083 400 5730)

    Thabang Setlhare (072 659 9690)

    Media enquiries

    Hlengiwe Nhlabathi

    Media Liaison Officer

    Ministry of Science and Technology

    064 754 8426 

    Story by: Department of Science and Technology, September 2018