Commonwealth Science and Industrial Research Organisation

Canberra, Australia

Commonwealth Science and Industrial Research Organisation

Canberra, Australia

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Bottje W.,University of Arkansas | Kong B.-W.,University of Arkansas | Reverter A.,Commonwealth Science and Industrial Research Organisation | Waardenberg A.J.,Commonwealth Science and Industrial Research Organisation | And 3 more authors.
BMC Systems Biology | Year: 2017

Background: We contrast the pectoralis muscle transcriptomes of broilers selected from within a single genetic line expressing divergent feed efficiency (FE) in an effort to improve our understanding of the mechanistic basis of FE. Results: Application of a virtual muscle model to gene expression data pointed to a coordinated reduction in slow twitch muscle isoforms of the contractile apparatus (MYH15, TPM3, MYOZ2, TNNI1, MYL2, MYOM3, CSRP3, TNNT2), consistent with diminishment in associated slow machinery (myoglobin and phospholamban) in the high FE animals. These data are in line with the repeated transition from red slow to white fast muscle fibres observed in agricultural species selected on mass and FE. Surprisingly, we found that the expression of 699 genes encoding the broiler mitoproteome is modestly-but significantly-biased towards the high FE group, suggesting a slightly elevated mitochondrial content. This is contrary to expectation based on the slow muscle isoform data and theoretical physiological capacity arguments. Reassuringly, the extreme 40 most DE genes can successfully cluster the 12 individuals into the appropriate FE treatment group. Functional groups contained in this DE gene list include metabolic proteins (including opposing patterns of CA3 and CA4), mitochondrial proteins (CKMT1A), oxidative status (SEPP1, HIG2A) and cholesterol homeostasis (APOA1, INSIG1). We applied a differential network method (Regulatory Impact Factors) whose aim is to use patterns of differential co-expression to detect regulatory molecules transcriptionally rewired between the groups. This analysis clearly points to alterations in progesterone signalling (via the receptor PGR) as the major driver. We show the progesterone receptor localises to the mitochondria in a quail muscle cell line. Conclusions: Progesterone is sometimes used in the cattle industry in exogenous hormone mixes that lead to a ~20% increase in FE. Because the progesterone receptor can localise to avian mitochondria, our data continue to point to muscle mitochondrial metabolism as an important component of the phenotypic expression of variation in broiler FE. © 2017 The Author(s).


Johnson F.,Sydney Water | White C.J.,University of Tasmania | van Dijk A.,Australian National University | Ekstrom M.,Commonwealth Science and Industrial Research Organisation | And 6 more authors.
Climatic Change | Year: 2016

Floods are caused by a number of interacting factors, making it remarkably difficult to explain changes in flood hazard. This paper reviews the current understanding of historical trends and variability in flood hazard across Australia. Links between flood and rainfall trends cannot be made due to the influence of climate processes over a number of spatial and temporal scales as well as landscape changes that affect the catchment response. There are also still considerable uncertainties in future rainfall projections, particularly for sub-daily extreme rainfall events. This is in addition to the inherent uncertainty in hydrological modelling such as antecedent conditions and feedback mechanisms. Research questions are posed based on the current state of knowledge. These include a need for high-resolution climate modelling studies and efforts in compiling and analysing databases of sub-daily rainfall and flood records. Finally there is a need to develop modelling frameworks that can deal with the interaction between climate processes at different spatio-temporal scales, so that historical flood trends can be better explained and future flood behaviour understood. © 2016 Springer Science+Business Media Dordrecht


