This scanner has a few bugs, and we’re glad about it

How many insect specimens do you think are in the Australian National Insect Collection? A few hundred thousand? A million?

Actually, at the moment, it has about 12 million specimens, and it’s growing by about 100,000 a year. Like many natural history collections around the globe, the ANIC holds thousands of holotypes – each the single specimen of a species that is used to define its characteristic features.

There are all sorts of uses for these specimens, and a lot of people outside the world of entomology have very good reasons for looking at them very closely. But they’re fragile things, and many of them are tiny, so they can’t really leave their cases. And photographs don’t capture all the detail that’s sometimes needed.

So how to make the necessary information available to the people who can use it, while keeping the precious specimens safe and available for research work? Digital 3D colour modelling is ideal, but there have been some major barriers to doing that effectively. The system most used at present – Micro Computed Tomography (Micro CT) can create amazingly accurate models. But it doesn’t capture the object’s natural colour, which is vital information for species identification. It can take many hours. It’s X-ray based, so it needs special safety equipment. The machines also cost around $100,000, and they’re not portable.

Well, there had to be a better way, didn’t there?

So Matt Adcock and his colleagues did some lateral thinking, and came up with InsectScan 3D. This re-imagines 3D image-gathering in a way that doesn’t need custom-made or high-cost equipment (some of it actually came from the local hardware megastore), and the image is in full colour. The entire system uses standard components, and costs less than $8000 for the hardware and software. The digital 3D models come out in a file size small enough to be sent by email and used in web pages. And to make it even better, we can 3D print them.

3D scanned images, printed in 3D. Image by Eleanor Gates-Stuart

3D scanned images, printed in 3D. Image by Eleanor Gates-Stuart

The process uses multiple photographs of the subject, mounted on a disc marked with a pattern of dots. Using a standard DSLR camera and a 2-axis turntable, the insect is photographed at different angles and focus depths. These are then plotted by a computer, using the dot pattern to gauge the angle from which the picture was taken.

In some cases the 3D image is more useful than conventional microscopy. Obviously, the actual specimen provides all the information, but it has to be examined under a microscope for features like the mouth area and hair surface on the head. Out-of-focus effect and other physical restrictions makes using a microscope to view the actual specimen more difficult than viewing the 3D model.

The possibilities for this system are varied. Entomologists and taxonomists already have a massive backlog of insect types which have not yet been digitised in any form, and this system can provide what they’ve been asking for: a network of automated instruments that can clear the backlog by quickly and accurately creating 3D images of type specimens.

Schools and universities can use 3D models of insects as rich education materials, so students can interact with insects without endangering the fragile specimens.

But the most interesting use could be in quarantine and biosecurity. Invasive insects and the diseases they carry are an ever-present threat to Australia‘s environment, its agricultural industries and the health of the population. With this affordable, portable and accurate scanning technology, quarantine officers could carry a 3D gallery of invasive insects with them on inspections to help identify pests. Suspect specimens could be scanned in 3D and sent straight to an expert entomologist for examination. High resolution image libraries will mean we can quickly extract, analyse and share rich information, supporting biodiversity discovery, species identification, quarantine control, and unlocking the value of our biological collections.

Sounds pretty good, doesn’t it? This technology is a finalist in the Smart 100 innovation awards, and there’s a people’s choice category. If you like it as much as we do, we’d really like you to vote for it. All you need to do is click the ‘Share on Facebook’ (or Twitter, or any of the others) button and that’s a vote.


New weapon against deadly Hendra virus

a micriscopic image of Hendra virus - bright organge cellular shape encapsulated in bright blue ring on yellow background

Electron micrograph of Hendra virus.

Last week Queensland’s Department of Heath announced they will soon begin testing a human antibody treatment against the deadly Hendra virus with the help of humans.

‘Hendra’ is a potentially fatal virus that can cause disease and death in horses and, occasionally, people. The virus is found in flying foxes, which are interestingly naturally immune to it.

The announcement of human trials is particularly exciting for us because of our intimate history with this virus and our involvement in the development of the monoclonal antibody in question – m102.4.

Hendra virus first came into the spotlight in 1994, when Queensland horse trainer Vic Rail, his stable hand and many of his horses, became ill to a mystery disease. Working with the then Queensland Department of Primary Industries (QDPI) our crack diagnostic team isolated and identified the virus, naming it Hendra after the Brisbane suburb where the outbreak occurred.

medium close shot of grey horse with neck over a wire fence

The Australian Veterinary Association recommends that all horses in Australia are vaccinated against the Hendra virus.

