Showing papers by "University of Adelaide published in 2002"

Asparagine hydroxylation of the HIF transactivation domain a hypoxic switch.

Abstract: The hypoxia-inducible factors (HIFs) 1α and 2α are key mammalian transcription factors that exhibit dramatic increases in both protein stability and intrinsic transcriptional potency during low-oxygen stress. This increased stability is due to the absence of proline hydroxylation, which in normoxia promotes binding of HIF to the von Hippel–Lindau (VHL tumor suppressor) ubiquitin ligase. We now show that hypoxic induction of the COOH-terminal transactivation domain (CAD) of HIF occurs through abrogation of hydroxylation of a conserved asparagine in the CAD. Inhibitors of Fe(II)- and 2-oxoglutarate–dependent dioxygenases prevented hydroxylation of the Asn, thus allowing the CAD to interact with the p300 transcription coactivator. Replacement of the conserved Asn by Ala resulted in constitutive p300 interaction and strong transcriptional activity. Full induction of HIF-1α and -2α, therefore, relies on the abrogation of both Pro and Asn hydroxylation, which during normoxia occur at the degradation and COOH-terminal transactivation domains, respectively.

FIH-1 is an asparaginyl hydroxylase enzyme that regulates the transcriptional activity of hypoxia-inducible factor

Abstract: Mammalian cells adapt to hypoxic conditions through a transcriptional response pathway mediated by the hypoxia-inducible factor, HIF. HIF transcriptional activity is suppressed under normoxic conditions by hydroxylation of an asparagine residue within its C-terminal transactivation domain, blocking association with coactivators. Here we show that the protein FIH-1, previously shown to interact with HIF, is an asparaginyl hydroxylase. Like known hydroxylase enzymes, FIH-1 is an Fe(II)-dependent enzyme that uses molecular O(2) to modify its substrate. Together with the recently discovered prolyl hydroxylases that regulate HIF stability, this class of oxygen-dependent enzymes comprises critical regulatory components of the hypoxic response pathway.

Truncation of the GABAA-Receptor γ2 Subunit in a Family with Generalized Epilepsy with Febrile Seizures Plus

Abstract: Recent findings from studies of two families have shown that mutations in the GABAA-receptor γ2 subunit are associated with generalized epilepsies and febrile seizures. Here we describe a family that has generalized epilepsy with febrile seizures plus (GEFS+), including an individual with severe myoclonic epilepsy of infancy, in whom a third GABAA-receptor γ2-subunit mutation was found. This mutation lies in the intracellular loop between the third and fourth transmembrane domains of the GABAA-receptor γ2 subunit and introduces a premature stop codon at Q351 in the mature protein. GABA sensitivity in Xenopus laevis oocytes expressing the mutant γ2Q351X subunit is completely abolished, and fluorescent-microscopy studies have shown that receptors containing GFP-labeled γ2Q351X protein are retained in the lumen of the endoplasmic reticulum. This finding reinforces the involvement of GABAA receptors in epilepsy.

On the formation of onion rings in friction stir welds

Abstract: Onion rings are the most prominent features of most friction stir welds. The origin and the effect of these on properties are not clearly understood. In this paper, an attempt has been made to explain the formation of onion rings. The formation of onion ring is found to be a geometric effect due to the fact that cylindrical sheets of material are extruded during each rotation of the tool and the cutting through the section of the material produces an apparent ‘Onion Rings’. It is postulated that the tool appears to wait for a very short time to produce frictional heat and extrude a cylindrical shaped material around to the retreating side of the joint. The spacing of the markings has been found to be equal to the forward motion of the tool in one rotation.

Mutations in the human ortholog of Aristaless cause X-linked mental retardation and epilepsy

Abstract: Mental retardation and epilepsy often occur together. They are both heterogeneous conditions with acquired and genetic causes. Where causes are primarily genetic, major advances have been made in unraveling their molecular basis. The human X chromosome alone is estimated to harbor more than 100 genes that, when mutated, cause mental retardation. At least eight autosomal genes involved in idiopathic epilepsy have been identified, and many more have been implicated in conditions where epilepsy is a feature. We have identified mutations in an X chromosome-linked, Aristaless-related, homeobox gene (ARX), in nine families with mental retardation (syndromic and nonspecific), various forms of epilepsy, including infantile spasms and myoclonic seizures, and dystonia. Two recurrent mutations, present in seven families, result in expansion of polyalanine tracts of the ARX protein. These probably cause protein aggregation, similar to other polyalanine and polyglutamine disorders. In addition, we have identified a missense mutation within the ARX homeodomain and a truncation mutation. Thus, it would seem that mutation of ARX is a major contributor to X-linked mental retardation and epilepsy.

