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SDG 13

A disease in search of a cause: a study of self-citation and press release pronouncement in the factoid of wind farms causing “vibroacoustic disease”.
18 May 2012
University of Sydney

Chapman, Simon;St.George, Alexis

Background In recent years, claims have proliferated that wind turbines cause a large variety of diseases. Two of these, “Wind Turbine Syndrome” (WTS) and “Vibroacoustic disease” (VAD) are frequently mentioned. Seventeen reviews of the evidence for wind turbines causing harm have concluded the evidence to be poor yet some regulatory authorities are now referencing health concerns as part of the rationale for set-back guidelines from residences, greatly reducing siting opportunities. Methods and Findings Google returns 158,000 hits for WTS and 298,000 for VAD. We conducted a search for all papers and citations on WTS or VAD, and searched for evidence for any association between wind turbine exposure and VAD. No papers on WTS were found in indexed journals. Thirty five papers on VAD were found, none reporting on an association between VAD and wind turbines. Of the 35 papers on VAD, 34 had a first author from a single Portuguese research group. Seventy four per cent of citations to these papers were self-citations by the group. Median self-citation rates in science are around 7%. Two unpublished case reports presented at conferences were found alleging that VAD was “irrefutably demonstrated” to be caused by wind turbines. Conclusions VAD has received virtually no scientific recognition beyond the group who invented the term. The claim that wind turbines cause VAD is a factoid that has gone “viral” in cyberspace and may be contributing to nocebo effects among those living near turbines.
Okamoto's space for the first Painlevé equation in Boutroux coordinates
22 June 2012
University of Sydney

Duistermaat, Johannes (Hans) J.;Joshi, Nalini

We study the completeness and connectedness of asymptotic behaviours of solutions of the first Painlev ́e equation d^2 y/ dx^2 = 6 y^2 + x, in the limit x → ∞, x ∈ C. This problem arises in various physical contexts including the critical behaviour near gradient catastrophe for the focusing nonlinear Schrodinger equation. We prove that the complex limit set of solutions is non-empty, compact and invariant under the flow of the limiting autonomous Hamiltonian system, that the infinity set of the vector field is a repellor for the dynamics and obtain new proofs for solutions near the equilibrium points of the autonomous flow. The results rely on a realization of Okamoto’s space, i.e., the space of initial values compactified and regularized by embedding in CP2 through an explicit construction of nine blow-ups.
Numerical investigation of the impact behaviour of bioinspired nacre-like aluminium composite plates
31 March 2014
University of Sydney

Flores-Johnson, E.A.;Shen, Luming;Guiamatsia, I.;Nguyen, Giang D.

Inspired by the hierarchical structure of nacre, an aluminium alloy (AA) 7075 based composite featuring layer waviness and cohesive interface is studied as a low weight impact resistant material. To investigate the mechanical response and the ballistic performance of this laminated structure, a numerical study of the proposed nacre-like composite plates made of 1.1-mm thick AA 7075 tablets bonded with toughened epoxy resin was performed using Abaqus/Explicit. Target thicknesses of 5.4-mm, 7.5-mm and 9.6-mm impacted by a rigid hemi-spherical projectile were simulated. The epoxy material was modelled using a user-defined interface cohesive element with compressive strength enhancement. A significant performance improvement was recorded for the 5.4-mm nacre-like plate (compared to the same thickness bulk plate), which was explained by the hierarchical structure facilitating both localised energy absorption (by deformation of the tablet) and more globalized energy absorption (by inter-layered delamination and friction). For a given projectile, however, the performance improvement of using the proposed composite decreased with increasing laminate thickness, which was attributed to the increased likelihood of ductile failure occurring prior to perforation in thicker bulk plates. For 5.4-mm thick plates impacted at high velocity, the nacre-like plate had a better ballistic performance than that of the plates made of continuous (flat and wavy) layers, which was attributed to the larger area of plastic deformation (observed in the nacre-like plate after impact) due to the tablets arrangement.
Structure of an atypical FeoB G-domain reveals a putative domain-swapped dimer.
29 April 2014
University of Sydney

Deshpande, Chandrika;McGrath, Aaron;Font, Josep;Guilfoyle, Amy;Maher, Megan;Jormakka, Mika

FeoB is a transmembrane protein involved in ferrous iron uptake in prokaryotic organisms. FeoB comprises a cytoplasmic soluble domain termed NFeoB and a C-terminal polytopic transmembrane domain. Recent structures of NFeoB have revealed two structural subdomains: a canonical GTPase domain and a five-helix helical domain. The GTPase domain hydrolyses GTP to GDP through a well characterized mechanism, a process which is required for Fe(2+) transport. In contrast, the precise role of the helical domain has not yet been fully determined. Here, the structure of the cytoplasmic domain of FeoB from Gallionella capsiferriformans is reported. Unlike recent structures of NFeoB, the G. capsiferriformans NFeoB structure is highly unusual in that it does not contain a helical domain. The crystal structures of both apo and GDP-bound protein forms a domain-swapped dimer.
Numerical simulations of quasi-static indentation and low velocity impact of Rohacell 51 WF foam
07 May 2014
University of Sydney

Flores-Johnson, E.A.;Li, Q.M.;Shen, Luming

Numerical simulations of quasi-static indentation and low velocity impact of low density polymethacrylimide (PMI) Rohacell 51 WF foam using indenters with different nose shapes (conical, truncated-conical, hemi-spherical and flat) were carried out using the finite element code LS-DYNA. A 2D axisymmetric model was generated. A strain-rate dependent material model and r-adaptive remeshing were used for low velocity impact simulations. Numerical predictions matched the available experimental data very well. Moreover, the predicted resistance force closely matched the empirical results. The results demonstrated the ability of the model to reproduce the deformation mechanisms of the penetration process of Rohacell 51 WF foam.
Numerical study of the hydrodynamic drag force in atomic force microscopy measurements undertaken in fluids
24 June 2014
University of Sydney

Mendez-Mendez, J.V.;Alonso-Rasgado, M.T.;Correia Faria, E.;Flores-Johnson, E.A.;Snook, R.D.

When atomic force microscopy (AFM) is employed for in vivo study of immersed biological samples, the fluid medium presents additional complexities, not least of which is the hydrodynamic drag force due to viscous friction of the cantilever with the liquid. This force should be considered when interpreting experimental results and any calculated material properties. In this paper, a numerical model is presented to study the influence of the drag force on experimental data obtained from AFM measurements using computational fluid dynamics (CFD) simulation. The model provides quantification of the drag force in AFM measurements of soft specimens in fluids. The numerical predictions were compared with experimental data obtained using AFM with a V-shaped cantilever fitted with a pyramidal tip. Tip velocities ranging from 1.05 to 105 µm/s were employed in water, polyethylene glycol and glycerol with the platform approaching from a distance of 6000 nm. The model was also compared with an existing analytical model. Good agreement was observed between numerical results, experiments and analytical predictions. Accurate predictions were obtained without the need for extrapolation of experimental data. In addition, the model can be employed over the range of tip geometries and velocities typically utilized in AFM measurements.
A numerical study of bioinspired nacre-like composite plates under blast loading
25 March 2015
University of Sydney

Flores-Johnson, E.A.;Luming, Shen;Guiamatsia, Irene;Nguyen, Giang D.

In this paper, a multi-layered composite inspired by the hierarchical structure of nacre and made of layers of aluminium alloy AA 7075 bonded with toughened epoxy resin is introduced for blast resistant applications. The performance of the proposed nacre-like 3.3-mm and 5.4-mm thick composite plates, made of 1.1-mm thick AA 7075 layers, under localised impulsive loading was numerically studied. The epoxy material was modelled using user-defined interface cohesive elements that properly take into account both strength and toughness enhancements under compression. As compared to bulk plates, the improvement in blast resistance performance was numerically observed in the nacre-like plates, which required larger loads to reach the onset of failure. In addition, a reduction of the peak velocity and maximum deflection of the back face was observed for the nacre-like plates. This improvement is explained by the hierarchical structure facilitating a globalized energy absorption by inter-layer interlocking, delamination and friction.
Static friction between rigid fractal surfaces
21 September 2015
University of Sydney

Alonso-Marroquin, Fernando;Huang, Pengyu;Hanaor, Dorian A. H.;Flores-Johnson, E. A.;Proust, Gwenaelle;Gan, Yixiang;Shen, Luming

Using spheropolygon-based simulations and contact slope analysis, we investigate the effects of surface topography and atomic scale friction on the macroscopically observed friction between rigid blocks with fractal surface structures. From our mathematical derivation, the angle of macroscopic friction is the result of the sum of the angle of atomic friction and the slope angle between the contact surfaces. The latter is obtained from the determination of all possible contact slopes between the two surface profiles through an alternative signature function. Our theory is validated through numerical simulations of spheropolygons with fractal Koch surfaces and is applied to the description of frictional properties of Weierstrass-Mandelbrot surfaces. The agreement between simulations and theory suggests that for interpreting macroscopic frictional behavior, the descriptors of surface morphology should be defined from the signature function rather than from the slopes of the contacting surfaces.
Gravitational collapse of spherically symmetric stars in noncommutative general relativity
17 February 2016
University of Sydney

Sun, Wen;Wang, Ding;Xie, Naqing;Zhang, Ruibin;Zhang, Xiao

Gravitational collapse of a class of spherically symmetric stars is investigated. We quantise the geometries describing the gravitational collapse by a deformation quantisation procedure. This gives rise to oncommutative spacetimes with gravitational collapse.
Movement of IS26-Associated Antibiotic Resistance Genes Occurs via a Translocatable Unit That Includes a Single IS26 and Preferentially Inserts Adjacent to Another IS26
07 March 2016
University of Sydney

Harmer, Christopher J;Moran, Robert A;Hall, Ruth M

TheinsertionsequenceIS26playsakeyroleindisseminatingantibioticresistancegenesinGram-negativebacteria, forming regions containing more than one antibiotic resistance gene that are flanked by and interspersed with copies of IS26. A model presented for a second mode of IS26 movement that explains the structure of these regions involves a translocatable unit consisting of a unique DNA segment carrying an antibiotic resistance (or other) gene and a single IS copy. Structures resembling class I transposons are generated via RecA-independent incorporation of a translocatable unit next to a second IS26 such that the ISs are in direct orientation. Repeating this process would lead to arrays of resistance genes with directly oriented copies of IS26 at each end and between each unique segment. This model requires that IS26 recognizes another IS26 as a target, and in transpo- sition experiments, the frequency of cointegrate formation was 60-fold higher when the target plasmid contained IS26. This re- action was conservative, with no additional IS26 or target site duplication generated, and orientation specific as the IS26s in the cointegrates were always in the same orientation. Consequently, the cointegrates were identical to those formed via the known mode of IS26 movement when a target IS26 was not present. Intact transposase genes in both IS26s were required for high- frequency cointegrate formation as inactivation of either one reduced the frequency 30-fold. However, the IS26 target specificity was retained. Conversion of each residue in the DDE motif of the Tnp26 transposase also reduced the cointegration frequency.
Homogentisate 1-2-Dioxygenase Downregulation in the Chronic Persistence of Pseudomonas aeruginosa Australian Epidemic Strain-1 in the CF Lung
07 March 2016
University of Sydney

Harmer, Christopher J;Wynn, Matthew;Pinto, Rachel;Cordwell, Stuart;Rose, Barbara R;Harbour, Colin;Triccas, James A;Manos, Jim

Some Pseudomonas aeruginosa strains including Australian Epidemic Strain-1 (AES-1 or AUS-01) cause persistent chronic infection in cystic fibrosis (CF) patients, with greater morbidity and mortality. Factors conferring persistence are largely unknown. Previously we analysed the transcriptomes of AES-1 grown in Luria broth, nematode growth medium for Caenorhabditis elegans assay (both aerobic) and artificial sputum medium (mainly hyp- oxic). Transcriptional comparisons included chronic AES-1 strains against PAO1 and acute AES-1 (AES-1R) against its chronic isogen (AES-1M), isolated 10.5 years apart from a CF patient and not eradicated in the meantime. Prominent amongst genes downregulated in AES-1M in all comparisons was homogentisate-1-2-dioxygenase (hmgA); an oxygen-dependent gene known to be mutationally deactivated in many chronic infection strains of P. aeruginosa. To investigate if hmgA downregulation and deactivation gave similar viru- lence persistence profiles, a hmgA mutant made in UCBPP-PA14 utilising RedS-recombinase and AES-1M were assessed in the C. elegans virulence assay, and the C57BL/6 mouse for pulmonary colonisation and TNF-α response. In C. elegans, hmgA deactivation resulted in significantly increased PA14 virulence while hmgA downregulation reduced AES-1M virulence. AES-1M was significantly more persistent in mouse lung and showed a significant increase in TNF-α (p<0.0001), sustained even with no detectable bacteria. PA14ΔhmgA did not show increased TNF-α. This study suggests that hmgA may have a role in P. aeruginosa persistence in chronic infection and the results provide a starting point for clarifying the role of hmgA in chronic AES-1.
A Type 2 A/C2 plasmid carrying the aacC4 apramycin resistance gene and the erm(42) erythromycin resistance gene recovered from two Salmonella enterica serovars
11 March 2016
University of Sydney

Harmer, Christopher J;Holt, Kathryn E;Hall, Ruth M

Objective: To determine the relationships between RepA/C2 plasmids carrying several antibiotic resistance genes found in isolates of Salmonella enterica serovars Ohio and Senftenberg from pigs. Methods: Illumina HiSeq was used to sequence seven S. enterica isolates. BLAST searches identified relevant A/C2 plasmid contigs, and contigs were assembled using PCR. Results: Two serovar Ohio isolates were ST329 and the five Senftenberg isolates were ST210. The A/C2 plasmids recovered from the seven isolates belong to Type 2 and contain two resistance islands. Their backbones were closely related, differing by five or fewer single nucleotide polymorphisms. The sul2-containing resistance island ARI-B is 19.9 kb and also contains the kanamycin and neomycin resistance gene aphA1, the tetracycline resistance gene tetA(D), and an erythromycin resistance gene, erm(42), not previously seen in A/C2 plasmids. A second 30.3 kb resistance island, RI-119, is in a unique location in the A/C2 backbone 8.2 kb downstream of rhs. RI-119 contained genes conferring resistance to apramycin, netilmicin, tobramycin (aacC4), hygromycin (hph), sulphonamides (sul1) and spectinomycin and streptomycin (aadA2). In one of the seven plasmids, this resistance region contained two IS26-mediated deletions. A discrete 5.7 kb segment containing the aacC4 and hph genes and bounded by IS26 on one side and the IR of Tn5393 on the other was identified. Conclusions: The presence of almost identical A/C2 plasmids in two serovars indicates a common origin. Type 2 A/C2 plasmids continue to evolve via addition of new resistance regions such as RI-119 and evolution of existing ones.
p39R861-4, a type 2 A/C2 plasmid carrying a segment from the A/C1 RA1
11 March 2016
University of Sydney

Anantham, S;Harmer, Christopher J;Hall, Ruth M

The largest plasmid in the strain 39R861, which is used as a plasmid size standard, was recovered by conjugation and sequenced to determine its exact size. Plasmid p39R861-4 transferred at high frequency. Though reported to be the A/C1 plasmid RA1, p39R861-4 is a 155794 bp Type 2 A/C2 plasmid in which a 39 kb segment derived from RA1 that includes a relative of the RA1 resistance island replaces 26.5 kb of the Type 2 backbone. p39R861-4 includes a single copy of IS10 and two resistance islands with a CR2-sul2 region in each of them. The 84 kb of backbone between the resistance islands is inverted relative to other known A/C plasmids and this inversion has arisen via recombination between the CR2-sul2 regions that are inversely oriented. The resistance islands prior to inversion were one related to but longer than that found in RA1, and a form of the ARI-B island identical to one found in the A/C2 plasmid R55. They contain genes conferring resistance to tetracycline (tetA(D)), sulphonamides (sul2) and florfenicol and chloramphenicol (floR). The tet(D) determinant is flanked by two IS26 in a transposon-like structure named Tntet(D). Both resistance islands contain remnants of the two ends of the integrative element GIsul2, consistent with the sul2 gene being mobilized by GIsul2 rather than by CR2.
Environmental Survival of Mycobacterium avium subsp. paratuberculosis in Different Climatic Zones of Eastern Australia.
04 April 2016
University of Sydney

Eppleston, J.;Begg, D. J.;Dhand, Navneet K.;Watt, B.;Whittington, R. J.

The duration of survival of both the S and C strains of Mycobacterium avium subsp. paratuberculosis in feces was quantified in contrasting climatic zones of New South Wales, Australia, and detailed environmental temperature data were collected. Known concentrations of S and C strains in feces placed on soil in polystyrene boxes were exposed to the environment with or without the provision of shade (70%) at Bathurst, Armidale, Condobolin, and Broken Hill, and subsamples taken every 2 weeks were cultured for the presence of M. avium subsp. paratuberculosis. The duration of survival ranged from a minimum of 1 week to a maximum of 16 weeks, and the provision of 70% shade was the most important factor in extending the survival time. The hazard of death for exposed compared to shaded samples was 20 and 9 times higher for the S and C strains, respectively. Site did not affect the survival of the C strain, but for the S strain, the hazard of death was 2.3 times higher at the two arid zone sites (Broken Hill and Condobolin) than at the two temperate zone sites (Bathurst and Armidale). Temperature measurements revealed maximum temperatures exceeding 60°C and large daily temperature ranges at the soil surface, particularly in exposed boxes.
The Influence of Meteorology on the Spread of Influenza: Survival Analysis of an Equine Influenza (A/H3N8) Outbreak.
04 April 2016
University of Sydney

Firestone, S. M.;Cogger, N;Ward, M. P.;Toribio, J. A.;Moloney, B. J.;Dhand, Navneet K.

The influences of relative humidity and ambient temperature on the transmission of influenza A viruses have recently been established under controlled laboratory conditions. The interplay of meteorological factors during an actual influenza epidemic is less clear, and research into the contribution of wind to epidemic spread is scarce. By applying geostatistics and survival analysis to data from a large outbreak of equine influenza (A/H3N8), we quantified the association between hazard of infection and air temperature, relative humidity, rainfall, and wind velocity, whilst controlling for premises-level covariates. The pattern of disease spread in space and time was described using extraction mapping and instantaneous hazard curves. Meteorological conditions at each premises location were estimated by kriging daily meteorological data and analysed as time-lagged time-varying predictors using generalised Cox regression. Meteorological covariates time-lagged by three days were strongly associated with hazard of influenza infection, corresponding closely with the incubation period of equine influenza. Hazard of equine influenza infection was higher when relative humidity was 30 km hour−1 from the direction of nearby infected premises were associated with increased hazard of infection. Through combining detailed influenza outbreak and meteorological data, we provide empirical evidence for the underlying environmental mechanisms that influenced the local spread of an outbreak of influenza A. Our analysis supports, and extends, the findings of studies into influenza A transmission conducted under laboratory conditions. The relationships described are of direct importance for managing disease risk during influenza outbreaks in horses, and more generally, advance our understanding of the transmission of influenza A viruses under field conditions.
Adsorption of Mycobacterium avium subsp. paratuberculosis to Soil Particles.
04 April 2016
University of Sydney

Dhand, Navneet K.;Toribio, Jenny-Ann L. M. L.;Whittington, Richard J.

