14th Aug 2019
My involvement with the field of Metabolomics is in my capacity as Liaison Scientist for the African Centre for Gene Technologies (ACGT) and as a committee member of Metabolomics South Africa (MSA). The ACGT represents the interests of three universities and two research councils in the Gauteng region (Wits, UJ, UP, CSIR and ARC. I coordinate ACGT’s Metabolomics capacity building activities which include, but are not limited to: meetings, workshops and symposiums; finding synergies between researchers and subsequently building linkages amongst ACGT partner institutions and relevant outside institutions. MSA is a non-profit organization seen as an opportunity to promote and improve the profile of metabolomics research and technology in South Africa, foster networking, training, capacity building, information sharing, mentoring, career opportunities, leadership training and professional development.
I discovered through one of our colleagues from the University of Edinburgh that a Metabolomics Conference was to be held at the World Forum in The Hague, Netherlands from 23-27 June 2019. Attending relevant information dissemination events like the 2019 International Metabolomics Conference, helps me perform my roles well for the ACGT and its partners and also enables me to keep up with the trends in metabolomics research. A decision was then made that I would be attending the conference. I therefore registered to attend the conference and began with the travel arrangements. The visa came out in the nick of time, they do say better late than never. I managed to conquer the usual worries of travelling: Did I pack enough clothes? Did I forget something? Constant reminder that whatever I do, I better not miss the flight. Thankfully, there were no glitches in my travel and all went well. As a bonus, the city of The Hague in itself is amazing with efficient public transport and some great sites.
There was a great South African presence at the workshop with delegates from University of Johannesburg, University of South Africa and North-West University. The conference provided an opportunity to listen to international metabolomics researchers from all over the world sharing their findings, an opportunity to network and identify relevant synergies so as to foster further collaboration amongst metabolomics researchers within SA and across the world. The ACGT already has relationships with some key international metabolomics players who have been assisting with capacity building activities over the past several years. This event provided an opportunity for some stakeholder management to continue to strengthen these relationships. This conference was also an opportunity to expand our contact list and open up new opportunities for collaborations and relationships with South Africans researchers.
My takeaway from this conference is simply that there is a significant and continuing growth of metabolomics all over the world. The discipline has diverse applications in health, agriculture and industry. The ACGT and MSA will do all in its power to assist in pushing African Metabolomics in the right direction and keeping it globally competitive. I would like to encourage anyone who is involved in metabolomics or metabolomics related work to attend future International Metabolomics Conference as this was a worthwhile experience.
My interests and professional involvements are not only limited to the field of metabolomics, I also continue to be involved in genomics and in life science research in aspects that include capacity building, fundraising and research coordination, nationally and internationally. For queries relating to any of the above fields, feel free to contact me at and we can discuss how I and/or the ACGT can be of assistance.
Story by: Molati Nonyane
19th Jul 2019
In the post-genomic era, life scientists are generating more data than ever. To enable researchers to manipulate and analyze their own data, the ACGT, together with the Centre for Bioinformatics and Computational Biology (CBCB, University of Pretoria) hosted a three-day workshop on the use of the operating system. Linux is open-source software allows researchers to analyze data generated on multiple platforms, in contrast to expensive vendor-specific software that require periodic license renewals.
The workshop was facilitated in conjunction with the CISCO Networking Academy, and a trainer from this academy, Mr Shaheem Sadien, facilitated the training sessions, with Professor Fourie Joubert providing context and practical examples on structural and next-generation sequencing data. Delegates were representative of all ACGT partner institutions (ARC, CSIR, UJ, UP and Wits), as well as the South African Medical Research Council. The delegates had wide-ranging interests, ranging from precision medicine, food technology, crop protection to animal genetics.
All delegates indicated that they would recommend the course to their colleagues, and their suggestions for future courses were noted. The trainers provided the delegates with ample online resources to work from in the future but there is a plan that in future workshops, the trainers will make time to assist each delegate with their own specific data sets. Should delegates complete the requisite online modules, they also receive a certificate of competence from CISCO.
Brief feedback from some of the delegates, on what they enjoyed most, can be found below:
“I really enjoyed the application of skills presented on the Thursday. But the rest of the course was definitely necessary to understand that section!”
“Doing the exercises in the class where you can ask questions and the lecturers were awesome.”