Structure of turbulent non-premixed jet flames in a diluted hot coflow

Abstract: Moderate and intense low oxygen dilution combustion is a newly implemented and developed concept to achieve high thermal efficiency and fuel savings while maintaining emission of pollutants at very low levels. It utilizes the concept of heat and exhaust gas recirculation to achieve combustion at a reduced temperature, a flat thermal field, and low turbulence fluctuations. An experimental burner is used in this study to simulate the heat and exhaust gas recirculation applied to a simple jet in a hot coflow. Temporally and spatially resolved measurements of reactive scalars are conducted on three different turbulent nonpremixed flames of a H2/CH4 fuel mixture at a fixed-jet Reynolds number, and different oxygen levels in the hot oxidant stream. The data were collected using the single-point Raman-Rayleigh-laser-induced fluorescence technique. The results show substantial variation in the flame structure and appearance with the decrease of the oxygen level. By reducing the oxygen level in the hot coflow, the flame becomes less luminous, the temperature increase in the reaction zone can get as low as 100 K, and the levels of CO and OH are substantially lowered. The levels of NO also decrease with decreasing the oxygen levels and at 3% by mass, it is less that 5 ppm. For this case, a widely distributed NO profile is found which is not consistent with profiles for other oxygen levels.

Pollen-mediated movement of herbicide resistance between commercial canola fields

Abstract: There is considerable public and scientific debate for and against genetically modified (GM) crops. One of the first GM crops, Brassica napus (oilseed rape or canola) is now widely grown in North America, with proposed commercial release into Australia and Europe. Among concerns of opponents to these crops are claims that pollen movement will cause unacceptable levels of gene flow from GM to non-GM crops or to related weedy species, resulting in genetic pollution of the environment. Therefore, quantifying pollen-mediated gene flow is vital for assessing the environmental impact of GM crops. This study quantifies at a landscape level the gene flow that occurs from herbicide-resistant canola crops to nearby crops not containing herbicide resistance genes.

Pluripotent cell division cycles are driven by ectopic Cdk2, cyclin A/E and E2F activities.

Abstract: Pluripotent cells of embryonic origin proliferate at unusually rapid rates and have a characteristic cell cycle structure with truncated gap phases. To define the molecular basis for this we have characterized the cell cycle control of murine embryonic stem cells and early primitive ectoderm-like cells. These cells display precocious Cdk2, cyclin A and cyclin E kinase activities that are conspicuously cell cycle independent. Suppression of Cdk2 activity significantly decreased cycling times of pluripotent cells, indicating it to be rate-limiting for rapid cell division, although this had no impact on cell cycle structure and the establishment of extended gap phases. Cdc2-cyclin B was the only Cdk activity that was identified to be cell cycle regulated in pluripotent cells. Cell cycle regulation of cyclin B levels and Y(15) regulation of Cdc2 contribute to the temporal changes in Cdc2-cyclin B activity. E2F target genes are constitutively active throughout the cell cycle, reflecting the low activity of pocket proteins such as p107 and pRb and constitutive activity of pRb-kinases. These results show that rapid cell division cycles in primitive cells of embryonic origin are driven by extreme levels of Cdk activity that lack normal cell cycle periodicity.

Avalanche behavior in yield stress fluids.

Abstract: We show that, above a critical stress, typical yield stress fluids (gels and clay suspensions) and soft glassy materials (colloidal glasses) start flowing abruptly and subsequently accelerate, leading to avalanches that are remarkably similar to those of granular materials. Rheometrical tests reveal that this is associated with a bifurcation in rheological behavior: for small stresses, the viscosity increases in time; the material eventually stops flowing. For slightly larger stresses the viscosity decreases continuously in time; the flow accelerates. Thus the viscosity jumps discontinuously to infinity at the critical stress. We propose a simple physical model capable of reproducing these effects.

In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species.