Attachment of Mycobacterium avium subsp. paratuberculosis to soil particles could increase their availability to farm animals, as well as influence the transportation of M. avium subsp. paratuberculosis to water sources. To investigate the possibility of such attachment, we passed a known quantity of M. avium subsp. paratuberculosis through chromatography columns packed with clay soil, sandy soil, pure silica, clay-silica mixture, or clay-silica complexes and measured the organisms recovered in the eluent using culture or quantitative PCR. Experiments were repeated using buffer at a range of pH levels with pure silica to investigate the effect of pH on M. avium subsp. paratuberculosis attachment. Linear mixed-model analyses were conducted to compare the proportional recovery of M. avium subsp. paratuberculosis in the eluent between different substrates and pH levels. Of the organisms added to the columns, 83 to 100% were estimated to be retained in the columns after adjustment for those retained in empty control columns. The proportions recovered were significantly different across different substrates, with the retention being significantly greater (P < 0.05) in pure substrates (silica and clay-silica complexes) than in soil substrates (clay soil and sandy soil). However, there were no significant differences in the retention of M. avium subsp. paratuberculosis between silica and clay-silica complexes or between clay soil and sandy soil. The proportion retained decreased with increasing pH in one of the experiments, indicating greater adsorption of M. avium subsp. paratuberculosis to soil particles at an acidic pH (P < 0.05). The results suggest that under experimental conditions M. avium subsp. paratuberculosis adsorbs to a range of soil particles, and this attachment is influenced by soil pH.
Association of farm soil characteristics with ovine Johne's disease in Australia
11 April 2016
University of Sydney

Dhand, Navneet K.;Eppleston, Jeff;Whittington, Richard J.;Toribio, Jenny-Ann L.M.L.

Speculation about the association of soil characteristics with the expression of ovine Johne’s disease (OJD) prompted this cross-sectional study. We enrolled 92 sheep flocks in Australia during 2004-05 and in each enrolled flock collected pooled faecal samples from an identified cohort (group of same age and sex) of sheep and soil samples from the paddocks grazed by this cohort of sheep. Faecal pools were cultured to create three outcome variables: positive or negative status of faecal pools (pool OJD status, binary); the log number of viable Mycobacterium avium subsp. paratuberculosis (MAP) organisms per gram of faeces (log pool MAP number, continuous); and the prevalence of faecal shedders (cohort OJD prevalence level, ordinal: low 10%). Separate statistical models were then developed to investigate the association between soil characteristics and each outcome variable. Sheep raised on soils with a higher percentage of organic carbon and clay had a higher OJD prevalence whereas, sheep grazing on soils with a higher content of sand and nitrogen had a lower OJD prevalence. Iron content of the soil was positively associated with OJD infection but the association between soil pH and OJD was inconclusive. Parent soil type, the only farm level factor, was not significant in any of the final models. Study results indicate a higher risk of OJD in sheep raised on soils with greater organic matter and clay content. We hypothesise that this is due to adsorption of MAP to clay and the consequent retention of the bacteria in the topsoil, thus making them available in higher numbers to grazing sheep. Keywords: risk factors, paratuberculosis, mycobacterium, cross-sectional study, organic carbon, clay, sand, pH, iron.
NEDD9 regulates 3D migratory activity independent of the Rac1 morphology switch in glioma and neuroblastoma.
16 September 2016
University of Sydney

Zhong, Jessie;Bach, Cuc T.;Shum, Michael S.Y.;O'Neill, Geraldine M.

Metastasizing tumor cells must transmigrate the dense extracellular matrix that surrounds most organs. The use of three-dimensional (3D) collagen gels has revealed that many cancer cells can switch between different modes of invasion that are characterized by distinct morphologies (e.g., rounded vs. elongated). The adhesion protein NEDD9 has the potential to regulate the switch between elongated and rounded morphologies; therefore, its role was interrogated in the invasion switch of glioblastoma and neuroblastoma tumors that similarly derive from populations of neural crest cells. Interestingly, siRNA-mediated depletion of NEDD9 failed to induce cell rounding in glioma or neuroblastoma cells, contrasting the effects that have been described in other tumor model systems. Given that Rac1 GTPase has been suggested to mediate the switch between elongated and rounded invasion, the functionality of the Rac1 morphology switch was evaluated in the glioma and neuroblastoma cells. Using both dominant-negative Rac1 and Rac1-specific siRNA, the presence of this morphologic switch was confirmed in the neuroblastoma, but not in the glioma cells. However, in the absence of a morphologic change following NEDD9 depletion, a significant decrease in the cellular migration rate was observed. Thus, the data reveal that NEDD9 can regulate 3D migration speed independent of the Rac1 morphology switch. IMPLICATIONS: NEDD9 targeting is therapeutically viable as it does not stimulate adaptive changes in glioma and neuroblastoma invasion.
Endogenous Environmental Variables In Stochastic Frontier Models
24 May 2017
University of Sydney

Amsler, Christine;Prokhorov, Artem;Schmidt, Peter

This paper considers a stochastic frontier model that contains environmental variables that affect the level of inefficiency but not the frontier. The model contains statistical noise, potentially endogenous regressors, and technical inefficiency that follows the scaling property, in the sense that it is the product of a basic (half-normal) inefficiency term and a parametric function of the environmental variables. The environmental variables may be endogenous because they are correlated with the statistical noise or with the basic inefficiency term. Several previous papers have considered the case of inputs that are endogenous because they are correlated with statistical noise, and if they contain environmental variables these are exogenous. One recent paper allows the environmental variables to be correlated with statistical noise. Our paper is the first to allow both the inputs and the environmental variables to be endogenous in the sense that they are correlated either with statistical noise or with the basic inefficiency term. Correlation of inputs or environmental variables with the basic inefficiency term raises non-trivial conceptual issues about the meaning of exogeneity, and technical issues of estimation of the model.
pCERC3 from a commensal ST95 Escherichia coli: A ColV virulence-multiresistance plasmid carrying a sul3-associated class 1 integron
09 March 2018
University of Sydney

Moran, Robert A;Holt, Kathryn E;Hall, Ruth M

The rare sulphonamide resistance gene sul3was found in the commensal Escherichia coli ST95 strain 22.1-R1 that was isolated in 2010 from the faeces of a healthy Australian adult. The genome of 22.1-R1 was sequenced and a 144,344 bp RepFII/FIB plasmid, pCERC3, carrying sul3 was assembled. The sul3 gene is part of a class 1 integron featuring a sul3-containing conserved segment (sul3-CS) that replaced the classic sul1-containing 3′-conserved segment (3′-CS) usually seen in class 1 integrons. The integron contained the cassette array dfrA12-orfFaadA2- cmlA1-aadA1-qacH, conferring resistance to trimethoprim, streptomycin, spectinomycin, chloramphenicol and quaternary ammonium compound. Two additional antibiotic resistance genes, blaTEM (ampicillin resistance) and tetA(B) (tetracycline) were adjacent to the integron, forming a single resistance region. In pCERC3, the sul3-type class 1 integron was flanked by sequence derived from the tnp and mer modules of Tn21 and was in the same location as In2, the sul1-containing In5-type class 1 integron of Tn21. At one end the sequence extends into Tn2670-derived sequence and then into sequence derived from the plasmid NR1 (R100). Examination of the sequences of eleven more complete sul3-containing plasmids in GenBank confirmed the relationship between sul3-associated integrons and Tn21/Tn2670/NR1. This suggests that the events that formed sul3- associated class 1 integrons occurred within the Tn21/Tn2670 context, most likely in NR1 or a related plasmid. The backbone of pCERC3 is most closely related to the backbones of ColV virulence plasmids and contains a complete ColV operon as well as several virulence associated genes and gene clusters. Hence, pCERC3 is both an antibiotic resistance and virulence plasmid.
Analysis of pCERC7, a small antibiotic resistance plasmid from a commensal ST131 Escherichia coli, defines a diverse group of plasmids that include various segments adjacent to a multimer resolution site and encode the same NikA relaxase accessory protein enabling mobilisation
09 March 2018
University of Sydney

Moran, Robert A;Hall, Ruth M

The ampicillin resistance plasmid pCERC7, carrying transposon Tn2 with an IS4 insertion, was detected in the draft genome of a commensal Escherichia coli isolate. The genome data also revealed that this isolate belongs to ST131, clade B. pCERC7 is 9712 bp comprised of a 3319 bp backbone, Tn2::IS4 (6388 bp) and 5 bp of target site duplication, and was present at a copy number of 40. pCERC7 is related to several plasmids composed of only the backbone, or the backbone with the Tn2 insertion in the same position. These plasmids have been found previously in Escherichia coli or Salmonella enterica recovered in several different countries from as early as the 1970s. This group was named the NTP16 group after the best studied example. pCERC7 was annotated using available information about plasmids in this group and additional analyses. The backbone includes genes for RNA I and RNA II to initiate replication and the Tn2 interrupts a gene found here to encode a protein 66% identical to the Romregulatory protein of ColE1. NTP16 family plasmids include a gene, previously designated mobA, that was found to encode a homologue (53% identical) of the NikA relaxase accessory protein of the conjugative IncI1 plasmid R64, which is known to bind to the R64 oriT. However, a nikB relaxase gene is not present, indicating that a relaxase must be supplied in trans for mobilisation by R64 to occur, as demonstrated previously for NTP16. Hence, MobA of NTP16 and relatives was renamed NikA. Upstream of nikA, we found a region closely related to the oriT of R64. pCERC7 and all members of theNTP16 family also include amultimer resolution site, nmr, similar to the cer site of ColE1. The backbone of the NTP16 family also includes genes for a demonstrated toxinantitoxin system, LsoAB. Several more distantly related groups of plasmids that include a very closely related nmr-nikA-oriT segment (99.4–93.7% DNA identity)were identified in theGenBank non-redundant DNA database. All use an RNA I/RNA II-Romsystemfor replication initiation, but each contains a unique fragment adjacent to the nmr site. The segment of theNTP16/pCERC7 group that encodes the LsoAB toxin-antitoxin systemis replaced by a different segment in other family groups. The point atwhich the sequences diverge is between the XerC and XerD sites of the dif site at one end of nmr, suggesting that the evolution of this broad group of plasmids involves XerC/ XerD recombination.
Effect of storage temperature on the stability of spray dried bacteriophage powders
04 April 2018
University of Sydney

Leung, Sharon S.Y.;Parumasivam, Thaigarajan;Nguyen, An;Gengenbach, Thomas;Carter, Elizabeth;Carrigy, Nicholas;Wang, Hui;Vehring, Reinhard;Finlay, Warren;Morales, Sandra;Britton, Warwick;Kutter, Elizabeth;Chan, Hak-Kim

This study aimed to assess the robustness of using a spray drying approach and formulation design in producing inhalable phage powders. Two types of Pseudomonas phages, PEV2 (Podovirus) and PEV40 (Myovirus) in two formulations containing different amounts of trehalose (70% and 60%) and leucine (30% and 40%) were studied. Most of the surface of the produced powders was found to be covered in crystalline leucine. The powders were stored at 4 °C and 20 °C under vacuum. The phage stability and in vitro aerosol performance of the phage powders were examined on the day of production and after 1, 3 and 12 months of storage. A minor titer loss during production was observed for both phages (0.2–0.8 log10 pfu/ml). The storage stability of the produced phage powders was found to be phage and formulation dependent. No further reduction in titer occurred for PEV2 powders stored at 4 °C across the study. The formulation containing 30% leucine maintained the viability of PEV2 at 20 °C, while the formulation containing 40% leucine gradually lost titer over time with a storage reduction of ∼0.9 log10 pfu/ml measured after 12 months. In comparison, the PEV40 phage powders generally had a ∼ 0.5 log10 pfu/ml loss upon storage regardless of temperature. When aerosolized, the total in vitro lung doses of PEV2 were of the order of 107 pfu, except the formulation containing 40% leucine stored at 20 °C which had a lower lung dose. The PEV40 powders also had lung doses of 106–107 pfu. The results demonstrate that spray dried Myoviridae and Podoviridae phage in a simple formulation of leucine and trehalose can be successfully stored for one year at 4 °C and 20 °C with vacuum packaging.
Evolution of regions containing antibiotic resistance genes in FII-2-FIB-1 ColV-ColIa virulence plasmids
16 May 2018
University of Sydney

Moran, Robert A;Hall, Ruth M

Three ColV virulence plasmids carrying antibiotic resistance genes were assembled from draft genome sequences of commensal ST95, ST131, and ST2705 Escherichia coli isolates from healthy Australians. Plasmids pCERC4, pCERC5, and pCERC9 include almost identical backbones containing FII-2 and FIB-1 replicons and the conserved ColV virulence region with an additional ColIa determinant. Only pCERC5 includes a complete, uninterrupted F-like transfer region and was able to conjugate. pCERC5 and pCERC9 contain Tn1721, carrying the tet(A) tetracycline resistance determinant in the same location, with Tn2 (blaTEM; ampicillin resistance) interrupting the Tn1721 in pCERC5. pCERC4 has a Tn1721/Tn21 hybrid transposon carrying dfrA5 (trimethoprim resistance) and sul1 (sulfamethoxazole resistance) in a class 1 integron. Four FII-2:FIB-1 ColVColIa plasmids in the GenBank nucleotide database have a related transposon in the same position, but an IS26 has reshaped the resistance gene region, deleting 2,069 bp of the integron 3¢-CS, including sul1, and serving as a target for IS26 translocatable units containing blaTEM, sul2 and strAB (streptomycin resistance), or aphA1 (kanamycin/neomycin resistance). Another ColV-ColIa plasmid containing a related resistance gene region has lost the FII replicon and acquired a unique transfer region via recombination within the resistance region and at oriT. Eighteen further complete ColV plasmid sequences in GenBank contained FIB-1, but the FII replicons were of three types, FII-24, FII-18, and a variant of FII-36.
Pavement condition and crashes
13 September 2018
University of Sydney

Yokoo, Toshihiro;Levinson, David;Marasteanu, Mihai

Change in weather state (such as the freeze-thaw cycle) leads to distresses in pave- ment materials. It has been hypothesized that poor pavement quality reduces the ability of roads to drain and reduces the ability of vehicles to resist skidding, and is thus associated with more crashes. This paper combines GIS data on crashes with a separate GIS database to test the hypothesis. Poor road quality is associated with more property damage and injury crashes. The interaction of road quality and curves was surprising, indicating that good pavement quality on curves increased the fatal, injury, and property-damage crash rate.
Constructing Authority in Disaster Relief Coordination
26 November 2018
University of Sydney

Koschmann, Matthew;Kopczynski, Jared;Opdyke, Aaron;Javernick-Will, Amy

The purpose of our study is to explore the social construction of authority in disaster relief coordination. We emphasize the ways in which stakeholders draw upon various discursive resources in order to establish or preserve their authority to act within a certain problem domain. We review literature on authority, coordination, communication, and collaborative work to provide a theoretical framework that informs our empirical examples. Next we present a case study of disaster relief coordination in the Philippines following Typhoon Yolanda (known internationally as Haiyan). Our case focuses on home reconstruction in the Cebu province of the Central Visayas region of the Philippines, one of the areas hardest hit by the storm where most of the homes were destroyed or severely damaged. This case demonstrates organizations do not have authority within this problem domain, but instead construct authority through practice and sensemaking in order to accomplish a variety of individual and collective goals; authority is in a constant state of negotiation as various organizations coordinate with each other (or not) to provide effective disaster relief. We conclude with a discussion about the contributions and implications of our research.
Characterizing Post-Disaster Reconstruction Training Methods and Learning Styles
26 November 2018
University of Sydney

Zerio, Alexander;Opdyke, Aaron;Javernick-Will, Amy

Large disasters damage or destroy infrastructure that is then reconstructed through programmes that train community members in construction techniques that reduce future risks. Despite the number of post-disaster reconstruction programmes implemented, there is a dearth of research on education and training in post-disaster contexts. To address this gap, we applied a mixed methods approach based upon experiential learning theory (ELT) to three shelter programmes administered in Eastern Samar, Philippines following Typhoon Haiyan. First, we characterize post-disaster training programmes based on learning modes and then, compared this to the learning styles of community members. To assess learning modes of training programmes, we analysed qualitative data from interview accounts of community members and aid organizations; and, to delineate community member’s learning style preferences, we analysed quantitative data from survey questionnaires. Findings show that aid organizations administered training largely in lecture format, aligning with the reflective observation mode of ELT, but lacked diversity in formats represented in other poles of ELT. Moreover, analysis revealed that community members tended to grasp new information in accordance with the concrete experimentation mode, then preferred transforming newly acquired knowledge via the reflective observation mode. The lecture-based training predominately administered by aid organizations partially aligned with community learning preferences, but fell short in cultivating other forms of knowledge acquisition known to enhance long-term learning.
Imaging mass spectrometry of frontal white matter lipid changes in human alcoholics
18 December 2018
University of Sydney

de la Monte, SM;Kay, J;Yalcin, EB;Kril, JJ;Sheedy, D;Sutherland, GT

BACKGROUND: Chronic alcohol use disorders (AUD) are associated with white matter (WM) degeneration with altered myelin integrity. Matrix assisted laser desorption ionization-imaging mass spectrometry (MALDI-IMS) enables high throughput analysis of myelin lipid biochemical histopathology to help characterize disease mechanisms. PURPOSE: This study utilized MALDI-IMS to investigate frontal lobe WM myelin lipid abnormalities in AUD. METHODS: Standardized cores of formalin-fixed WM from Brodmann Area 4 (BA4) and BA8/9 of 20 postmortem AUD and 19 control adult human brains were embedded in carboxymethyl-cellulose, cryo-sectioned (8 μm), thaw-mounted onto indium tin oxide (ITO) -coated glass slides, and sublimed with 2,5-dihydroxybenzxoic acid (DHB) matrix. Lipids were imaged by MALDI-time of flight in the negative ionization mode. Data were visualized with FlexImaging software v4.0 and analyzed with ClinProTools v3.0. RESULTS: Principal component analysis (PCA) and data bar plots of MALDI-IMS data differentiated AUD from control WM. The dominant effect of AUD was to broadly reduce expression of sphingolipids (sulfatides and ceramides) and phospholipids. Data bar plots demonstrated overall similar responses to AUD in BA4 and BA8/9. However, differential regional effects of AUD on WM lipid profiles were manifested by non-overlapping expression or discordant responses to AUD for a subset of lipid ions. CONCLUSIONS: Human AUD is associated with substantial inhibition of frontal lobe WM lipid expression with regional variability in these effects. MALDI-IMS can be used to characterize the nature of AUD-associated lipid biochemical abnormalities for correlation with lifetime exposures and WM degeneration, altered gene expression, and responses to abstinence or treatment.
Evidence supporting oxidative stress in a moderately affected area of the brain in Alzheimer’s disease
18 December 2018
University of Sydney

Youssef, P;Chami, B;Lim, J;Middleton, T;Sutherland, GT;Witting, PK

The pathogenesis of Alzheimer's disease (AD) remains to be elucidated. Oxidative damage and excessive beta-amyloid oligomers are components of disease progression but it is unclear how these factors are temporally related. At post mortem, the superior temporal gyrus (STG) of AD cases contains plaques, but displays few tangles and only moderate neuronal loss. The STG at post mortem may represent a brain region that is in the early stages of AD or alternately a region resistant to AD pathogenesis. We evaluated expression profiles and activity of endogenous anti-oxidants, oxidative damage and caspase activity in the STG of apolipoprotein ε4-matched human AD cases and controls. Total superoxide dismutase (SOD) activity was increased, whereas total glutathione peroxidase (GPX), catalase (CAT) and peroxiredoxin (Prx) activities, were decreased in the AD-STG, suggesting that hydrogen peroxide accumulates in this brain region. Transcripts of the transcription factor NFE2L2 and inducible HMOX1, were also increased in the AD-STG, and this corresponded to increased Nuclear factor erythroid 2-related factor (NRF-2) and total heme-oxygenase (HO) activity. The protein oxidation marker 4-hydroxynonenal (4-HNE), remained unchanged in the AD-STG. Similarly, caspase activity was unaltered, suggesting that subtle redox imbalances in early to moderate stages of AD do not impact STG viability.
An inverse analysis approach for the identification of the hygro-thermo-chemical model parameters of concrete
22 January 2019
University of Sydney

