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  • Africa Contributes SARS-CoV-2 Sequencing to COVID-19 Tracking

    Africa Contributes SARS-CoV-2 Sequencing to COVID-19 Tracking
    1st Apr 2020

    In recent years, laboratories on the continent have ramped up genomic sequencing capabilities, offering in-country analyses rather than outsourcing the job.

    Image from technostalls.com

    Three days after the confirmation of Nigeria’s first COVID-19 case, the genome sequencing results of the SARS-CoV-2 specimen were announced on March 1. The sputum samples, taken from an Italian consultant who entered Nigeria through Lagos on February 27 before traveling to the neighboring Ogun State, were analyzed at the African Center of Excellence for Genomics of Infectious Diseases (ACEGID) at Redeemer University. They became the first analysis of SARS-CoV-2 in Africa, signaling the continent’s contribution to the growing global body of evidence to understand the virus’s behavior outside China.

    “We have moved from being spectators to contributors and players in the field of infectious disease genomics,” Christian Happi, ACEGID director in Ede, Nigeria, who led the sequencing effort, tells The Scientist.

    Whether the tool is used for disease outbreaks or routine surveillance, we now have the capacity to perform in-country sequencing, which has traditionally been done through collaborations with laboratories outside the countries.

    —Chikwe Ihekweazu, Nigeria Centre for Disease Control

    Nigeria’s demonstration of rapid sequencing during a health emergency shows that African countries have capacities to monitor the progression of an infectious disease outbreak in real time to understand transmission patterns, says Chikwe Ihekweazu, the director general of the Nigeria Centre for Disease Control based in Abuja.

    Africa’s ability to sequence its own COVID-19 cases demonstrates that countries in the region have invested in diagnostic capabilities, says Ihekweazu. “Whether the tool is used for disease outbreaks or routine surveillance, we now have the capacity to perform in-country sequencing, which has traditionally been done through collaborations with laboratories outside the countries,” he tells The Scientist.

    The Africa Center for Disease Control (CDC) is encouraging countries that have the ability to sequence their own samples to do so, while those that cannot should send their samples to institutions such as ACEGID, Sofonias Kifle Tessema, the head of the genomic sequencing program at Africa CDC, tells The Scientist.

    Africa CDC says 4,871 total COVID-19 cases have been reported in 46 African countries with a total of 152 deaths and 340 recoveries as of March 30. ACEGID has enough expertise and equipment to sequence all confirmed cases from Africa so far, but would need more reagents and additional staff to support bigger outbreaks, says Happi. Each sequencing costs about $600 US.

    The center got its first equipment and staff in January 2014 from a World Bank investment of $8 million US that was part of a $165 million package for 19 higher education institutions specializing in STEM initiatives in eight West African nations.

    The need to enable Africa to contribute to the genomics revolution, and to reduce the knowledge and economic gaps between the rest of the world and Africa, prompted this investment, Happi says. “I wanted to use genomics technologies and to address health problems in Africa, especially infectious disease and facilitate outbreak response,” he says.

    Long before the coronavirus epidemic struck, in 2014, ACEGID sequencing gave the first accurate diagnosis of the Ebola virus in Nigeria.

    The ability to conduct genomic sequencing locally will contribute to the global fight against COVID-19, says Denis Chopera, the program executive manager of the Sub-Saharan African Network for TB/HIV Research Excellence at the Africa Research Institute (SANTHE) in KwaZulu-Natal in South Africa. “Viruses can easily change form to adapt to the environment and evade recognition by the immune system and drugs so it is crucial to understand all these aspects of this virus,” says Chopera. “Remember, it is a new virus and very little is known about it,” he adds. SANTHE has the expertise and resources for sequencing, but is not actively working on coronavirus samples as all laboratory tests are being conducted by the South Africa’s National Institute for Communicable Diseases.

    The World Health Organization has been supporting African governments with early detection by providing thousands of COVID-19 testing kits to countries, training dozens of health workers, and strengthening surveillance in communities, resulting in 46 countries being able test for COVID-19. So far, the number of cases in Africa is dwarfed by those on other continents.

    The initial cases detected in Africa were from travelers coming from countries with widespread outbreaks. “The Nigeria virus is similar to the viruses recently circulating in Europe, which is consistent with the travel history of the COVID-19 patient,” Ihekweazu says of the first case.

    “I do not think that the sequence can tell us why there are few cases in Africa at this point as it is highly likely that the climate in Africa is the reason. However, we will know whether the virus is changing to adapt to the climate, which is a possibility and this could result in more cases on the African continent,” Chopera tells The Scientist.

