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Carnegie Corporation Fellows Retreat, 14 October 2013

Carnegie Corporation

A Carnegie Corporation Fellows Research Day & Retreat was held on 14 October 2013, following on from the very successful Student Symposium hosted by the IDM in July 2012. The 2013 event brought together all the fellows from the infectious diseases components based in the IDM; their supervisors or hosts; Professor Valerie Mizrahi, Director, IDM; Professor Clive Gray HOD Immunology & who has led the IDM Education portfolio for 2013 which includes overall responsibility for the administration of the Carnegie Corporation awards; fellows based in the UCT Department of Molecular & Cell Biology; their supervisors or hosts; Professor Janet Hapgood, HOD, Molecular and Cell Biology (MCB); and four of the six 2013 IDM senior mentors, Professors Dave Beatty, Gay Elisha, Jacquie Greenberg, Bob Millar and Robert Wilkinson (apologies were given from Professors Wieland Gevers and Gregory Hussey). In response to requests from fellows after the 2012 research day, the event was held off campus, at the Silver Mist Mountain Lodge & Wine Estate, Constantia Nek, and included dinner with guest speaker Professor Stuart Saunders, retired former Vice Chancellor UCT & Dean of Medicine.

The Research Day provided an opportunity for the fellows to present their research, to listen to aspects of research topics aside from their own, to interact with each other, and hopefully to later apply new concepts and thinking to their own research. Commentary and questions were also forthcoming with each talk, from the staff and mentors present.

Professor Mizrahi introduced the programme, welcomed all and thanked in particular the organisors Professor Gray, Dr Heather Davies-Coleman (IDM Research Administration Manager) and Kathy Wood (CIDRI, IDM). Dr Nelleke Bak, Director, Postgraduate Centre, officially opened the day.

The programme consisted of a full day of presentations that included topics on TB as a disease, the associated genetic risk to TB, immunity, vaccines, and complications with diabetes; HIV and mouse models; HPV and the microbiome; Clostridium difficile; Avipox viruses; influenza; and malaria.

  Prof Valerie Mizrahi, Director, IDM
  Dr Nelleke Bak, Director, Postgraduate Office
09:40 SESSION 1. Tuberculosis  (Chair, Dr Claire Hoving, Postdoc Fellow) 
  09:40-09:55     Dr Sara Suliman
  09:55-10:10     Dr Emile Chimusa
  10:10-10:25     Dr Robert Thuku
  10:25-10:35     Antonina Wasuna
  10:35-10:45     One Dintwe
11:15 SESSION 2. HIV (Chair, Dr Tracy Meiring , Postdoc Fellow)
  11:15-11:30     Dr Chanel Avenant
  11:30-11:45     Dr Aderito Monjane
  11:45-11:55     Gama Bandawe
  11:55-12:05     Retsilisitsoe Moholisa
12:05 SESSION 3. HPV/pox (Chair, Dr Tolu Oni, Postdoc Fellow)
  12:05-12:20     Dr Tracy Meiring
  12:20-12:30     Aleyo Chabeda
  12:30-12:40     Kristy Offerman
  12:40-12:55     Dr Brian Kullin
14:00 SESSION 4. HIV (Chair, Dr Sara Suliman, Postdoc Fellow)
  14:00-14:10     Yashini Govender 
  14:10-14:20     Roslyn Ray
  14:20-14:30     Antoinette Labuschagné
14:30 SESSION 5. Influenza/malaria (Chair, Dr Emile Chimusa, Postdoc Fellow)
  14:30-14:40     Fredrick Nindo
  14:40-14:50     Dennis Ongarora
  14:50-15:05     Dr Michelle Fisher
15:20 SESSION 6. Tuberculosis (Chair, Dr Robert Thuku, Postdoc Fellow)
  15:20-15:35     Dr Claire Hoving
  15:35-15:50     Dr Tolu Oni
  15:50-16:00     Rubina Bunjun
  16:00-16:10     Zanele Ditse
  16:10-16:20     Munyaradzi Musvosvi
16:20 CLOSING REMARKS & DISCUSSIONS: Prof Janet Hapgood & Prof Clive Gray

The day ended in an opportunity to network with pre-dinner drinks, before a fitting end with Emeritus Professor Stuart Saunders as guest speaker at the dinner, giving the young academics some wise words and amusing anecdotes of life as an academic.