“Despite the fact that the course was provided in class, explaining concepts and allowing practice, a detailed online course is also provided. This repetition I think works well to allow lasting memorization of the course content – which is basically a language that needs to be remembered.“
Kindly also see the ACGT’s Facebook page for pictures of the event. The ACGT wishes to thank Mr Molati Nonyane, Ms Itseng Malao, Mr Shaheem Sadien and Prof Fourie Joubert for course content and organization. The ACGT is looking to host another iteration of this course in 2020. Kindly contact our Liaison Scientist, Mr Molati Nonyani () in this regard.
20th Jun 2019
There is no doubt that the stem cell field is generating a great deal of excitement and hope. Efforts are underway across the globe to find cures for incurable diseases. Yet despite these exciting developments, only a limited number of procedures are approved for routine therapy.
A spinal cord injury
Bone marrow transplantation, which has been performed for cancers and blood disorders for several decades, is one for the few universally approved and routinely practiced forms of stem cells therapy.
On 31 May 2019, Health24 published an article stating that stem cell treatment had improved the quality of life of a rugby player who sustained a spinal cord injury. Rugby injuries are often low velocity injuries and in many cases, the injuries that are sustained are incomplete.
The implication is that recovery is possible, to a greater or lesser degree, with follow up rehabilitation. To date, despite numerous research efforts and clinical trials, there is virtually no evidence that stem cells can cure spinal cord injury. Several factors are critical when assessing a case such as the one mentioned above. What was the origin of the cells used? How were they administered? Was the patient walking before the stem cells were administered?
Equally important, did the administration of the stem cells comply with the laws of the country, and since this is an unproven therapy, should it have been considered as a clinical trial? In the case of the latter, a number of critical steps would have needed to be followed.
While not wanting to detract from the great joy of seeing someone recover from a debilitating injury, accurate reporting is important if one is to ensure that vulnerable patients are not emotionally and financially exploited. There is regrettably a global trend involving “stem cell clinics” that seeks to treat a range of diseases using unproven stem cell therapies. Propagating the idea that there is a direct causal relationship between the administration of stem cells and a positive outcome, without considering all of the facts, may be misleading and may prompt other vulnerable patients to undertake similar unproven therapies.
It is therefore the responsibility of the person reporting the story to do so in a manner that is objective, and to avoid implicating direct causality unless this can be proven. Evidence-based and ethical marketing is also important in order to avoid misleading vulnerable patients and their families. An advertisement, currently running on one of the local radio stations, indicates that the future use of stored stem cells will “overcome my diabetes” and “treat my autism”.
While there is ongoing research in both of these areas, and many more, there is no guarantee that stem cells will be able to be used to treat these conditions in the future. Given the extent of the emotional involvement around matters pertaining to children, potential customers might be made to believe that by banking their newborn’s stem cells, “the child you have today will be protected tomorrow”.
While there is the potential that stored stem cells might well be used in the future for bone marrow transplantation or for regenerative medicine purposes, this information should be convened objectively, which includes placing the possibility of a future cure into perspective relative to the evidence currently available. Why is it important to proceed cautiously with new treatments that have the potential to cure previously incurable diseases?
One important reason is highlighted in a recent court decision in the US. As noted by the International Society for Cell and Gene Therapy, “this ruling an important step towards the regulation of an industry that has eluded regulatory oversight for many years, causing substantial financial, and in many cases, physical harm to patients through direct-to-consumer advertising of unproven and poorly tested “stem cell” treatments”.
In other words, as long as a treatment that eludes regulatory oversight does no harm, financial loss will be the only issue that needs to be contended with. However, in the case mentioned above, four patients were blinded by stem cells administered directly into their eye. And there are many more examples of cases in which patients have been harmed by unproven “stem-cell” therapies. The argument is often put forward that the use of the patient’s own stem cells does not require regulatory oversight.
Exploitation and possible harm
This is a complex matter, particularly since the cells are often processed in one form or another before being re-administered to the patients, which would qualify them as being “minimally-manipulated”. While there is no specific legislation governing this matter in South Africa, international best practice requires regulatory oversight with the use of such a product. To conclude, evidence-based and ethical reporting and marketing are necessary if patients are to benefit from the great strides being made in the stem cell field.