News Article | April 15, 2016
Site: www.spie.org

The first detection of a gravitational wave depended on large surfaces with excellent flatness, combined with low microroughness and the ability to mitigate environmental noise. Albert Einstein's general theory of relativity predicted that massive, accelerating bodies in deep space, such as supernovae or orbiting black holes, emit huge amounts of energy that radiate throughout the universe as gravitational waves. Although these "ripples in spacetime" may travel billions of light years, Einstein never thought the technology would exist that would allow for their detection on Earth. But a century later, the technology does exist at the Laser Interferometer Gravitational-Wave Observatory (LIGO). Measurements from two interferometers, 3000km apart in Louisiana and Washington State, have provided the first direct evidence of Einstein's theory by recording gravitational-wave signal GW150914, determined to be produced by two black holes coalescing 1.2 billion light years away. At the heart of the discovery lies fused silica optics with figure quality and surface smoothness refined to enable measurement of these incredibly small perturbations. Their design is an important part of LIGO's story. The black hole coalescence was detected as an upward-sweeping 'chirp' from 35 to 300Hz, which falls in the detectors' mid-frequency range that is plagued by noise from the optics. Left and right images show data from Hanford and Livingston observatories. Click to enlarge. (Caltech/MIT/LIGO Laboratory) "Most impressive are [the optics'] size combined with surface figure, coating uniformity, monolithic suspensions, and low absorption," says Daniel Sigg, a LIGO lead scientist at Caltech. LIGO's optics system amplifies and splits a laser beam down two 4km-long orthogonal tubes. The two beams build power by resonating between reflective mirrors, or 'test masses,' suspended at either end of each arm. This creates an emitted wavelength of unprecedented precision. When the split beam recombines, any change in one arm's path length results in a fringe pattern at the photodetector. For GW150914, this change was just a few times 10-18 meters. Reducing noise sources at each frequency improves interferometer sensitivity. Green shows actual noise during initial LIGO science run. Red and blue (Hanford, WA and Livingston, LA) show noise during advanced LIGO's first observation run, during which GW150914 was detected. Advanced LIGO's sensitivity goal (gray) is a tenfold noise reduction from initial LIGO. Click to enlarge. (Caltech/MIT/LIGO Laboratory) But the entire instrument is subject to environmental noise that reduces sensitivity. A noise plot shows the actual strain on the instruments at all frequencies, which must be distinguished from gravity wave signals. The optics themselves contribute to the noise, which most basically includes thermal noise and the quality factor, or 'Q,' of the substrate. "If you ping a wine glass, you want to hear 'ping' and not 'dink'. If it goes 'dink', the resonance line is broad and the entire noise increases. But if you contain all the energy in one frequency, you can filter it out," explains GariLynn Billingsley, LIGO optics manager at Caltech. That's the Q of the mirrors. Further, if the test mass surfaces did not allow identical wavelengths to resonate in both arms, it would result in imperfect cancellation when the beam recombines. And if non-resonating light is lost, so is the ability to reduce laser noise. Perhaps most problematic, the optics' coatings contribute to noise due to stochastic particle motion. Stringent design standards ameliorate these problems. In 1996, a program invited manufacturers to demonstrate their ability to meet the specifications required by initial LIGO's optics. Australia's Commonwealth Science and Industrial Research Organisation (CSIRO) won the contract. "It was a combination of our ability to generate large surfaces with excellent flatness, combined with very low microroughness," says Chris Walsh, now at the University of Sydney, who supervised the overall CSIRO project. "It requires enormous expertise to develop the polishing process to get the necessary microroughness (0.2-0.4nm RMS) and surface shape simultaneously." Master optician Achim Leistner led the work, with Bob Oreb in charge of metrology. Leistner pioneered the use of a Teflon lap, which provides a very stable surface that matches the desired shape of the optic during polishing and allows for controlled changes. "We built the optics to a specification that was different to anything we'd ever seen before," adds Walsh. Even with high-precision optics and a thermal compensation system that balances the minuscule heating of the mirror's center, initial LIGO was not expected to detect gravity waves. Advanced LIGO, begun in 2010 and completing its first observations when GW150914 was detected, offers a tenfold increase in design sensitivity due to upgrades that address the entire frequency range. "Very simply, we have better seismic isolation at low frequencies; better test masses and suspension at intermediate frequencies; and higher powered lasers at high frequencies," says Michael Landry, a lead scientist at the LIGO-Hanford observatory. At low frequencies, mechanical resonances are well understood. At high frequencies, radiation pressure and laser 'shot' noise dominate. But at intermediate frequencies (60-100 Hz), scattered light and beam jitter are difficult to control. "Our bucket is lowest here. And there are other things we just don't know," adds Landry. "The primary thermal noise, which is the component at intermediate frequency that will ultimately limit us, is the Brownian noise of the coatings." To improve signal-to-noise at intermediate frequencies, advanced LIGO needed larger test masses (340mm diameter). California-based Zygo Extreme Precision Optics won the contract to polish them. "We were chosen based on our ability to achieve very tight surface figure, roughness, radius of curvature, and surface defect specifications simultaneously," says John Kincade, Zygo's Extreme Precision Optics managing director. The test masses required a 1.9km radius of curvature, with figure requirements as stringent as 0.3nm RMS. After super-polishing to extremely high spatial frequency, ion beam figuring fine-tunes the curvature by etching the surface several molecules at a time. This allows reliable shape without compromising on ability to produce micro-roughness over large surfaces. Advanced LIGO input test mass champion data. Zygo achieved figuring accuracy to 0.08nm RMS over the critical 160mm central clear aperture, and sub-nanometer accuracy on the full clear 300mm aperture of many other samples. Click to enlarge. (Zygo Extreme Precision Optics) Dielectric coatings deposited on the high-precision surfaces determine their optical performance. CSIRO and the University of Lyon Laboratoire des Materiaux Avances shared the contract to apply molecule-thin alternating layers of tantalum and silica via ion-beam sputtering. Katie Green, project leader in CSIRO's optics group, says "the thickness of the individual layers are monitored as they're deposited. Each coating consists of multiple layers of particular thicknesses, with the specific composition of the layers varying depending on how the optic needs to perform in the detector." Additionally, gold coatings around the edges provide thermal shielding and act as an electrostatic drive. LIGO's next observation run is scheduled to begin in September 2016. And after Advanced LIGO reaches its design sensitivity by fine-tuning current systems, further upgrades await in the years 2018-2020 and beyond. "One question is how you reduce the thermal noise of the optics, in particular their coatings. But coating technologies make it hard to get more than a factor of about three beyond Advanced LIGO's noise level," says Landry. One possibility is operating at cyrogenic temperatures. But "fused silica becomes noisy at cold temperatures, and you need a different wavelength laser to do this," according to Billingsley. Another way of increasing the sensitivity at room temperature is to use 40km-arm-length interferometers. Other optics-related systems reduce noise. Advanced LIGO's test masses are suspended on fused silica fibers, creating monolithic suspension that reduces thermal noise and raises the system's resonant frequency compared with initial LIGO. "The Q of that system is higher so an entire band shrinks. That means opening up more space at lower frequencies, where binary black holes are," says Landry. In the 17th century, Galileo pointed a telescope to the sky and pioneered a novel way of observing the universe. Now, LIGO's detection of GW150914 marks another new era of astronomy. As advances in glass lenses enabled Galileo's discoveries, so have state-of-the-art optics made LIGO's discoveries possible. And with astronomy's track record of developing new generations of optical devices, both the astrophysical and precision optics communities are poised for an exciting future.