Bocciarelli, Massimiliano;Ranzi, Gianluca

Hygro-thermo-chemical models provide useful representations of the mechanisms of moisture transport and tem- perature variations that take place in concrete structures and that can influence their durability and service behaviour. Several material parameters need to be specified when performing a hygro-thermo-chemical simu- lation. While some of these parameters can be evaluated based on the concrete mix specifications or from data reported in the literature, some other parameters are not readily available from the literature, partly because of their large variability and partly because they do not possess a precise physical meaning. In this context, this pa- per presents a robust inverse analysis procedure for the identification of this latter set of material parameters. The inverse analysis problem is formulated by using temperature and relative humidity profiles taking place within a concrete component as input. The proposed approach is applied to evaluate the minimum number of temper- ature and relative humidity measurements that are necessary to be performed for a successful identification of the sought material parameters. Representative results of an extensive sensitivity analysis are presented to gain insight into the most effective locations within the concrete component for the measurements and instants in time when these measurements should be collected. The inverse analysis procedure is then presented and validated against a set of pseudo-experimental results affected by different levels of noise, highlighting the robustness of the proposed methodology when applied with the arrangements suggested in terms of discrete relative humidity and temperature measurements and monitoring periods.
Identification of the hygro-thermo-chemical-mechanical model parameters of concrete through inverse analysis
22 January 2019
University of Sydney

Bocciarelli, Massimiliano;Ranzi, Gianluca

A wide range of parameters is required in input when applying hygro-thermo-chemical-mechanical models to concrete components with the aim of determining the variations over time of temperature, relative humidity and shrinkage induced deformations. While a sub-set of these material parameters can be evaluated on the basis of the concrete mix specifications or from literature data, this paper presents a robust inverse analysis procedure for the identification of the remaining sub-set of parameters that are characterised by a large variability and, in some cases, do not have a precise physical meaning and are not amenable to a direct measurement. The particularity of this paper is to propose different strategies for the characterisation of these material parameters that account for the presence of different exposure conditions, as these affect the outcomes and requirements of the parameter identification procedure. After introducing the adopted hygro-thermo-chemical-mechanical model, representative results of an extensive sensitivity analysis are presented in the first part of the paper to give insight into most effective number, location and duration of measurements to be used in input of the inverse analysis. The inverse analysis procedure is then presented and applied to a number of selected scenarios to highlight its robustness considering different boundary conditions in terms of external temperature and relative humidity surrounding the concrete. The ability to characterise these parameters will support a wider use of these hygro-thermo-chemical-mechanical models, especially for those applications in which humidity and temperature profiles significantly influence the structural response, for example when predicting curling in industrial pavements and non-uniform shrinkage profiles in composite steel-concrete slabs.
Influence of type and dosage of micro-fibres on the physical properties of fibre reinforced mortar matrixes
22 January 2019
University of Sydney

Simões, T.;Costa, H.;Dias-da-Costa, D.;Júlio, E.

An experimental study is herein presented focusing the physical properties of fibre-reinforced mortar. A reference mortar mixture was adopted and three different types of reinforcement with micro fibres (steel, polypropylene and glass) were adopted, adding different volumetric dosages, ranging from 0.5% to 2%, in 0.5% increments. The influence of each type of fibre and dosage on the properties of the mixture, including workability, density, porosity, and Young’s modulus was analysed. In summary, it was observed that the workability was extremely reduced for polypropylene and glass fibres. It was found that this parameter has an important role in terms of porosity and bulk density. The latter property decreased until 8% when polypropylene or glass fibres were added to the reference mixture. However, the porosity was significantly higher for mixtures with those fibres, with values reaching nearly twice the porosity of the reference mixture. The dynamic Young’s modulus was not highly sensitive to the presence of steel fibres, with a reduction lower than 5% in all tested dosages. In the case of mixtures reinforced with polypropylene fibres and glass fibres, this reduction has reached at most 16% and 13%, respectively. This effect was even higher for the static Young’s modulus, experiencing a maximum reduction of 32%, for a 0.5% dosage of polypropylene fibres.
Comparison of Reynolds averaging Navier-Stokes (RANS) turbulent models in predicting wind pressure on tall buildings
24 January 2019
University of Sydney

Mohotti, D.;Wijesooriya, K.;Dias-da-Costa, D.

This paper presents a detailed comparison of using Reynolds Averaging Navier-Stokes (RANS) approach in predicting wind pressure on a super-tall 406 m slender tower with circular cross-section. The results obtained from wind tunnel tests using a rigid model approach in a boundary layer wind tunnel (BLWT) were compared to that of Computational Fluid Dynamics (CFD) numerical simulations. The main objective of this study is to critically investigate the possibility of using RANS turbulent model based CFD approach in tall building design. Three different RANS turbulence models were compared with the wind tunnel data in predicting flow characteristics. The detailed wind tunnel experimental procedure and numerical approach are discussed and presented. It was shown that the shear stress transport (SST) variant model,could predict pressure coefficients comparable to that of the wind tunnel experiments. The influence of flow separation point on flow characterisation and pressure prediction is highlighted. The improvement that can be made in the near-wall region in the finite volume mesh to achieve an accurate separation point is presented. The effects of Reynolds number produced in the wind tunnel and scaled-down numerical models were compared with the anticipated full-scale flow Reynolds number. Hence, it is shown that a correct modelling technique in CFD using RANS turbulence models can be used as an alternative design approach of super-tall structures to estimate wind-induced pressures.
Spin-orbit coupling controlled ground state in the Ir(V) perovskites A2ScIrO6 (A = Ba or Sr)
20 February 2019
University of Sydney

Kayser, Paula;Kennedy, Brendan J;Ranjbar, Ben;Kimpton, Justin;Avdeev, Maxim

The structural and magnetic properties of the two Ir(V) perovskites Ba2ScIrO6 and Sr2ScIrO6 have been established. The structures were refined using a combined neutron and Synchrotron data set. At room temperature the former has a cubic structure in space group Fm3 ̅m a = 8.1450(3) Å and the latter is monoclinic in P21/n with a = 5.6606(3) b= 5.6366(3) c = 7.9720(4) Å β = 89.977(5)°. Magnetization measurements show both oxides have magnetic moments close to zero as a consequence of strong spin-orbit coupling that results in a Jeff ~ 0 ground state. The distortion of the IrO6 octahedra in Sr2ScIrO6 is insufficient to generate crystal field splitting strong enough to quench the spin orbit coupling.
Magnetic and structural studies of Sc containing ruthenate double perovskites A2ScRuO6 (A = Ba, Sr).
20 February 2019
University of Sydney

Kayser, Paula;Injac, Sean;Ranjbar, Ben;Kennedy, Brendan J;Avdeev, Maxim;Yamaura, Kazunari

Ruthenium containing double perovskites A2ScRuO6 have been synthesized as polycrystalline powders and structurally characterized using a combination of synchrotron X-ray and neutron powder diffraction methods. When A = Ba a hexagonal 6L perovskite structure is obtained if the synthesis is conducted at ambient pressure and a rock-salt ordered cubic structure obtained if the sample is quenched from high pressures. The Sr oxide Sr2ScRuO6 is obtained with a rock-salt ordered corner sharing topology. Heat capacity and bulk magnetic susceptibility measurements show the three oxides are antiferromagnets. Cubic Ba2ScRuO6 undergoes a metal-insulator transition near 270 K and hexagonal Ba2ScRuO6 is a semiconductor with an activation energy of 0.207 eV. The magnetic structures of the two rock-salt ordered double perovskites were established using powder neutron diffraction, and are described by k = (001) and k = (000) for the Ba and Sr oxides respectively, corresponding to type I antiferromagnetic structures, with ferromagnetic layers stacked antiferromagnetically. The ambient pressure hexagonal polymorph of Ba2ScRuO6 has partial Sc-Ru ordering at both the face-sharing B2O9 dimer and corner sharing BO6 sites. The magnetic structure is described by k = (½ 0 0) with the basis vector belonging to the irreducible representation Γ3.
Structural and magnetic properties of the osmium double perovskites Ba2-xSrxYOsO6
20 February 2019
University of Sydney

Kayser, Paula;Injac, Sean;Kennedy, Brendan J;Vogt, Thomas;Avdeev, Maxim;Maynard-Casely, Helen;Zhaoming, Zhang

The crystal and magnetic structures of double perovskites of the type Ba2-xSrxYOsO6 have been studied by synchrotron X-ray and neutron powder diffraction methods, bulk magnetic susceptibility measurements and X-ray absorption spectroscopy. The structures were refined using a combined neutron and synchrotron data set and are based on ordered array of corner sharing YO6 and OsO6 octahedra, with the Ba/Sr cations being completely disordered. The structure evolves from cubic to monoclinic as the Sr content is increased, due to the introduction of cooperative tilting of the octahedra. Bulk magnetic susceptibility measurements demonstrate the oxides are all antiferromagnets. The decrease in symmetry results in a, non-linear, increase in the Neel temperature. Low temperature neutron diffraction measurements of selected examples show these to be type-I antiferromagnets. X-ray absorption spectra collected at the Os L3- and L2-edges confirm the Os is pentavalent in all cases, and there is no detectable change in the covalency of the Os cation as the A-cation changes. Analysis of the L3:L2 branching ratio shows that the spin-orbit coupling is constant and insignificant across the series.
Structure and phase transition in BaThO3: A combined neutron and synchrotron X-ray diffraction study
21 February 2019
University of Sydney

Gabriel L, Murphy;Brendan J, Kennedy;Zhaoming, Zhang;Avdeev, Maxim;Helen, Brand;Philip, Kegler;Evgeny V, Alekseev

The structure of BaThO3, obtained by solid state synthesis, was refined for the first time by the Rietveld method using a combination of synchrotron X-ray and neutron powder diffraction data. BaThO3 has an orthorhombic structure at room temperature, in space group Pbnm with a = 6.3491(5), b = 6.3796(4) and c = 8.9907(7) Å. Heating BaThO3 to above 700 °C results in a continuous transition to a second orthorhombic structure, in space group Ibmm, demonstrated by both in situ neutron and synchrotron X-ray powder diffraction measurements. The coefficient of volumetric thermal expansion for BaThO3 is determined to be 1.04 x 10-5 oC-1 from 50 to 625 oC (Pbnm phase), and 9.43 x 10-6 oC-1 from 800 to 1000 oC (Ibmm phase). BaThO3 was found to decompose upon exposure to atmospheric moisture resulting in the formation of ThO2. The thermal expansion of ThO2, which invariably co-exists with BaThO3, is also described.
Thermal Expansion Behavior in TcO2. Towards breaking the Tc-Tc bond.
21 February 2019
University of Sydney

Reynolds, Emily;Zhang, Zhaoming;Avdeev, Maxim;Thorogod, Gordon J;Poineau, Frederic;Czerwinski, Kenneth R;Kimpton, Justin A;Kennedy, Brendan J

The structure of TcO2 between 25 and 1000 °C has been determined in-situ using powder diffraction methods and is found to remain monoclinic in space group P21/c. The thermal expansion in TcO2 is highly anisotropic with negative thermal ex-pansion of the b-axis observed above 700 °C. This is the result of an anomalous expansion along the a-axis that is a consequence of weakening of the Tc-Tc bonds.
Thermal Expansion in BaRuO3 Perovskites – an unusual case of bond strengthening at high temperatures
21 February 2019
University of Sydney

Kayser, Paula;Injac, Sean;Kennedy, Brendan J;Menezes de Oliveira, Andre;Shirako, Yuichi;Hasegawa, Masashi

The temperature dependence of the structures of three polytypes of BaRuO3 have been investigated between room temperature and 1000 °C using high resolution Synchrotron X-ray diffraction. The structural studies reveal a systematic decrease in the Ru-Ru distance as the pressure required to prepare the polytype increases. The O-O distance across the shared face increases as the Ru-Ru separation decreases. The 9R and 4H polytypes undergo unexceptional changes with increasing temperature. In 6H-BaRuO3 there is an apparent increase in the Ru-Ru interaction around 650 °C and concurrent reduction in the O-O distance indicating an anomalous strengthening of the Ru-Ru interactions upon heating.
The impact of anion ordering on octahedra distortion and phase transitions in SrTaO2N and BaTaO2N
21 February 2019
University of Sydney

Wang, Chun-Hai;Kennedy, Brendan J;Menezes de Oliveira, Andre;Polt, Julia;Knight, Kevin S

In this work, we synthesized BaTaO2N and SrTaO2N using a two-step high temperature solid state reaction method and analysed the structural distortions, relative to the ideal cubic perovskite structure, according to group theory. From a complete distortion analysis/refinement using high resolution neutron diffraction data in the temperature range 8 K to 613 K, we identified tetragonal structures for BaTaO2N [P4/mmm (No 123)] and SrTaO2N [I4/mcm (No 140)]. In contrast to an anion-disordered cubic perovskite (Pm3 ̅m No 221) with Ta at the cell center, both systems show a site preference for oxygen anions in the two opposite corners (along the c axis) of the Ta-O/N octahedra rather than the four square corners in the ab plane (Γ3+ occupancy distortion), which induces a tetragonal elongation of the unit cell with the c axis being longer than the a axis. A further Ta-O/N octahedra displacement [R5-(a,0,0), rotation about the c axis] distortion was observed in SrTaO2N. This distortion mode is accompanied by an increased unit cell distortion that decreases as the temperature increases. Ultimately a second-order phase transition caused by the loss of the R5-(a,0,0) mode was observed at 400 – 450 K.
Structure and Magnetism in Sr1-xAxTcO3 Perovskites. The importance of the A-site cation.
22 February 2019
University of Sydney

Reynolds, Emily;Avdeev, Maxim;Thorogood, Gordon J;Poineau, Frederic;Czerwinski, Kenneth R;Kimpton, Justin A;Yu, Michelle;Kayser, Paula;Kennedy, Brendan J

The Sr1-xBaxTcO3 (x = 0, 0.1, 0.2) oxides were prepared and their solid-state and magnetic structure studied as a function of the temperature by x-ray and neutron powder diffraction. The refined Tc moments at room temperature and Nèel temperatures for Ba0.1Sr0.9TcO3 and Ba0.2Sr0.8TcO3 were 2.32(14) μβ and 2.11(13) μβ and 714 °C and 702 °C respectively. In contrast to expectations, the Nèel temperature in the series Sr1-xAxTcO3 decreases with increasing Ba content. This observation is consistent with previous experimental measurements for the two series AMO3 (M = Ru, Mn; A = Ca, Sr, Ba) where the maximum magnetic ordering temperature was observed for A = Sr. Taken with these previous results the current work demonstrates the critical role of the A-site cation in the broadening of the π* bandwidth and ultimately the magnetic ordering temperature.
Low temperature structure and the ferroelectric phase transitions in the CdTiO3 perovskite
22 February 2019
University of Sydney

Kennedy, Brendan J;Zhou, Qingdi;Zhao, Shipeng;Jia, Fanhao;Ren, Wei;Knight, Kevin S

The paraelectric-ferroelectric transition in CdTiO3 has been monitored using high resolution neutron diffraction data. This necessitated preparing a sample enriched in 114Cd. A subtle, but significant, anisotropy in the thermal expansion of the lattice parameters for CdTiO3 associated with the transition to the polar structure was observed. First-principles calculations are presented to understand energies, phonon dispersion, and structures of possible phases with different symmetries.
The ferroelectric phase of CdTiO3. A powder neutron diffraction study.
22 February 2019
University of Sydney

Kennedy, Brendan J;Zhou, Qingdi;Avdeev, Maxim

The synthesis of bulk samples of polycrystalline CdTiO3 in both the rhombohedral ilmenite and orthorhombic perovskite forms is described and the structures of these have been refined using powder neutron diffraction data. This involved the preparation of samples enriched in Cd-114. Cooling perovskite-type CdTiO3 to 4 K induces a ferroelectric phase transition, with the neutron data suggesting the low temperature structure is in Pna21. Mode analysis shows the polar mode to be dominant at low temperatures. The ilmenite-structure of CdTiO3 is compared with that of ZnTiO3. The refined scattering length of the Cd-114 is estimated to be 5.56 fm.
A Generalized Equatorial Model for the Accelerating Solar Wind
22 February 2019
University of Sydney

Tasnim, Samira;Cairns, Iver H.;Wheatland, Michael S.

A new theoretical model for the solar wind is developed that includes the wind’s acceleration, conservation of angular momentum, deviations from corotation, and nonradial velocity and magnetic ﬁeld components from an inner boundary (corresponding to the onset of the solar wind) to beyond 1 AU. The model uses a solution of the time-steady isothermal equation of motion to describe the acceleration and analytically predicts the Alfvénic critical radius. We ﬁt the model to near-Earth observations of the Wind spacecraft during the solar rotation period of 1–27 August 2010. The resulting data-driven model demonstrates the existence of noncorotating, nonradial ﬂows and ﬁelds from the inner boundary (r = rs)outward and predicts the magnetic ﬁeld B = (Br , B𝜙), velocity v = (vr , v𝜙), and density n(r , 𝜙, t), which vary with heliocentric distance r, heliolatitude 𝜙 , and time t in a Sun-centered standard inertial plane. Thedescription applies formally only in the equatorial plane. In a frame corotating with the Sun, the transformed velocity v ′ and a ﬁeld B′are not parallel, resulting in an electric ﬁeld with a component E′z along the z axis.The resulting E ′ × B′ = E ′ × B drift lies in the equatorial plane, while the 𝛁 B and curvature drifts are out of the plane. Together these may lead to enhanced scattering/heating of suﬃciently energetic particles. The model predicts that deviations 𝛿 v𝜙 from corotation at the inner boundary are common, with 𝛿 v𝜙(rs , 𝜙s , ts) comparable to the transverse velocities due to granulation and supergranulation motions. Abrupt changesin 𝛿 v𝜙(rs , 𝜙s , ts) are interpreted in terms of converging and diverging ﬂows at the cell boundaries and centers, respectively. Large-scale variations in the predicted angular momentum demonstrate that the solar wind can drive vorticity and turbulence from near the Sun to 1 AU and beyond.
Passive magnetic shielding in MRI-Linac systems.
01 March 2019
University of Sydney

Whelan, B;Kolling, S;Oborn, BM;Keall, P

Passive magnetic shielding refers to the use of ferromagnetic materials to redirect magnetic field lines away from vulnerable regions. An application of particular interest to the medical physics community is shielding in MRI systems, especially integrated MRI-linear accelerator (MRI-Linac) systems. In these systems, the goal is not only to minimize the magnetic field in some volume, but also to minimize the impact of the shield on the magnetic fields within the imaging volume of the MRI scanner. In this work, finite element modelling was used to assess the shielding of a side coupled 6 MV linac and resultant heterogeneity induced within the 30 cm diameter of spherical volume (DSV) of a novel 1 Tesla split bore MRI magnet. A number of different shield parameters were investigated; distance between shield and magnet, shield shape, shield thickness, shield length, openings in the shield, number of concentric layers, spacing between each layer, and shield material. Both the in-line and perpendicular MRI-Linac configurations were studied. By modifying the shield shape around the linac from the starting design of an open ended cylinder, the shielding effect was boosted by approximately 70% whilst the impact on the magnet was simultaneously reduced by approximately 10%. Openings in the shield for the RF port and beam exit were substantial sources of field leakage; however it was demonstrated that shielding could be added around these openings to compensate for this leakage. Layering multiple concentric shield shells was highly effective in the perpendicular configuration, but less so for the in-line configuration. Cautious use of high permeability materials such as Mu-metal can greatly increase the shielding performance in some scenarios. In the perpendicular configuration, magnetic shielding was more effective and the impact on the magnet lower compared with the in-line configuration.
Very narrow coronal mass ejections producing solar energetic particles
06 March 2019
University of Sydney

Bronarska, K.;Wheatland, Michael S.;Gopalswamy, N.;Michalek, G.