Not to do so exposes vulnerable people to exploitation and possible harm. It is critical that the South African Government provides an appropriate regulatory framework to allow patients to benefit from advances in the stem cell field while at the same time protecting them from exploitation and harm. This will also promote much needed research, investment and entrepreneurship in the stem cell field for the benefit of all of the people of our country.
Story by: Prof Michael Pepper for Health24
*Michael S. Pepper MBChB (Cape Town), PhD (Geneva), MD (Geneva), PD (Geneva)Professor, Dept. Immunology, Faculty of Health Sciences, University of PretoriaDirector, Institute for Cellular and Molecular Medicine, University of PretoriaDirector, SAMRC Extramural Unit for Stem Cell Research and Therapy
14th May 2019
The University of Cape Town, in partnership with the ACGT, DIPLOMICS and Stellenbosch University, hosted the Trans-Proteomic Pipeline (TPP) workshop which ran from the 21sttill the 22ndof March 2019.
The workshop, which followed the HUPO-PSI meeting, held from the 18thtill the 20thof March 2019, was facilitated by Dr Eric Deutsch and Mr Luis Mendoza from the Institute of Systems Biology (Seattle-USA). Dr Deutsch is a lead designer for the Systems Biology Experimental Management System. He is the Chair of the HUPO-PSI and is one of the leaders of the TPP project- that aims to provide a free and open-source suite of tools for the processing and analysis of proteomic tandem mass spectrometry data.
Mr Mendoza is a senior software engineer at the Institute for Systems Biology. He has been a main contributor to the development of the TPP for the past 14 years.
The two-day workshop was attended by 35 delegates from Universities in the Western Cape region (University of Cape Town, Stellenbosch University, University of the Western Cape and Cape Peninsula University of Technology) as well as delegates from other provinces (Gauteng and KZN).
The ACGT partnership was represented by four delegates at the workshop. The ACGT representatives hailed from the Council for Scientific and Industrial Research (Dr Previn Naiker and Dr Ireshyn Govender), the University of the Witwatersrand (Ms Genevieve Mezoh), and the University of Pretoria (Ms Denise Wilson). The delegates from the ACGT partnership are expected to transfer the knowledge gained from the TPP workshop by training their fellow unit/lab students/colleagues. A week after the workshop, Ms Denise Wilson reported that she was in the process of working with the Centre for Bioinformatics and Computational Biology (CBCB) at the University of Pretoria to install the TPP pipeline for command line execution on their Linux servers.
The next proteomics training workshop will be in November 2019 and it will focus on the open-source software package Skyline, data analysis and SWATH. Information regarding this workshop will be disseminated at a later stage.
Workshop programme: View here
Story by: The ACGT team, 14 May 2019
16th Apr 2019
Sanushka Naidoo, associate professor in the Department of Biochemistry, Genetics and Microbiology at the University of Pretoria (UP), was recently elected chairperson of the Next Einstein Forum’s (NEF) Community of Scientists programme. The NEF is a joint initiative of the Robert Bosch Stiftung Foundation and the African Institute for Mathematical Sciences (AIMS), which has centres in South Africa, Ghana, Senegal, Cameroon and Tanzania.
“The next Einstein could be African,” Prof Naidoo said. “It is up to us to find and nurture such upcoming generations of Einsteins. I am looking forward to presenting our NEF Community of Scientists vision and progress at the next World Economic Forum.”
The NEF provides opportunities for some of the brightest minds in Africa to look at the most persistent problems experienced on the continent and apply technology, engineering and mathematics as well as the social sciences to come up with possible solutions.
“I am honoured and humbled to be elected by such accomplished young scientists,” Prof Naidoo added. “I feel inspired and motivated to lead the community of scientists one step closer to achieving our vision.”
The KwaZulu-Natal-born professor’s vast experience in the field of plant biotechnology will stand her in good stead in her new position. She heads the Eucalyptus and Pine Pathogen Interactions group and works closely with the Forest Molecular Genetics Programme, part of the world-renowned Forestry and Agricultural Biotechnology Institute (FABI) at UP. She is also a committee member of Future Africa at the University of Pretoria.
She has also published more than 30 papers in international peer-reviewed journals, was awarded a Y-rating by the South African National Research Foundation (2015-2020), a Mellon Foundation Mentoring scholarship for her doctoral studies in plant biotechnology, and serves as president of the South African Genetics Society (2017-2020).