Bowerman A.F.,Commonwealth Science and Industrial Research Organisation | Bowerman A.F.,Australian National University | Newberry M.,Commonwealth Science and Industrial Research Organisation | Dielen A.-S.,Commonwealth Science and Industrial Research Organisation | And 10 more authors.
Plant Biotechnology Journal | Year: 2016

Starch phosphate ester content is known to alter the physicochemical properties of starch, including its susceptibility to degradation. Previous work producing wheat (Triticum aestivum) with down-regulated glucan, water dikinase, the primary gene responsible for addition of phosphate groups to starch, in a grain-specific manner found unexpected phenotypic alteration in grain and growth. Here, we report on further characterization of these lines focussing on mature grain and early growth. We find that coleoptile length has been increased in these transgenic lines independently of grain size increases. No changes in starch degradation rates during germination could be identified, or any major alteration in soluble sugar levels that may explain the coleoptile growth modification. We identify some alteration in hormones in the tissues in question. Mature grain size is examined, as is Hardness Index and starch conformation. We find no evidence that the increased growth of coleoptiles in these lines is connected to starch conformation or degradation or soluble sugar content and suggest these findings provide a novel means of increasing coleoptile growth and early seedling establishment in cereal crop species. © 2016 Society for Experimental Biology, Association of Applied Biologists and John Wiley and Sons Ltd.


News Article | October 29, 2016
Site: www.techrepublic.com

Despite having the same fitness level as everybody else at school, Gary Barber was never able to run as far as the other kids could because, at the age of four, he was diagnosed with a heart defect. The impact the heart defect had on Barber progressively worsened in his adult life. At one point, Barber, who is now 48, was unable to walk from the lounge room to the bathroom without having to stop halfway down the hallway to take a breath. "Imagine having somebody's hands around your throat, or you've got a really bad flu where there's pressure on your chest and you can't breathe properly. You're taking a quarter of your breath and you're trying to walk," Barber said. Toward the end of October 2015, Barber underwent emergency heart failure surgery after being admitted into Ipswich Hospital in Queensland, Australia. Barber's need for surgery came after frequently passing out and being told by his doctor the issue was his lungs and being overweight—not his heart. "My surgeon said I should have been on his [operating] table a minimum of four years ago," Barber said. Post-surgery, patients such as Barber are advised to undertake cardiac rehabilitation (CR) to reduce the risk of a second heart attack. As part of CR, patients are required to make regular visits to the hospital. But, according to Simon McBride, co-founder and CTO of Cardihab, the average cardiac rehab completion rate is only 30%. In hopes of increasing the completion rate, McBride introduced Cardihab, a smartphone application currently in pilot phase, designed to help patients recover from heart surgery remotely. Cardihab is a spin-off company from the Commonwealth Science and Industrial Research Organisation (CSIRO), and is also a participant of the HCF Catalyst accelerator program. He explained a key problem behind why people do not complete their CR program is due to accessibility and convenience. "The way normal cardiac rehab works is it's usually a 6-8 week long program where the person has to go to a clinic once or twice a week and that can really be inconvenient, especially for patients who have returned to work, or for rural remote patients," McBride said. Cardihab has been designed to collect data about a patient including how many steps a patient has taken, and their blood pressure and sugar levels, via Bluetooth-enabled monitors. The information is then uploaded to the cloud and shared with the patient's clinician, who can access it through an online portal. SEE: Healthcare IT's battle to keep sensitive data safe (TechRepublic) Based on research by the CSIRO, and through initial trials with Queensland Health, Cardihab has been able to reduce clinical hospital visits by 89% and improve cardiac rehab completion rates by 70%. While Barber said Cardihab has raised his personal awareness, it was not something he was initially open to trying. His initial thoughts about the program was that it was a " damn waste of time," but after completing the six-week Cardihab program with encouragement from one of the nurses, he said anyone who does not do the program would be a fool. "It made me more aware about what I was doing...I had a machine to be accountable to, I had a set of scales I had to be accountable to, and I had a blood pressure machine I had to be accountable to," Barber said. There were also conversational check-ups over the phone with the nurses, which would often involve discussions about why he was unable to take as many steps during certain days, Barber said, pointing out he's also a sufferer of gout and that restricted his movements. McBride said the application gives the opportunity to "empower" patients. "I think it's true to say getting patients more engaged is a big trend and something healthcare systems are trying to do. With [Cardihab], it gives people the ability to engage more with their care, and drive that feedback loop to the clinician and that's still the most important thing: The conversation between the patient and clinician is the heart of the cardiac rehab program; the technology just helps the clinician deliver that program in another way," Mcbride said. Although it has been a physical recovery, it has equally been an emotional one, too, Barber said. "When recovery is mentioned, what people don't understand is the emotional trauma. They don't understand the ongoing after affects," Barber said. While Barber believes there's still a long road ahead to full recovery, the results are already showing. He said it's now only taking him 10 minutes to feed the horses on his property, when it used to take 45 minutes.


PubMed | University of Queensland, Commonwealth Science and Industrial Research Organisation, Cobb Vantress Inc. and University of Arkansas
Type: | Journal: Biology open | Year: 2016

Mitochondrial content is a fundamental cellular bioenergetic phenotype. Previous work has hypothesised possible links between variation in muscle mitochondrial content and animal performance. However, no population screens have been performed in any production species. Here, we have designed a high throughput molecular approach to estimate mitochondrial content in commercial broilers. Technical validity was established using several approaches including its performance in monoclonal DF-1 cells, cross-tissue comparisons in tissues with differing metabolic demands (white fat


Walton A.,Commonwealth Science and Industrial Research Organisation | Gardner J.,Commonwealth Science and Industrial Research Organisation
Local Environment | Year: 2015

This research examined community acceptance of policy instruments that could be used to promote ongoing maintenance of domestic rainwater tank systems. Using an online survey of 533 tank owners in South East Queensland, Australia, the research investigated four sets of factors that influence policy acceptance: features of the policy, judgements of policy fairness and effectiveness, contextual framing, and individual attitudes and motivations towards tank maintenance. An experimental design incorporating choice modelling was employed. Results demonstrated that perceptions of policy fairness and effectiveness are important to acceptance. Policies that include enabling features associate with increased perceptions of effectiveness, and policies that use incentives are linked to increased perceptions of both fairness and effectiveness. Individual attitudes and motivations regarding tank maintenance were significant predictors of policy support. Perceptions of a person's own ability to undertake tank maintenance tasks were negative predictors of policy intervention, suggesting that people who believe they can carry out maintenance themselves may not see the need for a policy that encourages tank maintenance to exist. The findings are discussed in relation to issues of policy design. © 2014, © Crown in the Commonwealth of Australia 2014 .


