A Phenomic Scan of the Norfolk Island Genetic Isolate Identifies a Major Pleiotropic Effect Locus Associated with Metabolic and Renal Disorder Markers

Multiphenotype genome-wide association studies (GWAS) may reveal pleiotropic genes, which would remain undetected using single phenotype analyses. Analysis of large pedigrees offers the added advantage of more accurately assessing trait heritability, which can help prioritise genetically influenced phenotypes for GWAS analysis. In this study we performed a principal component analysis (PCA), heritability (h2) estimation and pedigree-based GWAS of 37 cardiovascular disease -related phenotypes in 330 related individuals forming a large pedigree from the Norfolk Island genetic isolate. PCA revealed 13 components explaining >75% of the total variance. Nine components yielded statistically significant h2 values ranging from 0.22 to 0.54 (P<0.05). The most heritable component was loaded with 7 phenotypic measures reflecting metabolic and renal dysfunction. A GWAS of this composite phenotype revealed statistically significant associations for 3 adjacent SNPs on chromosome 1p22.2 (P<1x10-8). These SNPs form a 42kb haplotype block and explain 11% of the genetic variance for this renal function phenotype. Replication analysis of the tagging SNP (rs1396315) in an independent US cohort supports the association (P = 0.000011). Blood transcript analysis showed 35 genes were associated with rs1396315 (P<0.05). Gene set enrichment analysis of these genes revealed the most enriched pathway was purine metabolism (P = 0.0015). Overall, our findings provide convincing evidence for a major pleiotropic effect locus on chromosome 1p22.2 influencing risk of renal dysfunction via purine metabolism pathways in the Norfolk Island population. Further studies are now warranted to interrogate the functional relevance of this locus in terms of renal pathology and cardiovascular disease risk.

Rice husk biochar and crop residue amendment in subtropical cropping soils: Effect on biomass production, nitrogen use efficiency and greenhouse gas emissions

We investigated the effect of maize residues and rice husk biochar on biomass production, fertiliser nitrogen recovery (FNR) and nitrous oxide (N2O) emissions for three different subtropical cropping soils. Maize residues at two rates (0 and 10 t ha−1) combined with three rates (0, 15 and 30 t ha-1) of rice husk biochar were added to three soil types in a pot trial with maize plants. Soil N2O emissions were monitored with static chambers for 91 days. Isotopic 15N-labelled urea was applied to the treatments without added crop residues to measure the FNR. Crop residue incorporation significantly reduced N uptake in all treatments but did not affect overall FNR. Rice husk biochar amendment had no effect on plant growth and N uptake but significantly reduced N2O and carbon dioxide (CO2) emissions in two of the three soils. The incorporation of crop residues had a contrasting effect on soil N2O emissions depending on the mineral N status of the soil. The study shows that effects of crop residues depend on soil properties at the time of application. Adding crop residues with a high C/N ratio to soil can immobilise N in the soil profile and hence reduce N uptake and/or total biomass production. Crop residue incorporation can either stimulate or reduce N2O emissions depending on the mineral N content of the soil. Crop residues pyrolysed to biochar can potentially stabilise native soil C (negative priming) and reduce N2O emissions from cropping soils thus providing climate change mitigation potential beyond the biochar C storage in soils. Incorporation of crop residues as an approach to recycle organic materials and reduce synthetic N fertiliser use in agricultural production requires a thorough evaluation, both in terms of biomass production and greenhouse gas emissions.

New genetic loci link adipose and insulin biology to body fat distribution

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10−8). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.

Genetic studies of body mass index yield new insights for obesity biology

Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P < 5 × 10−8), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for ~2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.

Defining the role of common variation in the genomic and biological architecture of adult human height

Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated approximately 2,000, approximately 3,700 and approximately 9,500 SNPs explained approximately 21%, approximately 24% and approximately 29% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes and pathways not highlighted in earlier efforts, such as signaling by fibroblast growth factors, WNT/beta-catenin and chondroitin sulfate-related genes. We identified several genes and pathways not previously connected with human skeletal growth, including mTOR, osteoglycin and binding of hyaluronic acid. Our results indicate a genetic architecture for human height that is characterized by a very large but finite number (thousands) of causal variants.

Genome-wide association and genetic functional studies identify autism susceptibility candidate 2 gene (AUTS2) in the regulation of alcohol consumption

Alcohol consumption is a moderately heritable trait, but the genetic basis in humans is largely unknown, despite its clinical and societal importance. We report a genome-wide association study meta-analysis of approximately 2.5 million directly genotyped or imputed SNPs with alcohol consumption (gram per day per kilogram body weight) among 12 population-based samples of European ancestry, comprising 26,316 individuals, with replication genotyping in an additional 21,185 individuals. SNP rs6943555 in autism susceptibility candidate 2 gene (AUTS2) was associated with alcohol consumption at genome-wide significance (P = 4 x 10(-8) to P = 4 x 10(-9)). We found a genotype-specific expression of AUTS2 in 96 human prefrontal cortex samples (P = 0.026) and significant (P < 0.017) differences in expression of AUTS2 in whole-brain extracts of mice selected for differences in voluntary alcohol consumption. Down-regulation of an AUTS2 homolog caused reduced alcohol sensitivity in Drosophila (P < 0.001). Our finding of a regulator of alcohol consumption adds knowledge to our understanding of genetic mechanisms influencing alcohol drinking behavior.

