Breakdown of postgraduate students and postdoctoral fellows in the CBTBR in 2009

Degrees conferred and postdoctoral fellowships completed
The CBTBR graduated 2 postdoctoral fellows, 9 PhD, 4 MSc, and 4 Honours students in 2009.

Dissertations and theses
MSc dissertation:

• Odelia Strauss- “Differences in gene expression between large and small clusters from the same family of Mycobacterium tuberculosis strains found in South Africa”.
• Alecia Falmer- “A Molecular characterization of drug resistant Mycobacterium tuberculosis isolates from different settings in South Africa”.
• Margaretha Bester - “Defining mechanisms that determine the levels of drug resistance in Mycobacterium tuberculosis”.

PhD theses:

• Mohube Betty Mowa – “Function and expression of class I ribonucleotide reductase small subunit-encoding genes in Mycobacterium tuberculosis and Mycobacterium smegmatis”.
• Suzanna Savvi – “Identification and characterisation of the vitamin B12-dependent methylmalonyl coenzyme A pathway in Mycobacterium tuberculosis”.
• Gian van der Spuy – “Analysis and application of evolutionary markers in the epidemiology of Mycobacterium tuberculosis”.
• Erika de Wit (nee Truter) - “Analysis of host determining factors in susceptibility to tuberculosis in the South African coloured population”.
• Andre Loxton – “The role of the regulatory T-cells during HIV/TB co-infection”.
• Novel Chegou – “An Evaluation of Novel Diagnostic Techniques in the Diagnosis of Latent and Active Tuberculosis”.
• Nonhlanhla Nene - “The effect of exposure to environmental mycobacteria on human immune responses against Mycobacterium tuberculosis”.
• Gail Louw – “Resistance to first-line anti-TB drugs by gene mutation and gene modulation”.
• Colleen Wright – “The contribution of fine needle aspiration biopsy in the diagnosis of mycobacterial lymphadenopathy with particular reference to children”.
• Madeleine Hanekom - “The Molecular Epidemiology of Mycobacterium tuberculosis: Host and Bacterial factors perpetuating the epidemic”.

Research interns (MRC sponsored)

• Dr M Hanekom (Clinical Intern) completed her PhD degree in the 4th year of her internship during 2009.
• Ms NC Ngombane (Research Intern) Registered for MSc degree in 2009
• Ms P Seepe (Research Intern) Registered for MSc degree in 2009

Recruitment of new postgraduate students
A number of new students have joined the team already or will do so during the course of 2010. 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, 4 PhD, 10 MSc and 4 Honours students into the CBTBR in 2009. At the Wits node, we enrolled 1 postdoctoral fellow, one PhD student (black female, upgraded from MSc) and five MSc students.

