By Glenn Marsh, CSIRO
The current outbreak of Ebola virus in West Africa is unprecedented in size, with nearly 4,800 confirmed or probable cases and more than 2,400 deaths. People have been infected in Guinea, Liberia, Sierra Leone, Nigeria and Senegal.
A second completely independent and significantly smaller Ebola virus outbreak has been detected in the Democratic Republic of the Congo.
Like all viruses, the Ebola virus has evolved since the outbreak began. So, how does this occur and how does it impact our attempts to contain the disease?
Ebolavirus and the closely related Marburgvirus genera belong to the Filoviridae family. Both of these genera contain viruses that may cause fatal haemorrhagic fevers.
The Ebola virus genus is made up of five virus species: Zaire ebolavirus (responsible for both of the current outbreaks), Sudan ebolavirus, Reston ebolavirus, Bundibugyo ebolavirus and Taï Forest ebolavirus.
In order to better understand the origin and transmission of the current outbreak in West Africa, researchers from the Broad Institute and Harvard University, in collaboration with the Sierra Leone Ministry of Health, sequenced 99 virus genomes from 78 patients.
The study, reported in Science, shows the outbreak resulted from a single introduction of virus into the human population and then ongoing human-to-human transmission. The scientists reported more than 300 unique changes within the virus causing the current West African outbreak, which differentiates this outbreak strain from previous strains.
Within the 99 genomes sequenced from this outbreak, researchers have recorded approximately 50 other changes to the virus as it spreads from person to person. Future work will investigate whether these differences are contributing to the severity of the current outbreak.
These 99 genome sequences have been promptly released to publicly available sequence databases such as Genbank, allowing scientists globally to investigate changes in these viruses. This is critical in assessing whether the current molecular diagnostic tests can detect these strains and whether experimental therapies can effectively treat the circulating strains.
How does Ebola evolve?
This is the first Ebola virus outbreak where scientists have sequenced viruses from a significant number of patients. Despite this, the Broad Institute/Harvard University study findings are not unexpected.
The Ebola virus genome is made up of RNA and the virus polymerase protein that does not have an error-correction mechanism. This is where it gets a little complicated, but bear with me.
As the virus replicates, it is expected that the virus genome will change. This natural change of virus genomes over time is why influenza virus vaccines must be updated annually and why HIV mutates to become resistant to antiretroviral drugs.
Changes are also expected when a virus crosses from one species to another. In the case of Ebola virus, bats are considered to be the natural host, referred to as the “reservoir host”. The virus in bats will have evolved over time to be an optimal sequence for bats.
Crossing over into another species, in this case people, puts pressure on the virus to evolve. This evolution can lead to “errors” or changes within the virus which may make the new host sicker.
Ebola viruses are known to rapidly evolve in new hosts, as we’ve seen in the adaptation of lab-based Ebola viruses to guinea pigs and mice. This adaptation occurred by passing a low-pathogenic virus from one animal to the next until the Ebola virus was able to induce a fatal disease. Only a small number of changes were required in both cases for this to occur.
While this kind of viral mutation is well known with other viruses, such as influenza virus, we are only truly appreciating the extent of it with the Ebola viruses.
What do the genetic changes mean?
The Broad Institute/Harvard University study reported that the number of changes in genome sequences from this current outbreak was two-fold higher than in previous outbreaks.
This could be due to the increased number of sequences obtained over a period of several months, and the fact that the virus has undergone many person-to-person passes in this time.
However, it will be important to determine if virus samples from early and late in the outbreak have differing ability to cause disease or transmit. The genetic changes may, for example, influence the level of infectious virus in bodily fluids, which would make the virus easier to spread.
Analysing this data will help us understand why this outbreak has spread so rapidly with devastating consequences and, importantly, how we can better contain and manage future outbreaks.
Glenn Marsh receives funding from Australian National Health and Medical Research Council and Rural Industries Research and Development Corporation.
