Aline Metris and colleagues at the Institute of Food Research and The Genome Analysis Centre recently won second prize in the National Institutes of Bioscience (NIB) Conference poster session.
Their poster described SalmoNet – a genome wide network of interactions between proteins in Salmonella bacteria. SalmoNet aims to integrate data from different levels, such as cellular metabolism, regulatory processes and protein-protein interactions. Salmonella bacteria are one of the leading causes of foodborne gastroenteritis, and SalmoNet is designed as a resource for scientists studying these bacteria, for example by allowing them to see whether a gene of interest interacts with others.
Photo: Rothamsted Research © 2015
The project initiated in József Baranyi’s group at IFR, as part of work to understand how Salmonella bacteria adapt to stress. Aline took a systems biology approach to this, looking at the whole organism and its gene and protein interaction networks.
These networks have been described for well- studied bacteria, such as E. coli, but not for food pathogens, so they needed to start from scratch. But a lack of gene expression data made it impossible to infer Salmonella’s regulatory networks by reverse engineering. So instead, they turned to genomic information across different strains.
This turned SalmoNet into a larger, multidisciplinary project, in collaboration with Dr Rob Kingsley of IFR and Dr Tamás Korcsmáros, a joint Fellow at IFR and TGAC, utilising the using skills of bioinformaticists, microbiologists and mathematical modellers on the Norwich Research Park.
Photo: Rothamsted Research © 2015
Aline’s career has embraced this multidisciplinary approach to research.
“I started studying chemical engineering, but was always interested in biology so I did a PhD in biotechnology, and then came to IFR to study bacterial modelling with József Baranyi,” she said.
“I like the combination of mathematics and biology; biology is not linear so to understand it there is a lot to gain taking mathematical and network approaches.”
“I started at IFR working on predictive microbiology, which looks at things like how salt levels affect the growth rate of bacteria. This uses empirical descriptive models, and there’s only so much you can do.”
At the NIB Conference, Aline noticed how systems biology approaches were becoming more and more mainstream.
“At the conference, it was good to see that so many people were moving away from the “one gene has one outcome” way of thinking, and that people were considering the importance of how genes are organised, and tackling problems from this point of view.”
Attending the conference helped Aline engage with other scientists encountering similar problems in different areas.
“For example, it was useful to meet with Mark Stevens from the Roslin Institute, who is studying salmonella in cattle. He’s shown how very small mutations have very large effects on infection of cattle. We are now interested to see how data his group have generated could be integrated into our model”
Future plans not only include integrating new data, but to continue to refine and expand the SalmoNet model and to make it user friendly for the wider scientific community. This will involve continuing to build the fruitful collaboration between the groups at IFR and TGAC.