10th July 2018
The end of June 2018 marked a significant moment in the South African metabolomics research space as the Metabolomics Association of South Africa (MASA) was officially affiliated to the International Metabolomics Society (IMS), effective 1st July 2018. Supported by the ACGT, in a stakeholder meeting held in January 2018 at the CSIR International Convention Centre (ICC) in Pretoria, local metabolomics representatives from several research institutions and industry, unanimously agreed to formally establish a non-profit organization, the MASA, and seek affiliation to the IMS. Such motion rose from the realisation of benefits of having a local structured platform that would provide the opportunity for collaboration among scientists in the field and related sciences, and connection between academia, government and industry. This would 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. Furthermore, the affiliation with the IMS provides international recognition, enhances the local association’s effectiveness and promotes awareness of locally and internationally available resources and joint initiatives of mutual benefits.
Thus, a committee was formed with at least one member representative from institutions that have active metabolomics research and development programs. The following were the individuals nominated into the committee:
- Dr Fidele Tugizimana (University of Johannesburg) – Chairperson
- Prof Duncan Cromarty (University of Pretoria) – Deputy Chairperson
- Prof Du Toit Loots (North-West University) – Secretary
- Dr Aurelia Williams (North-West University) – Deputy Secretary
- Dr Wilma Augustyn (Tshwane University of Technology) – Member
- Prof Geoffrey Candy (University of the Witwatersrand) – Member
- Dr David Tabb (Stellenbosch University) – Member
- Mr Molati Nonyane (African Centre for Gene Technologies) – Member
- Dr Nelson Soares (University of Cape Town) – Member, and
- Prof Gerhard Prinsloo (University of South Africa) – Member.
The MASA chairman, Dr Fidele Tugizimana, already serves on several IMS committees and was nominated to spearhead the registration and affiliation of MASA with the IMS. Dr Tugizimana, with the assistance of the committee, compiled the required documentation for the application for MASA to be affiliated with the IMS. The documents and application were submitted by Dr Tugizimana a few days before the 14th International Conference of the Metabolomics Society, held in Seattle from the 24-28th of June 2018.
The IMS president, Prof Jules Griffin, announced during the opening and closing sessions of the conference that the MASA was officially affiliated with the IMS. During the international affiliates meeting, the president of the IMS confirmed that the IMS will support the MASA’s activities, particularly in training and other activities which boost the profile of metabolomics research in SA. Prof Griffin also highlighted that he would be happy to join future MASA symposia or conferences, if the dates match his availability.
MASA will promote the growth and development of the field of metabolomics, particularly in South Africa and on the continent of Africa. MASA will also provide the opportunity for association and collaboration among scientists and connections between academia and industry in the field of metabolomics; provide opportunities for presentation of research achievements and for training workshops; promote the publication of meritorious research in the field; and furthermore, facilitate any other activities in support of and to benefit the above purposes.The affiliation will provide opportunities for bursaries and fellowships associated with the local metabolomics association.
The MASA committee will meet soon to lay out plans for future activities, branding, websites and other logistical steps. Once the MASA has gained further momentum, plans to host the International metabolomics conference in South Africa will be considered as per the IMS policy to rotate the conference location across the globe. The ACGT will continue to inform and update the metabolomics community on all developments.
For any queries or additional information, kindly contact Mr Molati Nonyane, ACGT Liaison Scientist (firstname.lastname@example.org or 012 420 6845).
1st June 2018
The 15th ACGT Regional Plant Biotechnology Forum took place on the 18th of May at the University of the Witwatersrand’s Professional Development Hub. Gathered, were sixty-seven plant scientists and delegates from the ACGT partnership (Agricultural Research Council, University of Johannesburg, University of Pretoria and the University of the Witwatersrand) as well as delegates from North West University and the University of South Africa. The theme of the forum was “Plant Genomes: From Genes to Networks”.
