Detecting malaria’s bad air: a breath test with a twist

Try looking at this image and not feeling an itch.

Try looking at this image and not feeling an itch.

By Pamela Tyers 

What’s the most deadly creature in the world? The lion? The shark? In fact, it’s a bit of a trick question (do humans count?)… but there is a fair argument that the humble mozzie is the world’s top killer.

Many species of mosquito carry deadly diseases such as malaria, yellow fever and west nile virus. Malaria in particular places a huge health and economic burden on developing countries. According to the World Health Organisation, almost 200 million people caught malaria and more than half a million of them died from it in 2013 alone.

Thankfully, Australian scientists have made a significant discovery that could lead to the development of new tests for diagnosing malaria – potentially saving millions of lives. By identifying distinctive chemicals in our breath, researchers have been able to detect whether someone is infected with the disease.

A team of our scientists joined with QIMR Berghofer Medical Research Institute and the Australian National University to look at the breath of volunteers who had been given a controlled malaria infection, as part of existing studies to develop new malaria treatments.

The research found that the levels of some normally almost undetectable chemicals increased markedly in their breath during the infection.

Stephen Trowell leads our research on the work. He is particularly excited because the new testing method allows us to diagnose malaria much earlier than with other tests.

“The increase in these chemicals were present at very early stages of infection, when many other methods would have been unable to detect the parasite in the body of people infected with malaria.”

“Overall, our breath could prove to be a much better alternative to blood tests for diagnosing the disease.”

The research, published today in the Journal of Infectious Diseases, was undertaken in two independent studies where experimental drug treatments were being tested in volunteers who had been given a very small dose of infection. Using a sophisticated analytical instrument, Stephen and the researchers identified four sulphur-containing compounds whose levels varied during the course of the malaria infection.

These sulphur-containing chemicals have not previously been associated with any disease and their concentrations changed in a consistent pattern over the course of the malaria infection, correlating with the severity of the infection. They effectively disappeared after the patients were cured.

By identifying distinctive chemicals in our breath, researchers have been able to detect whether someone is infected with malaria

By identifying distinctive chemicals in our breath, researchers have been able to detect whether someone is infected with malaria

Currently, diagnosing malaria involves using powerful microscopes to look for parasites in blood using a method discovered in 1880. As the world starts to work towards the elimination of malaria, there is an urgent need for more sensitive and convenient tests to detect early and hidden cases.

The team are now collaborating in regions where malaria is endemic to test for the chemicals in the breath of patients with the disease. They are also developing very specific, sensitive and cheap “biosensors” that could be used in the clinic and the field to breath test for malaria.

We’ve worked on developing a range of similar bioproducts – you can read more about them here.

For media enquiries, contact Andreas Kahl on andreas.kahl(at)csiro.au or +61 407 751 330.


Uncovering the mystery of stellar nurseries

The Cepheus Flare just one of the stellar nurseries in the night sky where stars are formed. Image: NASA Astronomy Picture of the Day/ Stephen Leshin

The Cepheus Flare just one of the stellar nurseries in the night sky where stars are formed. Image: NASA Astronomy Picture of the Day/Stephen Leshin

Claire-Elise Green wants to time travel. She wants to peer into the stellar nursery of the cosmos and understand how stars are formed, in their infancy, billions of years ago. To do this she needs access to multi-billion dollar telescopes, astronomical amounts of data and the time to work with the best and brightest in the field. Not something you can just Google.

This is why she is heading to the Max Planck Institute for Radio Astronomy in Bonn, Germany to work with the equipment, data and experts needed to further her PhD research. This isn’t a cheap European getaway by any stretch of the imagination.

The winner of the inaugural CSIRO Alumni 2015 Scholarship in Physics award: Claire-Elise Green

The winner of the inaugural CSIRO Alumni 2015 Scholarship in Physics award: Claire-Elise Green

But Claire-Elise took a big step towards financing this journey when she was selected as the first ever recipient of the CSIRO Alumni 2015 Scholarship in Physics award.

