5th Oct 2021
Four highly promising emerging plant biotechnology researchers attracted a large audience to a webinar aimed at spotlighting the next generation of researchers in the field in South Africa. The event drew 94 registrants, indicative of the quality of research on display by the emerging PhD graduates.
The webinar had diverse representation from all the ACGT partner research institutions. The presentations from the University partners (Johannesburg, Pretoria, and the Witwatersrand) centered around plant pathogens and how to curb their impact on economically important food crops, including viral, bacterial and fungal pathogens. The CSIR presented work on an engineered Agrobacterium repurposed to produce potent HIV antibodies in a tobacco production system.
The webinar was led by Professor Chrissie Rey, a highly experienced viral researcher focusing on the African subsistence crop Cassava. Professor Rey and other partner researchers instilled the discussions with decades of research experience and constructive suggestions.
The closing session focused on diversity in research and how the pandemic has affected the ability of scientists to network and gain viewpoints from different stakeholders. The speakers and audience agreed that a lot of collaborative opportunities existed in the South African biotechnology environment for further impact through combined critical mass. The ACGT will continue to find the synergies to move the research further along the development pipeline.
Meet our speakers on the day:
Dr Bulelani Sizani – (University of the Witwatersrand) – a post-doctoral research fellow at the department of Molecular and Cell Biology of the University of the Witwatersrand. In 2019, he completed his PhD at the University of Antwerp in plant systems Biology. His work focuses on the identification of disease resistance genes in cassava such as NLR encoding proteins. These genotypes can be selected by farmers and be used in breeding techniques for better improvement of cassava crops against CMD.
Title: Structural and functional characterization of NLRs proteins differentially expressed in Cassava plant inoculated with SACMV
Dr Dylan Zeiss (University of Johannesburg) – a post-doctoral research fellow at the University of Johannesburg. He then enrolled for an MSc in Biochemistry that was upgraded to a Doctoral degree in 2019. He graduated in 2020. His research focuses on plant-microbe interactions and how this knowledge may have applications within the South African agricultural sector for sustainable food production. Has used a metabolomics-based approach using liquid chromatography coupled to mass spectrometry (LC-MS) in combination with statistical modelling to monitor specialized plant metabolism in response to R. solanacearum infection.
Title: Metabolomic insights into the deployment of phytochemical defences in the tomato – Ralstonia solanacearum pathosystem
Dr David L. Nsibo (University of Pretoria)- currently a Lecturer at the Department of Plant and Soil Sciences of the University of Pretoria. In 2019, he completed his PhD in Plant Science at the Department of Plant and Soil Sciences, University of Pretoria and graduated in April 2020. His research is aimed at determining the extent and patterns of genetic variation in populations of foliar pathogens of cereals and to understand how these pathogens cause disease using an array of innovative molecular- and genomics-based tools.
Title: Population genetics of foliar pathogens of maize and the future of food and agriculture
Dr Advaita Singh (Council for Scientific and Industrial Research) – a researcher in the Biomanufacturing Technology Demonstration Group at the Council for Scientific and Industrial Research (CSIR), the largest R&D institution in Africa. He has qualifications from the University of the Witwatersrand and the University of Pretoria, having qualified as a protein biochemist. His expertise lies in the development of recombinant processes to produce biopharmaceuticals in various expression systems. Dr Singh forms part of a group which prioritizes supporting industry and other partners in the translation of technologies towards commercialization and impact.
Title: Plant-based production of highly potent anti-HIV antibodies with engineered posttranslational modifications.
The ACGT would like to thank you for all your suggestions on future webinars. Below are a few of the topics we hope to explore in the future as per your suggestions:
- Genome editing
- Drug discovery from Herbal Medicines
- Trends in analytical methods of medicinal plants
- Fermentation technology
- Systems biology in plant sciences
We look forward to hosting you on the next Plant Biotechnology Forum.
13th Sep 2021
Microbiomics research can be leveraged to develop innovative solutions towards food systems research and development. International domain experts recently convened to deliberate the opportunities and blind spots in the soil-plant-food-human gut microbiomics nexus. The event was inclusive of domain experts in each of the areas in the food system, from production to consumption. Countries and institutions represented were South Africa (University of Pretoria, University of Stellenbosch and CapeBio Technologies), Austria (Graz University of Technology), Netherlands (Wageningen University and Research), Germany (Julius Kühn Institut and the Helmholtz German Research Center for Environmental Health), as well as the USA (University of Pittsburgh).
