Four generations of sequencing: Is it ready for the clinic yet?

Next-generation sequencing techniques have revolutionized over the last decade providing researchers with low cost, high-throughput alternatives compared to the traditional Sanger sequencing methods. These sequencing techniques have rapidly evolved from first-generation to fourth-generation with very broad applications such as unravelling the complexity of the genome, in terms of genetic variations, and having a high impact on the biological field. In this review, we discuss the transition of sequencing from the second-generation to the third- and fourth-generations, and describe some of their novel biological applications. With the advancement in technology, the earlier challenges of minimal size of the instrument, flexibility of throughput, ease of data analysis and short run times are being addressed. However, the need for prospective analysis and effectiveness to test whether the knowledge of any given new variants identified has an effect on clinical outcome may need improvement.

Lipid-modified azurin of Neisseria meningitidis is a copper protein localized on the outer membrane surface and not regulated by FNR

The laz gene of Neisseria meningitidis is predicted to encode a lipid-modified azurin (Laz). Laz is very similar to azurin, a periplasmic protein, which belongs to the copper-containing proteins in the cupredoxin superfamily. In other bacteria, azurin is an electron donor to nitrite reductase, an important enzyme in the denitrifying process. It is not known whether Laz could function as an electron transfer protein in this important pathogen. Laz protein was heterologously expressed in Escherichia coli and purified. Electrospray mass spectrometry indicated that the Laz protein contains one copper ion. Laz was shown to be redox-active in the presence of its redox center copper ion. When oxidized, Laz exhibits an intense blue colour and absorbs visible light around 626 nm. The absorption is lost when exposed to diethyldithiocarbamate, a copper chelating agent. Polyclonal antibodies were raised against purified Laz for detecting expression of Laz under different growth conditions and to determine the orientation of Laz on the outer membrane. The expression of Laz under microaerobic and microaerobic denitrifying conditions was slightly higher than that under aerobic conditions. However, the expression of Laz was similar between the wild type strain and an fnr mutant, suggesting that Fumarate/Nitrate reduction regulator (FNR) does not regulate the expression of Laz despite the presence of a partial FNR box upstream of the laz gene. We propose that some Laz protein is exposed on the outer membrane surface of N. meningitidis as the αLaz antibodies can increase killing by complement in a capsule deficient N. meningitidis strain, in a dose-dependent fashion.

Utility of assessing nerve morphology in central cornea versus whorl area for diagnosing diabetic peripheral neuropathy

Purpose To compare small nerve fiber damage in the central cornea and whorl area in participants with diabetic peripheral neuropathy (DPN) and to examine the accuracy of evaluating these 2 anatomical sites for the diagnosis of DPN. Methods A cohort of 187 participants (107 with type 1 diabetes and 80 controls) was enrolled. The neuropathy disability score (NDS) was used for the identification of DPN. The corneal nerve fiber length at the central cornea (CNFLcenter) and whorl (CNFLwhorl) was quantified using corneal confocal microscopy and a fully automated morphometric technique and compared according to the DPN status. Receiver operating characteristic analyses were used to compare the accuracy of the 2 corneal locations for the diagnosis of DPN. Results CNFLcenter and CNFLwhorl were able to differentiate all 3 groups (diabetic participants with and without DPN and controls) (P < 0.001). There was a weak but significant linear relationship for CNFLcenter and CNFLwhorl versus NDS (P < 0.001); however, the corneal location x NDS interaction was not statistically significant (P = 0.17). The area under the receiver operating characteristic curve was similar for CNFLcenter and CNFLwhorl (0.76 and 0.77, respectively, P = 0.98). The sensitivity and specificity of the cutoff points were 0.9 and 0.5 for CNFLcenter and 0.8 and 0.6 for CNFLwhorl. Conclusions Small nerve fiber pathology is comparable at the central and whorl anatomical sites of the cornea. Quantification of CNFL from the corneal center is as accurate as CNFL quantification of the whorl area for the diagnosis of DPN.

Cross-border malaria: a major obstacle for malaria elimination

Movement of malaria across international borders poses a major obstacle to achieving malaria elimination in the 34 countries that have committed to this goal. In border areas, malaria prevalence is often higher than in other areas due to lower access to health services, treatment-seeking behaviour of marginalised populations that typically inhabit border areas, difficulties in deploying prevention programs to hard-to-reach communities, often in difficult terrain, and constant movement of people across porous national boundaries. Malaria elimination in border areas will be challenging, and key to addressing the challenges is strengthening of surveillance activities for rapid identification of any importation or reintroduction of malaria. This could involve taking advantage of technological advances, such as spatial decision support systems, which can be deployed to assist program managers to carry out preventive and reactive measures, and mobile phone technology, which can be used to capture the movement of people in the border areas and likely sources of malaria importation. Additionally, joint collaboration in the prevention and control of cross-border malaria by neighbouring countries, and reinforcement of early diagnosis and prompt treatment are ways forward in addressing the problem of cross-border malaria.

