Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR

With an increased emphasis on genotyping of single nucleotide polymorphisms (SNPs) in disease association studies, the genotyping platform of choice is constantly evolving. In addition, the development of more specific SNP assays and appropriate genotype validation applications is becoming increasingly critical to elucidate ambiguous genotypes. In this study, we have used SNP specific Locked Nucleic Acid (LNA) hybridization probes on a real-time PCR platform to genotype an association cohort and propose three criteria to address ambiguous genotypes. Based on the kinetic properties of PCR amplification, the three criteria address PCR amplification efficiency, the net fluorescent difference between maximal and minimal fluorescent signals and the beginning of the exponential growth phase of the reaction. Initially observed SNP allelic discrimination curves were confirmed by DNA sequencing (n = 50) and application of our three genotype criteria corroborated both sequencing and observed real-time PCR results. In addition, the tested Caucasian association cohort was in Hardy-Weinberg equilibrium and observed allele frequencies were very similar to two independently tested Caucasian association cohorts for the same tested SNP. We present here a novel approach to effectively determine ambiguous genotypes generated from a real-time PCR platform. Application of our three novel criteria provides an easy to use semi-automated genotype confirmation protocol.

Sibpair studies implicate chromosome 18 in essential hypertension

Interest in chromosome 18 in essential hypertension comes from comparative mapping of rat blood pressure quantitative trait loci (QTL), familial orthostatic hypotensive syndrome studies, and essential hypertension pedigree linkage analyses indicating that a locus or loci on human chromosome 18 may play a role in hypertension development. To further investigate involvement of chromosome 18 in human essential hypertension, the present study utilized a linkage scan approach to genotype twelve microsatellite markers spanning human chromosome 18 in 177 Australian Caucasian hypertensive (HT) sibling pairs. Linkage analysis showed significant excess allele sharing of the D18S61 marker when analyzed with SPLINK (P=0.00012), ANALYZE (Sibpair) (P=0.0081), and also with MAPMAKER SIBS (P=0.0001). Similarly, the D18S59 marker also showed evidence for excess allele sharing when analyzed with SPLINK (P=0.016), ANALYZE (Sibpair) (P=0.0095), and with MAPMAKER SIBS (P = 0.014). The adenylate cyclase activating polypeptide 1 gene (ADCYAP1) is involved in vasodilation and has been co-localized to the D18S59 marker. Results testing a microsatellite marker in the 3′ untranslated region of ADCYAP1 in age and gender matched HT and normotensive (NT) individuals showed possible association with hypertension (P = 0.038; Monte Carlo P = 0.02), but not with obesity. The present study shows a chromosome 18 role in essential hypertension and indicates that the genomic region near the ADCYAP1 gene or perhaps the gene itself may be implicated. Further investigation is required to conclusively determine the extent to which ADCYAP1 polymorphisms are involved in essential hypertension. © 2003 Wiley-Liss, Inc.

Association of HincII RFLP of low density lipoprotein receptor gene with obesity in essential hypertensives

Obese (BMI ≥ 26 kg/m 2; n = 51) and lean (BMI <26 kg/m 2; n = 61) Caucasian patients with severe, familial essential hypertension, were compared with respect to genotype and allele frequencies of a HincII RFLP of the low density lipoprotein receptor gene (LDLR). A similar analysis was performed in obese (n = 28) and lean (n = 68) normotensives. A significant association of the C allele of the T→C variant responsible for this RFLP was seen with obesity (χ 2 = 4.6, P = 0.029) in the hypertensive, but not in the normotensive, group (odds ratio = 3.0 for the CC genotype and 2.7 for CT). Furthermore, BMI tracked with genotypes of this allele in the hypertensives (P = 0.046). No significant genotypic relationship was apparent for plasma lipids. Significant linkage disequilibrium was, moreover, noted between the HincII RFLP and an ApaLI RFLP (χ 2 = 33, P<0.0005) that has previously shown even stronger association with obesity (odds ratio 19.6 for cases homozygous for the susceptibility allele and 15.2 for het-erozygotes). The present study therefore adds to our previous evidence implicating LDLR as a locus for obesity in patients with essential hypertension.

