Angiotensin-converting-enzyme gene polymorphism and heart failure: a case–control study

Heart failure (HF) is the final outcome of virtually all cardiovascular diseases and is a major and increasingly serious public health problem. The renin–angiotensin system plays an important role in the pathogenesis of cardiovascular disease. Insertion/deletion (I/D) polymorphism of the angiotensin-converting enzyme (ACE) has attracted significant attention; it has been extensively investigated in a spectrum of cardiovascular phenotypes because of its correlation with serum ACE activity. There is controversy regarding the association of ACE I/D polymorphism with cardiovascular disease. The aim of this study was to investigate whether ACE genotype is associated with HF by comparing cases and controls. The study sample consisted of 229 cases with HF due to coronary heart disease or idiopathic dilated cardiomyopathy and 230 controls recruited from the general population. The ACE I/D genotype was identified using a polymerase chain reaction assay. No evidence was found to support an association between ACE genotype and HF.     

Effects of a hydrological protection zone on the restoration of a raised bog: a case study from Northeast-Germany 1997–2008

We investigated the changes of water level and vegetation in a restored cut-over raised bog in response to a hydrological protection zone established around the bog. The restoration began 1997 and techniques involved ditch blocking within and around the bog to stimulate a return to conditions of intact bog ecosystems. In order to monitor the rehabilitation of the raised bog, water levels and vegetation have been recorded since before restoration measures began. The monitoring is ongoing, but an assessment of 15 year’s data (1994–2008) is presented. A hydrological protection zone with continuous high water levels could be established around the raised bog which minimizes the runoff of precipitation. Shortly after the first measures, the water levels increased significantly at all dipwells. Parallel to the increasing water levels a vascular plant species assemblage and a diverse Sphagnum community developed. In particular Sphagnum fimbriatum, S. palustre, S. recurvum and S. squarrosum spread efficiently. The cover of trees decreased significantly because of high water levels and ongoing acidification by Sphagnum spp. The high water levels have stimulated the re-vegetation and the hydrology self-regulation of the acrotelm. The successful regeneration of the acrotelm particularly became apparent in years with below-average precipitations (e.g. 2008), when the water levels in the central parts of the raised bog did not fall back to the low level reached in previous years, which had also remarkably water deficits (e.g. 2003).     

Biomarkers of pulmonary hypertension in patients with scleroderma: a case–control study

IntroductionSignificant pulmonary vascular disease is a leading cause of death in patients with scleroderma, and early detection and early medical intervention are important, as they may delay disease progression and improve survival and quality of life. Although several biomarkers have been proposed, there remains a need to define a reliable biomarker of early pulmonary vascular disease and subsequent development of pulmonary hypertension (PH). The purpose of this study was to define potential biomarkers for clinically significant pulmonary vascular disease in patients with scleroderma.MethodsThe circulating growth factors basic fibroblast growth factor, placental growth factor (PlGF), vascular endothelial growth factor (VEGF), hepatocyte growth factor, and soluble VEGF receptor 1 (sFlt-1), as well as cytokines (interleukin [IL]-1β IL-2, IL-4, IL-5, IL-8, IL-10, IL-12, IL-13, tumor necrosis factor-α, and interferon-γ), were quantified in patients with scleroderma with PH (n = 37) or without PH (n = 40). In non-parametric unadjusted analyses, we examined associations of growth factor and cytokine levels with PH. In a subset of each group, a second set of earlier samples, drawn 3.0±1.6 years earlier, were assessed to determine the changes over time.ResultssFlt-1 (p = 0.02) and PlGF (p = 0.02) were higher in the PH than in the non-PH group. sFlt-1 (ρ = 0.3245; p = 0.01) positively correlated with right ventricular systolic pressure. Both PlGF (p = 0.03) and sFlt-1 (p = 0.04) positively correlated with the ratio of forced vital capacity to diffusing capacity for carbon monoxide (DLCO), and both inversely correlated with DLCO (p = 0.01). Both PlGF and sFlt-1 levels were stable over time in the control population.ConclusionsOur study demonstrated clear associations between regulators of angiogenesis (sFlt-1 and PlGF) and measures of PH in scleroderma and that these growth factors are potential biomarkers for PH in patients with scleroderma. Larger longitudinal studies are required for validation of our results.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0712-4) contains supplementary material, which is available to authorized users.     

