A genetic variant located in miR-423 is associated with reduced breast cancer risk

Background/Aim: Since microRNAs (miRNAs) act as translational regulators of multiple genes, single nucleotide polymorphisms (SNP) in them can have potentially wide-ranging effects. Using an association approach, this research examined the effects of the rs6505162 SNP, an A>C polymorphism located in the premiRNA region of miR-423, on breast cancer development. Materials and Methods: Caucasian Australian women with breast cancer and controls matched for age and ethnicity were genotyped for rs6505162 and their genotypic and allelic frequencies analysed for significant differences. Results: Analysis indicated that there were significant differences between the case and control populations (χ 2=6.70, p=0.035), with the CC genotype conferring reduced risk of breast cancer development (odds ratio=0.50 95% confidence interval=0.27-0.92, p=0.03). Conclusion: Further functional research is required to determine the mechanism of action of this SNP on miRNA function.

Genetic variation in cytokine-related genes and migraine susceptibility

Migraine is classified by the World Health Organization (WHO) as being one of the top 20 most debilitating diseases. According to the neurovascular hypothesis, neuroinflammation may promote the activation and sensitisation of meningeal nociceptors, inducing the persistent throbbing headache characterized in migraine. The tumor necrosis factor (TNF) gene cluster, made up of TNFα, lymphotoxin α (LTA), and lymphotoxin β (LTB), has been implicated to influence the intensity and duration of local inflammation. It is thought that sterile inflammation mediated by LTA, LTB, and TNFα contributes to threshold brain excitability, propagation of neuronal hyperexcitability and thus initiation and maintenance of a migraine attack. Previous studies have investigated variants within the TNF gene cluster region in relation to migraine susceptibility, with largely conflicting results. The aim of this study was to expand on previous research and utilize a large case-control cohort and range of variants within the TNF gene cluster to investigate the role of the TNF gene cluster in migraine. Nine single nucleotide polymorphisms (SNPs) were selected for investigation as follows: rs1800683, rs2229094, rs2009658, rs2071590, rs2239704, rs909253, rs1800630, rs1800629, and rs3093664. No significant association with migraine susceptibility was found for any of the SNPs tested, with further testing according to migraine subtype and gender also showing no association for disease risk. Haplotype analysis showed that none of the tested haplotypes were significantly associated with migraine.

Molecular genetic analyses of RFLPs for PCR-amplified growth hormone gene, renal kallikrein gene and atrial natriuretic factor gene in essential hypertension

The present study examined polymorphisms of genes that might be involved in the onset of essential hypertension (HT). These included the (i) growth hormone gene (GH1), whose locus has recently been linked to elevated blood pressure (BP) in the stroke-prone SHR, although recent sib-pair analysis of a polymorphism near the human chorionic somatomammotropin gene (a member of the GH cluster) was unable to show linkage with HT; (ii) renal kallikrein gene (KLK1); and (iii) atrial natriuretic factor gene (ANF), where a primary defect in production or activity of kallikrein or ANF could cause NaCl retention and vasoconstriction. Association analyses were conducted to compare restriction fragment length polymorphisms (RFLPs) of each gene in 85 HT and 95 normotensive (NT) Caucasian subjects whose parents had a similar BP status at age ≥50 years. The frequency of the minor allele of (i) a RsaI RFLP in the promoter of GH1, amplified from leukocyte DNA by the polymerase chain reaction, was 0.15 in the HT group and 0.14 in the NT group (χ1=0.34, P=0.55); (ii) a TaqI RFLP for KLK1 was 0.035 in the HT group and 0.015 in the NT group (χ2=1.5, P=0.21); and (iii) a XhoI RFLP for ANF was 0.50 in HTs and 0.46 in NTs (χ2=0.20, P=0.65). Studies of HT pedigrees found one family in which the ANF locus and HT were not linked, owing to an obligate recombinant. The present data thus provide no evidence for involvement of the growth hormone, renal kallikrein, nor ANF gene in the causation of essential hypertension.

