25th June 2015
A team of British scientists representing an international, multi-organisational effort to curb the further spread of Ebola in Sierra Leone have released their first dataset of the virus’ genetic structure online on virological.org
The information is intended for the global scientific community to monitor the pathogen’s evolution in real-time and conduct research that can lead to more effective strategies against further outbreaks.
The team of scientists, funded by the Wellcome Trust, is using semi-conductor next-generation sequencing (NGS) technology developed by Thermo Fisher Scientific to generate data in a lab facilitated by Public Health England and International Medical Corps.
Head of Virology at the University of Cambridge, Professor Ian Goodfellow, travelled to Sierra Leone in December 2014 and then again in March 2015 to help set up a new diagnostics centre attached to an Ebola Treatment Centre in one of the country’s worst affected areas. Goodfellow returned a third time to study the virus at a molecular level using the sequencing technology.
“Sequencing the genome of a virus can tell us a lot about how it spreads and changes as it passes from person to person. While this information is invaluable to researchers, the rapid sharing of data does not always occur,” said Professor of the Virus Genomics laboratory at the Wellcome Trust Sanger Institute, Paul Kellam, Ph.D, who is leading the team to map the genomic data captured by Goodfellow and his colleagues.
“It used to take months to process samples that had to be brought back to labs in the UK for analysis. Having sequencing capabilities on the ground helps generate data in a matter of days or at the longest weeks, which should have a profound impact on how the Ebola virus is researched and inevitably addressed on a global scale,” continued Kellam.
Rapid sequencing enables epidemiologists to decipher the source of individual strains, helping to eliminate the need to rely on Ebola patients to find out how and where they contracted the Ebola virus, as different strains can be tracked as they are transmitted from person to person.
“Only by understanding the Ebola virus and other pathogens, which cause so much suffering in countries like Sierra Leone, can we take meaningful steps to protect communities from future outbreaks,” said Goodfellow. “My hope is that this technology will be used by the next generation of Sierra Leonean scientists and researchers to help provide a sustainable research and surveillance system in the future.”
The next-generation sequencing system was installed at the laboratory adjacent to an Ebola Treatment Centre in Makeni, which was funded by the UK’s Department for International Development. The next-generation sequencing system is also expected to be installed at the University of Makeni, where it will be used by local scientists to study Ebola and other pathogens that affect the region.
“We’ve learned many painful lessons from the Ebola outbreak, not least of which is that as a scientific community we must become less secretive with the data that is generated,” said Director of the Wellcome Trust, Dr Jeremy Farrar.
“The collective expertise of the world’s infectious disease experts is more powerful than any single lab, and the best way of tapping into this is to enhance the capacity to generate the data in the countries affected, rather than having to fly samples out to other countries and then to make the data openly and safely available, as soon as possible,” concluded Farrar.
Story by: Terri Chowles, eHealthNews.co.za
27th May 2015
Saturday, 25 April was World Malaria Day. This year’s theme was ‘Invest in the future, defeat malaria’. The University of Pretoria’s Centre for Sustainable Malaria Control (UP CSMC) believes that research is critical in combating malaria in a manner that is sustainable and without the potentially adverse health effects of toxic chemicals.
One of the ways in which the Centre interpreted this year’s theme, is that we should invest in our up-and-coming malaria researchers who develop new and innovative intervention methods to defeat this disease. As part of the Centre’s World Malaria Day activities, a group of 18 postgraduate students of the UP CSMC, who are working on malaria-related projects, travelled to rural Tonga in Mpumalanga Province, South Africa, to visit the Tonga Malaria Training Station, where they could get a more practical view of how the disease is fought on ground level.
Mr Aaron Mabuza, Malaria Control Programme Manager for Mpumalanga, spoke to the students about the work that he and his team are doing. He explained that one of the key programmes that the Tonga Malaria Training Station is involved with is the training and consequent management of insecticide spray workers who play a major role in Mpumalanga’s and South Africa’s control of the malaria vector (mosquito) itself.
