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Pilot study for master’s degree leads to PhD

19 April 2024 | Story André Damons | Photo Supplied

A pilot study for his master’s degree not only ignited Dr Milton Mogotsi’s passion but he was also inspired by the fact that this was a newly emerging field of research in the discipline of virology at the time. This eventually led to him pursuing a PhD and ing on his research.

Dr Mogotsi graduated on Thursday (18 April) with the degree Doctor of Philosophy with specialisation in Virology during the Faculty of Health Sciences at the University of the Free State (UFS) autumn graduation ceremonies. Prof Martin Nyaga, Head of the Next Generation Sequencing Unit (UFS-NGS) and an associate professor in the Division of Virology, was his promotor and Prof Trudi O’Neill from the Department of Microbiology and Biochemistry his co-promotor.

“It feels great! It was exhausting and overwhelming at times, but that light at the end of the tunnel will start to be brighter. I feel so proud of myself and very free. Nothing beats that liberating feeling that I have successfully completed a doctoral degree and now a new chapter of my life begins. I believe this post-PhD period is an excellent time for reflecting on my attributes and revising my CV, and with a PhD degree under my belt, I look forward to an abundance of opportunities that will soon open up,” says Dr Mogotsi after graduating.

Research

According to him, he was first introduced into this research concept when he was doing his master’s degree in microbiology. “Although it was more of a pilot study aiming to assess the feasibility of conducting this type of research on a larger scale, we made some interesting findings which we published in an international journal.

“I obtained my degree with distinction, receiving an award for Best Master’s Dissertation in Microbiology. The findings of this research really ignited my passion, and I was also inspired by the fact that this was a newly emerging field of research in the discipline of virology at the time, and of course in my master’s research there were some gaps and limitations which needed to be addressed. I then took a decision to pursue a PhD and expand on that research, and working with new-born babies is always enjoyable,” says Dr Mogotsi.

With his thesis titled “Longitudinal characterisation of the enteric virome of infants from the Free State, South Africa, using viral metagenomics”, Dr Mogotsi’s research aimed to characterise the total assemblage of all viruses that colonise the gastrointestinal tract of newborns, often referred to as the gut virome, using metagenomics.

“We know that the human gut undergoes some changes as the new-born baby becomes exposed to the numerous microorganisms, such as viruses, from the immediate environment. This once-in-a-lifetime occurrence can have life-long effects on the health and disease state of humans. Viral intestinal infections are among the leading causes of childhood hospitalisations and deaths, especially in Africa, and infants are at a greater risk of suffering severe illnesses due to their immature immune system,” he explains.

According to him, previous research had focused more on the investigating the population of bacteria present in the gut of new-borns, therefore, there’s a huge knowledge gap about viruses colonising this part of the human body. In South Africa, more attention has been on assessing the effectiveness of currently available vaccines and surveillance of specific disease-causing viruses such as rotavirus.

The research he was conducting, he continues, therefore, sought to characterise all intestinal viruses in healthy new-borns individuals, their source of origin, the changes in diversity and composition occurring over time, as well as their potential implications on the health of infants. “The findings of my study have provided more insights into what is known or new viruses are colonising the infants’ gut, as well as their evolution over time”, he adds.

PhD journey

Even though he had to put his PhD on hold for a year due to COVID-19, but with the resilience, persistence, and his ability to clear the roadblocks that were in his way, he managed to complete it. He also credits his supportive mentors and a community of colleagues and friends for their unwavering support throughout his academic journey.

“After a year-long delay, I was able to go ahead with the project and everything went well from sample collection and sample processing in the lab. The challenging part was analysing and interpreting the data as this involved advanced bioinformatics, but in the end, I was able to find solutions and make sense out of the results I got. The study was a great success with two publications in peer-reviewed international journals emanating from this study.

“Furthermore, I had an opportunity to present my research in local and international conferences. I have been to Ghana, Nigeria and Indonesia. Locally, I presented in a conference in Johannesburg and in Cape Town. More exciting was participating in the Three Minute Thesis (3MT) competition in which I emerged victorious, winning the National 3MT competition. The other award I received was from the Faculty of Health Sciences Research Forum, winning the Dr Lehlohonolo Mathengtheng Trophy for best PhD presentation”, says Dr Mogotsi.

Motivation

Dr Mogotsi says the fact that he comes from the township and received his secondary education from a township school always kept him motivated. He is well aware that there are many who look up to him, who are also inspired by what he has achieved.

“More importantly, my supervisor, Prof Nyaga, was very supportive and he is very active in his research field with genuine interest in student projects, while making time to provide adequate supervision and mentorship. His high standards of ensuring that students graduate with a strong publication record is commendable.”

As a coordinator of wet lab activities at the UFS-NGS Unit, Dr Mogotsi is currently involved in several projects as the unit is a World Health Organisation Collaborating Center for Vaccine Preventable Diseases and Pathogen Genomics. They are doing collaborative projects with several partners across the continent on the genomic surveillance of enteric viruses such as rotavirus, norovirus, sapovirus, astrovirus and adenoviruses.