HTERT MNS16A polymorphism in breast cancer: a case–control study

This case–control study aims to investigate the role of HTERT MNS16A polymorphism as a potential risk factors and/or a prognostic marker for breast cancer. 113 consecutive incident cases of histologically confirmed ductal breast cancer and 124 healthy controls were recruited. HTERT MNS16A polymorphism was genotyped (L: long allele, S: short allele); multivariate logistic regression was performed. No significant association was noted either at the overall analysis (OR?=?1.57, 95?% CI 0.84–2.93 for heterozygous LS carriers; OR?=?1.02, 95?% CI 0.54–1.95 for homozygous SS carriers) or at the subanalyses in premenopausal and postmenopausal women. With respect to survival analysis, HTERT MNS16A polymorphism was not associated with either disease-free survival or overall survival. HTERT MNS16A polymorphism does not seem to be a risk factor for breast cancer in the Caucasian Greek population. Further, larger studies from other countries and subjects seem to be needed as this novel polymorphism is being examined in depth.     

Abundance–suitability relationships for invasive species: Epiphyas postvittana as a case study

Biological Invasions - Prediction of the geographic distribution of an exotic species in a new environment is an important element of risk assessment as it provides an assessment of the spatial...     

Simulations of UV–visible spectra for analytical applications: phenothiazines as a case study

Simulation of UV–vis spectra over the whole absorption window requires not only an accurate approach for the estimation of electronic transitions' energies, but also to take properly into account solvent and band-broadening effects. Although the first, solvent, can be easily introduced in quantum-chemical calculations at both implicit and explicit levels, the second, band broadening, is more troublesome to evaluate. To this end, in this contribution, we propose a protocol aimed to correctly simulate the whole absorption UV–vis spectra of organic molecules based on time-dependent density functional theory, coupled with implicit and explicit solvent models, and on the use of a fitting procedure with respect to the experimental data in order to define the best band broadening. This protocol is applied to the simulation of absorption spectra of 10H-phenothiazine and three related molecules, N,N-diphenylamine, iminodibenzyl and 10H-phenothiazine-5-oxide, which appear as impurities during its industrial synthesis. The obtained results show not only that the main peak positions are reproduced with an error not exceeding 10 nm (in the 200–400 nm range) but also that the overall shape of the UV–vis spectra can be correctly simulated.     

Chronic tinnitus and BDNF/GDNF CpG promoter methylations: a case–control study

Brain-derived neurotrophic factor (BDNF) and Glial-derived neurotrophic factor (GDNF) are neurotrophic factors that play key roles in the auditory pathway. While the relationship between serum levels and polymorphisms of BDNF/GDNF and chronic tinnitus is emphasized in the literature, there is no study showing the link between the promoter methylations of these genes and tinnitus. For this purpose, the relationship between chronic tinnitus and peripheral blood derived BDNF/GDNF promoter methylations was investigated to identify their role in the pathophysiology of tinnitus. In this case–control study, we examined the possible effects of BDNF/GDNF methylations in the blood samples of patients with tinnitus complaints for more than 3 months. Sixty tinnitus subjects between the ages of 18–55 and 50 healthy control subjects in the same age group who were free of any otorhinolaryngology and systemic disease were selected for examination. Methylation of total 12 CpG sites in BDNF and GDNF promoter regions were determined by the bisulfite-pyrosequencing method. Statistically significant differences were detected between BDNF CpG6 and GDNF CpG3-5-6 methylation ratios in the comparison of control group and the chronic tinnitus patients (P?=?0.002, 0.0005, 0.00003, and 0.0029, respectively). To our knowledge, this is the first study in the literature investigating the relationship between chronic tinnitus and peripheral blood derived BDNF/GDNF promoter methylations. It is believed that the current results might be supported by investigating the relationships between BDNF/GDNF methylations and genotypes in future research using higher sample sizes.

     

Adsorption of HCN on reduced graphene oxides: a first–principles study

Journal of Molecular Modeling - Over the past few years, time-dependent ultrafast fluorescence spectroscopy method has been applied to the study of protein dynamics. However, observations from...     

Replication of recently identified systemic lupus erythematosus genetic associations: a case–control study

Introduction

We aimed to replicate association of newly identified systemic lupus erythematosus (SLE) loci.