Honours and awards to students

• Masters students Avani Bharuthram, Anastasia Koch and Krupa Naran were awarded scholarships from the National Research Foundation. They, and another new MSc student, Lusanda Mapela, were also awarded SATBAT grants to support their research projects.
• Students Anastasia Koch, Avani Bharuthram, Lusanda Mapela and Bintou Ahamdou Ahidjo were awarded a Postgraduate Merit Awards from Wits University
• Doctoral student Dudzile Ndwandwe and her supervisors, Digby Warner and Valerie Mizrahi, received a Mellon Postgraduate Mentoring Award from Wits University.
• Anastasia Koch was awarded a SATBAT bursary to attend the Johns Hopkins School of Public Health Graduate Summer Institute of Biostatistics and Epidemiology course, which she attended in June-July.
• Doctoral student, Bintou Ahmadou Ahidjo was selected as an ASM trainee and awarded a Global Health Fellowship to attend the 109th General Meeting of the American Society for Microbiology in Philadelphia, USA in May 2009
• Monique Williams and Duduzile Ndwandwe were awarded bursaries from the Cape Biotech TB Centre of Competence to attend the Advanced Design and Development of Tuberculosis Drugs Workshop held in Pretoria in August, 2009
• Doctoral student Atica Moosa was awarded a prestigious a Carl Storm Fellowship from the Gordon Research Conferences and a Whitehead Scientific Travel Award to support her attendance at the Vitamin B12 and Corphins Gordon Research Conference in August
• Two students from the Wits node were selected to present short talks on their research at the Gordon Research Conferences that they attended in Europe. Monique Williams, a Percy Fox Foundation Postdoctoral Fellow, presented a talk entitled, “Analysis of molybdopterin cofactor biosynthetic genes in mycobacteria” at the 6th GRC on Molybdenum & Tungsten Enzymes, held in Lucca, Italy, and doctoral student, Atica Moosa, talked on “The metabolism of vitamin B12 in Mycobacterium tuberculosis: role of alternate B12 cofactors” at the GRC on Vitamin B12 and Corphins, held in Oxford in August. This achievement is particularly notable as GRCs are considered to be among the most prestigious conferences in the world.
• Atica Moosa was awarded the 2nd prize in the Science Faculty Oral Presentation category at the 2nd Postgraduate Cross-Faculty Symposium, University of the Witwatersrand, 20-21 October 2009. She was awarded a prize of R 10,000.
• Dr. Cliff Magwira has been awarded a Global Infectious Diseases Research Training Program fellowship for short-term training in the laboratory of Dr. Petros Karakousis at Johns Hopkins University. He will take up this fellowship in early 2010.
• Duduzile Ndwandwe was awarded a Columbia University-southern African Fogarty AITRP pre-doctoral training grant for short-term training in TB Basic Sciences in the laboratories of Dr. Eric Rubin and Sarah Fortune at the Harvard School of Public Health. She will take up her fellowship in March 2010
• Ms Kim Hoek won third prize for her poster presented at the MRC TB Colloquium Held in Cape Town, South Africa, 3-4 June 2009.
• Ms Kim Hoek won third prize for her talk presented at the NIH ICORTA South Africa TB Aids Training Program meeting. Cape Town, South Africa, 18 July 2009.
• Hoek, K. 3rd Prize Oral Presentation - South African TB HIV Training (SATBAT) Meeting of Trainees, UCT Lung Institute, July 2009.
• Doctoral student Andile Ngwane received a Fogarty Fellowship for a research training visit for 6 months (June-November 2009) at the Public Health Research Institute (PHRI)in New Jersey, USA.
• Parsons S. “Best Poster prize”- Conference of the South African Association of Laboratory Animal Scientists, Durban, September 2009
• Fortuin, S. 1st Prize for Poster Presentation - Academic Year day, Tygerberg, Stellenbosch University, 13 August 2009.
• Fortuin, S. HUPO World Congress Toronto, Canada - HUPO 2009 Young Investigators award.
• Mlamla, Z. Runner up: Best Poster Presentation. Infectious Diseases Session, Academic Year day, Tygerberg, Stellenbosch University, 13 August 2009.
• Bester, M. Received  S2A3 Bronze medal.

Hosting of international exchange students
The Wits node hosted two international exchange students in 2009, Thomas Niemeier from the USA, and Julia Staffeldt from Germany. Thomas spent two months in the Wits node working under the supervision of Dr. Digby Warner. His visit was arranged through an HHMI program that enables talented undergraduates from US institutions to undertake short-term working visits in the laboratories of International Research Scholars. Julia, who is studying towards her Masters degree in Germany, spent nine months in the Wits node working under the supervision of Dr. Bavesh Kana.

Molecular Epidemiology Course
Prof. Rob Warren ran Molecular Epidemiology courses for African/Asian/South America fellows. In 2009 trainees from Ghana (K Bedzra, R Owusu), Dr L Erasmus  (NHLS), the AIEA (see below) visitors from East Asia, and for postgraduate students at the Honours level from the faculty of Health Sciences. This was a comprehensive course where 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. The participants from Africa and Asia also received a comprehensive manual and components such as standards, probes and internal markers to ensure that they could immediately begin DNA fingerprinting in their respective countries.

Tibotec Training courses
Ms Amour Venter conducted training during 2009 for Tibotec Inc. on study protocol numbers TMC207-C208 and TMC207-C209.  The training involved laboratory procedures for processing of tuberculosis specimens which are multi-drug resistant.  Tibotec has invited various countries to take part in the second stage of study C208, as well as in study C209.  They requested Amour to train all participating microbiology laboratories to follow the exact same procedures as described in the study Microbiology Manual.  This also involved training of the study monitors and clinical sites on some of the protocol procedures.

