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  • A beneficial Advanced Metabolomics Workshop is hosted by the ACGT at the University of Pretoria for metabolomics researchers from all over South Africa

    20th March 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).

    Useful tools

    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

    Hands on training

    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.

    Some fun was had too!

    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.

    The delegates and facilitators

    If you would like to view most of the pictures from this event, please visit our facebook page:

    https://www.facebook.com/ACGT.biotec/

    For any metabolomics-related capacity building and networking queries, kindly contact Mr Molati Nonyane, ACGT Liaison Scientist (az.ca1558877636.pu@e1558877636nayno1558877636n.ita1558877636lom1558877636, 0124206139).

  • Metabolomics South Africa (MSA) is officially launched during a Metabolomics Symposium in Pretoria

    Metabolomics South Africa (MSA) is officially launched during a Metabolomics Symposium in Pretoria
    20th March 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:

    https://www.facebook.com/ACGT.biotec/

  • SA Metabolomics Association established and officially affiliated to a prestigious international scientific body

    SA Metabolomics Association established and officially affiliated to a prestigious international scientific body
    10th July 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.

    Representatives from all the IMS international affiliates after their meeting in Seattle, USA. Dr Fidele Tugizimana is to the far right with president of the IMS, Prof Jules Griffin, next to him.

    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 (az.ca1558877636.pu@e1558877636nayno1558877636n.ita1558877636lom1558877636 or 012 420 6845).

  • From Genes to Networks: The ACGT plant forum creates a platform for future collaborations

    From Genes to Networks: The ACGT plant forum creates a platform for future collaborations
    1st June 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):

    1. 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.

    1. Dr Eshchar Mizrachi (University of Pretoria) – Reverse engineering networks of secondary growth and their evolution in plants
    2. Prof Chrissie Rey (University of the Witwatersrand) – Plant genes and networks: responses to geminivirus
    3. Dr Ansie Yseel (University of Pretoria) – Using a network based approach to interpret molecular profiling data
    4. Ms Katlego Masike (University of Pretoria) – Application of host-induced gene silencing to manage diseases in agriculturally important plants.
    5. Dr Christine Bizabani (University of the Witwatersrand) – Cassava responses to South Africa cassava mosaic virus: an ultimate battle of host and virus encoded microRNA
    6. Prof Dave Berger (University of Pretoria) –Transcriptional network analysis reveals candidate resistance mechanisms to grey leaf spot in maize
    7. Dr Patience Chatukuta (University of the Witwatersrand) – CRISPR and protoplast: Hand-in-hand towards high-throughput gene silencing in cassava
    8. 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.

    Forum speakers

    Story by: The ACGT team

  • New family of promising, selective silver-based anti-cancer drugs discovered

    4th April 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.

    Unusual compounds

    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.

    Story by: University of Johannesburg, for Eurekalert

  • Professor Lynn Morris awarded the 2018 TWAS Prize in the Medical Sciences

    Professor Lynn Morris awarded the 2018 TWAS Prize in the Medical Sciences
    8th March 2018

    Professor Lynn Morris

    In awarding Professor Lynn Morris with the 2018 TWAS Prize in the Medical Sciences category, the Academy praised her “pioneering studies on the neutralizing antibody response to HIV infection that has provided fundamental insights for HIV vaccine development”.

    The TWAS Prize, announced in December 2017, carries a cash award of US$15 000 and the winners will deliver a lecture about their research at TWAS’s 28th General Meeting in 2018, when they will receive a plaque and the prize money.

    Morris is a Highly Cited Researcher on the Clarivate Analytics list compiled annually that recognises leading researchers in the sciences and social sciences globally.

    Morris holds a joint appointment as Research Professor in the Faculty of Health Sciences at Wits University and Research Associate at the Centre for the Aids Programme of Research in South Africa (CAPRISA). She is the Head of the HIV Virology Laboratory within the Centre for HIV & STIs based at the National Institute for Communicable Diseases at the National Health Laboratory Services.

    In June 2017, Morris received the prestigious Harry Oppenheimer Fellowship Award for her scholarship and research excellence.

    Story by: The University of the Witwatersrand

  • UP scientist recognised by AU

    UP scientist recognised by AU
    15th February 2018

    Prof Robert Millar, Director of the Centre for Neuroendocrinology at the University of Pretoria, has been honoured with a Kwame Nkrumah Award for Scientific Achievement by the African Union in the category of Life and Earth Sciences at the Continental level. This is the highest level of the awards programme, which also recognises young scientists at a national level and women scientists at a regional level.

    The prize carries a grant of US$100 000.

    “I am deeply honoured by the African Union’s award which recognises the importance of our ongoing scientific research to improve lives all over the continent and in the training of young African scientists. The gathering of the heads of all African states was immensely impressive and underlines the potential to harness Africa’s science talent and make the continent a global player in research and I pledge my commitment to this endeavour. My group will continue to look for new and more effective treatments for diseases which lead to considerable suffering and pain,” said Prof Millar.

