Introducing The Edwards Group and ACPFG Bioinformatics

Biological research is becoming increasingly data intensive. DNA sequencers are now capable of reading thousands of millions of bases in a single run, microarrays can measure the expression of tens of thousands of genes, marker systems can interrogate tens of thousands of polymorphisms and the latest automated phenotyping systems can screen thousands of plants with little human intervention. Combined with the internet, which enables the open sharing of this data between international groups, data overload can generate a significant headache for researchers. While bioinformatics cannot provide an easy answer to this problem, it can promote quality research by making data accessible for integration and interrogation. The ACPFG Bioinformatics group aims to support research using two main approaches:

1. Supporting bioinformatics links within the ACPFG focus groups. No one understands the research problems like the researcher. Many researchers also have extensive bioinformatics skills, sometimes without knowing it. We aim to work with key members of each focus group to provide a direct path to advanced bioinformatics tools and training. These researchers can then apply their skills to their specific problems and support other staff within the focus group.

2. The second approach is to provide tools, capabilities and analysis which span focus groups. Examples include the development of a cereal molecular marker discovery database by Nikki Appleby, the integration of molecular genetic and genomic data by Chris Duran, and the development of high throughput sequence assembly and annotation tools by Michael Imelfort and Ping Zhang. These, and other systems aim to provide ACPFG researchers with access to the latest data and technology to support and promote their understanding of plant stress.

From left to right we have:
Mike Imelfort - Dave Edwards - Jacqueline Batley - Nikki Appleby - Ping Zheng
Missing: Peter Woon and Chris Duran

Introducing Andrew Hewitt and Recent Research at the Centre for Pesticide Application and Safety

The Centre for Pesticide Application and Safety (CPAS) is based at UQ Gatton in the Agricultural Mechanisation Building. They share this building with the Vocational Training Unit which is appropriate as CPAS is conducting an increasing number of workshops and training courses in Gatton and across Australia. The Centre's staff include Andrew Hewitt (Director), Chris O'Donnell (Principal Investigator), Gary Dorr (Research Scientist), Allen Bruce, Murray Byrnes, Brent Tangey and Elizabeth Quinn. It is hoped that as project activities increase, CPAS staff will expand in the near future. The Centre works closely with several other groups at UQ, especially within LCAFS as well as Chemical Engineering and the National Centre for Environmental Toxicology (EnTox).

The main focus of CPAS's research has always been the application of pesticides and sprays. The Centre trades under the name of the Centre for Spray Technology, Application Research and Training or C-START for commercial projects through UniQuest. The Centre has a wind tunnel equipped with a range of laser systems that are unique in Australia for the measurement of sprays. The work of the Centre is truly international in scope, with projects ranging from helping the U.S. State Department optimize spray applications for its war on drugs, to providing essential information to Australian agriculture for crop protection. The Centre's Director, Andrew Hewitt, spent over a decade working in the U.S. as Project Manager for the Spray Drift Task Force which invested over $30 million in research using the wind tunnel and other facilities currently located at UQ Gatton. Other members of the Centre staff have been involved in key aspects of spray application and modeling. Chris O'Donnell has studied the effects of climate change on weed distributions and is finalizing a major Grains Research and Development Corporation project to control difficult weeds. Gary Dorr is completing an ARC project into spray application and risk management for pesticides.

Some recent studies have investigated the effect of sprayer and nozzle selection on the application of sprays to grains, cotton and vineyard crops. The effectiveness of adjuvants on application technology has also been studied in depth both in wind tunnel and field studies.

CPAS also recently completed some studies into the effectiveness of new techniques for dipping sheep to control ectoparasites. This research should allow diazinon, a valuable chemical, to continue to be used under special permit conditions rather than being completely discontinued for such applications in Australia.

New fire fighting techniques using novel applications such as extremely high pressure to cut through vehicle or building walls and then provide a fine water mist for the extinguishment of fires have been tested.