The professor’s research interests include genetics, plant biotechnology as well as cell and environmental biology, and she currently teaches molecular genetics at UP. She is the main supervisor to two postdoctoral researchers (Dr Caryn Oates and Dr Erik Visser), two PhD students (Ms Lorraine Mhoswa and Mr Demissew Teshome), one MSc student (Ms Shannon Flemington) and two honours students (Shae Swanepoel and Kgopotso Pakwako).
Prof Naidoo first became involved with the NEF when she was awarded an NEF Fellowship (2017-2019), a programme that recognises the contribution of top young scientists and emerging leaders in Africa, and gives them the opportunity to grow their careers and present their work at the global NEF Spotlight Sessions. As part of the programme, fellows are expected to participate in national and continental policy formulation, cross-cutting research and innovation activities, lead public engagement around science and technology in Africa, and provide mentorship to early-career scientists and students.
During her tenure at the NEF, Prof Naidoo plans to focus on breaking down some of the barriers young African scientists face, such as lack of infrastructure, collaborative networks and resources. She says it’s important for people in leadership positions to remain positive and persevere despite challenges. Over the next two years, the NEF aims to strengthen ties with the community of scientists in order to offer them a strong support network that enables them to achieve their goals. The organisation also intends to build capacity and empower African scientists so they’re able to make use of international opportunities.
Prof Naidoo’s love affair with nature started at a young age. Her parents – both teachers – have always encouraged her to ask questions about the world around her. Her interest in plant science was piqued by a science teacher who encouraged learners to establish a nature club at school.
“We built a pond on the school premises and we watched a whole ecosystem develop over time. This became a teaching tool for our biology classes, and we were fascinated with how organisms depend on each other for survival.”
After matriculating, she enrolled for a degree in Cell and Environmental Biology at the University of KwaZulu-Natal (UKZN), and became interested in plant genetics. She completed her honours at UKZN before obtaining an MSc degree in plant biotechnology at the University of Stellenbosch, and her PhD at UP.
Her current research focuses on mechanisms that can confer broad-spectrum, long-lasting resistance by dissecting gene families and responses to pests and pathogens. With the development of new technologies, novel genetically modified crops are poised to increase yield and protect against pests and pathogens under harsh African climates.
When she’s not among the trees or in the lab, she loves spending time with her husband Tyrrell, her three children Tristan (15), Sunera (8) and Telana (7), and Dakota Rouge, whom she describes as “a beautiful King Charles Cavalier spaniel”. She also enjoys writing poetry and reading motivational books on leadership.
About 40% of the NEF fellows are women, and Prof Naidoo is quick to remind anyone that women have been integral to important scientific discoveries over the ages.
“I think of physicist Marie Curie, cytogeneticist Barbara McClintock and biochemist Jennifer Doudna as exemplars of women who have made impactful scientific breakthroughs. There are other types of contributions by women scientists that deserve attention too, such as Kenyan scientist Wangari Muta Maathai, who was the first African woman to win a Nobel Peace Prize for her efforts to combat deforestation. I believe that women will continue to break through glass ceilings and shape the future because of their passion and commitment to changing lives for the better.”
20th Mar 2019
The African Centre for Gene Technologies (ACGT), the University of Johannesburg and the University of Pretoria organized the 2019 Advanced Metabolomics Workshop that was held at the University of Pretoria from 13-15th March 2019. The workshop provided a capacity building platform to address key issues and challenges in the field of metabolomics.
The workshop was facilitated by this panel of elite metabolomics experts. The facilitators were Dr Reza Salek (International Agency for Research on Cancer, Lyon, France), Dr Karl Burgess (University of Edinburgh, Scotland, UK), Dr Fabien Jourdan (INRA Toulouse, France), Dr Justine Bertrand-Michel (INSERM Toulouse, France), Dr Naomi Rankin (University Hospital Wishaw, Scotland, UK), Dr Jasper Engel (Wageningen University & Research, The Netherlands) and Dr Fidele Tugizmana (University of Johannesburg, RSA).