The forum kicked off with a welcome address from Mr Thabo Khoza (ACGT) and Prof Chrissie Rey (University of the Witwatersrand). The programme was directed by Dr Farhahna Allie (University of Johannesburg) and Dr Dirk Swanevelderd (Agricultural Research Council ) who chaired the two sessions for the forum. The presentations were as follows: (Not all presentations are available due to work not being published yet):
- The keynote speaker: Dr Maria-Cecilia Costa (University of Cape Town) – Resurrection networks: insights into desiccation tolerance from gene co-expression networks
Dr Costa obtained her MSc in Brazil (her country of birth) then moved to the Netherlands to pursue a PhD in the Laboratory of Plant Physiology at Wageningen University. Her PhD resulted in six publications in publications such as Nature and Plant Physiology. Dr Costa is currently doing her post-doctorate at the University of Cape Town working on the analysis of the genome and transcriptome of Castanospermum austral. Her impressive resume made her a great candidate to be the keynote speaker at the forum. Her insightful address at the forum was on “Resurrection networks: insights into desiccation tolerance from gene co-expression networks”. Her presentation, which showcased how fast plants can move from a desiccated state to flowering after rehydration, kept the audience highly captivated. She also showed how networks change in dehydrated states and hydrated states. Her work shows promise for future collaborations with the delegates that attended the forum.
Dr Costa was followed by presentations from the University of Pretoria and the University of the Witwatersrand. These talks covered a variety of ways in which networks can be used in plants such as in the cassava research at the University of the Witwatersrand and the maize studies at the University of Pretoria.
- Dr Eshchar Mizrachi (University of Pretoria) – Reverse engineering networks of secondary growth and their evolution in plants
- Prof Chrissie Rey (University of the Witwatersrand) – Plant genes and networks: responses to geminivirus
- Dr Ansie Yseel (University of Pretoria) – Using a network based approach to interpret molecular profiling data
- Ms Katlego Masike (University of Pretoria) – Application of host-induced gene silencing to manage diseases in agriculturally important plants.
- Dr Christine Bizabani (University of the Witwatersrand) – Cassava responses to South Africa cassava mosaic virus: an ultimate battle of host and virus encoded microRNA
- Prof Dave Berger (University of Pretoria) –Transcriptional network analysis reveals candidate resistance mechanisms to grey leaf spot in maize
- Dr Patience Chatukuta (University of the Witwatersrand) – CRISPR and protoplast: Hand-in-hand towards high-throughput gene silencing in cassava
- Ms Ethel Mlunjwa (University of Pretoria) – Expression analysis of selected maize primary metabolism genes in response to Cercospora zeina inoculation in the glasshouse.
The presentations afforded the delegates an opportunity to identify ideal researchers to collaborate with in future. The ACGT will support and help facilitate any interest groups establishment that arises from the forum. The next forum will be hosted by the University of Johannesburg in September 2018. The ACGT will circulate the invitation once the date and topic has been confirmed.
The ACGT would like to thank Inqaba Biotec for sponsoring the forum.
Story by: The ACGT team
4th April 2018
A new family of very promising silver-based anti-cancer drugs has been discovered by researchers in South Africa. The most promising silver thiocyanate phosphine complex among these, called UJ3 for short, has been successfully tested in rats and in human cancer cells in the laboratory.
In research published in BioMetals, UJ3 is shown to be as effective against human esophageal cancer cells, as a widely-used chemotherapy drug in use today. Esophageal cancer cells are known to become resistant to current forms of chemotherapy.
“The UJ3 complex is as effective as the industry-standard drug Cisplatin in killing cancer cells in laboratory tests done on human breast cancer and melanoma, a very dangerous form of skin cancer, as well,” says Professor Marianne Cronjé, Head of the Department of Biochemistry at the University of Johannesburg.
“However, UJ3 requires a 10 times lower dose to kill cancer cells. It also focuses more narrowly on cancer cells, so that far fewer healthy cells are killed,” she says.
Fewer side effects
Apart from needing a much lower dose than an industry standard, UJ3 is also much less toxic.
“In rat studies, we see that up to 3 grams of UJ3 can be tolerated per 1 kilogram of bodyweight. This makes UJ3 and other silver phosphine complexes we have tested about as toxic as Vitamin C,” says Professor Reinout Meijboom, Head of the Department of Chemistry at the University of Johannesburg.
See the researchers commenting in this video.
If UJ3 becomes a chemotherapy drug in future, the lower dose required, lower toxicity and greater focus on cancer cells will mean fewer side effects from cancer treatment.
