26th Mar 2020
Modified gene editing machinery enables targeted disruptions of mitochondrial genes in rice and rapeseed plants.
Gene editing technologies have revolutionized the field of genetics, allowing researchers to make targeted changes to the DNA of various animal and plant nuclei, animal mitochondria, plant chloroplasts, and more. Missing from this list until recently, however, was plant mitochondrial DNA. The tools for delivering the necessary editing enzymes to plant mitochondria simply hadn’t been built.
Now, plant molecular biologist Shin-ichi Arimura of the University of Tokyo and colleagues have filled this gap, creating plant-friendly mitoTALENs—mitochondria-targeting gene editing tools based on transcription activator-like editing nucleases (TALENs).“This is an important paper—it’s the first demonstration that we can make targeted and heritable changes to mitochondrial DNA” in plants, Ian Small, a plant scientist at the University of Western Australia who was not involved in the research, writes in an email to The Scientist
Regular TALENs are composed of a DNA binding domain that can be readily engineered to recognize practically any DNA sequence, and a nuclease domain that chops up the DNA at that site, causing deletions. To target a mitochondrial gene, the team modified a plant-adapted TALEN such that it also included a mitochondrial homing signal, and engineered DNA binding domains to recognize particular genes of interest. The researchers then transferred a plasmid encoding a mitoTALEN into plants via agrobacteria—a common strategy used by plant geneticists.
In proof-of-principle experiments, the researchers designed two mitoTALENs, each targeting a particular mitochondrial gene: orf79 in rice and orf125 in rapeseed (canola). The resulting deletions enabled the researchers to confirm the genes’ hitherto suspected roles in male sterility—a natural phenomenon that prevents self-fertilization in certain hermaphroditic plants, thus promoting hybrid seed development. Indeed, disabling the genes reinstated self-fertilization in the two types of plants, the team showed.
Such male sterility genes, which are encoded in the maternally inherited mitochondria of certain plants, are desirable for agriculturalists wishing to produce hybrid crops that “grow faster, produce more, and are more resistant to disease,” explains Small. Thus, generally speaking, the goal is to activate such genes or introduce them into crop plants that lack them, rather than delete them, as Arimura’s team did.
While the plant mitoTALENs can’t yet deliver the “holy grail” of plant mitochondrial gene editing, this study is “an important first step,” says plant physiologist Ralph Bock of the Max Planck Institute of Molecular Plant Physiology who did not participate in the research. In the meantime, he adds, “one could use [the technology] to ask questions about the functions of mitochondrial genes.” (Nat Plants, 5:722–30, 2019)
Story by: Ruth Williams, for The Scientist, March 2020
19th Mar 2020
Following the call by the Government to practice social distancing in order to curb the spread of COVID-19, the ACGT staff will be working remotely and will be reachable via emails (please see our Contact Us page for our email addresses).
The ACGT is looking into ways to continue with its activities through the means of Webinars. More information on the Webinars will follow in the next few weeks.
12th Dec 2019
The African Centre for Gene Technologies (ACGT) partnered with the Council for Scientific and Industrial Research (CSIR), the University of Cape Town (UCT) and the Centre for Proteomic and Genomic Research (CPGR) to host the 2019 proteomics advanced workshop and symposium. The advanced workshop, which took place from the 18th to the 21st of November 2019, focused on the analysis of targeted proteomic and metabolomic data, using the open-source software package Skyline. The workshop was immediately followed by a national proteomics symposium, on the 22nd of November 2019, which provided emerging scientists in the field an ideal platform to showcase their work.
The four-day workshop was facilitated by Mr Brendan MacLean (MacCoss lab, University of Washington), Dr Birgit Schilling (Buck Institute for Research in Aging), Dr Ben Collins (Queen’s University Belfast and formerly Aebersold lab, ETH Zurich) and Dr Lindsay Pino (Garcia Lab, University of Pennsylvania and formerly MacCoss lab, University of Washington). The workshop had theory and practical sessions and covered a number of topics including:
- Brief introduction to targeted analysis;
- Skyline overview;
- Targeted Selected Reaction Monitoring: Method development and Data analysis;
- Targeted SWATH/ Data-Independent Acquisition: Introduction, Suitability (QC) test, library generation, data processing;
- Panaroma and AutoQC;
- Statistical group comparisons in Skyline; and
- Small molecule applications in Skyline.