Investigation of genetic diversity and development of vaccine for Chlamydia pecorum infections in koala (Phascolarctos cinereus)

Many wild koala populations in Australia continue to experience serious declines due to factors such as disease caused by Chlamydia. This thesis is the first of its kind to investigate diversity of the chlamydial infections in wild koala populations across Australia and has made significant progress towards the development of a vaccine for koalas. The findings in this study have demonstrated that it is feasible to develop a safe and effective recombinant vaccine against Chlamydia in both disease free as well as severely diseased koalas. Most importantly, this study is also first of its kind to evaluate a multi-component vaccine that should be effective against the range of Chlamydia pecorum strains circulating in both captive as well as wild koala populations.

Past 140-year environmental record in the northern South China Sea : evidence from coral skeletal trace metal variations

About 140-year changes in the trace metals in Porites coral samples from two locations in the northern South China Sea were investigated. Results of PCA analyses suggest that near the coast, terrestrial input impacted behavior of trace metals by 28.4%, impact of Sea Surface Temperature (SST) was 19.0%, contribution of war and infrastructure were 14.4% and 15.6% respectively. But for a location in the open sea, contribution of War and SST reached 33.2% and 16.5%, while activities of infrastructure and guano exploration reached 13.2% and 14.7%. While the spatiotemporal change model of Cu, Cd and Pb in seawater of the north area of South China Sea during 1986–1997 were reconstructed. It was found that in the sea area Cu and Cd contaminations were distributed near the coast while areas around Sanya, Hainan had high Pb levels because of the well-developed tourism related activities.

Intimate relationship status variations in violence against women : urban, suburban, and rural differences

Woman abuse varies across intimate relationship categories (e.g., marriage, divorce, separation). However, it is unclear whether relationship status variations in violence against women differ across urban, suburban, and rural areas. We test the hypothesis that rural females, regardless of their intimate partner relationship status, are at higher risk of intimate violence than their urban and suburban counterparts. Results indicate that marital status is an important aspect of the relationship between intimate victimization and geographic area and that rural divorced and separated females are victimized at rates exceeding their urban counterparts.

Cloning and characterization of microRNAs from Brassica napus

A library containing approximately 40,000 small RNA sequences was constructed for Brassica napus. Analysis of 3025 sequences obtained from this library resulted in the identification of 11 conserved miRNA families, which were validated by secondary structure prediction using surrounding sequences in the Brassica genome. Two 21 nt small RNA sequences reside within the arm of a pre-miRNA like stem-loop structure, making them likely candidates for novel non-conserved miRNAs in B. napus. Most of the conserved miRNAs were expressed at similar levels in a F1 hybrid B. napus line and its four double haploid progeny that showed marked variations in phenotypes, but many were differentially expressed between B. napus and Arabidopsis. The miR169 family was expressed at high levels in young leaves and stems, but was undetectable in roots and mature leaves, suggesting that miR169 expression is developmentally regulated in B. napus. © 2007 Federation of European Biochemical Societies.

A hybrid genetic algorithm for the energy-efficient virtual machine placement problem in data centers

Server consolidation using virtualization technology has become an important technology to improve the energy efficiency of data centers. Virtual machine placement is the key in the server consolidation technology. In the past few years, many approaches to the virtual machine placement have been proposed. However, existing virtual machine placement approaches consider the energy consumption by physical machines only, but do not consider the energy consumption in communication network, in a data center. However, the energy consumption in the communication network in a data center is not trivial, and therefore should be considered in the virtual machine placement. In our preliminary research, we have proposed a genetic algorithm for a new virtual machine placement problem that considers the energy consumption in both physical machines and the communication network in a data center. Aiming at improving the performance and efficiency of the genetic algorithm, this paper presents a hybrid genetic algorithm for the energy-efficient virtual machine placement problem. Experimental results show that the hybrid genetic algorithm significantly outperforms the original genetic algorithm, and that the hybrid genetic algorithm is scalable.

