Structural features associated with multiferroic behavior in the RX3(BO3)4 system.

The magnetoelectric effect in the RX3(BO3)4 system (R = Ho, Eu, Sm, Nd, Gd; X = Fe, Al) varies significantly with the cation R despite very similar structural arrangements. Our structural studies reveal a symmetry reducing tilting of the BO3 planes and of the FeO6 polyhedra in the systems exhibiting low magnetic field induced electric polarization. Neutron scattering measurements reveal a lack of magnetic ordering indicating the primary importance of the atomic structure in the multiferroic behavior of this system.

Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi.

Biofilms enhance rates of gene exchange, access to specific nutrients, and cell survivability. Haloarchaea in Deep Lake, Antarctica, are characterized by high rates of intergenera gene exchange, metabolic specialization that promotes niche adaptation, and are exposed to high levels of UV-irradiation in summer. Halorubrum lacusprofundi from Deep Lake has previously been reported to form biofilms. Here we defined growth conditions that promoted the formation of biofilms and used microscopy and enzymatic digestion of extracellular material to characterize biofilm structures. Extracellular DNA was found to be critical to biofilms, with cell surface proteins and quorum sensing also implicated in biofilm formation. Quantitative proteomics was used to define pathways and cellular processes involved in forming biofilms; these included enhanced purine synthesis and specific cell surface proteins involved in DNA metabolism; post-translational modification of cell surface proteins; specific pathways of carbon metabolism involving acetyl-CoA; and specific responses to oxidative stress. The study provides a new level of understanding about the molecular mechanisms involved in biofilm formation of this important member of the Deep Lake community.

Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function.

No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.

Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii.

TRAM domain proteins present in Archaea and Bacteria have a ß-barrel shape with anti-parallel ß-sheets that form a nucleic acid binding surface; a structure also present in cold shock proteins (Csps). Aside from protein structures, experimental data defining the function of TRAM domains is lacking. Here, we explore the possible functional properties of a single TRAM domain protein, Ctr3 (cold-responsive TRAM domain protein 3) from the Antarctic archaeon Methanococcoides burtonii that has increased abundance during low temperature growth. Ribonucleic acid (RNA) bound by Ctr3 in vitro was determined using RNA-seq. Ctr3-bound M. burtonii RNA with a preference for transfer (t)RNA and 5S ribosomal RNA, and a potential binding motif was identified. In tRNA, the motif represented the C loop; a region that is conserved in tRNA from all domains of life and appears to be solvent exposed, potentially providing access for Ctr3 to bind. Ctr3 and Csps are structurally similar and are both inferred to function in low temperature translation. The broad representation of single TRAM domain proteins within Archaea compared with their apparent absence in Bacteria, and scarcity of Csps in Archaea but prevalence in Bacteria, suggests they represent distinct evolutionary lineages of functionally equivalent RNA-binding proteins.

Donation After Circulatory Determination of Death Lung Transplantation for Pulmonary Arterial Hypertension: Passing the Toughest Test.

Lung transplantation (LTx) is a therapeutic option for severe pulmonary arterial hypertension (PAH) patients failing optimal medical therapy. The use of donation after circulatory determination of death (DCDD) donor lungs for PAH LTx has rarely been reported, primarily reflecting concerns that DCDD lungs represent extended criteria donors, at risk of morbidity and mortality. A retrospective study of all Alfred Hospital DCDD and DNDD (donation after neurologic determination of death) PAH LTx was undertaken. Protocolized fluid/inotrope/ventilator and extracorporeal membrane oxygenation (ECMO) strategies were utilized. Since our first DCDD LTx in 2006, 512 LTx have been performed. Of 31 PAH recipients, 11 received DCDD lungs (11% of DCDD LTx) and 20 received DNDD lungs (5% of DNDD LTx) (p = 0.04). Only one PAH patient died on the LTx waiting list. Peri-LTx ECMO was utilized in 3/11 (27%) DCDD and 6/20 (30%) DNDD PAH LTx (p = 0.68). Primary graft dysfunction, intensive care, and overall stay were the same in both groups. Survival at 1 and 8 years was 100% and 80% for DCDD versus 100% and 70% for DNDD LTx (p = 0.88), respectively. In conclusion, excellent results can be achieved for PAH LTx. DCDD donor lungs are not extended lungs per se having passed the toughest test.

New magnetic phase diagram of (Sr,Ca)2RuO4.

