17th Nov 2021
Single-cell RNA sequencing can reveal complex and rare cell populations, uncover regulatory relationships between genes, and track the trajectories of distinct cell lineages in development. The African Centre for Gene Technologies (ACGT) and researchers from the University of Zurich decided to host a webinar titled “The differential analyses and beyond for single cell RNA-sequencing data” on 03 November 2021.
In this webinar, Professor Mark Robinson shared his expertise in this field and demonstrated various strategies for differential analyses from multi-sample, multi-group single cell RNA-sequencing data. Prof Robinson’s research interests are in the application of statistical methods and data science to experimental data with biological applications within the context of genomics data types. Prof Robinson’s talk was followed by a presentation from Dr Simone Tiberi who focused on key considerations on single cell RNA-sequencing data with specific focus on quality control and RNA velocities. Dr Tiberi has interests in the development of cutting-edge statistical methods in bioinformatics, mostly for bulk and single-cell RNA-seq data.
The ACGT would like to credit the success of this event to the generosity of researchers from the Institute of Molecular Life Sciences at the University of Zurich in Switzerland; Professor Robinson and Dr Tiberi as well as Dr John Becker from the ACGT who chaired the session. The ACGT hopes that everyone who attended the webinar benefited in one way or another. This was not the first RNA-sequencing event organized by the ACGT and this group. A successful workshop was hosted in 2019. Unfortunately, one could not be hosted in 2020 as we were all adjusting to the pandemic and lockdowns. The ACGT will explore other topics in RNA-seq technologies that could be beneficial to members in the ACGT partnership and those who are active in these areas.
For more information, please contact Mr Molati Nonyane at or Tel: 012 420 6139.
16th Nov 2021
The second Metabolomics (MSA) Symposium was held on the 20-21 October 2021. This was another installation of efforts by members of the MSA committee of directors, the MSA subcommittees, the African Centre for Gene Technologies (ACGT) and the many other partners. What started off an idea three years ago, has grown into a very useful coming together of researchers and students with a common interest. The symposium was a to demonstrate the Metabolomics work that has been taking place in South Africa and by some of the members of the association.
The symposium was held over two days and attracted a crowd of over 100 participants. There were 24 speakers of diverse backgrounds and research experience. The event was especially designed to offer the younger speakers an opportunity to present their work and get some exposure. The sessions were chaired by Dr Aurelia Williams (North-West University), Dr Fidele Tugizimana (University of Johannesburg) and Prof Duncan Cromarty (University of Pretoria).
Here are some highlights from the symposium:
Keynote speakers included:
- Prof Alvaro Viljoen from Tshwane University of Technology whose talk was titled Metabolomics – an indispensable tool in medicinal plant research.
- Dr Tiffany Thomas from Columbia University Medical Center in the United States who presented on the structural and metabolic changes of red cells in hospitalized COVID-19 patients.
- Dr Volker Kruft from SCIEX who gave a talk on Clinical Metabolomics: The path to finding new markers.
- Molecular Networking by Dr Fidele Tugizimana and his young team from the University of Johannesburg.
- Validation of Metabolomics Data by Dr Mari van Wyk from North-West University (Potchefstroom).
The annual general meeting was held at the end of Day 1 and was used as an opportunity for MSA leadership to provide feedback of progress from the previous periods as well as insights into future MSA plans.
Best Speaker Awards:
- Anza T. Ramabulana from the University of Johannesburg was awarded the best speaker award for her talk titled Metabolomics and computational tools to characterize the chemical space of Momordica plant species.
- Chanel Pretorius from the University of Johannesburg was the other best speaker for her talk titled Metabolomic analysis of oat (Avena sativa L.) plants: A strategy for cultivar identification and differentiation.
The first MSA symposium was held not too long ago during the launch of MSA in 2019. This ACGT has been very invested in doing eve thing possible to facilitate the growth of MSA. It is very encouraging that momentum from all previous efforts has not been lost and that the MSA and its initiative is still ongoing. We would like to thank the speakers for donating their time and the attendees for making time to attend this event. We would like to thank the sponsors of this event and we look forward to future to working with you again in future events.
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.
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.
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.
19th Jul 2019
In the post-genomic era, life scientists are generating more data than ever. To enable researchers to manipulate and analyze their own data, the ACGT, together with the Centre for Bioinformatics and Computational Biology (CBCB, University of Pretoria) hosted a three-day workshop on the use of the operating system. Linux is open-source software allows researchers to analyze data generated on multiple platforms, in contrast to expensive vendor-specific software that require periodic license renewals.
The workshop was facilitated in conjunction with the CISCO Networking Academy, and a trainer from this academy, Mr Shaheem Sadien, facilitated the training sessions, with Professor Fourie Joubert providing context and practical examples on structural and next-generation sequencing data. Delegates were representative of all ACGT partner institutions (ARC, CSIR, UJ, UP and Wits), as well as the South African Medical Research Council. The delegates had wide-ranging interests, ranging from precision medicine, food technology, crop protection to animal genetics.
All delegates indicated that they would recommend the course to their colleagues, and their suggestions for future courses were noted. The trainers provided the delegates with ample online resources to work from in the future but there is a plan that in future workshops, the trainers will make time to assist each delegate with their own specific data sets. Should delegates complete the requisite online modules, they also receive a certificate of competence from CISCO.
Brief feedback from some of the delegates, on what they enjoyed most, can be found below:
“I really enjoyed the application of skills presented on the Thursday. But the rest of the course was definitely necessary to understand that section!”
“Doing the exercises in the class where you can ask questions and the lecturers were awesome.”
“Despite the fact that the course was provided in class, explaining concepts and allowing practice, a detailed online course is also provided. This repetition I think works well to allow lasting memorization of the course content – which is basically a language that needs to be remembered.“
Kindly also see the ACGT’s Facebook page for pictures of the event. 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 Nonyani () in this regard.
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).