SANTHE Masters trainees upskill in Texas

Wednesday, 7 November, 2018

Upasana Ramphal and Saiyuri Singh, SANTHE Masters trainees, at the Texas Biomedical Research Institute in San Antonio, USA.

SANTHE Masters trainees, Saiyuri Singh and Upasana Ramphal, both based at the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at the University of KwaZulu-Natal (UKZN) in Durban, South Africa, recently spent two months in Dr Kulkarni’s laboratory at the Texas Biomedical Research Institute, San Antonio, USA, learning modern scientific and molecular biology laboratory techniques needed to master their respective projects.

Asked why it was important they attend this training, they responded:

Singh: “Dr Kulkarni's laboratory specialises in Chromatin immunoprecipitation and luciferase assays and CRISPRi - a technique not widely known in South Africa - therefore this was a wonderful opportunity to learn novel lab techniques and bring them home, as well as to complete some of my Master's work.”

Ramphal: “My aim was to obtain as much knowledge and guidance during this trip and to receive training on all techniques possible, even aspects that do not pertain to my current Masters project. I wanted to observe the setup of a CRISPR laboratory and obtain hands-on training so that I may be competent in setting up a similar laboratory here at UKZN. The Kulkarni laboratory is involved in several exciting projects, all of which could result in publications. I wished to be a part of some of the projects so that I may be a part of the papers that may emerge from the collaboration between Dr Kulkarni and my supervisor, Dr Veron Ramsuran. I also wanted to complete as much of the practical components of my project as possible, using equipment, cohort samples and the expertise available on site. The institute as a whole is involved in some fascinating research and I wanted to interact with some of the scientists and build relationships that I may use to form collaborations of my own in the near future.”

What did their training entail?:

Singh: “I worked on my project by performing DNA electrophoretic mobility shift assays as well as luciferase assays. I learned the preparation steps for CRISPRi and how to perform many lab techniques independently that I hadn't done on my own before, including mini prep, maxi prep, qPCR (quantitative polymerase chain reaction), transformation, transfection using lipofectamine, restriction digestion, ligation, conventional PCR, colony PCR, agarose gel electrophoresis, polyacrylamide gel electrophoresis, gel extraction, western blot, wet transfer, chemiluminescence, media preparation, inoculation of broth, plating of E. coli. I attended the lab meetings of the president of the institution, Dr Larry Schlesinger, as well as various talks, presentations and journal clubs that took place within the institution. I mingled with the scientists and research assistants to learn a little about what each of them is working on.”

Ramphal: “I gained confidence and competence in the laboratory as a molecular scientist. I started my first week analysing genomic sequences and identifying possible SNP's (single nucleotide polymorphism's) that are linked to HLA (human leukocyte antigen) class I expression levels. These SNP's may also be a potential transcriptional binding site and may have a direct association in HIV disease outcomes. I have also become competent in cloning, transformation, transfection, sgRNA design and creation of a multiplex CRISPR-i/Cas9 system to effectively modify gene expression. I have performed several screening and PCR assays including conventional PCR, RT-PCR, qPCR and digital droplet PCR. I have had exposure to handling and culturing of various cell lines, florescence microscopy, DNA/RNA isolation, extraction and purification, and analysis of sanger sequencing data. I have also learned many good laboratory practices as well as aseptic techniques.”

Questioned as to whom they had encountered during their training, they said they had both interacted with Dr Smita Kulkarni and her technicians, Mr Hoang Nguyen and Mr Rodger Ewy, who were primarily responsible for their training. They also met weekly with Dr Larry Schlesinger, his staff and students, and daily with Dr Tim Anderson and his team of scientists. In addition, they attended weekly "meet and greet" sessions with all staff at the institute.

How did their trip benefit them?:

Singh: “This trip has immensely benefitted my development as a trainee. I now have the knowledge, skillset and confidence to perform assays independently. I have learned how to write protocols, conduct them and optimise them. I've gained confidence in bacterial work as well as working with tiny quantities in molecular work. I've learned techniques I didn't know existed, how fast-paced international science is, and the importance of laboratory training in furthering one's career. I've also gained a better understanding of my own project and the different methods of answering my research question.”

Ramphal: “I have gained the knowledge and background I require to be a successful scientist. Obviously, learning is a daily activity and I will continue on this path, however the experience I gained from this trip was memorable in so many ways. It exposed me to the culture of research and ignited a new found passion of wanting to know everything about everything. I have a new curiosity about science and the limitations that exist - which I want to overcome! I have gained the confidence that I previously lacked, by learning specialised techniques and novel approaches to experimentation. I have learned so much about the various types of equipment that can be used for the different aspects of my project design. This trip has enabled me to be a better researcher and to literally think out of the box and strive for the greatest of successes!”

As a final question, they were asked what they felt they could bring back to their laboratory at home. The said:

Singh: “I can teach my colleagues how to conduct a DNA EMSA (electrophoretic mobility shift assay) as well as when, how and why we use it. I can teach them how to conduct a luciferase assay, the science behind it, as well as the preparation steps involved such as primer design, restriction digestion, ligation, transformation and transfection.”

Ramphal: “I can set up a CRISPR laboratory with ease and initiate experimental design and protocol generation. I wish to express the difference in culture and level of science that is currently available to us, especially as SANTHE fellows. We have the opportunity to match, if not better, the high levels of international research.”

SANTHE subscribes to the fact that science is international by nature, that scientific exchange and international mobility are essential for training young scientists in general, and international collaboration is most often directly linked to high-quality science and innovation.