Master’s students build bacteria encyclopaedia

26 March 2010

The genetic make-up of bacteria is currently being mapped in the USA. Lund University is the only higher education institution in Sweden to establish an education partnership with the Joint Genome Institute (JGI). The partnership gives Swedish Master’s students the opportunity to help with the research on the genetic make-up of bacteria.

It is now possible to determine the DNA sequences of entire genomes cheaply and quickly. At the JGI in the US, the genomes of around 200 single-celled organisms have so far been mapped. The aim is to compile a Genomic Encyclopaedia of Bacteria and Archaea (GEBA). The bottleneck is finding people who can analyse the large quantities of data generated.

“When I heard that JGI was giving away genome data and looking for students for its GEBA project, I thought that it would be fantastic to bring this project to Lund”, says Dag Ahrén.

Dag Ahrén, who is a research fellow in microbiological ecology and the director of the Master’s programme in Bioinformatics, is in the process of developing genomics activities in Lund, together with his colleagues. The cooperation with JGI is a way to put Lund’s research on the map. It is also, in Dag Ahrén’s view, a way to offer education with very close links to research.

“We were one of the first universities outside the US to join the project, and we have adopted two bacteria genomes that our Master’s students will analyse in detail.”

The idea of the GEBA project is to choose to sequence ‘unknown’ bacteria, bacteria about which there is very little general information.

“It makes the entire project very exciting; we don’t really know what we expect to find, either from a biology, bioinformatics or genomics perspective”, says Dag Ahrén. “The idea is that our students will perform bioinformatic analyses to come up with hypotheses of how, for example, the bacteria Streptosporangium roseum works. Since we grow the bacteria, the hypotheses can then be tested in the lab by other students on the Master’s programme in Microbiology.”

Most of the students on the Master’s programme in Bioinformatics have a background in either computing or biology. In the first semester, they get a foundation in programming and the tools of bioinformatics. Now, in the second semester, they get the chance to use these tools.

At Kemicentrum, a dozen or so students sit and listen attentively to Dag Ahrén’s instructions. The data enables them to answer a lot of evolutionary and biological questions: what do these organisms do? What genes do they have? How have they evolved? For example, they will try to find an answer as to why the bacteria S. roseum has so many genes, unlike most other bacteria.

“This is an exciting, cutting-edge field and we get a lot of practical training here. It was the possibility to do analysis that made me switch from biology to bioinformatics”, says Randall Polgar from the USA, one of the students on the course.

One of the aims in adapting the programme to the GEBA project is to interest talented students in coming here. However, since the courses span so many fields – computer science, theoretical physics, medicine, biology and biochemistry – it is also good to have a core such as GEBA around which to structure the studies, according to Dag Ahrén.

“I see the work on the GEBA genomes as a common thread running through the programme. This project means that the students have something familiar on all the various courses and it holds the Master’s programme together.”

Besides the international contacts, a lot of cooperation across departmental and faculty boundaries is required to run the Bioinformatics programme. Dag Ahrén hopes that the programme in its new form can be seen as a model.
“I think people should try working together in different ways to create a programme that is sufficiently good and interesting to make prospective students say: ‘I want to study at Lund University.’”

Footnote: Archaea, like bacteria, are single-celled organisms without a cell nucleus, but the two groups are very different in terms of biochemistry and evolution. Archaea thrive in extreme environments, for example very salty, acidic or hot environments, but have recently been discovered in all sorts of environments.

- Pia Romare