Aims. Our main aim is to study the relationship between low-energy solar particles (energies below 1 MeV) and very narrow coronal mass ejections (“jets” with angular width ≤20 ◦ ). Methods. For this purpose, we considered 125 very narrow coronal mass ejections (CMEs) from 1999 to 2003 that are potentially associated with low-energy solar particles (LESPs). These events were chosen on the basis of their source location. We studied only very narrow CMEs at the western limb, which are expected to have good magnetic connectivity with Earth. Results. We found 24 very narrow CMEs associated with energetic particles such as ions (protons and 3 He), electrons, or both. We show that arrival times at Earth of energetic particles are consistent with onset times of the respective CMEs, and that in the same time intervals, there are no other potential sources of energetic particles. We also demonstrate statistical di ﬀ erences for the angular width distributions using the Kolmogorov–Smirnov test for angular widths for these 24 events. We consider a coherent sample of jets (mostly originating from boundaries of coronal holes) to identify properties of events that produce solar energetic particles (velocities, widths, and position angles). Our study presents a new approach and result: very narrow CMEs can generate low-energy particles in the vicinity of Earth without other activity on the Sun. The results could be very useful for space weather forecasting.
Effects of storage conditions on the stability of spray dried, inhalable bacteriophage powders
17 May 2019
University of Sydney

Leung, Sharon SY;Parumasivam, Thaigarajan;Gao, Fiona G;Carrigy, Nicholas B;Vehring, Reinhard;Finlay, Warren H;Morales, Sandra;Britton, Warwick J;Kutter, Elizabeth;Chan, Hak-Kim

This study aimed to develop inhalable powders containing phages active against antibiotic-resistant Pseudomonas aeruginosa for pulmonary delivery. A Pseudomonas phage, PEV2, was spray dried into powder matrices comprising of trehalose (0–80%), mannitol (0–80%) and L-leucine (20%). The resulting powders were stored at various relative humidity (RH) conditions (0, 22 and 60% RH) at 4 ºC. The phage stability and in vitro aerosol performance of the phage powders were examined at the time of production and after 1, 3 and 12 months storage. After spray drying, a total of 1.3 log titer reduction in phage was observed in the formulations containing 40%, 60% and 80% trehalose, whereas 2.4 and 5.1 log reductions were noted in the formulations containing 20% and no trehalose, respectively. No further reduction in titer occurred for powders stored at 0 and 22% RH even after 12 months, except the formulation containing no trehalose. The 60% RH storage condition had a destructive effect such that no viable phages were detected after 3 and 12 months. When aerosolised, the total lung doses for formulations containing 40%, 60% and 80% trehalose were similar (in the order of 105 pfu). The results demonstrated that spray drying is a suitable method to produce stable phage powders for pulmonary delivery. A powder matrix containing ≥ 40% trehalose provided good phage preservation and aerosol performances after storage at 0 and 22 % RH at 4 ºC for 12 months.
Microfluidic-assisted bacteriophage encapsulation into liposomes
17 May 2019
University of Sydney

Leung, Sharon SY;Morales, Sandra;Britton, Warwick;Kutter, Elizabeth;Chan, Hak-Kim

Microfluidics has recently emerged as a new method of manufacturing liposomes, which allows reproducible mixing in miliseconds on the nanoliter scale. Here we investigated the feasibility of a microfluidic flow focusing setup built from commercially available fittings to encapsulate phages into liposomes. Two types of Pseudomonas phages, PEV2 (Podovirus, ~65 nm) and PEV40 (Myovirus, ~220 nm), were used as model phages. A mixture of soy phosphatidylcholine and cholesterol at a ratio of 4:1 dissolved in absolute ethanol with a total solid content of 17.5 mg/mL was injected through the center inlet channel of a cross mixer. Phage suspensions were injected into the cross mixer from the two side channels intersecting with the center channel. The total flow rate (TFR) varied 160 – 320 µL/min and the organic/aqueous flow rate ratio (FRR) varied 1:3 to 2:3. The size of liposomes and the encapsulation efficiency both increased with increasing FRR and slightly decreased with increasing TFR. Due to the different size of the two studied phages, the size of liposomes encapsulating PEV2 were smaller (135 – 218 nm) than those encapsulating the Myovirus PEV40 (261 – 448 nm). Highest encapsulation efficiency of PEV2 (59%) and PEV40 (50%) was achieved at a TFR of 160 µL/ml and a FRR of 2:3. Generally, the encapsulation efficiency was slightly higher than that obtained from the conventional thin film hydration followed by extrusion method. In summary, the proposed microfluidic technique was capable of encapsulating phages of different size into liposomes with reasonable encapsulation efficiency and minimal titer reduction.
Jet nebulization of bacteriophages with different tail morphologies – structural effects
17 May 2019
University of Sydney

Leung, Sharon SY;Carrigy, Nicholas B;Vehring, Reinhard;Finlay, Warren H;Morales, Sandra;Carter, Elizabeth A;Britton, Warwick J;Kutter, Elizabeth;Chan, Hak-Kim

It was previously demonstrated that the loss of infectivity of a myovirus PEV44 after jet nebulization was closely related to a change in bacteriophage (phage) structure. In this follow-up study, we further examined the impact of jet nebulization on tailed phages, which constitute 96% of all known phages, from three different families, Podoviridae (PEV2), Myoviridae (PEV40) and Siphoviridae (D29). Transmission electron microscopy (TEM) identified major changes in phage structures after jet nebulization, correlating with their loss of infectivity. For the podovirus PEV2, jet nebulization had a negligible impact on activity (0.04 log10¬ pfu/mL loss) and structural change. On the other hand, the proportion of intact phages in the nebulised samples dropped from 50% to ~27% for PEV40 and from 15% to ~2% for D29. Phage deactivation of PEV40 measured by the TEM structural damage (0.52 log10¬ pfu/mL) was lower than that obtained by plaque assay (1.02 log10 pfu/mL), but within the range of variation (± 0.5 log10 pfu/mL). However, TEM quantification considerably underestimated the titer reduction of D29 phage, ~ 2 log pfu/mL lower than that obtained in plaque assay (3.25 log10 pfu/mL). In conclusion, nebulisation-induced titre loss was correlated with morphological damage to phages and in particular, the tail length may be an important consideration for selection of phages in inhaled therapy using jet nebulization.
Dichotomous well-defined nanostructure with weakly arranged ion packing explains the solvency of pyrrolidinium acetate
24 May 2019
University of Sydney

Jiang, Haihui Joy;Imberti, Silvia;Atkin, Rob;Warr, Gregory

Pyrrolidinium ionic liquids, especially pyrrolidinium acetate (PyrrAc), have demonstrated outstanding capacity for extracting lignin from biomass, as electrolytes for fuel cells and lithium ion batteries and as solvents for acid-catalysed reactions. In this work we show that the unusual liquid nanostructure of PyrrAc is the key to its versatility as a solvent compared to other ionic liquids. Neutron diffraction with multiple H/D isotopic substitutions reveals that the bulk nanostructure of PyrrAc is a bicontinuous network of interpenetrating polar and apolar domains. However, the arrangement of groups in both domains is strikingly different from that found in other ionic liquids. In the apolar regions, the pyrrolidinium rings are highly intercalated and disordered, with no preferred alignment between adjacent pyrrolidinium rings, which distinguishes it from both π−π stacking seen in imidazolium or pyridinium ionic liquids, and the tail-tail bilayer-like arrangements in linear alkylammonium ionic liquids. The H-bond network within the polar domain extends only to form finite clusters, with long bent H-bonds to accommodate electrostatics. Therefore, while PyrrAc unquestionably has well defined amphiphilic nanostructure, the disordered arrangement of groups in the polar and apolar domains enables it to accommodate a wide variety of solutes. The combination of well-defined polar/apolar nanostructure, but disordered arrangements of groups within domains, is therefore the origin of PyrrAc’s capacity for lignin extraction and as an electrolyte.
Geodynamic reconstruction of an accreted Cretaceous back-arc basin in the Northern Andes
31 July 2019
University of Sydney

Braz, Carmen;Seton, Maria;Flament, Nicolas;Muller, R. Dietmar

A complex history of subduction, back-arc basin formation, terrane accretion and transpressional shearing characterizes the evolution of the Caribbean and northern South American margin since Jurassic times. Quantitative plate tectonic reconstructions of the area do not include Jurassic-Cretaceous back-arc terranes of which there are both geological and geophysical observations. We developed a revised plate tectonic reconstruction based on geological observations and seismic tomography models to constrain the Jurassic-Cretaceous subduction history of eastern Panthalassa, along the western margin of the Caribbean region. This reconstruction considers the opening of a Northern Andean back-arc basin at 145 Ma, the Quebradagrande back-arc, closing at 120 Ma and followed by terrane accretion and northward translation along the South American margin starting at 100 Ma. This kinematic reconstruction is tested against two previously published tectonic reconstructions via coupling with global numerical mantle convection models using CitcomS. A comparison of modelled versus tomographically imaged mantle structure reveals that subduction outboard of the South American margin, lacking in previous tectonic models, is required to reproduce mid-mantle positive seismic anomalies imaged in P- and S-wave seismic tomography beneath South America, 500–2000 km in depth. Furthermore, we show that this subduction zone is likely produced by a back-arc basin that developed along the northern Andes during the Cretaceous via trench roll-back from 145 Ma and was closed at 100 Ma. The contemporaneous opening of the Quebradagrande back-arc basin with the Rocas Verdes back-arc basin in the southern Andes is consistent with a model that invokes return flow of mantle material behind a retreating slab and may explain why extension along the Peruvian and Chilean sections of the Andean margin did not experience full crustal break-up and back-arc opening during the late Jurassic-early Cretaceous Period.
Tectonic evolution of Western Tethys from Jurassic to present day: coupling geological and geophysical data with seismic tomography models
01 August 2019
University of Sydney

Hosseinpour, Maral;Williams, Simon;Seton, Maria;Barnett-Moore, Nicholas;Muller, R. Dietmar

The geodynamic evolution of the Western Tethys is characterized by multiple phases of rifting, seafloor spreading, subduction, and collisional events. Regional reconstructions are highly dependent on the kinematic history of the major plates bounding the Atlantic and Tethyan tectonic domains, as well as small micro-plates resulted from the fragmentation of northern Gondwanaland. The complexity of tectonic events in this area leads to major discrepancies between competing models about the timing, location, and polarity of subduction zones, for both the Cenozoic evolution and earlier phases. We focus on unravelling the Mesozoic evolution of the Western Tethys. We first reassessed kinematic models for the Early Jurassic–Late Cretaceous opening of the central, north central, and north Atlantic and used these as boundary conditions on the kinematic reconstructions of the Tethyan realm. We combined reconstructions of rifting and early seafloor spreading in northern Pangea that incorporate quantitative estimates of continental extension, and suggest a transtensional motion of Iberia relative to Europe in Early Cretaceous time to fit within the refined plate configuration of Central North Atlantic. We combined this regional framework with a recently published model for the motion of smaller blocks within the Western Tethys; from this model, we created synthetic isochrons for extinct oceanic basins and built evolving topological plate boundaries based on the new rigid plate model to derive a self-consistent and time-dependant model for the last 200 million years. We then examined the consistency of subduction history implied by the kinematic reconstructions, by comparing reconstructed plate boundary configurations to mantle velocity structure imaged by a range of seismic tomography models. Our results show that a satisfactory match can be made between Cenozoic subduction events in the Western Tethys region and observed shallow tomographic high-velocity material. However, the match is less clear for older subducted material. Correlations between surface reconstructions and deep Earth structure suggest that mid-deep mantle seismic features under present day Northeast-Central and Northwest Africa-Arabia may correspond with the Mesozoic subduction systems in the Vardar Ocean, Alpine Tethys, and Western Neotethys, respectively. These correlations support a model with intra-oceanic subduction of the Vardar Ocean from Middle Jurassic to Early Cretaceous, and mid-Early Cretaceous initiation of oceanic subduction in the Ligurian-Piemont Ocean. The results from the plate-tomography comparison suggest the existence of oceanic subduction in the Alpine Tethys Oceans in late early Cretaceous time. We investigated the uncertainties in the tectonic model in terms of absolute and relative plate motion and surface velocities and showed that choice of absolute reference frame can partially account for the lateral offset between the Vardar subduction zone and associated slab material in deep mantle; additional mismatches may be attributable to the limitations of our methodology, such as the assumption that slabs sink vertically. © 2016 Informa UK Limited, trading as Taylor & Francis Group.
Melanesian back-arc basin and arc development: Constraints from the eastern Coral Sea
01 August 2019
University of Sydney

Seton, Maria;Mortimer, Nick;Williams, Simon;Quilty, Patrick;Gans, Phil;Meffre, Sebastien;Micklethwaite, Steven;Zahirovic, Sabin;Moore, Jarrod;Matthews, Kara J

The eastern Coral Sea is a poorly explored area at the north-eastern corner of the Australian Tectonic Plate, where interaction between the Pacific and Australian plate boundaries, and accretion of the world's largest submarine plateau – the Ontong Java Plateau – has resulted in a complex assemblage of back-arc basins, island arcs, continental plateaus and volcanic products. This study combines new and existing magnetic anomaly profiles, seafloor fabric from swath bathymetry data, Ar–Ar dating of E-MORB basalts, palaeontological dating of carbonate sediments, and plate modelling from the eastern Coral Sea. Our results constrain commencement of the opening of the Santa Cruz Basin and South Rennell Trough to c. 48 Ma and termination at 25–28 Ma. Simultaneous opening of the Melanesian Basin/Solomon Sea further north suggests that a single > 2000 km long back-arc basin, with at least one triple junction existed landward of the Melanesian subduction zone from Eocene–Oligocene times. The cessation of spreading corresponds with a reorganisation of the plate boundaries in the area and the proposed initial soft collision of the Ontong Java Plateau. The correlation between back-arc basin cessation and a widespread plate reorganisation event suggests that back-arc basins may be used as markers for both local and global plate boundary changes.
Global plate boundary evolution and kinematics since the late Paleozoic
01 August 2019
University of Sydney

Matthews, Kara J;Maloney, Kayla T;Zahirovic, Sabin;Williams, Simon E;Seton, Maria;Muller, R. Dietmar

Many aspects of deep-time Earth System models, including mantle convection, paleoclimatology, paleobiogeography and the deep Earth carbon cycle, require high-resolution plate motion models that include the evolution of the mosaic of plate boundaries through time. We present the first continuous late Paleozoic to present-day global plate model with evolving plate boundaries, building on and extending two previously published models for the late Paleozoic (410–250 Ma) and Mesozoic-Cenozoic (230–0 Ma). We ensure continuity during the 250–230 Ma transition period between the two models, update the absolute reference frame of the Mesozoic-Cenozoic model and add a new Paleozoic reconstruction for the Baltica-derived Alexander Terrane, now accreted to western North America. This 410–0 Ma open access model provides a framework for deep-time whole Earth modelling and acts as a base for future extensions and refinement. We analyse the model in terms of the number of plates, predicted plate size distribution, plate and continental root mean square (RMS) speeds, plate velocities and trench migration through time. Overall model trends share many similarities to those for recent times, which we use as a first order benchmark against which to compare the model and identify targets for future model refinement. Except for during the period ~ 260–160 Ma, the number of plates (16–46) and ratio of “large” plates (≥ 107.5 km2) to smaller plates (~ 2.7–6.6) are fairly similar to present-day values (46 and 6.6, respectively), with lower values occurring during late Paleozoic assembly and growth of Pangea. This temporal pattern may also reflect difficulties in reconstructing small, now subducted oceanic plates further back in time, as well as whether a supercontinent is assembling or breaking up. During the ~ 260–160 Ma timeframe the model reaches a minima in the number of plates, in contrast to what we would expect during initial Pangea breakup and thus highlighting the need for refinement of the relative plate motion model. Continental and plate RMS speeds show an overall increase backwards through time from ~ 200 to 365 Ma, reaching a peak at 365 Ma of > 14 and > 16 cm/yr, respectively, compared to ~ 3 and ~ 5 cm/yr, respectively, at present-day. The median value of trench motion remains close to, yet above 0 cm/yr for most of the model timeframe, with a dominance in positive values reflecting a prevalence of trench retreat over advance. Trench advance speeds are excessive during the 370–160 Ma period, reaching more than four times that observed at present-day. Extended periods of trench advance and global continental and plate RMS speeds that far exceed present-day values warrant further investigation. Future work should test whether alternative absolute reference frames or relative motions would mitigate these high speeds, while still being consistent with geologic and geophysical observations, or alternatively focus on identifying potential driving mechanisms to account for such rapid motions. © 2016 Elsevier B.V.
Tectonic evolution and deep mantle structure of the eastern Tethys since the latest Jurassic
01 August 2019
University of Sydney

Zahirovic, Sabin;Matthews, Kara J;Flament, Nicolas;Muller, R. Dietmar;Hill, Kevin C;Seton, Maria;Gurnis, Michaell

The breakup of Pangea in the Jurassic saw the opening of major ocean basins at the expense of older Tethyan and Pacific oceanic plates. Although the Tethyan seafloor spreading history has been lost to subduction, proxy indicators from multiple generations of Tethyan ribbon terranes, as well as the active margin geological histories of volcanism and ophiolite obduction events can be used to reconstruct these ancient oceanic plates. The plate reconstructions presented in this study reconcile observations from ocean basins and the onshore geological record to provide a regional synthesis, embedded in a global plate motion model, of the India-Eurasia convergence history, the accretionary growth of Southeast Asia and the Tethyan-Pacific tectonic link through the New Guinea margin. The global plate motion model presented in this study captures the time-dependent evolution of plates and their tectonic boundaries since 160 Ma, which are assimilated as surface boundary conditions for numerical experiments of mantle convection. We evaluate subducted slab locations and geometries predicted by forward mantle flow models against P- and S-wave seismic tomography models. This approach harnesses modern plate reconstruction techniques, mantle convection models with imposed one-sided subduction, and constraints from the surface geology to address a number of unresolved Tethyan geodynamic controversies. Our synthesis reveals that north-dipping subduction beneath Eurasia in the latest Jurassic consumed the Meso-Tethys, and suggests that northward slab pull opened the younger Neo-Tethyan ocean basin from ~ 155 Ma. We model the rifting of ‘Argoland’, representing the East Java and West Sulawesi continental fragments, as a northward transfer of continental terranes in the latest Jurassic from the northwest Australian shelf – likely colliding first with parts of the Woyla intra-oceanic arc in the mid-Cretaceous, and accreting to the Borneo (Sundaland) core by ~ 80 Ma. The Neo-Tethyan ridge was likely consumed along an intra-oceanic subduction zone south of Eurasia from ~ 105 Ma, leading to a major change in the motion of the Indian Plate by ~ 100 Ma, as observed in the Wharton Basin fracture zone bends. We investigate the geodynamic consequences of long-lived intra-oceanic subduction within the Neo-Tethys, requiring a two-stage India-Eurasia collision involving first contact between Greater India and the Kohistan-Ladakh Arc sometime between ~ 60 and 50 Ma, followed by continent-continent collision from ~ 47 Ma. Our models suggest that the Sunda slab kink beneath northwest Sumatra in the mantle transition zone results from the rotation and extrusion of Indochina from ~ 30 Ma. Our results are also the first to reproduce the enigmatic Proto South China Sea slab beneath northern Borneo, as well as the Tethyan/Woyla slab that is predicted at mid-mantle depths south of Sumatra. Further east, our revised reconstructions of the New Guinea margin, notably the evolution of the Sepik composite terrane and the Maramuni subduction zone, produce a better match with seismic tomography than previous reconstructions, and account for a slab at ~ 30°S beneath Lake Eyre that has been overridden by the northward advancing Australian continent. Our plate reconstructions provide a framework to study changing patterns of oceanic circulation, long-term sea level driven by changes in ocean basin volume, as well as major biogeographic dispersal pathways that have resulted from Gondwana fragmentation and accretion of Tethyan terranes to south- and southeast-Eurasia. © 2016 Elsevier B.V.
The Late Cretaceous to recent tectonic history of the Pacific Ocean basin
01 August 2019
University of Sydney

