Genome-wide association study for radiographic vertebral fractures: A potential role for the 16q24 BMD locus

Vertebral fracture risk is a heritable complex trait. The aim of this study was to identify genetic susceptibility factors for osteoporotic vertebral fractures applying a genome-wide association study (GWAS) approach. The GWAS discovery was based on the Rotterdam Study, a population-based study of elderly Dutch individuals aged >55years; and comprising 329 cases and 2666 controls with radiographic scoring (McCloskey-Kanis) and genetic data. Replication of one top-associated SNP was pursued by de-novo genotyping of 15 independent studies across Europe, the United States, and Australia and one Asian study. Radiographic vertebral fracture assessment was performed using McCloskey-Kanis or Genant semi-quantitative definitions. SNPs were analyzed in relation to vertebral fracture using logistic regression models corrected for age and sex. Fixed effects inverse variance and Han-Eskin alternative random effects meta-analyses were applied. Genome-wide significance was set at p<5×10-8. In the discovery, a SNP (rs11645938) on chromosome 16q24 was associated with the risk for vertebral fractures at p=4.6×10-8. However, the association was not significant across 5720 cases and 21,791 controls from 14 studies. Fixed-effects meta-analysis summary estimate was 1.06 (95% CI: 0.98-1.14; p=0.17), displaying high degree of heterogeneity (I2=57%; Qhet p=0.0006). Under Han-Eskin alternative random effects model the summary effect was significant (p=0.0005). The SNP maps to a region previously found associated with lumbar spine bone mineral density (LS-BMD) in two large meta-analyses from the GEFOS consortium. A false positive association in the GWAS discovery cannot be excluded, yet, the low-powered setting of the discovery and replication settings (appropriate to identify risk effect size >1.25) may still be consistent with an effect size <1.10, more of the type expected in complex traits. Larger effort in studies with standardized phenotype definitions is needed to confirm or reject the involvement of this locus on the risk for vertebral fractures.

Combining HPLC-DAD and ICP-MS data for improved analysis of complex samples: Classification of the root samples from Cortex moutan

A combined data matrix consisting of high performance liquid chromatography–diode array detector (HPLC–DAD) and inductively coupled plasma-mass spectrometry (ICP-MS) measurements of samples from the plant roots of the Cortex moutan (CM), produced much better classification and prediction results in comparison with those obtained from either of the individual data sets. The HPLC peaks (organic components) of the CM samples, and the ICP-MS measurements (trace metal elements) were investigated with the use of principal component analysis (PCA) and the linear discriminant analysis (LDA) methods of data analysis; essentially, qualitative results suggested that discrimination of the CM samples from three different provinces was possible with the combined matrix producing best results. Another three methods, K-nearest neighbor (KNN), back-propagation artificial neural network (BP-ANN) and least squares support vector machines (LS-SVM) were applied for the classification and prediction of the samples. Again, the combined data matrix analyzed by the KNN method produced best results (100% correct; prediction set data). Additionally, multiple linear regression (MLR) was utilized to explore any relationship between the organic constituents and the metal elements of the CM samples; the extracted linear regression equations showed that the essential metals as well as some metallic pollutants were related to the organic compounds on the basis of their concentrations

Evaluation of the relationship between Chlamydia pecorum sequence types and disease using a species-specific multi-locus sequence typing scheme (MLST)

Chlamydia pecorum is globally associated with several ovine diseases including keratoconjunctivitis and polyarthritis. The exact relationship between the variety of C. pecorum strains reported and the diseases described in sheep remains unclear, challenging efforts to accurately diagnose and manage infected flocks. In the present study, we applied C. pecorum multi-locus sequence typing (MLST) to C. pecorum positive samples collected from sympatric flocks of Australian sheep presenting with conjunctivitis, conjunctivitis with polyarthritis, or polyarthritis only and with no clinical disease (NCD) in order to elucidate the exact relationships between the infecting strains and the range of diseases. Using Bayesian phylogenetic and cluster analyses on 62 C. pecorum positive ocular, vaginal and rectal swab samples from sheep presenting with a range of diseases and in a comparison to C. pecorum sequence types (STs) from other hosts, one ST (ST 23) was recognised as a globally distributed strain associated with ovine and bovine diseases such as polyarthritis and encephalomyelitis. A second ST (ST 69) presently only described in Australian animals, was detected in association with ovine as well as koala chlamydial infections. The majority of vaginal and rectal C. pecorum STs from animals with NCD and/or anatomical sites with no clinical signs of disease in diseased animals, clustered together in a separate group, by both analyses. Furthermore, 8/13 detected STs were novel. This study provides a platform for strain selection for further research into the pathogenic potential of C. pecorum in animals and highlights targets for potential strain-specific diagnostic test development.