Training was carried out at the following institutions:

TMC207-C208:

• Beijing Chest Hospital, Beijing, China – February 2009
• Siriraj Hospital, Bangkok, Thailand – February 2009
• Makati Medical Centre, Makati City, Manila, Philippines – February 2009
• FIOCRUZ (Fundação Oswaldo Cruz Hospital), Rio de Janeiro, Brazil – May 2009

TMC207-C209:

• Institute of Phthisiology and Pulmonology of the Academy of Medical Science of Ukraine, Kiev, Ukraine – September 2009
• Korean Institute of Tuberculosis, Microbiology Unit, Seoul, South Korea – October 2009
• Deneysel Tıp Arastırma Enstitusu, Istanbul, Turkey – November 2009

A pre-training session was conducted via teleconference for Tartu University Hospital, Microbiology Laboratory, Tartu, Estonia on 13 October 2009.

Training courses attended by staff and students

• Fortuin, S. National Proteomic Workshop, Bergen University, Bergen, Norway, April 2009.
• Dr M Moller, Ms E Truter, Dr MM Esterhuyse attended the Baltic Summer School 3-week course on "Genetic Basis of Medicine" in Kiel, Germany in September, 2009.

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

• Cedric Werely (PGWC) is a 5th year 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 Departmental allocation from Prof. Mizrahi’s HHMI grant was used to provide BSc Honours bursaries to four students (Mr. G. Beyleveld, Ms. J. Brener, Ms. C. Chang and Ms. A. Manilal) and support the running costs of these students as well as two others (Ms. N. Ebrahim and Ms. T. Ramatsebe). In addition, travel support for conference attendance was provided to one student (Ms. S. Saayman).