By Michael Brünig, CSIRO
Australian’s museums, galleries and other cultural institutions must adopt more of a digital strategy with their collections if they are to remain relevant with audiences.
Only about a quarter of the collections held by the sector have been digitised so far and a study out today says more needs to be done to protect and preserve the material, and make it available to people online.
Challenges and Opportunities for Australia’s Galleries, Libraries, Archives and Museums is a joint study by CSIRO and the Smart Services CRC.
It notes that Australia’s galleries, libraries, archives and museums (the GLAM sector) represent our accumulated achievements and experiences, inspire creativity and provide a place for us to connect with our heritage.
They are also crucial to our economy with the GLAM sector estimated to have a revenue of about A$2.5 billion each year. That’s not only a lot of paintings and artifacts, but a lot of jobs as well.
But despite its size and scope, we found that digital innovation in the sector has been inconsistent and isolated. If these cultural institutions don’t increase their use of digital technologies and services, they risk losing their relevance.
So what changes do they need to make in order to thrive in the digital economy?
Opening doors and minds
With Australia’s rapid uptake of online and mobile platforms, people are now choosing to access and share information in very different ways.
It’s safe to say that the only constant in this space is change. Research suggests that expectations for more personalised, better and faster services and more well-designed experiences will continue to increase.
This is why our cultural institutions need to review the kind of visitor experience they are providing. We found only a few organisations had made fundamental changes to their operations that would allow them to place digital services at their core, rather than as an add-on activity.
This is in contrast to the dramatic changes we’ve seen when it comes to adopting digital technologies in our daily lives.
In order to be successful, digital experiences need to be an integrated and cohesive part of an institution’s offering.
Take what is happening at the National Museum of Australia. It’s now possible to take a tour of the museum via a telepresence-enabled robot.
This means school students – particularly those in rural and regional Australia – can explore exhibits virtually, without even leaving the classroom. Interestingly, we hear that this actually increases their desire to visit the museum in person.
Digital-savvy innovations such as this need to be at the fore of our institutions’ thinking if they want to engage with the community and break down barriers to participation.
Engaging with the public
To be successful in this new era, institutions need to meet people on their own (digital) terms. We can no longer expect visitors to queue at the turnstiles waiting for opening time. Organisations need to bring experiences to the user so that they can access them wherever and however they prefer.
Some of Australia’s cultural institutions are starting to get this.
The NSW State Library has appointed a Wikipedian-In-Residence to contribute expertise and train the public in publishing information online.
The National Library of Australia has attracted a large online user base with its online Trove service attracting almost 70,000 unique users each day.
The Powerhouse Museum has made parts of their photographic collections available on Flickr via Creative Commons licensing. This has caused a surge in the level of use and allowed the public to contribute information, adding value to the collection.
While these examples provide a lot of hope for the sector, the unfortunate reality is that they are few and far between. Most of Australia’s cultural institutions have not kept pace with this change and are missing the opportunity to better connect and actually increase their revenue.
Australia’s eight national, state and territory art organisations hold archives that, if laid out flat end-to-end, would span 629km. This is on top of a staggering 100,000 million artworks, books and audio-visual items in Australia.
But only a quarter of these items are digitised, with some of Australia’s collections still being managed through “old school” mechanisms such as log books and card indices.
Imagine if there was a fire at one of our great institutions? We would risk losing cultural and heritage material of significance. Parts of our history could be completely lost. Even without such a devastating event, if we don’t make our collections more accessible, in a sense they’ll be lost to many of us anyway.
As a country, not only do we need to get moving when it comes to digitising our collections, we also need to explore new and innovative ways to do this. Traditionally, digitisation has meant scanning flat documents, photographing objects or creating electronic versions of catalogue data.
But what if we could do so much more? Researchers are now focused on the next challenge: digitising objects and spaces in three dimensions.