High-T(c) cuprates, iron pnictides, organic BEDT and TMTSF, alkali-doped C(60), and heavy-fermion systems have superconducting states adjacent to competing states exhibiting static antiferromagnetic or spin density wave order. This feature has promoted pictures for their superconducting pairing mediated by spin fluctuations. Sr(2)RuO(4) is another unconventional superconductor which almost certainly has a p-wave pairing. The absence of known signatures of static magnetism in the Sr-rich side of the (Ca, Sr) substitution space, however, has led to a prevailing view that the superconducting state in Sr(2)RuO(4) emerges from a surrounding Fermi-liquid metallic state. Using muon spin relaxation and magnetic susceptibility measurements, we demonstrate here that (Sr,Ca)(2)RuO(4) has a ground state with static magnetic order over nearly the entire range of (Ca, Sr) substitution, with spin-glass behaviour in Sr(1.5)Ca(0.5)RuO(4) and Ca(1.5)Sr(0.5)RuO(4). The resulting new magnetic phase diagram establishes the proximity of superconductivity in Sr(2)RuO(4) to competing static magnetic order.

Spin ice: magnetic excitations without monopole signatures using muon spin rotation.

Theory predicts the low temperature magnetic excitations in spin ices consist of deconfined magnetic charges, or monopoles. A recent transverse-field (TF) muon spin rotation (µSR) experiment [S. T. Bramwell et al., Nature (London) 461, 956 (2009)] reports results claiming to be consistent with the temperature and magnetic field dependence anticipated for monopole nucleation-the so-called second Wien effect. We demonstrate via a new series of µSR experiments in Dy(2)Ti(2)O(7) that such an effect is not observable in a TF µSR experiment. Rather, as found in many highly frustrated magnetic materials, we observe spin fluctuations which become temperature independent at low temperatures, behavior which dominates over any possible signature of thermally nucleated monopole excitations.

Li(Zn,Mn)As as a new generation ferromagnet based on a I-II-V semiconductor.

In a prototypical ferromagnet (Ga,Mn)As based on a III-V semiconductor, substitution of divalent Mn atoms into trivalent Ga sites leads to severely limited chemical solubility and metastable specimens available only as thin films. The doping of hole carriers via (Ga,Mn) substitution also prohibits electron doping. To overcome these difficulties, Masek et al. theoretically proposed systems based on a I-II-V semiconductor LiZnAs, where isovalent (Zn,Mn) substitution is decoupled from carrier doping with excess/deficient Li concentrations. Here we show successful synthesis of Li(1+y)(Zn(1-x)Mn(x))As in bulk materials. Ferromagnetism with a critical temperature of up to 50 K is observed in nominally Li-excess (y=0.05-0.2) compounds with Mn concentrations of x=0.02-0.15, which have p-type metallic carriers. This is presumably due to excess Li in substitutional Zn sites. Semiconducting LiZnAs, ferromagnetic Li(Zn,Mn)As, antiferromagnetic LiMnAs, and superconducting LiFeAs systems share square lattice As layers, which may enable development of novel junction devices in the future.

Biotechnological uses of enzymes from psychrophiles.

The bulk of the Earth's biosphere is cold (e.g. 90% of the ocean's waters are ≤ 5°C), sustaining a broad diversity of microbial life. The permanently cold environments vary from the deep ocean to alpine reaches and to polar regions. Commensurate with the extent and diversity of the ecosystems that harbour psychrophilic life, the functional capacity of the microorganisms that inhabitat the cold biosphere are equally diverse. As a result, indigenous psychrophilic microorganisms provide an enormous natural resource of enzymes that function effectively in the cold, and these cold-adapted enzymes have been targeted for their biotechnological potential. In this review we describe the main properties of enzymes from psychrophiles and describe some of their known biotechnological applications and ways to potentially improve their value for biotechnology. The review also covers the use of metagenomics for enzyme screening, the development of psychrophilic gene expression systems and the use of enzymes for cleaning.

Delta opioid receptors colocalize with corticotropin releasing factor in hippocampal interneurons.

The hippocampal formation (HF) is an important site at which stress circuits and endogenous opioid systems intersect, likely playing a critical role in the interaction between stress and drug addiction. Prior study findings suggest that the stress-related neuropeptide corticotropin releasing factor (CRF) and the delta opioid receptor (DOR) may localize to similar neuronal populations within HF lamina. Here, hippocampal sections of male and cycling female adult Sprague-Dawley rats were processed for immunolabeling using antisera directed against the DOR and CRF peptide, as well as interneuron subtype markers somatostatin or parvalbumin, and analyzed by fluorescence and electron microscopy. Both DOR- and CRF-labeling was observed in interneurons in the CA1, CA3, and dentate hilus. Males and normal cycling females displayed a similar number of CRF immunoreactive neurons co-labeled with DOR and a similar average number of CRF-labeled neurons in the dentate hilus and stratum oriens of CA1 and CA3. In addition, 70% of DOR/CRF dual-labeled neurons in the hilar region co-labeled with somatostatin, suggesting a role for these interneurons in regulating perforant path input to dentate granule cells. Ultrastructural analysis of CRF-labeled axon terminals within the hilar region revealed that proestrus females have a similar number of CRF-labeled axon terminals that contain DORs compared to males but an increased number of CRF-labeled axon terminals without DORs. Taken together, these findings suggest that while DORs are anatomically positioned to modulate CRF immunoreactive interneuron activity and CRF peptide release, their ability to exert such regulatory activity may be compromised in females when estrogen levels are high.