The award was setup in honour of the four physicists who sadly lost their lives – two years ago – in a tragic accident, with a view to helping young Australians finance their projects and research in physics.

After beating out 14 other entries, Claire-Elise was handed the award and the $5000 scholarship fund at a ceremony in Lindfield, NSW.

Before she heads off to Germany with her novelty over-sized cheque, we had a chance to sit down and speak with Claire-Elise about her research, her time with us and her passion for science.

Mastering Blob-ology

Claire-Elise’s scholarship winning project seeks to understand the birth of stars. So she scours the sky, looking for ancient molecular clouds in the deep dark recesses of space. These clouds play the role of stellar nurseries and look like large blobs with a radio telescope, so naturally she refers to this area of research as blob-ology.

Deep within the blob (and with the help of incredibly sensitive high resolution telescopes) you can find strings of gas and dust which appear within the cloud. These strings, called filaments, are the focus of Claire-Elise’s PhD, supervised by Dr. Maria Cunningham at UNSW, and our very own Dr Joanne Dawson.

Observations with James Clerk Maxwell Telescope (JCMT) of a molecular cloud and then the same region observed at higher resolution with The Atacama Large Millimeter/submillimeter Array (ALMA) Images: Rathborne et al. 2014 and 2015 papers

Blurry blob and clear blob: Observations through the Maxwell Telescope (JCMT) of a molecular cloud and then the same region observed at higher resolution with The Atacama Large Millimeter/submillimeter Array (ALMA). Images: Dr Jill Rathborne

In the process of star formation, dense regions of gas and dust within the molecular cloud collapse under gravity to form star forming cores. Most of these star forming cores have been found to lie on these dense filaments of gas like beads on a string. The role of these filaments in the star formation process, however, is currently unknown.

While she has had access to the Australian Compact Telescope Array near Narribri, and the Mopra Telescope, near Coonabarabran there is still lots of work to be done in this relatively new field of astrophysics and the time she will spend at the Max Planck Institute will further her understanding of the cosmic cabbage patch.

This PhD research into star formation is the culmination of many years of study back here on Earth.

A passionate scientist from a young age, Claire-Elise cites our Double Helix magazine as an early inspiration for all things scientific (please excuse the shameless self-promotion).

As she moved into high school she was fortunate enough to be part of a program designed to encourage young women to engage with science. Indeed, she chose to complete a Bachelor of Advanced Science majoring in Physics at University. And even though she was considering a double major including chemistry, we won’t fault her for taking the easy road and sticking to a single major!

In order to get some real world experience she completed two summer programs with our scientists where she collected her own data with the telescope at Parkes and the array of telescopes at Narrabri, she even used this opportunity to be get published.

Not only did she spend valuable time in the field where she could get her hands dirty and experience the realities of modern research, she also had the opportunity to rub shoulders with inspirational scientists like our own Dr Julie Banfield and Dr Jill Rathborne. Oh and she got to take a hayride on the world famous ‘Dish’ and take some memorable pictures.

Ever wanted to know the perks of being a scientist? How about riding the world famous Dish as it completes a “hayride” with you on board? from left to right: James Neild, Daniel Reardon, Tiffany Day, Claire-Elise Green, Sarah Hegarty. Image: Dr Yiannis Gonidakis

Ever wanted to know the perks of being a scientist? How about riding the world famous ‘Dish’ as it completes a “hayride” with you on board? From left to right: James Neild, Daniel Reardon, Tiffany Day, Claire-Elise Green, Sarah Hegarty. Image: Dr Yiannis Gonidakis

Through all these experiences and with the example set by her mentors like Dr Cunningham, Dr Dawson and Dr Rathborne, Claire-Elise developed into a scientist with a passion for encouraging more women to try science, as she says – they tend to “rock at it”.

Before she departs for Europe and the next stage of her research career, she hopes to find some time to indulge in her favourite pastimes: tending her vegetable and herb gardens and enjoying a bit of the old ‘Crafternoon tea’ (that’s an afternoon tea coupled with crafts if you are unfamiliar with the term). When you are searching for the answers to the some of the universe’s biggest questions, it pays to stay grounded.