Powerhouse pathway to neat cancer cell death
UJ3 appears to target the mitochondria, resulting in programmed cell death to kill cancer cells – a process called apoptosis. When a cancer cell dies by apoptosis, the result is a neat and tidy process where the dead cell’s remains are “recycled”, not contaminating healthy cells around them, and not inducing inflammation.
Certain existing chemotherapy drugs are designed to induce apoptosis, rather than “septic” cell death which is called necrosis, for this reason.
Cancer cells grow much bigger and faster, and make copies of themselves much faster, than healthy cells do. In this way they create cancerous tumors. To do this, they need far more energy than healthy cells do.
UJ3 targets this need for energy, by shutting down the “powerhouses” of a cancer cell, the mitochondria. The complex then causes the release of the “executioner” protein, an enzyme called caspase-3, which goes to work to dismantle the cell’s command centre and structural supports, cutting it up for recycling in the last stages of apoptosis.
See microscope images of human esophageal cancer cells treated with the UJ3 complex.
UJ3 complex and the others in the family are based on silver. This makes the starter materials for synthesizing the complex far more economical than a number of industry-standard chemotherapy drugs based on platinum.
“These complexes can be synthesized with standard laboratory equipment, which shows good potential for large scale manufacture. The family of silver thiocyanate phosphine compounds is very large. We were very fortunate to test UJ3, with is unusually ‘flat’ chemical structure, early on in our exploration of this chemical family for cancer treatment,” says Prof Meijboom.
Research on UJ3 and other silver thiocyanate phosphine complexes at the University is ongoing.
8th March 2018
In awarding Professor Lynn Morris with the 2018 TWAS Prize in the Medical Sciences category, the Academy praised her “pioneering studies on the neutralizing antibody response to HIV infection that has provided fundamental insights for HIV vaccine development”.
The TWAS Prize, announced in December 2017, carries a cash award of US$15 000 and the winners will deliver a lecture about their research at TWAS’s 28th General Meeting in 2018, when they will receive a plaque and the prize money.
Morris is a Highly Cited Researcher on the Clarivate Analytics list compiled annually that recognises leading researchers in the sciences and social sciences globally.
Morris holds a joint appointment as Research Professor in the Faculty of Health Sciences at Wits University and Research Associate at the Centre for the Aids Programme of Research in South Africa (CAPRISA). She is the Head of the HIV Virology Laboratory within the Centre for HIV & STIs based at the National Institute for Communicable Diseases at the National Health Laboratory Services.
In June 2017, Morris received the prestigious Harry Oppenheimer Fellowship Award for her scholarship and research excellence.
Story by: The University of the Witwatersrand
15th February 2018
Prof Robert Millar, Director of the Centre for Neuroendocrinology at the University of Pretoria, has been honoured with a Kwame Nkrumah Award for Scientific Achievement by the African Union in the category of Life and Earth Sciences at the Continental level. This is the highest level of the awards programme, which also recognises young scientists at a national level and women scientists at a regional level.
The prize carries a grant of US$100 000.
“I am deeply honoured by the African Union’s award which recognises the importance of our ongoing scientific research to improve lives all over the continent and in the training of young African scientists. The gathering of the heads of all African states was immensely impressive and underlines the potential to harness Africa’s science talent and make the continent a global player in research and I pledge my commitment to this endeavour. My group will continue to look for new and more effective treatments for diseases which lead to considerable suffering and pain,” said Prof Millar.
Prof Millar’s research is in the field of neuroendocrinology, where he has specialised in peptide regulators of reproductive hormones. He pioneered the discovery of the Gonadotropin Releasing Hormone (GnRH) prohormone, novel GnRH structures, and the first cloning of the GnRH I and GnRH II receptors. He has participated in and led a number of programmes developing GnRH analogues for use in a wide range of clinical pathologies.
His research has contributed to the development of the primary treatment for prostate cancer, the sole treatment for precocious puberty and treatments for hormone-dependent diseases in women such as endometriosis, as well as in vitro fertilisation.
He was the recipient of a National Science and Technology Forum (NSTF) Lifetime Achiever Award during 2013 to an individual for his outstanding contribution to Science, Engineering, Technology and Innovation (SETI) during his lifetime. In 2017 he received the Platinum Medal of the Medical Research Council and the Harry Oppenheimer Fellowship and Gold Medal. Prof Millar is a Fellow of the Royal Society (Edinburgh), a Fellow of the Royal Society of South Africa and a Fellow of the Academy of Science of South Africa (ASSAf). He has published 450 articles in internationally peer-reviewed journals (cited over 20 000 times) and has an H-index of over 70. Prof Millar is also an NRF A-rated scientist.