Because malaria vectors are considered endophilic, meaning that the mosquito vectors rest inside houses after taking a blood meal, it is possible to control the prevalence of the insects that carry the disease through indoor residual spraying (IRS). As the name implies, IRS involves applying a residual insecticide to the walls and other surfaces of a house. The insecticide will then kill mosquitoes and other insects that come into contact with these surfaces for several months. It is important to note that the process does not necessarily prevent people from being bitten by mosquitoes, but rather kills the insects when they come to rest on the surface after they have fed, thus preventing transmission of infection to other persons.
The Tonga Station is equipped with training facilities and accommodation for the spray workers undergoing training. Training usually takes place in August so that enough sprayers are available to cover the target area, because to be effective, IRS has to be applied to a very high proportion of households in an area – usually more than 80%. For the 2014/2015 malaria season, 321 temporary spray operators were trained and employed. In addition to the training of spray workers, the Station also runs yearly awareness and education campaigns to educate affected communities about malaria control and prevention strategies.
South Africa is one of the few countries in the world where dichlorodiphenyltrichloroethane, better known by the acronym DDT, is still used for vector control. Although use of this chemical is contentious, the responsible application thereof has been successful in reducing malaria transmission and related deaths in the three malaria-endemic provinces – Limpopo, Mpumalanga and KwaZulu-Natal. As the benefits in using chemicals for the control of malaria outweigh the human and environmental risks associated with these chemicals, there is agreement that public health efforts are needed to reduce reliance on chemicals. In an effort to find sustainable ways toward eliminating malaria, researchers at the UP CSMC are currently involved with various projects inter alia to determine the effects that chemicals used for insect control have on people living in the affected communities and also to find safer alternatives for vector control. Recently both Prof Tiaan de Jager (Director of the UP CSMC) and Prof Riana Bornman delivered plenary lectures on the topic at an international congress in Copenhagen. The UP CSMC’s work on insecticide exposure and health effects is internationally recognised.
According to Mr Mabuza there was an increase in the total number of malaria cases reported during the past season. He says that 75% of reported cases were however imported from other malaria areas and countries outside Mpumalanga, meaning that only 25% of cases contracted the disease locally in Mpumalanga. The case fatality rate was only slightly above the national and provincial norm of 0,5%. This relatively low mortality rate, he says, can be attributed to successful vector control through the spraying of houses, which is done between September and December each year. Another contributing factor to the low mortality rate in the province is the high rate of early diagnosis and treatment of malaria cases achieved by health workers in the province. Most diagnoses are still made using antigen-based malaria rapid diagnostic tests (RDTs) when a patient presents with symptoms at a clinic, but it is the second, more proactive testing approach employed by the programme that allows health workers to identify the majority of cases before they become too serious.
When a patient is diagnosed with malaria, health workers take blood smear samples from the patient’s immediate family members and close neighbours to determine if they were infected by the same parasite carrying mosquito. At present the blood smears are sent to the National Institute for Communicable Diseases (NICD) in Johannesburg for analysis, but the Station plans to analyse all samples locally once their own laboratory becomes operational.
Apart from the laboratory that will be available to staff at the Tonga Malaria Training Station in the future, the Station has also taken the first steps towards establishing a state-of-the-art insectary, which will allow researchers at the Station to study the behaviour of the mosquitoes that carry the deadly malaria parasite, thereby enabling them to develop more effective methods of vector control. The Station may also serve as a future field station for UP CSMC staff and students. The UP CSMC already has a satellite research facility in Vhembe District in Limpopo Province and Dr Sunday Ukpe from the UP CSMC is actively involved in promoting early diagnosis and the effective treatment of malaria in Mpumalanga.
The dedicated staff at the Tonga Malaria Training Station has been an inspiration to all the students who have had the opportunity to experience the practical side of the fight against a disease that they normally only get to study in a laboratory. All indications are that the team at the Station have made strides towards eliminating the disease in South Africa. According to Mr Mabuza, the largest remaining challenge is for them to find a way to effectively control the spread of the disease from neighbouring countries, where effective control strategies are largely lacking. He says that he firmly believes that it will be possible to eliminate the disease in South Africa by 2018, provided that countries where the disease is endemic work together towards achieving this goal. According to Prof de Jager, the UP CSMC is doing innovative and leading research to support the country and the African continent in efforts to eliminate malaria.