    Ihekweazu says a number of different factors can be contributing to the limited number of cases detected, and sequencing will provide evidence to show if SARS-CoV-2 is changing, if it’s acquired during hospitalization, and if importations from other countries are still causing outbreaks or if community transmission is driving numbers upward.

    For Akebe Luther King Abia, a Cameroonian environmental microbiologist at the University of KwaZulu-Natal in South Africa, the biggest contribution African scientists can bring are their experiences with previous outbreaks such as Ebola. After the first SARS-CoV outbreak of 2003, scientists within the continent started looking for other members of the coronavirus family in bats and developing methods to detect them, for instance. Medical personnel were trained and health infrastructure was improved to handle future emergencies. Following the previous SARS and Ebola outbreaks, Nigeria created the Nigerian Center for Disease Control and established a network of laboratories within the country for rapid identification of cases.

    “It is no doubt that most countries on the continent do not have sophisticated equipment, but the fact that they have been exposed to numerous diseases outbreaks has made most of them to be ready with what they have,” Abia tells The Scientist.

    Story by: Munyaradzi Makoni, for The Scientist

  • Gene Editing Reaches Plant Mitochondria

    Gene Editing Reaches Plant Mitochondria
    26th Mar 2020

    Modified gene editing machinery enables targeted disruptions of mitochondrial genes in rice and rapeseed plants.

     

    Gene editing technologies have revolutionized the field of genetics, allowing researchers to make targeted changes to the DNA of various animal and plant nuclei, animal mitochondria, plant chloroplasts, and more. Missing from this list until recently, however, was plant mitochondrial DNA. The tools for delivering the necessary editing enzymes to plant mitochondria simply hadn’t been built.

    Now, plant molecular biologist Shin-ichi Arimura of the University of Tokyo and colleagues have filled this gap, creating plant-friendly mitoTALENs—mitochondria-targeting gene editing tools based on transcription activator-like editing nucleases (TALENs).“This is an important paper—it’s the first demonstration that we can make targeted and heritable changes to mitochondrial DNA” in plants, Ian Small, a plant scientist at the University of Western Australia who was not involved in the research, writes in an email to The Scientist

     

    HITTING DELETE: Agrobacteria carrying a plasmid encoding a gene-specific, mitochondria-homing mitoTALEN infect cultured plant cells and deliver the genetic payload to the cells’ nuclei (1), where the DNA integrates into the genome. The encoded mitoTALEN protein is then produced and enters the mitochondria, deleting a portion of the target gene—in this case, a gene causing male sterility (2). The resulting transgenic plant can self-fertilize, producing abundant seeds (3). Illustration by GEORGE RETSECK

     

    Regular TALENs are composed of a DNA binding domain that can be readily engineered to recognize practically any DNA sequence, and a nuclease domain that chops up the DNA at that site, causing deletions. To target a mitochondrial gene, the team modified a plant-adapted TALEN such that it also included a mitochondrial homing signal, and engineered DNA binding domains to recognize particular genes of interest. The researchers then transferred a plasmid encoding a mitoTALEN into plants via agrobacteria—a common strategy used by plant geneticists.

    In proof-of-principle experiments, the researchers designed two mitoTALENs, each targeting a particular mitochondrial gene: orf79 in rice and orf125 in rapeseed (canola). The resulting deletions enabled the researchers to confirm the genes’ hitherto suspected roles in male sterility—a natural phenomenon that prevents self-fertilization in certain hermaphroditic plants, thus promoting hybrid seed development. Indeed, disabling the genes reinstated self-fertilization in the two types of plants, the team showed.

    Such male sterility genes, which are encoded in the maternally inherited mitochondria of certain plants, are desirable for agriculturalists wishing to produce hybrid crops that “grow faster, produce more, and are more resistant to disease,” explains Small. Thus, generally speaking, the goal is to activate such genes or introduce them into crop plants that lack them, rather than delete them, as Arimura’s team did.

    While the plant mitoTALENs can’t yet deliver the “holy grail” of plant mitochondrial gene editing, this study is “an important first step,” says plant physiologist Ralph Bock of the Max Planck Institute of Molecular Plant Physiology who did not participate in the research. In the meantime, he adds, “one could use [the technology] to ask questions about the functions of mitochondrial genes.” (Nat Plants, 5:722–30, 2019)

    Story by: Ruth Williams, for The Scientist, March 2020

  • ACGT activities during the COVID-19 pandemic

    19th Mar 2020

    Following the call by the Government to practice social distancing in order to curb the spread of COVID-19, the ACGT staff will be working remotely and will be reachable via emails (please see our Contact Us page for our email addresses).

    The ACGT is looking into ways to continue with its activities through the means of Webinars. More information on the Webinars will follow in the next few weeks.