You can hear more about Claire-Elise’s research in her own words on Thinkable.org. Don’t forget to vote for her while you are there.


Farming carbon can be a win for wildlife, if the price is right

Koalas are one of the threatened species that could benefit from carbon farming. christopher charles/Flickr, CC BY-NC-SA

Koalas are one of the threatened species that could benefit from carbon farming. christopher charles/Flickr, CC BY-NC-SA

Megan Evans, Australian National University; Anna Renwick, The University of Queensland; Josie Carwardine, CSIRO, and Tara Martin, CSIRO

Climate change and the loss of biodiversity are two of the greatest environmental issues of our time. Is it possible to address both of those problems at once?

In Australia, farmers and landholders will this week be able to apply for payments through the Federal government’s A$2.55 billion Emissions Reduction Fund. Bidders can request funding for projects that reduce emissions using agreed methods, which include approaches relevant to the transport, waste and mining sectors, as well as the land sector: for example, by managing or restoring forests.

Forests hold carbon in vegetation and soils and provide important habitat for native wildlife. Restoring forests in areas where they have been cleared in the past could be good for the climate, good for biodiversity, and generate additional income for landholders.

How well the Emissions Reduction Fund can achieve these benefits will depend on three things: the right approach, the right price, and the right location.

Farming carbon

There are a range of approaches available for restoring forests, and they vary in how quickly carbon can be sequestered, cost, and suitability for wildlife.

For example, fast-growing monocultures such as blue gum plantations can sequester carbon very rapidly, but don’t provide ideal habitat for wildlife. Planting a diversity of native trees and shrubs using an approach called environmental plantings is far more wildlife-friendly, but the costs are higher, and carbon is not stored as quickly.

A third possible approach is to assist the natural regeneration of vegetation. This can be done by fencing off cattle or by ceasing on-farm practises such as burning or disturbance with machinery. Assisted natural regeneration is the cheapest of these three possible methods, and is also good for biodiversity: our recent paper found that it could be a great option for restoring forests in agricultural landscapes across Queensland and northern New South Wales.

Brigalow woodlands allowed to regrow for 3-10 years. Image: John Dwyer

Regenerated brigalow woodlands after 50 years. Image: John Dwyer

Location, location, location

Across Australia, there are a number of places where growing carbon could be a more profitable option than the current land use. Some of these places are more important for biodiversity than others.

The mulga lands of western Queensland may be worth more as carbon farms than other uses. Image: Don Butler

If we’re interested in getting some wins for biodiversity while growing carbon forests, we need to think carefully about the possible opportunities and trade-offs, as the best places for sequestering carbon are not always the most beneficial for biodiversity, and vice versa.

In our recent paper, we found that it is possible to identify where growing forests could provide win-wins for both carbon and biodiversity.

For example, the top 25% of priority areas for environmental plantings could sequester 132 million tonnes of CO2 equivalent annually, which is almost a quarter of Australia’s annual emissions (excluding those caused by land-use change).

Relative priority areas for restoring 139 threatened ecosystems to 30% of original extent using environmental plantings, where carbon is stored at $20/tonne. Pink areas are higher priority, green is lower priority http://bioscience.oxfordjournals.org/content/65/4/372

These high-priority areas for environmental plantings could restore some of the most threatened ecosystems in Australia. There are 139 ecosystem types across the country that have lost more than 70% of their original extent. If it were possible to restore these ecosystems up to 30% of their original extent, they will have a better chance of surviving in the long term.

Restoring parts of the landscape with these ecosystems is a high priority for biodiversity – not only are the ecosystems rare, but many of the birds and animals that depend on these ecosystems are those that are most threatened. For example the brigalow woodlands of south east Queensland, of which less than 10% remain, are home to nationally threatened koalas and a host of other wildlife.

The right price

It will generally be more expensive to grow carbon forests that also provide benefits for biodiversity. This is because the places most profitable for land uses such as agriculture are often where the most threatened species and ecosystems are located.

