Crunching data to save lives

By Steve Kretzmann

Crunching data through specially designed computer software programmes in order to solve biological problems might, at first glance, not seem the most glamorous choice of occupation for those involved in the biological sciences.

However, while on the surface of things it would appear the bioinformatics teams spend their time huddled over computers creating and managing software programmes to process reams of information, the reality is that they are part of a global network of scientists whose ability to make sense of the biological information produced by researchers are ever expanding the frontiers of knowledge and are able to make a very real difference to entire communities of people.

One of the reasons bioinformatics came into being as a scientific specialisation was due to a desire to map out the human genome, and was given a major push by the founding of the human genome organisation (HUGO) in 1988 and the initiation of the human genome project in 1990, which sought to compile a complete map of our genetic structure.

A global project in which scientists sequenced billions of characters and examined exactly how they fitted together to create chemical messages at cellular level, it was necessary to harness information technology and computing power to complete the picture.

It took five years to map the entire human genome, which comprises three billion characters with 25 000 genes.

Bioinformatics, also known as computational biology, allowed scientists around the globe to contribute to a central data repository and also check their findings against what other people had been doing, thus both avoiding duplication and addressing the question: ‘how similar is what I’m doing to what’s already out there?’.

The mapping of the human genome revealed the potential of computational biology, as all living organisms have a genetic structure, including viruses and bacteria. Thus accessing, and contributing to, knowledge of the genetic structure of viruses, especially those that evolve rapidly, such as the HIV and flu viruses, can have huge benefits for medical research.

Sometimes, such information can result in world headlines, as was the case for former South African National Bioinformatics Institute senior lecturer Tulio de Oliviera in 2004.

Working at the University of the Western Cape and collaborating partner Oxford University at the time, de Oliviera’s knowledge of the HIV virus was a major factor in saving the lives of five Bulgarian nurses and a Palestinian doctor who were facing the death sentence in Libya after being accused of infecting hundreds of children there with HIV.

De Oliviera, as an expert witness in court, was able to help prove what exact strain of the over 60 strains of HIV the children had been infected with, and more importantly, when they had been infected.

Because de Oliviera, through the meticulous sampling of infected patients over time and sequencing the evolving virus genome, was able to show scientific evidence that the children had been infected three years prior to the accused even entering Libya, the medical workers – who were facing death by firing squad – were released.

While that story made world headlines, the ongoing work at SANBI is no less potent. Continuous data sampling of HIV infected patients means the identification of the scores of strains can be determined.

Using this information, combined with monitoring the efficacy of available ARVs, software programmes have been developed at SANBI, enabling clinicians to easily identify the strain of virus their patient has, and prescribe the drugs best suited to combat that strain.  

The beauty of this research is that it does not only apply to the HIV but to hundreds of other viruses afflicting both humans and animals

Sleeping sickness, scientifically known as trypanosomiasis, for instance, is another disease that afflicts hundreds of thousands of people in Africa.

The disease is not caused by a virus, but by a parasite. However, bioinformatics, while precise, is also flexible.

The parasite which causes sleeping sickness in humans and animals is transferred by the tsetse fly and what is fascinating to researchers like DST/NRF Research Chair in Bioinformatics and Health Genomics, Alan Chrisoffels, is that the fly is for the most part immune to this parasite. Mapping the fly’s genetic structure, hypothesises Christoffels, is the key to discovering what makes it immune.

“Once the tsetse fly genome is mapped out, it can be compared to the genomes that we have mapped out in other insects, such as the fruit fly and Anopheles mosquito which transmits malaria. We can then ask what is peculiar about this one. And not only what is peculiar about it but hone in even further and ask how does this fly protect itself?”

Once that information is known, it may be possible to develop the best possible drug to combat this disease which is causing the lives of millions of Africans to be lost. -- West Cape News