19th December 2017
A team of South African researchers which includes researchers from the University of Pretoria (UP) recently completed a study aimed at unlocking the unique genetic character of southern African populations. The study involved the genetic sequencing of 24 South African individuals of different ethnolinguistic origins, the results of which revealed a high level of genetic diversity and highlights the potential implications for disease susceptibility in Africans. The study was the first government-funded human genomics research study to be performed on African soil.
Funded by the National Department of Science and Technology (DST), the focus of the Southern African Human Genome Programme was to capture a full spectrum of diversity in populations that are under-represented from the genomic perspective. To achieve this, the sample group for the study was compiled to include ethnically self-identified individuals of different ancestries, after which whole-genome sequencing was used to study the differences in some of the major ethnolinguistic groups in the country. The sample group consisted of eight mixed-race or coloured individuals from the Western Cape, seven Sotho speakers from the Free State, eight Xhosa speakers from the Eastern Cape and one Zulu speaker from Gauteng.
The study aimed to explore the ancestral compositions of these individuals, including maternal and paternal lineages, using novel whole-genome sequence data. The results indicate that despite a short period of geographic and cultural separation between Nguni and Sotho-Tswana speakers, there are measurable genetic differences between them.
The team explains that these are in part the result of varying regional ancestral contributions, but also of a random process of genetic drift. Paternal ancestry was almost exclusively of African origin, while maternal ancestry was often of Khoesan origin, which is consistent with previous studies showing cross-cultural assimilation of female hunter gatherers into Nguni and Sotho-Tswana speaking farming communities. Coloured individuals in turn, showed varying proportions of admixture with Khoesan, African and European populations, as well as populations from the Indian sub-continent. After the inclusion of additional representative populations in the analysis, the study revealed a much stronger South Asian ancestry in the coloured individuals than indicated by previous studies.
Although African populations are known to harbour the greatest genetic diversity and have the highest per capita health burden, they are rarely included in large genome studies of disease association. The team says that this diversity provides both a challenge and an opportunity for biomedical research and the hope that Africans will one day benefit from genomic medicine.
Professor Michael Pepper, Director of the Institute for Cellular and Molecular Medicine, and a professor in the Department of Immunology in the Faculty of Health Sciences at UP, who is also the Unit Director of the South African Medical Research Council’s (SAMRC) Stem Cell Research and Therapy Unit, adds that the next step will be to use the knowledge gained through the team’s research to determine the potential impact the genetic variants could have on the health of individuals when health-related research is conducted.
The results of this study were published in Nature Communications on Tuesday, 12 December 2017
Story by: Ansa Heyl for the University of Pretoria News
5th December 2017
The 16th Annual World Congress of the Human Proteome Organisation (HUPO) was held at the Convention Centre Dublin in Ireland, from the 17th to the 21st of September 2017. HUPO is organised by the European Proteomics Association (EUPA) and the British Society for Proteomics Research (BSPR). The vision for HUPO2017 Congress was to “create a meeting that will bring together world leaders with a new generation of scientists to promote HUPO’s capabilities for advancing knowledge of the Human Proteome and the impact this will have on understanding health, disease and ageing”.
The congress ran six concurrent themes throughout the congress period. These themes were:
Cellular Proteomics; Drug & Biopharmaceutical Proteomics; Systems, Bioinformatics & Omics Data Integration; Disease & Clinical Proteomics; Precision & Personalised Proteomics; and the Human Proteome Project (HPP). In addition to the concurrent themes, there were exhibitions, networking and poster viewing sessions which were well attended by delegates. Poster presenters had an opportunity to share their work and also get some valuable suggestions from proteomics world experts that visited their posters.
