Single-nucleotide polymorphism versus microsatellite markers in a combined linkage and segregation analysis of a quantitative trait

Increasingly, single-nucleotide polymorphism (SNP) markers are being used in preference to microsatellite markers. However, methods developed for microsatellites may be problematic when applied to SNP markers. We evaluated the results of using SNPs vs. microsatellites in Monte Carlo Markov chain (MCMC) oligogenic combined segregation and linkage analysis methods. These methods were developed with microsatellite markers in mind. We selected chromosome 7 from the Collaborative Study on the Genetics of Alcoholism dataset for analysis because linkage to an electrophysiological trait had been reported there. We found linkage in the same region of chromosome 7 with the Affymetrix SNP data, the Illumina SNP data, and the microsatellite marker data. The MCMC sampler appears to mix with both types of data. The sampler implemented in this MCMC oligogenic combined segregation and linkage analysis appears to handle SNP data as well as microsatellite data and it is possible that the localizations with the SNP data are better

Heritability of risk-taking in adolescence: A longitudinal twin study

Adolescents are prone to risk-taking behaviors leading to adverse consequences such as substance abuse, accidents, violence, and victimization. However, little is known about the contribution of genetic and environmental factors to individual differences in the propensity for risk-taking. This study investigated developmental changes, longitudinal stability, and heritability of risk-taking using data from 752 adolescent twins including 169 MZ and 203 DZ pairs. The Balloon Analogue Risk Task (BART), an experimental behavioral measure of risk taking, was administered to the twins at age 12 and then re-administered to a part of this sample at age 14. Risk-taking increased with age, but individual differences showed a significant longitudinal stability. Genetic model fitting showed that at age 12, heritability of risk-taking was modest but significant in both sexes, whereas at age 14, heritability increased to 55% in males and became non-significant in females. The findings suggest that propensity for risk-taking as measured by BART can be a useful endophenotype for genetic studies of adolescent externalizing psychopathology, however, the utility of this measure may be limited by sex differences in heritability

Exploring the influence of food and temperature on North Sea sandeels using a new dynamic energy budget model

The zooplanktivorous schooling fish sandeels A. marinus comprise a quarter of North Sea fish biomass and are essential food for a number of marine mammals and birds. However, in recent decades there has been a decline in the abundance of older sandeels, with increased overwinter mortality proposed as a contributor. To survive winter animals require a minimum energy reserve which is determined by temperature, prey abundance, and possibly prey size. Here a new dynamic energy budget model is created to determine the influence of food and temperature on sandeel energy dynamics. The model hindcasts changes in energy and survival between 2000 and 2008, a period of pronounced stock decline in the northwestern North Sea. Overwinter starvation mortality was a large contributor towards a recent decline in sandeels in northern UK waters. Highest over-winter mortality rates were recorded for juveniles and not individuals aged 1 or over due to the effect of weight-specific metabolism. However, a sensitivity analysis of the model suggests that mortality rates are more sensitive to changes in copepod abundance in the build up to overwintering rather than temperature during overwintering. Further, projections show that temperature rises are negated by increases in large, but not small copepods. The conclusion is that food-driven size-selective starvation mortality contributed to the northwestern North Sea stock decline and that indirect food web effects of climate change are greater than direct physiological effects on sandeels

Timing of sandeel spawning and hatching off the East Coast of Scotland

The lesser sandeel, Ammodytes marinus, is a key forage fish species in the North Sea. Mean lengths and abundances of sandeels have declined steeply since the 1990’s and these are associated with declining breeding success of various seabird species on the east coast of Scotland, especially kittiwakes. The declining lengths have led to a mismatch between the peak in food demand arising from chick rearing, and the appearance of appropriately sized young sandeels in the foraging areas of the birds. A 10-year time series of sandeel larval samples between 2000 and 2009 offer a rare opportunity to analyze trends in spawning and hatch dates and determine whether they contributed to changes in mean lengths. By analyzing the abundance, length, and age distributions of sandeel larvae we were able to determine the temporal distribution of hatching rates each year, and back-track to the likely spawning dates of the sandeels. Estimated spawning dates showed no evidence of correlation with environmental cues such as tidal or lunar phases. However, hatch end dates varied by 20 days over the 10-year period and were correlated with the date of the seasonal minimum of sea bottom temperature. We show a significant decline between growth rate and 0-group length between 2000 and 2009, and suggest that changes in food quality and availability, rather than shifts in hatch dates, are likely to be responsible for current declines in the availability of sandeels to seabirds

A comfort assessment of existing cervical orthoses

Purpose: identify location and intensity of discomfort experienced by healthy participants wearing cervical orthoses. Method: convenience sample of 34 healthy participants wore Stro II, Philadelphia, Headmaster, and AspenVista® cervical orthoses for four-hour periods. Participants reported discomfort level (scale 0-6) and location. Results: participants reported mean discomfort for all orthoses over the four-hour test between ‘a little discomfort’ and ‘very uncomfortable’ (mean discomfort score=1.64, SD=1.50). Seven participants prematurely stopped tests due to pain and six reported maximum discomfort scores. Significant linear increase in discomfort with duration of wear was found for all orthoses. Significantly less discomfort was reported with Stro II than Headmaster and Philadelphia. Age correlated with greater perceived discomfort. Orthoses differed in the location discomfort was experienced. Conclusion: existing cervical orthoses cause discomfort influenced by design and duration of wear with orthoses' design the more significant factor. This work informed the design of a new orthosis and future orthoses developments

Trends in Sandeel Growth and Abundance off the East Coast of Scotland

Sandeels Ammodytes marinus are a crucial forage fish species in the North Sea, transferring zooplankton energy to higher trophic levels. However, there has been a sustained decline in sandeel abundance in the northwestern North Sea since 2000. Here we use field data to analyse year-to-year changes in A. marinus growth rate between 1997 and 2009 and assess whether variation in growth rate corresponded with variation in abundance. The signature of the reduction in abundance between 2000 and 2009 was a decline in age 1 sandeels, while no other age class declined. Analysis of age-length data showed that the decline in abundance coincided with a period of low growth. Growth performance indexes were correlated with zooplankton and phytoplankton biomass but not temperature. Further, we observed a significant correlation between larval growth rate and 0-group sandeel length during a period when hatch dates were relatively fixed; suggesting recent changes in length were influenced by food availability

Information recovery from low coverage whole-genome bisulfite sequencing.

