20th December 2018
The second Regional Plant Biotechnology Forum for 2018, co-hosted by the ACGT and the University of Johannesburg, centered around plant-pathogen interactions; a particular area of interest for numerous researchers in the partnership and beyond. As is appropriate in the “-omics” and systems biology era, the theme for the forum was “Advances in Plant Defense Responses: Towards Plant-Pathogen System Perspectives”. The topic was deliberately chosen to provide a platform for those who aim to unravel such responses from a wider systems perspective.
The wide variety of presentations, most with a focus on genome-wide approaches to deciphering plant defence systems, managed to attract in excess of 60 delegates from a range of universities, science councils (the majority being from ACGT partner institutions) as well as funders. The keynote speaker for the event was Dr Naadirah Moola, a researcher associated with both the University of Cape Town and the University of Ghent, Belgium. The title of her address was “A cereal killer’s killer: chitosan and plant defence”. Her address was followed by ten additional presentations, mostly from researchers associated with the Universities of Johannesburg and Pretoria. The presentations included studies utilizing technologies including transcriptomics, proteomics, multi-platform metabolomics, as well as combinations of the above. In addition, classical biochemical approaches were also utilised in addressing the research questions at hand.
The forum provided an excellent networking opportunity for researchers active in this field and exposed them to different approaches to elucidating plant-pathogen interactions in different systems.
The ACGT would like to sincerely thank the organizing team at ACGT (Thabo Khoza, Molati Nonyane and Itseng Malao), as well as UJ (Dr Farhahna Allie, Dr Ian Dubery and Dr Fidele Tugizimana).
For any queries about future Plant Biotechnology fora or suggestions for topics related to forums or workshops in this field, kindly contact Mr Thabo Khoza, ACGT Liaison Scientist, email@example.com.
18th December 2018
Two University of Pretoria (UP) academics have received prestigious A1 ratings by the National Research Foundation (NRF) for 2018, bringing the number of UP scientists rated in the A category to 14.
Prof. Don Cowan, Director of the Centre for Microbial Ecology and Genomics, has received an A1 rating, up from his previous A2 rating, while Prof. Mike Wingfield, founding director of UP’s Forestry And Biotechnology Institute (FABI), had his A1 rating renewed.
An NRF rating is a measure of the quality of a researcher, based on peer reviews of their publication performance and impact, including international recognition. A researcher in the A-rated category is recognised by all reviewers as a leading scholar in his/her field internationally for the high quality and wide impact – beyond a narrow field of specialisation – of his/her recent research outputs.
Prof. Cowan established the Centre for Microbial Ecology and Genomics in 2013. The Centre works on various aspects of soil microbial ecology, with a particular focus on hot and cold desert ecosystems. The team uses the latest metagenomic and bioinformatics methods to investigate the structure, function, adaptation and resilience of soil microbial communities, to further understanding of their roles in soil health, plant productivity and the provision of genetic resources. “I am absolutely delighted with the NRF rating result,” Prof. Cowan says. “One of the wonderful elements of academia is that it is possible to be rewarded for working on something about which one is passionate. But this is not a solo effort: I must also gratefully acknowledge and sincerely thank all those who have played their part, whether big or small, in this wonderful result: my research collaborators, my postdocs and students, my friends and my colleagues, and my wife.”
Prof. Wingfield’s research interests are focused on the broad area of forest health, particularly those caused by insect pests and pathogens of trees, and their patterns of global movement. Together with his colleagues and collaborators, the research team applies a wide range of biotechnology tools in order to better understand the biology and epidemiology of tree pests, and reduce the dramatic impact they are having globally. Asked about once again receiving an A1 NRF rating, Prof. Wingfield said, “This award belongs as much to me as it does to the amazing FABI team, including a wonderful group of colleagues, students and collaborators globally. I hope they will enjoy the fruits of the award with me and, more importantly, continue to have fun doing impactful research in the interests of forests and forestry globally.”
