Proteogenomics of selective susceptibility to endotoxin using circulating acute phase biomarkers and bioassay development in sheep: a review

Scientists have injected endotoxin into animals to investigate and understand various pathologies and novel therapies for several decades. Recent observations have shown that there is selective susceptibility to Escherichia coli lipopolysaccharide (LPS) endotoxin in sheep, despite having similar breed characteristics. The reason behind this difference is unknown, and has prompted studies aiming to explain the variation by proteogenomic characterisation of circulating acute phase biomarkers. It is hypothesised that genetic trait, biochemical, immunological and inflammation marker patterns contribute in defining and predicting mammalian response to LPS. This review discusses the effects of endotoxin and host responses, genetic basis of innate defences, activation of the acute phase response (APR) following experimental LPS challenge, and the current approaches employed in detecting novel biomarkers including acute phase proteins (APP) and micro-ribonucleic acids (miRNAs) in serum or plasma. miRNAs are novel targets for elucidating molecular mechanisms of disease because of their differential expression during pathological, and in healthy states. Changes in miRNA profiles during a disease challenge may be reflected in plasma. Studies show that gel-based two-dimensional electrophoresis (2-DE) coupled with either matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) or liquid chromatography-mass spectrometry (LC-MS/MS) are currently the most used methods for proteome characterisation. Further evidence suggests that proteomic investigations are preferentially shifting from 2-DE to non-gel based LC-MS/MS coupled with data extraction by sequential window acquisition of all theoretical fragment-ion spectra (SWATH) approaches that are able to identify a wider range of proteins. Enzyme-linked immunosorbent assay (ELISA), quantitative real-time polymerase chain reaction (qRT-PCR), and most recently proteomic methods have been used to quantify low abundance proteins such as cytokines. qRT-PCR and next generation sequencing (NGS) are used for the characterisation of miRNA. Proteogenomic approaches for detecting APP and novel miRNA profiling are essential in understanding the selective resistance to endotoxin in sheep. The results of these methods could help in understanding similar pathology in humans. It might also be helpful in the development of physiological and diagnostic screening assays for determining experimental inclusion and endpoints, and in clinical trials in future

Voice, deliberation, resistance and persuasion through networked journalism

The pervasive use of the World Wide Web by the general population has created a cultural shift in “our living world”. It has enabled more people to share more information about more events and issues in the world than was possible before its general use. As a consequence, it has transformed traditional news media’s approach to almost every aspect of journalism, with many organisations restructuring their philosophy and practice to include a variety of participatory spaces/forums where people are free to engage in deliberative dialogue about matters of public importance. Moreover, while news media were the traditional gatekeepers of information, today many organisations allow, to different degrees, the general public and other independent journalism entities to participate in the news production process, which may include agenda setting and content production. This paper draws from an international collective case study that showcases various approaches to networked online news journalism. It examines the ways in which different traditional news media models use digital tools and technologies for participatory communication of information about matters of public interest. The research finds differences between the ways in which public service, commercial and independent news media give voice to the public and ultimately their approach to journalism’s role as the Fourth Estate––one of the key institutions of democracy. The work is framed by the notion that journalism in democratic societies has a key role in ensuring citizens are informed and engaged with public affairs. An examination of four media models, the British Broadcasting Corporation (BBC), the Guardian, News Limited and OhmyNews, showcases the various approaches to networked online news journalism and how each provides different avenues for citizen empowerment. The cases are described and analysed in the context of their own social, political and economic setting. Semi-structured in-depth interviews with key senior journalists and editors provide specific information on comparisons between the distinctive practices of their own organisation. In particular these show how the ideal of democracy can be used as a tool of persuasion as much as a method of deliberation.

