Breakdown of postgraduate students and postdoctoral fellows in the CBTBR in 2011

Degrees conferred and postdoctoral fellowships completed
The CBTBR graduated 2 postdoctoral fellows, 4 PhD, 4 MSc, and 3 Honours students in 2011.

Dissertations and theses
MSc dissertation:

• Anastasia Koch - “Fitness costs of drug resistance mutations in mycobacteria”
• Zandile Mlamla - “Improving methods for genotypic drug resistance testing in Mycobacterium tuberculosis”
• Nokwanda Crystal Ngombane - “Immune profiles of recently exposed household contacts in a Tuberculosis endemic setting in the Western Cape”
• Prudy Seepe - “Differential expression of genes in clinical strains of mycobacterium tuberculosis in response to isoniazid”

PhD theses:

• Bintou Ahmadou Ahidjo – “Analysis of the role of VapBC toxin-antitoxin modules in growth, stress tolerance and drug tolerance in mycobacteria”
• Violet Chihota – “Use of genetic approaches to study the disease dynamics of Mycobacterium tuberculosis infection in Southern African regions with high tuberculosis incidence” Promoter: Prof RM Warren, Co-Promoter: Prof P van Helden.
• Carrie Kirsten – “Nitrogen metabolism and the regulation thereof in Mycobacterium smegmatis” Promoter: Prof I Wiid.
• Laurianne Loebenberg – “Environmental influences on innate and adaptive immune responses against Mycobacterium tuberculosis” Promoter: Prof G. Walzl

Research interns (MRC sponsored)

• Ms NC Ngombane (Research Intern) Registered for 3rd year of MSc degree and graduated in 2011.
• Ms P Seepe (Research Intern) Registered for 1st year of PhD degree in 2011

Recruitment of new postgraduate students
A number of new students have joined the team already or will do so during the course of 2012. Applications from other students are under consideration, pending availability of supervisory capacity, laboratory and office space and/or funding, including bursary support (see above). At the SU node, we enrolled 2 Postdoctoral fellows, 10 PhD, 12 MSc and 2 Honours students into the CBTBR in 2011. At the UCT node 1 Postdoctoral fellow, 2 PhD students and one Honours student were recruited. At the Wits node 2 Postdoctoral fellows and 4 MSc students were recruited in 2011.