In our analysis, we found that with a price on carbon equivalent to A$5 per tonne, it would not be profitable to restore threatened ecosystems up to 30% of their original extent. This means that without additional funding from another source, there is limited opportunity to achieve wins for biodiversity if the price on carbon is low.

However, a higher price of A$20 per tonne, reflecting Australia’s 2011-2013 carbon price, could allow up to half of the heavily cleared vegetation types to be restored up to 30% without any additional funding for biodiversity itself. At this A$20 price, we also found that it made more economic sense to farm carbon than the existing land use, in over 1.2 million hectares in Queensland.

This week’s Emissions Reduction Fund auction will be a good first test of how the current approach to carbon farming can provide the dual benefit of restoring habitat for native wildlife and addressing climate change. Our analysis shows that Australia’s climate policies could have a very significant impact on biodiversity – if we think carefully about the right approach, price, and location.

The Conversation

This article was originally published on The Conversation.
Read the original article.


Farmer counts a mouse: Australia’s first ever Mouse Census Week

Grain grower Richard Konzag, of Mallala in South Australia, says recording information about mouse numbers and activity on his property via the MouseAlert app was a simple but important exercise. Image credit: Grains Research and Development Corporation

Grain grower Richard Konzag, of Mallala in South Australia, says recording information about mouse numbers and activity on his property via the MouseAlert app was a simple but important exercise. Image credit: Grains Research and Development Corporation

By Emma Pyers

Our scientists are leading the nation’s first ever national game of cat and mouse, and we want you to join in the fun. Taking place this week, farmers and advisers throughout Australia’s grain-growing regions are being asked to get involved in the nation’s first ever Mouse Census Week by assessing mouse activity on their farms.

The census is taking place before seeding of winter crops – a critical time for locating mouse “hot spots” and determining whether numbers are at levels that could pose a risk to newly-sown crops. Farmers can record mouse activity via MouseAlert – a website and recently-released App aimed at improving early warning of possible plagues and rapid response to increases in mouse activity.

This video shows the sort of problem we are up against (and a warning, it’s not pretty):

We know from our own routine monitoring that mouse activity is currently low in Victoria and New South Wales, but has increased in South Australia with higher than normal abundance in some regions.

We now need farmers and agronomists to confirm this information for us on a much broader scale than we have ever been able to work before. Mouse Census Week will provide us, farmers, the grains industry and other researchers with an unprecedented bank of data about mouse activity in agricultural areas.

But we still need your help to keep up.  To make MouseAlert truly effective, we need farmers to give it a go – for their benefit and that of their farming neighbours. We encourage everyone to get involved and help us help you to get on the front foot and be better prepared before mouse numbers explode and damage occurs.

Farmers can download the new MouseAlert App ,which is part of the FeralScan phone App available in the iTunes store.

The mouse-monitoring programs are funded by the Grains Research and Development Corporation in collaboration with Landcare Research New Zealand, CSIRO and NSW Department of Primary Industries through the Invasive Animals CRC.


African cassava whitefly: getting to the root of the problem

The cassava whitefly is out to lunch with its friends, unfortunately this social gathering is a real problem for Africa's food security. Image: Sarina Macfadyen

The cassava whitefly is out to lunch with its friends, unfortunately this social gathering is a real problem for Africa’s food security. Image: Sarina Macfadyen

For a bug that’s only 1mm long, the African Cassava whitefly is causing a whole lot of trouble. This miniscule pest has become superabundant in East and Central African farmlands, destroying cassava crops and causing devastation to the food supply on multiple fronts. It’s estimated the whitefly is affecting the food security of more than 40 million African families in sub-Saharan Africa.

Enter a new research partnership with the Natural Resources Institute at the University of Greenwich, who are the recipients of funding from the Bill & Melinda Gates Foundation. This partnership of scientists spans five continents and includes a team of researchers from our biosecurity flagship, who shall conduct research and provide expert advice to East African scientists with the long-term aim of containing and controlling this pest.