The emerging role of extracellular vesicle-mediated drug resistance in cancers: Implications in advanced prostate cancer

Emerging evidence has shown that the extracellular vesicles (EVs) regulate various biological processes and can control cell proliferation and survival, as well as being involved in normal cell development and diseases such as cancers. In cancer treatment, development of acquired drug resistance phenotype is a serious issue. Recently it has been shown that the presence of multidrug resistance proteins such as Pgp-1 and enrichment of the lipid ceramide in EVs could have a role in mediating drug resistance. EVs could also mediate multidrug resistance through uptake of drugs in vesicles and thus limit the bioavailability of drugs to treat cancer cells. In this review, we discussed the emerging evidence of the role EVs play in mediating drug resistance in cancers and in particular the role of EVs mediating drug resistance in advanced prostate cancer. The role of EV-associated multidrug resistance proteins, miRNA, mRNA, and lipid as well as the potential interaction(s) among these factors was probed. Lastly, we provide an overview of the current available treatments for advanced prostate cancer, considering where EVs may mediate the development of resistance against these drugs.

Growth hormone resistance and somatomedins in children with end-stage liver disease awaiting transplantation

Background: The success of orthotopic liver transplantation as treatment for end-stage liver disease has prompted investigation of strategies to maintain or improve nutrition and growth in children awaiting transplantation, because malnutrition is an adverse prognostic factor. The purpose of this study was to evaluate the effect of recombinant human growth hormone therapy on body composition and indices of liver function in patients awaiting transplant. Methods: The study was designed as a placebo- controlled, double-blind, crossover trial. Patients received 0.2 U/kg growth hormone, subcutaneously, or placebo daily for 28 days during two treatment periods, separated by a 2-week washout period. Ten patients (mean age, 3.06 ± 1.15 years; range, 0.51-11.65 years, five men), with extrahepatic biliary atresia (n = 8) or two with Alagille's syndrome (n = 2), with end-stage liver disease, completed the trial while awaiting orthotopic liver transplantation. Height, weight, total body potassium, total body fat, resting energy expenditure, respiratory quotient, hematologic and multiple biochemical profile, number of albumin infusions, insulin-like growth factor-1 and 1, growth hormone binding protein (GHBP), and insulin-like growth factor binding protein-1 (IGFBP-1) and insulin-like growth factor binding protein (IGFBP-3) were measured at the beginning and end of each treatment period. Results: Growth hormone treatment was associated with a significant decline in serum bilirubin (-34.6 ± 16.5 μmol/l vs. 18.2 ± 11.59 μmol/l; p < 0.02) but there was no significant effect on any anthropometric or body composition measurements, or on any biochemical or hematologic parameters. Conclusions: These children with end-stage liver disease displayed growth hormone resistance, particularly in relation to the somatomedin axis. Exogenous growth hormone administration may be of limited value in these patients

Engineering cellulose nanofibre suspensions to control filtration resistance and sheet permeability

This study examines and quantifies the effect of adding polyelectrolytes to cellulose nanofibre suspensions on the gel point of cellulose nanofibre suspensions, which is the lowest solids concentration at which the suspension forms a continuous network. The lower the gel point, the faster the drainage time to produce a sheet and the higher the porosity of the final sheet formed. Two new techniques were designed to measure the dynamic compressibility and the drainability of nanocellulose–polyelectrolyte suspensions. We developed a master curve which showed that the independent variable controlling the behaviour of nanocellulose suspensions and its composite is the structure of the flocculated suspension which is best quantified as the gel point. This was independent of the type of polyelectrolyte used. At an addition level of 2 mg/g of nanofibre, a reduction in gel point over 50 % was achieved using either a high molecular weight (13 MDa) linear cationic polyacrylamide (CPAM, 40 % charge), a dendrimer polyethylenimine of high molecular weight of 750,000 Da (HPEI) or even a low molecular weight of 2000 Da (LPEI). There was no significant difference in the minimum gel point achieved, despite the difference in polyelectrolyte morphology and molecular weight. In this paper, we show that the gel point controls the flow through the fibre suspension, even when comparing fibre suspensions with solids content above the gel point. A lower gel point makes it easier for water to drain through the fibre network,reducing the pressure required to achieve a given dewatering rate and reducing the filtering time required to form a wet laid sheet. We further show that the lower gel point partially controls the structure of the wet laid sheet after it is dried. Halving the gel point increased the air permeability of the dry sheet by 37, 46 and 25 %, when using CPAM, HPEI and LPEI, respectively. The resistance to liquid flow was reduced by 74 and 90 %, when using CPAM and LPEI. Analysing the paper formed shows that sheet forming process and final sheet properties can be engineered and controlled by adding polyelectrolytes to the nanofibre suspension.