Honours and awards to students

• Mr. Germar Beukes from the Wits node was selected to give an oral presentation at the MRC Research Day and won the prize for best oral presentation by an MSc student.
• Dr. Melissa Chengalroyen from the Wits node won third prize for a poster presentation at the Wits Molecular Biosciences Research Thrust Symposium.
• Ms. Nicole Narrandes from the Wits node was selected to give oral presentations at two local conferences/meetings as testimony to the high quality of their research
• Ms. Duduzile Ndwandwe from the Wits node was awarded a K-RITH Collaborative Travel Award. Ms. Ndwandwe also received a Mellon Postgraduate Mentoring Award and a Postgraduate Merit award from Wits University.
• Dr. Christopher Ealand was awarded a Postdoctoral Fellowship from the Centre for the Aids Program of Research in South Arica.
• Ms. Lusanda Mapela was awarded an NRF prestigious MSc bursary.
• Mr. Sibusiso Senzani was awarded an Innovation NRF MSc bursary.
• Ms. Nabiela Moolla and Ms. Farzanah Hassim, newly appointed MSc students, were both awarded prestigious NRF bursaries
• Dr. Monique Williams and Ms. Atica Moosa were both awarded Keystone Symposia Global Health Travel Awards to attend the Keystone Symposium on Mycobacteria: Physiology, Metabolism and Pathogenesis - Back to the Basics, held in Vancouver in January 2011.
• Ms. Anastasia Koch received the Benfara Scholarship from UCT and a DAAD-NRF Joint Scholarship from the NRF.
• Ms. Krupa Naran was awarded a UCT Equity Scholarship and a DAAD-NRF Joint Scholarship from the NRF
• Ms. Zanele Ditse was awarded the Marion Beatrice Waddel Scholarship and an Equity Scholarship from UCT and a DAAD/NRF Joint Scholarship from the NRF. 
• Ms. Atica Moosa was awarded a Postgraduate Merit Award from Wits University.
• Stefanie Malan received a three month Novartis internship in drug discovery (1 July 2011 – 30 September 2011).
• Louw G. Visited as a Post Doctoral fellow at Harvard School of public health and Partners Organisation centre for Personalised genetic Medicine, Cambridge, USA.
• Louw G. Won 1st Prize in the Infectious disease session for a presentation by a young researcher under 35 years. Academic year day  (August 2011), Stellenbosch University
• A number of Scholarships to attend the 8th International Conference on the Pathogenesis of Mycobacterial Infections. Stockholm, Sweden, 30 June – 3 July 2011.
• Siame K., Basic Sciences Best Poster Prize at the 54th Academic Year day of the Faculty of Health Sciences of Stellenbosch University with a poster presentation entitled “Investigating the genome variation and evolution of Group 1 M. tuberculosis strains”.
• Bloem L. Second place for PhD poster presentation category at the 4th MRC Medical Research Day, 15th -15th October 2011.
• Malan S. Novartis internship in drug discovery and clinical research. Basel, Switzerland.  1 July – 30 September 2011.
• Le Roex N. Award to attend EMBO (European Molecular Biology Organisation) computational biology course, entitled “Computational Biology: Genomes, Cells and Systems”. Reykjavik, Iceland, 6-13 August 2011.
• Ehlers L. Award for Best Poster Presentation category Basic Sciences for, Effect of TB Treatment on Metabolic Hormone Profiles. Presented at Annual Academic Year Day. Cape Town, South Africa, 17-18 August 2011.
• Kleynhans L. Medroxyprogesterone acetate alters cytokine expression in response to Mycobacterium Bovis BCG in vitro and in PBMCs of contraceptive users.  Poster winner at the Infectious Disease session at the Annual Academic Day. Faculty of Health Sciences, Stellenbosch University, Cape Town, 17-18 August 2011.
• Blanckenberg J.  DRD Travel Grant: Research Visit Abroad.  To attend a GEO-PD meeting. Chicago, USA, 19-21 September 2011.
• Ehlers L. Harry Crossley Foundation Scholarship awarded for, Investigation of the underlying molecular mechanisms of immune modulation by the contraceptive Medroxyprogesterone acetate (MPA) on immune response to mycobacteria. R14 000 awarded for 2010-2011.
• Salie M. (2011) Deutscher Akademischer Austausch Dienst-National Research Foundation (DAAD-NRF) Joint In-Country Scholarship.
• Salie M. (2011) Columbia University-Southern Africa Fogarty AIDS and TB Training and Research Program.
• Salie M. (2011) Harry Crossley Foundation (Project funding).
• Wagman C. (2011) National Research Foundation Scarce Skills Scholarship.
• Wagman C. (2011) Stellenbosch University Postgraduate Merit Bursary.

Hosting of international exchange students
The SU node hosted Mr Rick Henrikson a chemical engineer (Ph.D. candidate at the UC Berkeley/UC San Francisco USA) for 1 month to work on a nanotech device for diagnosis of XTR-TB.

Molecular Epidemiology Course
Prof. Rob Warren ran Molecular Epidemiology courses for African/Asian/South America fellows. In 2011 trainees Lubabalo Macingwana, Carine Kunsevi, Razeenah Hunter, Brigetta Derendiger, D Stanley from CCTR and for postgraduate students at the Honours level from the faculty of Health Sciences. All participants had hands-on experience for the extraction of DNA from Mycobacteria tuberculosis, restriction enzyme digests, southern blotting, probe labelling and hybridisation. The course equipped all participants with the necessary skill to enable them to perform world class DNA fingerprinting.
FIND sponsored a HAIN test training course in Tanzania in 2011

Other Training courses
Amour Venter also conducted initiation training for the laboratory personnel involved with clinical drug trials on the following protocols:

• PanACEA – RUNMC – HR1 protocol; 26 May 2011
• Pfizer B1171003 protocol; 02 August 2011
• REMoxTB Laboratory Manual and Quality Manual update; 18 August 2011

