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 .
28th Sep 2020
The ACGT and MSA would like to congratulate Dr Fidele Tugizimana, the current chairman of Metabolomics South Africa (MSA), on his appointment to the board of directors for the International Metabolomics Society (IMS). Dr Tugizimana is a research scientist with the plant metabolomics research group at the University of Johannesburg. He is also a specialist scientist in the international R&D management of the Omnia (Pty) Ltd company (SA) and a scientific consultant in the L.E.A.F. Pharmaceuticals LLC (USA & Rwanda). Dr Tugizimana’s metabolomics research interests include host-pathogen interactions, immune response (at molecular level), chemometrics, bioinformatics and metabolite identification. He is an author/co-author of metabolomics papers in leading peer-reviewed scientific journals.
This appointment to the board of directors follows previous leadership involvement with the International Metabolomics Society as a secretary of the Early-career members Network (EMN) committee (2016-2017); (ii) member of the Data Standards and Strategy Tasks groups; and (iii) member of the International Organizing Committee for the International Metabolomics Conferences 2017 and 2019. The ACGT and MSA would like to congratulate its longtime partner and friend, Dr Tugizimana on his new role and we wish him all the luck.
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
18th Sep 2019
A team of academics from the Universities of Edinburgh, Pretoria and Johannesburg, in conjunction with the South Africa-based multinational fertilizer company, Omnia Group, Ltd, was recently awarded the Agri-Tech Catalyst grant by Innovate UK, the UK’s innovation agency.
The consortium submitted a proposal for improved cultivation and nutrition of the African staple, maize, to the Agricultural and Food Systems Innovation competition. Novel biostimulants will be screened and applied in greenhouse and field scale, and the effects on cultivation, as well as nutritional value of the crop, will be determined. The project will rely heavily on cooperation between industry and the academic partners.
The analyses will be conducted in appropriately equipped laboratories at the University of Edinburgh (EdinOmics platform, Dr Karl Burgess) as well as at the University of Johannesburg (Plant Metabolomics, Dr Fidele Tugizimana). The research component will be heavily metabolomics-based, relying on the latest high-throughput methods developed at UoE and UJ. Hence, technology and expertise transfer between the UK and SA will be a strong project outcome. In addition, stronger academic-industry partnerships will also be forged during the implementation of the programme. The African Centre for Gene Technologies (Mr Molati Nonyane and Dr John Becker) will provide coordination and oversight and exploit opportunities for further programme growth and development utilising this investment.
The project is envisaged to kick off in November 2019.
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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
20th Mar 2019
The African Centre for Gene Technologies (ACGT), the University of Johannesburg and the University of Pretoria organized the 2019 Advanced Metabolomics Workshop that was held at the University of Pretoria from 13-15th March 2019. The workshop provided a capacity building platform to address key issues and challenges in the field of metabolomics.
The workshop was facilitated by this panel of elite metabolomics experts. The facilitators were Dr Reza Salek (International Agency for Research on Cancer, Lyon, France), Dr Karl Burgess (University of Edinburgh, Scotland, UK), Dr Fabien Jourdan (INRA Toulouse, France), Dr Justine Bertrand-Michel (INSERM Toulouse, France), Dr Naomi Rankin (University Hospital Wishaw, Scotland, UK), Dr Jasper Engel (Wageningen University & Research, The Netherlands) and Dr Fidele Tugizmana (University of Johannesburg, RSA).
This workshop covered advanced metabolomics topics using a combination of lectures, interactive round table discussions and computer-based practical sessions. The topics covered in the workshop included applications of metabolomics (clinical, plant/agricultural, industrial), LC-MS/MS/NMR metabolite identification, simple and multivariate statistics, data standards and metabolomics resource, network-oriented metabolomics data mapping, advanced data analysis, lipidomics, metabolomics networks and using fragmentation to enhance metabolite IDs. Throughout the three days, the delegates also had a chance to ask project-specific questions and advice from the with facilitators.
The participants were from the ACGT partner institutions, as well as outside institutions including previously disadvantaged research institutions. There were participants from University of Pret
oria, University of Johannesburg, University of the Witwatersrand, Agricultural Research Council, Council for Scientific and Industrial Research, North-West University, University of South Africa, Tshwane University of Technology, University of the Free State, Walter Sisulu University, University of Cape Town and the University of Venda. Delegates exhibited different scientific backgrounds and had the chance to get to know each other through two-minute elevator-type flash presentations on the first day of each workshop.
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, Mrs Itseng Malao, Dr John Becker, Dr Fidele Tugizimana, and the European visitors 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 in Thermo Fisher Scientific and the Embassy of France in South Africa.
If you would like to view most of the pictures from this event, please visit our facebook page:
For any metabolomics-related capacity building and networking queries, kindly contact Mr Molati Nonyane, ACGT Liaison Scientist (, 0124206139).
20th Mar 2019
The 2019 Metabolomics symposium was held at the Innovation Hub from 11-12th March 2019. This symposium was aimed at principal investigators, postgraduate and PhD students currently performing or planning to work in the metabolomics field. This event was an opportunity for both local and international metabolomics researchers to share their findings, to network and identify synergies so as to foster further collaboration amongst metabolomics researchers within SA and across Europe. This symposium was mainly a platform to officially launch Metabolomics South Africa (MSA). 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. The symposium was a first official event hosted by MSA with the assistance of its partner, the ACGT.