3D numerical simulation of avascular tumour growth: effect of hypoxic micro-environment in host tissue

A three-dimensional (3D) mathematical model of tumour growth at the avascular phase and vessel remodelling in host tissues is proposed with emphasis on the study of the interactions of tumour growth and hypoxic micro-environment in host tissues. The hybrid based model includes the continuum part, such as the distributions of oxygen and vascular endothelial growth factors (VEGFs), and the discrete part of tumour cells (TCs) and blood vessel networks. The simulation shows the dynamic process of avascular tumour growth from a few initial cells to an equilibrium state with varied vessel networks. After a phase of rapidly increasing numbers of the TCs, more and more host vessels collapse due to the stress caused by the growing tumour. In addition, the consumption of oxygen expands with the enlarged tumour region. The study also discusses the effects of certain factors on tumour growth, including the density and configuration of preexisting vessel networks and the blood oxygen content. The model enables us to examine the relationship between early tumour growth and hypoxic micro-environment in host tissues, which can be useful for further applications, such as tumour metastasis and the initialization of tumour angiogenesis.

The role of H4 flagella in Escherichia coli ST131 virulence

Escherichia coli sequence type 131 (ST131) is a globally dominant multidrug resistant clone associated with urinary tract and bloodstream infections. Most ST131 strains exhibit resistance to multiple antibiotics and cause infections associated with limited treatment options. The largest sub-clonal ST131 lineage is resistant to fluoroquinolones, contains the type 1 fimbriae fimH30 allele and expresses an H4 flagella antigen. Flagella are motility organelles that contribute to UPEC colonisation of the upper urinary tract. In this study, we examined the specific role of H4 flagella in ST131 motility and interaction with host epithelial and immune cells. We show that the majority of H4-positive ST131 strains are motile and are enriched for flagella expression during static pellicle growth. We also tested the role of H4 flagella in ST131 through the construction of specific mutants, over-expression strains and isogenic mutants that expressed alternative H1 and H7 flagellar subtypes. Overall, our results revealed that H4, H1 and H7 flagella possess conserved phenotypes with regards to motility, epithelial cell adhesion, invasion and uptake by macrophages. In contrast, H4 flagella trigger enhanced induction of the anti-inflammatory cytokine IL-10 compared to H1 and H7 flagella, a property that may contribute to ST131 fitness in the urinary tract.

Voice, deliberation, resistance and persuasion through participatory journalism business models

The pervasive use of the World Wide Web by the general population has created a cultural shift throughout the world. It has enabled more people to share more information about more events and issues than was possible before its general use. As a consequence, it has transformed traditional news media’s approach to almost every aspect of journalism, with many organisations restructuring their philosophy and practice to include a variety of participatory spaces/forums where people are free to engage in deliberative dialogue about matters of public importance. This paper draws from an international collective case study that showcases various approaches to participatory online news journalism during the period 1997–2011 (Adams, 2013). The research finds differences in the ways in which public service, commercial, and independent news media give voice to the public, and ultimately in their approach to journalism’s role as the Fourth Estate––one of the key institutions of democracy. The work is framed by the notion that journalism in democratic societies has a crucial role in ensuring citizens are informed and engaged with public affairs. An examination of four media models, OhmyNews International, News Corp Australia (formerly News Limited), the Guardian and the British Broadcasting Corporation (BBC), showcases the various approaches to participatory online news journalism and how each provides different avenues for citizen engagement. Semistructured in-depth interviews with some of the key senior journalists and editors provide specific information on comparisons between the distinctive practices in each of their employer organisations.