Meanwhile, Dr Eshchar Mizrachi, a senior lecturer at FABI, is one of four scientists in South Africa to be awarded a highly prestigious P rating for research on understanding the molecular biology of polysaccharide metabolism, especially cellulose and xylan, during wood formation in Eucalyptus trees. This rating is assigned to researchers normally under 35 years of age who have held a doctorate or equivalent qualification for less than five years at the time of application. His research primarily focuses on constructing a model of the regulatory network (genes, proteins and pathways) that play a role in influencing the partitioning of carbon and the deposition of cellulose and xylan in wood, and identifying candidate pathways or processes for biotechnological improvement of trees (applied via breeding using molecular selection tools, or genetic modification).
Prof. Slippers, Director of FABI, said, “These recent ratings show that we do not only compete locally in terms of excellence, but also with the best in the world. It is exciting to have both established world leaders and upcoming young and leading scientists in FABI. That is good for the future of the institute and University, and shows that we have a vibrant academic environment.”
All three scientists are academically linked to the Department of Biochemistry, Genetics and Microbiology. Head of Department Prof. Paulette Bloomer said, “It is a true privilege to be the academic home of these world-leading scientists, to share their passion for discovering the fundamental basis of biology, and to do research that is locally and internationally relevant.”
In addition to these A and P ratings, so far in the current round of awards and renewals of NRF ratings, UP academics have received a total of no less than 30 new ratings, and 49 renewed ratings, of which 2 are A ratings, 20 are in the B category, with 43 C and 9 Y ratings. The University of Pretoria now hosts 507 rated researchers, representing about 12% of the total number of rated researchers in South Africa.
Prof. Stephanie Burton, UP Vice-Principal for Research and Postgraduate Education, said the University is proud of the achievements of all these academic colleagues. “We are one of the biggest producers of university research in the country and Africa, and we produce research that is relevant and which matters.”
Story by: Buyisiwe Nkonyane, University of Pretoria
9th October 2018
Capacity building is one of the objectives of the African Centre for Gene Technologies (ACGT) as a means to improve the skills level of South African scientists, especially in the field of bioinformatics data analysis. For African scientists to continue to produce quality work that is internationally recognized and competitive, there has to be continuous efforts to equip the scientists with the most relevant and applicable skills available. 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. For this reason, the ACGT organized a Linux course to benefit life scientists and introduce them to basic Linux concepts. The Linux course ran from the 25th to 28th September 2018 at the University of Pretoria, Hatfield campus at the Centre for Bioinformatics and Computational Biology (CBCB).
The course was facilitated by Mr Shaheem Sadien from the Cisco Networking Academy from Cape Town. Mr Sadien is a renowned lecturer and skilled technician with a wealth of over 12 years of experience and knowledge on networking, operating systems and applications. The lectures were kept as relaxed as possible with open discussions and computer-based practical sessions. The topics outlined below were covered during the course:
- The shell,
- the file system,
- files and directories,
- finding files,
- basic system commands,
- redirection with command and file pipes,
- basic grep, sed and awk,
- environment variables, and
- basic shell scripts.
The sessions were kept as interactive as possible to create a relaxed environment where the participants could ask questions and get the most out of the four days. The 25 delegates were from different research backgrounds and hailed mostly from the ACGT partner institutions; the Universities of Pretoria and the Witwatersrand, the Agricultural Research Council and Council for Scientific and Industrial Research.
Following conclusion of the workshop, there has been very positive feedback from the participants of the course. There was a general sense from the course evaluations that the course was informative, practical and interesting. Moving forward, there are plans to adjust some aspects of the course such as content and more bioinformatics-specific approaches. Keep an eye on the ACGT website and e-mail alerts for news of future iterations of the Linux workshop.
The ACGT and all of its partners would like to extend enormous gratitude to Mr Shaheem Sadien and Professor Fourie Joubert for running the course smoothly and successfully. The ACGT would also like to thank all the behind-the-scenes people that had a hand in putting this course together: Itseng Malao, Johann Swart and Vaughan Beckerling. The ACGT wishes all the participants good luck with their future work. Due to limited space, not all of the applicant could be hosted but the ACGT encourages those that were not placed this year to keep an eye out for future courses.
