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By Stephen Luntz

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Disability Due to Poor Protein Regulation
Genetic Clues to Inflammatory Bowel Disease
Ancient Supernovae Detected
Tying the Knot in Light
Mental Medications Double
Street Trees Affect Native Birds
A Skink in Time
Estuaries Capture Carbon

Disability Due to Poor Protein Regulation

The cause of an intellectual disability that is common in the men of a particular family has been traced to a mutation. However, instead of affecting the coding function of a gene, the mutation affects protein regulation.

The unnamed malfunction causes severe learning disabilities, aggression and epilepsy. With many men in an extended family of 100 being affected, but no women, it is clear the mutation is recessive and lies on the X chromosome.

“We’ve been researching this specific disability for 10 years and it’s taken us the last 3 years to convince ourselves that the protein regulation is the key,” says Prof Jozef Gecz of the University of Adelaide’s School of Paediatrics and Reproductive Health.

Most harmful mutations that have been identified cause proteins to be malformed or not produced at all. However, in this case the protein is formed perfectly but regulatory failures cause either an excess or deficiency in its quantity. Strangely, either too much or too little seems to trigger similar symptoms, although Gecz says “there are likely to be some differences”.

Gecz says the discovery will make genetic testing possible, allowing women to see if they are carriers with a 50% chance that any male children would have the disability unless they use IVF.

Gecz says that “this is just the tip of the iceberg in understanding the impact of altered gene regulation on intellectual disability – the gene regulatory landscape is much bigger than the protein coding landscape. We have already found, and I would expect to continue finding, a number of other intellectual disabilities linked with protein regulation over the next 20 years or so.”

Treatment options are not clear, but Gecz says: “We found the problem in the cell is that it does not use energy wisely – the mitochondria are somehow affected. The brain is a very energy-hungry organ, so it is not surprising it is affected.

“The long-term target is to boost the way the cell produces energy and tip the energy back to normality.”

Genetic Clues to Inflammatory Bowel Disease

A study of 75,000 people has identified many of the genetic locations responsible for inflammatory bowel disease (IBD).

“We’ve found 71 new loci – or sections – within genes, which are associated with the major inflammatory bowel diseases Crohn’s and ulcerative colitis,” says A/Prof Graham Radford-Smith of the Queensland Institute of Medical Research. “This is a big step forward for our ability to identify which genes are involved in the diseases.”

IBD affects one in 200 Australians and causes pain, diarrhoea and weight loss. Distinguishing the different forms of IBD can be a challenge, so Radford-Smith hopes the genetic markers will assist in this process, helping both future researchers and clinicians.

Nevertheless, knowing the form of IBD is of only limited assistance in controlling the disease. “At this stage the genetic factors are difficult to influence,” says Radford-Smith. “There is a limited amount you can do environmentally.”

However, smoking is known to dramatically raise the risks of certain forms of IBD while actually being protective against ulcerative colitis. There has been some success in treating Crohn’s disease with pig whipworm, while tests of the blocking of certain receptors is showing some promise for other forms of IBD.

Radford-Smith says it is not really understood why the same genes will trigger different forms of IBD in different individuals, but notes: “In Western societies ulcerative colitis grew first as our diets changed, but then Crohn’s disease overtook it.

We’re seeing the same pattern in Asian populations as they industrialise.

“The genome is not changing that fast: what is changing is the interaction with the microbiome, or bacteria in the gut.”

The findings were made using a newly designed chip for a Genome-Wide Association Study, and were published in Nature.

Ancient Supernovae Detected

A search of old images has turned up two distant super-luminous supernovae, adding to our limited information about events that put ordinary supernovae in the shade.

“The light of these supernovae contains detailed information about the infancy of the universe at a time when some of the first stars are still condensing out of the hydrogen and helium formed by the Big Bang,” says Dr Jeffrey Cooke of the Swinburne Centre for Astrophysics and Supercomputing.

Super-luminous supernovae are 10–100 times brighter than ordinary supernovae and are a more formal classification of hypernovae, which include any explosion significantly brighter than ordinary supernovae. The events are so rare that, despite their brightness, Cooke says only around 15 have been observed.

Keen to add to this limited sample, Cooke re-examined images taken by Hawaii’s Keck Telescope of galaxies with redshifts greater than 2, making them more than 10 billion years old. “Our program uses a novel image-stacking technique, and monitors tens of thousands of infant galaxies targeted because they are rapidly forming stars, which increased our chances of detecting the supernovae,” says Cooke.

The larger the star, the shorter its lifespan. Since explosions this powerful need stars of masses over 150 times the Sun, they can only occur shortly after the star was formed.

Cooke’s search found evidence of two super-luminous supernovae at red shifts of 2.05 and 3.9, winning publication in Nature. The previous record was 2.36.

Super-luminous supernovae have three known subcategories. The most exotic involves the conversion of gamma rays to electron–positron pairs. Since this light is required to counterbalance gravity, the conversion of too many photons to matter leads to the star’s collapse.

