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National metabolomics researchers agree to build a network to facilitate interaction February 2018 - A national Metabolomics Stakeholder Session was held on the 31st of January 2018 at the CSIR International Convention Centre in Pretoria. Representatives from several research institutions from different parts of the country were in attendance. The institutions included the University of Johannesburg, North-West University, University of Pretoria, Tshwane University of Technology, University of the Witwatersrand, Stellenbosch University, University of South Africa and the University of Cape Town. The meeting was intended to serve as a potential platform for the establishment of a formal society or network of South African metabolomics stakeholders. In this session, the benefits and expectations of such a society or network were also tabled. The event began with presentations from representatives of the various research institutions. The presentations were intended to offer the stakeholders in attendance an opportunity to appreciate the metabolomics research expertise, interests and offerings from the other institutions. The presentations were also an opportunity for the institutions to put on display their strengths and to highlight their needs which could hopefully be addressed by collaborations through the formal establishment of a society or network. Dr Fidele Tugizimana from the University of Johannesburg then presented on the operations and benefits of the International Metabolomics Society (IMS) as he is on several IMS committees. The presentations were followed by discussions about a path to the establishment of a more formal grouping of metabolomics stakeholders. It was highlighted that one of the goals for forming a society is improving the profile of metabolomics research and technology in South Africa and fostering networking, ...

UP scientist recognised by AU 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 ...

African genetic diversity could hold answer to unlocking disease susceptibility 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 ...

ACGT represented at HUPO 2017 in Dublin 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 ...

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

Advanced Proteomics Seminar and Workshop builds regional capacity November 2017 - The University of Pretoria (UP) hosted a Proteomics seminar and workshop, which they co-organised with the African Centre for Gene Technologies (ACGT) and the Council for Scientific and Industrial Research (CSIR). Over 20 delegates attended the events; which represented the majority of the ACGT’s partner institutions. Prof Ole Jensen visited South Africa during this period to give a plenary talk at the seminar, as well as to facilitate the subsequent two-day workshop. Prof Jensen is a Professor of protein mass spectrometry at the Department of Biochemistry and Molecular Biology, University of Southern Denmark (SDU), in Odense. His research focus includes chromatin biology and epigenetics, as well as “middle-down” proteomics approaches and mass spectrometry to study co-existing post-translational modifications and their cross-talk in proteins. The seminar took place on the 11th of October 2017 at UP’s Plant Sciences Complex Auditorium.  Dr John Becker (ACGT Centre Manager) made opening remarks and highlighted the progression of the proteomics workshops since their inception in 2012 under the leadership of Prof Duncan Cromarty from UP. After being introduced by Dr Stoyan Stoychev (CSIR), Prof Jensen gave a plenary talk on “One protein – many outcomes: Elucidating histone proteoform dynamics during aging by using Mass Spectrometry”. He was followed by other speakers from UP (Dr Duncan Cromarty and Ms Kim Sheva) and CSIR (Mr Ireshyn Govender and Dr Ashok Prabhu). The day ended off with the delegates, who were to attend the workshop taking place a day after the seminar, giving short presentations about their research studies which involved proteomics. The advanced proteomics workshop ...

Flagship Stem Cells Conference a great success October 2017 - Researchers from academia and science councils, industry representatives and scientific vendors came together for a national conference on Stem Cells Research and Therapy on the 26th and 27th of October 2017 at the Innovation Hub in Pretoria. The purpose was to showcase research performed under the MRC Flagship “Stem cell research and therapy- addressing South Africa’s disease burden”; awarded to the University of Pretoria in 2014. National stem cells stakeholders active in the field, but not necessarily funded through the flagship, also had the opportunity to showcase their research. The two-day event attracted close to 80 delegates from across South Africa, including delegates from Kwa-Zulu Natal and the Western Cape. Professor Michael Pepper, co-organizer of the event (with ACGT) welcomed delegates on the first day, after which Medical Research Council Vice-President, Professor Jeffrey Mphahlele, introduced the University Flagship Programme. Professor Mphahlele congratulated all involved in the Flagship, but also stressed the importance of translational research to delegates. Although the presentations over the remaining two days largely focused on scientific research, included in the programme was also presentations and deliberations on the legislative environment surrounding cell-based therapy; as well as legal issues in dealing with scientific data and privacy. Discussions were quite lively as researchers were exposed to high level work in the stem cells field from researchers that they don’t interact with frequently. Here, suggestions to post-graduate researchers, academics and industry; as well as opportunities identified for collaborative efforts, could be regarded as highly positive outcomes of the deliberations. The organizers were very fortunate to attract financial ...