Wright, Nicky M;Seton, Maria;Williams, Simon E;Muller, R. Dietmar

A vast ocean basin has spanned the region between the Americas, Asia and Australasia for well over 100 Myr, represented today by the Pacific Ocean. Its evolution includes a number of plate fragmentation and plate capture events, such as the formation of the Vancouver, Nazca, and Cocos plates from the break-up of the Farallon plate, and the incorporation of the Bellingshausen, Kula, and Aluk (Phoenix) plates, which have been studied individually, but never been synthesised into one coherent model of ocean basin evolution. Previous regional tectonic models of the Pacific typically restrict their scope to either the North or South Pacific, and global kinematic models fail to incorporate some of the complexities in the Pacific plate evolution (e.g. the independent motion of the Bellingshausen and Aluk plates), thereby limiting their usefulness for understanding tectonic events and processes occurring in the Pacific Ocean perimeter. We derive relative plate motions (with 95% uncertainties) for the Pacific-Farallon/Vancouver, Kula-Pacific, Bellingshausen-Pacific, and early Pacific-West Antarctic spreading systems, based on recent data including marine gravity anomalies, well-constrained fracture zone traces and a large compilation of magnetic anomaly identifications. We find our well-constrained relative plate motions result in a good match to the fracture zone traces and magnetic anomaly identifications in both the North and South Pacific. In conjunction with recently published and well-constrained relative plate motions for other Pacific spreading systems (e.g. Aluk-West Antarctic, Pacific-Cocos, recent Pacific-West Antarctic spreading), we explore variations in the age of the oceanic crust, seafloor spreading rates and crustal accretion and find considerable refinements have been made in the central and southern Pacific. Asymmetries in crustal accretion within the overall Pacific basin (where both flanks of the spreading system are preserved) have typically deviated less than 5% from symmetry, and large variations in crustal accretion along the southern East Pacific Rise (i.e. Pacific-Nazca/Farallon spreading) appear to be unique to this spreading corridor. Through a relative plate motion circuit, we explore the implied convergence history along the North and South Americas, where we find that the inclusion of small tectonic plate fragments such as the Aluk plate are critical for reconciling the history of convergence with onshore geological evidence. © 2015 Elsevier B.V.
Kinematic constraints on the Rodinia to Gondwana transition
07 August 2019
University of Sydney

Merdith, Andrew S;Williams, Simon E;Muller, R. Dietmar;Collins, Alan S

Earth's plate tectonic history during the breakup of the supercontinent Pangea is well constrained from the seafloor spreading record, but evolving plate configurations during older supercontinent cycles are much less well understood. A relative paucity of available palaeomagnetic and geological data for deep time reconstructions necessitates innovative approaches to help discriminate between competing plate configurations. More difficult is tracing the journeys of individual continents during the amalgamation and breakup of supercontinents. Typically, deep-time reconstructions are built using absolute motions defined by palaeomagnetic data, and do not consider the kinematics of relative motions between plates, even for occasions where they are thought to be ‘plate-pairs’, either rifting apart leading to the formation of conjugate passive margins separated by a new ocean basin, or brought together by collision and orogenesis. Here, we use open-source software tools (GPlates/pyGPlates) to assess quantitative plate kinematics inherent within alternative reconstructions, such as rates of relative plate motion. We analyse the Rodinia-Gondwana transition during the Neoproterozoic, investigating the proposed Australia-Laurentia configurations during Rodinia, and the motion of India colliding with Gondwana. We find that earlier rifting times provide more optimal kinematic results. The AUSWUS and AUSMEX configurations with rifting at 800 Ma are the most kinematically supported configurations for Australia and Laurentia (average rates of 57 and 64 mm/a respectively), and angular rotation of ∼1.4°/Ma, compared to a SWEAT configuration (average spreading rate ∼76 mm/a) and Missing-Link configuration (∼90 mm/a). Later rifting, at, or after, 725 Ma necessitates unreasonably high spreading rates of >130 mm/a for AUSWUS and AUSMEX and ∼150 mm/a for SWEAT and Missing-Link. Using motion paths and convergence rates, we create a kinematically reasonable (convergence below 70 mm/a) tectonic model that is built upon a front-on collision of India with Gondwana, while also incorporating sinistral strike-slip motion against Australia and East Antarctica. We use this simple tectonic model to refine a global model for the breakup of western Rodinia and the transition to eastern Gondwana. © 2017 Elsevier B.V.
Dynamic topography of passive continental margins and their hinterlands since the Cretaceous
07 August 2019
University of Sydney

Muller, R. Dietmar;Hassan, Rakib;Gurnis, Michael;Flament, Nicolas;Williams, Simon E

Even though it is well accepted that the Earth's surface topography has been affected by mantle-convection induced dynamic topography, its magnitude and time-dependence remain controversial. The dynamic influence to topographic change along continental margins is particularly difficult to unravel, because their stratigraphic record is dominated by tectonic subsidence caused by rifting. We follow a three-fold approach to estimate dynamic topographic change along passive margins based on a set of seven global mantle convection models. We first demonstrate that a geodynamic forward model that includes adiabatic and viscous heating in addition to internal heating from radiogenic sources, and a mantle viscosity profile with a gradual increase in viscosity below the mantle transition zone, provides a greatly improved match to the spectral range of residual topography end-members as compared with previous models at very long wavelengths (spherical degrees 2–3). We then combine global sea level estimates with predicted surface dynamic topography to evaluate the match between predicted continental flooding patterns and published paleo-coastlines by comparing predicted versus geologically reconstructed land fractions and spatial overlaps of flooded regions for individual continents since 140 Ma. Modelled versus geologically reconstructed land fractions match within 10% for most models, and the spatial overlaps of inundated regions are mostly between 85% and 100% for the Cenozoic, dropping to about 75–100% in the Cretaceous. Regions that have been strongly affected by mantle plumes are generally not captured well in our models, as plumes are suppressed in most of them, and our models with dynamically evolving plumes do not replicate the location and timing of observed plume products. We categorise the evolution of modelled dynamic topography in both continental interiors and along passive margins using cluster analysis to investigate how clusters of similar dynamic topography time series are distributed spatially. A subdivision of four clusters is found to best reveal end-members of dynamic topography evolution along passive margins and their hinterlands, differentiating topographic stability, long-term pronounced subsidence, initial stability over a dynamic high followed by moderate subsidence and regions that are relatively proximal to subduction zones with varied dynamic topography histories. Along passive continental margins the most commonly observed process is a gradual motion from dynamic highs towards lows during the fragmentation of Pangea, reflecting the location of many passive margins now over slabs sinking in the lower mantle. Our best-fit model results in up to 500 (± 150) m of total dynamic subsidence of continental interiors while along passive margins the maximum predicted dynamic topographic change over 140 million years is about 350 (± 150) m of subsidence. Models with plumes exhibit clusters of transient passive margin uplift of about 200 ± 200 m, but are mainly characterised by long-term subsidence of up to 400 m. The good overall match between predicted dynamic topography to geologically mapped paleo-coastlines makes a convincing case that mantle-driven topographic change is a critical component of relative sea level change, and indeed the main driving force for generating the observed geometries and timings of large-scale continental inundation through time. © 2017 International Association for Gondwana Research
Australian-Antarctic breakup and seafloor spreading: Balancing geological and geophysical constraints
07 August 2019
University of Sydney

Williams, Simon E;Whittaker, Joanne M;Halpin, Jacqueline A;Muller, R. Dietmar

The motion of diverging tectonic plates is typically constrained by geophysical data from preserved ocean crust. However, constraining plate motions during continental rifting and the breakup process relies on balancing evidence from a diverse range of geological and geophysical observations, often subject to differing interpretations. Reconstructing the evolution of rifting and breakup between Australia and Antarctica epitomizes the challenges involved in creating detailed models of Pangea breakup. In this example, differing degrees of emphasis on and alternative interpretations of offshore geophysical data, in particular magnetic anomalies and seismic reflection profiles, and onshore geological data, lead to starkly contrasting views of how the continents were configured at the onset of Mesozoic rifting. Here, we critically review reconstructions of rifting and breakup in the light of all available geological and geophysical data, including magnetic anomalies, fracture zones, conjugate crustal domains, amounts of continental extension, continental geology, plate boundary locations, break-up ages and stratigraphy. We identify the most viable plate tectonic reconstructions both with and without the input of the oldest, more controversial magnetic anomaly interpretations, and discuss implications for reconstructions of other margin pairs. Our analysis highlights key discrepancies between reconstructions based solely on geological piercing points, and those based on a range of constraints. These insights provide a powerful framework for reducing the range of viable models for Australian-Antarctic rifting, and provide key lessons for future efforts aimed at constraining pre- and syn-rift plate tectonic reconstructions. © 2018 Elsevier B.V.
The interplay of dynamic topography and eustasy on continental flooding in the late Paleozoic
09 August 2019
University of Sydney

Cao, Wenchao;Flament, Nicolas;Zahirovic, Sabin;Williams, Simon E;Muller, R. Dietmar

Global sea level change can be inferred from sequence stratigraphic and continental flooding data. These methods reconstruct sea level from peri-cratonic and cratonic basins that are assumed to be tectonically stable and sometimes called reference districts, and from spatio-temporal correlations across basins. However, it has been understood that long-wavelength (typically hundreds of km) and low-amplitude (<2 km) vertical displacements of the Earth's surface due to mantle flow, namely dynamic topography, can occur in the absence of crustal deformation. Dynamic topography can drive marine inundation or regional emergence of continents and must be taken into consideration for eustasy estimates. Our analysis indicates that the long-term trend in global-scale maximum flooding over the late Paleozoic generally correlates with global sea level curves. The first-order flooding history of North America correlates with some estimates of eustasy. The Paleozoic inundation of South America does not follow long-term sea level variations. The flooding lows during the Early Carboniferous and high during the Late Carboniferous are at odds with estimates of eustasy and can be explained by dynamic uplift and subsidence, respectively. Our dynamic topography models indicate that the Yangtze Platform of South China experienced significant dynamic subsidence during the transition from Permian to Triassic largely due to proto-Pacific subduction and its northward motion to collide with North China. The reference districts – Western New York, Oklahoma and Kansas, and West Texas in North America – were to some degree affected by dynamic uplift and subsidence associated with long-lived Panthalassa subduction zones, closure of the Rheic Ocean and large-scale upwelling above the African deep-mantle structure during late Paleozoic times. This indicates that some published global sea level curves may include non-eustatic signals such as dynamic uplift or subsidence. The interpretation of stratigraphic data gathered from these reference districts should be treated with caution to estimate global sea level variations. © 2019 Elsevier B.V.
The role of deep Earth dynamics in driving the flooding and emergence of New Guinea since the Jurassic
09 August 2019
University of Sydney

Harrington, Lauren;Zahirovic, Sabin;Flament, Nicolas;Muller, R. Dietmar

The paleogeography of New Guinea indicates fluctuating periods of flooding and emergence since the Jurassic, which are inconsistent with estimates of global sea level change since the Eocene. The role of deep Earth dynamics in explaining these discrepancies has not been explored, despite the strongly time-dependent geodynamic setting within which New Guinea has evolved. We aim to investigate the role of subduction-driven mantle flow in controlling long-wavelength dynamic topography and its manifestation in the regional sedimentary record, within a tectonically complex region leading to orogeny. We couple regionally refined global plate reconstructions with forward geodynamic models to compare trends of dynamic topography with estimates of eustasy and regional paleogeography. Qualitative corroboration of modelled mantle structure with equivalent tomographic profiles allows us to ground-truth the models. We show that predicted dynamic topography correlates with the paleogeographic record of New Guinea from the Jurassic to the present. We find that subduction at the East Gondwana margin locally enhanced the high eustatic sea levels from the Early Cretaceous (∼145 Ma) to generate long-term regional flooding. During the Miocene, however, dynamic subsidence associated with subduction of the Maramuni Arc played a fundamental role in causing long-term inundation of New Guinea during a period of global sea level fall. © 2017 Elsevier B.V
Global tectonic reconstructions with continuously deforming and evolving rigid plates
09 August 2019
University of Sydney

Gurnis, Michael;Yang, Ting;Cannon, John S;Turner, Mark;Williams, Simon E;Flament, Nicolas;Muller, R. Dietmar

Traditional plate reconstruction methodologies do not allow for plate deformation to be considered. Here we present software to construct and visualize global tectonic reconstructions with deforming plates within the context of rigid plates. Both deforming and rigid plates are defined by continuously evolving polygons. The deforming regions are tessellated with triangular meshes such that either strain rate or cumulative strain can be followed. The finite strain history, crustal thickness and stretching factor of points within the deformation zones are tracked as Lagrangian points. Integrating these tools within the interactive platform GPlates enables specialized users to build and refine deforming plate models and integrate them with other models in time and space. We demonstrate the integrated platform with regional reconstructions of Cenozoic western North America, the Mesozoic South American Atlantic margin, and Cenozoic southeast Asia, embedded within global reconstructions, using different data and reconstruction strategies. © 2018 Elsevier Ltd
Large fluctuations of shallow seas in low-lying Southeast Asia driven by mantle flow
09 August 2019
University of Sydney

Zahirovic, Sabin;Flament, Nicolas;Muller, R. Dietmar;Seton, Maria;Gurnis, Michael

The Sundaland continental promontory, as the core of Southeast Asia, is one of the lowest lying continental regions, with half of the continental area presently inundated by a shallow sea. The role of mantle convection in driving long-wavelength topography and vertical motion of the lithosphere in this region has often been ignored when interpreting regional stratigraphy, including a widespread Late Cretaceous-Eocene unconformity, despite a consensus that Southeast Asia is presently situated over a large-amplitude dynamic topography low resulting from long-term post-Pangea subduction. We use forward numerical models to link mantle flow with surface tectonics and compare predicted trends of dynamic topography with eustasy and regional paleogeography to determine the influence of mantle convection on regional basin histories. A Late Cretaceous collision of Gondwana-derived terranes with Sundaland choked the active margin, leading to slab breakoff and a ∼10–15 Myr-long subduction hiatus. A subduction hiatus likely resulted in several hundred meters of dynamic uplift and emergence of Sundaland between ∼80 and 60 Ma and may explain the absence of a Late Cretaceous-Eocene sedimentary record. Renewed subduction from ∼60 Ma reinitiated dynamic subsidence of Sundaland, leading to submergence from ∼40 Ma despite falling long-term global sea levels. Our results highlight a complete “down-up-down” dynamic topography cycle experienced by Sundaland, with transient dynamic topography manifesting as a major regional unconformity in sedimentary basins. © 2016. American Geophysical Union. All Rights Reserved.
Influence of mantle flow on the drainage of eastern Australia since the Jurassic Period
12 August 2019
University of Sydney

Salles, Tristan;Flament, Nicolas;Muller, R. Dietmar

Recent studies of the past eastern Australian landscape from present-day longitudinal river profiles and from mantle flow models suggest that the interaction of plate motion with mantle convection accounts for the two phases of large-scale uplift of the region since 120 Ma. We coupled the dynamic topography predicted from one of these mantle flow models to a surface process model to study the evolution of the eastern Australian landscape since the Jurassic Period. We varied the rainfall regime, erodibility, sea level variations, dynamic topography magnitude, and elastic thickness across a series of experiments. The approach accounts for erosion and sedimentation and simulates catchment dynamics. Despite the relative simplicity of our model, the results provide insights on the fundamental links between dynamic topography and continental-scale drainage evolution. Based on temporal and spatial changes in longitudinal river profiles as well as erosion and deposition maps, we show that the motion of the Australian plate over the convecting mantle has resulted in significant reorganization of the eastern Australian drainage. The model predicts that the Murray river drained eastward between 150 and ∼120 Ma, and switched to westward draining due to the tilting of the Australian plate from ∼120 Ma. First order comparisons of eight modeled river profiles and of the catchment shape of modeled Murray-Darling Basin are in agreement with present-day observations. The predicted denudation of the eastern highlands is compatible with thermochronology data and sedimentation rates along the southern Australian margin are consistent with cumulative sediment thickness. © 2017. American Geophysical Union. All Rights Reserved.
SPGM: A Scalable PaleoGeomorphology Model
12 August 2019
University of Sydney

Hassan, Rakib;Gurnis, Michael;Williams, Simon E.;Muller, R. Dietmar

Numerical models of landscape evolution are playing an increasingly important role in providing an improved understanding of geomorphic transport processes shaping Earth's surface topography. Improving theoretical underpinnings coupled with increasing computational capacity has led to the development of several open source codes written in low-level languages. However, adapting these codes to new functionality or introducing greater flexibility often requires significant recoding. Here we present a multi-process, scalable, numerical model of geomorphological evolution, built with a modular structure and geared toward seamless extensibility. We implement recent algorithmic advances that reduce the computational cost of flow routing – a problem that typically scales quadratically with the number of unknowns – to linear in time while allowing for parallel implementations of geomorphic transport processes. Our scalability tests demonstrate that such parallelizations can achieve an order of magnitude speedup on a typical desktop computer, making large-scale simulations more tractable. © 2018 The Author(s)
Oblique rifting: The rule, not the exception
13 August 2019
University of Sydney

Brune, Sascha;Williams, Simon E;Muller, R. Dietmar

Movements of tectonic plates often induce oblique deformation at divergent plate boundaries. This is in striking contrast with traditional conceptual models of rifting and rifted margin formation, which often assume 2-D deformation where the rift velocity is oriented perpendicular to the plate boundary. Here we quantify the validity of this assumption by analysing the kinematics of major continent-scale rift systems in a global plate tectonic reconstruction from the onset of Pangea breakup until the present day. We evaluate rift obliquity by joint examination of relative extension velocity and local rift trend using the script-based plate reconstruction software pyGPlates. Our results show that the global mean rift obliquity since 230 Ma amounts to 34° with a standard deviation of 24°, using the convention that the angle of obliquity is spanned by extension direction and rift trend normal. We find that more than ∼ 70% of all rift segments exceeded an obliquity of 20° demonstrating that oblique rifting should be considered the rule, not the exception. In many cases, rift obliquity and extension velocity increase during rift evolution (e.g. Australia-Antarctica, Gulf of California, South Atlantic, India-Antarctica), which suggests an underlying geodynamic correlation via obliquity-dependent rift strength. Oblique rifting produces 3-D stress and strain fields that cannot be accounted for in simplified 2-D plane strain analysis. We therefore highlight the importance of 3-D approaches in modelling, surveying, and interpretation of most rift segments on Earth where oblique rifting is the dominant mode of deformation. © 2018 Author(s).
Improving global paleogeography since the late Paleozoic using paleobiology
14 August 2019
University of Sydney