Report by Dr Heather Davies-Coleman


Carnegie Corporation Fellows Retreat



5th African Flow Cytometry Workshop, 2-6 September 2013

The 5th African Flow Cytometry Workshop was held at the University of Cape Town from 2nd to 6th September 2013. The goal of the workshop was to provide advanced training, through lectures and hands-on sessions, on the principles of flow cytometry, set-up and quality control of flow cytometry instruments, design and optimization of flow cytometry experiments and analysis and interpretation of flow cytometry data.  The overall aim of this biennial training event, now in its fifth year, is to develop expertise and build a critical mass of young African scientists studying cellular immunity to the three major pathogens, HIV, TB and malaria. These Workshops serve not only to enhance local African scientific capacity, but also contribute to the global health agenda. 

The workshop was preceded by the 'Infectious Diseases in Africa (IDA)' Symposium, a forum for providing cutting-edge knowledge of TB, HIV and malaria by international experts, organised by Prof Clive Gray (UCT) and Dr Guido Ferrari, Duke University. Students who were selected for the Flow Cytometry Workshop attended the Symposium and presented their research, placing the week's technical and practical training in the context of new developments in major disease research.

The 2013 African Flow Cytometry Workshop
Fifteen trainees from nine African countries participated in the event. Students were selected based on an abstract of their work. Thirty-four abstracts were received and scored by three experts in the field, and full sponsorship was provided for travel and accommodation in Cape Town for those selected. The organising committee consisted of Dr Wendy Burgers, Dr Tom Scriba, Dr Catherine Riou and Dr Elisa Nemes, all from the IDM. Additional teaching faculty for the Workshop included Prof Mike Betts, University of Pennsylvania, Dr Guido Ferrari, Duke University, Dr Steve Perfetto, Vaccine Research Center, NIH, Dr John Quinn, TreeStar and Dr Andreia Soares, UCT.

An assessment of flow cytometry knowledge was performed before and after the Workshop, and all students showed an improvement, with a median increase of 30%, which translated into a doubling of knowledge in most. An anonymous evaluation of the workshop was conducted, to evaluate the impact and experience of the trainees. Overall, the trainees expressed overwhelming enthusiasm for what they had learnt during the Workshop, which is best communicated in the selection of comments below:

"Perfect, so much of what I have read in papers now makes sense. I really went from 1% flow knowledge to 98.9%. I have had answers to things I didn't know I needed as well as things I did need to know. Really, it has been the best workshop I have ever attended."

 "It has been very helpful. I have learnt so much that I didn't know about flow cytometry. I now realize what we need to do on the machine and the analysis to ensure our data is valid and credible."

"With my little experience, I have been exposed to advanced knowledge on flow cytometry which is very good. I will be able to understand critically all the papers published, that address flow cytometry experiments and eventually I will be able to design such experiments in my own work."

"It will help our whole team to improve the quality of our data, [and] prepare me for my dream, a PhD."

Funding for the Workshop was obtained from a number of sources, including the Clinical Infectious Diseases Research Initiative (CIDRI, a Wellcome Trust initiative at the University of Cape Town), the South African Immunology Society (SAIS), the International Union of Immunological Societies (IUIS), the Canada-Africa Prevention Trials Network (CAPT), the Canadian Global Health Research Initiative (GHRI), BD Biosciences, Biocom Biotech, and Treestar.   

Report by Associate Professor Tom Scriba

IDA group



SACORE Annual Scientific Meeting, 31 August - 3 September 2013



The Southern Africa Centre for Research Excellence was established via a
Strategic Award from the Wellcome Trust. The consortium is comprised of:

  • 3 African universities with developing research environments
  • College of Medicine of the University of Malawi - CoM
  • University of Zimbabwe College of Health Sciences – UZ-CHS
  • University of Zambia School of Medicine – UNZA
  • 3 affiliated African institutions with established research environments:
  • University of Cape Town – UCT through CIDRI
  • Stellenbosch University – SU
  • Botswana-Harvard AIDS Institute Partnership – BHP
  • 4 United Kingdom universities with high quality research environments:
  • London School of Hygiene and Tropical Medicine – LSHTM
  • Barts and the London School of Medicine- BTL
  • University College London – UCL
  • University of Liverpool and the Liverpool School of Tropical Medicine  

The University of Cape Town hosted the Annual Scientific Meeting at the Vineyard Hotel Conference Centre in Newlands from 31st August to 3rd September 2013.