Researchers from the University of Wollongong with support from the Smart Services CRC are focusing on capturing 3D models and the textures of surfaces using low-cost equipment such as a Kinect camera from an Xbox.
At CSIRO, we’ve even used our own handheld scanner Zebedee to map culturally and environmentally significant sites suchb as the Jenolan Caves, Melbourne’s Shrine of Remembrance and even a semi-submerged wreckage of the HMQS Gayundah.
We’re also creating high-quality 2D and 3D image libraries based on the National Biological Collections, letting us document biodiversity in the digital era.
Embracing the digital economy
While our study reveals that Australia’s cultural institutions are certainly at risk of becoming “digital dinosaurs”, it also demonstrated how those organisations that are embracing digital are reaping the benefits.
It provides recommendations for the GLAM industry in order for it to maximise its digital potential, including:
- shifting to open access models and greater collaboration with the public
- exploring new approaches to copyright management that stimulate creativity and support creators
- building on aggregation initiatives such as the Atlas of Living Australia
- standardising preservation of “born digital” material to avoid losing access to digital heritage
- exploiting the potential of Australia’s Academic and Research Network (AARNet) and the National Broadband Network (NBN) for collection and collaboration.
By adopting these recommendations and building on some innovative examples in the sector, Australia’s GLAM industry will be well placed to embrace digital, rather than be engulfed by it.
By 2050, 95% of seabirds will have plastic in their gut. That is just one finding from our national marine debris research project, the largest sample of marine debris data ever collected anywhere in the world.
The statistic is just one prediction of what’s in store if we don’t come to grips with the growing problem of rubbish at sea.
The issue of marine debris was recently brought to the world’s attention by the search for missing Malaysian Airlines flight MH370, which was reportedly hampered by objects that look similar to aircraft remains.
When you consider that six million tonnes of fishing gear is lost in the oceans each year, yet derelict fishing gear doesn’t even crack the top ten most common items found during coastal clean-ups, you begin to grasp the scale of the problem.
Plastic not so fantastic
The Australian government has a “threat abatement plan” which aims to save marine animals from being harmed by rubbish. We set out to inform this plan by developing a better understanding of where exactly this rubbish comes from and how exactly it harms wildlife.
We surveyed the entire Australian coast at 100 km intervals, with help from school groups and citizen scientists. We found that our shorelines are littered with debris. About three-quarters of it is plastic and, although there are some large items, 95% of the items are just a few centimetres across, or smaller.
In Australian waters, you can expect to find anything from a few thousand to more than 40,000 pieces of plastic per square kilometre.
Our rubbish can travel huge distances, leaving behind a trail of destruction. We found that almost half (43%) of seabirds have plastic in their gut, with young birds being particularly susceptible. If the increasing trend of plastic production increases and no effort is made to curb the amount that finds its way into the oceans, then by 2050 nearly every seabird (95%) will have ingested some plastic.
Globally, about one-third of marine turtles are estimated to have ingested debris, and this figure has steadily increased since plastic production began in the 1950s.
Many turtles are killed and maimed by abandoned fishing nets each year, along with other species including whales, dolphins, dugongs, fish, crabs and crocodiles. In the past few years, we estimate that between 5,000 and 15,000 turtles have been ensnared by these “ghost nets” in the Gulf of Carpentaria alone.
Reining in our rubbish
Ocean trash is so dispersed that it is not practical to collect it at sea. It might sound obvious, but the most effective way to reduce the harmful effects of sea debris is to prevent it from getting there in the first place. Our research shows that the vast majority of this rubbish comes from the land, with large concentrations near our cities, rather than from litter dropped at sea.
Tackling the problem will mean getting people to change their ways. Here are three ways we can do it: education, rewards, and punishment.
As part of this project we engaged directly with nearly 6,000 students, teachers and members of the public, as well as reaching more than two million Australians and a wide international audience, all with the aim of changing attitudes towards ocean health.
We also focused on building foundations for the next generation of marine researchers through a mentoring program in which eight international and four Australian students participated intensively in the project.