GATK training for genome analysis: building bioinformatics capacity in the ACGT partnership October 2017 - The African Centre for Gene Technologies (ACGT) and the University of Pretoria’s Centre for Bioinformatics and Computational Biology (CBCB) co-hosted a genome analysis workshop from 23-27 October 2017. The hosts were extremely fortunate to have the week-long workshop facilitated by an expert group of scientists and software developers from the Broad Institute of Harvard and MIT. They included Dr Geraldine van der Auwera, Mr Hussein Elgridly and Mrs Kate Noblett. The team was supported by local bioinformatics expert and Director of the CBCB, Prof Fourie Joubert. This was the second capacity-building instance where the team facilitated the workshop in the Genome Analysis ToolKit (GATK) open-source software package. The toolkit was developed in the Data Sciences Platform at the Broad Institute, and offers a wide variety of tools with a focus on variant discovery and genotyping. The first GATK workshop was hosted by ACGT and CBCB in 2015. The workshop dealt with a number of genomics analysis topics and included data pre-processing and quality control; variant discovery and detailed sessions on setting up workflows in the toolkit. The approach was to have presentations on the specific sections, which was followed by hands-on exercises on the CBCB workstations throughout the five days. Delegates hailed from the ARC (including Stellenbosch), and the Universities of Pretoria, the Witwatersrand and Stellenbosch; and also included a delegate who traveled all the way from Newcastle University to attend. The attendees were at different levels of bioinformatic analysis experience and this was highlighted during the sessions where command line imputation was utilized. A consideration for ...

Revolutionary Genome Technology the Theme of Regional ACGT Scientific Forum July 2017 - Since the discovery of the three-dimensional structure of DNA in 1953 by James Watson and Francis Crick, molecular biologists have been studying the function of genes and genomes made up of the four bases of DNA. Scientists have had the ability to modify DNA through a number of enzymatic processes throughout recent decades, but these were mostly limited to manipulation of smaller pieces of DNA and vectors used for downstream analyses or genetic transformation of organisms. Precise, targeted genome engineering of organisms became a reality in 2012 when it was shown that an engineered Cas9 (an RNA-guided DNA endonuclease) could be used together with components of the bacterial defense system CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats). CRISPR-Cas9 has since revolutionized genome engineering in a range of organisms- including yeast, zebrafish, fruit flies, nematodes, plants, mice, monkeys and human embryos. A handful of researchers in South Africa has since started incorporating this, and other genome-engineering technologies, in their research endeavors. Considering the potential impact of this technology and its ability to address African research questions, it was appropriate to incorporate as the central theme in one of the series of ACGT regional scientific fora. The ACGT teamed up with the University of Pretoria to host a “Genome Editing” forum that cut across multiple biotechnology sectors. The forum was anchored by a leading genome editing specialist in the plant biotechnology sector, from the Karlsruhe Institute of Technology (KIT) in Germany, Professor Holger Puchta. Prof Puchta is the leader of the Botanical Institute at the research entity and Chair in ...

Analysing transcriptomes: ACGT community receives hands-on training June 2017 - A whole transcriptome sequencing (or RNA sequencing/RNA Seq) data analysis workshop was hosted for ACGT researchers from 15-19 May. The workshop was hosted by ACGT and facilitated by expert trainers from the University of Pretoria’s Centre for Bioinformatics and Computational Biology (CBCB, Prof Fourie Joubert) and the Agricultural Research Council’s Biotechnology Platform (Dr Charles Hefer and Dr Oliver Bezuidt). RNA Seq aims to unravel the sum of all transcripts in an organism at any given moment in time and is a key intermediate step in the central dogma. The coverage of the technology is also still superior to technologies aiming to measure the full complement of proteins and metabolites in a living system, but at the same time further removed from the phenotype of an organism. Hence, transcriptome analysis can give important clues to changes occurring in an organism following a variety of environmental cues or life stage transitions. The technology can be applied across multiple fields of study, and interest for the course was received from researchers and institutions with very different backgrounds and research aims. A total of 23 delegates could be accommodated for the week-long training event, hailing from the ARC (several different institutions), National Health Laboratory Service (NHLS), National Institute for Communicable Diseases (NICD), University of Pretoria (several medical, veterinary and agricultural delegates), as well as the University of the Witwatersrand. The workshop included a mix of lectures and hands-on practical sessions in the CBCB training laboratory. Delegates were given a holistic view of all the aspects contributing to a successful transcriptome analysis, including ...


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