Environments For Healthy Living (EFHL) Griffith birth cohort study : characteristics of sample and profile of antenatal exposures

Background The Environments for Healthy Living (EFHL) study is a repeated sample, longitudinal birth cohort in South East Queensland, Australia. We describe the sample characteristics and profile of maternal, household, and antenatal exposures. Variation and data stability over recruitment years were examined. Methods Four months each year from 2006, pregnant women were recruited to EFHL at routine antenatal visits on or after 24 weeks gestation, from three public maternity hospitals. Participating mothers completed a baseline questionnaire on individual, familial, social and community exposure factors. Perinatal data were extracted from hospital birth records. Descriptive statistics and measures of association were calculated comparing the EFHL birth sample with regional and national reference populations. Data stability of antenatal exposure factors was assessed across five recruitment years (2006–2010 inclusive) using the Gamma statistic for ordinal data and chi-squared for nominal data. Results Across five recruitment years 2,879 pregnant women were recruited which resulted in 2904 live births with 29 sets of twins. EFHL has a lower representation of early gestational babies, fewer still births and a lower percentage of low birth weight babies, when compared to regional data. The majority of women (65%) took a multivitamin supplement during pregnancy, 47% consumed alcohol, and 26% reported having smoked cigarettes. There were no differences in rates of a range of antenatal exposures across five years of recruitment, with the exception of increasing maternal pre-pregnancy weight (p=0.0349), decreasing rates of high maternal distress (p=0.0191) and decreasing alcohol consumption (p<0.0001). Conclusions The study sample is broadly representative of births in the region and almost all factors showed data stability over time. This study, with repeated sampling of birth cohorts over multiple years, has the potential to make important contributions to population health through evaluating longitudinal follow-up and within cohort temporal effects.

Molecular approaches to diagnosis and management of ovarian cancer

The recent advances in the understanding of the pathogenesis of ovarian cancer have been helpful in addressing issues in diagnosis, prognosis and management. The study of ovarian tumours by novel techniques such as immunohistochemistry, fluorescent in situ hybridisation, comparative genomic hybridisation, polymerase chain reaction and new tumour markers have aided the evaluation and application of new concepts into clinical practice. The correlation of novel surrogate tumour specific features with response to treatment and outcome in patients has defined prognostic factors which may allow the future design of tailored therapy based on a molecular profile of the tumour. These have also been used to design new approaches to therapy such as antibody targeting and gene therapy. The delineation of roles of c-erbB2, c-fms and other novel receptor kinases in the pathogenesis of ovarian cancer has led initially to the development of anti-c-erbB2 monoclonal antibody therapy. The discovery of BRCA1 and BRCA2 genes will have an impact in the diagnosis and the prevention of familial ovarian cancer. The important role played by recessive genes such as p53 in cancer has raised the possibility of restoration of gene function by gene therapy. Although the pathological diagnosis of ovarian cancer is still confirmed principally on morphological features, addition of newer investigations will increasingly be useful in addressing difficult diagnostic problems. The increasingly rapid pace of discovery of genes important in disease, makes it imperative that the evaluation of their contribution in the pathogenesis of ovarian cancer is undertaken swiftly, thus improving the overall management of patients and their outcome.