It is believed that during these events, known as “pair instability supernovae”, much of the core is turned into nickel-56, a radioactive isotope that decays to cobalt-56, leaving a characteristic light curve. “One of the events we have detected is definitely a nickel-56 supernova,” Cooke says. “The other one is hard to tell as we only have a small amount of data.”

The formation of stars above 150 solar masses was once thought impossible, but Cooke says the maximum is now believed to be 250 solar masses, particularly in the early universe when the metal content of the star formation regions was lower.

“Finding the first generation of stars is the current Holy Grail for astronomers,” says Cooke. “The distances of our supernovae overlap with the distances where we expect to find the first stars. Our search technique provides the means to detect and study the deaths of the first generation of stars and understand the chemical enrichment process of the universe from the beginning.”

Tying the Knot in Light

It may come as a surprise to non-physicists that it is possible to tie knots in light, but Dr Anton Desyatnikov of the Australian National University’s Nonlinear Physics Centre has taken this fact one step further and found that under certain conditions knots will form spontaneously.

The creation of knots requires an optical vortex with a dark core in a laser beam called a doughnut mode. The light around the core is twisted, and the darkness forms a thread like a straight line.

“It’s not so much knots of light but knots of darkness in light,” says Desyatnikov. “With an elliptically twisted laser beam, modes can nucleate by themselves and form links, rings and knots.

“The idea of a knot of light is something scientists have been exploring for years, and a few groups have managed to achieve just that by precisely engineering laser beams with ‘artificial’ or ‘hand-made’ knots. But what we’ve been working on are models in which the knots spontaneously form on their own, just like those annoying knots that you always get in electrical cables.”

Under certain circumstances a spinning mode causes knots to form spontaneously, Desyatnikov revealed in Scientific Reports. However, he says it is impossible to predict exactly where.

“Knots in matter are topologically protected, so they’re difficult to untie unless you take the Gordian knot approach,” says Desyatnikov, referring to the legendary knot that Alexander the Great supposedly disposed of by slicing with a sword.

While light can pass through itself and become unknotted in the process, new knots form almost immediately somewhere else. The new location is as unpredictable as the original.

In optical light the modes are just 10 microns across, or one-tenth the width of a human hair, but Desyatnikov says that similar objects can be created on a much larger scale using radio waves.

Desyatnikov says his work is “fundamental science” without an immediate application in mind. Nevertheless he adds: “This is a circulation of power, and could help us understand how power behaves. These knots of light could be useful for quantum computing and nanophotonics.”

Mental Medications Double

Australian consumption of antidepressants has doubled between 2000 and 2011, while there has been a 58% increase in the use of psychotropic medications in general.

Prof Iain McGregor, the author of an Australian and New Zealand Journal of Psychiatry paper measuring the rise, fears that much of the use is inappropriate.

“These results are surprising, somewhat worrying, and raise the question of why so many of us need drugs to be able to cope with modern life,” says McGregor. “The heavy use of antidepressants may reflect their increasing use in conditions other than depression: everything from anxiety disorders to treating pain.”

Although comparable studies in the US and UK showed similar trends, McGregor thought the 2006 introduction of the Better Access program, which allowed general practitioners to prescribe cognitive behavioural therapy, might have slowed the increase in antidepressant consumption, but this has not been the case.

McGregor believes the rise is driven by a combination of factors, including heavy advertising of two expensive antidepressant medications by their producers, reduction in the stigma about seeking help for depression, and the application of certain drugs to a broader range of conditions.

“Untreated depression is a terrible thing, but there is a body of evidence that shows if you only have mild to moderate depression you do just as well taking a placebo as antidepressant medication,” says McGregor.

However, drug trials are usually conducted by pharmaceutical companies. Freedom of Information requests have found that trials producing no benefits for their products are seldom published.

Antipsychotic drugs that were once used exclusively for schizophrenia are now often prescribed for bipolar disorder, dementia and attention deficit hyperactivity disorder. McGregor is particularly concerned about the last case, as he says there are no studies on the long-term effects of controlling unruly behaviour in children in this manner, and there is some evidence that antipsychotic drugs accelerate brain shrinkage.

McGregor agrees there is evidence for the effectiveness of psychotropic drugs in specific cases, but argues that “anyone with emotional problems should consider diet, exercise, lifestyle changes and psychological therapy”.

Moreover, he points out that in many cases older drugs no longer under patent are at least as effective, but have been displaced by more heavily advertised versions that are much more expensive.

Street Trees Affect Native Birds

The choice of street trees can have a major impact on the presence of native birds in suburban environments, a study in Diversity and Distributions reveals. The authors hope it will lead to a rethink of the recent trend towards using introduced species in Canberra’s suburbs.