A comparison of the structure of solute clusters formed during thermal ageing and irradiation.

Nanometre scale clusters form in Cu-containing reactor pressure vessel (RPV) steels during neutron irradiation. These clusters have a deleterious effect on mechanical properties, which can result in embrittlement and limit the reactor operating life. Thermal ageing of RPV steels can also induce the formation of solute clusters but it is not clear how similar these are to those formed during irradiation. In this work atom probe tomography, combined with detailed structural assessments of the structure of solute clusters, is used to address this issue. A series of thermal ageing heat treatments has been performed on several high- and low-Ni RPV welds to produce 1-4 nm diameter solute clusters. The same materials have also been neutron irradiated. The results show that CuMnNiSi enriched clusters formed during thermal ageing have, on average, higher Cu contents and lower Mn, Ni and Si contents than those found in irradiation-induced clusters. The effect of increasing bulk Ni is to encourage the formation of clusters with significantly higher Ni content, slightly higher Mn and Si contents and significantly lower Cu contents. At very high doses and dose rates MnNiSi enriched clusters can form even in high-Cu welds. Despite differences in the compositions of individual clusters formed during irradiation and during thermal ageing, clusters in both exhibit similar structure. In particular, well developed clusters in both materials have Cu-enriched cores whose peripheries are enriched in Ni, Mn and, in most cases, Si.

A sensitivity analysis of the maximum separation method for the characterisation of solute clusters.

Variants of the maximum separation method have become the de-facto methodologies for the characterisation of nanometre scale clusters in atom probe tomography (APT) data obtained from dilute solid solutions. All variants rely on a number of parameters and it is well known that the precise values for these parameters strongly influence estimates of cluster size and number density. Quantitative analyses require an improved understanding of the inter-relationship between user-defined parameters, experimental parameters such as detection efficiency and the resultant parameterisation of the microstructure. A series of simulations has been performed to generate clusters with a range of compositions (50-100%) and diameters (1.5-2.5 nm) in a dilute solid solution. The data were degraded to simulate the effects of the finite detection efficiencies and positioning uncertainties associated with the ECOPoSAP and LEAP-3000X HR. An extensive analysis of each resultant dataset, using a range of values for the maximum separation parameters was then performed. Optimum values for each material condition were identified and it is shown that it is possible to characterise cluster size, number density and matrix chemistry. However, accurate estimates of cluster compositions are more difficult and absolute measurements must be treated with caution. Furthermore, it is shown that D(MAX) must increase with decreasing detection efficiency and consequently clusters of a specific size will appear slightly larger in atom probes with a lower detection efficiency.

Atom probe tomography of reactor pressure vessel steels: an analysis of data integrity.

In this work, the importance of optimising experimental conditions for the analysis of reactor pressure vessel (RPV) steels using atom probe tomography is explored. The quality of the resultant atom probe data is assessed in terms of detection efficiency, noise levels and mass resolution. It is demonstrated that artefacts can exist even when experimental conditions have been optimised. In particular, it is shown that surface diffusion of some minority species, including P and Si, to major poles prior to field evaporation can be an issue. The effects were most noticeable during laser pulsing. The impact of surface migration on the characterisation of dislocations and grain boundaries is assessed. The importance of selecting appropriate regions of the reconstructed data for subsequent re-analysis is emphasised.

The Bosentan Patient Registry: long-term survival in pulmonary arterial hypertension.