Training courses attended by staff and students

• Dr. Bavesh Kana from the Wits node of the CBTBR attended several courses at the Epidemiology and Population Health Summer Institute at Columbia University (EPIC). Some of the EPIC courses he took included a study of randomized clinical trials, an introduction to observational epidemiology, and statistical analysis of complex data using SAS and SUDAAN. 6-17 June
• Dr. Bhavna Gordhan and Ms. Nicole Narrandes participated in the Basic and Advanced Immunology course hosted by the Faculty of Health Sciences at Wits University from 28th February - 4th March and 4th-8th April 2011.
• Dr. Bhavna Gordhan, Ms. Nicole Narrandes, Ms. Suzanne Nicholson, Mr. Germar Beukes, Mr. Sibusiso Senzani, Ms. Farzanah Hassim and Ms. Nabiela Moola attended a Laboratory and Safety & chemical Grades Seminal at University of Johannesburg, hosted by Merck, 25th January
• Dr. Christopher Ealand, Ms. Nicole Narrandes, Mr. Sibusiso Senzani participated in IEFA Emergency First Aid Level I course at the NHLS in Johannesburg on 11 November 2011.
• Mr Keith Siame, Ms Anzaan Dippenaar, Ms Mae Newton-Foot and Ms Louise Vos attended a Proteomics workshop on Tygerberg Campus presented by Dr. Salome Smit in May 2011.
• Ms Mae Newton-Foot and Ms Nastassja Steyn attended a fluorescent Microscopy course at CAF on Main Campus on 2-3 June 2011.
• Drs André Loxton and Daleen Kriel attended a Conference presentation skills workshop at STIAS, Stellenbosch University on 24 May 2011.
• Prof Rob Warren accessed an On-line Good Clinical Practise course in 2011.
• Ms Marisa Klopper attended the Basic epidemiology course presented by Dr Jo Barnes at SACEMA in April 2011.
• Ms Michelle Daya attended the EBI 2 day workshop at UWC in March 2011.
• Ms Michelle Daya attended the 16th Summer Institute in Statistical Genetics, Seattle, Washington, USA in June 2011.
• Miss Nikki Le Roux attended the EMBO practical course: “Computational Biology: Genomes, Cells and Systems” held in Reykjavik, Iceland, 6-13 August 2011.
• Ms Anzaan Dippenaar attended a course on “High throughput sequencing in disease studies” at the London School of Hygiene and Tropical Medicine (LSHTM), 12-15 September 2011.
• Dr Bienyameen Baker attended an international workshop for postgraduate supervisors at Stellenbosch University in September 2011.

Staff members studying for higher degrees (all registered at SU)

• Cedric Werely (PGWC) is a part-time PhD student, working on Arylamine N-acetyltransferase genes in Tuberculosis to study the influence of host genetics on disease susceptibility.

Other capacity development activities

• The SUN-IRG organized a database, statistics and Excel training workshop for the African-European Tuberculosis Consortium in Addis Ababa in October 2011 for African scientists.
• The SUN-IRG organized a capacity development and networking meeting between EDCTP-funded TB, malaria and HIV research networks in Addis Ababa during the EDCTP Forum in October 2011.

