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A Technical Guide for Wine Producers
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Biotech brief
Admittedly one will have to imagine the awesome technological advances of the next 50 years, but I think it is safe to say that they would probably also laugh at our concept of a modern computer, just as we find the computers of yester year pretty amusing (see the insert of a "modern" computer!). Nevertheless, irrespective of the jump in technology between "then and now", one cannot imagine that the use of computers will cause a bigger change in society than it did in the current era. The tempo at which computers have literally taken over our everyday lives has left many people reeling and marveling at the same time. Trying to keep up with the incredible amount of applications as well as changes in computing technology is almost futile. Even for people like me who are familiar with the everyday computer, the next generation of computing, or quantum computing, is so mind boggling it almost defies the classical laws of physics.
So you may ask, we are talking biotech, why the emphasis on computers? Well, in this modern computerized era, biotech researchers were quick to realize the huge impact computing can have on their research. From this realization, an entire new branch of computerized biotech research that harnesses the awesome power of today's computers, have evolved. This almost entire new scientific discipline (called bioinformatics) enables bio-scientists to model living processes within computer algorithms in order to gain a much better understanding of life as a whole.
The importance of bioinformatics has not escaped the South African scientific community. In recent years, the South African department of Science and Technology has made a significant investment in this regard and several bioinformatic nodes have been developed around the country. In Cape Town and Stellenbosch particular, these nodes are now well established (in Cape Town there is even a Cray "supercomputer" dedicated to bioinformatics research!) and facilitate various research projects, also in the wine industry. One such project is being conducted by Sven Kroppenstedt, a PhD student at the Institute for Wine Biotechnology, Stellenbosch University. In the next section, Sven discusses his work in a little more detail.
Computational Systems Biology: A tool towards understanding biological systems?
As mentioned in the preceding section, life in the 21st century is almost unimaginable without computers. What would we do without our daily internet surfing and email correspondence? And how would a modern winery cope without a computerized fermentation cellar for temperature control and wine stabilization, or a wine lab without a grape/wine analyzing system (e.g. grape scan)?
In biology in particular, the emergence of high-throughput data-generating technologies has led to the accumulation of a vast amount of information on genome sequences and gene expression, on protein interaction and enzyme kinetics, as well as on metabolic pathways and the "fluxes" through these pathways. For example, a modern "gene expression chip" can yield data sets in excess of 32000 data points, in a single experiment! This quantity of data can no longer be integrated through standard scientific approaches, but has to be "mined" for biologically relevant information. Ultimately, the ambition is to understand the functioning of a living organism from the information accumulated by modern science.
One possibility to give meaning to large sets of complex data is to develop mathematical models which would allow the computational simulation of processes taking place within living cells. Such mathematical modeling is now taking the center stage in many branches of biology, and its use and importance is likely to increase. The models can help us understand the distribution of certain control points within a specific pathway, and lead to more effective strategies to alter the flow of metabolic processes within a living system.
One of the main focus points of our group's research is to change the flux of a fermenting yeast cell towards higher accumulation of reserve carbohydrates, which would lead to a subsequent decrease in ethanol concentration.
By describing the behavior of the enzymes involved in the metabolism of reserve carbohydrates, e.g. trehalose and glycogen, in such a mathematical model using known, as well as new experimentally determined kinetic data, the model can present a platform allowing for the identification of the best suited targets for the alteration of metabolic fluxes within the system, and provide a powerful tool to optimize biotechnology applications.
"In silico" vs in "In vivo"
As a final thought it should be mentioned that current technology only allows for computers to describe models of actual living processes. The accuracy of these models must always still be validated by "conventional" experiments. Hopefully within the next 50 years or so, we can move beyond the current in silico barriers and use the models generated today to simulate life in such a way as to negate the need for today's (often controversial) in vivo testing procedures.
Albert Joubert IWBT, 021-8082188, e-mail albert@sun.ac.za
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