Story by: Ansa Heyl, University of Pretoria
11th February 2015
In the world of health and medicine, the word tobacco usually brings to mind cancer, emphysema and heart disease. But in recent years the plant’s tarnished reputation is getting a makeover from the development of pharmaceuticals through an effective, swift and cost-cutting technique that has been dubbed “biopharming.”
For more than seven years, the CSIR has been at the forefront of biopharming research and development (R&D) in South Africa and has active partnerships with global leaders in the field. Now, the CSIR’s antibody expression platform aims to enhance the organisation’s preparedness for hosting a national biopharming platform in support of an emerging South African bioeconomy. Consequently, the CSIR is poised to play a leadership role in support of the Department of Science and Technology’s new bioeconomy strategy.
According to Dr Tsepo Tsekoa, principal investigator of the antibody expression platform,”Technological development has resulted in plants increasingly becoming an attractive host for the recombinant production of proteins destined for agro-industrial, biomedical and pharmaceutical application. With the recent approval of a number of plant-produced biologics for human health use – and a strong pipeline in clinical trials – the concept of using plants as a source to produce recombinant vaccines and other biopharmaceutical proteins is now being realised. An example of this is the use of antibody-producing tobacco plants employed in the battle against rabies.”
“Plant-based expression systems are relatively inexpensive, readily scalable and fast; leveraging a niche in vaccines for neglected diseases, pandemic vaccines or emerging disease vaccines where other means of production may be too slow to respond or too expensive for mass roll-out,” noted Tsekoa.
Over the next few years, the platform will develop biopharming-related human capital and strengthen state-of-the-art competence through research exchanges; evaluate recombinant vaccine manufacturing technologies for rapid response to pandemic influenza in South Africa; and complete a proof of concept for expression of highly active and broadly neutralising HIV antibodies in preparation for national roll-out in partnership with a large international consortium.
“In addition, the production of ‘biobetters’ – which refers to a recombinant protein drug that is in the same class as an existing biopharmaceutical but is improved over the original, is an attractive option, as plant expression systems have been shown to produce biopharmaceuticals free of human infective viruses, prions and bacterial contaminants such as endotoxins. The technology has the potential to become a commercially attractive and universally accepted approach for vaccine, therapeutic and reagent protein manufacturing,” said Tsekoa.
The CSIR has a sound track record when it comes to biopharming R&D. The organisation has produced vaccines such as RabiVir, a plant-made antibody cocktail for rabies prophylaxis, plant-made subunit animal vaccines as well as a pipeline of other veterinary vaccine production technologies, including virus-like particles.
Story by: Kulani Chauke, Council for Scientific and Industrial Research
10th February 2015
The University of Pretoria (UP)’s vision acknowledges this institution’s prominent role in Africa and its commitment to fulfilling its social responsibilities. In this context it is clear that malaria, which has a devastating impact on the health of the citizens and the economies of many African countries, has been and continues to be a significant focus of research at UP. The University of Pretoria Centre for Sustainable Malaria Control (UP CSMC) is currently one of the leaders in malaria research in South Africa and is known for its unique integrated focus on malaria parasite biology, functional genomics, drug discovery efforts, innovative mosquito control strategies, public health management and community engagement. The Centre cooperates closely with the National Department of Health and other partner institutions throughout the country in their efforts to eradicate malaria in South Africa by 2018.
Worldwide an estimated 250 million clinical cases of malaria occur annually, and more than half a million deaths are reported. The majority of these deaths occur in sub-Saharan Africa and the victims are mostly children under the age of five years. Despite a marked reduction in the incidence of malaria over the past decade, fatality rates due to malaria remain high in South Africa. Since the malaria season is currently at its peak, the focus of many health care professionals is firmly on the timely diagnosis and treatment of this disease.