The workshop was chaired by Professor Lise Korsten, Co-Director of the DSI-NRF Centre of Excellence in Food Security. The workshop’s main aims were:
- to formally introduce this group of AgriMicrobiomics scientists from all over the globe to each other to encourage the creation of an AgriMicrobiome network
- to create a specialist group to collaborate on AgriMicrobiome research
- identify areas of collaboration amongst group members
- to seek and secure financial support for collaborative endeavours.
The trans-disciplinary and complementary approach of the speakers allowed for the identification of multiple opportunities to explore the role of microbes along the whole food system. The diversity of technical approaches and expertise housed at the various institutions were clearly indicative of the collective strength of the group, who indicated goodwill and a strong willingness to collaborate on the interdependent issues the One Health concept is facing. Several possible multi-institutional projects were identified, and progress is already underway to conceptualize and submit programmes for financial support.
The future focus of the group will be on the soil/water/commercial and indigenous crops/human gut interdependencies, following a One Health approach. The proposed work under discussion was relevant to multiple Sustainable Development Goals; including SDG1 (No Poverty), SDG 2 (Zero Hunger), SDG 4 (Quality Education), SDG 6 (Clean water and sanitation) as well as SDG 12 (Responsible Consumption and Production).
The African Centre for Gene Technologies and the DSI/NRF Centre of Excellence in Food Security would like to thank the following speakers for their time and highly constructive inputs during the event:
- Professor Lise Korsten, University of Pretoria
- Professor Don Cowan, Centre for Microbial Ecology and Genomics, University of Pretoria
- Professor Gabriele Berg, Graz University of Technology
- Professor Leo van Overbeek, Wageningen University and Research
- Professor Kornelia Smalla, Julius Kühn Institut
- Professor Michael Schloter, Helmholz Center Munich
- Stephen O’Keefe, African Microbiome Institute, University of Stellenbosch and University of Pittsburgh
- Dr Mubanga Kabwe, CapeBio Technologies
- Dr Jarishma Gokul, Department Plant and Soil Sciences, University of Pretoria.
The Organising Committee:
Prof Lise Korsten
Dr Jarishma Gokul
Mr Molati Nonyane
Dr John Becker
8th Mar 2021
In February 2021, the African Centre for Gene Technologies (ACGT) and INSERM Toulouse (France) organized a virtual Lipidomics workshop. Lipidomics is a newly emerged discipline that studies cellular lipids on a large scale, based on analytical chemistry principles and technological tools, particularly mass spectrometry.
Following from rapid advances in genomics, transcriptomics and proteomics, Lipidomics similarly seeks to elucidate the role of fats and lipids, especially in the context of a range of human diseases, at a high coverage and throughput rate. Due to the range of fatty acid length, conjugation and saturation status, it has been challenging to study all lipids in a single experiment. The event outlined different approaches to analysing different classes of lipids in targeted and untargeted approaches.
The workshop consisted of online lectures, a seminar and interactive discussions. The event was intended to ignite a deeper interest in Lipidomics and add more interesting research avenues to those who are already working on Lipidomics and related disciplines. The workshop covered topics that included: Introduction to Lipidomics, how Lipidomics converges with and complements other “-omics” technologies, analytical flow in global and targeted quantitative Lipidomics, as well as applications of Lipidomics. The latter had a specific focus on inflammation; as highlighted in a research case study, with high development potential, in treating inflammation.
The seminar highlighted that lipids play many essential roles in cellular functions, including cellular barriers, membrane matrices, signalling, and energy depots. As a result, the ACGT is reassured that Lipidomics is a fast-growing field not only in the world, but also in South Africa. The participants of the workshop were from various research institutions spread across South Africa and also included a few delegates from the rest of Africa. Potential international and local collaborative efforts were also evaluated. Plans are being put into place to have similar workshops in future and complementary Lipidomics-related capacity building efforts.