Corporate governance convergence and moral relativism

Research question / issue This paper frames the debate on corporate governance convergence in terms of the morality underlying corporate governance models. The claims and arguments of moral relativism are presented to provide theoretical structure to the moral aspects of corporate governance convergence, and ultimately the normative question of whether convergence should occur. Research findings / insights: The morality underlying different models of corporate governance has largely been ignored in the corporate governance convergence literature. A range of moral philosophies and principles that underlie the dominant corporate governance models are identified. This leads to a consideration of the claims and arguments of moral relativism relating to corporate governance. A research agenda around the claims of Descriptive and Metaethical moral relativism, and which ultimately informs the associated normative argument, is then suggested. Theoretical / Academic implications The application of moral relativism to the debate on corporate governance convergence presents a theoretical structure to the analysis and consideration of its moral aspects. This structure lends itself to further research, both empirical and conceptual. Practitioner / Policy implications The claims and arguments of moral relativism provide a means of analysing calls that are made for a culturally or nationally ‘appropriate’ model of corporate governance. This can assist in providing direction for corporate governance reforms and is of particular relevance for developing countries which have inherited Western corporate governance models through colonialism.

Young people's uses of music for well-being

The period between 15 and 25 years is characterised by much personal change and is the peak age of onset of mental health problems. This prompts an interest in everyday strategies that young people might use to support their well-being. Music use is the preferred leisure activity among young people yet little is known about how music is linked to well-being in this population. This study aimed to develop and test a model of the relationships between young people’s use of music and their well-being, drawing on theories from the music psychology and clinical psychology fields. A qualitative analysis of transcripts from focus groups with 11 participants aged 15–25 years revealed four ways in which music listening links with well-being: relationship building, modifying emotions, modifying cognitions and emotional immersion. These linking variables were operationalised using questionnaire scores and tested on a new sample of 107 young people. Results of a multiple mediation analysis revealed that music listening was significantly related to all four linking variables, but not directly related to well-being as measured by the Mental Health Continuum. Nevertheless, the four linking variables indirectly mediated the effect of music listening on social wellbeing. The findings are consistent with earlier research on the role of music in emotion regulation and social connection although there are clearly other factors involved in determining young peoples’ well-being. These findings will help inform music-based interventions for young people.

How does symptom burden differ in people with advanced CKD who are non-dialysis or currently receiving dialysis?

Background Chronic kidney disease (CKD) leads to a range of symptoms which are often under-recognised. Little is known about the full range of symptoms, particularly in who are pre-dialysis. Understanding symptom prevalence, distress, severity and frequency will help prioritise symptom management. Aims To examine symptom burden in advanced CKD (stages 4 and 5) and compare the symptom experience between those receiving dialysis or those who are pre-dialysis. Methods Using a cross-sectional design, a convenience sample of 436 people from three hospitals completed the Modified Dialysis Symptom Index (MDSI). Demographic and renal history data was also collected. Based on the 32 symptoms, we compared the prevalence, severity, distress and frequency of each symptom by treatment modality. Results Mean age was 48 years (range 18-87 years) and 53% were male. 75.5% (haemodialysis = 287; peritoneal dialysis = 42) were receiving dialysis and 24.5% (n = 107) were pre-dialysis. Overall, the mean symptom prevalence was 12.6 ± 7.9 and the most prevalent symptoms were fatigue (77%), bone or joint pain (60.3%) and itching (59.6%) across all CKD groups. The distress, severity and frequency of the symptoms were higher in the dialysis group. However, a higher frequency of psychological symptoms (worrying, feeling nervous and depression) were reported in the pre-dialysis group. Implication for clinical practice Patients with advanced CKD have a high symptom burden with those who are pre-dialysis needing greater psychological support. The MDSI could be used in nursing practice to screen patients for symptoms which could lead to timely and appropriate interventions.