For any other capacity building and networking queries, kindly contact Mr Molati Nonyane, ACGT Liaison Scientist (firstname.lastname@example.org, 012 420 6139).
13th September 2018
The proteomics community of South African came together for a week of proteomics events in the month of August 2018. In this week, two events organised by the ACGT, CSIR, DILPOMICS and the Universities of Cape Town and the Witwatersrand took place. The Advanced Proteomics Workshop was facilitated between the 20th and 22nd of August 2018; which was followed by the South African Proteomics Symposium a day later. Both these events were hosted at the Wits Parktown Health Sciences Campus.
The proteomics week kicked off with the Advanced Proteomics Workshop, which was facilitated by three world experts in the field. Each facilitator gave a series of lectures and hands-on exercises in the field which were highly respected for. In the three days dedicated to the workshop, the delegates were taught different aspect of Spatial Proteomics, Clinical Proteomics and Quality Control. The workshop began with Prof Kathryn Lilley (Research Group Head and Director, Cambridge Centre for Proteomics, University of Cambridge) taking the delegates through a series of lectures on Quantitative Proteomics and Spatial Proteomics. Included in Prof Lilley’s sessions were tutorials on Experimental Design, which enabled the delegates work on different scenarios to design effective experiments. These tutorials allowed the delegates to think outside the box and helped them think through their own experiments and how they would design them in the future.
Prof Stephen Pennington, a professor of Proteomics and Senior Fellow at the Conway Institute of Biomolecular and Biomedical Research at the University of College Dublin, took over from Prof Lilley and facilitated the Clinical Proteomics section of the workshop.
The last section of the workshop, Quality Control, was presented by Prof David Tabb. David Tabb is a Professor in the Division of Molecular Biology and Human Genetics at the Faculty of Medicine and Health Science at Stellenbosch University. Prof Tabb combined his lectures with tutorials and assisted the delegates to work with real proteomics data.
The workshop was attended by delegates from the following national institutions:
African Health Research Institute
Cape Peninsula University of Technology
Centre for Proteomic and Genomic Research
Council for Scientific and Industrial Research
Fort Hare University
The National Health Laboratory Services
The National Institute for Communicable Diseases
University of Cape Town
University of Johannesburg
University of Pretoria
University of the Western Cape
University of the Witwatersrand
The second part of the proteomics week saw seventy-two delegates gather at the Adler Museum of Medicine (Wits Parktown Health Sciences Campus) to attend the South African Proteomics Symposium.
The symposium was opened by Dr John Becker (ACGT – Centre manager) and Prof Michele Ramsay (Champion: Molecular Biosciences Research Thrust, University of the Witwatersrand). Prof Kathryn Lilley and Prof Stephen Pennington each gave a keynote address followed by presentations from top proteomics researchers in South Africa. These South African researchers represented the following institutions: African Health Research Institute, CSIR, CPGR, Fort Hare University, North West University, Stellenbosch University, University of Cape Town, University of the Western Cape as well as the University of the Witwatersrand. The following event sponsors also gave talks at the symposium: Microsep, Anatech Instruments and Separations. Click here to view the symposium booklet that contains the full programme as well poster abstracts for posters that were displayed at the symposium.
Both the workshop and symposium gave the delegates the platform to interact with world class proteomics researchers and to explore opportunities (postdoctoral fellowships, collaborative opportunities, etc.) that may arise from the proteomics week. This week also provided the delegates with a platform to network with each other for possible future collaborative opportunities- as well as to informally have discussions around the formation of a Proteomics Society of South Africa. The ACGT has made itself available to assist in the establishment of this society. This process will be guided by the proteomics community of South Africa that the society will serve.
The ACGT would like to thank the following sponsors for financial assistance to make the workshop and symposium possible: Anatech, CPGR, DIPLOMICS, inqaba biotec, Microsep, Separations and The Scientific Group.
