Whole-genome scan, in a complex disease, using 11,245 single-nucleotide polymorphisms: comparison with microsatellites

Despite the theoretical evidence of the utility of single-nucleotide polymorphisms (SNPs) for linkage analysis, no whole-genome scans of a complex disease have yet been published to directly compare SNPs with microsatellites. Here, we describe a whole-genome screen of 157 families with multiple cases of rheumatoid arthritis (RA), performed using 11,245 genomewide SNPs. The results were compared with those from a 10-cM microsatellite scan in the same cohort. The SNP analysis detected HLA*DRB1, the major RA susceptibility locus (P=.00004), with a linkage interval of 31 cM, compared with a 50-cM linkage interval detected by the microsatellite scan. In addition, four loci were detected at a nominal significance level (P<.05) in the SNP linkage analysis; these were not observed in the microsatellite scan. We demonstrate that variation in information content was the main factor contributing to observed differences in the two scans, with the SNPs providing significantly higher information content than the microsatellites. Reducing the number of SNPs in the marker set to 3,300 (1-cM spacing) caused several loci to drop below nominal significance levels, suggesting that decreases in information content can have significant effects on linkage results. In contrast, differences in maps employed in the analysis, the low detectable rate of genotyping error, and the presence of moderate linkage disequilibrium between markers did not significantly affect the results. We have demonstrated the utility of a dense SNP map for performing linkage analysis in a late-age-at-onset disease, where DNA from parents is not always available. The high SNP density allows loci to be defined more precisely and provides a partial scaffold for association studies, substantially reducing the resource requirement for gene-mapping studies.     

Satellite cell regulation of muscle mass is altered at old age.

Muscle mass is decreased with advancing age, likely due to altered regulation of muscle fiber size. This study was designed to investigate cellular mechanisms contributing to this process. Analysis of male Fischer 344 X Brown Norway rats at 6, 20, and 32 mo of age demonstrated that, even though significant atrophy had occurred in soleus muscle by old age, myofiber nuclear number did not change, resulting in a decreased myonuclear domain. Also, the number of centrally located nuclei was significantly elevated in soleus muscle of 32-mo-old rats, correlating with an increase in gene expression of MyoD and myogenin. Whereas total 5'-bromo-2'deoxyuridine (BrdU)-positive nuclei were decreased at older ages, BrdU-positive myofiber nuclei were increased. These results suggest that, with age, loss of muscle mass is accompanied by increased myofiber nuclear density that involves fusion of proliferative satellite cells, resembling ongoing regeneration. Interestingly, centrally located myofiber nuclei were not BrdU labeled. Rats were subjected to hindlimb suspension (HS) for 7 or 14 days and intermittent reloading during HS for 1 h each day (IR) to investigate how aging affects the response of soleus muscle to disuse and an atrophy-reducing intervention. After 14 days of HS, soleus muscle size was decreased to a similar extent at all three ages. However, myofiber nuclear number and the total number of BrdU-positive nuclei decreased with HS only in the young rats. IR was associated with an attenuation of atrophy in soleus muscles of 6- and 20- but not 32-mo-old rats. Furthermore, IR was associated with an increase in BrdU-positive myofiber nuclei only in young rats. These data indicate that altered satellite cell function with age contributes to the impaired response of soleus muscle to an intervention that attenuates muscle atrophy in young animals during imposed disuse.     

Identifying patterns in the diet of mackerel icefish (<Emphasis Type="Italic">Champsocephalus gunnari)</Emphasis> at South Georgia using bootstrapped confidence intervals of a dietary index