The ACGT would like to thank the INSERM Toulouse team of Dr Justine Bertrand-Michel, Dr Pauline Le Faouder and Dr Cénac Nicolas for facilitating this event. The ACGT and the 35 participants of the workshop thank the delegates for generously donating their time in preparing and in facilitating the talks.
For further information about developments in this field, contact Mr Molati Nonyane, ACGT Liaison Scientist, and visit the MSA website.
26th Oct 2020
The African Centre for Gene Technologies (ACGT) and Metabolomics South Africa (MSA) hosted another successful metabolomics webinar on the 14th of October 2020. This Metabolomics webinar series serves as a platform for discussions on key technologies, techniques or new data analyses that could be of relevance to the rest of the South African metabolomics community.
Professor Justin J.J. van der Hooft, an Assistant Professor at Wageningen University, facilitated a webinar on the challenges of metabolite annotation and identification in untargeted metabolomics experiments of complex mixtures, typically encountered in natural products and food research. Untargeted metabolomics approaches are now widely used, spanning various disciplines including natural products discovery and “foodomics”. This webinar focused on how recently developed tools inspired by natural language processing, facilitate metabolomics analyses.
Prof van der Hooft is currently developing computational metabolomics methodologies to decompose complex metabolite mixtures aided by natural language processing and genomic tools. His interests are in plant- and microbiome-associated metabolites and the food metabolome as prime examples; where expanded knowledge on the specialized metabolome will assist in understanding key metabolic drivers of growth and health.
Similar to previous events, this webinar proved very popular to a diverse audience. It was attended by 102 participants from across South Africa, as well as from some international research institutions. There was a great Q&A session that followed and this highlighted the need for more of these sorts of meetings. The resources for those who wish to enter the field or perform a specific metabolomics application was also highlighted.The ACGT and MSA wishes to thank Prof van der Hooft for his superb webinar and look forward to collaborative opportunities in the field.
For a recording of this webinar, or for more information and suggestions about potential advanced biotechnology-related events, please contact Mr Molati Nonyane at .
16th Jul 2020
The African Centre for Gene Technologies (ACGT) and Metabolomics South Africa (MSA) are always looking for ways to create more Metabolomics platforms for discussions and training. One such initiative was to start up a Metabolomics Webinar Series that will run throughout 2020. The idea is to have a webinar hosted by a local expert once a month or so to discuss a key technique or new data that could be of relevance to the rest of the South African metabolomics community.
The first webinar of the series was hosted by Dr Shayne Mason on the 9th July 2020 at 14:00. Dr Shayne Mason is from the Laboratory for Infectious Diseases in Human Metabolomics at the North-West University (NWU) Potchefstroom campus. Dr Mason is a research leader at NWU specializing in TB meningitis and biofluid analysis. Dr Mason completed not one, but two BSc degrees; one in Biochemistry and Microbiology and the other in Statistics and Applied Mathematics. He completed his PhD in 2016 as a joint degree between NWU and VU in Amsterdam in the field of nuclear magnetic resonance (NMR) metabolomics. Dr Mason has published over 20 publications in the field and assisted and/or supervised numerous postgraduate students.
Then idea for this webinar was birthed from a question. One of the issues that stood out at a previous ACGT/MSA workshop was “how does one interpret the NMR spectra to determine the metabolites?” This webinar is aimed at answering that question and more.
And Answer it did.
The webinar addressed one of the major challenges in metabolomics which is the identification of metabolites in a highly complex mixture of compounds that produce a forest of peaks in a NMR spectrum. Dr Mason gave a practical stepwise guide description of how to perform 1H-NMR metabolite profiling on multiple complex biological samples. This metabolite identification process, called metabolite profiling, involves fitting the mixture spectrum to a set of individual pure reference spectra obtained from known pure compounds. The fitting process yields not only the identity of the metabolites, but also the accurate concentration of those metabolites. The participants were given a path to successful metabolite profiling that would provide them with a table of metabolite names and their absolute or relative concentrations.
This webinar was attended by 128 participants from all over South Africa. There was a great Q&A session that followed and this highlighted the need for more of these sorts of meetings. Please look out for future communication about the next webinar and other ACGT events.