Sadly Vic and 14 of his horses succumbed to the virus, and since then several more outbreaks have occurred in horses in both Queensland and New South Wales. Of the seven human Hendra virus cases in Queensland, four people have sadly lost their lives.

Fast forward 19 years from the initial discovery and we have the development of the Equivac® HeV, the world’s first commercially available Hendra virus vaccine for horses – an achievement that was the culmination of a scientific and collaborative journey.

We have proven that this vaccine protects horses from a lethal exposure of the Hendra virus six months post vaccination, but what about protecting the health of people living and working around these beautiful animals?

The recent development of the ‘seek and destroy’ human monoclonal antibody known as m102.4 was truly a global effort. Our scientists were instrumental in the preliminary in vitro and in vivo (animal studies) work undertaken at the sophisticated high containment facilities at the Australian Animal Health Laboratory (AAHL) and provided critical expertise on the Hendra virus at the highest level of biosafety.

The laboratory-produced molecule works by attaching itself to the Hendra virus, preventing it from causing an infection.

The purpose of administering the monoclonal antibody is to treat Hendra virus infection in people and to improve the survival rate of those who have come in contact with infected horses. Although m102.4 has already been used on compassionate grounds to treat eleven people, ten of whom survived, no formal human safety trials have yet been undertaken. This is where the volunteers come in.

two female scientists conducting experiment in lab, fully suited in fully enlcosed biocontainment suits

Australian Animal Health Laboratory (AAHL) has been actively involved and has worked closely with QDPI and Queensland Health in each recorded Hendra virus incident since it first emerged in 1994.

Queensland’s Department of Health is seeking local volunteers for phase 1 safety trials of m102.4 which will be run at the Q-Pharm clinics at QIMR Berghofer Medical Research Institute under the supervision of Princess Alexandra Hospital’s respected Hendra virus specialist Dr Geoffrey Playford. You can find out more about the trial here.

The m102.4 was developed by Dr. Chris Broder at the Uniformed Services University of the Health Sciences, Maryland USA. Queensland Health has further developed the antibody (with funding from Australian Institute for Bioengineering and Nanotechnology) by purifying and making safer for human use. Queensland Health has developed batches of m102.4 to ensure sufficient supply for compassionate use. 

 


Bees backpacking in Brazil

Bee with a backpack...of the sensor variety.

Bee with a backpack…of the sensor variety.

By Emma Pyers

How do bees in the Amazon jungle compare to those in Tasmania? They get up earlier, for a start.

Paulo de Souza and his team have been tracking bees in the two regions using tiny backpack sensors as part of our Swarm Sensing Project to gather biological and ecological data to improve honey bee health.

The tiny backpacks are just a quarter of a centimetre square and are fitted to the back of the bees.

“We have already attached the micro-sensors to the backs of thousands of bees in Tasmania and the Amazon and we’re using the same surveillance technologies to monitor what each bee is doing, giving us a new view on bees and how they interact with their environment,” Paulo said.

Graph: Daily distribution of bees in Brazil and Tasmania

Daily distribution of bees in Brazil and Tasmania (click for large version)

“Once we have captured this information, we’ll be able to model it. This will help us understand how to manage our landscapes in order to benefit insects like bees, as they play such a key role in our lives. For example, one third of the food we eat relies on bees for pollination, that’s a pretty generous free service these humble insects provide us!”

Early modelling has shown one notable difference between the bees in Tasmania and those in the Amazon; Amazon bees are up and about very early in the morning while Tassie bees prefer to wait until the day warms up before they leave the hive.

But finding out what time bees get out of bed is only a tiny part of what the research can show us. For example the research will also look at the impacts of agricultural pesticides on honey bees by monitoring insects that feed at sites with trace amounts of commonly used chemicals.


A global buzz in micro sensing

We’re working with the Vale Institute of Technology in Rio de Janeiro, Brazil, on micro-sensory technology and systems (read  more about what Vale is up to here).

Working with researchers across the globe has its unique challenges as well as its rewards, and it’s the physical challenges that have been the most interesting.

“As the Africanised honey bees were very aggressive, the hive was placed in an isolated area away from housing and domestic animals – and isolation meant working in densely vegetated areas,” Paulo explained.  “We had to clear a path to the hive and we wore fully protective bee clothing which was tough given the extreme humidity and heat.”

The Brazilian media got a taste of what it was like to work in these conditions, when they suited up to interview Paulo and our colleagues from the Vale Institute of Technology about their work

Pressure from the press

Pressure from the press

The collapse in global populations

Bee health is important globally however, honey bee populations around the world are in danger.

Colony Collapse Disorder (CCD) – a phenomenon in which worker bees from a colony abruptly disappear – and Varroa mite are two major problems facing bee populations globally. While these two problems haven’t appeared in Australia, there is a very real risk.  And what happens if it does? Catastrophe!