Systematic review of interventions to improve the provision of information for adults with primary brain tumours and their caregivers

Background: Adults with primary brain tumors and their caregivers have significant information needs. This review assessed the effect of interventions to improve information provision for adult primary brain tumor patients and/or their caregivers. Methods: We included randomized or nonrandomized trials testing educational interventions that had outcomes of information provision, knowledge, understanding, recall, or satisfaction with the intervention, for adults diagnosed with primary brain tumors and/or their family or caregivers. PubMed, MEDLINE, EMBASE and Cochrane Reviews databases were searched for studies published between 1980 and June 2014. Results: Two randomized controlled, one non-randomized controlled, and 10 single group pre-post trials enrolled more than 411 participants. Five group, four practice/process change and four individual interventions assessed satisfaction (12 studies), knowledge (four studies) or information provision (2 studies). Nine studies reported high rates of satisfaction. Three studies showed statistically significant improvements over time in knowledge and two showed greater information was provided to intervention than control group participants, although statistical testing was not performed. Discussion: The trials assessed intermediate outcomes such as satisfaction, and only 4/13 reported on knowledge improvements. Few trials had a randomized controlled design and risk of bias was either evident or could not be assessed in most domains.

'Mutiny on the Bounty': The genetic history of Norfolk Island reveals extreme gender-biased admixture

Background The Pacific Oceania region was one of the last regions of the world to be settled via human migration. Here we outline a settlement of this region that has given rise to a uniquely admixed population. The current Norfolk Island population has arisen from a small number of founders with mixed Caucasian and Polynesian ancestry, descendants of a famous historical event. The ‘Mutiny on the Bounty’ has been told in history books, songs and the big screen, but recently this story can be portrayed through comprehensive molecular genetics. Written history details betrayal and murder leading to the founding of Pitcairn Island by European mutineers and the Polynesian women who left Tahiti with them. Investigation of detailed genealogical records supports historical accounts. Findings Using genetics, we show distinct maternal Polynesian mitochondrial lineages in the present day population, as well as a European centric Y-chromosome phylogeny. These results comprehensively characterise the unique gender-biased admixture of this genetic isolate and further support the historical records relating to Norfolk Island. Conclusions Our results significantly refine previous population genetic studies investigating Polynesian versus Caucasian diversity in the Norfolk Island population and add information that is beneficial to future disease and gene mapping studies.

Association of the microRNA-Single Nucleotide Polymorphism rs2910164 in miR146a with sporadic breast cancer susceptibility: A case control study

Background Breast cancer (BC) is primarily considered a genetic disorder with a complex interplay of factors including age, gender, ethnicity, family history, personal history and lifestyle with associated hormonal and non-hormonal risk factors. The SNP rs2910164 in miR146a (a G to C polymorphism) was previously associated with increased risk of BC in cases with at least a single copy of the C allele in breast cancer, though results in other cancers and populations have shown significant variation. Methods In this study, we examined this SNP in an Australian sporadic breast cancer population of 160 cases and matched controls, with a replicate population of 403 breast cancer cases using High Resolution Melting. Results Our analysis indicated that the rs2910164 polymorphism is associated with breast cancer risk in both primary and replicate populations (p = 0.03 and 0.0013, respectively). In contrast to the results of familial breast cancer studies, however, we found that the presence of the G allele of rs2910164 is associated with increased cancer risk, with an OR of 1.77 (95% CI 1.40–2.23). Conclusions The microRNA miR146a has a potential role in the development of breast cancer and the effects of its SNPs require further inquiry to determine the nature of their influence on breast tissue and cancer.

Serum bilirubin concentration is modified by UGT1A1 Haplotypes and influences risk of type-2 diabetes in the Norfolk Island Genetic Isolate

Background Located in the Pacific Ocean between Australia and New Zealand, the unique population isolate of Norfolk Island has been shown to exhibit increased prevalence of metabolic disorders (type-2 diabetes, cardiovascular disease) compared to mainland Australia. We investigated this well-established genetic isolate, utilising its unique genomic structure to increase the ability to detect related genetic markers. A pedigree-based genome-wide association study of 16 routinely collected blood-based clinical traits in 382 Norfolk Island individuals was performed. Results A striking association peak was located at chromosome 2q37.1 for both total bilirubin and direct bilirubin, with 29 SNPs reaching statistical significance (P < 1.84 × 10−7). Strong linkage disequilibrium was observed across a 200 kb region spanning the UDP-glucuronosyltransferase family, including UGT1A1, an enzyme known to metabolise bilirubin. Given the epidemiological literature suggesting negative association between CVD-risk and serum bilirubin we further explored potential associations using stepwise multivariate regression, revealing significant association between direct bilirubin concentration and type-2 diabetes risk. In the Norfolk Island cohort increased direct bilirubin was associated with a 28 % reduction in type-2 diabetes risk (OR: 0.72, 95 % CI: 0.57-0.91, P = 0.005). When adjusted for genotypic effects the overall model was validated, with the adjusted model predicting a 30 % reduction in type-2 diabetes risk with increasing direct bilirubin concentrations (OR: 0.70, 95 % CI: 0.53-0.89, P = 0.0001). Conclusions In summary, a pedigree-based GWAS of blood-based clinical traits in the Norfolk Island population has identified variants within the UDPGT family directly associated with serum bilirubin levels, which is in turn implicated with reduced risk of developing type-2 diabetes within this population.