After all, it was only 20 years ago that we faced a whitefly problem here in Australia. The closely related Silverleaf whitefly caused considerable damage to our soybean, cotton, and vegetable crops.

Our scientists will use their experience dealing with this closely related whitefly (Bemisa tabaci).

Our scientists will use their experience dealing with this closely related pest known as the Silverleaf whitefly to assist the East African scientists deal with the cassava whitefly.

Back then our scientists did some investigating to understand the tiny invader and to discover the best way of controlling it. Their research lead to the successful introduction of a biological control agent, a small wasp called Eretmocerus hayati, which kills the whitefly nymphs. The wasp did such a good job at controlling whiteflies that it became the basis of an effective and sustainable management program. The program combined the use of insecticides with on-farm practices such as crop rotation and maintaining plant refuges, which supported the survival of the wasps in the environment. By following the recommendations developed by our team, the integrated control measures reduced Silverleaf whitefly numbers significantly.

Now our scientists will bring their whitefly experience to Africa where the cassava whitefly is causing damage on two fronts: by feeding on plants and transmitting plant viruses that have caused two on-going and devastating pandemics – Cassava Mosaic Disease (CMD) and Cassava Brown Streak Disease (CBSD).

Due to this double-threat, cassava growers in the region have been exposed to devastating losses in a crop that is crucial to their food security.

African entomologist, Dr Andrew Kalyebi inspecting cassava plants at a trial site in Uganda. Credit: Sarina Macfadyen CSIRO

African entomologist, Dr Andrew Kalyebi inspecting cassava plants at a trial site in Uganda. I: Sarina Macfadyen

Since the 1990s, research efforts have focused almost entirely on developing virus-resistant cassava plants, with little attention being paid to understanding the underlying causes of the cassava whitefly population boom. This is a particular problem because even without the viruses, the whitefly causes 40% reductions in yield from feeding and reduced photosynthesis due to sooty moulds that cover the lower leaves of cassava plants.

This lack of research into the causes of cassava whitefly super-abundance is arguably the main reason why a lasting solution to cassava-virus pandemics also remains elusive.

Sadly, the region currently finds itself in a destructive cycle; the spread of these diseases is associated with the outbreaks in the cassava whitefly population and the larger the whitefly population the more rapid the spread of both pandemics.

We intend to get to the root cause of the whitefly problem and the experience of our scientists will be combined with the knowledge of East African scientists as they look to fight off the cassava whitefly and secure the crops for the long-term sustainability of the food supply. This new knowledge gained from the research will be used to develop rational interventions that will not only directly benefit hundreds of smallholder farmers in East Africa, but will also contribute to our understanding of this group of cryptic whitefly species that is of such global importance.

If you would like to see where we are working around the world, you can check out this interactive map, which showcases our other projects from around the globe.


Australia’s Next Top climate models

Some of Melbourne’s climate analogues for 2090 under a high emission scenario

Some of Melbourne’s climate analogues for 2090 under a high emission scenario

By Chris Gerbing

We all have an interest in whether rain will dampen our day and a curiosity about what the skies hold for next week. We are all impacted when the weather turns extreme, sometimes in devastating ways. And we have a yearning to know what the future might hold for our climate, so that we can plan ahead.

Weather and climate may never be completely predictable, but science has come far enough for us to be breaking new ground when it comes to projecting what Australia’s climate may look like decades – or even hundreds of years – in the future.

And here’s a sneak peak into the future – by the year 2090, Sydney could have the climate of Brisbane, and Melbourne could have the climate of Dubbo.

Climate models help us to understand our present weather and climate, and also allow us to consider plausible future scenarios of how the climate might change. Climate models are built using mathematical representations of the dynamic Earth system. Their fundamentals are based on the laws of physics including conservation of mass, energy and momentum. They create simulations to tell us what happened or what might happen under a range of different scenarios (such as greenhouse gas concentrations).

Check out this animation about climate models.