BACKGROUND/AIMS: The Bosentan Patient Registry (BPR) was a prospective, multicentre, Australian registry funded by Actelion Pharmaceuticals. The primary aim of the registry was to collect survival data in patients with pulmonary arterial hypertension (PAH) treated with bosentan. METHODS: The BPR was initiated in 15 specialized PAH centres. All patients on or starting bosentan were invited to enrol. Treating physicians notified the registry if patients discontinued bosentan, because of either a change in therapy, transplantation, intervention or death. Survival data were validated against the Australian Institute of Health and Welfare National Death Index. RESULTS: Between 2004 and 2007, a total of 528 patients (mean age 59 ± 17 years) were enrolled representing 69% of patients either previously taking or initiated on bosentan during that time. The BPR population was generally older with more advanced functional deficit than patients enrolled in randomized, placebo-controlled trials. Aetiology was idiopathic (iPAH) in 58% and connective tissue disease related (scleroderma (SSc)-PAH) in 42%. For iPAH patients, World Health Organisation functional classes II, III and IV at enrolment was 8.2%, 66.4% and 20.5%, and for the SSc-PAH cohort, 3.2%, 75.8% and 17.9% respectively. The observed annual mortality was 11.8% in patients with iPAH and 16.6% in patients SSc-PAH. CONCLUSION: This large Australian registry provides 'real life' information on the characteristics and management of PAH in clinical practice. Treatment with bosentan improved survival outcomes in both iPAH and SSc-PAH compared with historical controls. Age, disease severity and aetiology were critical factors in determining clinical outcomes.

Temperature-dependent global gene expression in the Antarctic archaeon Methanococcoides burtonii.

Methanococcoides burtonii is a member of the Archaea that was isolated from Ace Lake in Antarctica and is a valuable model for studying cold adaptation. Low temperature transcriptional regulation of global gene expression, and the arrangement of transcriptional units in cold-adapted archaea has not been studied. We developed a microarray for determining which genes are expressed in operons, and which are differentially expressed at low (4°C) or high (23°C) temperature. Approximately 55% of genes were found to be arranged in operons that range in length from 2 to 23 genes, and mRNA abundance tended to increase with operon length. Analysing microarray data previously obtained by others for Halobacterium salinarum revealed a similar correlation between operon length and mRNA abundance, suggesting that operons may play a similar role more broadly in the Archaea. More than 500 genes were differentially expressed at levels up to ≈ 24-fold. A notable feature was the upregulation of genes involved in maintaining RNA in a state suitable for translation in the cold. Comparison between microarray experiments and results previously obtained using proteomics indicates that transcriptional regulation (rather than translation) is primarily responsible for controlling gene expression in M. burtonii. In addition, certain genes (e.g. involved in ribosome structure and methanogenesis) appear to be regulated post-transcriptionally. This is one of few experimental studies describing the genome-wide distribution and regulation of operons in archaea.

Imaging the Fano lattice to 'hidden order' transition in URu(2)Si(2).

Within a Kondo lattice, the strong hybridization between electrons localized in real space (r-space) and those delocalized in momentum-space (k-space) generates exotic electronic states called 'heavy fermions'. In URu(2)Si(2) these effects begin at temperatures around 55 K but they are suddenly altered by an unidentified electronic phase transition at T(o) = 17.5 K. Whether this is conventional ordering of the k-space states, or a change in the hybridization of the r-space states at each U atom, is unknown. Here we use spectroscopic imaging scanning tunnelling microscopy (SI-STM) to image the evolution of URu(2)Si(2) electronic structure simultaneously in r-space and k-space. Above T(o), the 'Fano lattice' electronic structure predicted for Kondo screening of a magnetic lattice is revealed. Below T(o), a partial energy gap without any associated density-wave signatures emerges from this Fano lattice. Heavy-quasiparticle interference imaging within this gap reveals its cause as the rapid splitting below T(o) of a light k-space band into two new heavy fermion bands. Thus, the URu(2)Si(2) 'hidden order' state emerges directly from the Fano lattice electronic structure and exhibits characteristics, not of a conventional density wave, but of sudden alterations in both the hybridization at each U atom and the associated heavy fermion states.

The six-minute walk test: a useful metric for the cardiopulmonary patient.

Measurement of exercise capacity is an integral element in assessment of patients with cardiopulmonary disease. The 6-min walk test (6MWT) provides information regarding functional capacity, response to therapy and prognosis across a range of chronic cardiopulmonary conditions. A distance less than 350 m is associated with increased mortality in chronic obstructive pulmonary disease, chronic heart failure and pulmonary arterial hypertension. Desaturation during a 6MWT is an important prognostic indicator for patients with interstitial lung disease. The 6MWT is sensitive to commonly used therapies in chronic obstructive pulmonary disease such as pulmonary rehabilitation, oxygen, long-term use of inhaled corticosteroids and lung volume reduction surgery. However, it appears less reliable to detect changes in clinical status associated with medical therapies for heart failure. A change in walking distance of more than 50 m is clinically significant in most disease states. When interpreting the results of a 6MWT, consideration should be given to choice of predictive values and the methods by which the test was carried out.

