An update from James

The last three weeks have been absolutely incredible. I feel I have made great progress both in the training program and also in learning more about Irish people.  The third week started with Dr. Noel introducing me to CLUSTAL X and the principals of multiple alignment and pairwise alignments of sequences, both protein and nucleotide sequences. I begun working on the Plasmodium nucleotide sequences that I had begun within week one and two, and after getting the hang of it, I moved on to working with the Rickettsia nucleotide sequences which I had worked with for my MSc. project work.  I did multiple alignments of  both the protein and nucleotide sequences; with this done, I was able to observe areas within one of the genes I worked on which were absolutely conserved and also observe regions of variability. The importance of this was really appreciated when I began locating the sites within the gene that are used in diagnosing Rickettsia infections and in distinguishing the different species. I did the same with a second gene that we used in our studies on diagnosing Rickettsia infections.  Having completed this task, I moved on to the protein sequences of the segments of the two genes and using the skills I had learnt in the earlier weeks I began annotation of these sequences using other bioinformatics software. These analyses give insights into the functions of these genes and how they may function slightly differently in the various species of Rickettsia. The information can provide insights into why some organisms cause severe disease while others cause mild disease and with this knowledge new methods to control infectious diseases can be identified. What is amazing to me is that the data is freely available and, as long as you ask relevant biological questions, all you require is knowledge and skills on how to analyse these datasets and a computer with Internet access. It is an area where African scientists can contribute as much as scientists anywhere else in the World as long as they have the relevant knowledge and skills.

By the end of the month I felt I had done enough to take a break and discover more of Ireland! Dr. Murphy had told me about the DART (local train) that had beautiful views of the coast, and Dr. Maria had also told me about the Festival of World Cultures in Dun Laoghaire, south Dublin. On the last Saturday of the month I took the train into Dublin then took the DART down to Dun Laoghaire.  The DART heading to Dun Laoghaire was extremely full – I almost thought I was in a matatu (minibus) in Kenya, yet people weren’t pushing. It was a mixture of different languages, and I was sandwiched between Polish, Australians and Germans yet the ambiance was that of celebration. The festival was more than I imagined; the place had all kinds of entertainment and food from different countries. It had been a while since I had smelled Nyama choma (roast meat) and roasted bananas but all this was there and more!

Dun Laoghaire harbour

The climax of the day was when I saw the Kenyan flag and the words Najivunia kuwa Mkenya (proud to be Kenyan) had new meaning. I chatted with Kenyans as I moved on to other stands. I walked to almost all the stands, then headed down to the sea, but it’s quite rocky. By five PM, I was exhausted and headed back into Dublin. As I sat in the DART I saw great views of Seapoint and Sydney Parade where the sea was so calm as I saw a cruise ship sail away in the distance. As I looked into the sea all I could think of was how cultures can be so different, yet in all this difference one could take away something new from each country with its diverse cultures.  I walked around Dublin trying to remember all the areas Hayley had shown earlier in month, and finally discovered Temple Bar.  It quite rowdy compared to the rest of Dublin and for the first time since I arrived, I saw the Garda (police force) at work! I headed back to Maynooth later in the evening, physically tired but mentally refreshed to begin the new month and learn a lot more. 

Tony, Varma, James and Nadine in the reading room

The beginning of the month was quiet, Tony, Roshin, and Varma were winding up their projects and were leaving, and I got to sit in one of the lab meetings where they presented their project work. It was interesting as I picked a few tips as I prepare for my presentation back home. Nadine, my German friend, was also heading back home after a summer in Dr Martina’s lab. I am sad they are gone but excited for them since they finished their MSc! I wish them all the best in this long scientific journey.

James and Roisin in the reading room 

By the end of the week the lab was very quiet, however the Ph.D students should be arriving soon and the university is also reopening after the summer break, so the place will soon become extremely busy. As the month progresses I feel that I am learning something new each day. Dr. Murphy is always reminding me to use the tools I learn to produce something novel.  This is the challenge in my mind every morning as I head down Main Street; hopefully by the time I leave I will have several novel annotations of the Rickettsia genes which remain at the centre of my training. Finally, the weather has been absolutely beautiful this week!