Bioinformatics and Medicine

p53mutations Bioinformatics will have a series of important roles in the medicinal sciences. Biology and medicine are living in a time of rapidly increasing involvement of knowledge about processes at the molecular level, and bioinformatics can help cope with this rapid increase of required skills.
An important function for bioinformatics is explaining things at the molecular level. To do so, enzymes from pathogens or mutated native enzymes can be modelled by homology. These models can be used to explain the effects determined by molecular biology.

P63 mutations

Parasite activesite The human genome will be known and properly annotated in a few years. At that moment we know nearly all targets for medicins. Getting the same information for a parasite will enable us to make better medicins against infections with less side effects. After all, such a medicin should block a process that is crucial for the parasite, but it should of course not block the equivalent process in the host.

Parasite and active site

regulation Many research projects are aiming at the discovery of information about molecules or molecular interactions. Bioinformatics can help here. Correlated mutation analysis (CMA) is a technique to find co-variation in pairs of sequences. Bioinformaticists originally thought that CMA could be used to solve the protein folding problem, but it became clear that co-variation is a much better indicator for functional dependencies and inter-molecular contacts. It is more important for the medicinal sciences, however, to get an overview of entire process and not just about one or a few steps. Putting the pieces of the big jigsaw puzzle together, to get an overview of networks of interconnected steps is a typical task for bioinformatics.

Networks and regulation

GPCR Information about a molecule, or even a complicated network of interactions between proteins, is just the beginning. We want to understand the entire interplay of networks, and all forms of communication inside cells, between cells, between organs, and between organisms.
Bioinformatics is the ideal tool to integrate data at all levels from molecule to man. The G protein-coupled receptors (GPCRs) are our first attempt at integrating heterogenous data. This project, called GPCRDB, can be inspected at http://www.gpcr.org/7tm/. The GPCRDB combines all information about one class of molecules. It includes all known sequence, structure and mutation data with a large number of ligand binding studies and computational results. In the future we will extend this system with more data which will be automatically extracted from literature. We will also add new data types, such as expresion profiling data and automatically selected literature references. The importance of GPCRs is probably best illustrated by the fact that more than 30% of all known medicins act on a GPCR.

Schematic representation of a GPCR

array_spotter One of the new datatypes we intend to add to the GPCRDB is expression data. Expression data is collected with gene chips. A gene chip is an array of (thousands of) pieces of nucleic acid that all are complementary to a gene one wants to monitor. Adding a drop of cell extract will lead to hybridization, and if this hybridization is quantitative, one gets data about expression levels. In real life things are a bit more complicated, but from a bioinformatics point of view this is the minimal required knowledge.
Bioinformatics can help with the selection of probes to put on the chip, with the extraction of data from the chip, but most interestingly, a lot of bioinformatics will be needed

An array spotter

Bioinformatics and medicine will meet mainly in two ways.
First, collaborations on the research topics listed above will bring researchers together. Not only can bioinformatics be used to explain experimental results, but when used properly, bioinformatics can also generate ideas for new experiments to answer old questions, or stronger even, bioinformatics can raise new questions.

radboud Second, bioinformatics will have to become part of the curriculum of all medical students. Slogans like "Computers will take over in all corners of the world", or, "Without good computer skills you won't make it in the future", are surely overdone, but it is clear that a minimal amount of computer knowledge is an essential ingredient of the study of every student in the faculty of medical sciences. And what better way to generate this computer savvyness with a course that teaches the student skills he or she will use regularly throughout the career? Bioinformatics will provide just that: education of essential skills (searching and finding information using the WWW, using biomedical databases, etc.)

The faculty of medical sciences

It is not an exaggeration to state that the CMBI plays a leading role in the Dutch bioinformatics field, and probably also in Europe. This opens up beautiful opportunities for students and scientists.
In Nijmegen a student can get in contact with this science of the future called bioinformatics, but it is also possible to become a well-trained bioinformatician, ready for the challenges that come with the better jobs.
Experimental scientists in Nijmegen have better opportunities than at other universities in the Netherlands to discuss their research with bioinformaticians, and to collaborate with them. This potentially gives our experimental scientists a significant step ahead that "comes for free".