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  • The CRISPR Plant Genome Editing KIT

    9th Oct 2019

    The African Centre for Gene Technologies (ACGT) and the Agricultural Research Council (ARC) hosted a plant genome editing workshop between the 3rd and the 5th of September 2019 at the ARC’s Biotechnology Platform situated on the Onderstepoort Campus.

    Scientists from the Karlsrühe Institute of Technology, Germany (KIT) presented a “starter kit” for model plant CRISPR-related work in South Africa. The relationship with KIT began in 2017 with Professor Holger Puchta visiting South Africa on an ACGT invitation, to present a keynote address at one of the annual ACGT Regional Plant Biotechnology Forum series meetings. When the ACGT approached Prof Puchta to facilitate a three-day beginner’s workshop on plant genome editing with the CRISPR/Cas technology utilized in his laboratory, he recommended his trusted colleagues, Patrick Schindele and Angelina Schindele, to facilitate the workshop, who graciously accepted the invitation.

    The three-day workshop included both theory and practical sessions during which the participants were introduced to gene targeting in plants by using the CRISPR/Cas9-system.

    Topics covered in the sessions included:

    • Classification of the CRISPR/Cas-systems currently in use
    • Designing guide RNAs manually and with online tools
    • CRISPR construction and guide RNA cloning into the KIT group’s vectors using various cloning strategies, such as Gateway cloning
    • Current applications of CRISPR/Cas technologies looking beyond gene editing
    • Approaches to Agrobacterium transformation of model plants.

    Prof Puchta’s lab generously provided constructs for the participants to work on during the practical sessions. The relationship established with KIT will be an ongoing one. Prof Puchta’s lab has offered to assist participants who attended the workshop with their published constructs and other plant genome editing related queries. Queries must be directed to the ACGT. Inqaba Biotec partnered with ACGT and ARC as the major sponsor and generously provided the majority of reagents used in the workshop.

    The plant genome editing community in South Africa is a small but growing one. The workshop provided an opportunity for scientists in the field to be aware what other institutions in the region are doing in the plant genome editing space. Indeed, collaborative discussions have already been established between the ARC and the Council for Scientific and Industrial Research (CSIR) on a possible project as a direct result of this workshop. The participants were all enthusiastic about having a more cohesive community and the ACGT will facilitate the process by creating a CRISPR list server (contact ACGT’s Liaison Scientist, Mr Thabo Khoza, to gain access) and subsequently a Genome Editing Interest Group. The participant feedback indicated that both the extensive theoretical overview of the different technologies, combined with the KIT CRISPR experts’ practical experience, provided key insights into the technology during the practical sessions, with details often not provided in laboratory protocols or papers.

    Contact Thabo Khoza:

    For more workshop images, visit our ACGT Facebook page: Click here

    Story by: ACGT, October 2019

  • ACGT and FABI jointly hosts a Plant Phenotyping and Precision Agriculture workshop at Future Africa

    ACGT and FABI jointly hosts a Plant Phenotyping and Precision Agriculture workshop at Future Africa
    8th Oct 2019

    On Tuesday, September 17, the African Centre for Gene Technologies (ACGT), Forestry and Agricultural Biotechnology Institute (FABI) and Future Africa co-hosted a Plant Phenotyping and Precision Agriculture workshop at Future Africa on the University of Pretoria’s Hillcrest Campus. The event, which was themed “Opportunities and Needs in Research and Infrastructure” was attended by 66 delegates from a variety of national research, governmental and industry institutions.

    The workshop was opened by Dr Marinda Visser (Manager: Grain Research and Policy Centre at Grain SA) who emphasised the importance of research and development in the agricultural sector, as well as the need for better coordination and collaboration.

    The morning session was dedicated to introducing various aspects of phenotyping and precision agriculture to the delegates. This involved phenotyping at several different scales and applied to a variety of plant species. The programme and the national and international speakers who delivered the presentations are listed below:

    Morning presentations:

    Prof Carlos Poblete-Echeverria, Stellenbosch University Precision viticulture: digital technologies for monitoring and management of the vineyards
    Prof Dave Berger, FABI, University of Pretoria Deep learning for automated classification of maize diseases
    Dr Abraham Singels and Natalie Hoffman, SASRI, KZN Remote sensing of canopy cover and crop water status with drones to assist sugarcane breeding: Preliminary results
    Dr Nicky Taylor, University of Pretoria

     

    Assessing relatively simple tools for estimating canopy size in orchards
    Dr Moses Cho, CSIR Evolution in remote sensing of foliar nutrient and chlorophyll content as indicators of vegetation health
    Dr Nadia Shakoor, Donald Danforth Plant Science Centre, Missouri, USA

     

    Phenomics at scale: Driving advances in crop breeding with insights from diverse sensor platform technologies
    Dr Rosita Yocgo, African Institute of Mathematical Sciences, Rwanda

     

    A phenomics approach to the analysis of the influence of glutathione on leaf area and abiotic stress tolerance in Arabidopsis thaliana
    Dr Dirk Swanevelder, ARC Biotechnology Platform

     

    Plant phenotyping and remote sensing at the ARC
    Mr Maurits Voogt, eLEAF, Wageningen, Netherlands Making research work: how FruitLook evolved to generate impact at scale

     

    Adding to the diversity of speakers, delegates also represented institutions and initiatives that included: the University of Johannesburg, Tshwane University of Technology, the Royal Science and Technology Park: eSwatini, the Department of Science and Innovation, Corteva Agrisciences, Sensako Seed Company and Link Seed. ACGT and FABI post-graduates and researchers were very well represented.