Ontogenetic, inter-annual and regional variations in diet were investigated for mackerel icefish, Champsocephalus gunnari, in three successive summer seasons around South Georgia. Stomach contents from 2239 C. gunnari (130–560 mm total length) were examined. A bootstrapping technique was used to calculate confidence intervals for an index of relative importance of prey categories (% IRI_DC). Diet varied significantly between years and age classes but there was little regional difference in diet. In general, diet was dominated by krill, Euphausia superba and by the amphipod Themisto gaudichaudii. Smaller (younger) fish tended to prey on a higher proportion of T. gaudichaudii and small euphausiids such as Thysanoessa sp. and took smaller quantities of E. superba. In a season of poor krill availability (summer of 2003–2004) the proportion of krill in the diet, stomach fullness and fish condition (indicated by length–weight relationships) were significantly lower than in the other summer seasons. A large reduction (>80%) in the estimated annual (2005) biomass of the C. gunnari stock directly followed the season of poor krill availability. This decline was largely because of mortality of 2+ and 3+ fish, which were more krill dependent than 1+ fish. Younger fish appear to have survived, leading to an increase in the estimated population biomass in 2006.     

Assessment of Local Public Health Workers' Willingness to Respond to Pandemic Influenza through Application of the Extended Parallel Process Model

Background

Local public health agencies play a central role in response to an influenza pandemic, and understanding the willingness of their employees to report to work is therefore a critically relevant concern for pandemic influenza planning efforts. Witte''s Extended Parallel Process Model (EPPM) has been found useful for understanding adaptive behavior in the face of unknown risk, and thus offers a framework for examining scenario-specific willingness to respond among local public health workers. We thus aim to use the EPPM as a lens for examining the influences of perceived threat and efficacy on local public health workers'' response willingness to pandemic influenza.

Methodology/Principal Findings

We administered an online, EPPM-based survey about attitudes/beliefs toward emergency response (Johns Hopkins∼Public Health Infrastructure Response Survey Tool), to local public health employees in three states between November 2006 – December 2007. A total of 1835 responses were collected for an overall response rate of 83%. With some regional variation, overall 16% of the workers in 2006-7 were not willing to “respond to a pandemic flu emergency regardless of its severity”. Local health department employees with a perception of high threat and high efficacy – i.e., those fitting a ‘concerned and confident’ profile in the EPPM analysis – had the highest declared rates of willingness to respond to an influenza pandemic if required by their agency, which was 31.7 times higher than those fitting a ‘low threat/low efficacy’ EPPM profile.

Conclusions/Significance

In the context of pandemic influenza planning, the EPPM provides a useful framework to inform nuanced understanding of baseline levels of – and gaps in – local public health workers'' response willingness. Within local health departments, ‘concerned and confident’ employees are most likely to be willing to respond. This finding may allow public health agencies to design, implement, and evaluate training programs focused on emergency response attitudes in health departments.     

Host Responses to Intestinal Microbial Antigens in Gluten-Sensitive Mice

Background and Aims

Excessive uptake of commensal bacterial antigens through a permeable intestinal barrier may influence host responses to specific antigen in a genetically predisposed host. The aim of this study was to investigate whether intestinal barrier dysfunction induced by indomethacin treatment affects the host response to intestinal microbiota in gluten-sensitized HLA-DQ8/HCD4 mice.

Methodology/Principal Findings

HLA-DQ8/HCD4 mice were sensitized with gluten, and gavaged with indomethacin plus gluten. Intestinal permeability was assessed by Ussing chamber; epithelial cell (EC) ultra-structure by electron microscopy; RNA expression of genes coding for junctional proteins by Q-real-time PCR; immune response by in-vitro antigen-specific T-cell proliferation and cytokine analysis by cytometric bead array; intestinal microbiota by fluorescence in situ hybridization and analysis of systemic antibodies against intestinal microbiota by surface staining of live bacteria with serum followed by FACS analysis. Indomethacin led to a more pronounced increase in intestinal permeability in gluten-sensitized mice. These changes were accompanied by severe EC damage, decreased E-cadherin RNA level, elevated IFN-γ in splenocyte culture supernatant, and production of significant IgM antibody against intestinal microbiota.

Conclusion

Indomethacin potentiates barrier dysfunction and EC injury induced by gluten, affects systemic IFN-γ production and the host response to intestinal microbiota antigens in HLA-DQ8/HCD4 mice. The results suggest that environmental factors that alter the intestinal barrier may predispose individuals to an increased susceptibility to gluten through a bystander immune activation to intestinal microbiota.     