Methods

We selected the most associated SNP in 10 SLE loci. These 10 SNPs were analysed in 1,579 patients with SLE and 1,726 controls of European origin by single-base extension. Comparison of allele frequencies between cases and controls was done with the Mantel–Haenszel approach to account for heterogeneity between sample collections.

Results

A previously controversial association with a SNP in the TYK2 gene was replicated (odds ratio (OR) = 0.79, P = 2.5 × 10-⁵), as well as association with the X chromosome MECP2 gene (OR = 1.26, P = 0.00085 in women), which had only been reported in a single study, and association with four other loci, 1q25.1 (OR = 0.81, P = 0.0001), PXK (OR = 1.19, P = 0.0038), BANK1 (OR = 0.83, P = 0.006) and KIAA1542 (OR = 0.84, P = 0.001), which have been identified in a genome-wide association study, but not found in any other study. All these replications showed the same disease-associated allele as originally reported. No association was found with the LY9 SNP, which had been reported in a single study.

Conclusions

Our results confirm nine SLE loci. For six of them, TYK2, MECP2, 1q25.1, PXK, BANK1 and KIAA1542, this replication is important. The other three loci, ITGAM, STAT4 and C8orf13-BLK, were already clearly confirmed. Our results also suggest that MECP2 association has no influence in the sex bias of SLE, contrary to what has been proposed. In addition, none of the other associations seems important in this respect.     

The association between ANKH promoter polymorphism and chondrocalcinosis is independent of age and osteoarthritis: results of a case–control study

Introduction

Chondrocalcinosis (CC) most commonly results from calcium pyrophosphate crystal deposition (CPPD). The objective of this study is to examine the association between candidate single-nucleotide polymorphisms (SNPs) and radiographic CC.

Methods

SNPs in ankylosis human (ANKH), high ferritin (HFE), tissue non-specific alkaline phosphatase (TNAP), ecto-neucleotide pyrophosphatase 1 (ENPP1), and transferrin (TE) genes were genotyped in participants of the Genetics of Osteoarthritis and Lifestyle (GOAL) and Nottingham Osteoarthritis Case-Control studies. Adjusted genotype odds ratio (aOR_GENOTYPE), the OR for association between one additional minor allele and CC, was calculated and adjusted for age, gender, body mass index (BMI), and osteoarthritis (OA) by using binary logistic regression. Statistical significance was set at P ≤0.003 after Bonferroni correction for multiple tests.

Results

The -4bpG > A polymorphism in the 5′ untranslated region (5′ UTR) of ANKH associated with CC after Bonferroni correction. This was independent of age, gender, OA, and BMI; aOR_GENOTYPE (95% confidence interval, or CI) was 1.39 (1.14-1.69) (P = 0.001). rs3045 and rs875525, two other SNPs in ANKH, associated with CC; aOR_GENOTYPE (95% CI) values were 1.31 (1.09-1.58) (P = 0.005) and 1.18 (1.03-1.35) (P = 0.015), respectively; however, this was non-significant after Bonferroni correction.

Conclusions

This study validates the association between a functional polymorphism in the 5′ UTR of ANKH and CC and shows for the first time that this is independent of age and OA – the two key risk factors for CC. It shows that other SNPs in ANKH may also associate with CC. This supports the role of extracellular inorganic pyrophosphate in the pathogenesis of CC. The findings of this hospital-based study require replication in a community-based population.     

Post‐dispersal seed recovery by animals: is it a plant‐ or an animal‐driven process?

The ability of animals to find and consume hoarded seeds (i.e. seed recovery) is a key stage within the seed dispersal process. However, the ecology of seed recovery is still poorly understood. Here, we analyze the factors controlling seed recovery by scatter‐hoarding rodents in an oak‐dominated temperate forest. We examined the relative importance of intrinsic seed traits (i.e. plant‐driven) and extrinsic seed factors (i.e. animal‐driven) on the probability of seed recovery. We found that seed recovery is mainly driven by extrinsic seed factors, mostly related to animal behavior (pilfering frequency, microsite preference, predation risk, burial depth and cache size). Important intrinsic traits such as seed size, seed quality and seed‐drop timing were, on average, of lower significance in the probability of seed recovery (2.8‐times less important than extrinsic factors); only seed quality was an important intrinsic trait. On the other hand, larger and nutritionally more valuable seeds showed a removal–recovery tradeoff as they enhance seed removal and hoarding (increasing dispersal quality) but also favour seed recovery (increasing predation). We find that other mechanisms beyond seed traits (e.g. masting) are needed to decrease seed recovery and, thus, increase seed survival. We conclude that, as seed recovery is mostly driven by animal behavioural factors, it substantially differs from other previous stages of the seed dispersal process that are more dependent on seed traits. We argue that seed recovery needs further attention to advance our understanding of the ecology of seed dispersal and the role of secondary dispersers as a selective force for seeds.     

