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02 February 2022 | Story Leonie Bolleurs | Photo Leonie Bolleurs
Chané Enslin, master’s student in the UFS Centre for Environmental Management (CEM); Stephanie Graumnitz, Institute of Hydrobiology at the Technical University Dresden (TUD); Dr Dirk Jungmann, Head of Ecotoxicology and Biomonitoring in the Institute of Hydrobiology at TUD; Sihle Mlonyeni, master’s student in the Faculty of Applied Science at the Cape Peninsula Technical University; Dr Marinda Avenant, Senior Lecturer in the CEM at the UFS; Akani Baloyi, master’s student in the UFS Disaster Management Training and Education Centre for Africa; and Sphindile Dlamini, master’s student in the Department of Zoology and Entomology on the UFS Qwaqwa Campus.


The Centre for Environmental Management (CEM) at the University of the Free State (UFS), in collaboration with Dr Dirk Jungmann from the Technical University Dresden, recently presented a virtual summer school on Blackboard, titled: Monitoring of surface water quality: General framework, tools and implementing disaster management aspects in urban areas. 

The international group of 30 persons who attended the summer school mostly comprised postgraduate students and employees from, among others, the UFS and other tertiary institutions such as the Technical University Dresden (TUD), the Cape Peninsula University of Technology (CPUT), UNISA, the University of the Western Cape, Stellenbosch University, the University of Lesotho, and the University of Zimbabwe. Members of the Council for Scientific and Industrial Research also attended the summer school.

Experts present

Dr Marinda Avenant, Senior Lecturer in the CEM, believes the summer school provides students with a wonderful opportunity to be exposed to a topic, such as aquatic biomonitoring, over and above their normal postgraduate studies. “The presenters are all experts in their field and come from a range of disciplines (from hydrology and chemistry to the social aspects of water), as well as from different countries and perspectives,” she adds. 

Some interesting topics covered during the summer school included a panel discussion on water management challenges in Southern Africa. Head of CEM, Prof Paul Oberholser, participated in this live discourse. In 2021, he won the NSTF-Water Research Commission (WRC) Award for his contribution to water resource management in SA over the past five years.

Also contributing a perspective on surface water quality was affiliated professor in CEM, Prof Anthony Turton, who delivered the keynote address on Managing surface water quality as an element of disaster management in urban areas.

Dr Alice Ncube from the UFS Disaster Management Training and Education Centre (DiMTEC) presented on women and disasters (including a case study on a stokvel in Botshabelo), and Dr Inga Jacobs-Mata from the International Water Management Institute (IWMI) provided a social perspective on the water resources sector. 

Students excel 

Five master’s students representing the UFS, the Technical University Dresden (TUD), as well as the Cape Peninsula University of Technology (CPUT), assisted with the organisation of the summer school. The Volkswagen Foundation in Germany, which funded a first summer school in 2019, provided funding that was used to appoint the five students.

According to Dr Avenant, they made provision for the appointment of these students in their project proposal to the Volkswagen Foundation. “The students played a key role in the planning of the virtual summer school; they specially came up with ideas to make the virtual sessions more interesting,” she says.

Among others, they managed the technical aspects of the sessions, introduced the speakers, arranged social activities for the virtual platform, and they produced podcasts. The podcasts of the speakers were distributed to the participants over the extent of two months, in order to learn more about the presenters. 

“We were really impressed with the work of the students, who are all from the natural sciences,” says Dr Avenant.

News Archive

Newly operational sequencing unit in genomics at UFS
2016-09-09

Description: Next Generation Sequencing  Tags: Next Generation Sequencing

Dr Martin Nyaga and his research assistant,
Tshidiso Mogotsi in the Next Generation
Sequencing Laboratory.
Photo: Charl Devenish

The Next Generation Sequencing (NGS) unit at the UFS was established as an interdisciplinary facility under the Directorate for Research Development, Faculty of Health Sciences and Faculty of Natural and Agricultural Sciences.

The aim of the NGS facility is to aid internal and external investigators undertaking studies on Deoxyribonucleic acid (DNA) sequencing, assembly and bioinformatics approaches using the more advanced Illumina MiSeq NGS platform.

The NGS unit became operational in 2016 and is managed by Dr Martin Nyaga and administered through the office of the Dean, Faculty of Health Sciences, under the leadership of Prof Gert Van Zyl. Dr Nyaga has vast experience in microbial genomics, having done his PhD in Molecular Virology.

He has worked and collaborated with globally recognised centres of excellence in Prokaryotic and Eukaryotic genomics, namely the J. Craig Venter Institute and the Laboratory of Viral Metagenomics, Rega Institute, among others.

The unit has undertaken several projects and successfully generated data on bacterial, viral and human genomes. Currently, work is ongoing on bacterial and fungal metagenomics studies through 16S rRNA sequencing.

In addition, the unit is also working on plasmid/insert sequencing and whole genome sequencing of animal and human rotaviruses. The unit has capacity to undertake other kinds of panels like the HLA, Pan-cancer and Tumor 15 sequencing, among others.

Several investigators from the UFS including but not limited to Prof Felicity Burt, Prof Wijnand Swart, Dr Frans O’Neil, Dr Trudi O'Neill, Dr Charlotte Boucher, Dr Marieka Gryzenhout and Dr Kamaldeen Baba are actively in collaboration with the NGS unit.

The unit has also invested in other specialised equipment such as the M220 Focused-ultrasonicator (Covaris), 2100 Bioanalyzer system (Agilent) and the real-time PCR cycler, the Rotor-Gene Q (Qiagen), which both the UFS and external investigators can use for their research.

Investigators working on molecular and related studies are encouraged to engage with Dr Nyaga on how they would like to approach their genomics projects at the UFS NGS unit. 

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