  • Mother City provides backdrop for advanced biotech training workshop

    12th Dec 2019

    The African Centre for Gene Technologies (ACGT) partnered with the Council for Scientific and Industrial Research (CSIR), the University of Cape Town (UCT) and the Centre for Proteomic and Genomic Research (CPGR) to host the 2019 proteomics advanced workshop and symposium. The advanced workshop, which took place from the 18th to the 21st of November 2019, focused on the analysis of targeted proteomic and metabolomic data, using the open-source software package Skyline. The workshop was immediately followed by a national proteomics symposium, on the 22nd of November 2019, which provided emerging scientists in the field an ideal platform to showcase their work.

    The four-day workshop was facilitated by Mr Brendan MacLean (MacCoss lab, University of Washington), Dr Birgit Schilling (Buck Institute for Research in Aging), Dr Ben Collins (Queen’s University Belfast and formerly Aebersold lab, ETH Zurich) and Dr Lindsay Pino (Garcia Lab, University of Pennsylvania and formerly MacCoss lab, University of Washington). The workshop had theory and practical sessions and covered a number of topics including:

    • Brief introduction to targeted analysis;
    • Skyline overview;
    • Targeted Selected Reaction Monitoring: Method development and Data analysis;
    • Targeted SWATH/ Data-Independent Acquisition: Introduction, Suitability (QC) test, library generation, data processing;
    • Panaroma and AutoQC;
    • Statistical group comparisons in Skyline; and
    • Small molecule applications in Skyline.

    The participants represented various research institutions from across the country, including the Universities of Pretoria (UP), the Witwatersrand (Wits), Johannesburg (UJ), Stellenbosch, Cape Town, the CSIR and CPGR. The participants were also given an opportunity to engage with the experts on a one-to-one basis to discuss their projects.

    The symposium, which followed the workshop, had the workshop facilitators as keynote speakers as well as local researchers presenting their work. Local speakers hailed from a  number of South African institutions including UP, Wits, CSIR and UCT. The symposium was a great platform to showcase what has been transpiring in the field since the last national meeting, which took place at Wits in 2018. The symposium also gave emerging scientists the opportunity to network with established researchers in the field.

     

    Symposium talks:

    Dr Ben Collins (Queen’s University Belfast) –  Keynote speaker                                             

    Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage

     

    Dr Previn Naicker (CSIR)

    Development of sample preparation workflows and application to Clinical Proteomics

     

    Mr Matthys Potgieter (UCT)                                                                                                    

    MetaNovo: a probabilistic pipeline for peptide and polymorphism discovery in complex metaproteomic datasets

     

    Mr Brendan MacLean (University of Washington) – Keynote speaker

    Growth in the software ecosystem for targeted quantitative proteomics

                                

    Dr Tracy Hurrell (CSIR)

    Contextualizing the proteome of hepatocyte models

     

    Mr Andea Ellero (UP)

    Time course convergence of hepatocellular proteomic phenotypes seen in HepG2 spheroid cultures

     

    Mr Emmanuel Nweke (Wits)

    Deciphering the proteomic landscape of Pancreatic Ductal Adenocarcinoma in South African patients using SWATH mass spectrometry

                                

    Dr Birgit Schilling (Buck Institute for Research in Aging) – Keynote speaker

    Proteomic tools to decipher mechanisms of senescence in aging and age-related diseases

     

    Dr Shaun Garnett (UCT)

    Generating a proteomic profile of neurogenesis, through the use of human foetal neural stem cells

     

    Mr Daniel Mutithu (UCT)

    Metabolic profiling for biomarker discovery to understand pathogenesis of rheumatic heart disease

     

    Dr Lindsay Pino (University of Washington) – Keynote speaker

    Using an external reference material to harmonize and calibrate quantitative mass

    spectrometry data at scale

                                

    Establishing a community of practice for the proteomics society came up during the welcome address and closing remarks given by Prof Jonathan Blackburn from UCT and Mr Thabo Khoza from the ACGT. Mr Khoza highlighted that an informal platform (Google Groups) has been set up by the ACGT to encourage the researchers in the field to communicate more effectively. This platform is open to any researcher who wishes to join it.

    The workshop and symposium would have not been possible without the generous financial support from Anatech, Bruker, Inqaba Biotec, Microsep and The Scientific Group.

    The ACGT will engage with the community to plan and organise the next national proteomics workshop and national symposium for the year 2020.

    For any queries related to this, or other proteomics capacity-building and networking events, contact Mr Thabo Khoza, Liaison Scientist at: 

     

    To see more photos, please visit our ACGT Facebook page.

     

    Story by: ACGT, December 2019

  • 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