GoPrime: development of an in silico framework to predict the performance of real-time PCR primers and probes using foot-and-mouth disease virus as a model

Real-time PCR (rPCR) is a widely accepted diagnostic tool for the detection and quantification of nucleic acid targets. In order for these assays to achieve high sensitivity and specificity, primer and probe-template complementarity is essential; however, mismatches are often unavoidable and can result in false-negative results and errors in quantifying target sequences. Primer and probe sequences therefore require continual evaluation to ensure they remain fit for purpose. This paper describes the development of a linear model and associated computational tool (GoPrime) designed to predict the performance of rPCR primers and probes across multiple sequence data. Empirical data were generated using DNA oligonucleotides (n = 90) that systematically introduced variation in the primer and probe target regions of a diagnostic assay routinely used to detect foot-and-mouth disease virus (FMDV); an animal virus that exhibits a high degree of sequence variability. These assays revealed consistent impacts of patterns of substitutions in primer and probe-sites on rPCR cycle threshold (CT) and limit of detection (LOD). These data were used to populate GoPrime, which was subsequently used to predict rPCR results for DNA templates (n = 7) representing the natural sequence variability within FMDV. GoPrime was also applicable to other areas of the FMDV genome, with predictions for the likely targets of a FMDV-typing assay consistent with published experimental data. Although further work is required to improve these tools, including assessing the impact of primer-template mismatches in the reverse transcription step and the broader impact of mismatches for other assays, these data support the use of mathematical models for rapidly predicting the performance of rPCR primers and probes in silico

Illuminating spindle convex bodies and minimizing the volume of spherical sets of constant width

A subset of the d-dimensional Euclidean space having nonempty interior is called a spindle convex body if it is the intersection of (finitely or infinitely many) congruent d-dimensional closed balls. The spindle convex body is called a "fat" one, if it contains the centers of its generating balls. The core part of this paper is an extension of Schramm's theorem and its proof on illuminating convex bodies of constant width to the family of "fat" spindle convex bodies.Comment: 17 page

Replacement of soya bean meal with peas and faba beans in growing/finishing pig diets: effect on performance, carcass composition and nutrient excretion

There is now an increasing debate about the viability of using temperate-grown legumes in pig diets as a potential replacement for imported soya bean meal (SBM) and this is due to food security, sustainability and environmental concerns. Two trials were designed to examine nitrogen (N) retention, growth performance and carcass quality of grower and finisher pigs when fed nutritionally balanced SBM-free diets formulated to contain peas or faba beans at 300 g/kg, compared to an SBM-containing, pulse-free control diet. Trial 1 evaluated N digestibility/retention in four iso-energetic diets, comparing the SBM control with one diet formulated with peas and two with faba bean cultivars; a tannin-containing and a tannin-free variety. This trial employed a four by four Latin Square design with four male pigs housed in metabolism crates, fed twice daily at 0.9 of assumed ad libitum intake over four time periods during grower (30–55 kg) and finisher (55–95 kg) phases. Quantitative faecal and urine collection allowed determination of N coefficient of total tract apparent digestibility, coefficient of apparent metabolisability, and N balance. Results revealed that dietary treatment did not affect these N parameters (P > 0.05) during either the grower or finisher phase. Trial 2 evaluated growth performance (feed intake, daily live weight gain and feed conversion ratio) and carcass quality parameters. Five diets (based on SBM, peas and one of three faba bean cultivars) balanced for standard ileal digestible amino acids and net energy were each fed to eight replicates of individually housed entire male pigs over the same growth phases as Trial 1. The inclusion of three faba bean varieties allowed comparison of animal responses between tannin/tannin-free and spring vs. winter bean cultivars. At ∼95 kg, pigs were slaughtered and a comprehensive range of carcass measurements undertaken. Samples of shoulder backfat were also taken at slaughter to determine skatole and indole concentrations. As with N balance, feeding treatment did not affect performance data. Carcass parameters revealed pigs fed with the pea-based diet had a greater dressing percentage than those animals on faba bean-based diets. Pigs fed with the SBM or pea-based diets also had greater lean meat percentages than those on faba-bean diets. Mean skatole concentrations for all pigs were below the accepted maximum threshold level of 0.2 μg/g. In conclusion, it is suggested that peas and faba beans can be successfully fed in balanced pig diets throughout the grower/finisher periods as alternatives to SBM

Alzheimer’s disease cerebrospinal fluid biomarkers are not influenced by gravity drip or aspiration extraction methodology