Check out this video where Peter Norris, Tasmanian beekeeper, describes his first hand experience with CCD while working in the United Kingdom.

So it’s a good thing our scientists, and their colleagues in Tassie and Brazil, are on the case.

To learn more about how we’re trying to save honey bees around the world tune into ABC Catalyst at 8pm tonight.

CSIRO’s Swarm Sensing Project is a partnership with the University of Tasmania and receives funding from Vale, a Global mining company.


Will robots ResQu our rainforests from weeds?

By Carrie Bengston

Want to go for a walk in a rainforest? Join us!

We push our way past vines tangled around tree limbs in the dark, multilayered forest.  As we walk, we’re aware that we’re the only people in this tranquil environment. But it’s a place that’s home to rare and unique birds like the cassowary, a fantastic collection of fungi, and unusual mammals like the tree kangaroo. We step across clear, freshwater creeks (plus or minus leeches) and we listen to leaves rustle in the canopy as a thunderstorm approaches, rumbling in the distance.

Our rainforests are precious and incredibly biodiverse. For example, the rainforests of Far North Queensland, which include the iconic Daintree, occupy less than 0.2 per cent of Australia’s land mass. Yet they support more than ten percent of its flora, 36 per cent of its mammals and 48 per cent of its birds. Rainforests are confined to small patches clustered mostly in inaccessible, mountainous regions along the tropical coast. It’s important we look after these amazing habitats. Unfortunately, a purple-leafed weed, Miconia calvescens, has escaped from its natural habitat overseas via introduction into Aussie gardens and nurseries (which has since been banned) and has made its way into our World Heritage rainforests.

Miconia calvescens

The miconia calvescens, image: Forest & Kim Starr

Purple is a great colour. Don’t get us wrong. But these purple weeds have no place in our rainforests as they compete viciously for space, and squeeze out our native plants. The Miconia menace is taking over the rainforests of Tahiti and other countries. We don’t want that happening here. So we’ve called on an unlikely ally to stop Miconia getting a roothold – robotic technology.

We’ve been participating in a research project, Project ResQu, to trial robot helicopters that could do some of the weed spotting people currently do. Weed spotters work on the ground pushing through dense forest or flying above in manned helicopters, but robots can do the job better and safer. We recently put that to the test.

UAV in flight

UAV in flight. Image: Stefan Hrabar

The robots did well. The robot helicopters, fitted with radar and special cameras and given quirky names like ‘Hotel Golf’, found several Miconia infestations missed by other methods of surveillance. Here’s how we did it.

Will robots save the rainforest? They just might.

About Project ResQu:

Project ResQu is a two-year, $7M project led by the Australian Research Centre for Aerospace Automation (ARCAA) in a collaborative project between the Queensland University of Technology (QUT), CSIRO, Boeing and Insitu Pacific with the support of the Queensland State Government Department of Science, Information Technology, Innovation and the Arts.

Media contact: Emma Pyers, 03 5227 5123, 0409 031 658, emma.pyers@csiro.au


Watch-bees on the job

How much are bees worth to you?

Well, did you know they earn an estimated $4-$6B for Australia every year? Another way to look at it is – what price would you place on cashews, almonds, macadamias, strawberries and avocadoes? Among many others, these crops rely on bees for pollination.  In fact, around one in three bites of the food we eat owe its existence to bees, which is why it is a concern to learn that bee populations around the world are in trouble.

Bees on a frame

Healthy bees at work

Enter Destructive Varroa

Varroa mite (Varroa destructor) is in all beekeeping countries except ours. These sesame-seed-sized mites attach themselves to bees and suck their haemolymph (insects’ version of blood), making the bee more vulnerable to disease. No country has been able to eradicate Varroa once it’s established.

Varroa has been implicated in collapse of bee colonies. Adult worker bees suddenly leave the hive, dying somewhere else. The colony then falls apart. The underlying cause is often unclear, but devastated hives often contain Varroa mite. This may only be a coincidence, but it’s another reason to keep Australia Varroa mite-free as long as possible. Colony collapse has become a major problem – particularly in the US.

The good news is we’re unaffected – so far. The bad news is that when (and it is when, not if) Varroa mite arrives in Australia, local bees haven’t been exposed to it, so they’re extremely susceptible. There have already been a couple of scares in 2012. Varroa-carrying bees were found living in the loading cranes of a ship berthed off Sydney.

