Dr. Rafe Lyall

Dr. Rafe Lyall is a postdoctoral researcher at CPSBB. His research background includes components of both lab work and bioinformatics, with an emphasis towards next generation sequencing (NGS) and omics-based research over his postdoctoral career. His focus has been on plant stress tolerance and evolutionary development, particularly as they relate to desiccation tolerance seen in resurrection plants such as Xerophyta humilis and the Bulgarian species, Haberlea rhodopensis.

The purpose of his first visit to the University of Johannesburg was to train South African students in next generation sequencing (NGS) and provide general NGS expertise, as well as to familiarise himself with their metabolomics machines and analysis pipelines for later integration of omics datasets from the CropPrime project.

These training activities included:

1) Creating and organising a two-day RNA extraction practical course, which taught common RNA extraction protocols, gel visualisation and common pitfalls.

2) Compiling and running a two-part morning lecture series on NGS Technologies & Applications, which gave an overview of NGS (1st, 2nd and 3rd generation), common applications and important considerations for plant science.

3) Dr. Lyall also administered a week-long, hands-on Intro to Linux & Bioinformatics course, which allowed students to run through a transcriptomics pipeline from start to finish. Due to the lack of suitable high-performance computational service, he created the necessary material in Google Colaboratory Notebooks, which allowed individual students to run analysis independently using Google cloud servers. The ultimate goal is to run such a course on a larger scale. Thus, while in South Africa, he also helped set up further collaboration between the University of Cape Town (UCT) and CPSBB. The latter institution has helped fund the installation of a high-performance training server at UCT (run by UCT information services) which will serve as a central repository for bioinformatic analysis pipelines and courses across Africa. Hopefully this server can provide the necessary computational power to expand the reach of these courses to a wider audience (including other CropPrime partners) later in the project.

Finally, Dr. Lyall underwent metabolomics analysis training, both in terms of theory (Dr. Mhlongo), and hands-on experience (Dr. Akhona Myoli).