Analysis of human immunodeficiency virus type 1 drug resistance in children receiving nucleoside analogue reverse-transcriptase inhibitors plus nevirapine, nelfinavir, or ritonavir (Pediatric AIDS Clinical Trials Group 377)

In Pediatric AIDS Clinical Trials Group 377, antiretroviral therapy-experienced children were randomized to 4 treatment arms that included different combinations of stavudine, lamivudine (3TC), nevirapine (Nvp), nelfinavir (Nfv), and ritonavir (Rtv). Previous treatment with zidovudine (Zdv), didanosine (ddI), or zalcitabine (ddC) was acceptable. Drug resistance ((R)) mutations were assessed before study treatment (baseline) and at virologic failure. Zdv(R), ddI(R), and ddC(R) mutations were detected frequently at baseline but were not associated with virologic failure. Children with drug resistance mutations at baseline had greater reductions in virus load over time than did children who did not. Nvp(R) and 3TC(R) mutations were detected frequently at virologic failure, and Nvp(R) mutations were more common among children receiving 3-drug versus 4-drug Nvp-containing regimens. Children who were maintained on their study regimen after virologic failure accumulated additional Nvp(R) and 3TC(R) mutations plus Rtv(R) and Nfv(R) mutations. However, Rtv(R) and Nfv(R) mutations were detected at unexpectedly low rates.

Association of microRNA 17–92 cluster host gene (MIR17HG) polymorphisms with breast cancer

Breast cancer incidence and mortality rates are increasing despite our current knowledge on the disease. Ninety-five percent of breast cancer cases correspond to sporadic forms of the disease and are believed to involve an interaction between environmental and genetic determinants. The microRNA 17–92 cluster host gene (MIR17HG) has been shown to regulate expression of genes involved in breast cancer development and progression. Study of single-nucleotide polymorphisms (SNPs) located in this cluster gene could help provide a further understanding of its role in breast cancer. Therefore, this study investigated six SNPs in the MIR17HG using two independent Australian Caucasian case–control populations (GRC-BC and GU-CCQ BB populations) to determine association to breast cancer susceptibility. Genotyping was undertaken using chip-based matrix assisted laser desorption ionisation time-of-flight (MALDI-TOF) mass spectrometry (MS). We found significant association between rs4824505 and breast cancer at the allelic level in both study cohorts (GRC-BC p = 0.01 and GU-CCQ BB p = 0.03). Furthermore, haplotypic analysis of results from our combined population determined a significant association between rs4824505/rs7336610 and breast cancer susceptibility (p = 5 × 10−4). Our study is the first to show that the A allele of rs4824505 and the AC haplotype of rs4824505/rs7336610 are associated with risk of breast cancer development. However, definitive validation of this finding requires larger cohorts or populations in different ethnical backgrounds. Finally, functional studies of these SNPs could provide a deeper understanding of the role that MIR17HG plays in the pathophysiology of breast cancer.

Limitations of the manual supination resistance test

The aim of this study was to asses results obtained from a range of commonly performed lower extremity “open and closed” chain kinetic tests used for predicting foot function and correlate these test findings to data obtained from the Zebris WinFDM-T system®. When performed correctly these tests are thought to be indicators of lower extremity function. Podiatrists frequently perform examinations of joint and muscle structures to understand biomechanical function; however the relationship between these routine tests and forces generated during the gait cycle are not always well understood. This can introduce a degree of variability in clinical interpretation which creates conjecture regarding the value of these tests.

Inter-lamellar shear resistance confers compressive stiffness in the intervertebral disc: An image-based modelling study on the bovine caudal disc

