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By Stephen Luntz

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Thylacines Lacked Diversity
The Tasmanian tiger showed a similar lack of diversity to its devilish cousin, a study of museum samples reveals.

Dr Brandon Menzies of the University of Melbourne’s School of Biology collected DNA from a random sample of thylacine remains from different museums. He found genetic conformity at least as great as that endangering the survival of the Tasmanian devil.

“Hence, Tasmanian tigers may have faced similar environmental problems to the devils, had they survived,” says Menzies, although he acknowledges that the face-biting behaviour that is spreading cancer among the devils (AS, October 2011, p.5) was not a thylacine trait.

“Due to the similarly poor genetic diversity of the animals, this new data suggests that the genetic health of the Tasmanian tiger and devil may have been affected by the geographic isolation of Tasmania from mainland Australia approximately 10–13,000 years ago,” Menzies says.

Half the samples Menzies used were taken before the introduction of the bounty on thylacines in 1888, indicating that the lack of genetic diversity predates culling.

With 2000 bounties paid, the thylacine does not appear to have been particularly rare for a top predator of its size, but Menzies says that an estimated 2500 adults is not enough to maintain genetic diversity over a long period of time.

Given the coincidence in Tasmania’s two largest predators, Menzies is keen to investigate other local mammals. “Lots of resources – both government and private sector – are going to preserve the devil, but we should be looking at all the mammals in Tasmania,” he says.

“I’ve seen unpublished evidence suggesting the spotted-tailed quoll is less genetically diverse than the population on the mainland, based on mitochondrial DNA. We need to do sequencing to see what state they are in right now.”

DNA from mainland thylacines is too rare to provide a useful comparison at this point, and Menzies says that much effort is required to remove contamination from such old samples.

Arthritis Pain Is Outside the Joints
Much of the pain of arthritis is a result of inflammation of the muscles surrounding joints rather than in the joint itself, researchers from four Victorian institutions have found. Further investigation may open up paths to better treatment of arthritis, particularly in the lower limbs.

“Arthritis of the knee mostly affects the knee joint, and so far people have focused there,” says Dr Itamar Levinger of Victoria University’s Institute for Sport, Exercise and Active Living. “However, they have ignored that the knee is not an independent organ.”

Levinger was part of a team that combined people with different forms of expertise studying arthritis in knees. “We realised that pain would make people change their gait and the way they support the knee, and this would affect the muscles,” he says.

Samples of muscle from the quadriceps were taken during replacement knee surgery, and these also showed evidence of inflammation, the team reported in Arthritis and Rheumatism. “There are a number of markers of inflammation, and we need to investigate whether the profile of the muscle inflammation is the same of that in the knee,” Levinger says. If these are different, Levinger thinks that different drugs will be required to treat the two sorts of inflammation.

A program has begun to compare muscle function in people with and without arthritis of the knee as a stepping stone to learning about muscle inflammation. “With the better understanding of changes in muscle function coming out of this study we will be able to target exercise and drug therapy more effectively to keep this population active and increase their quality of life for longer,” Levinger says.

Further research is also required to see whether muscles around other arthritic joints are also affected. Levinger acknowledges that the effect on surrounding muscles is likely to be smaller in joints that do not carry as much weight as the knee.

Dementia-Fighting Molecule Revealed
A mechanism by which exercise fights dementia has been revealed, offering a path by which those unwilling or unable to get on the treadmill might keep their brains healthy.

“Ageing slows the production of new nerve cells, reducing the brain’s ability to form new memories,” says Dr Jana Vukovic of the Queensland Brain Institute. “But our research shows for the first time that the brain cells usually responsible for mediating immunity – microglia – have an inhibitory effect on memory during ageing. Furthermore, we have shown that a molecule produced by nerve cells – fractalkine – can reverse this process and stimulate stem cells to produce new neurons.”

Vukovic demonstrated that when the production of fractalkine was blocked while mice were exercising, they did not receive the mental benefits normally observed in mice encouraged to keep fit. The addition of fractalkine to cells in culture also increased the production of neuron precursors. The research was published in The Journal of Neuroscience.

Fractalkine plays an important role in the biochemistry of the human brain, and its production decreases with age. It also has roles in other parts of the body, such as the gut, and Vukovic says that the effects of the increased production of fractalkine due to exercise appear to be positive in every case. However, Vukovic says “it is a very large molecule, so getting it to cross the blood–brain barrier if it was given intravenously would be hard”.