A representative from the African Centre for Gene Technologies (ACGT), Mr Thabo Khoza, attended the congress. Mr Khoza is a Liaison Scientist at the ACGT and has been responsible for bringing the proteomics community together through symposiums and workshops for the past 4 years. This was the 2nd time Mr Khoza attended the HUPO congress. This time around, Mr Khoza was tasked to meet with a few world experts in the field to share ideas on forming a proteomics society for South Africa. Mr Khoza met with Prof Stephen Pennington (Chair of the Ireland HUPO organising team and Professor of Proteomics at the University College Dublin Conway Institute), Dr Maarten Dhaenens (President of the European Proteomics Association and researcher at Ghent University), Prof Kathryn Lilley (Director of the Cambridge Centre for Proteomics, University of Cambridge) and Prof Lennart Martens (Professor of Systems Biology at Ghent University, and Group Leader of the Computational Omics and Systems Biology group in Ghent, Belgium). All four world experts stressed the importance of a functioning society that would address the needs of the proteomics community and create an effective space for networking and collaboration.
Mr Khoza was able to identify a number of researchers who could potentially come to South Africa to facilitate future workshops for the South African proteomics community. These researchers presented some of the talks that stood out during the congress. The talks included those by Ben Collins, who gave a talk on “Quantitative Interaction Proteomics: Insights into Biological Systems” and Ruedi Aebersold, who gave a talk titled “The Protein in context”. Matthias Uhlen who’s talk was titled “The human protein atlas – implications for human biology, drug development and precision medicine” stressed the importance of transcriptomics, handling of big data, the focus of tissue-specific proteome and having a pathology atlas in addressing concerns associated with the human biology, drug development and precision medicine.
Through the interactions that Mr Khoza had at the congress, the ACGT plans to have two proteomics workshops in 2018 as well as engage the South African proteomics community to establish a proteomics society.
The congress was a great platform for networking. It was well attended by delegates from all over the world, with a common interest in proteomics and how it can be applied in humans and other systems. The next congress will be held in Orlando, USA from September 20th 2018 till the 3rd of October 2018.
13th November 2017
On the 18th of October 2017 the African Centre for Gene Technologies (ACGT) in conjunction with the Agricultural Research Council (ARC) hosted a Regional Plant Biotechnology Forum at the ARC’s Central Office Auditorium in Hatfield. The focus for this forum was “Plant-Soil Interactions”. This theme came in light of the national plant-soil working group initiative that the ARC is planning to create and coordinate. The forum was attended by a number of people from the ACGT’s partner institutions as well as outside institutions, including the University of Cape Town and industry representatives.
The organising committee were fortunate to secure Prof Wijnand Swart as the keynote speaker for the forum. Prof Swart is currently in the Department of Plant Sciences at the University of the Free State in Bloemfontein and Discipline Head in the Division of Plant Pathology. His research broadly focuses on using the taxonomic and functional diversity of microorganisms, above- and below ground, as bio-indicators of soil and plant health. His research interest made him a perfect fit for the forum’s theme. Prof Swart gave a fascinating talk titled “Phytobiomes: Key to understanding plant and soil health”.
Other equally fascinating talks came from Prof Joanne Dames (Rhodes University and Mycoroot), Prof Oleg Reva (University of Pretoria), Ms Francina Bopape (ARC), Dr Juan Venter (University of Pretoria), Dr Martin Myer (Biopower Institute) and Dr Fidele Tugizimana (University of Johannesburg).
The forum, like many of the ACGT fora, served as a platform for people from different institutions and labs to network as well as discuss future collaborative initiative. The plant-soil working group was a big topic during the networking session/lunch. The ACGT aims to work together with the ARC to establish and coordinate the working group and it will keep all interested stakeholders up to date with its progression.
The ACGT would like to thank Dr Charles Hefer and Dr Dirk Swanevelder from the ARC for assisting in organising the forum.
10th November 2017
The University of Pretoria (UP) hosted a Proteomics seminar and workshop, which they co-organised with the African Centre for Gene Technologies (ACGT) and the Council for Scientific and Industrial Research (CSIR). Over 20 delegates attended the events; which represented the majority of the ACGT’s partner institutions.
Prof Ole Jensen visited South Africa during this period to give a plenary talk at the seminar, as well as to facilitate the subsequent two-day workshop. Prof Jensen is a Professor of protein mass spectrometry at the Department of Biochemistry and Molecular Biology, University of Southern Denmark (SDU), in Odense. His research focus includes chromatin biology and epigenetics, as well as “middle-down” proteomics approaches and mass spectrometry to study co-existing post-translational modifications and their cross-talk in proteins.