Cao, Wenchao;Zahirovic, Sabin;Flament, Nicolas;Williams, Simon E;Golonka, Jan;Muller, R. Dietmar

Paleogeographic reconstructions are important to understand Earth's tectonic evolution, past eustatic and regional sea level change, paleoclimate and ocean circulation, deep Earth resources and to constrain and interpret the dynamic topography predicted by mantle convection models. Global paleogeographic maps have been compiled and published, but they are generally presented as static maps with varying map projections, different time intervals represented by the maps and different plate motion models that underlie the paleogeographic reconstructions. This makes it difficult to convert the maps into a digital form and link them to alternative digital plate tectonic reconstructions. To address this limitation, we develop a workflow to restore global paleogeographic maps to their present-day coordinates and enable them to be linked to a different tectonic reconstruction. We use marine fossil collections from the Paleobiology Database to identify inconsistencies between their indicative paleoenvironments and published paleogeographic maps, and revise the locations of inferred paleo-coastlines that represent the estimated maximum transgression surfaces by resolving these inconsistencies. As a result, the consistency ratio between the paleogeography and the paleoenvironments indicated by the marine fossil collections is increased from an average of 75ĝ€% to nearly full consistency (100ĝ€%). The paleogeography in the main regions of North America, South America, Europe and Africa is significantly revised, especially in the Late Carboniferous, Middle Permian, Triassic, Jurassic, Late Cretaceous and most of the Cenozoic. The global flooded continental areas since the Early Devonian calculated from the revised paleogeography in this study are generally consistent with results derived from other paleoenvironment and paleo-lithofacies data and with the strontium isotope record in marine carbonates. We also estimate the terrestrial areal change over time associated with transferring reconstruction, filling gaps and modifying the paleogeographic geometries based on the paleobiology test. This indicates that the variation of the underlying plate reconstruction is the main factor that contributes to the terrestrial areal change, and the effect of revising paleogeographic geometries based on paleobiology is secondary. © Author(s) 2017.
Oceanic microplate formation records the onset of India-Eurasia collision
14 August 2019
University of Sydney

Matthews, Kara J;Muller, R. Dietmar;Sandwell, David T

Mapping of seafloor tectonic fabric in the Indian Ocean, using high-resolution satellite-derived vertical gravity gradient data, reveals an extinct Pacific-style oceanic microplate ('Mammerickx Microplate') west of the Ninetyeast Ridge. It is one of the first Pacific-style microplates to be mapped outside the Pacific basin, suggesting that geophysical conditions during formation probably resembled those that have dominated at eastern Pacific ridges. The microplate formed at the Indian-Antarctic ridge and is bordered by an extinct ridge in the north and pseudofault in the south, whose conjugate is located north of the Kerguelen Plateau. Independent microplate rotation is indicated by asymmetric pseudofaults and rotated abyssal hill fabric, also seen in multibeam data. Magnetic anomaly picks and age estimates calculated from published spreading rates suggest formation during chron 21o (~47.3 Ma). Plate reorganizations can trigger ridge propagation and microplate development, and we propose that Mammerickx Microplate formation is linked with the India-Eurasia collision (initial 'soft' collision). The collision altered the stress regime at the Indian-Antarctic ridge, leading to a change in segmentation and ridge propagation from an establishing transform. Fast Indian-Antarctic spreading that preceded microplate formation, and Kerguelen Plume activity, may have facilitated ridge propagation via the production of thin and weak lithosphere; however both factors had been present for tens of millions of years and are therefore unlikely to have triggered the event. Prior to the collision, the combination of fast spreading and plume activity was responsible for the production of a wide region of undulate seafloor to the north of the extinct ridge and 'W' shaped lineations that record back and forth ridge propagation. Microplate formation provides a precise means of dating the onset of the India-Eurasia collision, and is completely independent of and complementary to timing constraints derived from continental geology or convergence histories. © 2015 Elsevier B.V.
Hazards and disasters in the Anthropocene: some critical reflections for the future
14 August 2019
University of Sydney

Dominey-Howes, Dale T.M.

The arrival of the Anthropocene presents many challenges—both theoretical and practical. Scholars in different disciplines, practitioners, the public and others, are all considering the meaning of the Anthropocene and how its arrival affects their ways of knowing and doing. Given that a dominant narrative of the Anthropocene is one of a coming crisis, hazard, and disaster experts from different disciplines have much to contribute. Here, I briefly summarize the trajectory of hazards’ and disasters’ research through to the present to provide the context to ask a series of critical questions that experts in hazard and disaster might address to make theoretical and practical contributions to making the Anthropocene as good as it might be. The questions considered are: how useful is the contemporary crisis narrative of the Anthropocene for understanding the planetary history of hazards and disasters, and coupled to this; is the modern language of disaster risk reduction useful for understanding past disasters; how do we give voice to the more-than-human experiences of Anthropocene disasters; is it possible to mitigate the impacts of future hazards and disasters within the Anthropocene without addressing the root causes of vulnerability; how do we make space for slow emergencies and what do slow emergencies mean for understanding hazard and disaster in the Anthropocene; and finally, does the scholarship of hazard and disaster provide evidence useful for informing the debate about an early or late-start for the Anthropocene? © 2018, The Author(s).
Quantitative stratigraphic analysis in a source-to-sink numerical framework
14 August 2019
University of Sydney

Ding, Xuesong;Salles, Tristan B;Flament, Nicolas;Rey, Patrice F

The sedimentary architecture at continental margins reflects the interplay between the rate of change of accommodation creation (δA) and the rate of change of sediment supply (δS). Stratigraphic interpretation increasingly focuses on understanding the link between deposition patterns and changes in δA=δS, with an attempt to reconstruct the contributing factors. Here, we use the landscape modelling code pyBadlands to (1) investigate the development of stratigraphic sequences in a source-to-sink context; (2) assess the respective performance of two well-established stratigraphic interpretation techniques: the trajectory analysis method and the accommodation succession method; and (3) propose quantitative stratigraphic interpretations based on those two techniques. In contrast to most stratigraphic forward models (SFMs), pyBadlands provides self-consistent sediment supply to basin margins as it simulates erosion, sediment transport and deposition in a source-to-sink context. We present a generic case of landscape evolution that takes into account periodic sea level variations and passive margin thermal subsidence over 30 million years, under uniform rainfall. A set of post-processing tools are provided to analyse the predicted stratigraphic architecture. We first reconstruct the temporal evolution of the depositional cycles and identify key stratigraphic surfaces based on observations of stratal geometries and facies relationships, which we use for comparison to stratigraphic interpretations. We then apply both the trajectory analysis and the accommodation succession methods to manually map key stratigraphic surfaces and define sequence units on the final model output. Finally, we calculate shoreline and shelf-edge trajectories, the temporal evolution of changes in relative sea level (proxy for δA) and sedimentation rate (proxy for δS) at the shoreline, and automatically produce stratigraphic interpretations. Our results suggest that the analysis of the presented model is more robust with the accommodation succession method than with the trajectory analysis method. Stratigraphic analysis based on manually extracted shoreline and shelf-edge trajectory requires calibrations of time-dependent processes such as thermal subsidence or additional constraints from stratal terminations to obtain reliable interpretations. The 3-D stratigraphic analysis of the presented model reveals small lateral variations of sequence formations. Our work provides an efficient and flexible quantitative sequence stratigraphic framework to evaluate the main drivers (climate, sea level and tectonics) controlling sedimentary architectures and investigate their respective roles in sedimentary basin development. © Author(s) 2019.
The Dynamic Topography of Eastern China Since the Latest Jurassic Period
14 August 2019
University of Sydney

Cao, Xianzhi;Flament, Nicolas;Muller, R. Dietmar;Li, Shanzhong

Some changes in the topography of eastern China since Late Jurassic times cannot be well explained by lithospheric deformation. Here we analyze global mantle flow models to investigate how mantle-driven long-wavelength topography may have contributed to shaping the surface topography of eastern China. Paleodrainage directions suggest that a southward tilted topography once existed in eastern north China in the latest Jurassic Period, which is different from that at present day (southeastward tilting). Our model dynamic topography reveals a southward tilting topography between 160 and 150 Ma, followed by southeastward tilting and rapid subsidence, which is compatible with paleodrainage directions and tectonic subsidence of the Ordos Basin. The Cretaceous anomalous subsidence of the Songliao and North Yellow Sea basins, as well as the Cenozoic anomalous subsidence of the East China Sea Shelf Basin, can also be explained by dynamic topography. An apatite fission track study in the Taihang Mountains reveals four stages of evolution: Late Jurassic fast unroofing, Cretaceous slow unroofing, early Cenozoic fast unroofing, and late Cenozoic slow unroofing. We propose that mantle flow influenced this surface unroofing because the model predicts Late Jurassic dynamic uplift, Cretaceous dynamic subsidence, early Cenozoic dynamic uplift, and late Cenozoic dynamic subsidence. Apatite fission track data from northern south China are also in reasonable agreement with predicted dynamic topography between 80 and 30 Ma. The spatial and temporal agreement between geological observations and model dynamic topography indicates that mantle flow has had a significant influence in shaping the surface topography of eastern China. ©2018. American Geophysical Union. All Rights Reserved.
Global patterns in Earth's dynamic topography since the Jurassic: The role of subducted slabs
14 August 2019
University of Sydney

Rubey, Michael;Brune, Sascha;Heine, Christian J;Davies, Rhodri D;Williams, Simon E;Muller, R. Dietmar

We evaluate the spatial and temporal evolution of Earth's long-wavelength surface dynamic topography since the Jurassic using a series of high-resolution global mantle convection models. These models are Earth-like in terms of convective vigour, thermal structure, surface heat-flux and the geographic distribution of heterogeneity. The models generate a degree-2-dominated spectrum of dynamic topography with negative amplitudes above subducted slabs (i.e. circum-Pacific regions and southern Eurasia) and positive amplitudes elsewhere (i.e. Africa, north-western Eurasia and the central Pacific). Model predictions are compared with published observations and subsidence patterns from well data, both globally and for the Australian and southern African regions. We find that our models reproduce the long-wavelength component of these observations, although observed smaller-scale variations are not reproduced. We subsequently define geodynamic rules for how different surface tectonic settings are affected by mantle processes: (i) locations in the vicinity of a subduction zone show large negative dynamic topography amplitudes; (ii) regions far away from convergent margins feature long-term positive dynamic topography; and (iii) rapid variations in dynamic support occur along the margins of overriding plates (e.g. the western US) and at points located on a plate that rapidly approaches a subduction zone (e.g. India and the Arabia Peninsula). Our models provide a predictive quantitative framework linking mantle convection with plate tectonics and sedimentary basin evolution, thus improving our understanding of how subduction and mantle convection affect the spatiooral evolution of basin architecture. © 2017 Author(s).
Oceanic crustal carbon cycle drives 26-million-year atmospheric carbon dioxide periodicities
14 August 2019
University of Sydney

Muller, R. Dietmar;Dutkiewicz, Adriana

Atmospheric carbon dioxide (CO2) data for the last 420 million years (My) show long-term fluctuations related to supercontinent cycles as well as shorter cycles at 26 to 32 My whose origin is unknown. Periodicities of 26 to 30 My occur in diverse geological phenomena including mass extinctions, flood basalt volcanism, ocean anoxic events, deposition of massive evaporites, sequence boundaries, and orogenic events and have previously been linked to an extraterrestrial mechanism. The vast oceanic crustal carbon reservoir is an alternative potential driving force of climate fluctuations at these time scales, with hydrothermal crustal carbon uptake occurring mostly in young crust with a strong dependence on ocean bottom water temperature. We combine a global plate model and oceanic paleo-age grids with estimates of paleo-ocean bottom water temperatures to track the evolution of the oceanic crustal carbon reservoir over the past 230 My. We show that seafloor spreading rates as well as the storage, subduction, and emission of oceanic crustal and mantle CO2 fluctuate with a period of 26 My. A connection with seafloor spreading rates and equivalent cycles in subduction zone rollback suggests that these periodicities are driven by the dynamics of subduction zone migration. The oceanic crust-mantle carbon cycle is thus a previously overlooked mechanism that connects plate tectonic pulsing with fluctuations in atmospheric carbon and surface environments. Copyright © 2018 The Authors.
The GPlates Portal: Cloud-Based Interactive 3D Visualization of Global Geophysical and Geological Data in a Web Browser
14 August 2019
University of Sydney

Muller, R. Dietmar;Qin, Xiaodong;Sandwell, David T;Dutkiewicz, Adriana;Williams, Simon E;Flament, Nicolas;Maus, Stefan;Seton, Maria

The pace of scientific discovery is being transformed by the availability of 'big data' and open access, open source software tools. These innovations open up new avenues for how scientists communicate and share data and ideas with each other and with the general public. Here, we describe our efforts to bring to life our studies of the Earth system, both at present day and through deep geological time. The GPlates Portal (portal.gplates.org) is a gateway to a series of virtual globes based on the Cesium Javascript library. The portal allows fast interactive visualization of global geophysical and geological data sets, draped over digital terrain models. The globes use WebGL for hardware-accelerated graphics and are cross-platform and cross-browser compatible with complete camera control. The globes include a visualization of a highresolution global digital elevation model and the vertical gradient of the global gravity field, highlighting small-scale seafloor fabric such as abyssal hills, fracture zones and seamounts in unprecedented detail. The portal also features globes portraying seafloor geology and a global data set of marine magnetic anomaly identifications. The portal is specifically designed to visualize models of the Earth through geological time. These space-time globes include tectonic reconstructions of the Earth's gravity and magnetic fields, and several models of long-wavelength surface dynamic topography through time, including the interactive plotting of vertical motion histories at selected locations. The globes put the on-the-fly visualization of massive data sets at the fingertips of end-users to stimulate teaching and learning and novel avenues of inquiry. © 2016 Müller et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Global kinematics of tectonic plates and subduction zones since the late Paleozoic Era
15 August 2019
University of Sydney

Young, Alexander;Flament, Nicolas;Maloney, Kayla T.;Williams, Simon E;Matthews, Kara J;Zahirovic, Sabin;Muller, R. Dietmar

Detailed global plate motion models that provide a continuous description of plate boundaries through time are an effective tool for exploring processes both at and below the Earth's surface. A new generation of numerical models of mantle dynamics pre- and post-Pangea timeframes requires global kinematic descriptions with full plate reconstructions extending into the Paleozoic (410 Ma). Current plate models that cover Paleozoic times are characterised by large plate speeds and trench migration rates because they assume that lowermost mantle structures are rigid and fixed through time. When used as a surface boundary constraint in geodynamic models, these plate reconstructions do not accurately reproduce the present-day structure of the lowermost mantle. Building upon previous work, we present a global plate motion model with continuously closing plate boundaries ranging from the early Devonian at 410 Ma to present day. We analyse the model in terms of surface kinematics and predicted lower mantle structure. The magnitude of global plate speeds has been greatly reduced in our reconstruction by modifying the evolution of the synthetic Panthalassa oceanic plates, implementing a Paleozoic reference frame independent of any geodynamic assumptions, and implementing revised models for the Paleozoic evolution of North and South China and the closure of the Rheic Ocean. Paleozoic (410–250 Ma) RMS plate speeds are on average ∼8 cm/yr, which is comparable to Mesozoic–Cenozoic rates of ∼6 cm/yr on average. Paleozoic global median values of trench migration trend from higher speeds (∼2.5 cm/yr) in the late Devonian to rates closer to 0 cm/yr at the end of the Permian (∼250 Ma), and during the Mesozoic–Cenozoic (250–0 Ma) generally cluster tightly around ∼1.1 cm/yr. Plate motions are best constrained over the past 130 Myr and calculations of global trench convergence rates over this period indicate median rates range between 3.2 cm/yr and 12.4 cm/yr with a present day median rate estimated at ∼5 cm/yr. For Paleozoic times (410–251 Ma) our model results in median convergence rates largely ∼5 cm/yr. Globally, ∼90% of subduction zones modelled in our reconstruction are determined to be in a convergent regime for the period of 120–0 Ma. Over the full span of the model, from 410 Ma to 0 Ma, ∼93% of subduction zones are calculated to be convergent, and at least 85% of subduction zones are converging for 97% of modelled times. Our changes improve global plate and trench kinematics since the late Paleozoic and our reconstructions of the lowermost mantle structure challenge the proposed fixity of lower mantle structures, suggesting that the eastern margin of the African LLSVP margin has moved by as much as ∼1450 km since late Permian times (260 Ma). The model of the plate-mantle system we present suggests that during the Permian Period, South China was proximal to the eastern margin of the African LLSVP and not the western margin of the Pacific LLSVP as previous thought. © 2018 China University of Geosciences (Beijing) and Peking University
Alignment between seafloor spreading directions and absolute plate motions through time
15 August 2019
University of Sydney

Williams, Simon E;Flament, Nicolas;Muller, R. Dietmar

The history of seafloor spreading in the ocean basins provides a detailed record of relative motions between Earth's tectonic plates since Pangea breakup. Determining how tectonic plates have moved relative to the Earth's deep interior is more challenging. Recent studies of contemporary plate motions have demonstrated links between relative plate motion and absolute plate motion (APM), and with seismic anisotropy in the upper mantle. Here we explore the link between spreading directions and APM since the Early Cretaceous. We find a significant alignment between APM and spreading directions at mid-ocean ridges; however, the degree of alignment is influenced by geodynamic setting, and is strongest for mid-Atlantic spreading ridges between plates that are not directly influenced by time-varying slab pull. In the Pacific, significant mismatches between spreading and APM direction may relate to a major plate-mantle reorganization. We conclude that spreading fabric can be used to improve models of APM. ©2016. American Geophysical Union. All Rights Reserved.
Oceanic Residual Topography Agrees With Mantle Flow Predictions at Long Wavelengths
15 August 2019
University of Sydney

Yang, Ting;Moresi, Louis N;Muller, R. Dietmar;Gurnis, Michael

Dynamic topography, the surface deflection induced by sublithosheric mantle flow, is an important prediction made by geodynamic models, but there is an apparent disparity between geodynamic model predictions and estimates of residual topography (total topography minus lithospheric and crustal contributions). We generate synthetic global topography fields with different power spectral slopes and spatial patterns to investigate how well the long-wavelength (spherical degrees 1 to 3) components can be recovered from a discrete set of samples where residual topography has been recently estimated. An analysis of synthetic topography, along with observed geoid and gravity anomalies, demonstrates the reliability of signal recovery. Appropriate damping factors, which depend on the maximum degree in the spherical harmonic expansion that is used to fit the samples, must be applied to recover the long-wavelength topography correctly; large damping factors smooth the model excessively and suppress residual topography amplitude and power spectra unrealistically. Recovered long-wavelength residual topographies based on recent oceanic point-wise estimates with different spherical expansion degrees agree with each other and with the predicted dynamic topography from mantle flow models. The peak amplitude of the long-wavelength residual topography from oceanic observations is about 1 km, suggesting an important influence of large-scale deep mantle flow. ©2017. American Geophysical Union. All Rights Reserved.
In search of early life: Carbonate veins in Archean metamorphic rocks as potential hosts of biomarkers
16 August 2019
University of Sydney

Peters, Carl A.;Piazolo, Sandra;Webb, Gregory E.;Dutkiewicz, Adriana;George, Simon C.