Story by: The ACGT team, September 2018
For more photos from these events, please visit our Facebook page: ACGT Facebook page
10th September 2018
Science, technology and innovation enabling sustainable and inclusive development in a changing world
Twenty years after the adoption of the first White Paper on Science and Technology (DST) in 1996, the Department of Science and Technology began developing a new draft White Paper on Science, Technology and Innovation (STI), which was approved by Cabinet last week. The new document will ensure a growing role for STI in building a more prosperous and inclusive society. It focuses on using STI to accelerate inclusive economic growth, make the economy more competitive and improve people’s everyday lives.
The review of the 1996 White Paper, which included broad consultation within the national system of innovation, showed that, while there has been good progress in the implementation of this document, South Africa has not yet fully benefited from the potential of STI to advance the objectives of the National Development Plan. The STI institutional landscape is a case in point. It has been expanded and there has been a threefold increase in publications, significant growth in the participation of black people and women in the research and development workforce, and a rise in doctoral graduation rates. However, challenges remain, and the national system of innovation is still not fully inclusive.
Since the adoption of the 1996 White Paper, the world has changed. The Fourth Industrial Revolution, which is rapidly transforming the way people interact, transact and learn is already well advanced in the developing world. To enable South Africa’s effective participation in this new world order, which is bringing increasing automation and digitisation, the Department of Science and Technology has developed a new policy document.
The new draft policy focuses on two main goals, namely, to ensure that South Africa benefits from STI for economic growth, social development and transformation, and to respond to the risks and opportunities brought by rapid global technological advancement and other global changes.
With rapid change comes increasing uncertainty about the future, particularly for emerging markets like South Africa’s. The new draft White Paper has considered a number of megatrends spanning the geopolitical, economic, social, technological and environmental spheres.
These megatrends include a growing population, increased consumption driven by an expanding middle class in emerging economies, the rise of China and India, and the impact on the natural environment. The degree to which countries prepare for these changes will determine whether they thrive.
Some of the megatrends are creating market opportunities. For example, the growth of a middle class in emerging economies, and the high proportion of young people in the total population in Africa – the so-called “youth bulge” – are stimulating manufacturing, widening markets for mobile telephones and creating job opportunities for ICT-enabled young entrepreneurs in the services sector. South Africa can benefit from these opportunities by using technology to modernise sectors such as agriculture and mining and increase exports to growing markets. Innovation is required to address needs arising from these megatrends, such as protecting the environment and improving service delivery.
Rapid technological change is driving some of these megatrends to shape a world that will soon look very different. The lines between physical, digital and biological systems are becoming blurred, and governments around the world are planning for the impact of the Fourth Industrial Revolution. In particular, it is necessary to prepare for the ways in which artificial intelligence and advances in ICT will change the way society and the economy function.
Already, traditional jobs are being lost due to automation and traditional commerce is being disrupted by the move to online, just-in-time personalised services and products. The role of cryptocurrencies in the digital economy is uncertain. The possibilities are exciting and the implications vast.
STI lies at the heart of the preparation for this emerging future, and South Africa therefore needs to build on progress in areas such as biotechnology, nanotechnology, advanced manufacturing, and ICT research and innovation. This White Paper proposes policy interventions to accelerate skills development, leverage ICT, commit to openness, and support inter- and transdisciplinary research. It also puts in place mechanisms to institutionalise foresight capacity to assist collaborative planning across government for STI.
Overview of the new draft White Paper
The new draft White Paper focuses on the following:
- Raising the profile of STI in South Africa by instilling an innovation culture in South African society and integrating STI into cross-cutting government planning at the highest levels.
- Strengthening partnerships between business, government, academia and civil society, creating a more enabling environment for STI.
- Focusing on innovation for social benefit and for fundamental economic transformation.
- Expanding and transforming the human resource base of the national system of innovation.
- Increasing investment, both public and private, in STI.
Raising the profile of STI in South Africa
- South Africa needs to set its innovation agenda at the highest level of government and business so that all actors pursue the same objectives and pool resources where possible. The Presidency will therefore chair an STI Plenary meeting, involving business leaders, academic experts in the field of STI, government departments that have a focus on STI, and leaders from civil society. Among other matters, the STI Plenary will discuss STI priorities.