The seminar took place on the 11th of October 2017 at UP’s Plant Sciences Complex Auditorium. Dr John Becker (ACGT Centre Manager) made opening remarks and highlighted the progression of the proteomics workshops since their inception in 2012 under the leadership of Prof Duncan Cromarty from UP. After being introduced by Dr Stoyan Stoychev (CSIR), Prof Jensen gave a plenary talk on “One protein – many outcomes: Elucidating histone proteoform dynamics during aging by using Mass Spectrometry”. He was followed by other speakers from UP (Dr Duncan Cromarty and Ms Kim Sheva) and CSIR (Mr Ireshyn Govender and Dr Ashok Prabhu). The day ended off with the delegates, who were to attend the workshop taking place a day after the seminar, giving short presentations about their research studies which involved proteomics.
The advanced proteomics workshop ran for two days (12 and 13 October 2017) at the ACGT Centre for Bioinformatics and Computational Biology (CBCB) at the FABI Square building. Delegates for the workshop were carefully selected based on their motivation to attend this specialised training workshop. Prof Jensen facilitated the two-day workshop with the primary focus being post-translational modifications of proteins. The workshop was interactive which allowed the attendees to ask questions which were specifically related to their research. The workshop also included practical sessions as well as round-table discussions in which the attendees had an opportunity to ask more in-depth questions about their research. Prof Jensen, Prof Cromarty and Dr Stoychev facilitated the round-table discussions.
These events are part of the ACGT’s strategic plan to build and increase capacity in the field of proteomics. Some of the delegates have attended these training workshops since the “Introduction to proteomics” stages. With each year, the ACGT have (and will continue to) focus on modifying the training workshops to suit the community, as well to advance the expertise in proteomics so that our South African community can keep up with the rest of the global proteomics community. Researchers in the partnership are welcome to contact Mr Thabo Khoza, who is driving capacity-building initiatives in this field at ACGT, to discuss specific training and networking requirements and suggestions for future events (email@example.com).
The ACGT would like to thank Prof Cromarty and Dr Stoychev for assisting in organising the forum as well as facilitating some sessions at the workshop.
30th October 2017
Researchers from academia and science councils, industry representatives and scientific vendors came together for a national conference on Stem Cells Research and Therapy on the 26th and 27th of October 2017 at the Innovation Hub in Pretoria. The purpose was to showcase research performed under the MRC Flagship “Stem cell research and therapy- addressing South Africa’s disease burden”; awarded to the University of Pretoria in 2014. National stem cells stakeholders active in the field, but not necessarily funded through the flagship, also had the opportunity to showcase their research.
The two-day event attracted close to 80 delegates from across South Africa, including delegates from Kwa-Zulu Natal and the Western Cape. Professor Michael Pepper, co-organizer of the event (with ACGT) welcomed delegates on the first day, after which Medical Research Council Vice-President, Professor Jeffrey Mphahlele, introduced the University Flagship Programme. Professor Mphahlele congratulated all involved in the Flagship, but also stressed the importance of translational research to delegates. Although the presentations over the remaining two days largely focused on scientific research, included in the programme was also presentations and deliberations on the legislative environment surrounding cell-based therapy; as well as legal issues in dealing with scientific data and privacy. Discussions were quite lively as researchers were exposed to high level work in the stem cells field from researchers that they don’t interact with frequently. Here, suggestions to post-graduate researchers, academics and industry; as well as opportunities identified for collaborative efforts, could be regarded as highly positive outcomes of the deliberations.
The organizers were very fortunate to attract financial support from nine scientific vendors. Funds were largely utilized to cover travel and accommodation costs for delegates as well as a networking event for attendees on the evening of the first day. The organizers would like to extend their sincere gratitude to the vendors for their financial assistance, without which the event would not have been possible.
Attendees were very supportive of potential future scientific events to showcase research and provide a platform for networking. The ACGT and researchers in the field are evaluating the possibility and means to host similar events in future.
Financial support for the event was kindly provided by:
- Whitehead Scientific
- Separations Scientific
- ThermoFisher Scientific
- The Scientific Group
- Inqaba biotec
The organizers would also like to express their sincere gratitude to G Studio (and specifically Ms Jacomina Visser), who provided design and layout services for a conference programme and website- absolutely free of charge. See the conference web link here: