Integrated analysis of epigenomic and genomic changes by DNA methylation dependent mechanisms provides potential novel biomarkers for prostate cancer

Epigenetic silencing mediated by CpG methylation is a common feature of many cancers. Characterizing aberrant DNA methylation changes associated with tumor progression may identify potential prognostic markers for prostate cancer (PCa). We treated two PCa cell lines, 22Rv1 and DU-145 with the demethylating agent 5-Aza 2’–deoxycitidine (DAC) and global methylation status was analyzed by performing methylation-sensitive restriction enzyme based differential methylation hybridization strategy followed by genome-wide CpG methylation array profiling. In addition, we examined gene expression changes using a custom microarray. Gene Set Enrichment Analysis (GSEA) identified the most significantly dysregulated pathways. In addition, we assessed methylation status of candidate genes that showed reduced CpG methylation and increased gene expression after DAC treatment, in Gleason score (GS) 8 vs. GS6 patients using three independent cohorts of patients; the publically available The Cancer Genome Atlas (TCGA) dataset, and two separate patient cohorts. Our analysis, by integrating methylation and gene expression in PCa cell lines, combined with patient tumor data, identified novel potential biomarkers for PCa patients. These markers may help elucidate the pathogenesis of PCa and represent potential prognostic markers for PCa patients.

Facial motion engages predictive visual mechanisms

We employed a novel cuing paradigm to assess whether dynamically versus statically presented facial expressions differentially engaged predictive visual mechanisms. Participants were presented with a cueing stimulus that was either the static depiction of a low intensity expressed emotion; or a dynamic sequence evolving from a neutral expression to the low intensity expressed emotion. Following this cue and a backwards mask, participants were presented with a probe face that displayed either the same emotion (congruent) or a different emotion (incongruent) with respect to that displayed by the cue although expressed at a high intensity. The probe face had either the same or different identity from the cued face. The participants' task was to indicate whether or not the probe face showed the same emotion as the cue. Dynamic cues and same identity cues both led to a greater tendency towards congruent responding, although these factors did not interact. Facial motion also led to faster responding when the probe face was emotionally congruent to the cue. We interpret these results as indicating that dynamic facial displays preferentially invoke predictive visual mechanisms, and suggest that motoric simulation may provide an important basis for the generation of predictions in the visual system.

Facial emotion modulates the neural mechanisms responsible for short interval time perception

Emotionally arousing events can distort our sense of time. We used mixed block/event-related fMRI design to establish the neural basis for this effect. Nineteen participants were asked to judge whether angry, happy and neutral facial expressions that varied in duration (from 400 to 1,600 ms) were closer in duration to either a short or long duration they learnt previously. Time was overestimated for both angry and happy expressions compared to neutral expressions. For faces presented for 700 ms, facial emotion modulated activity in regions of the timing network Wiener et al. (NeuroImage 49(2):1728–1740, 2010) namely the right supplementary motor area (SMA) and the junction of the right inferior frontal gyrus and anterior insula (IFG/AI). Reaction times were slowest when faces were displayed for 700 ms indicating increased decision making difficulty. Taken together with existing electrophysiological evidence Ng et al. (Neuroscience, doi: 10.3389/fnint.2011.00077, 2011), the effects are consistent with the idea that facial emotion moderates temporal decision making and that the right SMA and right IFG/AI are key neural structures responsible for this effect.

Insights into a multidrug resistant Escherichia coli pathogen of the globally disseminated ST131 lineage : genome analysis and virulence mechanisms

Escherichia coli strains causing urinary tract infection (UTI) are increasingly recognized as belonging to specific clones. E. coli clone O25b:H4-ST131 has recently emerged globally as a leading multi-drug resistant pathogen causing urinary tract and bloodstream infections in hospitals and the community. While most molecular studies to date examine the mechanisms conferring multi-drug resistance in E. coli ST131, relatively little is known about their virulence potential. Here we examined E. coli ST131 clinical isolates from two geographically diverse collections, one representing the major pathogenic lineages causing UTI across the United Kingdom and a second representing UTI isolates from patients presenting at two large hospitals in Australia. We determined a draft genome sequence for one representative isolate, E. coli EC958, which produced CTX-M-15 extended-spectrum β-lactamase, CMY-23 type AmpC cephalosporinase and was resistant to ciprofloxacin. Comparative genome analysis indicated that EC958 encodes virulence genes commonly associated with uropathogenic E. coli (UPEC). The genome sequence of EC958 revealed a transposon insertion in the fimB gene encoding the activator of type 1 fimbriae, an important UPEC bladder colonization factor. We identified the same fimB transposon insertion in 59% of the ST131 UK isolates, as well as 71% of ST131 isolates from Australia, suggesting this mutation is common among E. coli ST131 strains. Insertional inactivation of fimB resulted in a phenotype resembling a slower off-to-on switching for type 1 fimbriae. Type 1 fimbriae expression could still be induced in fimB-null isolates; this correlated strongly with adherence to and invasion of human bladder cells and bladder colonisation in a mouse UTI model. We conclude that E. coli ST131 is a geographically widespread, antibiotic resistant clone that has the capacity to produce numerous virulence factors associated with UTI.