Variants in Neuropeptide Y Receptor 1 and 5 Are Associated with Nutrient-Specific Food Intake and Are Under Recent Selection in Europeans

There is a large variation in caloric intake and macronutrient preference between individuals and between ethnic groups, and these food intake patterns show a strong heritability. The transition to new food sources during the agriculture revolution around 11,000 years ago probably created selective pressure and shaped the genome of modern humans. One major player in energy homeostasis is the appetite-stimulating hormone neuropeptide Y, in which the stimulatory capacity may be mediated by the neuropeptide Y receptors 1, 2 and 5 (NPY1R, NPY2R and NPY5R). We assess association between variants in the NPY1R, NPY2R and NPY5R genes and nutrient intake in a cross-sectional, single-center study of 400 men aged 40 to 80 years, and we examine whether genomic regions containing these genes show signatures of recent selection in 270 HapMap individuals (90 Africans, 90 Asians, and 90 Caucasians) and in 846 Dutch bloodbank controls. Our results show that derived alleles in NPY1R and NPY5R are associated with lower carbohydrate intake, mainly because of a lower consumption of mono- and disaccharides. We also show that carriers of these derived alleles, on average, consume meals with a lower glycemic index and glycemic load and have higher alcohol consumption. One of these variants shows the hallmark of recent selection in Europe. Our data suggest that lower carbohydrate intake, consuming meals with a low glycemic index and glycemic load, and/or higher alcohol consumption, gave a survival advantage in Europeans since the agricultural revolution. This advantage could lie in overall health benefits, because lower carbohydrate intake, consuming meals with a low GI and GL, and/or higher alcohol consumption, are known to be associated with a lower risk of chronic diseases.     

Changes in EMG activity in the upper trapezius muscle due to local vibration exposure

Exposure to vibration is suggested as a risk factor for developing neck and shoulder disorders in working life. Mechanical vibration applied to a muscle belly or a tendon can elicit a reflex muscle contraction, also called tonic vibration reflex, but the mechanisms behind how vibration could cause musculoskeletal disorders has not yet been described. One suggestion has been that the vibration causes muscular fatigue. This study investigates whether vibration exposure changes the development of muscular fatigue in the trapezius muscle. Thirty-seven volunteers (men and women) performed a sub-maximal isometric shoulder elevation for 3 min. This was repeated four times, two times with induced vibration and two times without. Muscle activity was measured before and after each 3-min period to look at changes in the electromyography parameters. The result showed a significantly smaller mean frequency decrease when performing the shoulder elevation with vibration (?2.51 Hz) compared to without vibration (?4.04 Hz). There was also a slightly higher increase in the root mean square when exposed to vibration (5.7% of maximal voluntary contraction) compared to without (3.8% of maximal voluntary contraction); however, this was not statistically significant. The results of the present study indicate that short-time exposure to vibration has no negative acute effects on the fatiguing of upper trapezius muscle.     

Improving goniometer accuracy by compensating for individual transducer characteristics

Flexible goniometers are useful for direct movement measurements. Crosstalk due to rotation between the endblocks is well known. However, even without any rotation, some crosstalk can occur. The objective of this study was to elucidate the effect of, and compensate for, the inherent crosstalk in biaxial goniometers, with specific relevance for applications with one dominating movement direction. Six biaxial goniometers (M110, Biometrics Ltd., Gwent, UK) were evaluated. A precision jig, for simulating pure flexion/extension angles, was constructed. Each sensor produced a consistent and specific crosstalk pattern, when tested over a ±100° range of motion. A procedure for correction for the inherent crosstalk of individual goniometer, based on polynomial adjust, is presented. The method for compensation, which reduced the root mean square error from, on average for the six goniometers, 3.7° (range 1.8–10.1°) to 0.35° (0.12–0.55°), might be required for obtaining valid goniometer measurements, e.g. of valgus/varus of the knee during gait flexion/extension movements.