A new Atlantis

Not this one. It's the Atlantis Hotel in the Bahamas.

Not this one. It’s the Atlantis Hotel in the Bahamas.

Wouldn’t it be good if there were a spare ecosystem we could try things out on before making a decision about how we use resources? Sadly, there’s no Earth II, but at least we have Atlantis.

No, not the fabled sunken city, but a marine ecosystem modelling tool that lets resource managers and coastal planners test drive their decisions before they commit to them in the real world.

We’ve developed a model that encompasses oceanography, chemistry and biology, and simulates ecological processes such as consumption, migration, predation and mortality.

The United Nations rated Atlantis as the best ecosystem model in the world for looking at alternative management strategies for fisheries, and regional versions are being used in management strategy evaluation for more than 30 ecosystems in a wide range of places.

Before models like Atlantis were available, decisions about resource use were made in isolation. We’d make our plans about things like fisheries or water quality based on what we knew about fisheries or water quality, rather than on their effects on the entire system. And decisions like these – that don’t look at the system as a whole, interdependent web – can often be on the wrong side of the law of unintended consequences.

So Beth Fulton got to work and created Atlantis.

It gathers information including ocean currents, and the way the food system works, all the way up from phytoplankton – tiny plants that exist in oceans and underpin the marine food chain. They build up through to seaweed and sea grasses, different kinds of fish, to marine mammals like dugongs, sharks and seabirds. The modelling incorporates the ways people interact with the oceans and the Earth, and includes coastal industries such as ports and fisheries, along with the social and economic pressures that drive resource use decisions.

A conceptual diagram of Atlantis

A conceptual diagram of Atlantis

Atlantis has its longest usage history in south-eastern Australia. This is a marine area of about 4 million square kilometres, and home to Australia’s largest fishery. It’s also – literally – a hot spot for ocean warming. There the ocean temperature is rising faster than anywhere else, and the Australian current that extends down the eastern seaboard to Victoria is pushing further south to Tasmania.

The carbon dioxide that’s sucked up into the ocean is making the water more acidic. The balance of marine species, and their range, is likely to alter as the climate warms. We’ll still have fish and still be eating them, but there will need to be some major decisions made about how best to manage fisheries.

One of the beauties of the Atlantis model is that it can be re-calibrated with new data as the effects of warming oceans begin to be felt. This will be vital to making far-reaching decisions that can no longer be based on the old certainties.

For more on our work in oceans, head to our website.


Business beams with new solar cells

The CSIRO research team

The sun provides a huge amount of energy for us and our work on solar cells is helping to capture it.

By Emily Lehmann

Blessed with beautiful beaches and plenty of sunshine, it’s easy to argue that Australia is the lucky country.

Of all our major cities, Perth takes the cake as the sunniest with an average 3200 hours of sunshine annually. Even well-seasoned Melbournians, who live in our least sunny city, get to enjoy an average of 2200 hours of sunshine a year.

So it might not be so hard to believe that Australia is home to the highest solar radiation per square metre of any continent. Not only does this reinforce why ‘slip, slop, slap’ should be every local’s mantra, this high degree of sunshine means that we have some of the best solar energy resources in the world.

Right now, only 1.1 per cent of our electrical energy comes from solar, but this could soon change as new technologies come to market.

Solar cells – like the flexible kind we’re printing – are fast becoming an important player in the renewable energy mix. Thin and lightweight, solar cells can be plastered to almost any surface to harness the sun’s energy and bring you sustainable power.

Solar energy is a business opportunity for Australian industry that’s projected to be worth about US$160 billion internationally by 2023.

Solar cell

A new skin for solar energy. Dyesol’s perovskite based cell is highly efficient.

We’ve been working with Dyesol, a local small-to-medium-sized enterprise (SME) to tap into this growing market and help them become the first to commercialise a new kind of solar cell based on perovskite material.

Dyesol develops cutting edge, clean energy generation solutions for consumers and hopes to be able to offer perovskite solar cells as a competitive alternative to the more widely-used thin-film photovoltaic (PV) cells.