p53 codon 72 polymorphism is associated with susceptibility to hepatocellular carcinoma in the Turkish population: a case–control study

The tumor suppressor p53 gene plays a crucial role in preventing carcinogenesis through its ability to induce cell cycle arrest and apoptosis following DNA damage and oncogene activation. A guanine (G)/cytosine (C) common single nucleotide polymorphism (SNP) at second position of codon 72 in exon 4 of p53 gene determines a arginine (Arg) to proline (Pro) (Arg72Pro) aminoacidic substitution within the proline-rich domain of p53 protein. Arg72 and Pro72 allele are different from a biochemical and biological point of view and many reports suggest that they can modulate individual cancer susceptibility. To determine the association of the p53 Arg72Pro polymorphism with the risk of hepatocellular carcinoma (HCC) development in a Turkish population, a hospital-based case–control study was designed consisting of 119 subjects with HCC and 119 cancer-free control subjects matched for age, gender, smoking and alcohol status. The genotype frequency of the p53 Arg72Pro polymorphism was determined by using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. Our data shows that the Pro/Pro genotype of the p53 Arg72Pro polymorphism is associated with increased risk of HCC development in this Turkish population (OR = 3.20, 95% CI: 1.24–8.22, P = 0.02). Furthermore, according to stratified analysis, a significant association was observed between the homozygote Pro/Pro genotype and HCC risk in the subgroups of male gender (OR = 3.01, 95% CI: 1.14–7.97, P = 0.03) and patients with hepatitis B virus (HBV)-related HCC (OR = 4.04, 95% CI: 1.46–11.15, P = 0.007). Because our results suggest for the first time that the Pro/Pro homozygote of p53 Arg72Pro polymorphism may be a genetic susceptibility factor for HCC (especially in the male gender and HBV-infected patients) in the Turkish population, further independent studies are required to validate our findings in a larger series, as well as in patients of different ethnic origins.     

Population densities and density–area relationships in a community with advective dispersal and variable mosaics of resource patches

Many communities comprise species that select resources that are patchily distributed in an environment that is otherwise unsuitable or suboptimal. Effects of this patchiness can depend on the characteristics of patch arrays and animal movements, and produce non-intuitive outcomes in which population densities are unrelated to resource abundance. Resource mosaics are predicted to have only weak effects, however, where patches are ephemeral or organisms are transported advectively. The running waters of streams and benthic invertebrates epitomize such systems, but empirical tests of resource mosaics are scarce. We sampled 15 common macroinvertebrates inhabiting distinct detritus patches at four sites within a sand-bed stream, where detritus formed a major resource of food and living space. At each site, environmental variables were measured for 100 leaf packs; invertebrates were counted in 50 leaf packs. Sites differed in total abundance of detritus, leaf pack sizes and invertebrate densities. Multivariate analysis indicated that patch size was the dominant environmental variable, but invertebrate densities differed significantly between sites even after accounting for patch size. Leaf specialists showed positive and strong density–area relationships, except where the patch size range was small and patches were aggregated. In contrast, generalist species had weaker and variable responses to patch sizes. Population densities were not associated with total resource abundance, with the highest densities of leaf specialists in sites with the least detritus. Our results demonstrate that patchy resources can affect species even in communities where species are mobile, have advective dispersal, and patches are relatively ephemeral.     

