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  • To single cell RNA-sequencing data and beyond: a tale of a successful webinar

    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 ETH University of Zürich co-hosted a webinar titled “Differential analyses and beyond for single cell RNA-sequencing data” on 3 November 2021.

    In this webinar, Professor Mark Robinson shared his expertise in the 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 of single cell RNA sequencing data, specifically focusing 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.

    A total of 40 delegates registered for the event, representing various South African Universities and science councils. The delegates hailed from diverse backgrounds, including agricultural, medical and veterinary sciences. The two presentations were followed by a stimulating discussion session from various viewpoints.

    Single-cell RNA Seq methodology has previously been deployed in the country, hence a hands-on data analyses workshop was also co-hosted by the ACGT and ETH Zürich in 2019 in Pretoria.  Unfortunately, an event could not be hosted in 2020 due to the pandemic. Transcriptomics analyses remains a rich area of growth for South Africa and the continent and the community can look forward to further follow-up events, as well as how transcriptomics interlinks and complements other “omics” approaches.

    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 Zürich in Switzerland: Professor Robinson and Dr Tiberi. The ACGT hopes that everyone who attended the webinar benefited in one way or another. The ACGT will continue to 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.

  • The Second MSA Symposium exhibits South African talent in the field of Metabolomics

    16th Nov 2021

    The second Metabolomics South Africa (MSA) Symposium was held on the 20-21st of October 2021. This was yet another installation of networking and training 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 as an idea three years ago, has grown into a highly useful coming together of researchers and students with common interests. The symposium was intended to demonstrate the Metabolomics work that has been taking place in South Africa by 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 from diverse backgrounds and research experiences. The event was especially designed to offer the younger speakers an opportunity to present their work and gain 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.

    Training sessions:

    • 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 AGM

    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 awarded the additional 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 during the launch of MSA in 2019. This ACGT has been very invested in doing everything 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 many initiatives are still ongoing. We would like to thank the speakers for donating their time and the attendees for accommodating this event. We would like to thank the sponsors of the event and look forward to working with you again in future events.

    For additional queries, kindly contact Mr Molati Nonyane, or visit the MSA website at www.metabolomics-sa.co.za

     

  • The future of South African plant biotechnology research and innovation is bright!

    The future of South African plant biotechnology research and innovation is bright!
    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
    • Biopharming
    • 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.

  • InnovateUK programme unearths beneficial mechanisms of novel agricultural biostimulants in the African agricultural staple maize

    16th Sep 2021

    An internationally funded consortium working towards increasing yield and nutritional value of staple crops in Africa recently concluded an InnovateUK-funded programme. Despite the restrictions on travel due to COVID-19, the programme delivered promising results after being initiated in November 2019. The consortium was led by the University of Edinburgh, in collaboration with Omnia Nutriology®, the University of Pretoria (through the African Centre for Gene Technologies) and the University of Johannesburg.

    An innovative approach was followed by combining high-throughput, high coverage metabolomics analyses of individual plant growth-promoting rhizobacteria (PGPR or biostimulant strains), as well as novel combinations of the strains. Analyses were also undertaken of maize plants grown under controlled conditions, as well as at different field sites in the main maize growing areas of South Africa, treated with the biostimulants. The field trials provided ample plant material for detailed analyses of metabolite changes between the treatments, and hence gave insights into the mechanisms by which these biostimulants increased yield and altered metabolites with direct association to yield and nutritional benefits of the staple.

    A number of programme outputs have been achieved, that will target different audiences in the academic and agricultural industries. Included are two review manuscripts (one published), three peer-reviewed manuscripts (in preparation), an interview article in the UK Crop Production Magazine, three conference presentations and a video for public dissemination (currently being finalized).

    In addition, a demonstration site for African smallholder farmers is also being planned and will be implemented as soon as South African COVID restrictions allow. The demonstration site will extend knowledge on general soil health and optimal maize growth to smallholder farmers (as an introduction); through hands-on experience as well as extension manuals.

    The programme established and strengthened ties between multiple research organizations, from both the academic and industry side, and has opened new avenues to further explore refinement of the biostimulants under study.

    The consortium would like to sincerely thank InnovateUK, the United Kingdom’s innovation agency; as well as Omnia Nutriology®, for providing financial support to make the research programme possible.

     

     

  • AgriMicrobiomics workshop highlights African and international critical mass in food systems research

    AgriMicrobiomics workshop highlights African and international critical mass in food systems research
    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:

    1. to formally introduce this group of AgriMicrobiomics scientists from all over the globe to each other to encourage the creation of an AgriMicrobiome network
    2. to create a specialist group to collaborate on AgriMicrobiome research
    3. identify areas of collaboration amongst group members
    4. 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:

    1. Professor Lise Korsten, University of Pretoria
    2. Professor Don Cowan, Centre for Microbial Ecology and Genomics, University of Pretoria
    3. Professor Gabriele Berg, Graz University of Technology
    4. Professor Leo van Overbeek, Wageningen University and Research
    5. Professor Kornelia Smalla, Julius Kühn Institut
    6. Professor Michael Schloter, Helmholz Center Munich
    7. Stephen O’Keefe, African Microbiome Institute, University of Stellenbosch and University of Pittsburgh
    8. Dr Mubanga Kabwe, CapeBio Technologies
    9. Dr Jarishma Gokul, Department Plant and Soil Sciences, University of Pretoria.

    Keep an eye out for future events, inclusive of discussion sessions and online training, in the field of AgriMicrobiomics.

    The Organising Committee:
    Prof Lise Korsten
    Dr Jarishma Gokul
    Mr Molati Nonyane
    Dr John Becker

  • Lipidomics: unravelling the role of small molecules with big impacts on health

    Lipidomics: unravelling the role of small molecules with big impacts on health
    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.

  • Another successful episode of the Metabolomics webinar series

    Another successful  episode of the Metabolomics webinar series
    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 .

    The ACGT is looking forward to your participation in future webinars and events.

  • Researcher from the University of Johannesburg secures a position on the International Metabolomics Society board of directors

    Researcher from the University of Johannesburg secures a position on the International Metabolomics Society board of directors
    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.

    Congratulations!

     

     

  • The Launch of the 2020 Metabolomics Webinar Series

    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.

    The ACGT is looking forward to your participation in future webinars and events. For more information and suggestions about future events, please contact Mr Molati Nonyane at .

  • Life Scientists receive training in Linux

    Life Scientists receive training in Linux
    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.