Abstract: During the last decade microsatellites or SSRs (simple sequence repeats) have been proven to be the markers of choice in plant genetics research and for breeding purposes because of their hypervariability and ease of detection. However, development of these markers is expensive, labour intensive and time consuming, in particular, if they are being developed from genomic libraries. In the context of large-scale sequencing and genomics programmes in various cereal species at different laboratories, a large set of expressed sequence tags (ESTs) is being generated, which can be used to search for microsatellites. Keeping in view the importance of such type of SSRs, available ESTs of some cereal species like barley, maize, oats, rice, rye and wheat were investigated for a study of abundance, frequency and distribution of various types of microsatellites. SSRs were present in about 7% to 10% of the total ESTs in the investigated cereal genomes. On the basis of surveying EST sequences amounting to 75.2 Mb in barley, 54.7 Mb in maize, 43.9 Mb in rice, 3.7 Mb in rye, 41.6 Mb in sorghum and 37.5 Mb in wheat, the frequency of SSRs was 1/7.5 kb in barley, 1/7.5 kb in maize, 1/6.2 kb in wheat, 1/5.5 kb in rye and sorghum and 1/3.9 kb in rice. The overall average SSR frequency for these species is 1/6.0 kb. Trimeric repeats are the most abundant (54% to 78%) class of microsatellit es followed by dimeric repeats (17% to 40%). Among the trimeric repeats the motifs CCG are the most common in all the cases ranging from 32% in wheat to 49% in sorghum. When all these SSRs were analysed for assessing their potential to develop new markers, unique primer pairs could be designed for 30% to 70% of the total non-redundant microsatellites which are up to 3% of total ESTs in the studied species.

Direct Detection and Characterization of Shiga Toxigenic Escherichia coli by Multiplex PCR for stx1, stx2, eae, ehxA, and saa

Abstract: We recently described a novel megaplasmid-encoded adhesin produced by certain Shiga toxigenic Escherichia coli (STEC) strains that lack the locus for enterocyte effacement (LEE) pathogenicity island. This adhesin, designated Saa (STEC autoagglutinating adhesin), may be a marker for a subset of LEE-negative STEC strains capable of causing severe gastrointestinal and systemic diseases in humans. In this study, we developed a pentavalent PCR assay for the detection of saa as well as other proven and putative STEC virulence genes (stx1, stx2, eae, and ehxA). The five primer pairs used in the assay do not interfere with each other and generate amplification products of 119, 180, 255, 384, and 534 bp.

D branes on group manifolds and fusion rings

Abstract: In this paper we compute the charge group for symmetry preserving D-branes on group manifolds for all simple, simply-connected, connected compact Lie groups G.

REDOX regulation of early embryo development.

Abstract: Preimplantation embryonic development is associated with a change in preference in energy metabolism pathways. Although oxidative phosphorylation is obligatory in most species throughout preimplantation development, an increasing role for energy derived from glycolysis is associated with compaction and blastulation. Such a shift in metabolic pathway preference is desirable as the embryo faces an increasingly hypoxic environment in utero. We hypothesize that this shift in metabolic preference is associated with a change in the reduction-oxidation (REDOX) state within the embryo, affecting not only the energy production required for development, but also the activity of REDOX-sensitive transcription factors, which may alter gene expression patterns. Shifts in intracellular REDOX state may also contribute to spatial differences in cell activity, especially after compaction, and perhaps even major embryonic events such as fertilization, genome activation and cellular differentiation.

Twisted K-theory and K-Theory of Bundle Gerbes

Abstract: In this note we introduce the notion of bundle gerbe K-theory and investigate the relation to twisted K-theory. We provide some examples. Possible applications of bundle gerbe K-theory to the classification of K-brane charges in nontrivial backgrounds are briefly discussed.

T-ray computed tomography.

Abstract: We demonstrate a tomographic imaging modality that uses pulsed terahertz (THz) radiation to probe the optical properties of three-dimensional (3D) structures in the far-infrared. This THz-wave computed tomography (T-ray CT) system provides sectional images of objects in a manner analogous to conventional CT techniques such as x-ray CT. The transmitted amplitude and phase of broadband pulses of THz radiation are measured at multiple projection angles. The filtered backprojection algorithm is then used to reconstruct the target object, including both its 3D structure and its frequency-dependent far-infrared optical properties.

Chemistry of inorganic arsenic in soils: II. Effect of phosphorus, sodium, and calcium on arsenic sorption.