Identifying ways to increase fractalkine production, other than through exercise, may also prove difficult but Vukovic says it may be possible to identify molecules that trigger the fractalkine pathway to produce more brain cells.

Vukovic is not sure of the reasons why microglia become more likely to suppress neurone production with age, but she says it is clear that they become increasingly pro-inflammatory with time.

Bass Strait’s Signature
Water from Bass Strait has a unique signature that can be identified using deep-diving ocean gliders even after it has merged with the East Australian Current.

Bass Strait is quite shallow, so the amount of water flowing through it is small compared with the major ocean currents. Dr Mark Baird of CSIRO’s Wealth from Oceans Flagship says that a volume equivalent to 16 Olympic swimming pools discharges into the Tasman Sea each second before being swept north and encountering the East Australian Current near Jervis Bay in southern NSW.

The Bass Strait water is relatively cool as a result of evaporation, so it sinks to a depth of 400–800 metres north-east of Flinders Island in what is known as the Bass Strait Cascade.

The water retains a distinctive temperature and salinity profile for as long as 5 years, and this can be measured to great accuracy by the ocean gliders deployed by CSIRO.

“We have seen for the first time a 200 metre-tall, 40 km-wide disc formed from water that originated in Bass Strait that amazingly remains undiluted as it travels hundreds of kilometres,” Baird says.

Baird explains that heat flow by conduction within water is slow, and that “waters of different densities tend not to mix. Instead they lie on top of each other.” The waters rotate around like air pockets around a low-pressure cell once they reach the open ocean.

In winter the temperature gap between Bass Strait and the wider ocean is greatest, so there are annual pulses of water that maintain their character thereafter.

The exploration of the water’s path, along with new data for the Tasman Leakage (see The Pacific Ocean Leaks, below), help to explain why Bass Strait water has been detected as far away as Albany in Western Australia.

“We like to know where all the water goes,” says Baird before adding that there is a particular reason to explore the Bass Strait water further. Exposure to the atmosphere means that this water is rich in oxygen and carbon dioxide, and carries both of these to the depths.

As well as playing a minor role in removing atmospheric carbon, it has been proposed that the oxygen in these waters may allow pelagic fish to forage at depths that would be impossible elsewhere. Baird says this has yet to be confirmed by direct observations.

The research was published in Geophysical Research Letters.

The Pacific Ocean Leaks
The largely unstudied Tasman Leakage has been investigated to reveal the volume of water flowing from the Pacific to the Indian Ocean south of Tasmania and the way in which this water makes the journey.

A vast current of water known as the Antarctic Circumpolar Current (ACC) flows eastward at southern latitudes. However, Dr Erik van Sebille of the University of NSW Climate Change Research Centre says that a gap of 300–400 km exists between Tasmania and the ACC, through which the Tasman Leakage flows.

In one sense the leakage is vast, averaging 4 sverdrups. “One sverdrup is one million cubic metres per second,” van Sebille explains. “The outflow of all the rivers in the world adds up to about 1 sverdrup.”

However, by oceanic standards the Tasman Leakage is small. The flow from the Pacific to the Indian Ocean through the Indonesian Throughflow is three or four times as large.

The movement is part of the global thermohaline system. Water flows from the Atlantic Ocean around the planet at great depth, most of it eventually rising in the Pacific. It then returns through the Indonesian Archipelago and south of Tasmania, before exiting the Indian Ocean in a similar gap between South Africa and the ACC.

As important as these flows are to the global ocean, little has been known about them. “It’s much easier to track large eddies as you can see them from satellites,” van Sebille says. “So people hoped this was how most of the water flowed.”

Unfortunately, van Sibelle’s high resolution ocean circulation model has found that more than half the flow occurs either in far smaller swirls or slow background currents.

“The East Australian Current sheds some very large eddies, but these break up into smaller and smaller filaments,” van Sebille says. He has published these findings in Geophysical Research Letters.

The size of the flow varies significantly, and in some years falls almost to zero. Van Sebille says that peak flows occur when the winds associated with the ACC move south, leaving a larger bottleneck for the leakage to traverse. The relationship of these winds to factors such as the El Niño Southern Oscillation remains poorly understood.

Warming Alters Ocean Salinity
Global warming is intensifying patterns of ocean salinity faster than climate models predict, with serious implications for the climate of coastal cities.