Perovskite solar cells are an attractive option as the material cost is low and they are highly efficient to manufacture. Yet, at this stage it’s uncertain whether the product would have stability and durability over the long-term compared to other solar cells currently on the market.

Together, we’re working to investigate this limitation and improve the process for making perovskite solar cells so that Dyesol can produce a high-quality, sought after product.

We’ve undertaken two Department of Industry projects together, where our flexible electronics experts were brought into Dyesol’s business to help them identify the best way to take the technology forward.

Now, through a longer term partnership, we hope to help Dyesol capture the opportunities that this technology – and our great solar potential – offers Australia and turn their idea into a profitable and globally competitive business.

Want  to find the right expertise and tools to overcome technical challenges and grow your business? Connect with our SME Engagement Centre now.


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.


Cracking good science on egg allergens

scientists with egg

Pathum Dhanapala (Deakin) and Tim Doran (CSIRO) have made a breakthrough in their bid to create allergy-free eggs. Image: Mitch Bear

This article was written by Lucie Van den Berg and first appeared in the Herald Sun

What came first – the chicken with the switched off allergen gene, or the allergy-free egg? Our scientists have been working with Deakin University to develop an egg that doesn’t cause allergic reactions, and it’s all about changing the chicken.

In a world first, the team has also created synthetic versions of all four egg white proteins in the lab.

Our own Dr Tim Doran, and Deakin University’s Associate Professor Cenk Suphioglu, said it was one of the first critical steps towards developing allergy-free eggs to make life easier for people with allergies and improve the safety of medications made with eggs, such as flu vaccines.

There are 40 proteins in egg white, but four major ­allergens that cause the ­majority of reactions.

Almost 9 per cent of Victorian infants have an egg ­allergy at 12 months of age, which can lead to dermatitis, asthma, vomiting or gut irritation.

Dr Doran, who has a daughter with such an allergy, said they were used in such a wide range of foods and products, including cosmetics and medication.

Associate Professor Suphioglu said they created all four versions of egg white proteins in the lab and switched off the allergenic ­response in one protein, which is responsible for the majority of allergies.

“We have developed the synthetic versions of the allergens, which are more pure and standardised than the natural extract, which would be useful for both skin-prick testing and immunotherapy,” he said.

Immunotherapy aims to give people tiny amounts of the allergen in a controlled medical setting to induce ­desensitisation or tolerance.

The advantage of switching off the allergenic part of the egg white protein would be that the patient would be less likely to have a dangerous allergic reaction during treatment.

Together with PhD candidate Pathum Dhanapala, the scientist’s ultimate aim is to modify the proteins in egg whites to produce chickens that lay allergy-free eggs.

Professor Mimi Tang, from the Murdoch Childrens Research Institute and Royal Children’s Hospital, said the synthetic protein could one day be useful in immunotherapy trials for allergies, but it was very early to be talking about clinical applications of the research.

“I think the major barriers to overcome with this product for it to be useful is to determine if it can be used to modulate immune responses and induce desensitisation or tolerance,” Prof Tang said.

The research is published in the journal Molecular ­Immunology.


Another kind of Southern Lights

Noctiluca scintillans bllom with Hobart in the background

Noctiluca scintillans bloom with Hobart in the background

So there you are, trying to take some pictures of the Aurora Australis, and there’s too much light. When there shouldn’t be. Blue light.

If you jumped to the conclusion that this was an alien invasion, you probably like science fiction. You’d also be right. But the aliens are from Earth, appearing in a place they don’t belong. However, they’re happily making it their home. Jellyfish expert Lisa-Anne Gershwin was in the right place at the right time to identify what was happening.

Microscopic image of Noctiluca scintillans

Up close and personal with Noctiluca scintillans, commonly known as ‘sea sparkle’.

It’s a dinoflagellate called Noctiluca scintillans (which actually means ‘sparkling night’ in Latin). They’re phytoplankton – single-celled creatures, not strictly an animal, not exactly a plant. Seen separately, they look like tiny colourless lily-pads. But when the conditions are right, they look like something else altogether. Sometimes they bloom – countless tiny creatures, all massed together.