Directional dominance on stature and cognition in diverse human populations

Homozygosity has long been associated with rare, often devastating, Mendelian disorders1, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness2. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power3, 4. Here we use runs of homozygosity to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and find statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment (P < 1 × 10−300, 2.1 × 10−6, 2.5 × 10−10 and 1.8 × 10−10, respectively). In each case, increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months’ less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing evidence that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples5, 6, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection7, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.

Citizens breaking out of filter bubbles: Urban screens as civic media

Social media platforms risk polarising public opinions by employing proprietary algorithms that produce filter bubbles and echo chambers. As a result, the ability of citizens and communities to engage in robust debate in the public sphere is diminished. In response, this paper highlights the capacity of urban interfaces, such as pervasive displays, to counteract this trend by exposing citizens to the socio-cultural diversity of the city. Engagement with different ideas, networks and communities is crucial to both innovation and the functioning of democracy. We discuss examples of urban interfaces designed to play a key role in fostering this engagement. Based on an analysis of works empirically-grounded in field observations and design research, we call for a theoretical framework that positions pervasive displays and other urban interfaces as civic media. We argue that when designed for more than wayfinding, advertisement or television broadcasts, urban screens as civic media can rectify some of the pitfalls of social media by allowing the polarised user to break out of their filter bubble and embrace the cultural diversity and richness of the city.

Dimethyl sulfide and other biogenic volatile organic compound emissions from branching coral and reef seawater: Potential sources of secondary aerosol over the Great Barrier Reef

Volatile organic compounds (VOCs) in the headspace of bubble chambers containing branches of live coral in filtered reef seawater were analysed using gas chromatography with mass spectrometry (GC-MS). When the coral released mucus it was a source of dimethyl sulfide (DMS) and isoprene; however, these VOCs were not emitted to the chamber headspace from mucus-free coral. This finding, which suggests that coral is an intermittent source of DMS and isoprene, was supported by the observation of occasional large pulses of atmospheric DMS (DMSa) over Heron Island reef on the southern Great Barrier Reef (GBR), Australia, in the austral winter. The highest DMSa pulse (320 ppt) was three orders of magnitude less than the DMS mixing ratio (460 ppb) measured in the headspace of a dynamically purged bubble chamber containing a mucus-coated branch of Acropora aspera indicating that coral reefs can be strong point sources of DMSa. Static headspace GC-MS analysis of coral fragments identified mainly DMS and seven other minor reduced sulfur compounds including dimethyl disulfide, methyl mercaptan, and carbon disulfide, while coral reef seawater was an indicated source of methylene chloride, acetone, and methyl ethyl ketone. The VOCs emitted by coral and reef seawater are capable of producing new atmospheric particles < 15 nm diameter as observed at Heron Island reef. DMS and isoprene are known to play a role in low-level cloud formation, so aerosol precursors such as these could influence regional climate through a sea surface temperature regulation mechanism hypothesized to operate over the GBR.

Germination biology and occurrence of pol-yembryony in two forms of cats claw creeper vine, Dolichandra unguis-cati (Bignonia-ceae): implications for its invasiveness and management

Cat’s claw creeper, Dolichandra unguis-cati (L.) Lohmann (syn. Macfadyena unguis-cati (L.) Gentry) is a major environmental weed in Australia. Two forms (‘long’ and ‘short’ pod) of the weed occur in Australia. This investigation aimed to evaluate and compare germination behavior and occurrence of polyembryony in the two forms of the weed. Seeds were germinated in growth chambers set to 10/20 °C, 15/25 °C, 20/30 °C, 30/45 °C and 25 °C. Germination and polyembryony were monitored over a period of 12 weeks. For all the treatments in this study, seeds from the short pod form exhibited significantly higher germination rates and higher occurrence of polyembryony than those from the long pod form. Seeds from the long pod form did not germinate at the lowest temperature of 10/20 °C; in contrast, those of the short pod form germinated under this condition, albeit at a lower rate. Results from this study could explain why the short pod form of D. unguis-cati is the more widely distributed form in Australia, while the long pod form is confined to a few localities. The results have implication in predicting future ranges of both forms of the invasive D. unguis-cati, as well as inform management decisions for control of the weed.