- To ensure that STI is integrated into the planning of relevant government departments and that the STI programmes have sufficient funding, an Interministerial Committee on STI, chaired by the Minister of Science and Technology, will be formed.
- To provide the necessary data on and analysis of STI progress and enablers, the National Advisory Council on Innovation will be strengthened.
Strengthening partnerships among business, government, academia and civil society
While government has an important role to play in enabling and stimulating STI, it cannot do it alone.
The White Paper therefore has a strong focus on including business in STI planning (at the level of the STI Plenary, but also at the level of, for example, the mining or agricultural sector level) and on support measures for business, for instance, by means of incentives for small and medium enterprises and the direct funding of research and development through Sector Innovation Funds.
- The White Paper also draws civil society formally into STI planning and aims to empower civil society to distribute the benefits of technology to communities, as well as to help identify and support grassroots innovators.
Creating a more enabling environment for STI
- All government departments working in areas that affect STI will embrace a national innovation compact to ensure that there is policy coherence across the national innovation system, and that immigration, education, trade, competition and procurement policies, to name a few, support innovation.
- The various incentives offered by government for STI will be aligned to ensure synergy rather than duplication in using the available funding, and their administration will be improved to ensure effectiveness.
- Government procurement will support locally developed technologies.
- Local innovation systems will be stimulated by, for example, walk-in innovation centres for communities and more incubators, and encouraging the involvement of local universities.
- Measures to create greater access to STI information such as solutions developed at universities will be created through an open science approach.
Focusing on innovation for social benefit and for fundamental economic transformation
- Civil society will be involved in high-level government planning for STI programmes and will be supported through training, funding and networks to play a stronger role.
- Support for grassroots and social innovation, when linked to provincial and local development strategies, will have significant transformative results.
- The intellectual property regime for publicly funded research and development (R&D) will be reviewed to expand South Africa’s patenting. Intellectual property generated from publicly funded R&D will be used to help increase black and female ownership of new technology-based companies.
- Government itself will become more innovative in using digital information and innovative technologies for service delivery. This will involve accelerated digitisation, establishing innovation units in STI-intensive departments, and increasing the movement of human resources between government, science councils and business, among other things.
Expanding and transforming the science and human resource base of the national system of innovation
- A policy nexus will be developed to achieve collaboration, increased funding, and policy coherence to improve educational outcomes from early childhood and school level (to increase the number of Grade 12 university exemption passes with Science and Mathematics – the pipeline) and higher education (to further increase the number of PhDs produced, and improve the representation of blacks and women).
- Internships and training opportunities abroad are to be expanded.
- The untapped potential of historically disadvantaged universities and universities of technology will be used.
- There will be increased support for research, both basic and transdisciplinary.
Increasing investment, both public and private, in STI
South Africa’s gross expenditure on research and development as a percentage of GDP, which is currently about 0,76%, needs to be increased to 1,5% over the next decade. This will be done through improved incentives for business R&D, contributions to public STI by provincial governments, and expanding measures to attract foreign funding for South African STI.
An annual STI investment framework, linked to the national STI agenda, will be developed to direct the allocation of public funding to priority STI programmes.
Implementing the White Paper
The White Paper sets the high-level, long-term policy direction for the next five to 15 years. It will be implemented through regularly updated decadal plans, which will be based on performance evaluation and foresight, as well as collaborative planning with relevant business sectors and government departments. The decadal plans will detail the deliverables, partnerships and funding required, as well as the indicators that will be used to measure progress. To this end, the National Advisory Council on Innovation is currently undertaking a foresight exercise for South Africa.
The truest test of this White Paper will be the impact that it has in realising the potential of STI to support the achievement of the National Development Plan and to help change the reality of South African’s lives over time.
The next steps
This is a draft White Paper released for public consultation. Members of the public have 30 days to make inputs. After the comments have been integrated, we intend to have a summit on 9 November 2018 to engage various stakeholders on the White Paper before taking the final document to Cabinet for approval.
For the full document visit www.dst.gov.za.