This was what the Aurora Australis photographers saw. All it takes is a good rain, which washes nutrients into the coastal water, combined with a gentle wind to concentrate these tiny creatures into a mass.

These blooms are almost certainly more common than we know, but most go unnoticed because they occur away from places where humans are likely to see them.

They make their own light, using a chemical reaction. Bioluminescence is found in almost every phylum, with different sorts of creatures having different colours of light, and using it for different purposes. It can be a startling effect to would-be predators, a warning to others, a call for help, or a way to recognise a potential mate. In this particular case it’s probably a startling effect, simply because the other explanations indicate greater cognitive function than is likely in single-celled creatures.

A kick gives a lightshow

A kick gives a lightshow

At South Arm in Tasmania, where a recent bloom occurred, the beach was blue for kilometres in both directions, glowing and flashing for most of the night. A band 1-2m wide along the beach was glowing quite brightly, and with each lapping wavelet it flashed a brilliant blue. The wave wash on the sand left behind a bed of twinkles.

Dipping your hand in it gave the skin an eerie Avatar-like appearance. A handful of sand thrown into the water elicited a brilliant flash of dots. And a piece of seaweed dipped into the water then flicked produced an amazing arc of light followed by an explosion of light when they hit the water. A kick of the water gave a similar arc and explosion, but even more brightly.

Sounds beautiful, doesn’t it? And it was, except here comes the ‘but’.

They’re an introduced species, penetrating the Southern Ocean, and they’re notorious for fish kills.

The majority of dinoflagellates are more plant-like than animal-like: they photosynthesise. Noctiluca doesn’t. Because it has no chloroplasts, it has to get food the old fashioned way, by eating something else. Mainly the ‘something else’ is other phytoplankton, but has been known to eat copepods (small crustaceans) and even occasionally tiny fish fry. Adjusted for scale, this is the equivalent of a human being eaten by a clam.

It’s been implicated in the decline of fisheries in other areas. Although it does not appear to be toxic itself, it accumulates and excretes high levels of ammonia into the surrounding area while it’s gorging itself on phytoplankton.

So, not all good. But it’s so beautiful, all we can say is…
WOW written in sand DSC_0148


Rotating sea cucumbers is kind of a big deal

Thelenota ananas (the Prickly Redfish)

Thelenota ananas (the Prickly Redfish)

By Chris Gerbing 

The poor old sea cucumber doesn’t fare very well in the oceanic food chain. They’re slow-moving, (cu)cumbersome creatures that are considered a delicacy by us humans… and they even cop the brunt of Nemo’s swim up comedy routine. But they’re also an important source of income for many coastal communities around the world, particularly in the South Pacific. This is why they need to be rotated (but we’ll get to that in a bit).

Sea cucumbers, when processed and dried, are turned into bêche-de-mer, which is considered a delicacy in Chinese culture. Demand for bêche-de-mer has increased markedly in the last few decades.

The ugly cousins of the star fish are part of the benthic family of marine organisms. These bottom dwelling creatures are slow and sluggish and literally cannot move quickly enough to save themselves. That combined with their easy accessibility and high value means that sea cucumber fisheries around the world are easily overfished and many fisheries have collapsed.

In Australia, the Queensland east coast bêche-de-mer fishery is perhaps Queensland’s oldest, with harvesting starting in the mid-nineteenth century and continuing up until the beginning of WWII. A revival of the fishery did not occur until the late 1980s. With this resurgence new management systems were introduced to protect the fishery. Since then various management strategies have been implemented to align with management acts and regulations that influence this fishery.

The modern Australian bêche-de-mer fishery provides to the livelihoods of fishers from coastal communities in northern Queensland. It is typical of many small scale fisheries in Queensland and Australia in that it is difficult to do a detailed stock assessment, and hence there have been few undertaken.

Queensland East Coast Beche-de-mer fishery management zones

Queensland East Coast Beche-de-mer fishery management zones

This is where the rotating sea cucumbers might start to make sense.