Exchange visits

• Ms. Philippa Black from the SU node of the CBTBR spent ~ 6 months at the Wits node on an exchange visit. Ms. Black was trained at the Wits node on methodology for saturating transposon mutagenesis in Mycobacterium tuberculosis. In addition, Ms. Black learnt key new methodologies in gene cloning, gene manipulation and transformation of various mycobacterial species. Upon her return, this expertise has now been transferred to the SU node which has resulted in strengthening of collaborative linkages between the Wits and SU nodes
• Ms. Dudu Ndwandwe, a PhD student currently based at the Wits node with co-spuervision from Dr. Digby Warner and Prof. Valerie Mizrahi at the UCT node, received a K-RITH Collaborative Travel Award to support an exchange visit to the Harvard School of Public Health. The purpose of Ms. Ndwandwe’s visit was to conduct a proteomics analysis of mutant strains generated during her PhD studies
• Dr. Monique Williams from the SU node is collaborating with Dr. Bavesh Kana and Ms. Nicole Narrandes at the Wits node on a project aimed further understanding the biosynthetic pathway for molybdopterin cofactor (MoCo) biosynthesis. This is a collaborative project that also involves the UCT node and will soon include Dr. Gilla Kaplan from the Public Health Research Institute in the USA. Dr. Williams has recently been awarded a CU-SA Fogarty Fellowship to spend three months in Dr. Kaplan’s laboratory to obtain training on animal models for TB infection. Her work will specifically involve the use of mutant defective for MoCo biosynthesis
• Dr. Garth Abrahams was appointed on 1 April 2011 to the position of Research Officer in the UCT node of the CBTBR, funded by the HIT-TB grant (sub-award from FNIH on a grant from the Bill & Melinda Gates Foundation). This is a three-year contract position. Dr. Abrahams has been seconded, full-time to the laboratory of Dr. Clifton E. Barry III and Dr. Helena Boshoff (Tuberculosis Research Section, NIAID, NIH) for the duration of this contract appointment. He is working on the HIT-TB project and therefore interacts closely with the postdoctoral fellow in the UCT node who is also working on this project
• The IIDMM is a hub of tuberculosis and infectious disease immunology research and has a steady stream of international visitors throughout the year. Many of these visitors who included Prof David Russell (Cornell University), Prof. Gilla Kaplan (UMDNJ), Prof. Douglas Young (Imperial College), Prof. William Bishai (K-RITH & JHU), and Dr. Ken Duncan (Bill & Melinda Gates Foundation) send time with staff and students in the UCT node
• Dudu Ndwandwe and Dr. Digby Warner received a K-RITH Collaborative Travel Award to support an exchange visit by Ms. Ndwandwe to the laboratory of Dr. Sarah Fortune at the Harvard School of Public Health. The purpose of this visit was to continue the proteomics work that Dudu had initiated in Dr. Fortune’s lab during her Fogarty AITRP Pre-doctoral training fellowship in 2010. Ms. Ndwandwe’s visit was unfortunately cut short owing to illness in her family. The visit was nonetheless reasonably productive and generated some new data as part of Ms. Ndwandwe’s doctoral project
• Louw G. Visited as a Post Doctoral fellow at Harvard School of public health and Partners Organisation centre for Personalised Genetic Medicine, Cambridge, USA
• Doctoral student Andile Ngwane received a Fogarty Fellowship for a research training visit for 3 months (January-March 2011) at the Public Health Research Institute (PHRI) in New Jersey, USA.
• PhD student Melanie Grobbelaar visited the lab of Prof WR Bishai for Microarray training at the Johns Hopkins University, Baltimore, Maryland, USA in May – July 2011
• Tom Evans of AERAS visited on 16 Feb 2011 for discussions on future collaborations
• Jill Winter of the Catalysis Foundation spent time with the SUN-IRG at the field sites and laboratory for the ongoing study
• Prof Cliff Barry of the NIH visited on the 28 July 2011 as part of the ongoing collaboration
• Dr Leander Grode of the vaccine company, VPM , Germany visited several times to discuss the ongoing vaccine trial
• Prof Henry Boom of Cleveland University, USA, visited on 7-8 November 2011 for the TBRU meeting and the ongoing proteogenomics collaborative study
• Alex Lastovich, senior manager at BD, USA visited for the kick-off meeting of the BDFACSCAP study on 5 December 2011
• Prof Eileen Hoal visited Prof Erwin Schurr at McGill University, Montreal in October to discuss ongoing collaboration
• Profs Eileen Hoal and Paul van Helden visited Prof Vic Rutten and Dr Ad Koets at Utrecht Veterinary School, Netherlands, in June to discuss ongoing collaboration.
• Dr David Hain (Hain Lifescience, Germany), Prof Christie Jeon (Dept Epidemiology, Harvard University), Prof Eric Bottger (Institute of Medical Microbiology, University of Zurich), Prof Goerge Huber (University of Pittsburgh, USA), Prof William MacKenzie (Centers for Disease Control, USA), Dr Patrice Matchaba (Novartis, USA) and Dr Bernd Eisele (Vakzine Projekt Management, Germany) all visited to discuss collaborative projects with the SU node
• Dr C de Chastellier, INSERM, France – November - Discussions on EM and Mycothiol pathway

International Atomic Energy Agency (IAEA)
The International Atomic Energy Agency (IAEA) awarded eight candidates a two-month fellowship to be trained in theory and practical techniques in molecular diagnostic methods of communicable diseases. The emphasis was on the application of these techniques for the detection of mutations in genes associated with drug resistance in TB. The following candidates were trained in the 2011 training course on Drug resistance: Dezemon Zingue from Burkina Faso, Aristid Herve Ekollo Mbange and Pride Mbuh Teyim from Cameroon, Dieudonne Ouassa Timothee from Cote d'Ivoire, Samuel Kudzawu from Ghana, Imane Chaoui from Morocco, Ruth Umoh and Emmanuel Chibuike Wenah from Nigeria, Muataz Eldirdery from Sudan, Leila Jeljeli from Tunisia and Patrick Kaonga from Zambia.

For the past 11 years we have been involved in development and transfer of molecular technology to various countries in Africa through funding mostly from the IAEA. In this initiative we use tuberculosis as a model disease to transfer molecular technology. Our involvement includes planning and report meetings with IAEA (Prof. T Victor), the running of training workshops in Africa and the hosting of African Fellows for training purposes. Advice is given electronically to numerous participating countries and 35 students were trained between 2004 and 2011. The technologies and experience have helped other countries in Africa to get a better understanding of tuberculosis, and the value of these initiatives are shown in collaborative papers.