Lapalikar G.V.,Commonwealth Science and Industrial Research Organisation | Taylor M.C.,Commonwealth Science and Industrial Research Organisation | Warden A.C.,Commonwealth Science and Industrial Research Organisation | Scott C.,Commonwealth Science and Industrial Research Organisation | And 2 more authors.
PLoS ONE | Year: 2012

Two classes of F 420-dependent reductases (FDR-A and FDR-B) that can reduce aflatoxins and thereby degrade them have previously been isolated from Mycobacterium smegmatis. One class, the FDR-A enzymes, has up to 100 times more activity than the other. F 420 is a cofactor with a low reduction potential that is largely confined to the Actinomycetales and some Archaea and Proteobacteria. We have heterologously expressed ten FDR-A enzymes from diverse Actinomycetales, finding that nine can also use F 420H 2 to reduce aflatoxin. Thus FDR-As may be responsible for the previously observed degradation of aflatoxin in other Actinomycetales. The one FDR-A enzyme that we found not to reduce aflatoxin belonged to a distinct clade (herein denoted FDR-AA), and our subsequent expression and analysis of seven other FDR-AAs from M. smegmatis found that none could reduce aflatoxin. Certain FDR-A and FDR-B enzymes that could reduce aflatoxin also showed activity with coumarin and three furanocoumarins (angelicin, 8-methoxysporalen and imperatorin), but none of the FDR-AAs tested showed any of these activities. The shared feature of the compounds that were substrates was an α,β-unsaturated lactone moiety. This moiety occurs in a wide variety of otherwise recalcitrant xenobiotics and antibiotics, so the FDR-As and FDR-Bs may have evolved to harness the reducing power of F 420 to metabolise such compounds. Mass spectrometry on the products of the FDR-catalyzed reduction of coumarin and the other furanocoumarins shows their spontaneous hydrolysis to multiple products. © 2012 Lapalikar et al.


PubMed | Commonwealth Science and Industrial Research Organisation
Type: Journal Article | Journal: PloS one | Year: 2012

Two classes of F(420)-dependent reductases (FDR-A and FDR-B) that can reduce aflatoxins and thereby degrade them have previously been isolated from Mycobacterium smegmatis. One class, the FDR-A enzymes, has up to 100 times more activity than the other. F(420) is a cofactor with a low reduction potential that is largely confined to the Actinomycetales and some Archaea and Proteobacteria. We have heterologously expressed ten FDR-A enzymes from diverse Actinomycetales, finding that nine can also use F(420)H(2) to reduce aflatoxin. Thus FDR-As may be responsible for the previously observed degradation of aflatoxin in other Actinomycetales. The one FDR-A enzyme that we found not to reduce aflatoxin belonged to a distinct clade (herein denoted FDR-AA), and our subsequent expression and analysis of seven other FDR-AAs from M. smegmatis found that none could reduce aflatoxin. Certain FDR-A and FDR-B enzymes that could reduce aflatoxin also showed activity with coumarin and three furanocoumarins (angelicin, 8-methoxysporalen and imperatorin), but none of the FDR-AAs tested showed any of these activities. The shared feature of the compounds that were substrates was an ,-unsaturated lactone moiety. This moiety occurs in a wide variety of otherwise recalcitrant xenobiotics and antibiotics, so the FDR-As and FDR-Bs may have evolved to harness the reducing power of F(420) to metabolise such compounds. Mass spectrometry on the products of the FDR-catalyzed reduction of coumarin and the other furanocoumarins shows their spontaneous hydrolysis to multiple products.


PubMed | Australian National University and Commonwealth Science and Industrial Research Organisation
Type: Journal Article | Journal: Plant biotechnology journal | Year: 2016

Starch phosphate ester content is known to alter the physicochemical properties of starch, including its susceptibility to degradation. Previous work producing wheat (Triticum aestivum) with down-regulated glucan, water dikinase, the primary gene responsible for addition of phosphate groups to starch, in a grain-specific manner found unexpected phenotypic alteration in grain and growth. Here, we report on further characterization of these lines focussing on mature grain and early growth. We find that coleoptile length has been increased in these transgenic lines independently of grain size increases. No changes in starch degradation rates during germination could be identified, or any major alteration in soluble sugar levels that may explain the coleoptile growth modification. We identify some alteration in hormones in the tissues in question. Mature grain size is examined, as is Hardness Index and starch conformation. We find no evidence that the increased growth of coleoptiles in these lines is connected to starch conformation or degradation or soluble sugar content and suggest these findings provide a novel means of increasing coleoptile growth and early seedling establishment in cereal crop species.

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