Surface salinity away from rivers depends on the local balance of rainfall and evaporation. Dr Susan Wijffels of CSIRO says that most saline oceans lie at subtropical latitudes “where we get deserts on land”, while the equatorial belt and high polar regions are fresher. “Warming of the Earth’s surface and lower atmosphere is expected to strengthen the water cycle, which is largely driven by the ability of warmer air to hold and redistribute more moisture,” explains Dr Richard Matear of CSIRO’s Wealth from Oceans Flagship.

Previous research has confirmed a qualitative shift matching expectations, but has not been able to compare the extent with expectations.

Wijffels says that she, Matear and American colleagues have used data from Argo floats and historical measurements from research vessels to show there has been a 4% intensification in this trend over the past 50 years. “Previously people used a ‘kitchen sink approach’ amalgamating all the data. We’ve been able to use the Argo floats to provide detailed information about the salinity in particular places at particular seasons, and then conducted statistical analysis comparing this with the more patchy samples from earlier times.”

These findings were compared to global models coupling changes in the atmosphere and ocean. They found that change is happening twice as fast as most models predict given measured planetary warming.

If this trend continues, a warming of 3°C will result in a 24% acceleration in the water cycle. While local variations will complicate the picture, Wijffels says this means that in areas where rainfall exceeds evaporation the gap will increase by almost one-quarter, with the reverse also the case.

“On land there is some variation caused by local recycling, but for most coastal cities the ocean conditions should predominate,” Wijffels says.

The conclusion is ominous for Australian cities. Wijffels notes that rainfall may not change dramatically in drier regions, but “an increase in evaporation can increase stress during droughts”.

Wijffels admits she does not know why the models are underestimating water cycle changes, but says that modelling of cloud radiation feedback is poorly constrained.

She says it is unclear whether limitations in the water cycle modelling might be affecting estimates of the sensitivity of temperature to carbon dioxide increases.

Blood Test Like Magic
The inspiration for a potentially life-saving blood test came from watching the second Harry Potter film, supporting the inventor’s claim that scientists should look for inspiration beyond their peers.

Current blood tests either require training to interpret them or facilities that aren’t available in much of the developing world. Consequently, in emergencies people may be given the wrong type of blood in a transfusion. The situation is even more serious when it comes to disease diagnosis.

A/Prof Wei Shen of Monash University’s Faculty of Engineering was looking for an easy-to-read way to report the results of multiple tests when he saw Harry Potter and the Chamber of Secrets. Although he admits he is not a fan of the books, Shen was struck by the scene where Harry writes a question in a diary and sees the answer appear on the page. “The artist’s vision showed us that non-conventional mechanisms for reporting results using paper-based sensors should be explored,” Shen says.

He coated paper with a hydrophobic reagent, but left areas in the shape of the letters of blood types with a plus and minus to indicate the blood’s rhesus status. Each of these areas were coated with appropriate antibodies so that they would change colour in the presence of blood of the appropriate type. “We’ve compared 99 samples with mainstream blood typing instruments, and we have had no disagreement,” Shen says.

The idea has been patented and is being developed with Australian company Haemokinesis, with the test results published in Angewandte Chemie.

Shen says that for practical purposes the antibodies need to be proven stable, but “the literature contains examples of antibodies that last up to 6 months without freezing”. Tests for diseases such as HIV will make the idea even more valuable.

“We need to train students to have an open mind,” Shen says. “From the scientific literature they can learn ways to make tests more reliable and more efficient, but not how to make them more user-friendly.

“When we talk of the literature we need to think of more than just the scientific literature. In the past we have cited Alice in Wonderland in one of our papers.”

Although others have suggested it, so far Shen has not written to J.K. Rowling or the filmmaker to reveal the value of their ideas.

Laser Helps Kenya Inherit the Wind
Australian technology is being put to use in possibly the world’s most exciting renewable energy location, contributing to the transformation of millions of lives.

Lake Turkana in northern Kenya is an extraordinary, perhaps unique, location from the perspective of wind power. In Australia a site with average winds of 6 m/s is considered excellent for wind harvesting, but at Lake Turkana typical wind speeds are over 11 m/s.

“Energy density is a function of the cube of the wind speed,” notes Mr John Sutton of the CRC for Contamination Assessment and Remediation of the Environment (CRCCARE). Consequently there is eight times as much energy in wind that is twice as fast.

