Grasping nettles: cellular heterogeneity and other confounders in epigenome-wide association studies

Platform technologies for measurement of CpG methylation at multiple loci across the genome have made ambitious epigenome-wide association studies affordable and practicable. In contrast to genetic studies, which estimate the effects of structural changes in DNA, and transcriptomic studies, which measure genomic outputs, epigenetic studies can access states of regulation of genome function in particular cells and in response to specific stimuli. Although many factors complicate the interpretation of epigenetic variation in human disease, cell-specific methylation patterns and the cellular heterogeneity present in peripheral blood and tissue biopsies are anticipated to cause the most problems. In this review, we suggest that the difficulties may be exaggerated and we explore how cellular heterogeneity may be embraced with appropriate study designs and analytical tools. We further suggest that systematic mapping of the loci influenced by age, sex and genetic polymorphisms will bring important biological insights as well as improved control of epigenome-wide association studies

Using single nucleotide polymorphisms as a means to understanding the pathophysiology of asthma

Asthma is the most common chronic childhood disease in the developed nations, and is a complex disease that has high social and economic costs. Studies of the genetic etiology of asthma offer a way of improving our understanding of its pathogenesis, with the goal of improving preventive strategies, diagnostic tools, and therapies. Considerable effort and expense have been expended in attempts to detect specific polymorphisms in genetic loci contributing to asthma susceptibility. Concomitantly, the technology for detecting single nucleotide polymorphisms (SNPs) has undergone rapid development, extensive catalogues of SNPs across the genome have been constructed, and SNPs have been increasingly used as a method of investigating the genetic etiology of complex human diseases. This paper reviews both current and potential future contributions of SNPs to our understanding of asthma pathophysiology

Identification of Variegated Coloring in Skin Tumors: Neural Network vs. Rule-Based Induction Methods

The use of neural networks for automatic identification of variegated coloring, which is believed to be one of the most predictive features for malignant melanoma, is described. The Nestor development system (NDS) was chosen for neural network implementation. At the heart of NDS is a three-layer neural network called a restricted Coulomb energy (RCE) network. The learning scheme and the database for detection of variegated coloring are discussed. Results are reporte

Proficiency of clinical laboratories in and near Monterrey, Mexico, to detect vancomycin-resistant enterococci.

Early detection of vancomycin-resistant enterococci is important for preventing its spread among hospitalized patients. We surveyed the ability of eight hospital laboratories in and near Monterrey, Mexico, to detect vancomycin resistance in Enterococcus spp. and found that although laboratories can reliably detect high-level vancomycin resistance, many have difficulty detecting low-level resistance

Economic Values for Perennial Ryegrass Traits in New Zealand Dairy Farm Systems

Perennial ryegrass (Lolium perenne L.) is the main species used in dairy pastures throughout New Zealand. There are approximately 30 perennial ryegrass cultivars sold commercially in New Zealand, but currently there is no evaluation system which allows farmers to compare the potential impact of different cultivars on the profitability of their farm business. Such an economic evaluation system requires information on performance values (PV) for cultivars which quantifies their performance with respect to the major productivity traits (herbage accumulation (HA, kg DM/ha), nutritive value and persistence) relative to a genetic base, and economic values (EV, Doyle and Elliott 1983) which estimate the additional profit resulting from each unit change in the trait of interest (Equation 1). Economic value = Δ operating profit/Δ trait of interest (1) This paper describes a system modelling approach developed to estimate EV for seasonal HA of pasture in the major dairying regions of New Zealand. This information is used in the DairyNZ Forage Value Index system (www.dairynzfvi.co.nz) which is being developed to include information on all three productivity traits for commercially available ryegrass cultivars

Lactobacillus plantarum MB452 enhances the function of the intestinal barrier by increasing the expression levels of genes involved in tight junction formation