The detection of early life signatures using hydrocarbon biomarkers in Precambrian rocks struggles with contamination issues, unspecific biomarkers and the lack of suitable sedimentary rocks due to extensive thermal overprints. Importantly, host rocks must not have been exposed to temperatures above 250 °C as at these temperatures biomarkers are destroyed. Here we show that Archean sedimentary rocks from the Jeerinah Formation (2.63 billion yrs) and Carawine Dolomite (2.55 billion yrs) of the Pilbara Craton (Western Australia) drilled by the Agouron Institute in 2012, which previously were suggested to be suitable for biomarker studies, were metamorphosed to the greenschist facies. This is higher than previously reported. Both the mineral assemblages (carbonate, quartz, Fe-chlorite, muscovite, microcline, rutile, and pyrite with absence of illite) and chlorite geothermometry suggest that the rocks were exposed to temperatures higher than 300 °C and probably ∼400 °C, consistent with greenschist-facies metamorphism. This facies leads to the destruction of any biomarkers and explains why the extraction of hydrocarbon biomarkers from pristine drill cores has not been successful. However, we show that the rocks are cut by younger formation-specific carbonate veins containing primary oil-bearing fluid inclusions and solid bitumens. Type 1 veins in the Carawine Dolomite consist of dolomite, quartz and solid bitumen, whereas type 2 veins in the Jeerinah Formation consist of calcite. Within the veins fluid inclusion homogenisation temperatures and calcite twinning geothermometry indicate maximum temperatures of ∼200 °C for type 1 veins and ∼180 °C for type 2 veins. Type 1 veins have typical isotopic values for reprecipitated Archean sea-water carbonates, with δ13CVPDB ranging from −3‰ to 0‰ and δ18OVPDB ranging from −13‰ to −7‰, while type 2 veins have isotopic values that are similar to hydrothermal carbonates, with δ13CVPDB ranging from −18‰ to −4‰ and δ18OVPDB ranging from −18‰ to −12‰. Evidently, the migration and entrapment of hydrocarbons occurred after peak metamorphism under temperatures congruous with late catagenesis and from fluids of different compositions. The relatively high temperatures of vein formation and the known geotectonic history of the rocks analysed suggest a probable minimum age of 1.8 billion yrs (Paleoproterozoic). Our results demonstrate that post peak-metamorphic veins provide an exciting opportunity in the search for evidence of early life. The integration of petrological and organic geochemical techniques is crucial for any future studies that use biomarkers to reconstruct the early biosphere.
Formation of Australian continental margin highlands driven by plate-mantle interaction
21 August 2019
University of Sydney

Muller, R. Dietmar;Flament, Nicolas;Matthews, Kara J;Williams, Simon E;Gurnis, Michael

Passive margin highlands occur on most continents on Earth and play a critical role in the cycle of weathering, erosion, and atmospheric circulation. Yet, in contrast to the well-developed understanding of collisional mountain belts, such as the Alps and Himalayas, the origin of less elevated (1-2 km) passive margin highlands is still unknown. The eastern Australian highlands are a prime example of these plateaus, but compared to others they have a well-documented episodic uplift history spanning 120 million years. We use a series of mantle convection models to show that the time-dependent interaction of plate motion with mantle downwellings and upwellings accounts for the broad pattern of margin uplift phases. Initial dynamic uplift of 400-600 m from 120-80 Ma was driven by the eastward motion of eastern Australia's margin away from the sinking eastern Gondwana slab, followed by tectonic quiescence to about 60 Ma in the south (Snowy Mountains). Renewed uplift of ~700 m in the Snowy Mountains is propelled by the gradual motion of the margin over the edge of the large Pacific mantle upwelling. In contrast the northernmost portion of the highlands records continuous uplift from 120 Ma to present-day totalling about 800 m. The northern highlands experienced a continuous history of dynamic uplift, first due to the end of subduction to the east of Australia, then due to moving over a large passive mantle upwelling. In contrast, the southern highlands started interacting with the edge of the large Pacific mantle upwelling ~40-50 million years later, resulting in a two-phase uplift history. Our results are in agreement with published uplift models derived from river profiles and the Cretaceous sediment influx into the Ceduna sub-basin offshore southeast Australia, reflecting the fundamental link between dynamic uplift, fluvial erosion and depositional pulses in basins distal to passive margin highlands. © 2016 Elsevier B.V.
Disaster declarations associated with bushfires, floods and storms in New South Wales, Australia between 2004 and 2014
21 August 2019
University of Sydney

Sewell, Thomas;Stephens, Ruby;Dominey-Howes, Dale T.M.;Bruce, Eleanor;Perkins-Kirkpatrick, Sarah

Australia regularly experiences disasters triggered by natural hazards and New South Wales (NSW) the most populous State is no exception. To date, no publically available spatial and temporal analyses of disaster declarations triggered by hazards (specifically, bushfires, floods and storms) in NSW have been undertaken and no studies have explored the relationship between disaster occurrence and socio-economic disadvantage. We source, collate and analyse data about bushfire, flood and storm disaster declarations between 2004 and 2014. Floods resulted in the most frequent type of disaster declaration. The greatest number of disaster declarations occurred in 2012-2013. Whilst no significant Spearman's correlation exists between bushfire, flood and storm disaster declarations and the strength of the El Niño/Southern Oscillation (ENSO) phase, we observe that bushfire disaster declarations were much more common during El Niño, and flood disaster declarations were five times more common during La Niña phases. We identify a spatial cluster or 'hot spot' of disaster declarations in the northeast of the State that is also spatially coincident with 43% of the most socio-economically disadvantaged Local Government Areas in NSW. The results have implications for disaster risk management in the State. © The Author(s) 2016.
Effect of cholesterol on the dipole potential of lipid membranes
04 September 2019
University of Sydney

Clarke, Ronald J.

The membrane dipole potential, ψd, is an electrical potential difference with a value typically in the range 150 – 350 mV (positive in the membrane interior) which is located in the lipid headgroup region of the membrane, between the linkage of the hydrocarbon chains to the phospholipid glycerol backbone and the adjacent aqueous solution. At its physiological level in animal plasma membranes (up to 50 mol%), cholesterol makes a significant contribution to ψd of approximately 65 mV; the rest arising from other lipid components of the membrane, in particular phospholipids. Via its effect on ψd, cholesterol may modulate the activity of membrane proteins. This could occur through preferential stabilization of protein conformational states. Based on its effect on ψd, cholesterol would be expected to favour protein conformations associated with a small local hydrophobic membrane thickness. Via its membrane condensing effect, which also produces an increase in ψd, cholesterol could further modulate interactions of polybasic cytoplasmic extensions of membrane proteins, in particular P-type ATPases, with anionic lipid headgroups on the membrane surface, thus leading to enhanced conformational stabilization effects and changes to ion pumping activity.
General and specific interactions of the phospholipid bilayer with P-type ATPases
05 September 2019
University of Sydney

Hossain, Khondker R.;Clarke, Ronald J.

Protein structure and function are modulated via interactions with their environment, representing both the surrounding aqueous media and lipid membranes that have an active role in shaping the structural topology of membrane proteins. Compared to a decade ago, there is now an abundance of crystal structural data on membrane proteins, which together with their functional studies have enhanced our understanding of the salient features of lipid-protein interactions. It is now important to recognize that membrane proteins are regulated by both: (1) general lipid-protein interactions, where the general physicochemical properties of the lipid environment affect the conformational flexibility of a membrane protein; and (2) by specific lipid-protein interactions, where lipid molecules directly interact via chemical interactions with specific lipid-binding sites located on the protein. However, due to local differences in membrane composition, thickness and lipid packing, local membrane physical properties and hence the associated lipid-protein interactions also differ due to membrane location, even for the same protein. Such a phenomenon has been shown to be true for one family of integral membrane ion pumps, the P2-type adenosine triphosphatases (ATPases). Despite being highly homologous, individual members of this family have distinct structural and functional activity and are an excellent candidate to highlight how the local membrane physical properties and specific lipid-protein interactions play a vital role in facilitating the structural rearrangements of these proteins necessary for their activity. Hence in this review, we focus on both the general and specific lipid-protein interactions and will mostly discuss the structure-function relationships of the following P2-type ATPases, Na+,K+-ATPase (NKA), gastric H+,K+-ATPase (HKA) and sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA), in concurrence with their lipid environment.
Electrostatic stabilization plays a central role in autoinhibitory regulation of the Na+,K+-ATPase
05 September 2019
University of Sydney

Jiang, Qiucen;Garcia, Alvaro;Han, Minwoo;Cornelius, Flemming;Apell, Hans-Jurgen;Khandelia, Himanshu;Clarke, Ronald J.

The Na+,K+-ATPase is present in the plasma membrane of all animal cells. It plays a crucial role in maintaining the Na+ and K+ electrochemical potential gradients across the membrane, which are essential in numerous physiological processes, e.g. nerve, muscle and kidney function. Its cellular activity must, therefore, be under tight metabolic control. Consideration of eosin fluorescence and stopped-flow kinetic data indicates that the enzyme’s E2 conformation is stabilized by electrostatic interactions, most likely between the N-terminus of the protein’s catalytic α-subunit and the adjacent membrane. The electrostatic interactions can be screened by increasing ionic strength, leading to a more evenly balanced equilibrium between the E1 and E2 conformations. This represents an ideal situation for effective regulation of the Na+,K+-ATPase’s enzymatic activity, since protein modifications which perturb this equilibrium in either direction can then easily lead to activation or inhibition. The effect of ionic strength on the E1:E2 distribution and the enzyme’s kinetics can be mathematically described by the Gouy-Chapman theory of the electrical double-layer. Weakening of the electrostatic interactions and a shift towards E1 causes a significant increase in the rate of phosphorylation of the enzyme by ATP. Electrostatic stabilization of the Na+,K+-ATPase’s E2 conformation, thus, could play an important role in regulating the enzyme’s physiological catalytic turnover.
Extracellular allosteric Na+ binding to the Na+,K+-ATPase in cardiac myocytes
10 September 2019
University of Sydney

Garcia, Alvaro;Fry, Natasha A. S.;Karimi, Keyvan;Liu, Chia-chi;Apell, Hans-Jurgen;Rasmussen, Helge H.;Clarke, Ronald J.

Whole cell patch clamp measurements of the current, Ip, produced by the Na+,K+-ATPase across the plasma membrane of rabbit cardiac myocytes show an increase in Ip over the extracellular Na+ concentration range 0 – 50 mM. This is not predicted by the classical Albers-Post scheme of the Na+,K+-ATPase mechanism, where extracellular Na+ should act as a competitive inhibitor of extracellular K+ binding, which is necessary for the stimulation of enzyme dephosphorylation and the pumping of K+ ions into the cytoplasm. The increase in Ip is consistent with Na+ binding to an extracellular allosteric site, independent of the ion transport sites, and an increase in turnover via an acceleration of the rate-determining release of K+ to the cytoplasm, E2(K+)2 → E1 + 2K+. At normal physiological concentrations of extracellular Na+ of 140 mM it is to be expected that binding of Na+ to the allosteric site would be nearly saturated. Its purpose would seem to be simply to optimize the enzyme’s ion pumping rate under its normal physiological conditions. Based on published crystal structures, a possible location of the allosteric site is within a cleft between the α- and β-subunits of the enzyme.
Polar interactions play an important role in the energetics of the main phase transition of phosphatidylcholine membranes
10 September 2019
University of Sydney

Garcia, Alvaro;Zou, Haipei;Hossain, Khondker R.;Xu, Qikui Henry;Buda, Annabelle;Clarke, Ronald J.

Conformational changes of membrane proteins are accompanied by deformation in the surrounding lipid bilayer. To gain insight into the energetics of membrane deformation, the phase behavior of dimyristoylphosphatidylcholine (DMPC) membranes in the presence of dipole potential, ψd, modifiers were investigated by differential scanning calo-rimetry. 7-Ketocholesterol, which weakens ψd and reduces membrane-perpendicular dipole-dipole repulsion, causes a discrete second peak on the high temperature side of the main transition, whereas 6-ketocholestanol, which strength-ens ψd and increases membrane-perpendicular dipole-dipole repulsion merely produces a shoulder. Measurements on pure DMPC vesicles showed that the observed temperature profile could not be explained by a single endothermic pro-cess, i.e. breaking of van der Waals forces between hydrocarbon chains alone. Removal of NaCl from the buffer caused an increase in the main transition temperature and the appearance of an obvious shoulder, implicating polar interac-tions. Consideration of the phosphatidylcholine headgroup dipole moment indicates direct interactions between phosphatidylcholine dipoles are unlikely to account for the additional process. It seems more likely the breaking of an in-plane hydrogen-bonded network consisting of hydrating water dipoles together with zwitterionic lipid headgroups is responsible. The evidence presented supports the idea that the breaking of van der Waals forces between lipid tails required for the main phase transition of PC membranes is coupled to partial breaking of a hydrogen-bonded network at the membrane surface.
Evidence for ATP interaction with phosphatidylcholine bilayers
10 September 2019
University of Sydney

Garcia, Alvaro;Pochinda, Simon;Elgaard-Jorgensen, Paninnguaq N.;Khandelia, Himanshu;Clarke, Ronald J.

ATP is a fundamental intracellular molecule and is thought to diffuse freely throughout the cytosol. Evidence obtained from nucleoside-sensing sarcolemmal ion channels and red blood cells, however, suggest that ATP is compartmentalised or buffered, especially beneath the sarcolemma, but no definitive mechanism for restricted diffusion or potential buffering system has been postulated. In this study, we provide evidence from alterations to membrane dipole potential, membrane conductance, changes in enthalpy of phospholipid phase transition, and from free energy calculations that ATP associates with phospholipid bilayers. Furthermore, all-atom molecular dynamics simulations show that ATP can form aggregates in the aqueous phase at high concentrations. ATP interaction with membranes provides a new model to understand the diffusion of ATP through the cell. Coupled with previous reports of diffusion restriction in the subsarcolemmal space, these findings support the existence of compartmentalized or buffered pools of ATP.
Cholesterol depletion inhibits Na+,K+-ATPase activity in a near-native membrane environment
10 September 2019
University of Sydney

Garcia, Alvaro;Lev, Bogdan;Hossain, Khondker R.;Gorman, Amy;Diaz, Dil;Pham, T. H. Nguyen;Cornelius, Flemming;Allen, Toby W.;Clarke, Ronald J.

Cholesterol’s effects on Na+,K+-ATPase reconstituted in phospholipid vesicles have been extensively studied. However, previous studies have reported both cholesterol-mediated stimulation and inhibition of Na+,K+-ATPase activity. Here, using partial reaction kinetics determined via stopped-flow experiments, we studied cholesterol’s effect on Na+,K+-ATPase in a near-native environment in which purified membrane fragments were depleted of cholesterol with methyl-β-cyclodextrin (mβCD). The mβCD-treated Na+,K+-ATPase had significantly reduced overall activity and exhibited decreased observed rate constants for ATP phosphorylation (ENa+3 → E2P, i.e. phosphorylation by ATP and Na+ occlusion from the cytoplasm) and K+ deocclusion with subsequent intracellular Na+ binding (E2K+2 → E1Na+3). However, cholesterol depletion did not affect the observed rate constant for K+ occlusion by phosphorylated Na+,K+-ATPase on the extracellular face and subsequent dephosphorylation (E2P → E2K+2). Thus, partial reactions involving cation binding and release at the protein’s intracellular side were most dependent on cholesterol. Fluorescence measurements with the probe eosin indicated that cholesterol depletion stabilizes the unphosphorylated E2 state relative to E1, and the cholesterol depletion-induced slowing of ATP phosphorylation kinetics was consistent with partial conversion of Na+,K+-ATPase into the E2 state, requiring a slow E2 → E1 transition before the phosphorylation. Molecular dynamics simulations of Na+,K+-ATPase in membranes with 40 mol% cholesterol revealed cholesterol interaction sites that differ markedly among protein conformations. They further disclosed state-dependent effects on membrane shape, with the E2 state being likely disfavored in cholesterol-rich bilayers relative to the E1P state because of a greater hydrophobic mismatch. In summary, cholesterol extraction from membranes significantly decreases Na+,K+-ATPase steady-state activity.
Evolutionary analysis of the lysine-rich N-terminal cytoplasmic domains of the gastric H+,K+-ATPase and the Na+,K+-ATPase
10 September 2019
University of Sydney

Diaz, Dil;Clarke, Ronald J.

The catalytic α-subunits of both the Na+,K+-ATPase and the gastric H+,K+-ATPase possess lysine-rich N-termini which project into the cytoplasm. Due to conflicting experimental results it is currently unclear whether the N-termini play a role in ion pump function or regulation, and, if they do, by what mechanism. Comparison of the lysine frequencies of the N-termini of both proteins with those of all of their extramembrane domains showed that the N-terminal lysine frequencies are far higher than one would expect simply from exposure to the aqueous solvent. The lysine frequency was found to vary significantly between different vertebrate classes, but this is due predominantly to a change in N-terminal length. As evidenced by a comparison between fish and mammals, an evolutionary trend towards an increase of the length of the N-terminus of the H+,K+-ATPase on going from an ancestral fish to mammals could be identified. This evolutionary trend supports the hypothesis that the N-terminus is important in ion pump function or regulation. In placental mammals, one of the lysines is replaced by serine (Ser-27), which is a target for protein kinase C. In most other animal species a lysine occupies this position and hence no protein kinase C target is present. Interaction with protein kinase C is thus not the primary role of the lysine-rich N-terminus. The disordered structure of the N-terminus may, via increased flexibility, facilitate interaction with another binding partner, e.g. the surrounding membrane, or help to stabilize particular enzyme conformations via the increased entropy it produces.
Glutathionylation-dependence of N+-K+-pump currents can mimic reduced subsarcolemmal Na+ diffusion
10 September 2019
University of Sydney

Garcia, Alvaro;Liu, Chia-Chi;Cornelius, Flemming;Clarke, Ronald J.;Rasmussen, Helge H.

The existence of a subsarcolemmal space with restricted diffusion for Na+ in cardiac myocytes has been inferred from a transient peak electrogenic Na+-K+ pump current beyond steady state on re-exposure of myocytes to K+ after a period of exposure to K+-free extracellular solution. The transient peak current is attributed to enhanced electrogenic pumping of Na+ that accumulated in the diffusion-restricted space during pump inhibition in K+-free extracellular solution. However, there are no known physical barriers that account for such restricted Na+ diffusion, and we examined if changes of activity of the Na+-K+ pump itself cause the transient peak current. Re-exposure to K+ reproduced a transient current beyond steady state in voltage clamped ventricular myocytes as reported by others. Persistence of it when the Na+ concentration in patch pipette solutions perfusing the intracellular compartment was high and elimination of it with K+-free pipette solution could not be reconciled with restricted subsarcolemmal Na+ diffusion. The pattern of the transient current early after pump activation was dependent on transmembrane Na+- and K+ concentration gradients suggesting the currents were related to the conformational poise imposed on the pump. We examined if the currents might be accounted for by changes in glutathionylation of the β1 Na+-K+ pump subunit, a reversible oxidative modification that inhibits the pump. Susceptibility of the β1 subunit to glutathionylation depends on the conformational poise of the Na+-K+ pump, and glutathionylation with the pump stabilized in conformations equivalent to those expected to be imposed on voltage clamped myocytes supported this hypothesis. So did elimination of the transient K+-induced peak Na+-K+ pump current when we included glutaredoxin 1 in patch pipette solutions to reverse gluthathionylation. We conclude that transient K+-induced peak Na+-K+ pump current reflects the effect of conformation-dependent β1 pump subunit glutathionylation, not restricted subsarcolemmal diffusion of Na+.
Interaction of N-terminal peptide analogues of the Na+,K+-ATPase with membranes
10 September 2019
University of Sydney

Nguyen, Khoa;Garcia, Alvaro;Sani, Marc-Antoine;Diaz, Dil;Dubey, Vikas;Clayton, Daniel;Dal Poggetto, Giovanni;Cornelius, Flemming;Payne, Richard J.;Separovic, Frances;Khandelia, Himanshu;Clarke, Ronald J.