Conjugation of carcinogens by 6 class glutathione S-transferases : mechanisms and relevance to variations in human risk

Conjugation of chemicals with glutathione (GSH) can lead to decreased or increased toxicity. A genetic deficiency in the GSH S-transferase μ class gene M1 has been hypothesized to lead to greater risk of lung cancer in smokers. Recently a gene deletion polymorphism involving the human θ enzyme T1 has been described; the enzyme is present in erythrocytes and can be readily assayed. A rat θ class enzyme, 5-5, has structural and catalytic similarity and the protein was expressed in the Salmonella typhimurium tester strain TA1535. Expression of the cDNA vector increased the mutagenicity of ethylene dibromide and several methylene dihalides. Mutations resulting from the known GSH S-transferase substrate 1,2-epoxy-3-(4′nitrophenoxy)propane were decreased in the presence of the transferase. Expression of transferase 5-5 increased mutations when 1,2,3,4-diepoxybutane (butadiene diepoxide), 4-bromo-1,2-epoxybutane, or 1,3-dichloracetone were added. The latter compound is a model for the putative 1,2-dibromo-3-chloropropane oxidation product 1-bromo-3-chloroacetone. These genotoxicity and genotyping assays may be of use in further studies of the roles of GSH S-transferase θ enzymes in bioactivation and detoxication and any changes in risk due to polymorphism.

Fred’s Flow (Canada) and Murphy Well (Australia) : thick komatiitic lava flows with contrasting compositions, emplacement mechanisms and water contents

Two Archaean komatiitic flows, Fred’s Flow in Canada and the Murphy Well Flow in Australia, have similar thicknesses (120 and 160 m) but very different compositions and internal structures. Their contrasting differentiation profiles are keys to determine the cooling and crystallization mechanisms that operated during the eruption of Archaean ultramafic lavas. Fred’s Flow is the type example of a thick komatiitic basalt flow. It is strongly differentiated and consists of a succession of layers with contrasting textures and compositions. The layering is readily explained by the accumulation of olivine and pyroxene in a lower cumulate layer and by evolution of the liquid composition during downward growth of spinifex-textured rocks within the upper crust. The magmas that erupted to form Fred’s Flow had variable compositions, ranging from 12 to 20 wt% MgO, and phenocryst contents from 0 to 20 vol%. The flow was emplaced by two pulses. A first ~20-m-thick pulse was followed by another more voluminous but less magnesian pulse that inflated the flow to its present 120 m thickness. Following the second pulse, the flow crystallized in a closed system and differentiated into cumulates containing 30–38 wt% MgO and a residual gabbroic layer with only 6 wt% MgO. The Murphy Well Flow, in contrast, has a remarkably uniform composition throughout. It comprises a 20-m-thick upper layer of fine-grained dendritic olivine and 2–5 vol% amygdales, a 110–120 m intermediate layer of olivine porphyry and a 20–30 m basal layer of olivine orthocumulate. Throughout the flow, MgO contents vary little, from only 30 to 33 wt%, except for the slightly more magnesian basal layer (38–40 wt%). The uniform composition of the flow and dendritic olivine habits in the upper 20 m point to rapid cooling of a highly magnesian liquid with a composition like that of the bulk of the flow. Under equilibrium conditions, this liquid should have crystallized olivine with the composition Fo94.9, but the most magnesian composition measured by electron microprobe in samples from the flow is Fo92.9. To explain these features, we propose that the parental liquid contained around 32 wt% MgO and 3 wt% H2O. This liquid degassed during the eruption, creating a supercooled liquid that solidified quickly and crystallized olivine with non-equilibrium textures and compositions.