From ‘free’ to fee: Acceptability of airline ancillary fees and the effects on customer behavior

Businesses in various consumer service industries have begun to unbundle their service offerings by introducing numerous fees for products and services that were previously provided as “free.” Anecdotal evidence in the media indicates that these fees cause widespread public displeasure, frustration, and outrage. This paper develops a framework of fee acceptability, negative emotions, and dysfunctional customer behavior, which is tested using data from the airline industry. Findings identify the strongest effects on betrayal in the case of baggage fees, followed by charges for comfort. Also, betrayal has a direct effect on complaining, whereas anger mediates the relationship between betrayal and negative word of mouth.

Mathematical modelling of gas production and compositional shift of a CSG (coal seam gas) field: Local model development

In this work we discuss the development of a mathematical model to predict the shift in gas composition observed over time from a producing CSG (coal seam gas) well, and investigate the effect that physical properties of the coal seam have on gas production. A detailed (local) one-dimensional, two-scale mathematical model of a coal seam has been developed. The model describes the competitive adsorption and desorption of three gas species (CH4, CO2 and N2) within a microscopic, porous coal matrix structure. The (diffusive) flux of these gases between the coal matrices (microscale) and a cleat network (macroscale) is accounted for in the model. The cleat network is modelled as a one-dimensional, volume averaged, porous domain that extends radially from a central well. Diffusive and advective transport of the gases occurs within the cleat network, which also contains liquid water that can be advectively transported. The water and gas phases are assumed to be immiscible. The driving force for the advection in the gas and liquid phases is taken to be a pressure gradient with capillarity also accounted for. In addition, the relative permeabilities of the water and gas phases are considered as functions of the degree of water saturation.

Developing pictorial conceptual metaphors as a means of understanding and changing the Australian health system for Indigenous people

This paper describes the development of Pictorial Conceptual Metaphors, created out of a literature review on gendered Indigenous health and wellbeing that depicts the inherited effects of the ‘system’ past, present and future. The Pictorial Conceptual Metaphors are pictures that were created to tell the story of colonisation and its inherited and ongoing impacts on Indigenous people’s health and wellbeing. Aboriginal historical experiences, past, present and future are briefly overviewed in order to unpack and communicate to readers the significance and impact of these experiences on Aboriginal health, and ultimately, to bring about understanding to initiate change within the Australian health system. Systemic racism, embedded in the Australian health system, excludes and discriminates against Indigenous peoples through a lack of cultural consideration resulting in a cumulative and ongoing negative effect on Indigenous people’s health (Dudgeon et al. 2014; Fredericks 2008; Marmot 2011; Queensland Government 2012). Systemic action research identifies actions and processes in large systems such as health and education in order to bring about systemic change. Our intention to highlight the systemic changes needed in the Australian health system to improve Indigenous people’s health and wellbeing require us to understand the processes involved in bringing about systemic change. For this to occur, we needed to ‘see the system’ in order to identify the system dynamics in operation. The Pictorial Conceptual Metaphors are the first step in ‘seeing the system’; they illustrate the past and the present, and identify the preferred future for Indigenous health and wellbeing outcomes

The IFITM5 mutation c.-14C > T results in an elongated transcript expressed in human bone; And causes varying phenotypic severity of osteogenesis imperfecta type V

Background The genetic mutation resulting in osteogenesis imperfecta (OI) type V was recently characterised as a single point mutation (c.-14C > T) in the 5' untranslated region (UTR) of IFITM5, a gene encoding a transmembrane protein with expression restricted to skeletal tissue. This mutation creates an alternative start codon and has been shown in a eukaryotic cell line to result in a longer variant of IFITM5, but its expression has not previously been demonstrated in bone from a patient with OI type V. Methods Sanger sequencing of the IFITM5 5' UTR was performed in our cohort of subjects with a clinical diagnosis of OI type V. Clinical data was collated from referring clinicians. RNA was extracted from a bone sample from one patient and Sanger sequenced to determine expression of wild-type and mutant IFITM5. Results: All nine subjects with OI type V were heterozygous for the c.-14C > T IFITM5 mutation. Clinically, there was heterogeneity in phenotype, particularly in the manifestation of bone fragility amongst subjects. Both wild-type and mutant IFITM5 mRNA transcripts were present in bone. Conclusions The c.-14C > T IFITM5 mutation does not result in an RNA-null allele but is expressed in bone. Individuals with identical mutations in IFITM5 have highly variable phenotypic expression, even within the same family.