Recently a series of large field studies into the application of a bacterial pesticide (Bacillus thuringiensis) for the control of bagworm in oil palm in Malaysia was completed. The studies compared different application systems using aircraft, vehicle and hand-held ground based spraying systems.

The Centre also recently completed a series of field studies into improving applications of sprays to grapes in Victoria. This research will be supplemented with additional laboratory work in Gatton and will improve the quality of fruit at harvest from vineyards.

Several studies have been conducted for the Australian and U.S. forestry industries. The U.S. Forest Service has an ongoing link with the centre for such research.

Several studies and modeling exercises have been conducted to facilitate risk assessment for particle dispersion. A large study was conducted for the mining industry and additional work has been conducted to develop new models for pesticide drift exposure risk assessments. Valuable tools have been provided for future testing and modeling of exposure pathways to protect humans and the environment while allowing effective crop and forest protection.

The centre has conducted research to assist the Australian banana growing industry following the extensive crop damage periods in Northern Queensland.

The centre has also conducted many studies to develop improved application and control techniques for mosquito and vector control in Queensland and other parts of Australia and the world. An ARC, state government and industry-funded PhD project will soon commence to develop additional information in the control of adult mosquitoes.

The centre is looking forward to expanding its ties with other groups within the School and University and is expecting a solid growth curve in the future for its key activities of applied research, education and training. For further information on the activities of the centre, please contact Andrew Hewitt at a.hewitt@uq.edu.au.

Spotlight on LCAFS postgraduate Students

The science of Cappuccino. Sapna Kamath has just completed a very important PhD project on the science of foaming milk. When we have a Cappuccino coffee we want a nice fine foam which will last for the time it takes us to drink the coffee. However, in the dairy industry foaming of cold milk can be a problem; for example, it can cause a lot of waste when foam is left in vats and pipes and has to be flushed out during cleaning. So the aim of Sapna's project was find out what factors made milk foam at both low and high temperatures.

When milk is foamed for Cappuccino coffee, steam is injected into the milk along with air so it produces a good volume of foam at about 65ºC. Therefore to study foaming of milk at this temperature, Sapna was able to use a commercial coffee machine. However, she needed to study the foaming of milk at different temperatures so she developed a foaming apparatus based on compressed air that she could use to foam milk (preheated in a microwave oven if necessary) at any temperature. In this way she was able to compare foam formation in the temperature range at 5 - 85ºC.

The foams formed at different temperatures were quite different. In general the most stable foams formed at 45ºC.

Sapna literally pulled milk apart to see which components affected its foaming capacity. The fat has a large effect and can prevent milk foaming at certain temperatures. Furthermore, when the fat is broken down to its constituent fatty acids, milk foams very poorly and cannot be used for Cappuccino. On the hand, the protein component (especially the casein) is responsible for forming a stable foam. Under some conditions, Sapna was able to make milk foams which lasted several hours and would be ideal for Cappuccino. Sapna's work will no doubt help the Dairy Industry, which funded her project, to provide milk which consistently gives a good foam for Cappuccino coffee. The insight she has gained into the mechanisms of foaming will also help the industry to control foaming during milk processing.

Sapna is supervised by Assoc Professor Hilton Deeth.

Plant Breeding Research. Lee Hickey, supervised by Mark Dieters, Ian Delacy and Olena Kravchuk, is one of LCAFS Honours students. To date his research has resulted in a draft of a first publication, with a second on its way. Lee also featured on the ABC TV program Landline last month. In October, he will travel to Argentina to present some of his findings at the International Pre-harvest Sprouting Symposium. Lee plans to start a PhD working on breeding for disease resistance (including yellow-spot, rusts and pre-harvest sprouting) when he has finished his honours year.

