This time around, our teaching course was made possible by our TrypTag project, funded by the Wellcome Trust. We applied for extra funds so we could transfer the genetic engineering technologies we developed for TrypTag into the hands of African researchers; to get the research techniques to the parts of the world that really suffer from parasitic diseases.
Our course focused on tools for analysing parasites and what makes them tick, particularly using genetic tools. We mostly looked at Plasmodium (malaria), Trypanosoma (sleeping sickness) and Leishmania (leishmaniasis). To teach the malaria side of the course we had the excellent Kirk Deitsch (Cornell University, New York) and Oliver Billker (Sanger Institute, Cambridge). On the trypanosome and Leishmania side we had Keith Gull (University of Oxford) and Sue Vaughan (Oxford Brookes University), along with the TrypTag team: Jack Sunter, Sam Dean and me!
So what was the course all about?
We focused on the tools to help young African scientists (starting their Master's or PhDs) take control of their research - from learning about free genome data and bioinformatics experiments, to computational and genetic tools to make discoveries about parasite biology.
A major part of the course was tools for handling DNA: PCR for detecting genes in a sample, amplifying DNA to clone it into a plasmid, and working with software (ApE) to design cloning strategies for gene tagging, deletion and RNA interference/siRNA knockdown. Teaching how to design a PCR or cloning experiment, rather than just teaching how to do the experimental technique, was very popular.
We also taught how to use the sequence resources you need for working with DNA: How to get the most from genome databases, like PlasmoDB for malaria and TriTrypDB for trypanosomes and Leishmania. The course also covered bioinformatics experiments, thinking how to test a biological hypothesis using existing data from genome data. The students quickly recognised the power of this approach, particularly given genome sequence resources are free! Many were immediately applying these ideas to their areas of research.
We also tried, for the first time ever, using the TrypTag.org website as the start point for a bioinformatics experiment. The students were challenged to start with a protein localisation patterns to identify protiens likely involved in particular aspects of parasite energy metabolism, then test whether any of these were unique to trypanosomes making them a potential drug target.
This was the perfect stress test for the new TrypTag.org website and server. It coped with up to a page view per second, and downloads of 10 images per second, with no problems. All over a slightly unreliable internet connection in Ghana! Many thanks to the scientific computing at the Sir William Dunn School of Pathology in Oxford for helping make this happen.
Overall the course was a great success, with very positive feedback from the students and local research staff. The students were smart, engaged and hard-working. It will be exciting to see what these young people can achieve over the next few years.