Additionally we developed an online national marine debris database which allows members of the public to contribute data about litter they find at their local beach. We also engaged with existing initiatives such as Clean Up Australia, Tangaroa Blue, the Surfrider Foundation and other groups that are cleaning up Australia’s beaches.
Together, all of these organisations and citizen scientists contribute to the improved understanding of the types, amounts and sources of debris we find on Australia’s coastline.
Meanwhile, we have tackled the specific issue of derelict fishing gear in the Gulf of Carpentaria- most of which comes from overseas sources- by identifying a “pinch point” in the gulf near the port of Weipa where ghost nets can be collected relatively easily and cheaply, before they reach high-density turtle areas.
Economists often emphasise the important role of incentives in modifying behaviour. South Australia’s container deposit legislation has helped to reduce the number of plastic drinks containers entering the environment by a factor of three, suggesting that incentive schemes can positively impact on levels of waste.
…and the stick
Regulation can be effective, but it needs to be targeted to have the best chance of success.
Using our coastal survey data and interviews with more than 40 coastal councils around Australia, we found evidence for two main drivers behind marine debris: general public behaviour, and illegal dumping of refuse.
Similarly, we found that local council outreach, which presumably affects user behaviour, and anti-dumping campaigns were both effective in reducing the debris found in coastal areas.
Making a difference
Littering isn’t the only cause of the problem. Even toothpaste and personal care products can have plastic microbeads in them which end up in the marine environment and are mistakenly eaten by a range of species. Awareness is a major issue here, but there are guides being developed to help consumers make informed choices about the products they use.
Working together, scientists, industry partners, coastal managers and citizen scientists can make significant strides to reduce sea debris impacts in coastal areas and in the marine environment.
Ultimately, however, the throwaway culture ingrained in our society needs to change if we are to tip the scales back in favour of the wildlife in our oceans.
Britta Denise Hardesty’s research was co-funded by Shell Australia’s National Social Investment Program and CSIRO’s Oceans and Atmosphere Flagship. TeachWild is an innovative national partnership between CSIRO, Earthwatch and Founding Partner Shell Australia to gather the data needed to bridge the information gap and tackle the global issue of marine debris.
Chris Wilcox’s research was co-funded by Shell Australia’s National Social Investment Program and CSIRO’s Oceans and Atmosphere Flagship. TeachWild is an innovative national partnership between CSIRO, Earthwatch and Founding Partner Shell Australia to gather the data needed to bridge the information gap and tackle the global issue of marine debris.
Australia is not what you’d call over-burdened with water, and yet we grow vast amounts of wheat and other grains. To continue to do so, we need to use the water we have as efficiently as possible. To do more with less.
Together with the Grains Research and Development Corporation, we started a multi-pronged project to increase the water use efficiency of grain production in Australia. And it worked so well that two of our scientists, James Hunt and John Kirkegaard, have just shared a Eureka Prize for it.
Their research has shown that it’s possible to increase the long term average winter crop yield, without increasing input costs. This would lift the average Australian wheat yield by around 25 per cent across all regions. They have also shown an increase in the long term average yields of winter grain crops, including barley and canola.
To make sure they covered all types of climate and soil conditions, they worked with 16 regional grower groups and research institutions across Australia, from the WA Sandplain to Tasmania.
They studied the many factors that influence water use efficiency and looked into the kinds of management practices that lead to more efficient use of water.
Instead of looking at a single crop or a single paddock, the research focussed on the capacity of the whole farm, and then assessed the farm’s potential for production and profitability, as well as the risks that might be associated with a change in the water use regime.
Some of the results returned big numbers. Improved summer fallow management, including weed management and stubble retention can lead to a 60 per cent increase in grain yield. The use of a legume crop after two consecutive grain crops can lead to increases in a range between 16 and 83 per cent.