8th Jun 2020
The African Centre for Gene Technologies (ACGT) together with the University of Pretoria’s Centre for Bioinformatics and Computational Biology (CBCB) and the CISCO Networking Academy, have been hosting the annual Linux for Life Scientists Workshops for three straight years now. This year’s course was facilitated fully online; a completely different format from that of previous years due to the current COVID-19 situation.
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. Researchers use open-source Linux to analyse the huge amounts of data they generate on multiple platforms. Linux is an alternative to expensive vendor-specific software that require periodic license renewals.
The workshop was facilitated by Mr Shaheem Sadien (CISCO Networking Academy) and Professor Fourie Joubert (University of Pretoria). The Linux course facilitated over five webinars spread out over 2 weeks in May 2020. The first webinar served as an introduction to Linux and the rest of the webinars that followed covered navigation, essential commands, resources, clusters and queuing. The workshop participants were representative of all ACGT partner institutions (ARC, CSIR, UJ, UP and Wits), as well as the National Institute for Communicable Diseases (NICD), Tshwane University of Technology (TUT), University of Cape Town (UCT) and University of the Western Cape (UWC).
The ACGT wishes to thank Mr Molati Nonyane, Ms Itseng Malao, Mr Shaheem Sadien and Prof Fourie Joubert for course content and organization. The ACGT is looking to host another iteration of this course in 2020. Kindly contact our Liaison Scientist, Mr Molati Nonyane () in this regard. The ACGT plans to continue with these kinds capacity building efforts to improve the skills level of South African scientists, especially in the field of bioinformatics and data analysis.
5th Nov 2019
Life science researchers from and around Gauteng, gathered at the University of Pretoria for a Bioprospecting Regulations Forum on the 23rd of October 2019. This information sharing day was intended give the life science community an overview of the national legislative provisions on bioprospecting and biodiversity in South Africa and to address the concerns of the researchers on how these relate to their work. For context, “Bioprospecting economy is based on searching for, collecting, harvesting and extracting living or dead indigenous species or derivatives and genetic material thereof for commercial or industrial purposes.”
There was a clear need for these discussions between the Department of Environment, Forestry and Fisheries (DEFF) personnel and Life Science researchers on the bioprospecting regulations. The meeting consisted of presentations that provided definitions and clarifications on different aspects of bioprospecting and biodiversity regulations in South Africa. The attendees were guided through key regulatory frameworks for bioprospecting, the Nagoya protocol, permits, compliance and benefits sharing. Healthy discussions and debates occurred throughout and after the presentations. Some of the discussion points were on how long the permit applications take, differences between bioprospecting vs scientific/basic research permits, amendments to the Biodiversity Act, the importance of the Nagoya Protocol and provincial level capacity and limitations.
The African Centre for Gene Technologies (ACGT) believes that the forum will improve the communication between the DEFF and the researchers applying for permits and also believes that interests are now more aligned. This event raised significant awareness on national bioprospecting regulations and addressed the concerns of the researchers in attendance. The ACGT is looking forward to working with the DEFF on other future initiatives such as this one. We would like to thank Ms Natalie Feltman and Mrs Lactitia Tshitwamulomoni from the DEFF and the delegates that were in attendance, for their contributions to the success of this event.
For more info on the event; visit our Facebook page: link or contact Mr Molati Nonyane for further information at
29th Oct 2019
Calendar events are a great motivator and serve as a milestone to plan for and to work towards. Researchers from academia and science councils, clinicians, industry representatives and scientific vendors came together for one such networking event- the 5th National Cell and Gene Therapy Meeting, on the 26th and 27th of September 2019 at the Innovation Hub in Pretoria. The purpose of the meeting was for stakeholders active in the field to showcase their research. The two-day event attracted close to 70 delegates from across South Africa.
The stakeholders presented their efforts to find therapies for different diseases and ailments. The work presented touched on a range of applications and possibilities; from the different uses of multiple cell types and genes to different ways to administer said cells in therapeutic treatments. Lively discussions followed almost every talk that due to the high quality and relevance of the work being presented. Symposium panel discussion sessions focused on relevant issues around cell and gene therapy such as CAR-T cells, genome editing, technology exploitation and possible harms.