Genome-wide association study of intraocular pressure identifies the GLCCI1/ICA1 region as a glaucoma susceptibility locus

To discover quantitative trait loci for intraocular pressure, amajor risk factor for glaucoma and the only modifiable one,weperformed agenome-wide association studyonadiscoverycohort of2175individualsfromSydney, Australia. We found a novel association between intraocular pressure and a common variant at 7p21 near to GLCCI1 and ICA1. The findings in this region were confirmed through two UK replication cohorts totalling 4866 individuals (rs59072263, Pcombined = 1.10 × 10-8). A copy of the G allele at this SNP is associated with an increase in mean IOP of 0.45 mmHg (95%CI = 0.30-0.61 mmHg). These results lend support to the implication of vesicle trafficking and glucocorticoid inducibility pathways in the determination of intraocular pressure and in the pathogenesis of primary open-angle glaucoma.

Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's Esophagus

Barrett's esophagus is an increasingly common disease that is strongly associated with reflux of stomach acid and usually a hiatus hernia, and it strongly predisposes to esophageal adenocarcinoma (EAC), a tumor with a very poor prognosis. We report the first genome-wide association study on Barrett's esophagus, comprising 1,852 UK cases and 5,172 UK controls in the discovery stage and 5,986 cases and 12,825 controls in the replication stage. Variants at two loci were associated with disease risk: chromosome 6p21, rs9257809 (P combined = 4.09 × 10-9; odds ratio (OR) = 1.21, 95% confidence interval (CI) =1.13-1.28), within the major histocompatibility complex locus, and chromosome 16q24, rs9936833 (P combined = 2.74 × 10-10; OR = 1.14, 95% CI = 1.10-1.19), for which the closest protein-coding gene is FOXF1, which is implicated in esophageal development and structure. We found evidence that many common variants of small effect contribute to genetic susceptibility to Barrett's esophagus and that SNP alleles predisposing to obesity also increase risk for Barrett's esophagus. © 2012 Nature America, Inc. All rights reserved.

Genome-wide study of familial juvenile hyperuricaemic (gouty) nephropathy (FJHN) indicates a new locus, FJHN3, linked to chromosome 2p22.1-p21

Familial juvenile hyperuricaemic (gouty) nephropathy (FJHN), is an autosomal dominant disease associated with a reduced fractional excretion of urate, and progressive renal failure. FJHN is genetically heterogeneous and due to mutations of three genes: uromodulin (UMOD), renin (REN) and hepatocyte nuclear factor-1beta (HNF-1β) on chromosomes 16p12, 1q32.1, and 17q12, respectively. However, UMOD, REN or HNF-1β mutations are found in only ~45% of FJHN probands, indicating the involvement of other genetic loci in ~55% of probands. To identify other FJHN loci, we performed a single nucleotide polymorphism (SNP)-based genome-wide linkage analysis, in six FJHN families in whom UMOD, HNF-1β and REN mutations had been excluded. Parametric linkage analysis using a 'rare dominant' model established linkage in five of the six FJHN families, with a LOD score >+3, at 0% recombination, between FJHN and SNPs at chromosome 2p22.1-p21. Analysis of individual recombinants in two unrelated affected individuals defined a ~5.5 Mbp interval, flanked telomerically by SNP RS372139 and centromerically by RS896986 that contained the locus, designated FJHN3. The interval contains 28 genes, and DNA sequence analysis of the most likely candidate, solute carrier family 8 member 1 (SLC8A1), did not identify any abnormalities in the FJHN3 probands. FJHN3 is likely located within a ~5.5 Mbp interval on chromosome 2p22.1-p21, and identifying the genetic abnormality will help to further elucidate mechanisms predisposing to gout and renal failure.

