Modern-day Rosetta Stone helping to decode biological life

The discovery of the Rosetta Stone, which enabled the decoding of hieroglyphics, helped to open up historical treasures and put historical events into perspective. Today Bioinformatics, the modern-day Rosetta Stone in Biology, is as significantly, helping to decode biological life in the finest detail.

Bioinformatics is a crosscutting scientific discipline for the management of large amounts of biological data. It incorporates the application of computer science, informatics, and mathematical and statistical techniques to this data. A variety of software programs allow researchers to query the resulting databanks to interpret the data and generate new knowledge at a rate not otherwise possible. Its potential impact is significant in areas such as the automation of medical and veterinary diagnosis, the treatment and management of diseases, forensic analyses, agricultural advancement and even the prediction and understanding of animal and human behaviour. The most well known application is probably the analysis of data from the human genome project (the sequencing of all the genetic information in the human body).

Where is South Africa in this important, rapidly advancing field of technology? “South African researchers certainly have the intellectual capacity and the technological ability to become part of the international research community that already benefits from the enormous quantity of biological data generated daily”, said South African-born Dr David Landsman, branch chief of Computational Biology at the National Centre for Biotechnology Information (NCBI) in the US.

Dr Landsman delivered a prestigious bioinformatics lecture at the launch of the state-of-the-art Unit for Bioinformatics and Computational Biology at the University of Pretoria (UP) this week. “Local researchers deserve reliable infrastructure and financial support that would allow them to access this stream of data, such as high-speed Internet access to cope with the large quantity of data downloads that are required. However, this is currently not possible for South African researchers,” he said.

User statistics of the NCBI database – one of the three largest bioinformatics databases in the world – indicate exponential growth in the use and quantity of this data. About 400 000 users access the NCBI database every month, while about 1 000 gigabytes of information are downloaded per day. In the region of four trillion of gene sequence comparisons are performed every year, during which time the database doubles. The Unit for Bioinformatics and Computational Biology forms part of the African Centre of Gene Technologies (ACGT), which is a joint venture between UP and the CSIR under the SERA banner. The new unit also hosts the Pretoria node of the National Bioinformatics Network (NBN), which is an initiative of the Department of Science and Technology. The Pretoria node incorporates the CSIR, University of the North and ARC Onderstepoort. Dr Landsman currently chairs the Scientific Advisory Board of the NBN.

In his research Dr Landsman, a leading international bioinformatics expert, concentrates on finding new information in the human genome and has indeed discovered potential new genes. “We have found that much of the DNA that is generally discarded as nonsensical has interesting characteristics and provides clues towards function, for example a defunct gene (also known as a pseudo gene) may regain function. Our research looks at how changes in the genome affect cellular function. Interesting regions have been identified, which warrant the design of more experiments,” he said.

The Bioinformatics and Computational Biology Unit at UP is currently working on various projects, including the development of new drugs for malaria. It has recently been involved in the annotation (functional description of gene products) of the Ehrlichia ruminantium genome, the causative agent of heartwater disease in cattle. There is an increasing involvement in bioinformatics related to forestry and plant biotechnology. This Unit is accommodated in the ultra-modern new building and facilities of the Forestry and Agricultural Biotechnology Institute ( FABI) of the University of Pretoria.