News Archive

Open letter from Prof Jonathan Jansen to all UFS students

2014-02-22

Dear Students of the University of the Free State

In the past four years there has emerged a new consensus on the three campuses of the University of the Free State (UFS) about the things that divide us – such as racism, sexism and homophobia. Students and campus leaders have worked hard to develop this new consensus in residences and in the open spaces on campus. There can be no doubt that new bonds of friendship have developed across the markers of race, ethnicity, class, religion and sexual orientation. I bear witness to these new solidarities every day on the campus.

You chose a white student to head up the transformation portfolio on the SRC. You chose a black captain to head up the university’s first team in rugby. You chose a white “prime” as head of residence to lead a predominantly black men’s residence. You chose a South African woman of Indian descent as Rag Queen and last week, a black student from Cape Town as the men’s Rag winner—choices not possible and never made before in our campus history. Many of you have intimate friends who come from different social or cultural or religious backgrounds. You learn together, share rooms together, pray together and party together. In other words, in the day to day workings of this university campus, you have demonstrated to campus, city and country that we can overcome the lingering effects of racism and other maladies in this new generation. You have helped create a university community inclusive of people of diverse religions, abilities, class and sexual orientation.

I have said this repeatedly that from time to time this new consensus will be tested – when a minority of students, and they are a small and dwindling minority, still act as if these are the days of apartheid. And when that consensus is tested as it was this week, and as it will be tested in the future, only then we will be able to assess the strength and durability of our progress in creating a new South African campus culture of human togetherness based on respect, dignity and embrace.

The real test of our leadership, including student leadership, is how we respond when our transformation drive is threatened.

Let me say this: I have absolute faith in you, as students of this great university, to stand together in your condemnation of these vile acts of violence and to move together in your determination to maintain the momentum for the Human Project of the University of the Free State. We have come too far to allow a few criminals to derail what you have built together in recent years.

There will, no doubt, be unscrupulous people on all sides of the political spectrum wanting to milk this tragedy for their own narrow purposes. There will be false information, rumours and exaggerations by those who wish to inflame a bad situation to gain mileage for their agendas. That is inevitable in a country that is still so divided.

I ask you, through all of this, to keep perspective. Two or ten or even twenty students behaving badly do not represent 30,000 students; a minority of violent and hateful persons do not represent the ideals, ambitions and commitments of the majority. At the same time, let us be realistic – anyone who thinks you can drive transformation without resistance clearly does not understand the difficult process of change.

The events of the week remind us, however, that we still have a long road to walk in deepening social and academic transformation at our university. Yes, we have invested hundreds of hours in training and mentorship; we have created new structures – such as the Institute for Reconciliation and Social Justice – to capture the energy and imagination of students driving transformation; we have created many opportunities for students to study and travel on this and other continents to enable cross-cultural learning; we have established formal and informal opportunities to dialogue about difficult issues on and off campus between students and their leaders; and we crafted new curricula to enable teaching and learning on the big questions of our times.

But this is clearly not enough, and so I have decided on the following immediate next steps:

We will meet for several hours next week to think about how we can deepen the transformation of our university after this terrible incident.
We will arrange a University Assembly on the events of the past week so that we speak with one voice on human wrongs and to re-commit to human rights and we will continue with open forum discussions during the months to come.
We will review the entire spectrum of programmes, from orientation to residence life to the undergraduate curriculum, to determine how effective our interventions really are in reaching all students with respect to basic issues of human rights.
We will review our media and communications strategy to determine how far and deep our messages on human rights travel across all sectors of the university community. In this regard it is important that the campus be blanketed on a regular basis with our condemnation of human wrongs and our commitment to human rights.
We will commission the Institute for Reconciliation and Social Justice to review the events of the past week and make recommendations on how we can improve the campus environment so that all students are protected from harm inside residences, classrooms and in open spaces of the campus.
We will take the questions raised during this week into the academic community and to the general staff of the university so that all personnel also engage with our own roles and responsibilities with respect to campus transformations.
We undertake to make annual report-backs on transformation to all stakeholders in public forums so that students and staff and external communities can track the progress of the university on matters of human rights on campus.

I wish to thank my staff for acting firmly as soon as this tragic event came to our attention. We worked through the night to find and identify the perpetrators. We traced the two students and immediately handed them to the police. They were expelled. And throughout this process we offered counselling and support to the victim of this violent act.

The two former students were expelled and will now face justice in the criminal courts. It is hoped that in the course of time they will come to their senses and seek restoration and reconciliation with the student they so callously harmed. They are not part of the university community anymore.

That is the kind of university we are.

Jonathan D Jansen
Vice-Chancellor and Rector
University of the Free State
20 February 2014

Note: The use of the word ‘campus’ refers to all three campuses of the UFS, namely the Bloemfontein Campus, South Campus and Qwaqwa Campus.

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