The cost of whole-genome bisulfite sequencing (WGBS) remains a bottleneck for many studies and it is therefore imperative to extract as much information as possible from a given dataset. This is particularly important because even at the recommend 30X coverage for reference methylomes, up to 50% of high-resolution features such as differentially methylated positions (DMPs) cannot be called with current methods as determined by saturation analysis. To address this limitation, we have developed a tool that dynamically segments WGBS methylomes into blocks of comethylation (COMETs) from which lost information can be recovered in the form of differentially methylated COMETs (DMCs). Using this tool, we demonstrate recovery of ∼30% of the lost DMP information content as DMCs even at very low (5X) coverage. This constitutes twice the amount that can be recovered using an existing method based on differentially methylated regions (DMRs). In addition, we explored the relationship between COMETs and haplotypes in lymphoblastoid cell lines of African and European origin. Using best fit analysis, we show COMETs to be correlated in a population-specific manner, suggesting that this type of dynamic segmentation may be useful for integrated (epi)genome-wide association studies in the future

Influence of antigen density and TLR ligands on preclinical efficacy of a VLP-based vaccine against peanut allergy.

BACKGROUND Virus-like particle (VLP) Peanut is a novel immunotherapeutic vaccine candidate for the treatment of peanut allergy. The active pharmaceutical ingredient represents cucumber mosaic VLPs (CuMVTT -VLPs) that are genetically fused with one of the major peanut allergens, Ara h 2 (CuMVTT -Ara h 2). We previously demonstrated the immunogenicity and the protective capacity of VLP Peanut-based immunization in a murine model for peanut allergy. Moreover, a Phase I clinical trial has been initiated using VLP Peanut material manufactured following a GMP-compliant manufacturing process. Key product characterization studies were undertaken here to understand the role and contribution of critical quality attributes that translate as predictive markers of immunogenicity and protective efficacy for clinical vaccine development. METHOD The role of prokaryotic RNA encapsulated within VLP Peanut on vaccine immunogenicity was assessed by producing a VLP Peanut batch with a reduced RNA content (VLP Peanut low RNA). Immunogenicity and peanut allergen challenge studies were conducted with VLP Peanut low RNA, as well as with VLP Peanut in WT and TLR 7 KO mice. Furthermore, mass spectrometry and SDS-PAGE based methods were used to determine Ara h 2 antigen density on the surface of VLP Peanut particles. This methodology was subsequently applied to investigate the relationship between Ara h 2 antigen density and immunogenicity of VLP Peanut. RESULTS A TLR 7 dependent formation of Ara h 2 specific high-avidity IgG antibodies, as well as a TLR 7 dependent change in the dominant IgG subclass, was observed following VLP Peanut vaccination, while total allergen-specific IgG remained relatively unaffected. Consistently, a missing TLR 7 signal caused only a weak decrease in allergen tolerability after vaccination. In contrast, a reduced RNA content for VLP Peanut resulted in diminished total Ara h 2 specific IgG responses, followed by a significant impairment in peanut allergen tolerability. The discrepant effect on allergen tolerance caused by an absent TLR 7 signal versus a reduced RNA content is explained by the observation that VLP Peanut-derived RNA not only stimulates TLR 7 but also TLR 3. Additionally, a strong correlation was observed between the number of Ara h 2 antigens displayed on the surface of VLP Peanut particles and the vaccine's immunogenicity and protective capacity. CONCLUSIONS Our findings demonstrate that prokaryotic RNA encapsulated within VLP Peanut, including antigen density of Ara h 2 on viral particles, are key contributors to the immunogenicity and protective capacity of the vaccine. Thus, antigenicity and RNA content are two critical quality attributes that need to be determined at the stage of manufacturing, providing robust information regarding the immunogenicity and protective capacity of VLP Peanut in the mouse which has translational relevance to the human setting

Estimating DNA coverage and abundance in metagenomes using a gamma approximation

Motivation: Shotgun sequencing generates large numbers of short DNA reads from either an isolated organism or, in the case of metagenomics projects, from the aggregate genome of a microbial community. These reads are then assembled based on overlapping sequences into larger, contiguous sequences (contigs). The feasibility of assembly and the coverage achieved (reads per nucleotide or distinct sequence of nucleotides) depend on several factors: the number of reads sequenced, the read length and the relative abundances of their source genomes in the microbial community. A low coverage suggests that most of the genomic DNA in the sample has not been sequenced, but it is often difficult to estimate either the extent of the uncaptured diversity or the amount of additional sequencing that would be most efficacious. In this work, we regard a metagenome as a population of DNA fragments (bins), each of which may be covered by one or more reads. We employ a gamma distribution to model this bin population due to its flexibility and ease of use. When a gamma approximation can be found that adequately fits the data, we may estimate the number of bins that were not sequenced and that could potentially be revealed by additional sequencing. We evaluated the performance of this model using simulated metagenomes and demonstrate its applicability on three recent metagenomic datasets