    In the afternoon session, facilitated by Prof Bernard Slippers (Director: FABI, UP), delegates were tasked to discuss issues around opportunities to meet needs for infrastructure and facilities, academic – government – industry alignment, and opportunities for South Africa, Africa and international communities. These crowd-sourced inputs will now provide a foundation for developing a network of interested parties and contain numerous ideas for projects and further development.

    A more formal report on the feedback emanating from the groupwork is in preparation. There was strong agreement that a follow-up event is required and planning will commence shortly.

    In closure, Prof Bernard Slippers thanked all the speakers and delegates, as well as the organizing committee.

    For more photos, please visit out Facebook page: click here

  • SA researchers introduced to the field at the National Metabolomics Platform

    14th Aug 2019

    The 2019 Introductory Metabolomics Workshop was held at the National Metabolomics Platform, based at North-West University’s (NWU) Potchefstroom Campus from 05-07th August 2019. This workshop was a collaborative effort between the African Centre for Gene Technologies (ACGT), NWU and the recently established Metabolomics South Africa (MSA).  The workshop provided a capacity building opportunity to help delegates that are in the earlier stages of the research to build a foundation with sound metabolomics techniques and tools.

    The workshop was facilitated by a panel of local metabolomics experts from several institutions from all over the country. The facilitators from North-West University were Dr Aurelia Williams, Prof Du Toit Loots, Dr Mari van Reenen, Dr Shayne Mason, Dr Zander Lindeque, Mr Emile Jansen van Rensburg and Ms Zinandre Stander. The facilitators from the University of Johannesburg included Dr Fidele Tugizimana and Mr Msizi Mhlongo. University of Pretoria was represented by Prof Duncan Cromarty and the University of Cape Town by Dr Zandile Mlamla.

    The focus on day one of the workshop was on the different metabolomics workflows, experimental design and the application of metabolomics in different disciplines and industries. On the second day of workshop the delegates were given an opportunity to participate in real wet lab experiments using NMR and Mass spectroscopy. On the final day of the workshop, the focus was mostly on data handling and interpretation. This involved normalization, quality assurance, statistics, metabolite identification and metabolomics resources.

    The participants were from multiple research institutions from all over South Africa. There were participants from the Universities of Pretoria, Johannesburg, the Witwatersrand, Council for Scientific and Industrial Research, North-West University, University of South Africa, Tshwane University of Technology, University of Cape Town, University of Limpopo and the University of KwaZulu-Natal. Below is a few takes offered by the delegates about the workshop:

    “The content of the course was well balanced to suite newbies and experienced researchers in metabolomics. It was a great mix of people at different levels of research and different themes which made it rich.” 

    “The course is very insightful to beginners, gives an idea of how to tackle metabolic profiling as well as how to analyse the data. Personally, the course has answered a lot of questions I had, and it inspired me.”

    “The statistical analysis was extensively covered and will be very useful in considering the best possible statistical tool to use on one’s data.”

    “ I enjoyed learning about the different applications of metabolomics and how various types of research questions can be answered through the platform.” 

    “The area of research is still evolving and there is the need to prepare next generation of researchers for the task ahead to apply it in various fields apart from the human area alone.”

    “I found the workshop well- structured, comprehensive and rich in content.”

     

    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, Dr Aurelia Williams, Mrs Itseng Malao, Dr John Becker and Dr Fidele Tugizimana 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: Shimadzu, Microsep, Separations and the Scientific Group. You are welcome to visit our facebook page for more visuals from the event.

     

     

     

     

  • Stem cell treatment – excitement is understandable but let’s tread carefully

    20th Jun 2019

     

    Stem cells not a panacea.

    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.

    No guarantee

    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”.

    Complex matter

    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

  • UCT, ACGT, SU and DIPLOMICS host the Trans-Proteomic Pipeline (TPP) Workshop

    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

  • ‘The next Einstein could be African’ – newly elected UP head of Next Einstein Forum’s Community of Scientists

    'The next Einstein could be African’ – newly elected UP head of Next Einstein Forum’s Community of Scientists
    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.

    Prof S. Naidoo

    “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.”

     

    Story by: ©University of Pretoria, News. April 12, 2019

  • ACGT’s Liaison Scientist Attends a Multi-Stakeholder Partnership Facilitation Course in the Netherlands

    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

  • Plant-Pathogen Systems Under The Spotlight At Regional Forum

    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, .

     

  • UP receives boost in NRF ratings

    UP receives boost in NRF ratings
    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.”

    NRF A1 rated UP academics Prof Don Cowan (left) and Prof Mike Wingfield

    Story by: Buyisiwe Nkonyane, University of Pretoria

  • ACGT life scientists trained in Linux use for data analysis

    ACGT life scientists trained in Linux use for data analysis
    9th Oct 2018

    The Centre for Bioinformatics and Computational Biology

    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 ACGT and capacity building
    • The shell,
    • the file system,
    • files and directories,
    • permissions,
    • finding files,
    • basic system commands,
    • redirection with command and file pipes,
    • basic grep, sed and awk,
    • processes,
    • 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.

    The Delegates during the interactive sessions

    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 (, 012 420 6139).