Variations in acculturation and Australian physical education teacher education students' receptiveness to an alternative pedagogical approach to games teaching

Background The development of intelligent, thinking performers as a central theme in Physical Education curriculum documents worldwide has highlighted the need for an evolution of teaching styles from the dominant reproductive approach. This has prompted an Australian university to change the content and delivery of a games unit within their Physical Education Teacher Education (PETE) course and adopt a productive student centred approach that is compatible with current curriculum directives. The significance of prospective physical educators’ biographies on their receptiveness to this pedagogical innovation was studied to help recognise and understand potential differences and subsequently guide programme development to help improve the impact of teacher education. Purpose To investigate whether past school and sporting experiences are powerful influences on Australian PETE recruits’ initial perspectives about effective physical education teaching practice and their receptiveness to an alternative pedagogical approach. Participants and Setting 49 first year pre-service PETE students (53% male; 47% female; mean age 18.88 ± 1.57 years) undertaking a compulsory unit on games teaching at an Australian university volunteered to take part in the study and were grouped according to their highest level of representation in games, either school/club (n=13), regional (n=20), or state/national (n=16). Students experienced the constraints-led approach as learners and teachers during an 8-week games unit informed by nonlinear pedagogy and underpinned by motor learning theory. Data collection and Analysis Prior to the commencement of the unit participants completed part A of a two part mixed response questionnaire aimed at gathering data about their physical education and sporting background. The data were summarised using descriptive statistics. Pre and post intervention, participants completed part B responding, via Likert Scale with their opinion of the importance of each sub-component of the traditional reproductive style for an effective games teaching session. This resulted in a traditional reproductive games teaching belief score. For each sub-component, participants were invited to respond in more detail to justify their opinions. A one-way between groups analysis of variance (ANOVA), Tukey’s HSD Post Hoc Test and a two - tailed, paired samples t test were used to analyse the quantitative data. Content analysis was used to analyse the qualitative data. Findings The traditional, reproductive approach was the most frequently reported teaching approach used by the physical education teachers and sports coaches of participants in all groups. Prior to the commencement of the alternate games unit, participants in each representative level group held very strong custodial traditional reproductive games teaching beliefs. After experiencing the alternative games unit there were statistically significant differences in the traditional reproductive games teaching belief mean scores for each group, This combined with participants’ qualitative responses indicated a receptiveness to the alternative pedagogy. Conclusions The results of this present study show that, contrary to previous research undertaken in North America, in Australia, it is possible for PETE educators to change beliefs in order to overcome the constraint of acculturation and provide PETE students with the knowledge, understanding and belief in an alternate approach to teaching games in physical education compatible with curriculum documents.

Diurnal variations in ocular aberrations of human eyes

Purpose: To investigate the diurnal variations in ocular wavefront aberrations over two consecutive days in young adult subjects. Materials and methods: Measurements of both lower-order (sphero-cylindrical refractive powers) and higher-order (3rd and 4th order aberration terms) ocular aberrations were collected for 30 young adult subjects at ten different times over two consecutive days using a Hartmann-Shack aberrometer. Fifteen subjects were myopic and 15 were emmetropic. Five sets of measurements were collected each day at approximately 3 hourly intervals, with the first measurement taken at ~9 am and the final measurement at ~9 pm. Results: Spherical equivalent refraction (p = 0.029) and spherical aberration (p = 0.043) were both found to undergo significant diurnal variation over the two measurement days. The spherical equivalent was typically found to be at a maximum (i.e. most hyperopic) at the morning measurement, with a small myopic shift of 0.37 ± 0.15 D observed over the course of the day. The mean spherical aberration of all subjects (0.038 ± 0.048 μm) was found to be positive during the day and gradually became more negative into the evening, with a mean amplitude of change of 0.036 ± 0.02 μm. None of the other considered sphero-cylindrical refractive power components or higher-order aberrations exhibited significant diurnal variation over the two days of the experiment (p>0.05). Except for the lower-order astigmatism at 90/180 deg (p = 0.040), there were no significant differences between myopes and emmetropes in the magnitude and timing of the observed diurnal variations (p>0.05). Conclusions: Significant diurnal variations in spherical equivalent and spherical aberration were consistently observed over two consecutive days of measurement. Research and clinical applications requiring precise refractive error and wavefront measurements should take these diurnal changes into account when interpreting wavefront data.