    Prof Millar’s research is in the field of neuroendocrinology, where he has specialised in peptide regulators of reproductive hormones. He pioneered the discovery of the Gonadotropin Releasing Hormone (GnRH) prohormone, novel GnRH structures, and the first cloning of the GnRH I and GnRH II receptors. He has participated in and led a number of programmes developing GnRH analogues for use in a wide range of clinical pathologies.

    His research has contributed to the development of the primary treatment for prostate cancer, the sole treatment for precocious puberty and treatments for hormone-dependent diseases in women such as endometriosis, as well as in vitro fertilisation.

    He was the recipient of a National Science and Technology Forum (NSTF) Lifetime Achiever Award during 2013 to an individual for his outstanding contribution to Science, Engineering, Technology and Innovation (SETI) during his lifetime. In 2017 he received the Platinum Medal of the Medical Research Council and the Harry Oppenheimer Fellowship and Gold Medal. Prof Millar is a Fellow of the Royal Society (Edinburgh), a Fellow of the Royal Society of South Africa and a Fellow of the Academy of Science of South Africa (ASSAf). He has published 450 articles in internationally peer-reviewed journals (cited over 20 000 times) and has an H-index of over 70. Prof Millar is also an NRF A-rated scientist.

     

    Prof Robert Millar
    Prof Robert Millar

     

    Story by: Department of University Relations, University of Pretoria

  • African genetic diversity could hold answer to unlocking disease susceptibility

    African genetic diversity could hold answer to unlocking disease susceptibility
    19th December 2017

    A team of South African researchers which includes researchers from the University of Pretoria (UP) recently completed a study aimed at unlocking the unique genetic character of southern African populations. The study involved the genetic sequencing of 24 South African individuals of different ethnolinguistic origins, the results of which revealed a high level of genetic diversity and highlights the potential implications for disease susceptibility in Africans. The study was the first government-funded human genomics research study to be performed on African soil.

    Funded by the National Department of Science and Technology (DST), the focus of the Southern African Human Genome Programme was to capture a full spectrum of diversity in populations that are under-represented from the genomic perspective. To achieve this, the sample group for the study was compiled to include ethnically self-identified individuals of different ancestries, after which whole-genome sequencing was used to study the differences in some of the major ethnolinguistic groups in the country. The sample group consisted of eight mixed-race or coloured individuals from the Western Cape, seven Sotho speakers from the Free State, eight Xhosa speakers from the Eastern Cape and one Zulu speaker from Gauteng.

    The study aimed to explore the ancestral compositions of these individuals, including maternal and paternal lineages, using novel whole-genome sequence data. The results indicate that despite a short period of geographic and cultural separation between Nguni and Sotho-Tswana speakers, there are measurable genetic differences between them.

    The team explains that these are in part the result of varying regional ancestral contributions, but also of a random process of genetic drift. Paternal ancestry was almost exclusively of African origin, while maternal ancestry was often of Khoesan origin, which is consistent with previous studies showing cross-cultural assimilation of female hunter gatherers into Nguni and Sotho-Tswana speaking farming communities. Coloured individuals in turn, showed varying proportions of admixture with Khoesan, African and European populations, as well as populations from the Indian sub-continent. After the inclusion of additional representative populations in the analysis, the study revealed a much stronger South Asian ancestry in the coloured individuals than indicated by previous studies.

    Although African populations are known to harbour the greatest genetic diversity and have the highest per capita health burden, they are rarely included in large genome studies of disease association. The team says that this diversity provides both a challenge and an opportunity for biomedical research and the hope that Africans will one day benefit from genomic medicine.

    Professor Michael Pepper, Director of the Institute for Cellular and Molecular Medicine, and a professor in the Department of Immunology in the Faculty of Health Sciences at UP, who is also the Unit Director of the South African Medical Research Council’s (SAMRC) Stem Cell Research and Therapy Unit, adds that the next step will be to use the knowledge gained through the team’s research to determine the potential impact the genetic variants could have on the health of individuals when health-related research is conducted.

    Professor Michael Pepper
    Professor Michael Pepper

    The results of this study were published in Nature Communications on Tuesday, 12 December 2017

     

     

     

     

     

     

    Story by: Ansa Heyl for the University of Pretoria News

  • ACGT represented at HUPO 2017 in Dublin

    ACGT represented at HUPO 2017 in Dublin
    5th December 2017

    The 16th Annual World Congress of the Human Proteome Organisation (HUPO) was held at the Convention Centre Dublin in Ireland, from the 17th to the 21st of September 2017. HUPO is organised by the European Proteomics Association (EUPA) and the British Society for Proteomics Research (BSPR).  The vision for HUPO2017 Congress was to “create a meeting that will bring together world leaders with a new generation of scientists to promote HUPO’s capabilities for advancing knowledge of the Human Proteome and the impact this will have on understanding health, disease and ageing”.