The results also revealed that matching nitrogen supply to the soil type produce yield increases of up to 91 per cent.
In a world that needs to be fed, these are important findings. If we can do more to work to our conditions, it’s an all-round win.
So big congratulations to James and John, for making less more.
More than 2 200 years ago, legend has it, Archimedes got into a bath and had a lightbulb moment. He worked out that you could use the amount of water it displaces to measure the volume of an irregularly-shaped object. He was supposedly so excited about this that he jumped out, and ran, dripping wet and naked, down the street yelling ‘Eureka!’ (Ancient Greek for ‘I’ve found it’).
This story might not be entirely true, even though it deserves to be. But something that is unquestionably true is that several of our peeps had their very own Eureka moment, winning an Australian Museum Eureka Award, while fully clothed.
Here’s what they did to earn it.
WUE Initiative team (James Hunt, John Kirkegaard, CSIRO and Stuart Kearns, GRDC)
Department of Agriculture Landcare Eureka Prize for Sustainable Agriculture.
One of the biggest limiting factors for Australian agriculture is water. CSIRO and the Grains Research Development Corporation have been working on a five-year research project – the WUE Initiative – to increase water use efficiency in grain farming.
The results showed that it’s possible to a significantly improve water use efficiency in the southern and western growing regions, demonstrating an increase in the long term average winter crop yield without increasing input costs, and lifting average Australian wheat yield by around 25 per cent across all regions.
Two thirds of the yield gains from improved WUE come from pre-crop management.
Hendra Virus Research Team
Australian Infectious Diseases Research Centre Eureka Prize for Infectious Diseases Research
Well, what can we say? Horses and their owners all over Australia are very, very grateful for Equivac® HeV. This vaccine was the culmination of years of painstaking work by the Hendra Virus Research Team. It was also a novel approach to preventing a disease that kills humans – developing a vaccine for the horses that pass it on to humans, and who are also vulnerable to it. Hendra Virus has killed four out of the seven people it has infected – and with the help of this vaccine, they might be the last.
Science Photography Prize
Mark is a microscopist in CSIRO’s Bioimaging & Plant Development unit. He has developed a technique using a scanning electron microscope, to look deeper into plant cell tissues. His images speak for themselves.
We’d also like to congratulate the other CSIRO finalist at the Eureka’s last night:
The AIBL Research Team (CSIRO Lead Scientist Lance Macaulay)
University of New South Wales Eureka Prize for Excellence in Interdisciplinary Scientific Research
This – the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing – is a truly massive multidisciplinary undertaking. It’s a long-term study to discover which are the biomarkers, cognitive characteristics, and health and lifestyle factors that determine whether a person will develop symptomatic Alzheimer’s Disease. It has more than a thousand participants, and is now showing positive results both in detecting biomarkers and developing diagnostic tests.
And finally, a congratulations to the winner of the CSIRO Leadership in Science award, Professor Terence Speed from the Walter and Eliza Hall Institute of Medical Research.
At the Institute, the team that Terry leads uses computational mathematics to help researchers interpret massive amounts of experimental data.
Terry’s extraordinary leadership in the field extends well beyond the walls of the Institute. His techniques for improved DNA data analysis are distributed free-of-charge and used by thousands of researchers around the world. He is one of the world’s most cited scientists—not only in mathematics, but in computer science, biology and biochemistry.
Congratulations to all the finalists and winners of this year’s Eureka Prizes. Archimedes would be proud.
And boy, does this baby have back.
Australia’s new $120m marine research vessel, Investigator, is a thing of beauty. We’ve been watching Investigator get built step-by-step over in Singapore and have shared with you some of the key moments of its birth.
Investigator is now only hours away from arriving at its home port of Hobart. We’re hoping to welcome the big ship at 10am Tuesday morning with a flotilla.
You can follow all the action on Twitter using #RVInvestigator from around 8am tomorrow.
And for your dinner table conversation tonight, here are some sweet facts about the big ship:
- This will be Australia’s biggest ever marine research vessel.