Ninety delegates including students, supervisors, Steering Committee members as well as members of the SACORE Scientific Advisory Committee attended the meeting. The main purpose of the meeting was to encourage networking and mentoring of the students by the supervisors. As the consortium comprises members from 6 African countries as well as the United Kingdom, the ASM is the only opportunity for all to meet to present and discuss their research. To further provide these opportunities, 4 workshops were held on the first day:

  • Understanding and intervening in tuberculosis in Southern Africa convened by Professor Robert J Wilkinson from the University of Cape Town
  • Parasitology convened by Professor Paul Kelly from Queen Mary University of London
  • Pharmacology convened by Professor Paul Kelly and led by Professor Gary Maartens from University of Cape Town
  • Statistics convened by Professor Frances Cowan and led by Dr Colette Smith from University College London


The opening ceremony took place on Saturday 31st August 2013 after the workshops at 17h45. The delegates were welcomed by the Director of SACORE, Moffat Nyirenda from the College of Medicine, University of Malawi and the Director of CIDRI, Robert J Wilkinson.

Moffat NyirendaRobert Wilkinson




The opening plenary entitled "Immunogenetic insights into the pathogenesis of Coeliac Disease", was delivered by Praveen Kumar from Barts and the London Medical School. Professor Kumar is a member of the International Scientific Advisory Committee.

Praveen Kumar


The following 2 days were devoted to presentations from all the SACORE students as well as their supervisors. There was a dominant focus on issues related to infectious diseases and pharmacokinetics but there were also presentations on projects on non-communicable diseases such as stroke, diabetes and carcinoma.

The programme also included social events to encourage networking and outings were organised to Robben Island, Table Mountain and the Victoria and Alfred Waterfront.

The meeting ended with a braai around the pool area at the Vineyard Hotel on the evening of 3rd September. The ISAC (Anne Buve, Institute of Tropical Medicine in Belgium, Praveen Kumar, Barts and the London School, UK and Thumbi Ndung'u, University of Kwazulu-Natal, South Africa) commended the SACORE Steering Committee and the organisers for an excellent meeting. It was particularly gratifying to see the good progress of the students' research projects since the last ASM held in September 2012.

Sponsorship for the dinner on Sunday 1st September was generously provided by BD Biosciences. Ms Nazma Mansoor represented BD Biosciences at the conference.


SACORE meetingSACORE meetingSACORE meetingSACORE meetingSACORE meetingSACORE meetingSACORE group





EMBO AIDS-Related Mycoses Meeting, 3-5 July 2013

Embo workshop 2013

A three-day meeting of researchers was held at the IIDMM from 3-5 July 2013 to address public health, as well as clinical and basic science aspects of fungal infections that cause disease in patients with HIV infection. While tuberculosis is recognised as a common cause of morbidity and mortality amongst HIV infected patients in sub-Saharan Africa it is certainly not the only cause. Collectively fungal diseases (such as cryptococcal meningitis and pneumocystis pneumonia) result in a substantial number of hospitalisations and deaths amongst HIV infected patients globally. Even amongst patients treated for cryptococcal meningitis, mortality is over 50% in routine care settings. Despite this high disease burden and major contribution to HIV-related mortality, fungal diseases in HIV have not had sufficient public health or research prioritisation. The major aims of this meeting were to bring together both HIV and fungal researchers to share their research findings, engage in discussion, develop collaborations and find ways in which the relative neglect of fungal diseases on the global HIV public health and research agenda could be reversed.

Co-funding for this workshop was provided by the Clinical Infectious Diseases Research Initiative (CIDRI) based at the IIDMM, along with other funders.

Participants from all over the world attended this meeting, and plenary presentations were given by world-leading scientists and covered topics including the effect of HIV/AIDS on antifungal immunity, the epidemiology, surveillance and public health aspects of these infections, the fungal diseases (both from the host and pathogen perspective, including sessions on Candida, Pneumocystis, Cryptococcus and other fungi), fungal-related immune reconstitution inflammatory syndrome, antifungal treatment options and the way forward.  Considerable time was given to general discussion during this meeting and several important action points were agreed by consensus of all participants. A consensus statement from the workshop is being developed for public presentation.

The meeting was attended by 88 individuals including 29 invited speakers. There were 8 short talks chosen from submitted poster abstracts. There were 21 students/postdoctoral fellows in attendance, most of whom presented posters, and 17 of whom were from Africa. Nearly half the participants were from South Africa and other countries represented include;  Australia, Brazil, Canada, Germany, Italy, Malawi, Nigeria, Taiwan, Tanzania, the Netherlands, Uganda, United Kingdom, USA, Vietnam and Zimbabwe.

Embo Workshop 2013 delegates

Full programme available at: www.aids-and-mycoses-2013.co.za