This workshop covered advanced metabolomics topics using a combination of lectures, interactive round table discussions and computer-based practical sessions. The topics covered in the workshop included applications of metabolomics (clinical, plant/agricultural, industrial), LC-MS/MS/NMR metabolite identification, simple and multivariate statistics, data standards and metabolomics resource, network-oriented metabolomics data mapping, advanced data analysis, lipidomics, metabolomics networks and using fragmentation to enhance metabolite IDs. Throughout the three days, the delegates also had a chance to ask project-specific questions and advice from the with facilitators.
The participants were from the ACGT partner institutions, as well as outside institutions including previously disadvantaged research institutions. There were participants from University of Pret
oria, 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, University of the Free State, Walter Sisulu University, University of Cape Town and the University of Venda. 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 ACGT would also like to wish all the participants of the workshops all the luck with their work and future in metabolomics. Furthermore, the ACGT sends much deserved gratitude to all the members of the organizing committee; Mr Molati Nonyane, Mrs Itseng Malao, Dr John Becker, Dr Fidele Tugizimana, and the European visitors for all of their efforts in making this event a success. The ACGT would also like to extend their gratitude to the sponsors of this event in Thermo Fisher Scientific and the Embassy of France in South Africa.
If you would like to view most of the pictures from this event, please visit our facebook page:
For any metabolomics-related capacity building and networking queries, kindly contact Mr Molati Nonyane, ACGT Liaison Scientist (, 0124206139).
20th Mar 2019
The 2019 Metabolomics symposium was held at the Innovation Hub from 11-12th March 2019. This symposium was aimed at principal investigators, postgraduate and PhD students currently performing or planning to work in the metabolomics field. This event was an opportunity for both local and international metabolomics researchers to share their findings, to network and identify synergies so as to foster further collaboration amongst metabolomics researchers within SA and across Europe. This symposium was mainly a platform to officially launch Metabolomics South Africa (MSA). MSA is a non-profit organization seen as an opportunity to promote and improve the profile of metabolomics research and technology in South Africa, foster networking, training, capacity building, information sharing, mentoring, career opportunities, leadership training and professional development. The symposium was a first official event hosted by MSA with the assistance of its partner, the ACGT.
The first day of the symposium was themed “Metabolomics, where are we?”. Topics discussed throughout the day included the overview of metabolomics in South Africa, good metabolomics data, role of metabolomics in health sciences, lipidomics and plant metabolomics. The discussions on the second day of the symposium were under the theme “Metabolomics, informatics, statistics and applications” and covered topics such as metabolomics networks, statistical models, NMR metabolomics and lipidomic profiling. At the end of each day, attempts were made to finish off with round table discussions to address burning issues or questions on the day’s talks as well as other issues regarding to metabolomics or MSA.
It is worth mentioning several key speakers that participated and contributed to the symposium. The speakers mentioned below are all key contributors to the field of Metabolomics and we are thankful that they shared their work and experiences. These were the presenters at the event in no specific order:
- Dr Reza Salek is currently with the International Agency for Research on Cancer, Lyon, France. Dr Salek has extensive experience in metabolomics research in academia, industry and research institutes with extensive metabolomics knowledge, both analytical and data handling. Dr Salek has worked in clinical trial settings and is interested in setting up workflow infrastructures for metabolomics data handling and analysis using cloud computing.
- Dr Karl Burgess is from the University of Edinburgh, Scotland, UK. Most of Dr Burgess’s workfocuses on the use of mass spectrometry in biomedical research, particularly in the understanding of infectious disease. This multidisciplinary research area builds on his fruitful collaborations with cell biologists, engineers, bioinformaticians, instrumentation developers and clinicians.
- Dr Fabien Jourdan is a research scientist at the French National Research Institute for Agricultural Research (INRA). Dr Jourdan develops computational methods to study human genome-scale metabolic network aimed at retrieving parts of the metabolism affected by genetic or environmental perturbations. These methods are mainly applied to toxicology and human health.
- Dr Naomi Rankin is from the University Hospital Wishaw, Scotland, UK. Dr Rankin’s research interests focus on the use of NMR for metabolite profiling and advanced lipoprotein profiling of serum and plasma samples. She is particularly interested in the use of these methods in epidemiology/clinical trials, especially with a view towards translation of NMR molecular profiling approaches into the clinic.
- Dr Jasper Engel is a researcher at Biometris at Wageningen University & Research. Dr Engel’s primary research interests are in applied statistics. He is interested in the development and careful evaluation of statistical approaches for processing and analysis of complex high-dimensional data sets, and their application in high-dimensional chemical, biological or medical problems. Over the last several years his research has mainly focused on method development for analysis of metabolomics experiments.