The participants represented various research institutions from across the country, including the Universities of Pretoria (UP), the Witwatersrand (Wits), Johannesburg (UJ), Stellenbosch, Cape Town, the CSIR and CPGR. The participants were also given an opportunity to engage with the experts on a one-to-one basis to discuss their projects.
The symposium, which followed the workshop, had the workshop facilitators as keynote speakers as well as local researchers presenting their work. Local speakers hailed from a number of South African institutions including UP, Wits, CSIR and UCT. The symposium was a great platform to showcase what has been transpiring in the field since the last national meeting, which took place at Wits in 2018. The symposium also gave emerging scientists the opportunity to network with established researchers in the field.
Dr Ben Collins (Queen’s University Belfast) – Keynote speaker
Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage
Dr Previn Naicker (CSIR)
Development of sample preparation workflows and application to Clinical Proteomics
Mr Matthys Potgieter (UCT)
MetaNovo: a probabilistic pipeline for peptide and polymorphism discovery in complex metaproteomic datasets
Mr Brendan MacLean (University of Washington) – Keynote speaker
Growth in the software ecosystem for targeted quantitative proteomics
Dr Tracy Hurrell (CSIR)
Contextualizing the proteome of hepatocyte models
Mr Andea Ellero (UP)
Time course convergence of hepatocellular proteomic phenotypes seen in HepG2 spheroid cultures
Mr Emmanuel Nweke (Wits)
Deciphering the proteomic landscape of Pancreatic Ductal Adenocarcinoma in South African patients using SWATH mass spectrometry
Dr Birgit Schilling (Buck Institute for Research in Aging) – Keynote speaker
Proteomic tools to decipher mechanisms of senescence in aging and age-related diseases
Dr Shaun Garnett (UCT)
Generating a proteomic profile of neurogenesis, through the use of human foetal neural stem cells
Mr Daniel Mutithu (UCT)
Metabolic profiling for biomarker discovery to understand pathogenesis of rheumatic heart disease
Dr Lindsay Pino (University of Washington) – Keynote speaker
Using an external reference material to harmonize and calibrate quantitative mass
spectrometry data at scale
Establishing a community of practice for the proteomics society came up during the welcome address and closing remarks given by Prof Jonathan Blackburn from UCT and Mr Thabo Khoza from the ACGT. Mr Khoza highlighted that an informal platform (Google Groups) has been set up by the ACGT to encourage the researchers in the field to communicate more effectively. This platform is open to any researcher who wishes to join it.
The workshop and symposium would have not been possible without the generous financial support from Anatech, Bruker, Inqaba Biotec, Microsep and The Scientific Group.
The ACGT will engage with the community to plan and organise the next national proteomics workshop and national symposium for the year 2020.
For any queries related to this, or other proteomics capacity-building and networking events, contact Mr Thabo Khoza, Liaison Scientist at:
To see more photos, please visit our ACGT Facebook page.
Story by: ACGT, December 2019
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.
9th Oct 2019
The African Centre for Gene Technologies (ACGT) and the Agricultural Research Council (ARC) hosted a plant genome editing workshop between the 3rd and the 5th of September 2019 at the ARC’s Biotechnology Platform situated on the Onderstepoort Campus.
Scientists from the Karlsrühe Institute of Technology, Germany (KIT) presented a “starter kit” for model plant CRISPR-related work in South Africa. The relationship with KIT began in 2017 with Professor Holger Puchta visiting South Africa on an ACGT invitation, to present a keynote address at one of the annual ACGT Regional Plant Biotechnology Forum series meetings. When the ACGT approached Prof Puchta to facilitate a three-day beginner’s workshop on plant genome editing with the CRISPR/Cas technology utilized in his laboratory, he recommended his trusted colleagues, Patrick Schindele and Angelina Schindele, to facilitate the workshop, who graciously accepted the invitation.