The Na+,K+-ATPase, which is present in the plasma membrane of all animal cells, plays a crucial role in maintaining the Na+ and K+ electrochemical potential gradients across the membrane. Recent studies have suggested that the N-terminus of the protein’s catalytic α-subunit is involved in an electrostatic interaction with the surrounding membrane, which controls the protein’s conformational equilibrium. However, because the N-terminus could not yet be resolved in any X-ray crystal structures, little information about this interaction is so far available. In measurements utilising poly-L-lysine as a model of the protein’s lysine-rich N-terminus and using lipid vesicles of defined composition, here we have identified the most likely origin of the interaction as one between positively charged lysine residues of the N-terminus and negatively charged headgroups of phospholipids (notably phosphatidylserine) in the surrounding membrane. Furthermore, to isolate which segments of the N-terminus could be involved in membrane binding, we chemically synthesized N-terminal fragments of various lengths. Based on a combination of results from RH421 UV/visible absorbance measurements and solid-state 31P and 2H NMR using these N-terminal fragments as well as MD simulations it appears that the membrane interaction arises from lysine residues prior to the conserved LKKE motif of the N-terminus. The MD simulations indicate that the strength of the interaction varies significantly between different enzyme conformations.
Quantitative calculation of the role of the Na+,K+-ATPase in thermogenesis
10 September 2019
University of Sydney

Clarke, Ronald J.;Catauro, Michelina;Rasmussen, Helge H.;Apell, Hans-Jurgen

The Na+,K+-ATPase is accepted as an important source of heat generation (thermogenesis) in animals. Based on information gained on the kinetics of the enzyme’s partial reactions we consider via computer simulation whether modifications to the function of the combined Na+,K+-ATPase/plasma membrane complex system could lead to an increased body temperature, either through the course of evolution or during an individual’s lifespan. The enzyme’s kinetics must be considered because it is the rate of heat generation which determines body temperature, not simply the amount of heat per enzymatic cycle. The results obtained indicate that a decrease in thermodynamic efficiency of the Na+,K+-ATPase, which could come about by Na+ substituting for K+ on the enzyme’s extracellular face, could not account for increased thermogenesis. The only feasible mechanisms are an increase in the enzyme’s expression level or an increase in its ion pumping activity. The major source of Na+,K+-ATPase-related thermogenesis (72% of heat production) is found to derive from passive Na+ diffusion into the cell, which counterbalances outward Na+ pumping to maintain a constant Na+ concentration gradient across the membrane. A simultaneous increase in both Na+,K+-ATPase activity and the membrane's passive Na+ permeability could promote a higher body temperature.
Cone-beam CT reconstruction with gravity-induced motion.
03 October 2019
University of Sydney

Shieh, CC;Barber, J;Counter, W;Sykes, J;Bennett, P;Heng, SM;White, P;Corde, S;Jackson, M;Ahern, V;Feain, I;O'Brien, R;Keall, P

Fixed-gantry cone-beam computed tomography (CBCT), where the imaging hardware is fixed while the subject is continuously rotated 360° in the horizontal position, has implications for building compact and affordable fixed-gantry linear accelerators (linacs). Fixed-gantry imaging with a rotating subject presents a challenging image reconstruction problem where the gravity-induced motion is coupled to the subject's rotation angle. This study is the first to investigate the feasibility of fixed-gantry CBCT using imaging data of three live rabbits in an ethics-approved study. A novel data-driven motion correction method that combines partial-view reconstruction and motion compensation was developed to overcome this challenge. Fixed-gantry CBCT scans of three live rabbits were acquired on a standard radiotherapy system with the imaging beam fixed and the rabbits continuously rotated using an in-house programmable rotation cradle. The reconstructed images of the thoracic region were validated against conventional CBCT scans acquired at different cradle rotation angles. Results showed that gravity-induced motion caused severe motion blur in all of the cases if unaccounted for. The proposed motion correction method yielded clinically usable image quality with <1 mm gravity-induced motion blur for rabbits that were securely immobilized on the rotation cradle. Shapes of the anatomic structures were correctly reconstructed with <0.5 mm accuracy. Translational motion accounted for the majority of gravity-induced motion. The motion-corrected reconstruction represented the time-averaged location of the thoracic region over a 360° rotation. The feasibility of fixed-gantry CBCT has been demonstrated. Future work involves the validation of imaging accuracy for human subjects, which will be useful for emerging compact fixed-gantry radiotherapy systems.
Platy pyroxene: New insights into spinifex texture
21 November 2019
University of Sydney

Lowrey, Jack R.;Ivanic, Tim J.;Wyman, Derek A.;Roberts, Malcolm P.

New evidence has emerged for a different type of platy spinifex texture that has not previously been documented in the existing literature, in this case from 2.8 Ga high-Mg basalts in the Murchison Domain of the Yilgarn Craton, where petrographic and geochemical evidence shows that the dominant platy mineral is pyroxene, rather than olivine. In our samples, two scales of plates are evident. Larger plates have lengths and widths that are approximately equal and range from ~1000 to 15 000 mm, with thicknesses typically ≲120 mm. These plates have ≲25 mm thick augite rims, and cores that are now a mixture of low-temperature hydrous alteration minerals. They occur in sets of similarly oriented crystals, and typically intersect other sets of crystals at oblique angles. A second population of smaller augite-only plates occur within the interstices of the larger plates; they have lengths and widths that range from 200 to 1500 mm, and thicknesses that are typically ≲50 mm. Pyroxene dendrites are also a typical component of this texture and represent a third scale of crystal growth, which probably crystallized shortly before the remaining liquid quenched to glass. All scales of pyroxene contained within this texture exhibit skeletal features and are considered to have crystallized rapidly. We discuss possible conditions that led to the crystallization of platy habits instead of the typical acicular ones. The exposed volcanic sequence in our study area is volcanologically similar to other Archean komatiites, such as those from the 2.7 Ga Abitibi greenstone belt, for example, and has probably experienced a similar cooling history; however, apart from having similar textures, we cannot demonstrate a komatiitic association. Liquid compositions, estimated from chilled flow margins, are distinctly lower in MgO (14.4-15.8wt %) and higher in SiO2 (50.9-52.1wt %) than those for most platy olivine spinifex-textured komatiites; from these compositions, we calculate dry liquidus temperatures of 1312-1342°C and mantle potential temperatures of 1440-1480°C. On the basis of these temperatures we question whether a mantle plume is a necessary element of their petrogenesis. 'Platy olivine spinifex' is an igneous texture that characterizes komatiites and its observation in outcrops or drill core (typically prior to, or in lieu of chemical analysis) leads geologists to classify a rock as a komatiite. Field descriptions may therefore drive assumptions and interpretations surrounding the prevailing tectonic or geodynamic setting at the time of emplacement. We emphasize the importance of careful discrimination between a variety of spinifex textures within a local volcanological framework and caution against the habit of making direct interpretations of rock type based on the existence of spinifex textures alone. © The Author 2017.
Local structure adaptations and oxide ionic conductivity in the Type III stability region of (1–x)Bi2O3∙xNb2O5
21 November 2019
University of Sydney

Wind, Julia;Sharma, Neeraj;Yaremchenko, Aleksey A;Kharton, Vladislav V;Blom, Douglas A;Vogt, Thomas;Ling, Chris D

Starting from a previously published stoichiometric model for the commensurate Type III phase in the (1–x)Bi2O3∙xNb2O5 system, Bi94Nb32O221 (x = 0.254), we have developed a crystal-chemical model of this phase across its solid-solution range 0.20 ≤ x ≤ 0.26. After using annular dark-field scanning transmission electron microscopy to identify the metal sites that support non-stoichiometry, we show that the maximum possible range of that non-stoichiometry is 0.198 ≤ x ≤ 0.262, perfectly consistent with the experimental result. Inter-site cation defects on these sites provide some local coordinative flexibility with respect to the surrounding oxygen sublattice, but not enough to create continuous fluorite-like channels like those found in the high-temperature incommensurate Type II phase. This explains the reduced oxide-ionic conductivity of Type III compared to Type II at all temperatures and compositions, regardless of which phase is thermody-namically stable under those conditions. The solid-solution model shows that oxygen disorder and vacancies are both re-duced as x increases, which also explains why Type III becomes relatively more stable, and why oxide ionic conductivity decreases, as x increases.
Stability and range of the type II Bi1-xWxO1.5+1.5x solid solution
22 November 2019
University of Sydney

Wind, Julia;Kayser, Paula;Zhang, Zhaoming;Radosavljevic Evans, Ivana;Ling, Chris D

We have established the stability and range of the cubic type II phase of Bi1-xWxO1.5+1.5x using a combination of X-ray diffraction, neutron diffraction and X-ray absorption spectroscopy. Type II is a high temperature modification that can be obtained by quenching/rapid cooling of samples with compositions between x = 0.148 to x = 0.185. Slower cooling rates yield the stable low temperature polymorph, the tetragonal type Ib phase (Bi rich samples), and mixtures of type Ib and Aurivillius phase (W-rich samples). Throughout the entire solid solution range, type II exhibits a (3+3) dimensional incommensurate modulation with modulation vectors slightly smaller than 1/3 based on a cubic fluorite type subcell (δ-Bi2O3). The main structural motifs are well-defined tetrahedra of WO6 octahedra in a δ-Bi2O3-matrix, with additional W being incorporated on corners and face centers of the approximate commensurate 3×3×3 supercell in octahedral coordination, confirmed by XANES analysis of the W L3-edge. Impedance measurements reveal oxide ionic conductivities comparable to those of yttria-stabilised zirconia even after a decrease in ionic conductivity of about half an order of magnitude on thermal cycling due to transition to the tetragonal type Ib phase.
Durable Superhydrophobic Surfaces Via Spontaneous Wrinkling of Teflon
28 November 2019
University of Sydney

Scarratt, L.R.J.;Hoatson, B.S.;Wood, E.S.;Hawkett, B.S.;Neto, Chiara

We report the fabrication of both single-scale and hierarchical superhydrophobic surfaces, created by exploiting the spontaneous wrinkling of a rigid Teflon AF film on two types of shrinkable plastic substrates. Sub-100 nm to micrometric wrinkles were reproducibly generated by this simple process, with remarkable control over the size and hierarchy. Hierarchical Teflon AF wrinkled surfaces showed extremely high water repellence (contact angle 172°) and very low contact angle hysteresis (2°), resulting in droplets rolling off the surface at tilt angles lower than 5°. The wrinkling process intimately binds the Teflon AF layer with its substrate, making these surfaces mechanically robust, as revealed by macroscale and nanoscale wear tests: hardness values were close to that of commercial optical lenses and aluminum films, resistance to scratch was comparable to commercial hydrophobic coatings, and damage by extensive sonication did not significantly affect water repellence. By this fabrication method the size of the wrinkles can be reproducibly tuned from the nanoscale to the microscale, across the whole surface in one step; the fabrication procedure is extremely rapid, requiring only 2 min of thermal annealing to produce the desired topography, and uses inexpensive materials. The very low roll-off angles achieved in the hierarchical surfaces offer a potentially up-scalable alternative as self-cleaning and drag-reducing coatings.
Boundary flow on end-grafted PEG brushes
04 December 2019
University of Sydney

Charrault, E.;Lee, T.;Easton, C.D.;Neto, Chiara

We investigated the boundary conditions for flow of a Newtonian liquid over soft interfaces by measuring hydrodynamic drainage forces with colloid probe atomic force microscopy in a viscous liquid. The investigated soft surfaces are end-grafted brushes of thiolated poly(ethylene glycol) (PEG), of molecular weight 1k and 30k, grafted-to gold. The conditions for brush preparation were optimized as to meet the stringent conditions required for surface force measurements, namely reproducible and uniform surface composition and roughness. The fit of a slip model to the experimental data returned a slip length of 16 nm on the PEG 1k brush and 25 nm on the PEG30k brush. The slip length can be interpreted as a penetration length, which accounts for flow within the top half of the brush for the PEG30k case, and within the brush and surface roughness for the PEG1k case. These findings confirm earlier simulation studies by our group on the flow of liquids within polymer brushes.
Patterned polymer coatings increase the efficiency of dew harvesting
04 December 2019
University of Sydney

Al-Khayat, Omar;Hong, Jun Ki;Beck, David M.;Minett, Andrew I.;Neto, Chiara

Micropatterned polymer surfaces, possessing both topographical and chemical characteristics, were prepared on three-dimensional copper tubes and used to capture atmospheric water. The micropatterns mimic the structure on the back of a desert beetle that condenses water from the air in a very dry environment. The patterned coatings were prepared by the dewetting of thin films of poly-4-vinylpyridine (P4VP) on top of polystyrene films (PS) films, upon solvent annealing, and consist of raised hydrophilic bumps on a hydrophobic background. The size and density distribution of the hydrophilic bumps could be tuned widely by adjusting the initial thickness of the P4VP films: the diameter of the produced bumps and their height could be varied by almost 2 orders of magnitude (1−80 μm and 40−9000 nm, respectively), and their distribution density could be varied by 5 orders of magnitude. Under low subcooling conditions (3 °C), the highest rate of water condensation was measured on the largest (80 μm diameter) hydrophilic bumps and was found to be 57% higher than that on flat hydrophobic films. These subcooling conditions are achieved spontaneously in dew formation, by passive radiative cooling of a surface exposed to the night sky. In effect, the pattern would result in a larger number of dewy nights than a flat hydrophobic surface and therefore increases water capture efficiency. Our approach is suited to fabrication on a large scale, to enable the use of the patterned coatings for water collection with no external input of energy.
Disasters, Queer Narratives, and the News: How Are LGBTI Disaster Experiences Reported by the Mainstream and LGBTI Media?
06 December 2019
University of Sydney

McKinnon, Scott;Gorman-Murray, Andrew;Dominey-Howes, Dale T.M.

The media plays a significant role in constructing the public meanings of disasters and influencing disaster management policy. In this article, we investigate how the mainstream and LGBTI media reported—or failed to report—the experiences of lesbian, gay, bisexual, transgender, and intersex (LGBTI) populations during disasters in Brisbane, Australia and Christchurch, New Zealand. The implications of our work lie within recent disasters research suggesting that marginalized populations—including LGBTI peoples—may experience a range of specific vulnerabilities during disasters on the basis of their social marginality. In this article, we argue that LGBTI experiences were largely absent from mainstream media reporting of the Brisbane floods and Christchurch earthquake of 2011. Media produced by and about the LGBTI community did take steps to redress this imbalance, although with uneven results in terms of inclusivity across that community. We conclude by raising the possibility that the exclusion or absence of queer disaster narratives may contribute to marginality through the media’s construction of disasters as experienced exclusively by heterosexual family groups.
Substrate range and enantioselectivity of epoxidation reactions mediated by the ethene-oxidising Mycobacterium strain NBB4
13 December 2019
University of Sydney

Cheung, Samantha;McCarl, Victoria;Holmes, Andrew;Coleman, Nicholas;Rutledge, Peter J

Mycobacterium strain NBB4 is an ethene-oxidizing micro-organism isolated from the estuarine sediments of Botany Bay. In pursuit of new systems for biocatalytic epoxidation, we report the capacity of strain NBB4 to convert a diverse range of alkene substrates to epoxides. A colorimetric assay based on 4-(4- nitrobenzyl)pyridine (NBP) has been developed to allow the rapid characterisation and quantification of biocatalytic epoxide synthesis. Using this assay we have demonstrated that ethene-grown NBB4 cells epoxidise a wide range of alkenes, including terminal (propene, 1-butene, 1-hexene, 1-octene and 1-decene), cyclic (cyclopentene, cyclohexene), aromatic (styrene, indene), and functionalised substrates (allyl alcohol, dihydropyran and isoprene). Apparent specific activities have been determined and range from 2.5 to 12.0 nmol min-1 per milligram of cell protein. The enantioselectivity of epoxidation by Mycobacterium strain NBB4 has been established using styrene as a test substrate; (R)-styrene oxide is produced in enantiomeric excesses greater than 95%. Thus the ethene monooxygenase of Mycobacterium NBB4 has a broad substrate range and promising enantioselectivity, confirming its potential as a biocatalyst for alkene epoxidation.
Supramolecular beta-cyclodextrin adducts of boron-rich DNA metallointercalators containing dicarba-closo-dodecaborane
19 December 2019
University of Sydney

Ching, H. Y. Vincent;Clarke, Ronald J.;Rendina, Louis M.

A chiral, isomeric series of novel boron-rich PtII metallointercalators ([PtL2(phen)](NO3)2: L = (x)-(1,y-closo-carboran-1-yl)pyrid-z-ylmethanol: x = R, S; y = 7, 12; z = 3, 4) wre prepared and fully characterized. By means of variable-temperature NMR spectroscopy, different combinations of Δ-head-to-tail, head-to-head, and Λ-head-to-tail rotamers were identified, and the free energies of activation for Pt–N bond rotation were determined for the pyrid-4-yl complexes with ΔG‡307 = 16.1 ± 0.3 kcal mol–1 and ΔG‡325 = 16.2 ± 0.5 kcal mol–1 for the 1,7-carboranyl derivative and ΔG‡307 = 16.4 ± 0.5 kcal mol–1 and ΔG‡325 = 16.2 ± 0.5 kcal mol–1 for the 1,12-carboranyl derivative. The corresponding 2:1 host–guest β-cyclodextrin (β-CD) adducts ([PtL2(phen)·2β-CD](NO3)2) were also prepared and fully characterized by high resolution electrospray ionization mass spectrometry and 2D-1H{11B} nuclear Overhauser enhancement spectroscopy and rotating-frame Overhauser effect spectroscopy NMR experiments. The interaction of the novel supramolecular adducts with calf thymus DNA was investigated by means of linear dichroism, ultraviolet-visible spectroscopy, thermal denaturation, and isothermal titration calorimetry experiments which revealed a bimodal binding regime with DNA intercalation favored at low [drug]/[DNA] ratios, while at higher drug loading, surface aggregation was observed. Furthermore, the data were also consistent with some degree of dissociation of the β-CD host–guest adducts upon DNA binding. When we used a single binding-site model, interpreted as a weighted average of all of the possible equilibrium interactions, the compounds showed high affinity for ct-DNA with Kassoc ranging from (1.3 ± 0.1) × 105 M–1 to (5.7 ± 0.4) × 105 M–1. In general, the overall DNA-binding behavior was enthalpically driven with a minor or unfavorable entropic component, which is consistent with the thermodynamics of an intercalation-dominated process. A higher degree of DNA intercalation was observed for the R-isomer in the pyrid-3-yl compounds, and the opposite trend was observed in the case of pyrid-4-yl derivatives.

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