Cytokine mRNA expression and IFN-γ production of immunised nematode resistant and susceptible lambs against natural poly-generic challenge

IL-2, IL-4 and IFN-γ mRNA expression, and production of IFN-γ was examined in mesenteric lymph node cells (MLNC) and CD4+ enriched T cell populations of nematode resistant (R) and susceptible (S) line lambs by use of RT-PCR and ELISA. Five R and S line lambs that were immunised by repeated oxfendazole-abbreviated infections and 5 non-immunised R and S line lambs were used. All lambs grazed nematode infected pasture for 107 days. Immunisation enhanced the resistant status in both R and S lambs. MLNC obtained from slaughtered animals were stimulated with Con A or T. colubriformis specific antigen. Non-stimulated MLNC of immunised lambs expressed higher levels of IL-4 mRNA and lower levels of IL-2 mRNA than non-immunised lambs. MLNC of immunised R and S line lambs stimulated with antigen for 24 h expressed detectable amounts of IL-4 mRNA that was not seen in non-immunised controls. CD4+ T cell enriched cell populations of immunised R and S lambs and non-immunised R lambs expressed moderate to high levels of IL-4 mRNA. Con A stimulated MLNC of immunised R and S lambs expressed high levels IFN-γ mRNA and produced high amounts of IFN-γ. Lower levels were present in non-immunised controls. The results indicate that R line lambs and immunised S line lambs respond to natural nematode challenge with a predominating IL-4 cytokine response when compared to non-immunised S lambs.

A framework for generating realistic traffic for distributed denial-of-service attacks and flash events

An intrinsic challenge associated with evaluating proposed techniques for detecting Distributed Denial-of-Service (DDoS) attacks and distinguishing them from Flash Events (FEs) is the extreme scarcity of publicly available real-word traffic traces. Those available are either heavily anonymised or too old to accurately reflect the current trends in DDoS attacks and FEs. This paper proposes a traffic generation and testbed framework for synthetically generating different types of realistic DDoS attacks, FEs and other benign traffic traces, and monitoring their effects on the target. Using only modest hardware resources, the proposed framework, consisting of a customised software traffic generator, ‘Botloader’, is capable of generating a configurable mix of two-way traffic, for emulating either large-scale DDoS attacks, FEs or benign traffic traces that are experimentally reproducible. Botloader uses IP-aliasing, a well-known technique available on most computing platforms, to create thousands of interactive UDP/TCP endpoints on a single computer, each bound to a unique IP-address, to emulate large numbers of simultaneous attackers or benign clients.

Mating compatibility between bactrocera invadens and bactrocera dorsalis (Diptera: Tephritidae)

The invasive fruit fly, Bactrocera invadens Drew, Tsuruta & White, is a highly polyphagous fruit pest that occurs predominantly in Africa yet has its origins in the Indian subcontinent. It is extremely morphologically and genetically similar to the Oriental fruit fly, Bactrocera dorsalis (Hendel); as such the specific relationship between these two species is unresolved. We assessed prezygotic compatibility between B. dorsalis and B. invadens using standardized field cage mating tests, which have proven effectiveness in tephritid cryptic species studies. These tests were followed by an assessment of postzygotic compatibility by examining egg viability, larval and pupal survival, and sex ratios of offspring produced from parental and subsequent F1 crosses to examine for hybrid breakdown as predicted under a two-species hypothesis. B. dorsalis was sourced from two countries (Pakistan and China), and each population was compared with B. invadens from its type locality of Kenya. B. invadens mated randomly with B. dorsalis from both localities, and there were generally high levels of hybrid viability and survival resulting from parental and F1 crosses. Furthermore, all but one hybrid cross resulted in equal sex ratios, with the single deviation in favor of males and contrary to expectations under Haldane's rule. These data support the hypothesis that B. dorsalis and B. invadens represent the same biological species, an outcome that poses significant implications for pest management and international trade for sub-Saharan Africa.

Physical mechanisms underlying the strain-rate-dependent mechanical behavior of kangaroo shoulder cartilage

Due to anatomical and biomechanical similarities to human shoulder, kangaroo was chosen as a model to study shoulder cartilage. Comprehensive enzymatic degradation and indentation tests were applied on kangaroo shoulder cartilage to study mechanisms underlying its strain-rate-dependent mechanical behavior. We report that superficial collagen plays a more significant role than proteoglycans in facilitating strain-rate-dependent behavior of kangaroo shoulder cartilage. By comparing the mechanical properties of degraded and normal cartilages it was noted that proteoglycan and collagen degradation significantly compromised strain-rate-dependent mechanical behavior of the cartilage. Superficial collagen contributed equally to the tissue behavior at all strain-rates. This is different to studies reported on knee cartilage and confirms the importance of superficial collagen on shoulder cartilage mechanical behavior. A porohyperelastic numerical model also indicated that collagen disruption would lead to faster damage of the shoulder cartilage than when proteoglycans are depleted.