Powerful new tool produces proteins in 3-D

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The amazing depth of atomic-scale 3D structural information now available via Aquaria.

By Andrew Warren

If you’re a regular at the gym or an early morning boot-camp fanatic, it’s possible that the first thing you picture when you think of protein is the powder you use to make your post-workout recovery shake.

But when our scientists discuss protein, they’re talking about the many thousands of molecules that act as the essential building blocks of life as we know it. Because proteins are so important to constructing life, researchers need a way to visualise the exact ways in which they fit together so that they can better understand the functions they play in our bodies.

With this in mind, a team of international programmers and bioinformaticians (think biology, computer science and maths mixed together) led by our very own Dr Seán O’Donoghue have created a new web-based tool named Aquaria that can create unprecedented 3-D representations of protein structures.

Aquaria is based on the Protein Data Bank, an online resource which houses more than 100,000 structures of proteins that contains a wealth of detail about the molecular processes of life. But Sean and his teams were conscious that few biologists were taking full advantage of the site. The Protein Data Bank is designed for and by biologists who are expert in structures; however for most biologists, its organisation can be confusing.

So, they created Aquaria to make this valuable information more accessible and easier to use for discovery purposes.

Freely and publicly accessible, Aquaria can help scientists like ecologists, nutritionists and agriculture, biosecurity and medical researchers to streamline their discovery process and gain new insight into protein structures.

Sean’s team added additional layers of information (like genetic differences) to the basic protein structure and made it accessible in a fast, easy-to-use interface that’s visualised in a fully 3D environment.

“We’ve added protein sequences that don’t yet have a structure, but are similar to something in the Protein Data Bank,” says Sean.

“That meant we first had to find all these similarities. We took over 500,000 protein sequences and compared every one of them with the 100,000 known protein structures, and that has given us around 46 million computer models.

ICAM-1 a

This image shows an example of one of the many spectacular molecular structures that science has determined at atomic resolution. This is the Aquaria view of Intercellular Adhesion Molecule 1, a protein that occurs on the surface of endothelial and immune system cells.

“For example, you can add Single Nucleotide Polymorphisms (SNPs) that cause protein changes, then visualise exactly where those changes occur in the protein structure. This provides valuable insight into why proteins sometimes completely change their function as a result of one small change in the DNA code.

“You can then ask interesting questions like ‘Does this set of SNPs cluster in 3D?’ and the answers to such questions can set new research directions.”

Aquaria was developed in collaboration with Dr Andrea Schafferhans from the Technical University of Munich, and is hosted with support of a grant from Amazon Web Services.

To learn more about Aquaria, you can take part in a special webinar scheduled for 9am Tuesday, 3 February (AEDST).


Viva Parkes-Vegas!

Viva Parkes-Vegas!

When stars collide: Elvis meets The Dish

By Glen Nagle

The town of Parkes, NSW – home of our famous Parkes Radio Telescope – has slipped on its Blue Suede Shoes.

In the second week of January each year, Parkes marks the birthday of Elvis Presley with a massive festival celebrating everything Elvis. It started over 20 years ago as a one-day get together of just a few hundred fans. In 2015, the festival has grown to cover a week of events, shows, parades and exhibits and over 15,000 visitors more than doubling the town’s population.

Along with one of the largest collections of Elvis memorabilia on permanent display at the Henry Parkes Visitor Centre (donated by Wiggles performer, Greg Page), the Parkes Elvis Festival is one of the town’s major icons.

The other great icon of course is the Dish – our very own Parkes radio telescope – so combining these two great icons into one stellar event was always going to be, quite literally, a match made in Heaven.

'Return to sender' took on a new meaning for the Dish last night.

‘Return to sender’ took on a new meaning for the Dish last night.

On Wednesday, 7th January an inaugural concert was held at the Dish to help mark the opening night of the Festival – and to celebrate what would have been the King’s 80th birthday the following day.

Starring popular Elvis tribute artist, Shakin’ Rick Mackaway, and backed by the fabulous rock band, The Wilsonics, the dinner and show night attracted hundreds of people from across the region and as far and wide as Canberra, Wollongong, Sydney, Adelaide and Melbourne.

Storm clouds threatened earlier in the day, but nothing was going to rain on this parade of love for the King and the Dish. The clouds almost magically bypassed the telescope and the brightest stars in heaven came out for an incredible night of songs, dancing and laughter against the impressive backdrop of Australia’s iconic radio telescope.

Shakin' Rick, rockin' in to the night.

Shakin’ Rick, rockin’ in to the night.

Continuing to observe the heavens throughout the show, the Dish even performed during the intermission with several large moves enthralling the audience and provoking  questions about both the science behind, and the history of, the Dish.

As the evening came to a close with a final encore performance and the audience departed, the number one question was, “Are you going to do it again next year?!”

Hmmm? Elvis and the Dish 2! Two icons, exciting audiences everywhere with music and astronomy.

The possibilities are endless. Watch this space.