“We found that suburbs with more than 30% native street trees have 11% more bird species of all types than those with exotic street trees,” say Dr Karen Ikin of the Centre of Excellence for Environmental Decisions. “More birds were also found in nature reserves next to the suburbs. This shows that how we manage our urban areas has a significant effect on wildlife in surrounding locations.”

While Canberra took pride in the 1970s from its status as the “bush capital”, introduced species have become dominant in the newest suburbs, both because they allow more sunlight in winter and since the 2003 bushfires have been considered less flammable.

Ikin says she grouped all exotic species together, and has not investigated how fruit trees, which are often popular with both native and introduced birds, compare with the oaks and elms chosen for many new suburbs.

Ikin has previous demonstrated that large eucalypts support far more biodiversity than small ones in urban parks (AS, December 2012, p.46). While birds are the prime beneficiaries, Ikin’s colleague Prof David Lindenmayer notes that even tiger quolls have been observed using suburban Canberra’s streets as connection corridors where eucalypts have been planted.

“Research shows that people enjoy seeing and hearing birds around their home, work and recreational spaces, even if they are not interested in what the individual species are. So having charismatic and colourful ‘native favourites’ that ordinary people can recognise can improve their well-being,” Ikin says.

A Skink in Time

The discovery of a new species of skink may have come just in time to prevent its extinction from habitat loss.

The coastal plains skink (Ctenotus ora) has unwisely decided to make its home in the sand dunes between Dunsborough and Mandurah, south of Perth. The area is experiencing a population boom, with development threatening the skink’s territory.

However, since the publication in Zootaxa of evidence that C. ora is a different species from the widespread C. labillardieri, moves have been made to ensure the coastal plains skink’s survival.

“The discovery of a new species is a momentous occasion in science,” says Mr Geoffrey Kay of the Fenner School of Environment and Society at the Australian National University, one of the skink’s discoverers. “To find something as-yet undetected, so close to one of the country’s largest cities, demonstrates how much we’ve still got to discover.”

Only small numbers of the skink have been found, although Kay acknowledges it may have unrecognised habitat.

Specimens of C. ora had been collected and marked as examples of its larger cousin until Kay noted that not only does it only grow to 6 cm long, but the coastal plains skink has a smooth black back and a distinct line of dots on its flank while C. labillardieri’s back is mottled. Genetic analysis revealed substantial mitochondrial and nucleic DNA differences between the two species.

Kay says evidence is emerging that south-west WA’s extraordinary biodiversity (AS, October 2006, p.43) extends to its reptile populations, although often the differences are not visible from morphology alone. “In some cases, by using new genetic techniques and technology we’re finding what we thought was only one species is in fact nine or ten very different ones,” says Kay. He attributes this diversity to alternating periods of wet and arid conditions, leading to populations often becoming isolated “islands within the desert”.

While Kay is pleased the WA government is treating the coastal plains skink as potentially a priority one species for protection, he is concerned that other examples of the state’s rich flora and fauna may be lost before they are identified.

Estuaries Capture Carbon

Australian estuaries are doing their bit to halt global warming while those studied overseas are acting in the other direction, a Southern Cross University study has found.

While estuaries are frequently flushed with organic material picked up by rivers in flood, sea grasses and algae in the estuaries can fix a lot of carbon dioxide from the water column. Overseas research has found that estuaries release net CO2 into the atmosphere, but Dr Damien Maher of Southern Cross University’s Centre for Coastal Biogeochemistry Research says this has mostly been conducted in heavily degraded environments.

Maher estimated the behaviour of the Hastings River, Camden Haven and Wallis Lake estuaries on the NSW coast. While they are too close together to be representative of Australian conditions as a whole, the three have minimal climate variation, allowing a comparison of the effects of other factors.

“These estuaries were selected because they represent a natural gradient in estuarine types in terms of geomorphology, river flow and habitat coverage,” says Maher. “This enabled us to determine how these factors control the carbon cycle at the estuary scale.”

Maher acknowledges that “errors accumulate” in trying to estimate something so complex, so his team adopted two independent methods. “We measured the concentration of dissolved CO2 in the water. If this is less than under normal conditions, the estuary is absorbing carbon from the atmosphere. If it is greater it is releasing it.

“We also measured the carbon coming into the estuary from the catchment, how much was fixed by sea grasses, macroalgae and phytoplankton, and how much was exported to the ocean.” Maher was pleased with how well the figures matched.

More carbon was absorbed in summer than at other times, but Maher says the seasonal patterns varied between the three estuaries, and might differ again in years of heavy rainfall. “We couldn’t be sure these results apply for tropical estuaries where there is a huge amount of organic material during the wet season and very little during the dry,” he notes.

The estuaries absorbed 14–53 grams of carbon per square metre per year on average, while in two cases substantially more was flushed to the ocean. The estuaries absorbed enough carbon to offset a small village rather than the nearby cities of Port Macquarie and Newcastle.

Maher says excess nutrients in the water supply can lead to algal blooms that cut off sunlight, killing sea grasses and driving estuaries towards becoming net emitters.