Interethnic studies of TNF polymorphisms confirm the likely presence of a second MHC susceptibility locus in ankylosing spondylitis

The objective of this study was to investigate TNF promoter region polymorphisms for association with susceptibility to ankylosing spondylitis (AS). The TNF -238 and -308 polymorphisms were genotyped in 306 English AS cases and 204 ethnically matched healthy B27-positive controls, and 96 southern German AS cases, 58 B27-positive and 251 B27-negative ethnically matched controls. Additionally, the TNF -376 polymorphism was genotyped in the southern German cases and controls. In the southern German AS patients a significant reduction in TNF -308.2 alleles was seen, compared with B27 positive controls (odds ratio 0.4, P= 0.03, 95% confidence interval 0.2-0.9), but no difference in allele frequencies was observed at TNF -238. Significant association between AS and both TNF -238 and TNF -308 was excluded in the English cases. These results confirm previous observations in the southern German population of association between TNF promoter region polymorphisms and AS, but the lack of association in the English population suggests that these polymorphisms themselves are unlikely to be directly involved. More likely, a second, non-HLA-B, MHC locus is involved in susceptibility to AS in these two populations.

Improved root t method to evaluate consolidation test results - Discussion

Taylor (1948) suggested the method for determination of the settlement, d, corresponding to 90% consolidation utilizing the characteristics of the degree of consolidation, U, versus the square root of the time factor, square root of T, plot. Based on the properties of the slope of U versus square root of T curve, a new method is proposed to determine d corresponding to any U above 70% consolidation for evaluation of the coefficient of consolidation, Cn. The effects of the secondary consolidation on the Cn value at different percentages of consolidation can be studied. Cn, closer to the field values, can be determined in less time as compared to Taylor's method. At any U in between 75 and 95% consolidation, Cn(U) due to the new method lies in between Taylor's Cn and Casagrande's Cn.

Genetic analysis of resistance to root-lesion nematode (Pratylenchus thornei) in wheat

The inheritance of resistance to root-lesion nematode was investigated in five synthetic hexaploid wheat lines and two bread wheat lines using a half-diallel design of F1 and F2 crosses. The combining ability of resistance genes in the synthetic hexaploid wheat lines was compared with the performance of the bread wheat line 'GS50a', the source of resistance to Pratylenchus thornei used in Australian wheat breeding programmes. Replicated glasshouse trials identified P. thornei resistance as polygenic and additive in gene action. General combining ability (GCA) of the parents was more important than specific combining ability (SCA) effects in the inheritance of P. thornei resistance in both F1 and F2 populations. The synthetic hexaploid wheat line 'CPI133872' was identified as the best general combiner, however, all five synthetic hexaploid wheat lines possessed better GCA than 'GS50a'. The synthetic hexaploid wheat lines contain novel sources of P. thornei resistance that will provide alternative and more effective sources of resistance to be utilized in wheat breeding programmes

Rhizoctonia crown and root rot of the pasture legume, sulla (Hedysarum coronarium)

Rhizoctonia solani AG-2-2 was isolated from wilting and dying plants of sulla (Hedysarum coronarium), which is currently being assessed in eastern and southern Australia for its potential as a pasture and forage legume. Infected plants in the field had extensive rotting of the taproot, lateral roots and crown. Koch's postulates were fulfilled using three inoculation methods. The disease may pose a considerable threat to the potential use of H. coronarium in the dryland, grazing farming systems of Australia, with resistance offering the most viable option for minimising its impact.

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.

Locus Bonus : The Relationship of the Roman Villa to its Environment in the Vicinity of Rome

The aim of this study is to examine the relationship of the Roman villa to its environment. The villa was an important feature of the countryside intended both for agricultural production and for leisure. Manuals of Roman agriculture give instructions on how to select a location for an estate. The ideal location was a moderate slope facing east or south in a healthy area and good neighborhood, near good water resources and fertile soils. A road or a navigable river or the sea was needed for transportation of produce. A market for selling the produce, a town or a village, should have been nearby. The research area is the surroundings of the city of Rome, a key area for the development of the villa. The materials used consist of archaeological settlement sites, literary and epigraphical evidence as well as environmental data. The sites include all settlement sites from the 7th century BC to 5th century AD to examine changes in the tradition of site selection. Geographical Information Systems were used to analyze the data. Six aspects of location were examined: geology, soils, water resources, terrain, visibility/viewability and relationship to roads and habitation centers. Geology was important for finding building materials and the large villas from the 2nd century BC onwards are close to sources of building stones. Fertile soils were sought even in the period of the densest settlement. The area is rich in water, both rainfall and groundwater, and finding a water supply was fairly easy. A certain kind of terrain was sought over very long periods: a small spur or ridge shoulder facing preferably south with an open area in front of the site. The most popular villa resorts are located on the slopes visible from almost the entire Roman region. A visible villa served the social and political aspirations of the owner, whereas being in the villa created a sense of privacy. The area has a very dense road network ensuring good connectivity from almost anywhere in the region. The best visibility/viewability, dense settlement and most burials by roads coincide, creating a good neighborhood. The locations featuring the most qualities cover nearly a quarter of the area and more than half of the settlement sites are located in them. The ideal location was based on centuries of practical experience and rationalized by the literary tradition.