The intervertebral disc withstands large compressive loads (up to nine times bodyweight in humans) while providing flexibility to the spinal column. At a microstructural level, the outer sheath of the disc (the annulus fibrosus) comprises 12–20 annular layers of alternately crisscrossed collagen fibres embedded in a soft ground matrix. The centre of the disc (the nucleus pulposus) consists of a hydrated gel rich in proteoglycans. The disc is the largest avascular structure in the body and is of much interest biomechanically due to the high societal burden of disc degeneration and back pain. Although the disc has been well characterized at the whole joint scale, it is not clear how the disc tissue microstructure confers its overall mechanical properties. In particular, there have been conflicting reports regarding the level of attachment between adjacent lamellae in the annulus, and the importance of these interfaces to the overall integrity of the disc is unknown. We used a polarized light micrograph of the bovine tail disc in transverse cross-section to develop an image-based finite element model incorporating sliding and separation between layers of the annulus, and subjected the model to axial compressive loading. Validation experiments were also performed on four bovine caudal discs. Interlamellar shear resistance had a strong effect on disc compressive stiffness, with a 40% drop in stiffness when the interface shear resistance was changed from fully bonded to freely sliding. By contrast, interlamellar cohesion had no appreciable effect on overall disc mechanics. We conclude that shear resistance between lamellae confers disc mechanical resistance to compression, and degradation of the interlamellar interface structure may be a precursor to macroscopic disc degeneration.

Staphylococcus epidermidis as a cause of bacteremia

Staphylococcus epidermidis is a biofilm-producing commensal organism found ubiquitously on human skin and mucous membranes, as well as on animals and in the environment. Biofilm formation enables this organism to evade the host immune system. Colonization of percutaneous devices or implanted medical devices allows bacteria access to the bloodstream. Isolation of this organism from blood cultures may represent either contamination during the blood collection procedure or true bacteremia. S. epidermidis bloodstream infections may be indolent compared with other bacteria. Isolation of S. epidermidis from a blood culture may present a management quandary for clinicians. Over-treatment may lead to patient harm and increases in healthcare costs. There are numerous reports indicating the difficulty of predicting clinical infection in patients with positive blood cultures with this organism. No reliable phenotypic or genotypic algorithms currently exist to predict the pathogenicity of a S. epidermidis bloodstream infection. This review will discuss the latest advances in identification methods, global population structure, pathogenicity, biofilm formation, antimicrobial resistance and clinical significance of the detection of S. epidermidis in blood cultures. Previous studies that have attempted to discriminate between invasive and contaminating strains of S. epidermidis in blood cultures will be analyzed.

Evaluation of transgenic bananas expressing anti-apoptotic genes for resistance against Fusarium wilt

The banana industry worldwide is under threat from a fungal disease known as Fusarium wilt, a disease for which there is no chemical control. Conventional breeding approaches to generate resistant banana varieties are lengthy and very difficult. As such, genetic engineering for disease resistance is considered the most viable control option. In this PhD thesis, genetically modified banana plants were generated using several different stress tolerance genes. When challenged with Fusarium wilt in glasshouse trials, some lines showed increased resistance to the disease. The promising elite lines generated in this study will now require testing in field trials.

Fire resistance of light gauge steel frame wall systems lined with gypsum plasterboards

Light gauge steel frame (LSF) wall systems are increasingly used in residential and commercial buildings as load bearing and non-load bearing elements. Conventionally, the fire resistance ratings of such building elements are determined using approximate prescriptive methods based on limited standard fire tests. However, recent studies have shown that in some instances real building fire time-temperature curves could be more severe than the standard fire curve, in terms of maximum temperature and rate of temperature rise. This has caused problems for safe evacuation and rescue activities, and in some instances has also lead to the collapse of buildings earlier than the prescribed fire resistance. Therefore a detailed research study into the performance of LSF wall systems under both standard fire and realistic fire conditions was undertaken using full scale fire tests to understand the fire performance of different LSF wall configurations. Both load bearing and non-load bearing full scale fire tests were performed on LSF walls configurations which included single layer, double layer, externally insulated wall panels made up of different steel sections and thicknesses of gypsum plasterboards. The non-load bearing fire test results were utilized to understand the factors affecting the fire resistance of LSF walls, while loading bearing fire test results led to development of simplified methods to predict the fire resistance ratings of load bearing LSF walls exposed to both standard and realistic design fires. This paper presents the results of full scale experimental study and highlights the effects of standard and realistic fire conditions on fire performance of LSF walls.