Haemochromatosis and HLA--H

The recently identified can didate gene, HLA-H, for haemochromatosis (HH) by Feder et al. generated considerable scientific interest coupled with a degree of uncertainty about the likely involvement of this gene in this common iron metabolism disorder, Feder et al. found a single point mutation resulting in an amino acid substitution (C282Y) that was homozygous in 148 (83%) of their patients, heterozygous in 9 patients (5%) but completely absent in 21 patients (12%). They proposed that the lack of a causative mutation in HLA-H in 12% of their patients was because these cases were not linked to chromosome 6p. A significant weakness in this argument is that all familial studies of the disorder so far have concluded that HH is due to a single major HLA-linked gene5-7. The ultimate test for a candidate gene is the clear segregation of a mutation with the disorder in all patients. Thus, some of the uncertainty surrounding the role of HLA-H in HH may be resolved by the identification of complete concordance of the C282Y mutation (or some other mutation) in HLA H with disease status in HH families. One potential problem in the design of such an experimental analysis is that a number of studies have shown the presence of a predominant ancestral haplotype in all HH populations examined: Australian, French, Italian, UK and US Thus in the analysis of a putative causative mutation, it is important to include families with...

Raising Children in Single-Parent Families

Children from single-parent families fare more poorly on multiple outcomes than those in two-parent families. Most explanations for these differences assume that compromised parenting and parent mental health play a central role. This chapter explores the contribution of a range of factors to the parenting and mental health of single mothers using data from approximately 1000 Australian single mothers with a child aged 4–5 or 8–9 years. The findings show that single mothers are more likely than couple mothers to experience parenting and mental health difficulties; however, they also face heightened adversity in their home and extra-familial environments. Importantly, this comparison of single and couple mothers facing similar levels of adversity shows no difference in poor parenting practices, although single mothers remain more vulnerable to psychological distress. These findings have policy implications since they challenge the prevailing view that single-parent families inherently provide sub-optimal environments for raising children.

Evaluating a model of parental influence on youth physical activity

Objective To test a conceptual model linking parental physical activity orientations, parental support for physical activity, and children's self-efficacy perceptions with physical activity participation. Participants and setting The sample consisted of 380 students in grades 7 through 12 (mean age, 14.0±1.6 years) and their parents. Data collection took place during the fall of 1996. Main outcome measures Parents completed a questionnaire assessing their physical activity habits, enjoyment of physical activity, beliefs regarding the importance of physical activity, and supportive behaviors for their child's physical activity. Students completed a 46-item inventory assessing physical activity during the previous 7 days and a 5-item physical activity self-efficacy scale. The model was tested via observed variable path analysis using structural equation modeling techniques (AMOS 4.0). Results An initial model, in which parent physical activity orientations predicted child physical activity via parental support and child self-efficacy, did not provide an acceptable fit to the data. Inclusion of a direct path from parental support to child physical activity and deletion of a nonsignificant path from parental physical activity to child physical activity significantly improved model fit. Standardized path coefficients for the revised model ranged from 0.17 to 0.24, and all were significant at the p<0.0001 level. Conclusions Parental support was an important correlate of youth physical activity, acting directly or indirectly through its influence on self-efficacy. Physical activity interventions targeted at youth should include and evaluate the efficacy of individual-level and community-level strategies to increase parents’ capacity to provide instrumental and motivational support for their children's physical activity.

Gender, sexuality, and rurality in the mining industry

Sexuality is a subject that has been, at best, marginal in the significant body of literature that has examined gender and mining in contemporary Western nations. This is despite the fact that academics have circled, if not almost bumped into the topic in closely related discussions of hegemonic masculinity and mining work, and of patriarchal familial relations and mining communities. This scholarship has documented what has been and remains women’s primary relationship to mining—that is, as a “mining wife.” How patriarchal relations are manifest in and emerge from this state of affairs has been critiqued with research on the gendered implications of housing arrangements in mining towns, the division of household labor, changing shift-work mining rosters, and the gendered consequences of strikes and mine closures (Williams 1981; Gibson 1992; Gibson-Graham 1996; Rhodes 2005; McDonald, Mayes, and Pini 2012). Despite the centrality of the heterosexual relationship—and indeed heteronormativity—to these discussions, scholars of gender and mining have had little to say on the subject of sexuality. In response to this lacuna, this chapter takes an exploratory lens to the subject of sexuality and the mining industry. We approach the task from the perspective that the mining industry is gendered as masculine. That is, definitions of mining mobilize around masculinized notions of physicality, technical competence with machinery, and strength, as well as emphasize the harshness and dirtiness of the work (Mayes and Pini 2010).