Exchange visits and strengthening of collaborative linkages

• The Wits node hosted a number of international visitors during 2009. Prof. Česlovas Venclovas from the Institute of Biotechnology in Vilnius, Lithuania visited the Wits node for a week in March. Prof. Venclovas is an International Research Scholar of the HHMI and is a renowned authority on protein structure prediction. The purpose of this visit was to further develop a collaborative study between Prof. Venclovas and members of Wits node on the structure and function of proteins involved in DNA repair and replication in mycobacteria.
• Dr. Garth Abrahams (postdoctoral fellow) spent 4 months (March-June) working at the NIAID (NIH) I the laboratory of collaborator, Dr. Clifton E. Barry. Dr. Abrahams worked under the supervision of former MMRU member, Dr. Helena Boshoff, on a project supported by the IMTB grant from the Bill & Melinda Gates Foundation
• In July, Digby Warner visited the laboratory of Prof. John McKinney at the Ecole Polytechnique Fédérale de Lausanne (EPFL) in Switzerland to discuss the collaborative study on mechanisms of propionate metabolism in M. tuberculosis that is underway in both laboratories and funded the Swiss/South Africa Joint Research Programme. 
• The Wits node hosted Dr. Sarah Fortune, from the Harvard School of Public Health, and two members of her laboratory, Rupal Shah and Chris Ford. Accompanying them was Prof. Barry Bloom, Harvard University Distinguished Service Professor and Joan L. and Julius H. Jacobson Professor of Public Health and Dr. Jill Conley from the Howard Hughes Medical Institute. Prof. Bloom is a former Dean of the Harvard School of Public Health and a pioneer in the field of tuberculosis research.
• Dr. William R. Bishai, a leading TB researcher from Johns Hopkins University in Baltimore, USA, visited the Wits node in October. He met with staff and students and the Wits node  and with other Wits researchers with an interest in TB/HIV research.
• Long-time collaborator, Prof. Gilla Kaplan (PHRI, New Jersey) also visited the Wits node in October, where she discussed ongoing and future collaboration with Prof. Mizrahi and Dr. Kana.
• Prof. Eric Rubin from the Harvard School of Public Health visited the Wits node on 16 November 2009. He presented a seminar on his work on regulated protein degradation in mycobacteria and spent the rest of the day interacting with staff and students in the Wits node.
• Dr. Warner visited visited Dr. Alex Zawaira and Prof. Jonathan Blackburn at the IIDMM (UCT) to discuss possible collaborative projects.
• Doctoral student Andile Ngwane went for research training visit for 6 months (June-November 2009) at the Public Health Research Institute (PHRI)in New Jersey, USA.
• Masters student James Hove Mazorodze visited the Lab of Dr Chantal de Chastellier at INSERM in Marseille, France during the month of October 2009.
• Prof. S Kaufmann (Director, Max Planck Institute of Infection Biology, Berlin), Prof. M Maeurer (Infectious Disease Control, Karolinska Institute, Sweden) Prof. G Bunje (University of Oslo, Norway) – 6 April - Review of field, lab and database activities for the Bill and Melinda Gates Foundation funded Grand Challenge project ‘Biomarkers of protective Immunity against TB in Africa’ (GC6).
• Prof. G Kaplan (Public Health Research Institute Center, International Center for Public Health, New Jersey, USA) – October - To meet with various members of the Department and foster collaborations.
• Dr. I Honeyborne (University College, London, Dr S Gillespie's lab) – July and  October – Discuss project looking for Mycobacterium tuberculosis biomarkers in sputum of TB patients. She worked in our lab for several months and quantified the amounts of Mtb RNA in sputum throughout TB treatment. Some of the sputum samples will also be used for microarray analysis overseas.
• Prof. R Koup, Dr. M Rhoederer (NIH, USA) – November - Discuss ways in which to collaborate.
• Dr. Donata Sizemore (Senior Director of Vaccine Assesment, AERAS Global TB Vaccine Foundation, Maryland, USA) – December - Assessment of laboratory adherence to Standard Laboratory Operating Procedures specifically for the Bill and Melinda Gates Foundation funded Grand Challenge project ‘Biomarkers of protective Immunity Against TB in Africa’ (GC6). 
• Prof E Bottger,  Univ Zurich - Lab meeting to discuss milestones of current projects as well as new collaborations.
• Prof M Borgdorff,  Univ Amsterdam, Netherlands - Discussions on Molecular Epidemiology.
• Dr V Schoellhorn,    Aid-Diagostika, Germany - Discussions on collaboration wrt validation of a diagnostic.
• Prof A Steyn,  Univ Alabama, USA - Discussions on the ESAT-6 systems.
• Prof R Hernandez Pando, Mexico - Discussions on current collaborations and design of new projects.
• Dr A Trollip, SA - Discussions on collaboration and the establishment of a new research field site in Nelson Mandela Bay, Eastern Cape.
• Dr S Verver KNCV The Netherlands - Discussions on possible collaboration and reseach funding.
• Prof B Bishai, USA - Discussions on TB research in South Africa and collaboration with the HHI HIV/TB institute in Natal.
• Dr D Warner - Mycobacteriology, WITS - April, June - Discussions on ESAT-6 systems and drug resistance.
• Prof M Murray,  Harvard Univ, USA -  March, April - Discussions on new epidemiology tools.
• Dr du Toit Loots and Prof C Reinecke - NWU Potchefstroom – March - Discussions on metabolomics.
• Dr P de Haas - Zambart, Lusaka, Zambia – July - Discussions on Zamstar study.
• Prof R Huard - Assistant Professor of Clinical Pathology, Columbia University, New York, USA, - July - Discussions on strain diversity.
• Prof A Christoffels - SANBI, UWC – July, September, October - Discussions on bioinformatics.
• Dr S Sampson - Imperial College, London, UK – August - Discussions on ESAT-6 systems.
• Dr H Boom - TBRU, Case Western Univ, USA – March - Discussions on BMGF-funded project.
• Dr K Jacobson and Ms C Jeon , Harvard Univ, USA - Mentoring purposes.
• Dr D Park, Univ California, San Diego, USA - Mentoring purposes.
• Dr C de Chastellier, INSERM, France – November - Discussions on EM and Mycothiol pathway.
• Prof E Shurr, McGill University, Montreal, Canada – April - Discussions on genetic epidemiology of TB.

International Atomic Energy Agency (IAEA)
For the past 10 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 22 students were trained between 2004 and 2009. The technologies and experience have helped other countries in Africa to get a better understanding of tuberculosis, and the value of this initiative is shown in collaborative papers.

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 2009: Mr Kofi Bedzra and Mr Richard Owusa from Ghana.