Resistance of selected strawberry cultivars to root-knot nematode species (Meloidogyne spp.)

Strawberry runner production areas in Queensland are assessed for the presence of Pratylenchus vulnus (lesion nematode) and Meloidogyne hapla (root-knot nematode) as part of the approval process for sites used in runner production under the approved runner scheme. M. hapla is known to infest strawberry. The ability of three other Meloidogyne species occurring in Queensland to infest this host was investigated. The species M. arenaria, M. incognita and M. javanica, in addition to M. hapla, were able to reproduce on strawberry roots of the cultivar 'Joy', which sustained higher nematode reproduction rates than 'Jewel' and 'Sweet Charlie'. The ability of species other than M. hapla to infest strawberry needs to be recognised in site selection for runner production, and in screening cultivars for resistance to nematodes.

Resistance of Brassicaceae plants to root-knot nematode (Meloidogyne spp.) in northern Australia

Brassicaceae plants have the potential as part of an integrated approach to replace fumigant nematicides, providing the biofumigation response following their incorporation is not offset by reproduction of plant-parasitic nematodes on their roots. Forty-three Brassicaceae cultivars were screened in a pot trial for their ability to reduce reproduction of three root-knot nematode isolates from north Queensland, Australia: M. arenaria (NQ1), M. javanica (NQ2) and M. arenaria race 2 (NQ5/7). No cultivar was found to consistently reduce nematode reproduction relative to forage sorghum, the current industry standard, although a commercial fodder radish (Raphanus sativus) and a white mustard (Sinapis alba) line were consistently as resistant to the formation of galls as forage sorghum. A second pot trial screened five commercially available Brassicaceae cultivars, selected for their biofumigation potential, for resistance to two nematode species, M. javanica (NQ2) and M. arenaria (NQ5/7). The fodder radish cv. Weedcheck, was found to be as resistant as forage sorghum to nematode reproduction. A multivariate cluster analysis using the resistance measurements, gall index, nematode number per g of root and multiplication for two nematode species (NQ2 and NQ5/7) confirmed the similarity in resistance between the radish cultivar and forage sorghum. A field trial confirmed the resistance of the fodder radish cv. Weedcheck, with a similar reduction in the number of Meloidogyne spp. juveniles recovered from the roots 8 weeks after planting. The use of fodder radish cultivars as biofumigation crops to manage root-knot nematodes in tropical vegetable production systems deserves further investigation.

Mapping species differences for adventitious rooting in a Corymbia torelliana x Corymbia citriodora subspecies variegata hybrid

Quantitative trait loci (QTL) detection was carried out for adventitious rooting and associated propagation traits in a second-generation outbred Corymbia torelliana x Corymbia citriodora subspecies variegata hybrid family (n=186). The parental species of this cross are divergent in their capacity to develop roots adventitiously on stem cuttings and their propensity to form lignotubers. For the ten traits studied, there was one or two QTL detected, with some QTL explaining large amounts of phenotypic variation (e.g. 66% for one QTL for percentage rooting), suggesting that major effects influence rooting in this cross. Collocation of QTL for many strongly genetically correlated rooting traits to a single region on linkage group 12 suggested pleiotropy. A three locus model was most parsimonious for linkage group 12, however, as differences in QTL position and lower genetic correlations suggested separate loci for each of the traits of shoot production and root initiation. Species differences were thought to be the major source of phenotypic variation for some rooting rate and root quality traits because of the major QTL effects and up to 59-fold larger homospecific deviations (attributed to species differences) relative to heterospecific deviations (attributed to standing variation within species) evident at some QTL for these traits. A large homospecific/heterospecific ratio at major QTL suggested that the gene action evident in one cross may be indicative of gene action more broadly in hybrids between these species for some traits.