Bee pupae infected with Varroa mite

Varroa mite on bee pupae

Australia is currently free of Varroa mite but not of Asian honey bees which is their natural host. We’re already on alert, which is why horticultural industries, the honeybee industry and the Australian Government created a National Bee Pest Surveillance Program, managed nationally by Plant Health Australia.

Unfortunately no amount of surveillance can guarantee pests are kept out, so an early warning system is necessary.

The most likely entry point for Varroa mite is through Australia’s east coast ports, especially from vessels from New Zealand and South-East Asia.

The National Bee Pest Surveillance Program now has 126 sentinel hives. These are hives of healthy European honey bees that are placed at high-risk locations, an average of six per location. These hives are tested every two months using mite-killing chemicals, to provide early detection for Varroa mites and another major honey bee pest, Tropilaelaps mites that could be carried by exotic bees on a ship or in the cargo. Samples of bees are taken from sentinel hives every two months.

But how do they know which ports to put the hives at? Enter data analytics.

The shipping news

Working out the best sites for the hives involved taking multiple data sets containing details on exotic bee interceptions, ships involved, ports of origin, destinations and types of cargo carried.

We used a technique called random effects modelling, a way of drawing out the relevant information when the precise characteristics of the members of the dataset– in this case the cargo, the last country of call and arrival port– are not all the same and difficult to quantify.

We started with shipping data. There is comprehensive information on those vessels that have arrived in Australia, when and from where. We matched this with records of exotic bee interceptions – sometimes on vessels, in machinery, or nesting on the outside of containers at ports.  We then collected maps and aerial pictures of all Australian ports, to produce models of potential bee habitats. To know what to put into the models, we had to find out how far bees can swarm (5km maximum for Asian honey bees and 2km for European honey bees). We also had to learn how long a vessel would need to be in port for bees to find a place to swarm to. If there isn’t enough time for scout bees to find a suitable site or a second set of bees to visit and ‘approve’ it, the colony will not swarm. That’s also assuming it has a queen and is a genuine swarm. This was not always possible to establish with confidence from the interception data.

Some ports with desert or industrial areas nearby ports were ruled out because they have no habitat suitable for honey bees that are within swarming range. This also ruled out ports where the berthing location is relatively distant from the coast.

Data were then assessed to establish what cargo came to the more ‘bee-hospitable’ ports, where the vessels arrived from and how long the voyage had been. Voyages of 300 days or longer were excluded on the basis that the bees wouldn’t survive a trip of that length.

The country of origin and type of cargo are also important considerations. Asian honey bees in particular like to nest in nooks in machinery which is subsequently shipped as cargo. These bees are less keen on – perhaps unsurprisingly – the barren hulls of empty vessels.

Asian honey bees

Asian honey bees

All this information and consideration have combined to produce a surveillance system that is likely to use resources effectively as possible and head off exotic and infected bees before they do any damage.

So, next time you’re enjoying a handful of almonds, spare a thought for the bees that pollinated it and for the data analysis that goes into keeping those bees healthy.


Mite as well call Australia home – the immigration success story of the redlegged earth mite

 

Picture bean plant damaged by redlegged earth mite

Redlegged earth mite damage on a faba bean

By Adam Harper

Whenever communities emigrate from far away, they do their best to adapt and succeed in their new environment. Some groups succeed better than others. One population of Australian immigrants has been particularly good at adapting – the rather aptly named Halotydeus destructor, more commonly known as the redlegged earth mite (RLEM for short).

These pinhead-sized pests emigrated from South Africa in the early part of last century. They’ve settled into their new home so well that they are now the most expensive pest for Australian grain growers, at least in southern Australia, causing losses of about $45 million a year. An infestation is a triple threat – it can kill seedlings, reduce productivity and quality of older plants and lower the seed yield in spring. Pesticide treatment for RLEM costs about $20.5 million a year.

Picture of redlegged earth mite

The redlegged earth mite has adapted well to Australian conditions

Not only are they the most expensive pest, they are also showing resistance to some insecticides. What’s more, they’re expanding their range into climatic regions in Australia different from the ones they occupied in their native South Africa. We don’t yet know how far they are capable of extending their range. All these factors mean RLEM could spell disaster for grain growers. Fortunately University of Melbourne PhD student Matthew Hill recently completed his research on this problem.

In collaboration with his supervisors at The University of Melbourne and CSIRO, Matt found how the distribution of RLEM had changed in Australia and what this may mean for grain growers. He used historical data collected on RLEM to show how it is expanding its distribution. His research will help growers not affected by RLEM understand the risks RLEM could pose.