- Dr Justine Bertrand-Michel is the co-director of the MetaToul Lipidomic facility at INSERM in Toulouse, France. Dr Bertrand-Michel is a lipidomics expert and she was invited to this symposium because of her work in lipidomics a field that most people in metabolomics have shown a keen interest in.
- Dr Fidele Tugizimana is the chairman of MSA, a research scientist at the University of Johannesburg, a specialist scientist in the international R&D management of the Omnia (Pty) Ltd company (SA) and a scientific consultant in the L.E.A.F. Pharmaceuticals LLC (USA & Rwanda). Dr Tugizimana applies metabolomics approaches in plant-environment interactions (involving abiotic/biotic stresses, beneficial microorganisms, etc.).
- Prof Du Toit Loots is the secretary of MSA and a key member of the national metabolomics platform based at the North-West University in Potchefstroom. Prof Loots has made a substantial contribution to the advancement of metabolomics, by means of developing much of the published methodology and applications in terms of identifying new markers for better disease characterization, diagnostics and treatment since 2002.
- Dr Aurelia A. Williams is the deputy secretary of MSA and a senior lecturer at the biochemistry department of the North-West University. Her research interests include characterizing the impact of molecular traits, metabolism and the immune response on disease pathogenesis. She believes metabolomics will serve as a tool in better characterizing infectious diseases such as HIV/AIDS, HIV-associated comorbidities, virus-host interactions, treatment response mechanisms and pathogenesis-associated phenotypes.
- Dr Zandile C. Mlamla is a committee member of MSA and a post-doctoral research fellow at the Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town (UCT). Her research is currently aimed towards the validation of urinary biomarkers of Tuberculosis Disease. She continues to gain experience and expertise in the cutting-edge field of MS-based lipidomics.
The future of South African metabolomics will be in great hands if the student sessions over the two days are anything to go by. On day one, the student presenters were Mr Efficient Ncube from the University of Johannesburg, Mr Emile Jansen van Rensburg and Ms Monique Combrink both from the North-West University. The student session on day two was by three students from the North-West University in Ms Karin Terburgh, Mrs Zinandre´ Stander and Christiaan van Zyl. The students presented their ongoing work and they received great contributions from the people that attended the symposium in the form of question and suggestions.
Well over 140 delegates from over 25 institutions attended this symposium. They consisted of principal investigators, post-doctorates, researchers, post graduate students and several industry players. The hope is that most of them will register as member of MSA and take an active role in the growth of MSA and metabolomics in general. The ACGT and MSA would like to thank all the delegates who registered to attend this event as well as all the members of the organizing committee; Mr Molati Nonyane, Mrs Itseng Malao, Dr John Becker, Dr Fidele Tugizimana, MSA Committee and the European visitors for all of their efforts in putting together this event. The ACGT and MSA would also like to extend their gratitude to the sponsors of this event in Shimadzu, Thermo Fisher Scientific, Microsep/Waters and the Embassy of France in South Africa. Please look out for more MSA and/or ACGT events similar to this symposium in the future.
If you would like to view more of the pictures from this event, please visit our facebook page:
26th Feb 2019
The Africa Centre for Gene Technologies (ACGT), in conjunction with the University of Zurich, University of Pretoria and the Agricultural Research Council, hosted a successful whole transcriptome sequencing (RNA sequencing or RNASeq) data analysis workshop for researchers from the 1st to the 8th of February 2019. The workshop was held at the Hatfield campus of the University of Pretoria.
RNA sequencing 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 workshop started with two days of introductory courses in Linux and R. The introductory courses were facilitated by Professor Fourie Joubert from the University of Pretoria and Dr Rian Pierneef from the Agricultural Research Council. These courses offered the delegates basic command line skills needed to manipulate RNA sequencing data.
The two days of introductory courses were followed by a four-day interactive and hands-on RNA Sequencing workshop. The workshop was facilitated by renowned experts and academics from the Institute of Molecular Life Sciences at the University of Zurich in Switzerland: Professor Mark Robinson and Dr Simone Tiberi. Professor Mark Robinson is involved in research that applies statistical methods and data science to experimental data with biological applications within the context of genomics data types. Dr Simone Tiberi is a post-doctoral research fellow who is working on the development of cutting-edge statistical methods in bioinformatics, mostly for bulk and single-cell RNASeq data.
