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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 ...

CSIR and UP partner up to facilitate the “Introduction to Proteomics” Workshop May 2017 - The ACGT, UP and CSIR recently hosted an Introduction to Proteomics Workshop which ran from the 11th to the 12th of May 2017 at the University of Pretoria Medical School.  The workshop was in response to the “Workshops and Training Needs” survey that was sent out to the ACGT in which an introductory proteomics workshop was highlighted as a need. The workshop was attended by researchers new to the field of proteomics. Delegates hailed from the University of Pretoria (UP), the Agricultural Research Council, the University of the Witwatersrand as well as Vaal University of Technology and Cape Town University. Dr Stoyan Stoychev (Council for Scientific and Industrial Research, CSIR) and Prof Duncan Cromarty (UP Immunology) lead the team of researchers who facilitated the workshop. The first day of the workshop was facilitated by Ms Chanelle Pillay (UP), Dr Previn Naiker (CSIR), Prof Cromarty and Dr Stoychev. The second day was facilitated by Ms Kim Sheva (UP), Ireshyn Govender (CSIR) and Dr Stoychev.  Topics covered included: mass spectrometry basics, proteomics experimental design and sample preparation, mass spectrometry-based workflows, MALDI-IMS, as well as data processing and interpretation.  The delegates also got a chance to discuss their individual projects with the facilitators as well as complete a group assignment in which they were given different proteomics scenarios to work through.  All the workshop facilitators have been through extensive Proteomics training provided by Prof Katherine Lilley and Prof Lennart Martens over the past four years and Dr Stoychev and Prof Cromarty are leading proteomics researchers in South Africa. The ACGT will ...

ACGT and UJ host second open-source Metabolomics workshop for partnership May 2017 - A highly successful Metabolomics workshop was hosted by the ACGT and the University of Johannesburg from 6 to 10 March 2017 at the University of Pretoria’s Centre for Bioinformatics and Computational Biology (CBCB). This event built on the first open-source metabolomics workshop, also facilitated by ACGT and UJ in 2016, and is based on the European EMBL course. A number of European metabolomics experts returned to facilitate the event, and a number of new experts also joined the facilitation team. These included (Europe): Dr Reza Salek (University of Cambridge), Drs Karl Burgess, Naomi Rankin and Justin van der Hooft (University of Glasgow), Dr Jos Hageman (Wageningen University) and Dr Fabien Jourdan (INRA, France). Local trainers included Drs Fidele Tugizimana and Edwin Madala from the University of Johannesburg. The theme of the workshop was Study Design, Informatics and Statistics and included numerous lectures as well as hands-on data analysis and statistics sessions. An internet-based participatory quiz at the end of each session allowed participants to test their knowledge in a very informal manner, and was received very well by the delegates. The response to the workshop registration was overwhelming and not all delegates could be accommodated due to space constraints. Those who did take part in the workshop were representative of four of the five ACGT partner institutions and included principal investigators (UP, Wits, UJ) as well as post-graduate researchers (UP, CSIR and UJ). Feedback received from the delegates was extremely positive. Herewith a few quotations from attendees: It provides a week-long introduction to all the core concepts in Metabolomics. Both ...

ACGT and DST host first Metagenomics Symposium March 2017 - The Centre secured a metagenomics expert for a national metagenomics symposium, which was hosted on the 23rd of November 2016. Professor Peter Golyshin (Bangor University, Wales) is a well-known international metagenomics expert and agreed to be the keynote at the national event held at the Department of Science and Technology (DST). A number of national institutions and prominent local researchers were also represented (69 in total), including the Universities of Pretoria, North-West, Cape Town, the Western Cape, VUT, TUT, UNISA, the ARC as well as the CSIR. Research from the CSIR, UP, NWU, UWC as well as UCT was showcased at the event. The symposium ended with a discussion about collaborative opportunities in the field, and it was agreed that the ACGT would make available the research interests, expertise and relevant infrastructure of those in the field of metagenomics on its website.

ACGT facilitates open-source bioinformatics for proteomics workshop February 2017 - A detailed three-day open-source proteomics workshop focusing on targeted proteomics and the use of the software package Skyline (this software package can be utilised regardless of hardware utilised in the different institutions and has become highly popular in the proteomics community) was hosted from the 6th to the 8th of December 2016 at the University of the Witwatersrand. The workshop was conducted by Mr Brendan MacLean (who is the chief developer of the software) and Mr Brian Searle (both from the MacCoss lab, Washington University) as well as Dr Birgit Schilling (Gibson lab, Buck Institute). Both institutes are located in the United States. Various advanced topics were covered during the three-day workshop, and delegates from multiple institutions attended. Invitations were also extended to proteomics researchers outside of the region, and researchers hailing from the Universities of Cape Town and Limpopo were also in attendance at the workshop.