RLEM was first found in WA in 1917. By the 1920s it had spread to Victoria. Its ability to use a wide range of host plants (grain crops, pasture species, clover, and many broad-leaved weeds) meant that it spread easily and quickly. Matthew compiled three data sets, showing the recorded distribution of RLEM in its native South Africa, its invasive range in Australia in the 1960s, and its present-day range in Australia. He used these to develop models describing the environmental conditions this mite experienced in each case. His models show that RLEM has expanded beyond the range predicted by its distribution in South Africa. Today, RLEM can be found in hotter and drier inland regions of Australia.

Several factors may have helped RLEM expand into inland Australia. First, changing farming practices have meant a greater uptake of minimum or no tillage systems, as well as an increase in area under irrigation in the eastern states. Second, climate changes such as a small increase in winter rainfall may have also helped. Third, and perhaps most worryingly, RLEM may have undergone an adaptive genetic shift.

That means Australian RLEM populations may have different physiological traits that make them more tolerant to these new dry and hot environments. When Matthew compared mites from Australia and South Africa, the Australian mites were able to move around at higher temperatures than those from South Africa. Australian mites also recover more quickly from damaging cold temperatures. This shows that RLEM has adapted well to its new Australian home. However, the question still remains; how far is it capable of expanding its distribution?

Matt Hill gathering samples of mites in southern NSW

Matt Hill sampling mites from roadside vegetation in agricultural areas of southern NSW

Dr Garry McDonald at the University of Melbourne has been developing models that predict the risk of a RLEM outbreak each season, based on the weather patterns in a region. RLEMs are generally active in the cool, wet part of the year. Eggs laid in spring go into a suspended growth state over summer to protect them from drying out. Identifying the weather conditions that trigger egg hatching as the autumn weather cools is a crucial part of Garry’s models. Discovering these triggers will help growers more accurately predict when to watch out for RLEM. To discover exactly what the triggers are, Garry compiled data from various research trials conducted by state departments, CSIRO and universities over the past 50 years. He is now using this data to tease out the climate triggers for egg hatching. So far he has found that rainfall, then temperature, act in concert to regulate egg development and hatching.

Interestingly, the triggers in the western region appear to be different from those in the southern-eastern region. This supports some of Matthew’s findings that suggest there may be un-documented differences between populations in the western and southern-eastern regions. Once these triggers are validated across a range of sites, Garry can determine if they will be useful for growers currently managing RLEM, and whether different management strategies should be developed for the two regions.

Current research is aimed at giving growers advance notice of the risk or severity of an RLEM outbreak. However, to confidently predict outbreak risk, the factors that influence RLEM at both the regional and field levels need to be combined.

The work was funded by The University of Melbourne, CSIRO and the Grains Research and Development Corporation, and conducted as part of the National Invertebrate Pest Initiative.

For further information please contact Dr Nancy Schellhorn NIPI Leader nancy.schellhorn@csiro.au


Getting crazy ants under control

By Emily Lehmann

One of the world’s most invasive pests – the yellow crazy ant – is anything but a small problem in Australia’s top end.

Called ‘crazy’ for their erratic and frantic movements, these unwelcome critters were accidentally introduced into Australia and are a threat to native wildlife including other ant species.

Their capacity for destruction has been most devastatingly felt on Christmas Island where crazy ant supercolonies have formed and killed more than 20 million red crabs.

That’s why we have been leading efforts to control and eradicate the pest ant species across northern Australia.

We're keeping these crazy critters in check.
We’re keeping these crazy critters in check.

As part of this mission, we’ve helped local company Yolngu Business Enterprises (YBE2) join the effort by developing a new service in crazy ant control.

Operating in north-east Arnhem Land, YBE2 is contracted to undertake rehabilitation work at Rio Tinto Alcan’s Gove Bauxite mine. The Gove area is ridden with yellow crazy ants.

Crazy ant infestations pose a significant challenge to mining and effective rehabilitation, as digging up the earth risks spreading them. The site needs to be continually monitored and treated to clear it of any colonies.

Through the Researchers in Business program, our ant ecologist Dr Ben Hoffmann worked with the YBE2 team on the ground to develop protocols to monitor the land, and identify and collect data to accurately map ant infestations using a GPS system.

About 200 hectares of infested area was mapped by YBE2 staff and underwent treatment. Since the project ended, a further 200 hectares has been mapped for treatment later this year.

The team gained valuable data on the impact the ants and treatments have on the local environment, which could be used to improve YBE2’s rehabilitation processes.

This research and development has given YBE2 the capacity to monitor and capture data from the land, secured them a contract to control crazy ants on the mine site and will potentially open up new business opportunities.

It’s also putting a halt to the spread of yellow crazy ants, helping to protect the Australian environment.

Read more about our work with small and medium-sized businesses or our biosecurity research.


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