The spectrum of structural abnormalities on CT scans from patients with CF with severe advanced lung disease.

RATIONALE: In cystic fibrosis (CF), lung disease is the predominant cause of morbidity and mortality. Little is known about the spectrum of structural abnormalities on CT scans from patients with CF with severe advanced lung disease (SALD). No specific CT scoring system for SALD is available. OBJECTIVES: To design a quantitative CT scoring system for SALD, to determine the spectrum of structural abnormalities in patients with SALD and to correlate the SALD system with an existing scoring system for mild CF lung disease and pulmonary function tests (PFTs). METHODS: 57 patients with CF contributed one CT made during screening for lung transplantation. For the SALD system, lung tissue was divided into four components: infection/inflammation (including bronchiectasis, airway wall thickening, mucus and consolidations), air trapping/hypoperfusion, bulla/cysts and normal/hyperperfused tissue. The volume proportion of the components was estimated on a 0-100% scale; mean volumes for the whole lung were computed. Scores were correlated with Brody-II scores and PFTs. RESULTS: The SALD system identified a wide spectrum of structural abnormalities ranging from predominantly infection/inflammation to predominantly air trapping/hypoperfusion. SALD infection/inflammation scores correlated with Brody-II scores (r(s) = 0.36-0.64) and SALD normal/hyperperfusion scores correlated with forced expiratory volume in 1 s (FEV(1); r(s) = 0.37). Reproducibility for both systems was good. CONCLUSIONS: A CT scoring system was developed to characterise the structural abnormalities in patients with SALD. A wide spectrum was observed in SALD, ranging from predominantly air trapping to predominantly infection/inflammation-related changes. This spectrum may have clinical implications for patients with SALD.

Hippocampal dynorphin immunoreactivity increases in response to gonadal steroids and is positioned for direct modulation by ovarian steroid receptors.

The hippocampal formation (HF) is involved in modulating learning related to drug abuse. While HF-dependent learning is regulated by both endogenous opioids and estrogen, the interaction between these two systems is not well understood. The mossy fiber (MF) pathway formed by dentate gyrus (DG) granule cell axons is involved in some aspects of learning and contains abundant amounts of the endogenous opioid peptide dynorphin (DYN). To examine the influence of ovarian steroids on DYN expression, we used quantitative light microscopic immunocytochemistry to measure DYN levels in normal cycling rats as well as in two established models of hormone-treated ovariectomized (OVX) rats. Rats in estrus had increased levels of DYN-immunoreactivity (ir) in the DG and certain CA3 lamina compared with rats in proestrus or diestrus. OVX rats exposed to estradiol for 24 h showed increased DYN-ir in the DG and CA3, while those with 72 h estradiol exposure showed increases only in the DG. Six hours of estradiol exposure produced no change in DYN-ir. OVX rats chronically implanted with medroxyprogesterone also showed increased DYN-ir in the DG and CA3. Next, dual-labeling electron microscopy (EM) was used to evaluate the subcellular relationships of estrogen receptor (ER) alpha-, ERbeta and progestin receptor (PR) with DYN-labeled MFs. ERbeta-ir was in some DYN-labeled MF terminals and smaller terminals, and had a subcellular association with the plasmalemma and small synaptic vesicles. In contrast, ERalpha-ir was not in DYN-labeled terminals, although some DYN-labeled small terminals synapsed on ERalpha-labeled dendritic spines. PR labeling was mostly in CA3 axons, some of which were continuous with DYN-labeled terminals. These studies indicate that ovarian hormones can modulate DYN in the MF pathway in a time-dependent manner, and suggest that hormonal effects on the DYN-containing MF pathway may be directly mediated by ERbeta and/or PR activation.

Statistical analysis of atom probe data: detecting the early stages of solute clustering and/or co-segregation.

Statistical analysis of atom probe data has improved dramatically in the last decade and it is now possible to determine the size, the number density and the composition of individual clusters or precipitates such as those formed in reactor pressure vessel (RPV) steels during irradiation. However, the characterisation of the onset of clustering or co-segregation is more difficult and has traditionally focused on the use of composition frequency distributions (for detecting clustering) and contingency tables (for detecting co-segregation). In this work, the authors investigate the possibility of directly examining the neighbourhood of each individual solute atom as a means of identifying the onset of solute clustering and/or co-segregation. The methodology involves comparing the mean observed composition around a particular type of solute with that expected from the overall composition of the material. The methodology has been applied to atom probe data obtained from several irradiated RPV steels. The results show that the new approach is more sensitive to fine scale clustering and co-segregation than that achievable using composition frequency distribution and contingency table analyses.