The three-day workshop included both theory and practical sessions during which the participants were introduced to gene targeting in plants by using the CRISPR/Cas9-system.
Topics covered in the sessions included:
- Classification of the CRISPR/Cas-systems currently in use
- Designing guide RNAs manually and with online tools
- CRISPR construction and guide RNA cloning into the KIT group’s vectors using various cloning strategies, such as Gateway cloning
- Current applications of CRISPR/Cas technologies looking beyond gene editing
- Approaches to Agrobacterium transformation of model plants.
Prof Puchta’s lab generously provided constructs for the participants to work on during the practical sessions. The relationship established with KIT will be an ongoing one. Prof Puchta’s lab has offered to assist participants who attended the workshop with their published constructs and other plant genome editing related queries. Queries must be directed to the ACGT. Inqaba Biotec partnered with ACGT and ARC as the major sponsor and generously provided the majority of reagents used in the workshop.
The plant genome editing community in South Africa is a small but growing one. The workshop provided an opportunity for scientists in the field to be aware what other institutions in the region are doing in the plant genome editing space. Indeed, collaborative discussions have already been established between the ARC and the Council for Scientific and Industrial Research (CSIR) on a possible project as a direct result of this workshop. The participants were all enthusiastic about having a more cohesive community and the ACGT will facilitate the process by creating a CRISPR list server (contact ACGT’s Liaison Scientist, Mr Thabo Khoza, to gain access) and subsequently a Genome Editing Interest Group. The participant feedback indicated that both the extensive theoretical overview of the different technologies, combined with the KIT CRISPR experts’ practical experience, provided key insights into the technology during the practical sessions, with details often not provided in laboratory protocols or papers.
Contact Thabo Khoza:
For more workshop images, visit our ACGT Facebook page: Click here
Story by: ACGT, October 2019
8th Oct 2019
On Tuesday, September 17, the African Centre for Gene Technologies (ACGT), Forestry and Agricultural Biotechnology Institute (FABI) and Future Africa co-hosted a Plant Phenotyping and Precision Agriculture workshop at Future Africa on the University of Pretoria’s Hillcrest Campus. The event, which was themed “Opportunities and Needs in Research and Infrastructure” was attended by 66 delegates from a variety of national research, governmental and industry institutions.
The workshop was opened by Dr Marinda Visser (Manager: Grain Research and Policy Centre at Grain SA) who emphasised the importance of research and development in the agricultural sector, as well as the need for better coordination and collaboration.
The morning session was dedicated to introducing various aspects of phenotyping and precision agriculture to the delegates. This involved phenotyping at several different scales and applied to a variety of plant species. The programme and the national and international speakers who delivered the presentations are listed below:
Adding to the diversity of speakers, delegates also represented institutions and initiatives that included: the University of Johannesburg, Tshwane University of Technology, the Royal Science and Technology Park: eSwatini, the Department of Science and Innovation, Corteva Agrisciences, Sensako Seed Company and Link Seed. ACGT and FABI post-graduates and researchers were very well represented.
In the afternoon session, facilitated by Prof Bernard Slippers (Director: FABI, UP), delegates were tasked to discuss issues around opportunities to meet needs for infrastructure and facilities, academic – government – industry alignment, and opportunities for South Africa, Africa and international communities. These crowd-sourced inputs will now provide a foundation for developing a network of interested parties and contain numerous ideas for projects and further development.
A more formal report on the feedback emanating from the groupwork is in preparation. There was strong agreement that a follow-up event is required and planning will commence shortly.
In closure, Prof Bernard Slippers thanked all the speakers and delegates, as well as the organizing committee.
For more photos, please visit out Facebook page: click here
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
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