Waking Up to New Horizons

Nicholas Kachel:

Our Canberra Deep Space Communication Complex just received a signal, sent at the speed of light, from 4.8 billion kilometres away. Who was it from? What was it about? Find out below…

Originally posted on Universe @ CSIRO:

I guess we all love to sleep in on a Sunday morning, maybe just snoozing under the doona, laying there for a few hours before getting up for a late brunch. Ah! Luxury.

On Sunday 7th December 2014, the New Horizons spacecraft, 5 billion kilometres away from the warmth of Earth, had little time to sleep in. It was ‘wake up’ day. The final awakening from hibernation for the next 2 years until well after its encounter with rapidly approaching dwarf planet, Pluto, set for the 14th July 2015.

Waiting back on Earth to hear the spacecraft’s morning ‘alarm’ go off was the giant 70 metre antenna dish at the CSIRO-managed, Canberra Deep Space Communication Complex – Deep Space Station 43 (DSS43).

Covering a distance of nearly 4.8 billion kilometres, New Horizons signal was travelling through space at the speed of light, telling home that it had…

View original 322 more words


World Soil Day: a chance to worship the ground we walk on

By Leon Braun

It’s downtrodden, underfoot and often under appreciated, yet so crucial to our existence that one of our scientists describes it as “the complex natural medium that supports all life on Earth”. It holds our crops, stores and purifies our water, and provides habitat for amazing creatures like the giant Gippsland earthworm, which can reach up to 3 m in length. But most of us only think about it when we’re trying to get it out of footy socks on laundry day.

It’s soil – and today (and all next year) it gets a bit of long-overdue recognition. December 5 is World Soil Day, and the United Nations has declared 2015 to be International Year of Soils. That’s a good thing, because globally, soils are under threat: from erosion, poor land management and urbanisation. At the same time, we need soils more than ever to produce the food we need for a growing population, to help manage climate change and to ensure ecosystem health.

Cracked soil at Chowilla, South Australia.

Cracked soil at Chowilla, South Australia.

Luckily for Australia’s soils, they have CSIRO looking out for them. We started researching soils in 1929, published the first soil map of Australia in 1944, and have been working hard ever since to improve our understanding and management of soils. We’re looking at ways to make agricultural soils more productive and to ensure they’re used sustainably, so future generations can continue to reap their bounty. And we’re working internationally too, so it’s not just Australia that benefits.

Our latest achievement (with allies from around the country) is the Soil and Landscape Grid of Australia, a digital map of Australia’s soils with two billion ‘pixels’ of about 90 by 90 metres, down to a depth of two metres below the surface. It contains information such as water holding capacity, nutrients and clay, and has applications for everyone from farmers deciding where to plant their crops to conservationists looking for habitats for endangered native species. You can read more about it here.

We’re also home to the Australian National Soil Archive, which has just gotten a new home in Canberra. The archive contains about 70,000 samples from almost 10,000 sites across Australia, the oldest dating back to 1924. Each sample represents a time capsule of the Australian landscape at the time it was collected, so we can measure things like caesium dispersal from the British nuclear tests at Maralinga and the impact of phosphate-based fertilisers on agricultural land. The archive is a vital national asset for soil researchers and industry, and has even been used by the Australian Federal Police to examine the potential of new forensic methods. Finally, data from the archive powers our first official app, SoilMapp, which puts information about Australian soils at your fingertips. This is incredibly useful, whether you’re growing canola on a farm in Western Australia or planning a major roads project in Victoria.

So as you go through your day today, eat your lunch, wipe your shoes, just remember: it takes 2000 years to form 10 centimetres of fertile soil suitable for growing our food, but just moments for that soil to blow away or get covered in a layer of asphalt. Something to think about next time you sit down to a meal – or do your laundry.


Sports science is getting gnarly, dude

The future of surfing? Credit: Seth de Roulet / Red Bull Content Pool

A laptop backpack: the future of surfing, or a sure-fire way to get dropped in on? Credit: Seth de Roulet / Red Bull Content Pool

A company more traditionally associated with energy drinks has been busy making waves in the world of sports science. Red Bull recently took two top professional surfers and a team of scientists to Mexico to test a range of new performance-enhancing technologies in one of the harshest arenas possible: an overhead, barreling wave breaking only a few feet over a bed of sand and rock.

We’re all for trying out new technologies in novel conditions, but this was a particularly impressive feat – the surfers were hooked up with all sorts of electronic equipment before paddling out into the lineup and doing their thing. At one point, surfer Jake Marshall even managed to ride some amazing waves with a laptop strapped to his back.

Surfing is a sport that is usually described in terms of instinct, intuition and unpredictability – so studies like this are providing scientists with amazing insights into areas of surfing that have previously held an almost mystical status. As well as hooking up the surfers with wi-fi headsets for instant feedback from coaches on land, and pressure-sensing feet ‘booties’ to analyse and optimise how they controlled their boards, the scientists were even able to measure surfer ‘stoke’ levels using a waterproof EEG.

You can watch the video here:

We’ve done a fair bit of sports science ourselves, too. Most recently, we partnered with Melbourne company Catapult Sports to deliver a new wireless athlete tracking device using our Wireless Ad-hoc System for Positioning (WASP) technology. The device, called ClearSky, gives coaches the ability to monitor their athletes more accurately in indoor and GPS-poor environments.