Malaria is endemic in three provinces in South Africa (Limpopo, Mpumalanga and KwaZulu-Natal), but this does not mean that the other provinces are malaria free. The disease is transmitted by female Anopheles mosquitoes that carry the malaria parasite, and although malaria prevention and control strategies are being vigorously implemented in the provinces where malaria is endemic, similar strategies in the rest of the country are unfortunately lagging behind.
It is interesting to note that even though malaria is not endemic in Gauteng, this province is none the less classified as one of the high-incidence malaria areas in South Africa, with most of the reported cases occurring in the Ekurhuleni, Johannesburg and West Rand Districts. More than 80% of the patients diagnosed with malaria in these districts hail from Mozambique and other African countries and have travelled to South Africa in search of employment.
Since many of these migrants are in the country illegally, they are reluctant to seek medical attention when they become ill. This often leads to delayed diagnosis and treatment, and consequently to a high mortality rate among people from this group. Unfortunately the Gauteng Department of Health’s campaign aimed at educating migrants about the disease has been hampered by the fact that they are difficult to reach as they often have no fixed addresses or are afraid of prosecution should their illegal status become known.
In recent years ‘taxi malaria’ or ’Odyssean malaria’ – which refers to malaria transmitted by translocated parasite-carrying mosquitoes – has become another cause for concern in the South African provinces where malaria is non-endemic, since malaria is often excluded as a possible diagnosis in the case of patients who have not visited areas where the disease is endemic. According to the National Institute for Communicable Diseases (NICD), road traffic arriving from areas in and around South Africa where malaria is endemic is a very likely source of most of the infected mosquitoes responsible for Odyssean malaria cases.
As the disease mimics many other conditions, such as influenza, meningitis, viral hepatitis, septicaemia and tick-bite fever, misdiagnosis is common and results in treatment being delayed, which in turn leads to a high incidence of severe and complicated malaria and a high fatality rate.
The Plasmodium falciparum malaria strain, which accounts for the majority of malaria cases in South Africa, causes almost all severe and fatal instances of the disease. Symptoms of malaria typically include fever, rigours, headache and muscle pain, but a definitive diagnosis can usually be made by the detection of the parasite during a microscopic examination of a blood smear, or by using a rapid malaria antigen test. Most hospitals and clinics in the country have the capacity to make a definitive diagnosis by using either one of these methods. Malaria is generally treated with antimalarial drugs combined with medications to control fever, anti-seizure medications when needed, and fluids and electrolytes. The severity of a patient’s condition and the likelihood of chloroquine resistance will determine the types of medication administered.
In October 2014 the UP CSMC was awarded the status of Medical Research Council (MRC) Collaborating Centre for Malaria Research, which means that it is now part of a network of MRC Collaborating Centres for Malaria Research that will collectively provide a multi-disciplinary approach to malaria research; synergise efforts on malaria research to achieve common goals; and facilitate scientific collaboration among malaria researchers in southern Africa. The Centre will also receive funding from the MRC to further develop the infrastructure needed in order to continue to engage in cutting-edge research on innovative, safe and effective vector control methods.
In recent years the management and treatment of malaria has improved significantly and there is even talk of a vaccine that could eradicate the burden of this devastating disease in many of the world’s poorest countries. With the huge increase in available resources and brainpower focused on fighting this disease, it is beginning to seem more likely that the ambitious goal of eradicating malaria by 2018 could indeed be achieved.
Story by: Ansa Heyl, University of Pretoria
11th December 2014
The ACGT hosted the 5th national proteomics workshop in September 2014; facilitated by two world renowned proteomics experts, Prof Kathryn Lilley from Cambridge University and Prof Lennart Martens from Ghent University. The workshops were held at two nodes; at the University of Pretoria from the 10th-12th of September and at Stellenbosch University from the 15th – 17th of September.
