By Dr. Daniel Oehme
Over the millennia our ability to utilise plants in many different ways has allowed us to flourish as a species. Most importantly, they turn our waste carbon dioxide into oxygen.
But we have also used plants to provide shelter, to publish and transmit information on paper and as a food source. In fact, developing new ways to utilise plants has even led to population explosions throughout time, such as when we first developed granaries to store grain thousands of years ago. In these modern times of climate change, global warming, ever-increasing populations and fossil fuels, plants have never been more important.
We need to ensure that there is enough plant biomass available to satisfy the world’s needs as well as ensuring there is enough to preserve habitats, act as a carbon sink and supply us with enough oxygen. To do this we must find ways to increase biomass yields, increase land available for plant production, reduce the risk to crop yields from pests and disease, limit wasted biomass and optimise plant properties to better suit specific applications such as increasing nutritional composition for human health.
IBM is acutely aware of the importance of plants and is developing and utilising a number of approaches in agriculture. Precision agriculture is one approach combining real-time data such as weather and soil quality with predictive analytics to allow the best decisions to be made when planting, fertilising and harvesting crops. Another approach, in collaboration with Mars, has used bioinformatics to sequence the genome of cocoa
Leveraging the technologies developed from other life sciences studies and developing specialised algorithms, IBM was able to identify genes that produced healthier and better tasting cocoa plants. Both of these approaches utilise IBM’s expertise in Big Data and Analytics.
Here in Australia I am part of a team at the IBM Research Collaboratory for Life Sciences – Melbourne working in collaboration with researchers in the ARC Centre of Excellence in Plant Cell Walls. We are using computational biology to examine the structure of the wall that surrounds all plant cells. We are investigating how the plant cell wall is produced, its structure and organisation and how it gets deconstructed.
In work just published in the journal Plant Physiology we used molecular dynamics techniques and high performance computing to model the major component of plant cell walls: cellulose. Our results strongly suggest that the fibres of cellulose are much smaller than previously believed. We are now investigating how these cellulose fibres interact with each other and other wall components to form the plant cell wall. Through these studies we intend to produce more accurate models of the plant cell wall and make predictions about how changes will affect the plant’s physical properties.
The possible application areas are vast. In the area of food security, we could optimise the properties of plant cell walls to make plants that are more drought/salt tolerant or more resistant to disease pathogens. In the area of human health, we hope to increase the nutritional composition of plant cell walls. In the paper and textiles industry, we could increase the physical strength of the plant cell wall making plants better for pulping or fibre production. In the area of biofuels, our studies should help to limit the effect of recalcitrance leading to more efficient ethanol extraction.
Supercomputers, such as the IBM Blue Gene/Q that we used at the University of Melbourne’s Victorian Life Sciences Computation Initiative (VLSCI), are essential in these type of projects where we examine the dynamics of biological systems at the nanoscale. Such work requires simulation of the motion of each atom and to do this we must calculate how all these atoms interact.
This must be done for many millions of time steps – a process that would take years on a standard desktop computer but days on a supercomputer. Supercomputing accelerates science and that is what the University of Melbourne and IBM Research set out to do with the formation of the VLSCI and the Collaboratory. Our work with the ARC Centre of Excellence in Plant Cell Walls is an excellent example of the success of these two organisations and the importance of plant research to the world.
Over the past few decades the major focus of life sciences research has been on animals and humans. In many ways, today we are at a similar position with plant research. We predict this research to grow dramatically in the coming years and it’s exciting to be at the forefront of the field.