For more information
Veronica Mohapeloa (083 400 5730)
Thabang Setlhare (072 659 9690)
Media Liaison Officer
Ministry of Science and Technology
064 754 8426
30th September 2016
In early September, the ACGT teamed up with WITS and UP’s 2016 iGem team to sponsor and host a 2-day informative workshop and symposium on Synthetic Biology. Synthetic biology is a multidisciplinary field of science that involves the design and construction of novel artificial biomolecular components, pathways or networks in organisms or the redesign of existing natural biological systems. Although still in its infancy, Synthetic biology is rapidly expanding and has shown huge potential and benefit in a diverse number of applications, including the development of cheaper drugs, the treatment of antibiotic resistant infections, genetic disorders, therapies to treat diseases such as cancer, biofuel production.
The 2-day event was well attended and included participants from the CSIR, ARC, UP, WITS and the Department of Environmental Affairs. The workshop was interactive and delegates had the opportunity to hear about and discuss some of activities and approaches in the field that are currently being explored in South America, UK and South Africa. On the first day, a workshop was facilitated by Dr. Fernán Federici, assistant professor at the Pontifical Catholic University of Chile and a research fellow at the University of Cambridge. Dr. Federici introduced open source technologies for science, education and bioengineering as well as started open discussions about how to implement new collaborative frameworks in Africa and Latin America. Dr. Geoffrey Baldwin, a Reader in Biochemistry in the Department of Life Sciences and Centre for Synthetic Biology and Innovation (CSynBI) at Imperial College London, also presented on his work on the BASIC method for standard DNA assembly approaches.
On the second day, delegates were treated to a keynote address by Dr. Baldwin titled: “Engineering Biology in the Genomic Age: the Synthetic Biology Revolution” as well a presentation by the 2016 UP iGEM team on their WattsAptamer project, where they described the design of “Synthetic laccases and DNA aptamers for thylakoid tethering in photo-electrochemical cells”.
These two events provided an informative platform for an exchange of ideas and interdisciplinary discussions as well as the potential for new collaborations. The ACGT is committed to supporting and hosting events that benefit Biotechnology and the Bioscience Community, particularly our partners, so for more information on upcoming workshops, symposia and bioinformatics training events, visit the events page on the ACGT website (www.acgt.co.za), like us on Facebook (http://www.facebook.com/ACGT.biotec) or contact Farhahna Allie at az.ca1547650433.ju@e1547650433illaf1547650433
* Thank you to Whitehead Scientific for sponsorship towards these events
19th August 2011
CSIR Biosciences joined the University of Pretoria’s Pharmacology Department in co-hosting a national symposium followed by a workshop on proteomics. The successful event drew close to 70 delegates from across the country to a two-day symposium held on 11 and 12 July followed by an oversubscribed two-day hands-on workshop. The symposium was a follow-up to an inaugural meeting that was hosted by the Universities of Pretoria and the Witwatersrand in 2009. (more…)
22nd March 2010
The ACGT was recently represented at the Food and Agricultural Organisation of the United Nations (FAO) International technical conference on Agricultural Biotechnologies in Developing Countries (ABDC-10). (more…)
22nd February 2010
A world-class building promising to be an excellent example of a green building that is both effective and user-friendly will be erected at the University of Pretoria.
A sod-turning ceremony was held at the construction site of the new Plant Science building on Friday 29 January 2010. In her welcoming speech Prof Cheryl de la Rey, Vice-Chancellor and Principal of the University of Pretoria, described the occasion as symbolic of the successes of the Faculty of Natural and Agricultural Sciences and the University of Pretoria. Prof de la Rey said that this event marked the University’s commitment to 2010 as the International Year of Biodiversity and that it was a “celebration of past successes and new beginnings”.
Click here to read more
21st February 2010
February 2010 Related info National Health Laboratory Service
The ACGT was recently represented at the annual SAMI (South African Malaria Initiative) Conference 2010 in Cape St Francis. The meeting, which was held from 26 – 28 January, was followed by an open SAMI Steering Committee Meeting. (more…)