It works much like a GPS, but instead of using satellites in space, ClearSky uses fixed reference nodes that are located either within or just outside of a building. You can read more about the benefits of it here.

ClearSky can triangulate an athlete’s position to 20cm accuracy. Credit: Catapult Sports

ClearSky can triangulate an athlete’s position to 20cm accuracy. Credit: Catapult Sports

Of course, it doesn’t take a scientist to figure out how useful this technology could be on a cloudy day at a Melbourne AFL match when traditional GPS coverage is low. But it also has great applications for other (editor’s note: wussier) sports that are played undercover, like American football, basketball and soccer.

Indeed, the Catapult client list is a veritable who’s who of the international sporting world: the New York Giants (NFL), Orlando Magic (NBA), AC Milan (soccer), the Socceroos (soccer), Brisbane Broncos (rugby league), New Zealand Silver Ferns (basketball) and dozens of others. Many of these organisations are either already using ClearSky, or are preparing to do so.

Obviously, this is a winning technology that can be applied across a diverse range of sports. Who knows, maybe one day ClearSky will even be used to track the performance of professional surfers in a wave pool in the middle of Melbourne?

But in the meantime, some mysteries of surfing – like why the waves were always better yesterday, who stole my wax, and where surfing commentators get their t-shirts from – will forever remain unanswered.

Find out more about WASP here. 


Sensing your diagnosis on the spot

On the spot blood analysis provides immediate results to doctors and patients.

On the spot blood analysis provides immediate results to doctors and patients.

By Emily Lehmann

“We’ve got your test results back and…” *Gulp*

Does that feeling sound familiar? Having any kind of medical test can be nerve-wracking – not just because of the necessary probing – but for the fear of a potential diagnosis while you wait for the results.

Thanks to developments in point-of-care testing, the waiting game is over for certain crucial blood tests which can be performed and analysed on the spot using sensitive ‘biosensor’ devices. These are the types of instruments that doctors or diabetics use to measure blood sugar levels.

Test results can be provided immediately so that you can avoid the potentially unnecessary stress that often comes with waiting. There’s the opportunity to get onto treatment and the path back to better health faster – and it’s also much more efficient for healthcare providers.

We’ve been working with Universal Biosensors, a small-to-medium sized (SME) manufacturer who makes these devices locally, to help them improve their products and test for a broader range of diseases.

The project started through the Researchers in Business program, which brought on board our materials expert Dr Helmut Thissen. Helmut has since been working alongside the company to develop a new coating material that will make the biosensor test strips more sensitive.

This will allow the devices to be used for a range of new tests (immunoassays) not currently available in point-of-care testing and could lead to time and cost savings for already-stretched healthcare providers.

This exciting R&D project will enable Universal Biosensors to grow and export more high-end products internationally, while improving healthcare for patients around the globe.

Check out this video to learn more about the work we’re doing with this growing manufacturer:

Universal Biosensors was connected to our researchers through our SME Engagement Centre, which helps Aussie SMEs find the right science to overcome technical challenges and grow their business.

We’re continuing to work with the company to create superior products ready for the market, supported by Victorian State Government’s Technology Voucher Program.


To map and protect: how our 3D Zebedee technology is helping re-build New Zealand

By Emily Lehmann 

Situated on the Pacific Ring of Fire, our Kiwi neighbours in New Zealand (NZ) are rattled by up to 20,000 earthquakes a year.

While most of these are minor, some can be catastrophic – like the 6.3 magnitude earthquake that shook Christchurch in 2011. This earthquake devastatingly claimed 185 lives and the country’s second largest city continues to rebuild from it three years on.

Unfortunately, there’s likelihood of another large magnitude quake – which fall above six on the Richter scale – rocking the country one day again in future.

To prepare for this, NZ has very stringent building regulations; and the 25,000 earthquake prone buildings that the country is estimated to have are the focus of maintenance and restoration efforts to ensure their stability.

In an effort to earthquake proof at-risk buildings, NZ-based building restoration company Solutions By Zeal is using our 3D laser mapping technology to survey buildings to highlight structural areas in need of strengthening or restoration.

Our technology is helping protect buildings in New Zealand from earthquake damage .

Our technology is helping protect buildings in New Zealand from earthquake damage.

ZEB1 – the commercial product of our Zebedee technology – is a handheld technology that allows users to create 3D maps of a desired location by simply walking through it.

The company found that by using ZEB1 to create accurate floor plans, elevations and wall widths, that they can save a massive 50 to 80 per cent on their measurement costs.

They have also found the technology particularly useful for measuring old buildings where there are no architectural plans.

Earthquake-strengthening and restoration work is just one of the many applications that the technology is being used for – from security and forestry, to mapping manufacturing production lines.

Zebedee has mapped some of the world’s most iconic landmarks, including the Leaning Tower of Pisa, as well as national treasures like the Jenolan Caves near the Blue Mountains and Fort Lytton in Brisbane.

ZEB1 is licensed to GeoSLAM, a spinout company of 3D Laser Mapping and CSIRO. Read more about our 3D mapping technology.


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