Abstract: There are more than 10000 arsenic (As) contaminated sites in Australia. The ability of soils at these contaminated sites to sorb As is highly variable and appreciable amounts of As have been recorded in the subsurface soils. The potential risk of surface and ground water contamination by As at these sites is a major environmental concern. Factors that influence adsorption capacity of soils influence the bioavailability and subsequent mobility of As in soils. In the present study we investigated the effect of PO4(3-) and Na+ and Ca2+ on the sorption of AsV and AsIII by an Oxisol, a Vertisol, and two Alfisols. The presence of P (0.16 mmol L(-1)) greatly decreased AsV sorption by soils containing low amounts of Fe oxides ( 800 mmol kg(-1)). However, AsV sorption substantially decreased from 0.63 to 0.37 mmol kg(-1) as P concentration was increased from 0.16 to 3.2 mmol L(-1) in selected soils. This suggests increased competition between P and AsV for soil sorption sites, through either the higher affinity or the effect of mass action of the increasing concentration of P in solution. A similar effect of P on AsIII sorption was observed in the low sorbing Alfisol and high affinity Oxisol. However, the amount of AsIII sorbed by the Oxisol was much greater than the Alfisol for all treatments. The presence of Ca2+ increased the amount of AsV sorbed compared with that of Na+ and was manifested through changes in the surface charge characteristics of the soils. A similar trend in AsIII sorption was recorded with changes in index cation, although the effect was not as marked as recorded for AsV.

Gastric emptying in diabetes: clinical significance and treatment.

Abstract: The outcome of recent studies has led to redefinition of concepts relating to the prevalence, pathogenesis and clinical significance of disordered gastric emptying in patients with diabetes mellitus. The use of scintigraphic techniques has established that gastric emptying is abnormally slow in approx. 30-50% of outpatients with long-standing Type 1 or Type 2 diabetes, although the magnitude of this delay is modest in many cases. Upper gastrointestinal symptoms occur frequently and affect quality of life adversely in patients with diabetes, although the relationship between symptoms and the rate of gastric emptying is weak. Acute changes in blood glucose concentration affect both gastric motor function and upper gastrointestinal symptoms. Gastric emptying is slower during hyperglycaemia when compared with euglycaemia and accelerated during hypoglycaemia. The blood glucose concentration may influence the response to prokinetic drugs. Conversely, the rate of gastric emptying is a major determinant of post-prandial glycaemic excursions in healthy subjects, as well as in Type 1 and Type 2 patients. A number of therapies currently in development are designed to improve post-prandial glycaemic control by modulating the rate of delivery of nutrients to the small intestine.

The role of lifestyle modification in polycystic ovary syndrome

Abstract: Polycystic ovary syndrome (PCOS) is a common endocrine condition with reproductive and metabolic consequences, including anovulation, infertility and an increased prevalence of diabetes mellitus. Obesity, central obesity and insulin resistance are strongly implicated in its etiology and reduction of these risk factors should be a central treatment focus. Short-term weight loss has been consistently successful in reducing insulin resistance and restoring ovulation and fertility. However, problems arise with maintaining weight loss and precisely quantifying the associated long-term benefits of risk factor change. Although recent research indicates modest long-term lifestyle changes might reduce the extent of impaired glucose tolerance and delay the conversion to diabetes mellitus in the general population, this has not yet been examined in women with PCOS. Current conservative treatment should emphasize sustainable weight loss through dietary modification and exercise. Modifying additional lifestyle factors, including alcohol consumption, psychosocial stressors and smoking, are also crucial in long-term treatment of PCOS.

Predicting settlement of shallow foundations using neural networks

Abstract: Over the years, many methods have been developed to predict the settlement of shallow foundations on cohesionless soils. However, methods for making such predictions with the required degree of accuracy and consistency have not yet been developed. Accurate prediction of settlement is essential since settlement, rather than bearing capacity, generally controls foundation design. In this paper, artificial neural networks (ANNs) are used in an attempt to obtain more accurate settlement prediction. A large database of actual measured settlements is used to develop and verify the ANN model. The predicted settlements found by utilizing ANNs are compared with the values predicted by three of the most commonly used traditional methods. The results indicate that ANNs are a useful technique for predicting the settlement of shallow foundations on cohesionless soils, as they outperform the traditional methods.

Displacement-based seismic analysis for out-of-plane bending of unreinforced masonry walls

Abstract: This paper addresses the problem of assessing the seismic resistance of brick masonry walls subject to out-of-plane bending. A simplified linearized displacement-based procedure is presented along with recommendations for the selection of an appropriate substitute structure in order to provide the most representative analytical results. A trilinear relationship is used to characterize the real nonlinear force–displacement relationship for unreinforced brick masonry walls. Predictions of the magnitude of support motion required to cause flexural failure of masonry walls using the linearized displacement-based procedure and quasi-static analysis procedures are compared with the results of experiments and non-linear time-history analyses. The displacement-based procedure is shown to give significantly better predictions than the force-based method. Copyright © 2002 John Wiley & Sons, Ltd.