Rad51 supports triple negative breast cancer metastasis

In contrast to extensive studies on familial breast cancer, it is currently unclear whether defects in DNA double strand break (DSB) repair genes play a role in sporadic breast cancer development and progression. We performed analysis of immunohistochemistry in an independent cohort of 235 were sporadic breast tumours. This analysis suggested that RAD51 expression is increased during breast cancer progression and metastasis and an oncogenic role for RAD51 when deregulated. Subsequent knockdown of RAD51 repressed cancer cell migration in vitro and reduced primary tumor growth in a syngeneic mouse model in vivo. Loss of RAD51 also inhibited associated metastasis not only in syngeneic mice but human xenografts and changed the metastatic gene expression profile of cancer cells, consistent with inhibition of distant metastasis. This demonstrates for the first time a new function of RAD51 that may underlie the proclivity of patients with RAD51 overexpression to develop distant metastasis. RAD51 is a potential biomarker and attractive drug target for metastatic triple negative breast cancer, with the capability to extend the survival of patients, which is less than 6 months.

Homemade cookbooks : a recipe for sharing

In this paper we contribute to the growing body of research into the use and design of technology in the kitchen. This research aims to identify opportunities for designing technologies that may augment existing cooking traditions and in particular familial recipe sharing practices. Using ethnographic techniques, we identify the homemade cookbook as a significant material and cultural artifact in the family kitchen. We report on findings from our study by providing descriptive accounts of various homemade cookbooks, and offer design considerations for digitally augmenting homemade cookbooks.

The challenges of meeting the needs of children with Autism Spectrum Disorders (ASD) during out of hospital interactoins with Paramedics

This poster presents the results of a critical review of the literature on the intersection between paramedic practice with Autism Spectrum Disorder (ASD) and previews the clinical and communication challenges likely to be experienced with these patients. Paramedics in Australia provide 24/7 out-of-hospital care to the community. Although their core business is to provide emergency care, paramedics also provide care for vulnerable people as a consequence of the social, economic or domestic milieu. Little is known about the frequency of use of emergency out-of-hospital services by children with ASD and their families. Similarly, little is known about the attitudes and perceptions of paramedics to children with ASD and their emergency health care. However, individuals with ASD are likely to require paramedic services at some point across the life span and may be more frequent users of health services as a consequence of the challenges they face. The high rate of co-morbidities of people diagnosed with ASD is reported and includes seizure disorders, gastro-intestinal disorders, metabolic disorders, hormonal dysfunction, ear, nose and throat infections, hearing impairment, hypertension, allergies/anaphylaxis, immune disorders, migraine and diabetes, gross/fine motor skill dysfunction, premature birth, birth defects, obesity and mental illness. Individuals with ASD may frequently experience concurrent communication, behaviour and sensory challenges. Consequently, Paramedics can encounter difficulties gathering important patient information which may compromise sensitive care. These interactions occur often in high pressure and emotionally challenging environments, which add to the difficulties in communicating the treatment and transport needs of this population.

Review of Public Trustee Files - Families and generational asset transfers: Making and challenging wills in contemporary Australia

The Public Trustee file review was designed to address research questions relating to will disputes and socio-cultural and family norms, expectations and obligations that underpin challenges to wills. Findings from this review will augment the earlier review of all adjudicated succession law cases in Australia between January and December 2011. The research team obtained 139 cases for the review. Within the reviewed cases, parties generally needed some kind of formalised assistance to resolve disputes and almost a third ended up going to court. Most claims launched to contest wills were successful i.e. led to a change in distribution. The existence of poor and/or complex personal relationships between beneficiaries, disputants and/or the deceased were a feature of most cases involving will disputes, particularly where disputes were escalated to court. There are significant costs of will contestation both for the estate and the individuals involved in disputes. Previous research has identified that in addition to the direct costs is the indirect cost of extending the time for probate of the will. This review highlights that one of the most significant costs of will contestation is the damage to familial relationships that appears to both drive and be worsened by contestation. Findings of this review highlight the role of Public Trustees in providing financial management and advocacy services to protect and support vulnerable people in the community such as those with impaired capacity, as well as offering services such as will drafting and deceased estate administration.