Management agencies and industry have attempted to mitigate risk to sea cucumber populations by introducing rotational fishing zones that limit the catch, spread the activity and improve the overall sustainability of the fishery. A management strategy that humans have used on land for centuries, rotational harvesting has been less commonly applied to marine resources.

This strategy has been applied in the Australian east coast fishery and seen the creation of 154 fishing zones that can be fished for single 15 day periods every three years. Essentially, the zones are rotated…but the effectiveness of this strategy needed testing.

Research published this week  by a CSIRO research team has shown that there are clear advantages to a spatial rotation harvest strategy. Using a quantitative modeling approach, the team showed that rotating the harvest zone improves the biological and economic performance of the fishery. They also found that lengthening the rotations out to six years can be helpful too.

The greatest benefit of rotational harvesting was measured for the slowest growing slugs in the sea, and also for the tastiest, who suffer under high fishing intensity.

Holothuria scabra (the sandfish)

Holothuria scabra (the sandfish)

This finding has applications for sea cucumber fisheries across Australian waters, as well as regional fisheries in South Pacific countries and south-east Asia. There are also global applications, particularly in other fisheries like abalone, geoduck clams and sea urchins that can be susceptible to overfishing.

There is potential for expansion of the Australian sea cucumber fishery in terms of both volume and value of products by spreading the fishery effort widely. We cannot say however if this will lead to sea cucumbers appearing on many local menus any time soon. But in the meantime, please keep your sea cucumbers rotating!


Extreme makeover for surgical implants

Implant modelsThis story is part of our spotlight series on #CSIROhealth. From apps to 3D printing, global epidemics to preventative wellbeing, we’re working in many ways, across many industries, to keep you healthy. More on our website

Plastic surgery is a booming business in Australia. In fact, we spend over $1 billion each year on surgical procedures and treatments, with liposuction, breast augmentation and rhinoplasty topping the list.

While many patients simply want to change their appearance or chase the fountain of youth, plastic surgery can make the biggest difference to people who are recovering from trauma, or who are suffering from other debilitating medical conditions.

For those that have been in a road or industrial accident, or who have had a cancerous tumour removed, reconstructive surgery can return function to affected body parts, boost confidence and put patients on the path to full recovery.

That’s why we’ve partnered with Australian medical devices company Anatomics to develop better surgical implants that can be used in these types of procedures. Last year we worked together to 3D print a titanium heel bone implant, saving cancer sufferer Len Chandler’s leg and making headlines around the world.

Now, we’ve helped Anatomics develop a new type of polyethylene (plastic) implant, specifically designed for repairing and augmenting bones in the head, skull and face.

These new implants can repair and augment bones in the head, skull and face.

These new implants can repair and augment bones in the head, skull and face.

This new implant is called PoreStar, named after the star shaped particle used in its manufacturing process, to create a porous structure. PoreStar is the first in a new class of implant material with bone like architecture. Unlike other implants, PoreStar has an open pore structure that resembles real bone.

“To create this implant we took a known material in polyethylene which has a history of being approved for use in the human body,” Dr Mike O’Shea from our biomedical manufacturing team says.

“We then took some inspiration from manufacturing processes that are used in different industries. We drew on our knowledge in structural fibres, moulding and biomedical scaffolds.”

Close-up of PoreStar structure

The star-like particles of PoreStar more closely resemble trabecular bone.

By bringing together all of this expertise, the team was able to develop a product that had higher porosity, giving it improved malleability and flexibility. This means that surgeons can actually shape and mould the implants in the operating theatre.

Anatomics CEO Andrew Batty says the implants are designed from 3D CT scans, meaning they are customised for individual patients, which can improve surgical outcomes.

“It’s rewarding being able to develop a product that has the potential to help so many people around the world.”

“What’s more, we’ve really been able to tap into the local industry. Thanks to this new product, we were able to set up a manufacturing facility for the implants right here in Melbourne.”

Building on this success, the team is now looking toward the opening of the Biomedical Materials Transformation Facility a $46 million initiative that will bring together CSIRO, Monash University and 20 industry partners to focus on taking biomedical products from the bench to prototype, and ultimately to market.

Learn more about our work in biomedical manufacturing on our website.


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