4th Apr 2018
One of the objectives of the African Centre for Gene Technologies (ACGT) is to improve the advanced biotechnology skills level of scientists in South Africa. The quality of the work done locally should match, or even exceed, related work from any part of the world and the best way to do that is through continuous capacity building efforts.
To this end, the ACGT recently facilitated two metabolomics workshops to provide a platform to address key issues and challenges in the field of metabolomics, including subsequent data analyses. The two workshops were meant for different audiences and were held at the University of Pretoria. The first was an Introductory Workshop that ran from the 12th to the 14th of March 2018. This event was aimed at those who have limited knowledge of metabolomics techniques and applications. The second, an Advanced Workshop, subsequently ran on the 15th and 16th of March 2018 and covered more advanced topics in the field. The latter workshop was intended for those with existing metabolomics knowledge and already working with some metabolomics techniques, or are actively engaged in data analyses emanating from metabolomics experiments.
Both workshops were designed to include a mixture of lectures, interactive round-table discussions and computer-based practical sessions. The Introductory Workshop covered topics that ranged from experimental design, introduction to techniques, applications of metabolomics, analysis of metabolomics data, metabolite identification, statistics and metabolomics data interpretation. The Advanced Metabolomics Workshop focused on advanced data analysis, quantitative metabolomics, metabolomics networks and data sharing.
The participants hailed from the ACGT partner institutions, as well as institutions outside the partnership, including previously disadvantaged research institutions (University of Pretoria, 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 and the Central University of Technology (Free State). 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 workshops were facilitated by a team of renowned metabolomics experts, both local and international. The local facilitators included Dr Fidele Tugizimana and Professors Ian Dubery and Paul Steenkamp from the University of Johannesburg. The international facilitators included Dr Reza Salek from the University of Cambridge, Dr Jos Hageman from Wageningen University, Dr Fabien Jourdan from the French National Research Institute for Agricultural Research, and Drs Naomi Rankin and Karl Burgess (both from the University of Glasgow).
Following the brief ice breaker presentations by the individual participants on their backgrounds and areas of interest, the workshops then proceeded onto a variety of subjects that influence and shape metabolomics research. Web tools and practical applications of metabolomics were demonstrated, as well as hands-on exercises that focused on data analysis and interpretation. The sessions were kept as interactive as possible to create a relaxed environment where the participants could ask questions pertaining to their own work.
The ACGT and all of its partners would like to extend enormous gratitude to all those who contributed to making these workshops a success, including the facilitators who again took a lot of time out of their busy schedules to contribute to capacity building in South Africa. The ACGT would also like to wish all the participants of the workshops all the luck with their work and future in metabolomics.
There has since been positive feedback from the participants of both workshops. There was a general sense from the workshop evaluations that the workshops were informative, practical and interesting. The participants enjoyed interacting with the expert facilitators from different parts of the globe. They felt that the facilitators were knowledgeable and showed willingness to help. Moving forward, there are plans to adjust the duration of the course to increase subject coverage, as well as to include additional practical sessions. Due to limited space, the Centre could not host everyone that applied, but the ACGT encourages those that were not placed this year to keep an eye out for future workshops.
The workshops represent one of the means towards building a sense of community- further building on a stakeholder session that was facilitated earlier in 2018 towards the establishment of a more formal grouping of metabolomics stakeholders. More news on the establishment of an association to follow soon.
For any metabolomics-related capacity building and networking queries, kindly contact Mr Molati Nonyane, ACGT Liaison Scientist ( email@example.com,
012 420 6139 )
8th Mar 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 Feb 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 Dec 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 Dec 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 Nov 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 Nov 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 (firstname.lastname@example.org).
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 Oct 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:
27th Oct 2017
The African Centre for Gene Technologies (ACGT) and the University of Pretoria’s Centre for Bioinformatics and Computational Biology (CBCB) co-hosted a genome analysis workshop from 23-27 October 2017. The hosts were extremely fortunate to have the week-long workshop facilitated by an expert group of scientists and software developers from the Broad Institute of Harvard and MIT. They included Dr Geraldine van der Auwera, Mr Hussein Elgridly and Mrs Kate Noblett. The team was supported by local bioinformatics expert and Director of the CBCB, Prof Fourie Joubert. This was the second capacity-building instance where the team facilitated the workshop in the Genome Analysis ToolKit (GATK) open-source software package. The toolkit was developed in the Data Sciences Platform at the Broad Institute, and offers a wide variety of tools with a focus on variant discovery and genotyping. The first GATK workshop was hosted by ACGT and CBCB in 2015.