QUT Library advances the use of open public tools to navigate genetic inventions and builds research networks

Many emerging economies are dangling the patent system to stimulate bio-technological innovations with the ultimate premise that these will improve their economic and social growth. The patent system mandates full disclosure of the patented invention in exchange of a temporary exclusive patent right. Recently, however, patent offices have fallen short of complying with such a mandate, especially for genetic inventions. Most patent offices provide only static information about disclosed patent sequences and even some do not keep track of the sequence listing data in their own database. The successful partnership of QUT Library and Cambia exemplifies advocacy in Open Access, Open Innovation and User Participation. The library extends its services to various departments within the university, builds and encourages research networks to complement skills needed to make a contribution in the real world.

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world’s poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16–45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.

Genetic analysis of GRIA2 and GRIA4 genes in migraine

Background Migraine is a brain disorder affecting ∼12% of the Caucasian population. Genes involved in neurological, vascular, and hormonal pathways have all been implicated in predisposing individuals to developing migraine. The migraineur presents with disabling head pain and varying symptoms of nausea, emesis, photophobia, phonophobia, and occasionally visual sensory disturbances. Biochemical and genetic studies have demonstrated dysfunction of neurotransmitters: serotonin, dopamine, and glutamate in migraine susceptibility. Glutamate mediates the transmission of excitatory signals in the mammalian central nervous system that affect normal brain function including cognition, memory and learning. The aim of this study was to investigate polymorphisms in the GRIA2 and GRIA4 genes, which encode subunits of the ionotropic AMPA receptor for association in an Australian Caucasian population. Methods Genotypes for each polymorphism were determined using high resolution melt analysis and the RFLP method. Results Statistical analysis showed no association between migraine and the GRIA2 and GRIA4 polymorphisms investigated. Conclusions Although the results of this study showed no significant association between the tested GRIA gene variants and migraine in our Australian Caucasian population further investigation of other components of the glutamatergic system may help to elucidate if there is a relationship between glutamatergic dysfunction and migraine.

Genetic polymorphisms in miRNAs targeting the estrogen receptor and their effect on breast cancer risk

Breast cancer is the cancer that most commonly affects women worldwide. This type of cancer is genetically complex, but is strongly linked to steroid hormone signalling systems. Because microRNAs act as translational regulators of multiple genes, including the steroid nuclear receptors, single nucleotide polymorphisms (SNPs) in microRNAs genes can have potentially wide-ranging influences on breast cancer development. Thus, this study was conducted to investigate the relationships between six SNPs (rs6977848, rs199981120, rs185641358, rs113054794, rs66461782, and rs12940701) located in four miRNA genes predicted to target the estrogen receptor (miR-148a, miR-221, miR-186, and miR-152) and breast cancer risk in Caucasian Australian women. By using high resolution melt analysis (HRM) and polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP), 487 samples including 225 controls and 262 cases were genotyped. Analysis of their genotype and allele frequencies indicated that the differences between case and control populations was not significant for rs6977848, rs66461782, and rs12940701 because their p-values are 0.81, 0.93, 0.1 which are all above the threshold value (p=0.05). Our data thus suggests that these SNPs do not affect breast cancer risk in the tested population. In addition, rs199981120, rs185641358, and rs113054794 could not be found in this population, suggesting that these SNPs do not occur in Caucasian Australians.

Quantitative genetic parameters for body traits at different ages in a cultured stock of giant freshwater prawn (Macrobrachium rosenbergii) selected for fast growth

The aim of the current study was to estimate heritabilities and correlations for body traits at different ages (Weeks 10 and 18 after stocking) in a giant freshwater prawn (Macrobrachium rosenbergii) population selected for fast growth rate in Vietnam. The dataset consisted of 4650 body records (2432 and 2218 records collected at Weeks 10 and 18, respectively) in the full pedigree comprising a total of 18 387 records. Variance and covariance components were estimated using restricted maximum likelihood fitting a multi-trait animal model. Estimates of heritability for body traits (bodyweight, body length, cephalothorax length, abdominal length, cephalothorax width and abdominal width) were moderate and ranged from 0.06 to 0.11 and from 0.11 to 0.22 at Weeks 10 and 18, respectively. Body-trait heritabilities estimated at Week 10 were not significantly lower than at Week 18. Genetic correlations between body traits within age and genetic correlations for body traits between ages were generally high. Our results suggested that selection for high growth rate in GFP can be undertaken successfully before full market size has been reached.