Privacy, modesty, hospitality and the design of Muslim homes in Australia

The home environment is conceptualised in prolific ways within the academic literature. A home is an unparalleled base for human settlement and habitation that embodies a sensorial space that is layered with personal memories and traces of history. The success of a home in providing a strong ‘sense of place’ depends on various factors such as geographical location, monetary funds or personal perceptions. A home too, is an influential medium that allows its dwellers to express, perform and continue their cultural traditions and religious faiths. Traditional Islamic teachings and practices involve guidelines that apply directly to the domestic space. The principles of privacy, modesty and hospitality are paramount to these guidelines and each has a significant influence upon the design of Muslim homes and the home owners’ or dwellers’ domestic behaviours. Despite a significant increase of Muslim population in Australia over the last decade, very little is known about their perceptions of domestic life and their use of domestic spaces within an Australian context. This research investigated on how Muslims in Brisbane live and adapt within their Australian homes and if these homes meet their personal and familial needs to perform their daily activities, as well as maintaining and practising their Islamic faiths and traditions. Specific attention has been given to their perceptions on tripartite principles of privacy, modesty, and hospitality (PMH) and how they achieve these three objectives. A qualitative case study approach was used to investigate six Muslim families living in four Brisbane suburbs, consisting of: a) Case Study 1: three Muslim families residing in one suburb of Brisbane and, b) Case Study 2: three international Muslim students living in three different Brisbane suburbs. This research indicates that apart from minor ‘design-related’ difficulties, case study participants were able to continue to perform their daily activities within their current homes through minor changes to the use of the available interior spaces. Above all, case study participants opined that their current Australian homes provide them with adequate safety and privacy for their families without any major disturbances. Insight gained from these cases suggests that greater research attention needs to be given to the potential development of Australian home designs that are adaptable to the ever-changing needs of the Australian multicultural society. Awareness of the multifactorial nature of the influences on Muslims’ perceptions of home and their use of domestic space is needed if architects, building designers, engineers and builders are to be properly equipped to meet the needs of their Muslim clients.

Common variants in the CYP2C19 gene are associated with susceptibility to endometriosis

Objective: To follow-up previous studies highlighting a possible role for cytochrome P450, family 2, subfamily C, 19 (CYP2C19) in susceptibility to endometriosis by searching for additional variants in the CYP2C19 gene that may be associated with the disease. Design Case-control study. Setting Academic research. Subject(s) The cases comprised 2,271 women with surgically confirmed endometriosis; the controls comprised 939 women with self-report of no endometriosis and 1,770 unscreened population samples. Intervention(s) Sequencing of the CYP2C19 region and follow-up of 80 single nucleotide polymorphisms (SNPs) in two case-control samples. Main Outcome Measure(s) Allele frequency differences between cases and controls. Result(s) Sequencing of the CYP2C19 gene region resulted in the detection of a large number of known and novel SNPs. Genotyping of 80 polymorphic SNPs in 901 endometriosis cases and 939 controls resulted in study-wide significant association signals for SNPs in moderate or complete linkage disequilibrium with rs4244285, a functional SNP in exon 5 that abrogates CYP2C19 function through the creation of an alternative splice site. Evidence of association was also detected for another functional SNP in the CYP2C19 promoter, rs12248560, which was highlighted in our previous study. Conclusion(s) Functional variants in CYP2C19 may contribute to endometriosis susceptibility in both familial and sporadic cases. © 2014 by American Society for Reproductive Medicine.