The workshop dealt with a number of genomics analysis topics and included data pre-processing and quality control; variant discovery and detailed sessions on setting up workflows in the toolkit. The approach was to have presentations on the specific sections, which was followed by hands-on exercises on the CBCB workstations throughout the five days.
Delegates hailed from the ARC (including Stellenbosch), and the Universities of Pretoria, the Witwatersrand and Stellenbosch; and also included a delegate who traveled all the way from Newcastle University to attend. The attendees were at different levels of bioinformatic analysis experience and this was highlighted during the sessions where command line imputation was utilized. A consideration for future courses could potentially be to bring those delegates less familiar with this aspect up to speed in a separate prior training event. Notwithstanding, feedback from delegates was overwhelmingly positive and will be utilized for planning similar subsequent events in the genome analysis field for partnership researchers.
The ACGT and its partner institutions will continue to build capacity in bioinformatics analyses in the “-omics” space; and would like to invite all who require such analyses as part of their research to engage us and tell us about their specific training needs.
The ACGT would like to sincerely thank the Broad facilitators, including Prof Joubert, for their investment in time and effort in preparing and facilitating this workshop.
11th Jul 2017
Since the discovery of the three-dimensional structure of DNA in 1953 by James Watson and Francis Crick, molecular biologists have been studying the function of genes and genomes made up of the four bases of DNA. Scientists have had the ability to modify DNA through a number of enzymatic processes throughout recent decades, but these were mostly limited to manipulation of smaller pieces of DNA and vectors used for downstream analyses or genetic transformation of organisms.
Precise, targeted genome engineering of organisms became a reality in 2012 when it was shown that an engineered Cas9 (an RNA-guided DNA endonuclease) could be used together with components of the bacterial defense system CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats). CRISPR-Cas9 has since revolutionized genome engineering in a range of organisms- including yeast, zebrafish, fruit flies, nematodes, plants, mice, monkeys and human embryos.
A handful of researchers in South Africa has since started incorporating this, and other genome-engineering technologies, in their research endeavors. Considering the potential impact of this technology and its ability to address African research questions, it was appropriate to incorporate as the central theme in one of the series of ACGT regional scientific fora. The ACGT teamed up with the University of Pretoria to host a “Genome Editing” forum that cut across multiple biotechnology sectors.
The forum was anchored by a leading genome editing specialist in the plant biotechnology sector, from the Karlsruhe Institute of Technology (KIT) in Germany, Professor Holger Puchta. Prof Puchta is the leader of the Botanical Institute at the research entity and Chair in Molecular Biology and Biochemistry. Professor Puchta’s keynote presentation was entitled “Double-Strand Break Induced Genome Engineering in Plants: Past, Present, Future”. The remainder of the presentations were from South African-based researchers and included:
- Ms Prashika Singh (Wits)- Using obligate heterodimeric TALENs to mutate Hepatitis B virus DNA
- Prof Patrick Arbuthnot (Wits)- Disabling Hepatitis B virus with CRISPR/Cas9 from Staphylococcus aureus
- Dr Victoria Maloney (UP)- CRISPR gene editing in trees
- Mr Donovin Coles (UP)- Lessons learned from genome editing in Arabidopsis thaliana
- Mr Ezio Fok (CSIR)- Interrogating the dark matter of the genome using gene editing tools.
The presentations were all of an exceptionally high standard and feedback received from delegates was very positive. Sufficient time was was set aside for networking between sessions and following conclusions of the event over lunch.
The event attracted a total of 61 delegates, including principal investigators and post-graduate students, with some as far afield as Cape Town. Notably, there was also representation from two entities in industry. From the deliberations, it was clear that researchers in different biotechnology sectors could benefit strongly from networking and collaboration with researchers in other sectors, should cross-cutting technologies be the central focus.
The ACGT and its partners are currently evaluating how best to build capacity in this developing field in the country. What is certain is that more events on this exciting and rapidly evolving topic will be forthcoming.
The ACGT wishes to express its sincere gratitude to especially Mr Thabo Khoza and Itseng Malao (both ACGT) as well as Dr Bridget Crampton for co-organizing the event; and the University of Pretoria for acting as hosts.