The workshop covered theoretical aspects of RNA sequencing such as new technologies, applications, experimental design, batch effects, dimension reduction, clustering, quality control, limma, normalization quantification and differential expression, among other things. There were also one-on-one sessions with delegates to address their specific queries or to clarify any issues that may have arisen. The delegates hailed mostly from the ACGT partner institutions; University of Pretoria, University of Johannesburg, University of the Witwatersrand and the Agricultural Research Council. The feedback from the delegates was very positive in how the course was designed, organized and conducted. The ACGT is hopeful that the course will be beneficial to all the researchers that came to the workshop and to those that work close with them.
The ACGT and all of its partners would like to extend enormous gratitude to Professor Mark Robinson, Dr Simone Tiberi, Dr Rian Pierneef and Professor Fourie Joubert for sharing their 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 Centre wishes all the participants the best of luck with applying their newly learned skill to their work.
To view some additional pictures from the event please visit our facebook page.
29th Jan 2019
Wageningen University and Research (WUR) is a higher institute of learning based in the Netherlands that specialises in the areas of food and food production, living environment, and health, lifestyle and livelihood. WUR opens its doors to the international community and offers short courses in the areas that the institution specialises in. One such course came to ACGT’s attention as it related closely to what the ACGT as an organization is mandated to achieve and the projects that the ACGT is involved in.
The institution offers a short course (three weeks) called “Facilitating Multi-Stakeholder Partnerships to Foster Sustainable Food Systems”. This course was deemed quite applicable for ACGT staff as the Centre is itself a multiple stakeholder partnership mandated to build capacity in the area of advanced biotechnology for five institutions (three universities and two science councils).
The ACGT found it necessary to send one of its staff members, Mr Thabo Khoza – Liaison Scientist at ACGT, to the Netherlands to attend this three-week course in order to enable ACGT staff to be better multi-stakeholder facilitators. The course ran from the 22nd of October 2018 till the 9th of November 2018.
The course took the participants on a journey of (1) establishing what sort of a multiple stakeholder partnerships (MSPs) are required for different projects and needs, (2) who to involve in such MSPs, (3) how to design the required MSP, and (4) how to facilitate the MSP to yield desired outcomes. While all four mentioned steps are crucial in ending up with an MSP that works, step 4 would require the most effort and resources from the MSP facilitator. This effort is especially highlighted when dealing with different stakeholders who have different interests and varying levels of influence. The course gave the participants a number of tools to use in the facilitation process to make sure that the MSP is a success. Each tool would be chosen based on the stakeholders involved as well as on the type of MSP that has been created.
The course had theory and practical components to it. The participants were divided into groups at the beginning of the course and they were tasked to come up with a problem (project) that would require an intervention of an MSP. Throughout the course, the participants would then have to apply what they were learning in their project. At different levels of formulating their MSPs, the participants would give presentations on how they applied what they have learned during their projects.
The participants were also given a real life problem to design an MSP on. This scenario took the participants to Friesland where they had to design a pathway of creating a cooperative that would address the biodiversity problems that are faced in the Friesland region. The participants had to interview farmers, government officials, business owners, nature reserve experts, activists and civil society. The participants then, based on the interviews and what they had been learning at Wageningen, created a roadmap for establishing this cooperative. This roadmap was presented to the community of Friesland where all the stakeholders were invited. The presentation took about two hours with Mr Khoza being the master of ceremonies, together with a fellow participant from Indonesia. The MSP design suggested by the course participants was well received with the project lead promising to use the suggested roadmap.
The course came to an end with participants giving presentations based on their individual MSP that they want to set up when returning to their home countries. The course facilitators as well as the course participants gave suggestions at the end of each presentation.
The course was also a great platform for networking as it was attended by individuals from 14 different countries representing different sectors and expertise such as government and policy makers, scientists and NGOs. The participants have an active network and are actively looking for opportunities for collaboration.
The ACGT hopes that Mr Khoza will put into practice the knowledge he acquired at Wageningen University and Research especially in creating new initiatives for the ACGT community, such as the Proteomics Society for South Africa.
Story by: ACGT Team, January 2018
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