The title of Lee's Honours project is Bread Wheat - Selection for Resistance to Pre-Harvest Sprouting. Pre-harvest sprouting (PHS) in wheat (Triticum aestivum L.) is the germination of grain when it is still in the head of a crop that is standing in the field. Pre-harvest sprouting is usually a consequence of unfavourable weather conditions (rain and/or high humidity) when the crop is mature, but not yet harvested. Germination of the grain prior to harvest causes a major reduction in quality - sprouted grain is not suitable for making bread, and is undesirable for all applications, including use as feed for cattle and other livestock.

Wheat growing in a controlled temperature glasshouse (maintained at 23ºC), fitted with low-pressure sodium lamps to supplement natural light levels and extend the photoperiod. An environment such as this allows control over temperature and water availability, two major factors responsible for affecting the development of dormancy in maturing grain.

Screening for grain dormancy in the laboratory. Most Australian wheat cultivars germinate rapidly within the first few days of testing due to a lack of grain dormancy

Pre-harvest sprouting can affect crops in all regions of the Australian wheat-belt but is most frequent in northern New South Wales and Queensland where the harvest period coincides with the beginning of the summer storm season. Each season, growers lose money when their wheat is downgraded due to PHS. In one year alone, widespread rain at harvest resulted in an estimated loss of $500 million throughout eastern Australia. Pre-harvest sprouting is also a serious problem internationally. Seed dormancy is an adaptive characteristic of many plant species that delays germination to avoid unfavourable conditions for plant establishment and growth. In wheat, dormancy provides a major source of genetic variation for resistance to pre-harvest sprouting. Dormancy can be easily measured in laboratory germination tests, where environmental variation is controlled to maximise expression of genetic differences in the rate of germination.

There is no useful level of dormancy in the wheat varieties that are currently grown in Australia. Lee's project aims to investigate ways to rapidly introduce genes controlling grain dormancy into commercial varieties of bread wheat, but specifically seeks to examine the following questions:

Preliminary results have shown that: - Dormant and non-dormant lines can be accurately identified using grain from plants grown in a controlled environment glasshouse. This will enable rapid screening using plants grown at any time of year. - Selection for increased dormancy in the F2 can produce an F3 population with similar levels of dormancy to the most dormant parent. - Marker-assisted selection if applied to F2 individuals with >14 days of dormancy, is able to identify individuals which carry 2 copies of a major dormancy gene and that all produce F3 progeny with a dormant phenotype (i.e. <14 days).

Pre-harvest sprouting - germination of wheat grain while still in the head in the field

10th International Conference on Environmental Science and Technology
5 to 7 September 2007 in Greece
This conference maintains and upgrades the synthetic and integrated approach towards protection and restoration of the environment, by bringing together engineers, scientists, students, managers and other professionals from different countries, involved in various aspects of environmental science and technology. This synthetic approach, in combination with the integration of environmental issues with economic and social aspects, is a prerequisite for adopting sustainable solutions to the numerous contemporary environmental problems. Main topics are Environmental dynamics; Global environmental change and ecosystems management; Environmental restoration and ecological engineering; Environmental sustainability; Health and the Environment; Water resources and river basin management; Wastewater and sludge treatment; Air pollution and control.

Greenhouse 2007: the latest Science and Technology
2 to 5 October 2007 in Sydney
The conference will be one of the most significant climate change events held in the southern hemisphere this year and will feature many examples of industry and government approaches to tackling climate change, as well as presentations on the latest Australian and international science findings. Themes covered include biosequestration; climate change impacts and adaptation; climate modeling; communicating climate change; energy efficiency.

Next Generation Biofuels Markets
4 and 5 October 2007 in Amsterdam
This conference examines the technologies and processes availalble to migrate to the next generation of biofuels.

Biofuels Markets Africa
5 and 6 November 2007 in Cape Town
This two day conference will address strategies to develop Biofuels business opportunities in Africa, looking at regulation policies, investment opportunities, current success stories and looking ahead to next generation technologies. With speakers from all stakeholder areas of the industry this is an essential event for all parties both within Africa & globally.