Indeed the wind is so powerful at Lake Turkana that the $775 million Lake Turkana Wind Power Project will actually avoid sites with the highest average wind speed for fear of wearing out the turbines and gearboxes too quickly. “The German Wind Energy Association, who assessed the site, said they had never seen anything like it,” Sutton says.

A few degrees from the Equator, Lake Turkana gets the northern trade winds in one season and the southern equivalent in the other. The jet stream comes unusually close to the surface of the Earth here, and the valley’s shape acts like a funnel.

The project will install 365 turbines, with a combined capacity of 300 MW. Kenya’s total generating capacity is a little over 1 GW but demand is rising rapidly.

While Lake Turkana offers an extraordinary resource, capturing it poses challenges. The area is so remote that the project will require the installation not only of a high voltage powerline but also a road capable of transporting the poles. Consequently it is essential to place each turbine to maximise the available energy.

CRCCARE has developed Doppler lidar (Light Detection and Ranging) technology, which bounces laser beams off dust particles in the atmosphere to detect the speed and direction at which they are travelling. Originally used to measure wind shear around airports, CRCCARE saw opportunities for pollution control. “For example, it helps large miners to dramatically reduce the cost of monitoring and controlling dust pollution from mining, stockpiling and ship-loading activities,” Sutton says.

Others have attempted to use lidar to measure the wind around wind farms, but Sutton says the version CRCCARE is using is far more powerful. “Some lidars are powerful but at frequencies that damage the eye, so you can’t use them. Others could only measure vertically, or for distances of about 6 km under normal conditions,” he says.

“We operate at 700 Hz, allowing us to bring in next-generation algorithms that enable us to create 3D vectors with accuracy of 0.3–0.4 m/s and a few degrees over distances of 20 km for full hemispheric scans.”

Lake Turkana will be the first wind farm to benefit from CRCCARE’s technology, but Sutton says that as well as identifying the best turbine locations it can be used to validate the models currently used, which he says “contains a degree of witchcraft”. This is important in getting wind farms approved, as uncertainties in wind conditions can make it difficult for developers to gain financing.

Canadian company Catch The Wind is exploring the use of lidar to predict changes in wind direction, allowing turbines to be tilted for maximum benefit. Sutton says: “Our system is complementary with that. They’re looking at areas for two to four windmills, whereas we have a bigger picture. Our system could provide warning not just to the wind farm operator but to the grid of when there will be a drop in the wind so there is time to bring back-up systems online.”

Biofuel Bonanza
The native Australian legume Pongamia pinnata could be the basis for a new industry in Queensland’s north, replacing fossil fuels and breaking the poverty cycle in indigenous communities.

Pongamia seeds are 40% oil, and the crop is so bountiful that Peter Gresshoff of the University of Queensland’s Centre of Excellence for Integrative Legume Research (CILR) estimates that a hectare can produce 3–5 tonnes of biofuel per year.

Test plantings have been conducted at Roma and Hope Vale, both of which have plenty of cleared land suitable for expansion. CILR is seeking funding to plant 3000 hectares at Hope Vale.

Numerous attempts have been made to establish agricultural industries in or near Hope Vale, but Gresshoff says these have foundered because “it’s too far from markets”. While transport costs have made commercial agriculture unviable, the mining industry in the far north has a huge need for diesel, which currently has to be brought in at considerable expense.

Pongamia offers a solution utilising the rich, red soils of Hope Vale, and would provide work in a community with high levels of unemployment. “It’s a native species that has already grown in the area for thousands of years,” Gresshoff says.

Besides the large crop, Pongamia offers many advantages over other sources of biofuel. As a legume it fixes its own nitrogen, avoiding the need for expensive fertilisers that can pollute local waterways. It is also very long-lasting, only needing replanting every 35 years because the tree becomes too large for the modified olive tree-shakers used to harvest the crop.

“This is very important because most plants are very susceptible to stress during the seedling stage,” Gresshoff says. Watering may be required in the early years, but once established Pongamia is highly resistant to drought and flooding, and can survive five times as much salt as soybeans.

While 4–5 years are required to produce commercial quantities of seeds, limited flowering occurs in the first year. “This is very exciting for us because it means we can cross-breed and quickly see if desirable traits have been inherited,” Gresshoff says.

With one million square kilometres of Pongamia-suitable land in Australia, most of it not considered viable for food crops, the tree could easily meet current demand for 20 billion litres of diesel.

Moreover, Gresshoff says that the invention of a process to produce jet fuel from plant oil has generated interest from airlines in Darwin and Cairns as refuelling sites.