Dr Rachel Chikwamba to serve on African Union panel and Medical Research Board January 2017 - Dr Rachel Chikwamba, CSIR Group Executive: Strategic Alliances and Communication, was recently appointed to the African Union (AU) high-level committee on Science, Technology and Innovation Strategy for Africa 2024 (STISA 2024) and to the South African Medical Research Board. Rachel will join a nine-member High-Level African Panel on Emerging Technologies, which is composed of eminent experts who advise the AU and all its affiliates on harnessing emerging technologies. In June 2014, the AU adopted a long-term STISA 2024 roadmap to underpin its Agenda 2063, with its main drive as the diversification of sources of economic growth and lifting the continent’s population out of poverty. The strategy aims to foster social and economic transformation by developing human capital, innovation, value addition, industrialisation and entrepreneurship. STISA 2024 has identified six priority areas namely: Eradicating hunger and ensuring nutrition and food security; prevention and control of diseases and ensuring wellbeing; communication (physical and intellectual mobility); natural resources management and climate change; peace and security and wealth creation. A major recognition in STISA 2024 is that the continent needs to apply existing and emerging technologies to realise the AU vision. Rachel will also serve on the South African Medical Research Board for the period 2016 to 2019 together with 15 other distinguished leaders. Story by: Anna Semenya, CSIR News

Plant-Based Biologics proves a popular and relevant field of biotechnology at ACGT Regional Plant Forum December 2016 - The ACGT, in conjunction with the CSIR, hosted the 12th Regional Plant Biotechnology Forum on the 8th of September at the CSIR’s International Convention Centre (ICC). The forum focused on “Plant-based biologics” and saw over 50 delegates in attendance. The forum kicked off with Dr Rachel Chikwamba, CSIR Executive for Strategic Alliances and Communications, giving a brief welcome and introducing the forum’s key-note speaker, Professor Herta Steinkellner. Herta is a professor at the University of Natural Resources and Life Sciences (BOKU) in Vienna, Austria. She has expertise in N-glycosylation in plants, recombinant protein production in plants as well as protein glycan engineering.  She gave a presentation titled “In planta engineering of post-translational protein modification to enhance biological activity”, which was very well received by the audience and sparked interest in future collaborations between her institution, BOKU, and the CSIR. Other contributors to the forum included CSIR’s Dr Tsepo Tsekoa and Dr Maretha O’Kennedy, Dr Priyen Pillay from the University of Pretoria and Dr Mauritz Venter from the biotechnology company Azargen.   Dr Tsekoa’s presentation was on plant-made antibodies for passive immunisation, while Dr O’Kennedy gave a talk on affordable plant-produced vaccines and biologics through innovative science. Dr Pillay gave a talk on his PhD work, performed at the University of Pretoria, which focused on the contribution of agrofiltration to VP1 recombinant protein degradation. Dr Venter, co-founder and CEO of AzarGen Biotechnologies, gave a talk on “Entrepreneurial endeavours in Plant Biotechnology” and took the audience on a very entertaining journey of how he started his own successful biotechnology company.  The ...

Bringing Silicon to Life December 2016 - A new study is the first to show that living organisms can be persuaded to make silicon-carbon bonds—something only chemists had done before. Scientists at Caltech “bred” a bacterial protein to have the ability to make the man-made bonds, a finding that has applications in several industries. Molecules with silicon-carbon, or organosilicon, compounds are found in pharmaceuticals as well as in many other products, including agricultural chemicals, paints, semiconductors, and computer and TV screens. Currently, these products are made synthetically, since the silicon-carbon bonds are not found in nature. The new research, which recently won Caltech’s Dow Sustainability Innovation Student Challenge Award (SISCA) grand prize, demonstrates that biology can instead be used to manufacture these bonds in ways that are more environmentally friendly and potentially much less expensive. “We decided to get nature to do what only chemists could do—only better,” says Frances Arnold, Caltech’s Dick and Barbara Dickinson Professor of Chemical Engineering, Bioengineering and Biochemistry, and principal investigator of the new research, published in the Nov. 24 issue of the journal Science. The study is also the first to show that nature can adapt to incorporate silicon into carbon-based molecules, the building blocks of life. Scientists have long wondered if life on Earth could have evolved to be based on silicon instead of carbon. Science-fiction authors likewise have imagined alien worlds with silicon-based life, like the lumpy Horta creatures portrayed in an episode of the 1960s TV series Star Trek. Carbon and silicon are chemically very similar. They both can form bonds to four atoms simultaneously, making them ...

Biotechnology: A growing field in the developing world November 2016 - The developing world is achieving significant growth in a broad cross-section of biotechnology fields, many of them directly tied to food production, health and other dimensions of human well-being, says a new analysis commissioned by the CAS-TWAS Centre of Excellence in Biotechnolgy. The first-of-its kind report, ‘Biotechnology in Developing Countries: Growth and Competitiveness’ was released today by the Beijing-based centre, which is organized by the Chinese Academy of Sciences (CAS), and The World Academy of Sciences (TWAS). The CAS-TWAS Centre of Excellence for Biotechnology report provides an assessment of research and patents in the field across the global South. “This report is, to the best of my knowledge, the first extensive document summarizing the development status of a specific technology area in the developing world,” writes Bai Chunli, the president of both CAS and TWAS, in the foreword. “It provides a strong, valuable assessment of biotechnology activities in developing countries, as measured in scientific publications and patents.” Simultaneously, it highlights the important role of international collaboration in the rapid pace of growth in the field, especially in sub-Saharan Africa. The report found that from 2004 to 2015: Biotechnology research has grown steadily, with a 117% increase in published studies. However, biotechnology research from the developing world is less cited in other research papers – only about 83% as much. Over 85% of the biotech papers that were co-authored by science-and-technology lagging countries resulted from international collaborations. Countries in sub-Saharan Africa in particular benefited from international collaboration, resulting in a notably high impact. Patent filings in the developing world have been most active in ...


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