Along with the Bureau of Meteorology, we’ve used as many as 40 climate models, produced by international global climate modelling groups, to create projections for Australia’s climate, all the way out to the year 2090. The projections consider up to 15 regions of Australia, a small set of plausible future greenhouse gas scenarios and four future time periods.

Climate change projections are presented as a range of possibilities. This occurs because different models produce different projections. Even though they are based on the same physical laws, such as conservation of mass, moisture and energy, each climate model treats regional processes in the oceans and atmosphere slightly differently. It is important to explore the full range of possibilities in any impact assessment.

Even if we significantly reduce our greenhouse gas emissions as under an intermediate scenario, Melbourne’s annual average climate could look more like that of Adelaide’s, and Adelaide’s climate could be more like that of Griffith in New South Wales.

Eastern Australian coastal sites could see a climate shift to those currently typical of locations hundreds of kilometres north along the coast. Sydney’s climate could resemble that of Port Macquarie, and Coffs Harbour’s climate resembling that of the Gold Coast (by 2050; intermediate emissions).

These analogues, and others for more than 400 towns, can be found using a climate analogues tool –  one of 13 tools that can be found on the Climate Change in Australia website.

This research received funding from the Department of Environment under the Regional Natural Resource Management Planning for Climate Change Fund. Additional funding was provided by CSIRO and the Bureau of Meteorology.

We have published two articles over on The Conversation which takes a deeper look into the details of these climate models and projections.


Science with heart: 5 ways we’re helping medical research in Australia (and the world)

The CardioCel patch.

The CardioCel patch.

Australian company Admedus has been making headlines recently for its innovative medical material, CardioCel. The tiny, flexible patch, made using part of a cow’s heart, is being used to treat potentially devastating birth defects like congenital heart disease – and it’s taking the international medical community by storm.

What’s more, we’re proud as punch to say that we were integrally involved in its success.

Our researchers worked with Admedus to assess the suitability of CardioCel for use in stem cell therapy in heart failure patients by comparing it with another commonly-used product. We found that CardioCel was well suited to cardiovascular cell therapy, and that it could have potentially groundbreaking applications in other areas of stem cell delivery too.

It’s since been implanted in more than 1200 patients across Australia, Europe, North America and Asia.

This is just one of many medical success stories we’ve been a part of. So, just because we like the number five, here’s five more:

3D printed titanium heel bones? Why not

When a Victorian man was facing amputation of his leg due to bone cancer in his heel bone, his doctor turned to us for help. Professor Peter Choong, from Melbourne’s St Vincent Hospital, knew about our work in titanium 3D printing and wondered if we could print a workable heel bone transplant, thus removing the need for amputation. We helped turn his vision – a metallic implant which could support a human body’s weight – into a world first-reality.

Putting blood tests on the spot

We’re working with Universal Biosensors to trial on-the-spot testing and results for a range of crucial blood tests. The immediacy of results means that patients avoid the dreadful stress that comes with waiting, as well as receiving treatment faster.  By broadening the application of point-of-care testing, we will see time and cost savings for already-stretched healthcare providers. Not bad for a little prick.

Supercomputers for (sort of) super hearts

Using the same technology that drives state-of-the-art video games, we created a ‘virtual heart’ simulation that the Victor Chang Cardiac Research Institute are using to better diagnose and treat heart rhythm disease. Who said nothing good ever came from gaming?

Winning the waiting game in our hospitals
Our Demand Prediction Analysis Tool can predict bed demand in hospital emergency rooms by the hour, day and week, greatly easing the pressure on their emergency wards. A similar technology has already been rolled out in more than 30 hospitals in Queensland (hello, Schoolies!) and is currently being trialled in Victoria.

Know your enemy
Collectively, Alzheimer’s and Type 2 diabetes impact the lives of millions of Australians. Their symptoms on the surface are known only too well – but how they affect us on the cellular level is a mystery to many. We brought the science behind the illnesses to life, using animations that explain very complex biological processes related to each disease with scientific accuracy. This is a truly unique way of zooming in on what happens inside our body, but can’t be seen with the naked eye.

For more information on our medical research, check out the health hub on our new website.


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