- It has ten internal storeys.
- It has three diesel-electric engines, capable of generating enough electricity to power a small suburb.
- It can collect weather data 20km into the atmosphere and within a 150km radius from the ship.
- It can map the sea floor to any depth. Only 12 per cent of Australia’s ocean terrain has been mapped.
- It will take 50 days to fit the ship with super techy equipment once it arrives.
- There’s a gym onboard.
So why is any of this important? Australia’s oceans are estimated to contribute $42 billion annually to our economy, increasing to over $100 billion in ten years. And yet there’s so little we actually know about them – we know more about the moon than we do our own deepest oceans.
What may we learn from Investigator? We’ve never been able to collect fish and biological samples in our deep oceans before. So we’re likely to discover new species. We’ve never been able to map the ocean floor to any depth before, so now we can describe the ocean floor in Australian waters, which means we could find new resources. And the weather radar on the top of the ship, it will allow us to collect data at sea, for the first time.
This ship is the bee’s knees of marine research… and it will put Australia at the forefront of ocean research globally.
Oh, and before you ask about MH370…
We certainly have the necessary sophisticated sonar technologies to undertake the search, but let’s look at the size of the job at hand.
Let’s assume that we don’t need to refuel the ship or change the crew onboard and we can operate continuously. We would need to tow a piece of equipment called a side-scan sonar, which has a beam width of 500 metres at a speed of 2 knots, and the latest size of the search area was 60,000 square kilometres.
This means it would take Investigator 3.8 years to map the search area. That’s working 24hrs a day, 365 days a year.
Send us your best snap of Investigator as it comes into Hobart harbour for a chance to win a LEGO model of the ship AND a tour of Investigator for you and three friends later this year. Use #RVInvestigator when posting your image to Twitter or Facebook, or email it directly to us at firstname.lastname@example.org by 5pm Tuesday 9 September. Winners will be announced Wednesday at midday. Creative selfies with Investigator are highly encouraged.
Follow the action on Twitter with #RVInvestigator.
Media enquiries: Sarah Schofield on +61 3 6232 5197, +61 417 028 016 or email@example.com
As World Water Week draws to a close, we want to tell you about a water management project we’re involved with in the developing world.
The Koshi River basin covers some of the poorest parts of China, India and Nepal. The river stretches more than 700km, from China in the north, down through Nepal and across the Himalayas, and finally feeds into the Ganges River. Millions of people live in the region – many of them in flood-prone areas – and rely on the river and the fertile floodplain for their livelihoods.
We’re helping to manage the river better and improve the circumstances of the people living there.
The area is subject to floods, droughts landslides and flows of debris. Erosion also leads to heavy sedimentation, and rivers have been known to change their course.
The effects of climate change aren’t helping, either. Glaciers in the upper reaches of the Basin are melting, bringing water and sediments down to the plains. The people of the Koshi River Basin are in an increasingly vulnerable situation. The impacts of climate change are disturbing water supply and agricultural production. Adding more pressure, the demand for energy and food production is rising.
Raising the stakes even higher, the Koshi Basin also has areas of significant biodiversity, including a UNESCO World Heritage Site.
With funding from the Department of Foreign Affairs and Trade – Australian Aid, we’re working with partners including the International Centre for Integrated Mountain Development, the International Water Management Institute and eWater to develop an integrated modelling framework for the entire basin. We’re helping to develop water balance models that capture the relationship between climate (both rainfall and temperature) and stream-flow (and flood risk) in the Koshi River Basin.
We’re also working on characterising the seasonality and variability of stream flow, and, if possible, the expected trends in stream-flow. We’ll also develop techniques for understanding the likelihood of particular stream-flow estimates.
We aim to use the research and knowledge gained from these projects to allow a regionally coordinated approach to developing and managing the Koshi Basin’s water resources. The people of the area, and the environment, should both benefit.