This three-day workshop was a follow-up from the 2012 and 2013 Proteomics workshops that were facilitated by Prof Lilley and the 2013 Proteomics-Bioinformatics workshop facilitated by Prof Martens. The 1st two days of the workshop were packed with a series of lectures and practical sessions from both professors. The topics covered on day 1 and 2 included: introduction to proteomics, basics of mass spectrometry, quantitative proteomics approaches, data processing of quantitative methods, identification and interpretation of MS proteomics data, experimental design and protein inference. On the 3rd day, round-table discussions were conducted and the participants had the opportunity to engage with the two professors, as well as local proteomics experts, regarding their own projects and discuss topics such as sample preparation; experimental design; quantifying methods to be employed, biological interpretation of MS data and validation methods.
The Gauteng leg of the workshop was well represented by attendees from the ACGT partner institutions (Council for Scientific and Industrial Research, Agricultural Research Council, the Universities of Johannesburg, Pretoria and Witwatersrand). There were also attendees from Rhodes University, University of South Africa, University of Free State and Protechnik Laboratories. The Western Cape leg of the workshop had participants from Stellenbosch University, University of Cape Town, the Agricultural Research Council and Cape Peninsula University of technology.
The workshop was very well received at both nodes with some of the participants sharing comments such as “Both speakers were very knowledgeable and were good at explaining difficult concepts. I thought the course was excellent and extremely useful”, and “The lecturers (Profs Lilley and Martens) were excellent at conveying complex topics in an easy to understand way. They were extremely knowledgeable and helpful during discussion sessions. I would highly recommend utilising their expertise in future workshops.”
The facilitators were also impressed with the attendees and were able to pitch the lectures according to the needs of the participants at the different nodes. The success of the workshop made it possible for the both facilitators informing the ACGT team that they would be happy to come back in 2015 and present a more evolved proteomics workshop.
3rd December 2014
The 10th Regional Plant Forum was held on the 30th of October 2014 at the University of the Witwatersrand’s Professional Development Hub. The ACGT partnered with Prof Chrissie Rey, from the University of the Witwatersrand, to plan and organise the 10th Forum under the theme of “Crop Improvement and Genetic Transformation”.
The forum drew an audience of over 50 people representing all the ACGT partner institutions as well as outside attendees, including the African Centre for Crop Improvement (ACCI) in KZN as well as the Department of Science and Technology. The attendees had the pleasure of hearing talks from two prominent scientists in the field and keynote speakers for the forum, Dr Sandy Snyman and Prof Johan Burger.
Dr Sandy Snyman is a senior researcher in the biotechnology facility at the South African Sugercane Research Institute (SASRI) based in Kwa-Zulu Natal. Whilst with SASRI, Dr Snyman has initiated and implemented several tissue culture protocols in different aspects of the institute. She also has a particular interest in biosafety risk assessment relating to genetically modified organisms (GMOs).
Prof Johan Burger is Chair of the Genetics department of Stellenbosch University and his research programme deals with viral diseases as well as molecular genomics of grapevine. Prof Burger serves on a number of steering committees that deal with the study of virus and virus-like diseases of grapevine as well as grape genome programs.
The forum also included talks from Dr Lerato Matsaunyane from University of Johannesburg/ Agricultural Research Council (ARC), Dr Inge Gazendam from the ARC, Prof Chrissie Rey from Wits, Dr Kingstone Mashingaidze from the ARC and Mr Wayne Barnes from the forum sponsor, Thermo Fisher Scientific.
The forum served as an opportunity for the 50+ delegates to network and talk about future collaborative efforts. A need for workshops for plant biotechnologists was also highlighted and the ACGT will look into ways of bringing such workshops within reach for its partner institutions as from 2015.
To access the presentations, please click on the title below:
Dr Sandy Snyman (SASRI) – “In vitro manipulations and strategies for the improvement of sugarcane cultivars in South Africa”
Dr Lerato Matsaunyane (UJ) – “Analysis of the unintended and unexpected effects of transgene insertion on the endogenous host genome”
Prof Johan Burger (SU) – “Of vineyards, viromes and VNPs – lessons in virus variability and versatility”
Dr Inge Gazendam (ARC) – “The application of genetic transformation at the ARC-VOPI to improve plant traits”
Prof Chrissie Rey (Wits) – “Stacking genes for multiple trait genetic modification”
Dr Kingstone Mashingaidze – “Public-private partnerships for deployment of GM traits to smallholder farmers”
25th November 2014
Prof Ian Dubery from the Department of Biochemistry and his Plant Metabolomics Research Group were awarded the Chromatographer of the Year Award for 2014.
