21st Jan 2019
RNA Seq aims to unravel the sum of all transcripts in an organism at any given moment in time and can give important clues to changes occurring in an organism following a variety of environmental cues or life stage transitions. The ACGT, in conjunction with the Universities of Zurich, Pretoria and the Agricultural Research Council, will host a whole transcriptome sequencing (RNA sequencing or RNA Seq) data analysis workshop for researchers in Pretoria during the first week of February 2019. In preparation for the workshop, there will also be introductory sessions to Linux and R for those accepted to attend the workshop.
Important dates:· 01 February 2019 (Friday) – Introduction to Linux
· 04 February 2019 (Monday) – Introduction to R
· 05-08 February 2019 (Tuesday to Friday) – RNA Seq WorkshopTopics:
· Theoretical aspects (technologies and applications, experimental design, batch effects, dimension reduction, clustering, QC, limma, normalization)
· Environment setup (Organizing files, running QC on datasets)
· Differential expression
· Advanced topics (Geneset testing, single cell pre-processing, workflow)
· One-on-one sessions with delegates to address their specific queries or to clarify any issues that may have arisen.
The Facilitators:The workshop will include a mix of lectures and hands-on practical sessions facilitated by renowned and expert academics. The facilitators will include:
· Professor Mark Robinson: Professor of Statistical Genomics at the Institute of Molecular Life Sciences at the University of Zurich in Switzerland – Research interests are in the application of statistical methods and data science to experimental data with biological applications within the context of genomics data types.
· Doctor Simone Tiberi: Post-Doctoral Research Fellow, also from the University of Zurich, who works on on the development of cutting-edge statistical methods in bioinformatics, mostly for bulk and single-cell RNA-seq data.
· Professor Fourie Joubert: Bioinformaticist and Director of the Centre for Bioinformatics and Computational Biology at the University of Pretoria.
· Doctor Rian Pierneef: Bioinformatics Research Scientist at the Biotechnology Platform of the Agricultural Research Council.Application Process:
Should you be interested in attending this course, please provide your details and your reasons for attending the course before noon on Wednesday, 23 January 2019.
Please use this link to apply:
Kindly be as descriptive as possible in answering questions as selections will be based on the answers you provided. If you know someone else who stands to benefit from this course, kindly forward this email to the relevant party. Please note that incomplete applications will not be considered. We look forward to receiving your applications.
On behalf of the organising committee
African Center for Gene Technologies
Experimental Farm, South Street
University of Pretoria
Tel: +27 12 420 6139/ +27 71 887 0438
20th Dec 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 Dec 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
28th Nov 2018
The African Centre for Gene Technologies (ACGT) reached out to numerous metagenomics researchers throughout the country and determined that most of their capacity-building needs were data orientated. A large number of metagenomics stakeholders generate huge amounts of data from samples derived from diverse environments. The stakeholders felt they were not getting maximum value out of vast amount of metagenomics data they have gathered due to limitations in skills to effectively analyse and interpret the data. The ACGT decided to assist in addressing this issue by organizing multiple training initiatives starting with a metagenomics data visualization & data interpretation workshop.
The metagenomics data visualization & data interpretation workshop ran from 12-14th November 2018 at the University of Pretoria and was facilitated by a local expert, Dr Rian Pierneef. Dr Pierneef is a bioinformatics research scientist at the Biotechnology Platform of the Agricultural Research Council. Dr Pierneef specializes in biological data analysis and has conducted numerous research studies on prokaryotes in the agricultural environment. The three-day workshop focused on using R for metagenomics data visualization. R is a programming language and free software environment for statistical computing and graphics. The R language is widely used among statisticians and data miners for developing statistical software and data analysis. The workshop started with introducing R to the workshop attendees and then proceeded to direct the attendees through the use of R packages for metagenomics analysis and data visualization.
The delegates were from different research backgrounds and hailed mostly from the ACGT partner institutions; University of Pretoria, Agricultural Research Council and Council for Scientific and Industrial Research. The lectures were kept as relaxed as possible with open discussions and computer-based practical sessions. Through the interactive sessions, the attendees were able to obtain advice and assistance that was specific to their individual projects. There was a general sense from the course evaluations that the course was relevant, practical and beneficial. The ACGT and all of its partners would like to extend enormous gratitude to Dr Rian Pierneef for sharing his time and expertise with the attendees. The ACGT would also like to thank Professor Fourie Joubert and Mrs Itseng Malao for all of their assistance in organizing this event. The ACGT wishes all the participants the best of luck with applying their new earned skill to their work. Due to limited space, not all of the applicants 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).
Here is a link to some of the images taken during the event:
9th Oct 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 (email@example.com, 012 420 6139).
13th Sep 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 Sep 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
10th Jul 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 Jun 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 Apr 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.