Hypoxia-inducible Factor-1α mRNA Contains an Internal Ribosome Entry Site That Allows Efficient Translation during Normoxia and Hypoxia

Abstract: HIF-1α is the regulated subunit of the HIF-1 transcription factor, which induces transcription of a number of genes involved in the cellular response to hypoxia. The HIF-1α protein is rapidly degraded in cells supplied with adequate oxygen but is stabilized in hypoxic cells. Using polysome profile analysis, we found that translation of HIF-1α mRNA in NIH3T3 cells is spared the general reduction in translation rate that occurs during hypoxia. To assess whether the 5′UTR of the HIF-1α mRNA contains an internal ribosome entry site (IRES), we constructed a dicistronic reporter with the HIF-1α 5′UTR inserted between two reporter coding regions. We found that the HIF-1α 5′UTR promoted translation of the downstream reporter, indicating the presence of an IRES. The IRES had activity comparable to that of the well-characterized c-myc IRES. IRES activity was not affected by hypoxic conditions that caused a reduction in cap-dependent translation, and IRES activity was less affected by serum-starvation than was cap-dependent translation. These data indicate that the presence of an IRES in the HIF-1α 5′UTR allows translation to be maintained under conditions that are inhibitory to cap-dependent translation.

Obesity increases the risk of spontaneous abortion during infertility treatment.

Abstract: Objective: This study examines the relationship between body mass and the risk of spontaneous abortion in a large cohort of patients who received infertility treatment. Research Methods and Procedures: This is a retrospective study using data on pregnancies (n = 2349) achieved after treatment in a tertiary medical center from 1987 to 1999. One pregnancy per subject was included, and the subjects were stratified into five body mass groups based on body mass index (BMI): underweight, <18.5 kg/m2; normal, 18.5 to 24.9 kg/m2; overweight, 25 to 29.9 kg/m2; obese, 30 to 34.9 kg/m2; and very obese, ≥35 kg/m2. Logistical regression analysis was used. Results: The overall incidence of spontaneous abortion was 20% (476 of 2349). The effect of BMI on the risk of spontaneous abortion was significant after adjusting for several independent risk factors. Compared with the reference group (BMI 18.5 to 24.9 kg/m2), underweight women had a similar risk of spontaneous abortion, whereas there was progressive increase of risk in overweight, obese, and very obese groups (p < 0.05, p < 0.01, and p < 0.001, respectively). Discussion: Of all known risk factors for spontaneous abortion, the control of obesity has great significance because it is noninvasive, potentially modifiable, possibly amenable to low cost, and self-manageable by patients. This study established a positive relationship between BMI and the risk of spontaneous abortion in women who became pregnant after assisted reproductive technology treatment.

Random and Mixed Effects

Abstract: Models with mixed effects contain both fixed and random effects. Fixed effects are what we have been considering up to now; the only source of randomness in our models arises from regarding the cases as independent random samples. Thus in regression we have an additive measurement error that we assume is independent between cases, and in a GLM we observe independent binomial, Poisson, gamma ... random variates whose mean is a deterministic function of the explanatory variables.

The Coronary Slow Flow Phenomenon – A New Coronary Microvascular Disorder

Abstract: The coronary slow flow phenomenon is an angiographic finding characterized by delayed distal vessel opacification in the absence of significant epicardial coronary disease. Case-control and observational studies of patients with this phenomenon were conducted to determine the associated clinical features and prognosis. Patients with coronary slow flow (n = 47) differed from controls (n = 47), more often being current smokers (32 vs. 9%; p < 0.01) and presenting with rest pain requiring urgent admission (74 vs. 21%; p < 0.001), usually to the coronary care unit (66 vs. 17%; p < 0.01). During a median 21-month follow-up of 64 slow flow patients, 84% had recurrent chest pain. Based upon these findings and those of previous investigators, it is speculated that coronary slow flow is a new disease entity characterized by acute but recurrent perturbations of microvascular function.

Leak detection in pipelines using the damping of fluid transients

Abstract: Leaks in pipelines contribute to damping of transient events. That fact leads to a method of finding location and magnitude of leaks. Because the problem of transient flow in pipes is nearly linear, the solution of the governing equations can be expressed in terms of a Fourier series. All Fourier components are damped uniformly by steady pipe friction, but each component is damped differently in the presence of a leak. Thus, overall leak-induced damping can be divided into two parts. The magnitude of the damping indicates the size of a leak, whereas different damping ratios of the various Fourier components are used to find the location of a leak. This method does not require rigorous determination and modeling of boundary conditions and transient behavior in the pipeline. The technique is successful in detecting, locating, and quantifying a 0.1% size leak with respect to the cross-sectional area of a pipeline.