ChromSA Chromatographer of the Year award for 2014 is awarded to the Metabolomics Research Group of the University of Johannesburg, for their publications of applications of new chromatographic techniques and those relating to established chromatographic technique applications. Their metabolomics research involves both chromatography and mass spectrometry and is focussed on secondary plant metabolites and their importance in disease resistance in plants.
The research team comprises Prof Ian Dubery; Prof Paul Steenkamp; Dr Lizelle Piater; Dr Ntakadzeni Madala; Dr Heino Heyman; Ms Nombuso Ndlovu and Mr Fidele Tugizimana.
Story by: UJ Newsletter, Faculty of Science, University of Johannesburg
21st November 2014
The Medical Research Council (MRC) invited higher education institutions, science councils and registered non-profit research organisations in South Africa, Zimbabwe and Mozambique to submit applications to become part of their new initiative, MRC Collaborating Centres for Malaria Research. The University of Pretoria’s Centre for Sustainable Malaria Control (UP CSMC) recently received word that their application has been successful. The network of MRC collaborating centres for malaria research will collectively provide a multidisciplinary approach to malaria research; synergise efforts on malaria research to achieve common goals; and facilitate scientific collaboration among malaria researchers in Southern Africa.
The collaborating centres involved in the initiative will receive an annual core grant for an initial period of three years and will become members of the MRC network for malaria research. The UP CSMC, in particular, will receive funding from the MRC to further develop the infrastructure that will enable it to continue to engage in cutting-edge research on innovative vector control methods that are safe and effective. In addition, institutions selected to form part of the initiative will be given a preferential opportunity to participate in national multicentre studies based on the priorities defined in the MRC’s national malaria research plan.
‘To get the status of an MRC collaborating centre is not only recognition at the highest national level, but is also giving credibility to the researchers, and opening up international opportunities’, says Prof Tiaan de Jager, Deputy Dean: Research, Faculty of Health Sciences at UP and Director of the UP CSMC.
The UP CSMC has pioneered research on a range of methods for sustainable malaria control – from the biochemical and the biological to the chemical and the physical. Current research in the Centre focuses on how best to manage these methods at a transdisciplinary level. Community involvement and education are addressed as part of health promotion and there is a commitment to change affected communities’ behaviour towards malaria. Environmentally friendly ways of delivering chemicals for malaria prevention are among the novel ideas being explored. The focus of the UP CSMC is safer malaria control and management.
Southern African countries, such as South Africa, Namibia, Botswana and Swaziland, which are situated on the fringe of malaria transmission in Africa, have all seen a reduction in malaria cases over the last decade; in fact, most of these countries now meet the pre-elimination criteria of the World Health Organisation (WHO) and are set to eliminate malaria by 2018. That being said, a lot of work still needs to be done towards eradicating the disease completely, but through education and research into new and innovative methods of fighting the disease we can imagine a day when the whole of Southern Africa will be malaria-free.
Story by: Ansa Heyl, UP News, University of Pretoria
2nd October 2014
The Chief Executive of Standard Bank, Mr Sim Tshabalala, the Executive Chair of Dimension Data Middle East and Africa, Dr Andile Ngcaba, and the Chief Executive Officer of the Human Sciences Research Council, Prof. Olive Shisana, are among the experts who make up the new the National Advisory Council on Innovation (NACI) Council.
The Minister of Science and Technology, Naledi Pandor, announced the appointment of nineteen new members of the NACI Council at a welcoming ceremony held in Pretoria today, 30 September 2014.
NACI is a statutory body established by the National Advisory Council on Innovation Act, 1997 (Act No. 55 of 1997), to advise the Minister of Science and Technology and Cabinet on all matters pertinent to innovation. NACI provides advice to the Minister on the role and contribution of science, mathematics, innovation and technology in South Africa’s social and economic development.