Numerical investigation of deformation and failure mechanisms of osteopontin-hydroxyapatite interfaces and mineralized collagen fibril arrays

This thesis is a comprehensive study of deformation and failure mechanisms in bone at nano- and micro-scale levels. It explores the mechanical behaviour of osteopontin-hydroxyapatite interfaces and mineralized collagen fibril arrays, through atomistic molecular dynamics and finite element simulations. This thesis shows some main factors contributing to the excellent material properties of bone and provides some guidelines for development of new artificial biological materials and medical implants.

Nonprofit Service Delivery for Government : Accountability Relationships and Mechanisms

When government purchases social services under contract from a nonprofit organisation, a clear accountability relationship is created. The NPO must give an account for the use of the funds and achievement of outcomes to the funder. This paper explores how accountability is enacted in two different types of funding relationships in Queensland. Support is found for the argument that different relationships have different approaches to accountability.

Stress at the synapse : signal transduction mechanisms of adrenal steroids at neuronal membranes

As the key neuron-to-neuron interface, the synapse is involved in learning and memory, including traumatic memories during times of stress. However, the signal transduction mechanisms by which stress mediates its lasting effects on synapse transmission and on memory are not fully understood. A key component of the stress response is the increased secretion of adrenal steroids. Adrenal steroids (e.g., cortisol) bind to genomic mineralocorticoid and glucocorticoid receptors (gMRs and gGRs) in the cytosol. In addition, they may act through membrane receptors (mMRs and mGRs), and signal transduction through these receptors may allow for rapid modulation of synaptic transmission as well as modulation of membrane ion currents. mMRs increase synaptic and neuronal excitability; mechanisms include the facilitation of glutamate release through extracellular signal-regulated kinase signal transduction. In contrast, mGRs decrease synaptic and neuronal excitability by reducing calcium currents through N-methyl-D-aspartate receptors and voltage-gated calcium channels by way of protein kinase A- and G protein-dependent mechanisms. This body of functional data complements anatomical evidence localizing GRs to the postsynaptic membrane. Finally, accumulating data also suggest the possibility that mMRs and mGRs may show an inverted U-shaped dose response, whereby glutamatergic synaptic transmission is increased by low doses of corticosterone acting at mMRs and decreased by higher doses acting at mGRs. Thus, synaptic transmission is regulated by mMRs and mGRs, and part of the stress signaling response is a direct and bidirectional modulation of the synapse itself by adrenal steroids.

Cytokine expression and secretion by skeletal muscle cells : regulatory mechanisms and exercise effects

Cytokines are important mediators of various aspects of health and disease, including appetite, glucose and lipid metabolism, insulin sensitivity, skeletal muscle hypertrophy and atrophy. Over the past decade or so, considerable attention has focused on the potential for regular exercise to counteract a range of disease states by modulating cytokine production. Exercise stimulates moderate to large increases in the circulating concentrations of interleukin (IL)-6, IL-8, IL-10, IL-1 receptor antagonist, granulocyte-colony stimulating factor, and smaller increases in tumor necrosis factor-α, monocyte chemotactic protein-1, IL-1β, brain-derived neurotrophic factor, IL-12p35/p40 and IL-15. Although many of these cytokines are also expressed in skeletal muscle, not all are released from skeletal muscle into the circulation during exercise. Conversely, some cytokines that are present in the circulation are not expressed in skeletal muscle after exercise. The reasons for these discrepant cytokine responses to exercise are unclear. In this review, we address these uncertainties by summarizing the capacity of skeletal muscle cells to produce cytokines, analyzing other potential cellular sources of circulating cytokines during exercise, and discussing the soluble factors and intracellular signaling pathways that regulate cytokine synthesis (e.g., RNA-binding proteins, microRNAs, suppressor of cytokine signaling proteins, soluble receptors).

Is climate change litigation an effective strategy for promoting greater action to address climate change? What other legal mechanisms might be appropriate?

In recent times a widespread consensus on the reality and gravity of anthropogenic climate change has emerged. Perceived inadequacies in the Australian government’s legal and policy responses to climate change issues have resulted in environmental activists increasingly turning to the courts as a strategy to promote greater action to address adverse climate impacts. The efficacy of this strategy for achieving climate goals is limited by the time and expense of litigating, the restrictions inherent in environmental law administrative challenges, and the possibility that judicial decisions may be overruled by the legislature. To date, climate change litigation in Australia has met with varied success, yet its significance extends beyond the court room as an important mechanism for raising public, political and commercial awareness about climate change issues. Ultimately, however, the types of far-reaching changes needed to mitigate and manage adverse climate impacts require strong regulatory backing. The most effective approach to addressing the complex challenges posed by climate change is a coordinated suite of regulatory measures spearheaded by the Federal Government.