The meeting was also used to launch the special edition of the South African Medical Journal on Cell & Gene Therapy. The attendees were fortunate to receive a free copy of the journal to take home. The issue presented another opportunity and platform to showcase the great work that is being done by the different SA groups and researchers.
At the end of the two days, Professor Michael Pepper from the University of Pretoria made a strong plea for stakeholders to contribute to ongoing development and drafting of specific policies and legislation governing Cell and Gene Therapy in South Africa. It is critical to have appropriate regulatory frameworks to allow patients to benefit from advances in the field, while at the same time protecting them from exploitation and harm.
The organizers (Prof Michael Pepper, Dr Janine Scholefield and the ACGT Team) would like to thank Haemotec, Separations Scientific, the Scientific Group, inqaba biotec, Beckman Coulter, Whitehead Scientific and ACGT for the financial support. Without their contribution the travel and accommodation arrangements for some of the delegates would not have been possible. The organizers would also like to extend their sincere gratitude to the speakers and panellists for their participation in the meeting. The speakers represented the Universities of Pretoria, Cape Town, the Witwatersrand, Stellenbosch as well as the South African Medical Research Council, Royal Holloway University of London, Council for Scientific and Industrial Research, Biolawgic (Pty) Ltd, University College Cork, Ireland and the Albert’s Cellular Therapy centre (ACT). Without their involvement this event would not have been possible. We hope to see the delegates again at the next meeting. The date for the next meeting will be communicated soon. For more images use this link.
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.
14th Aug 2019
My involvement with the field of Metabolomics is in my capacity as Liaison Scientist for the African Centre for Gene Technologies (ACGT) and as a committee member of Metabolomics South Africa (MSA). The ACGT represents the interests of three universities and two research councils in the Gauteng region (Wits, UJ, UP, CSIR and ARC. I coordinate ACGT’s Metabolomics capacity building activities which include, but are not limited to: meetings, workshops and symposiums; finding synergies between researchers and subsequently building linkages amongst ACGT partner institutions and relevant outside institutions. MSA is a non-profit organization seen as an opportunity to promote and improve the profile of metabolomics research and technology in South Africa, foster networking, training, capacity building, information sharing, mentoring, career opportunities, leadership training and professional development.
I discovered through one of our colleagues from the University of Edinburgh that a Metabolomics Conference was to be held at the World Forum in The Hague, Netherlands from 23-27 June 2019. Attending relevant information dissemination events like the 2019 International Metabolomics Conference, helps me perform my roles well for the ACGT and its partners and also enables me to keep up with the trends in metabolomics research. A decision was then made that I would be attending the conference. I therefore registered to attend the conference and began with the travel arrangements. The visa came out in the nick of time, they do say better late than never. I managed to conquer the usual worries of travelling: Did I pack enough clothes? Did I forget something? Constant reminder that whatever I do, I better not miss the flight. Thankfully, there were no glitches in my travel and all went well. As a bonus, the city of The Hague in itself is amazing with efficient public transport and some great sites.
There was a great South African presence at the workshop with delegates from University of Johannesburg, University of South Africa and North-West University. The conference provided an opportunity to listen to international metabolomics researchers from all over the world sharing their findings, an opportunity to network and identify relevant synergies so as to foster further collaboration amongst metabolomics researchers within SA and across the world. The ACGT already has relationships with some key international metabolomics players who have been assisting with capacity building activities over the past several years. This event provided an opportunity for some stakeholder management to continue to strengthen these relationships. This conference was also an opportunity to expand our contact list and open up new opportunities for collaborations and relationships with South Africans researchers.
My takeaway from this conference is simply that there is a significant and continuing growth of metabolomics all over the world. The discipline has diverse applications in health, agriculture and industry. The ACGT and MSA will do all in its power to assist in pushing African Metabolomics in the right direction and keeping it globally competitive. I would like to encourage anyone who is involved in metabolomics or metabolomics related work to attend future International Metabolomics Conference as this was a worthwhile experience.
My interests and professional involvements are not only limited to the field of metabolomics, I also continue to be involved in genomics and in life science research in aspects that include capacity building, fundraising and research coordination, nationally and internationally. For queries relating to any of the above fields, feel free to contact me at and we can discuss how I and/or the ACGT can be of assistance.
Story by: Molati Nonyane