Development and use of genomics mining and visualization tools for prokaryotes. Analysis of gene regulatory networks of Lactococcus lactis

PhD ceremony: Mr. A. de Jong, 12.45 uur, Academiegebouw, Broerstraat 5, Groningen

Dissertation: Development and use of genomics mining and visualization tools for prokaryotes. Analysis of gene regulatory networks of Lactococcus lactis

Promotor(s): prof. J. Kok, prof. O.P. Kuipers

Faculty: Mathematics and Natural Sciences

The last few years we've seen an exponential increase of the data describing the genetic content (the genomes) and their expression (the transcriptome) of bacteria. It’s a big challenge to gain biological knowledge using this data. Anne de Jong describes in his thesis how complex datasets can be reduced to and visualized as relatively simple structured models. These models make it for men possible to extract valuable biological information.

The BAGEL-method is developed by De Jong to search in the large number of bacterial DNA-sequences for genes encoding proteins (bacteriocins) having a potential anti-microbial property. This unique method is accessible via a user-friendly webserver and led to the discovery of novel active bacteriocins. The results are now available in scientific publications. Eventually, these novel bacteriocins could contribute to the reduction of excessive use of antibiotics or to the development of alternative anti-microbial strategies. Furthermore, his thesis describes PePPER, a webserver that can be used to discover gene regulation processes by making use of existing databases and literature data. Finally, a number of technologies described by De Jong are used to make a computer model of the bacterium Lactococcus lactis when it’s growing in milk. This model is a valuable resource of fermentation of milk by this industrial and economical important lactic acid bacterium, which is the first step in the cheese making process.