<p>Abstract</p> <p>Background</p> <p>Intestinal barrier function is important for preserving health, as a compromised barrier allows antigen entry and can induce inflammatory diseases. Probiotic bacteria can play a role in enhancing intestinal barrier function; however, the mechanisms are not fully understood. Existing studies have focused on the ability of probiotics to prevent alterations to tight junctions in disease models, and have been restricted to a few tight junction bridging proteins. No studies have previously investigated the effect of probiotic bacteria on healthy intestinal epithelial cell genes involved in the whole tight junction signalling pathway, including those encoding for bridging, plaque and dual location tight junction proteins. Alteration of tight junction signalling in healthy humans is a potential mechanism that could lead to the strengthening of the intestinal barrier, resulting in limiting the ability of antigens to enter the body and potentially triggering undesirable immune responses.</p> <p>Results</p> <p>The effect of <it>Lactobacillus plantarum </it>MB452 on tight junction integrity was determined by measuring trans-epithelial electrical resistance (TEER) across Caco-2 cell layers. <it>L. plantarum </it>MB452 caused a dose-dependent TEER increase across Caco-2 cell monolayers compared to control medium. Gene expression was compared in Caco-2 cells untreated or treated with <it>L. plantarum </it>MB452 for 10 hours. Caco-2 cell RNA was hybridised to human oligonucleotide arrays. Data was analysed using linear models and differently expressed genes were examined using pathway analysis tools. Nineteen tight junction-related genes had altered expression levels in response to <it>L. plantarum </it>MB452 (modified-P < 0.05, fold-change > 1.2), including those encoding occludin and its associated plaque proteins that anchor it to the cytoskeleton. <it>L. plantarum </it>MB452 also caused changes in tubulin and proteasome gene expression levels which may be linked to intestinal barrier function. Caco-2 tight junctions were visualised by fluorescent microscopy of immuno-stained occludin, zona occludens (ZO)-1, ZO-2 and cingulin. Caco-2 cells treated with <it>L. plantarum </it>MB452 had higher intensity fluorescence of each of the four tight junction proteins compared to untreated controls.</p> <p>Conclusions</p> <p>This research indicates that enhancing the expression of genes involved in tight junction signalling is a possible mechanism by which <it>L. plantarum </it>MB452 improves intestinal barrier function.</p

Development of a Forage Evaluation System for Perennial Ryegrass Cultivar and Endophyte Combinations in New Zealand Dairy Systems

An economic index for perennial ryegrass (Lolium perenne L.) cultivars is a relatively new concept, although recently introduced in Ireland (McEvoy et al. 2011). By contrast, in dairy cattle breeding, the concept of an economic index rating animals and economic values underlying that index is well entrenched (Philipson et al. 1994; Veerkamp, 1998). Historically, forage evaluation data for individual cultivars were either displayed using absolute numbers for seasonal dry matter production within a season or across all seasons with a notation to indicate statistical differences, or percentage values where a reference cultivar is 100. The adoption of an economic index and routine evaluation approach for perennial ryegrass provides a method to identify traits of economic importance to focus plant breeding efforts better and to provide clarity for farmers around predicting cultivars that will maximise farm profit. It also allows for routine tracking of genetic gain of individual traits and the economic index. In this paper, the economic based forage evaluation techniques now used in New Zealand for perennial ryegrass cultivar/endophyte combinations are presented

A cross-sectional survey of the acceptability of data collection processes for validation of a European point prevalence survey of healthcare-associated infections and antimicrobial use

BACKGROUND: Statistical measurements alone are insufficient to ensure robust data for point prevalence surveys (PPS) of healthcare-associated infections (HAI). Data quality is determined by the type of data, data collection methods and available resources. Data collectors’ views regarding the acceptability of data collection process for validation studies are also important to consider. AIM: To explore data collectors’ views on the acceptability of data collection processes used for a European validation PPS of HAI and antimicrobial use (AMU). METHODS: An anonymous online survey was conducted with 67 data collectors from 10 European countries involved in the study. FINDINGS: Twenty-five (64.1%) participants viewed AMU data collection as easy/quite easy whereas only five (12.8%) thought HAI data collection was easy/quite easy. Six (17%) participants indicated that incentives and 21 (56.8%) that disincentives were possibly/definitely present for reporting cases of HAI. Engagement of staff was not thought to have adversely affected data collection as only one (2.6%) and five (15.4%) participants thought involvement of hospital PPS teams and administration was low/very low, respectively. DISCUSSION: Participants believed the approaches used were appropriate but that more training was required prior to data collection, some case definitions should be reviewed and the number of variables reduced

The WD40 Domain Is Required for LRRK2 Neurotoxicity

BACKGROUND:Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinson disease (PD). LRRK2 contains an "enzymatic core" composed of GTPase and kinase domains that is flanked by leucine-rich repeat (LRR) and WD40 protein-protein interaction domains. While kinase activity and GTP-binding have both been implicated in LRRK2 neurotoxicity, the potential role of other LRRK2 domains has not been as extensively explored. PRINCIPAL FINDINGS:We demonstrate that LRRK2 normally exists in a dimeric complex, and that removing the WD40 domain prevents complex formation and autophosphorylation. Moreover, loss of the WD40 domain completely blocks the neurotoxicity of multiple LRRK2 PD mutations. CONCLUSION:These findings suggest that LRRK2 dimerization and autophosphorylation may be required for the neurotoxicity of LRRK2 PD mutations and highlight a potential role for the WD40 domain in the mechanism of LRRK2-mediated cell death