Rheumatoid arthritis–associated autoantibodies in non–rheumatoid arthritis patients with mucosal inflammation: a case–control study

IntroductionRheumatoid arthritis–associated autoantibodies (RA-AAB) can be present in serum years before clinical onset of rheumatoid arthritis (RA). It has been hypothesized that initiation of RA-AAB generation occurs at inflamed mucosal surfaces, such as in the oral cavity or lungs. The aim of this study was to assess systemic presence of RA-AAB in patients without RA who had oral or lung mucosal inflammation.MethodsThe presence of RA-AAB (immunoglobulin A [IgA] and IgG anti-cyclic citrullinated peptide 2 antibodies (anti-CCP2), IgM and IgA rheumatoid factor (RF), IgG anti-carbamylated protein antibodies and IgG and IgA anti-citrullinated peptide antibodies against fibrinogen, vimentin and enolase) were determined in sera of non-RA patients with periodontitis (PD, n = 114), bronchiectasis (BR, n = 80) or cystic fibrosis (CF, n = 41). Serum RA-AAB levels were compared with those of periodontally healthy controls (n = 36). Patients with established RA (n = 86) served as a reference group. Association of the diseases with RA-AAB seropositivity was assessed with a logistic regression model, adjusted for age, sex and smoking.ResultsLogistic regression analysis revealed that IgG anti-CCP seropositivity was associated with BR and RA, whereas the association with PD was borderline significant. IgA anti-CCP seropositivity was associated with CF and RA. IgM RF seropositivity was associated with RA, whereas the association with BR was borderline significant. IgA RF seropositivity was associated with CF and RA. Apart from an influence of smoking on IgA RF in patients with RA, there was no influence of age, sex or smoking on the association of RA-AAB seropositivity with the diseases. Anti-CarP levels were increased only in patients with RA. The same held for IgG reactivity against all investigated citrullinated peptides.ConclusionAlthough overall levels were low, RA-AAB seropositivity was associated with lung mucosal inflammation (BR and CF) and may be associated with oral mucosal inflammation (PD). To further determine whether mucosal inflammation functions as a site for induction of RA-AAB and precedes RA, longitudinal studies are necessary in which RA-AAB of specifically the IgA isotype should be assessed in inflamed mucosal tissues and/or in their inflammatory exudates.     

Reservoir design and operation: effects on aquatic biota—a case study of planktonic copepods

Copepod assemblages from two cascade reservoirs were analyzed during two consecutive years. The upstream reservoir (Chavantes) is a storage system with a high water retention time (WRT of 400 days), and the downstream one (Salto Grande) is a run-of-river system with only 1.5 days WRT. Copepod composition, richness, abundance, and diversity were correlated with the limnological variables and the hydrological and morphometric features. Standard methods were employed for zooplankton sampling and analysis (vertical 50-μm net hauls and counting under a stereomicroscope). Two hypotheses were postulated and confirmed through the data obtained: (1) compartmentalization is more pronounced in the storage reservoir and determines the differences in the copepod assemblage structure; and (2) the assemblages are more homogeneous in the run-of-river reservoir, where the abundance decreases because of the predominance of washout effects. For both reservoirs, the upstream zone is more distinctive. In addition, in the smaller reservoir the influence of the input from tributaries is stronger (turbid waters). Richness did not differ significantly among seasons, but abundance was higher in the run-of-river reservoir during summer.     

Integrating farmers’ knowledge on toxic plants and grassland management: a case study on Colchicum autumnale in Austria

High densities of Colchicum autumnale may endanger grassland management in Austria. As the toxic components persist in hay and silage, the continuation of the management of these grasslands, which are often characterised by a high biodiversity, is uncertain. Farmers possess valuable and context-specific know-how on toxic plants and grassland management. This study aims at assessing the contribution of farmers’ knowledge to nature conservation research on toxic plants in grasslands. In total, we conducted 170 face-to-face interviews with farmers managing grasslands with C. autumnale in four areas of Lower Austria. In addition, the farmers were invited to regional workshops to discuss C. autumnale, control measures and related problems. We also encouraged farmers to carry out on-farm experiments. To provide triangulation of the participatory with academic research results, C. autumnale was mapped in three municipalities, covering in total 686 ha. The majority of all grassland plots were extensively managed meadows. More than half of them were not fertilised and were subject to nature conservation regulations. Farmers reported an increase of C. autumnale on 44% of all grassland plots. Of these, grassland management has been extensified in 64%. About 27% of all farmers regarded C. autumnale as a problem. Among farmers who sold hay, 48% considered it as problematic. The field survey showed that C. autumnale covers up to 73% of grasslands. Farmers’ knowledge is an important contribution to nature conservation research and should be included in the design and implementation of agri-environmental schemes so that long-term extensive grassland management can be assured.