    The congress ran six concurrent themes throughout the congress period.  These themes were:
    Cellular Proteomics; Drug & Biopharmaceutical Proteomics; Systems, Bioinformatics & Omics Data Integration; Disease & Clinical Proteomics; Precision & Personalised Proteomics; and the Human Proteome Project (HPP). In addition to the concurrent themes, there were exhibitions, networking and poster viewing sessions which were well attended by delegates. Poster presenters had an opportunity to share their work and also get some valuable suggestions from proteomics world experts that visited their posters.

    A representative from the African Centre for Gene Technologies (ACGT), Mr Thabo Khoza, attended the congress. Mr Khoza is a Liaison Scientist at the ACGT and has been responsible for bringing the proteomics community together through symposiums and workshops for the past 4 years. This was the 2nd time Mr Khoza attended the HUPO congress.  This time around, Mr Khoza was tasked to meet with a few world experts in the field to share ideas on forming a proteomics society for South Africa. Mr Khoza met with Prof Stephen Pennington  (Chair of the Ireland HUPO organising team and Professor of Proteomics at the University College Dublin Conway Institute), Dr Maarten Dhaenens (President of the European Proteomics Association and researcher at Ghent University), Prof Kathryn Lilley (Director of the Cambridge Centre for Proteomics, University of Cambridge) and Prof Lennart Martens (Professor of Systems Biology at Ghent University, and Group Leader of the Computational Omics and Systems Biology group in Ghent, Belgium).  All four world experts stressed the importance of a functioning society that would address the needs of the proteomics community and create an effective space for networking and collaboration.

    Mr Khoza was able to identify a number of researchers who could potentially come to South Africa to facilitate future workshops for the South African proteomics community. These researchers presented some of the talks that stood out during the congress. The talks included those by Ben Collins, who gave a talk on “Quantitative Interaction Proteomics: Insights into Biological Systems” and Ruedi Aebersold, who gave a talk titled “The Protein in context”. Matthias Uhlen who’s talk was titled “The human protein atlas – implications for human biology, drug development and precision medicine” stressed the importance of transcriptomics, handling of big data, the focus of tissue-specific proteome and having a pathology atlas in addressing concerns associated with the human biology, drug development and precision medicine.

    Through the interactions that Mr Khoza had at the congress, the ACGT plans to have two proteomics workshops in 2018 as well as engage the South African proteomics community to establish a proteomics society.

    The congress was a great platform for networking.  It was well attended by delegates from all over the world, with a common interest in proteomics and how it can be applied in humans and other systems. The next congress will be held in Orlando, USA from September 20th 2018 till the 3rd of October 2018.

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  • The Plant-Soil community comes together at the Agricultural Research Council

    The Plant-Soil community comes together at the Agricultural Research Council
    13th November 2017

    On the 18th of October 2017 the African Centre for Gene Technologies (ACGT) in conjunction with the Agricultural Research Council (ARC) hosted a Regional Plant Biotechnology Forum at the ARC’s Central Office Auditorium in Hatfield.  The focus for this forum was “Plant-Soil Interactions”. This theme came in light of the national plant-soil working group initiative that the ARC is planning to create and coordinate. The forum was attended by a number of people from the ACGT’s partner institutions as well as outside institutions, including the University of Cape Town and industry representatives.

    The organising committee were fortunate to secure Prof Wijnand Swart as the keynote speaker for the forum. Prof Swart is currently in the Department of Plant Sciences at the University of the Free State in Bloemfontein and Discipline Head in the Division of Plant Pathology.  His research broadly focuses on using the taxonomic and functional diversity of microorganisms, above- and below ground, as bio-indicators of soil and plant health.  His research interest made him a perfect fit for the forum’s theme. Prof Swart gave a fascinating talk titled “Phytobiomes: Key to understanding plant and soil health”.

    Other equally fascinating talks came from Prof Joanne Dames (Rhodes University and Mycoroot), Prof Oleg Reva (University of Pretoria), Ms Francina Bopape (ARC), Dr Juan Venter (University of Pretoria), Dr Martin Myer (Biopower Institute) and Dr Fidele Tugizimana (University of Johannesburg).

    The forum, like many of the ACGT fora, served as a platform for people from different institutions and labs to network as well as discuss future collaborative initiative. The plant-soil working group was a big topic during the networking session/lunch. The ACGT aims to work together with the ARC to establish and coordinate the working group and it will keep all interested stakeholders up to date with its progression.

    The ACGT would like to thank Dr Charles Hefer and Dr Dirk Swanevelder from the ARC for assisting in organising the forum.

    Programme

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