Introduction: Cerebrospinal fluid (CSF) biomarkers, although of established utility in the diagnostic evaluation of Alzheimer's disease (AD), are known to be sensitive to variation based on pre-analytical sample processing. We assessed whether gravity droplet collection versus syringe aspiration was another factor influencing CSF biomarker analyte concentrations and reproducibility. Methods: Standardized lumbar puncture using small calibre atraumatic spinal needles and CSF collection using gravity fed collection followed by syringe aspirated extraction was performed in a sample of elderly individuals participating in a large long-term observational research trial. Analyte assay concentrations were compared. Results: For the 44 total paired samples of gravity collection and aspiration, reproducibility was high for biomarker CSF analyte assay concentrations (concordance correlation [95%CI]: beta-amyloid1-42 (Aβ42) 0.83 [0.71 - 0.90]), t-tau 0.99 [0.98 - 0.99], and phosphorylated tau (p-tau) 0.82 [95 % CI 0.71 - 0.89]) and Bonferroni corrected paired sample t-tests showed no significant differences (group means (SD): Aβ42 366.5 (86.8) vs 354.3 (82.6), p = 0.10; t-tau 83.9 (46.6) vs 84.7 (47.4) p = 0.49; p-tau 43.5 (22.8) vs 40.0 (17.7), p = 0.05). The mean duration of collection was 10.9 minutes for gravity collection and <1 minute for aspiration. Conclusions: Our results demonstrate that aspiration of CSF is comparable to gravity droplet collection for AD biomarker analyses but could considerably accelerate throughput and improve the procedural tolerability for assessment of CSF biomarkers

Composition of bird nests is a species-specific characteristic

Bird nests represent an extended phenotype of individuals expressed during reproduction and so exhibit variability in composition, structure and function. Descriptions of nests based on qualitative observations suggest that there is interspecific variation in size and composition but there are very few species in which this has been confirmed. For these species, data of the amounts of different materials indicate that nest construction behaviour is plastic and affected by a variety of factors, such as prevailing temperature, geographic location, and availability of materials. The lack of data on nest composition is hampering our understanding of how nests achieve their various functions and how different species solve the problem of building a nest that will accommodate incubation and allow successful hatching of eggs. This study deconstructed nests of four species of the Turdidae, four species of the Muscicapidae, and six species of the Fringillidae and quantified the size of the nests and their composition. These data were used to test: (1) whether nest size correlated with adult bird mass; (2) whether it was possible to distinguish between species on the basis of their nest composition; and (3) whether, within a species, it was possible to distinguish between the cup lining and the rest of the nest based on composition. Most but not all nest dimensions correlated with bird mass. Principal component analysis revealed species differences based on nest composition and discriminant analysis could distinguish cup lining from the outer nest based on material composition. Intraspecific variation in composition varied among species and in general fewer types of material were found in the cup lining than the outer nest. These data provide insight into how nests are constructed by the different species and in conjunction with studies of the mechanical, thermal and hydrological properties of a nest, will begin to reveal how and why individual species select particular combinations of materials to build a nest

Defining the relative performance of isothermal assays that can be used for rapid and sensitive detection of foot-and-mouth disease virus

This study describes the first multiway comparison of portable isothermal assays for the detection of foot-and-mouth disease virus (FMDV), benchmarked against real-time reverse transcription RT-PCR (rRT-PCR). The selected isothermal chemistries included reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA). The analytical sensitivity of RT-LAMP was comparable to rRT-PCR (101 RNA copies), while RT-RPA was one log10 less sensitive (102 RNA copies). Diagnostic performance was evaluated using a panel of 35 samples from FMDV-positive cattle and eight samples from cattle infected with other vesicular viruses. Assay concordance for RT-LAMP and RT-RPA was 86?98% and 67?77%, respectively, when compared to rRT-PCR, with discordant samples consistently having high rRT-PCR cycle threshold values (no false-positives were detected for any assay). In addition, a hierarchy of sample preparation methods, from robotic extraction to simple dilution of samples, for epithelial suspensions, serum and oesophageal-pharyngeal (OP) fluid were evaluated. Results obtained for RT-LAMP confirmed that FMDV RNA can be detected in the absence of RNA extraction. However, simple sample preparation methods were less encouraging for RT-RPA, with accurate results only obtained when using RNA extraction. Although the evaluation of assay performance is specific to the conditions tested in this study, the compatibility of RT-LAMP chemistry with multiple sample types, both in the presence and absence of nucleic acid extraction, provides advantages over alternative isothermal chemistries and alternative pen-side diagnostics such as antigen-detection lateral-flow devices. These characteristics of RT-LAMP enable the assay to be performed over a large diagnostic detection window, providing a realistic means to rapidly confirm positive FMD cases close to the point of sampling

Glasgow’s Floating Estuarine Wetlands Baseline Monitoring Report

No abstract available

Glasgow’s Floating Estuarine Wetlands Long-Term Ecosystem Services and Function Monitoring and Evaluation Plan

No abstract available

Psychology and aggression

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68264/2/10.1177_002200275900300301.pd