The NACI Council members are drawn from various sectors and are people of distinction, influence and expertise in their fields.
The Council will be headed by the Vice Chancellor and Principal of the University of Pretoria, Prof. Cheryl de la Rey. Prof. De la Rey was the Chief Executive Officer of the Council on Higher Education before serving as Deputy Vice Chancellor and Professor of Psychology at the University of Cape Town. She also served as the Executive Director of Research Promotion at the National Research Foundation.
Announcing the new members, the Minister said “I am pleased with the calibre of the Council members and the wealth of knowledge and expertise that they bring to this institution, which is a key priority for government. All appointees bring an impressive range of skills and experience from a diverse range of backgrounds. I am sure you will make a valuable contribution to the innovation of the country.”.
Minister Pandor further expressed her appreciation for the excellent work done by by the outgoing members, particularly Dr Steve Lennon,who chaired the Council for two terms.”I especially want to thank the outgoing Chairperson, Dr Steve Lennon, for his tireless commitment and dedication to the work of NACI.”
Members of the new NACI council:
- Prof. Cheryl de la Rey (Chairperson)
- Prof. Anton Eberhard
- Adv. Louisa Zondo
- Dr Azar Jammine
- Dr Shadrack Moephuli
- Dr Andile Ngcaba
- Prof. Olive Shisana
- Dr Sibusiso Sibisi
- Dr Albert van Jaarsveld
- Mr Dhesigen Naidoo
- Mr Kevin Nassiep
- Mr Garth StrachanMr Sim Tshabalala
- Ms Clare Busetti
- Ms Zanele Monnakgotla
- Ms Nonkululeko Nyembezi-Heita
- Prof. Roseanne Diab
- Prof. Glenda Gray
- Prof. Jennifer Ann Thomson
Source: Department of Science and Technology Press release 30 September 2014
1st October 2014
Annotating and assembling genomes can be a daunting task for biologists. Navigating the command line, installing MAKER, mounting directoriess, working in Linux and Mother Nature could not keep these delegates from conquering and learning genome assembly and annotation using the MAKER software.
Professors Mark Yandell and Barry Moore facilitated a genome annotation and assembly workshop using the MAKER software from the 15th-19th September 2014. Held at the University of Pretoria’s Bioinformatics and Computational Biology Unit, the course was hosted by the African Centre for Gene Technologies and the Genomics Research Institute. The Department of Science and Technology co-sponsored the event by providing scholarships for participants from outside Pretoria as well as lunches for all participants.
Participants from all five ACGT partner institutions, ACGT affiliate the University of Limpopo and the University of the Western Cape participated in the 3 day course. The exuberant course presenters made learning the abstract content both easy and fun for participants. These outstanding lectures were followed by hands-on data analysis sessions.
As an observer, not battling the command line during this course, it was heartening to see all the participants running their analyses and not giving up. Those command line “fundi’s” present assisted their fellow delegates with camaraderie and patience I have not witnessed in a while. With all the positive attitude in the room, not even the blistering heat stopped the presenters and delegates running their analyses. Mark, Barry and Fourie were ever willing to lend a hand or fill the time while the analyses were running with some good coding humour. There were a lot of laughs, smiles and wide eyes as we continued throughout the three-day course.
On the 18th of September, course presenters assisted delegates in analysing their data and addressing any specific questions that were not addressed during the course. Prof Brenda Wingfield hosted Mark and Barry on the 19th of September, during which time members of her lab held group sessions with the presenters to discuss their projects.
Overall, the course was received positively by the delegates. The presenters were in turn suitably impressed by the level and enthusiasm of the delegates.
The workshop presented forms part of a series of bioinformatics training courses hosted by ACGT and its partners to address specific needs in bioinformatics skills training. For more information on upcoming bioinformatics training events, visit the events page on the ACGT website (www.acgt.co.za) or like us on Facebook (http://www.facebook.com/ACGT.biotec).