The first day of the symposium was themed “Metabolomics, where are we?”. Topics discussed throughout the day included the overview of metabolomics in South Africa, good metabolomics data, role of metabolomics in health sciences, lipidomics and plant metabolomics. The discussions on the second day of the symposium were under the theme “Metabolomics, informatics, statistics and applications” and covered topics such as metabolomics networks, statistical models, NMR metabolomics and lipidomic profiling. At the end of each day, attempts were made to finish off with round table discussions to address burning issues or questions on the day’s talks as well as other issues regarding to metabolomics or MSA.
It is worth mentioning several key speakers that participated and contributed to the symposium. The speakers mentioned below are all key contributors to the field of Metabolomics and we are thankful that they shared their work and experiences. These were the presenters at the event in no specific order:
- Dr Reza Salek is currently with the International Agency for Research on Cancer, Lyon, France. Dr Salek has extensive experience in metabolomics research in academia, industry and research institutes with extensive metabolomics knowledge, both analytical and data handling. Dr Salek has worked in clinical trial settings and is interested in setting up workflow infrastructures for metabolomics data handling and analysis using cloud computing.
- Dr Karl Burgess is from the University of Edinburgh, Scotland, UK. Most of Dr Burgess’s workfocuses on the use of mass spectrometry in biomedical research, particularly in the understanding of infectious disease. This multidisciplinary research area builds on his fruitful collaborations with cell biologists, engineers, bioinformaticians, instrumentation developers and clinicians.
- Dr Fabien Jourdan is a research scientist at the French National Research Institute for Agricultural Research (INRA). Dr Jourdan develops computational methods to study human genome-scale metabolic network aimed at retrieving parts of the metabolism affected by genetic or environmental perturbations. These methods are mainly applied to toxicology and human health.
- Dr Naomi Rankin is from the University Hospital Wishaw, Scotland, UK. Dr Rankin’s research interests focus on the use of NMR for metabolite profiling and advanced lipoprotein profiling of serum and plasma samples. She is particularly interested in the use of these methods in epidemiology/clinical trials, especially with a view towards translation of NMR molecular profiling approaches into the clinic.
- Dr Jasper Engel is a researcher at Biometris at Wageningen University & Research. Dr Engel’s primary research interests are in applied statistics. He is interested in the development and careful evaluation of statistical approaches for processing and analysis of complex high-dimensional data sets, and their application in high-dimensional chemical, biological or medical problems. Over the last several years his research has mainly focused on method development for analysis of metabolomics experiments.
- Dr Justine Bertrand-Michel is the co-director of the MetaToul Lipidomic facility at INSERM in Toulouse, France. Dr Bertrand-Michel is a lipidomics expert and she was invited to this symposium because of her work in lipidomics a field that most people in metabolomics have shown a keen interest in.
- Dr Fidele Tugizimana is the chairman of MSA, a research scientist at the University of Johannesburg, a specialist scientist in the international R&D management of the Omnia (Pty) Ltd company (SA) and a scientific consultant in the L.E.A.F. Pharmaceuticals LLC (USA & Rwanda). Dr Tugizimana applies metabolomics approaches in plant-environment interactions (involving abiotic/biotic stresses, beneficial microorganisms, etc.).
- Prof Du Toit Loots is the secretary of MSA and a key member of the national metabolomics platform based at the North-West University in Potchefstroom. Prof Loots has made a substantial contribution to the advancement of metabolomics, by means of developing much of the published methodology and applications in terms of identifying new markers for better disease characterization, diagnostics and treatment since 2002.
- Dr Aurelia A. Williams is the deputy secretary of MSA and a senior lecturer at the biochemistry department of the North-West University. Her research interests include characterizing the impact of molecular traits, metabolism and the immune response on disease pathogenesis. She believes metabolomics will serve as a tool in better characterizing infectious diseases such as HIV/AIDS, HIV-associated comorbidities, virus-host interactions, treatment response mechanisms and pathogenesis-associated phenotypes.
- Dr Zandile C. Mlamla is a committee member of MSA and a post-doctoral research fellow at the Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town (UCT). Her research is currently aimed towards the validation of urinary biomarkers of Tuberculosis Disease. She continues to gain experience and expertise in the cutting-edge field of MS-based lipidomics.
The future of South African metabolomics will be in great hands if the student sessions over the two days are anything to go by. On day one, the student presenters were Mr Efficient Ncube from the University of Johannesburg, Mr Emile Jansen van Rensburg and Ms Monique Combrink both from the North-West University. The student session on day two was by three students from the North-West University in Ms Karin Terburgh, Mrs Zinandre´ Stander and Christiaan van Zyl. The students presented their ongoing work and they received great contributions from the people that attended the symposium in the form of question and suggestions.
Well over 140 delegates from over 25 institutions attended this symposium. They consisted of principal investigators, post-doctorates, researchers, post graduate students and several industry players. The hope is that most of them will register as member of MSA and take an active role in the growth of MSA and metabolomics in general. The ACGT and MSA would like to thank all the delegates who registered to attend this event as well as all the members of the organizing committee; Mr Molati Nonyane, Mrs Itseng Malao, Dr John Becker, Dr Fidele Tugizimana, MSA Committee and the European visitors for all of their efforts in putting together this event. The ACGT and MSA would also like to extend their gratitude to the sponsors of this event in Shimadzu, Thermo Fisher Scientific, Microsep/Waters and the Embassy of France in South Africa. Please look out for more MSA and/or ACGT events similar to this symposium in the future.
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