Ovine reference materials and assays for prion genetic testing

Background  

Genetic predisposition to scrapie in sheep is associated with several variations in the peptide sequence of the prion protein gene (PRNP). DNA-based tests for scoring PRNP codons are essential tools for eradicating scrapie and for evaluating rare alleles for increased resistance to disease. In addition to those associated with scrapie, there are dozens more PRNP polymorphisms that may occur in various flocks. If not accounted for, these sites may cause base-pair mismatching with oligonucleotides used in DNA testing. Thus, the fidelity of scrapie genetic testing is enhanced by knowing the position and frequency of PRNP polymorphisms in targeted flocks.     

Effect of a single acupuncture treatment on surgical wound healing in dogs: a randomized,single blinded,controlled pilot study

Background  

The aim of the study was to investigate the effect of acupuncture on wound healing after soft tissue or orthopaedic surgery in dogs.     

Prediction of haplotypes for ungenotyped animals and its effect on marker-assisted breeding value estimation

Background

In livestock populations, missing genotypes on a large proportion of animals are a major problem to implement the estimation of marker-assisted breeding values using haplotypes. The objective of this article is to develop a method to predict haplotypes of animals that are not genotyped using mixed model equations and to investigate the effect of using these predicted haplotypes on the accuracy of marker-assisted breeding value estimation.

Methods

For genotyped animals, haplotypes were determined and for each animal the number of haplotype copies (nhc) was counted, i.e. 0, 1 or 2 copies. In a mixed model framework, nhc for each haplotype were predicted for ungenotyped animals as well as for genotyped animals using the additive genetic relationship matrix. The heritability of nhc was assumed to be 0.99, allowing for minor genotyping and haplotyping errors. The predicted nhc were subsequently used in marker-assisted breeding value estimation by applying random regression on these covariables. To evaluate the method, a population was simulated with one additive QTL and an additive polygenic genetic effect. The QTL was located in the middle of a haplotype based on SNP-markers.

Results

The accuracy of predicted haplotype copies for ungenotyped animals ranged between 0.59 and 0.64 depending on haplotype length. Because powerful BLUP-software was used, the method was computationally very efficient. The accuracy of total EBV increased for genotyped animals when marker-assisted breeding value estimation was compared with conventional breeding value estimation, but for ungenotyped animals the increase was marginal unless the heritability was smaller than 0.1. Haplotypes based on four markers yielded the highest accuracies and when only the nearest left marker was used, it yielded the lowest accuracy. The accuracy increased with increasing marker density. Accuracy of the total EBV approached that of gene-assisted BLUP when 4-marker haplotypes were used with a distance of 0.1 cM between the markers.

Conclusions

The proposed method is computationally very efficient and suitable for marker-assisted breeding value estimation in large livestock populations including effects of a number of known QTL. Marker-assisted breeding value estimation using predicted haplotypes increases accuracy especially for traits with low heritability.     

Survival of Candida parapsilosis yeast in olive oil

Candida parapsilosis is a human opportunistic pathogen yeast isolated from different habitats like animals, man, pickled cucumber, fruit juices, and water. Recent studies have demonstrated that C. parapsilosis can survive in olive oil for very long periods even exceeding 24 months. The survival of two strains of C. parapsilosis named DAPES 1890 and 1892, previously isolated from extra virgin olive oil, was influenced by the state of hydration of the cells and the polyphenols concentration of olive oil. When the cells of the two strains of C. parapsilosis were inoculated under a liophilized form into olive oil containing 45–312 mg/kg of total polyphenols, their survival in some olive oil samples reached approximately 18 months. However, if the above-mentioned inoculum was rehydrated with 1 % of distilled water, then the survival of both yeast strains in some samples of oil exceeded 24 months. The two yeast strains, recovered from the olive oil samples after 24 months of storage, showed, under SEM, spherical shapes with and without buds according to whether the inoculum was made up of rehydrated or lyophilized cells. The survival of all the C. parapsilosis strains was also negatively influenced by the polyphenols concentration of the olive oil samples inoculated both with lyophilized and rehydrated yeast cells. In the oily habitat, the polyphenols sorption to the C. parapsilosis yeast surface was observed, and during storage the polyphenols reacted with the yeast cell walls according to their concentration in the inoculated olive oil.     

THE COMPETITIVE DEMANDS OF ELITE MALE RINK HOCKEY

The aim of this study was to simulate the activity pattern of rink hockey by designing a specific skate test (ST) to study the energy expenditure and metabolic responses to this intermittent high-intensity exercise and extrapolate the results from the test to competition. Six rink hockey players performed, in three phases, the 20-metre multi-stage shuttle roller skate test, a tournament match and the ST. Heart rate was monitored in all three phases. Blood lactate, oxygen consumption, ventilation and respiratory exchange ratio were also recorded during the ST. Peak HR was 190.7±7.2 beats · min⁻¹. There were no differences in peak HR between the three tests. Mean HR was similar between the ST and the match (86% and 87% of HR_max, respectively). Peak and mean ventilation averaged 111.0±8.8 L · min⁻¹ and 70.3±14.0 L ^· min⁻¹ (60% of V_Emax), respectively. VO_2max was 56.3±8.4 mL · kg⁻¹ · min⁻¹, and mean oxygen consumption was 40.9±7.9 mL · kg^{−1 ·} min⁻¹ (70% of VO_2max). Maximum blood lactate concentration was 7.2±1.3 mmol · L-1. ST yielded an energy expenditure of 899.1±232.9 kJ, and energy power was 59.9±15.5 kJ · min⁻¹. These findings suggest that the ST is suitable for estimating the physiological demands of competitive rink hockey, which places a heavy demand on the aerobic and anaerobic systems, and requires high energy consumption.     

Allogeneic mesenchymal stem cell infusion for the stabilization of focal segmental glomerulosclerosis

Focal segmental glomerulosclerosis (FSGS) is the most frequent acquired renal condition resulting in end stage kidney disease in children. We describe a cell therapy treatment with human allogeneic bone marrow mesenchymal stem cells (MSC) in a 13-year-old patient developing recurrent FSGS after renal transplantation, which was not responding to conventional therapy.This treatment relied on the following measurements:clinical and laboratory evaluation of renal function, proteome array, biopsy, short tandem repeat assay.Before MSC treatment, the patient needed weekly plasmapheresis to achieve proteinuria-to-creatininuria ratio below 5. After three MSC infusions without adverse events, the patient has a stable renal function and the proteinuria target was reached without plasmapheresis. In addition, some circulating inflammatory factors decreased and their levels were still low after one year.This is the first report of an MSC treatment in an FSGS patient. Even though different factors may have contributed to the clinical results, after MSC infusion a stable reduction in the serum level of several inflammatory factors has been registered and the patient does not need anymore plasmapheresis to keep proteinuria under control.In addition, this encouraging single case let us identify some putative efficacy biomarkers that could be of clinical interest in chronic kidney diseases.     

Analysis of meristic and mitochondrial DNA variation in Syngnathus abaster (Teleostea: Syngnathidae) from two western Mediterranean lagoons

Syngnathus abaster is a euryhaline pipefish distributed in the Mediterranean, Black Sea, and the north-eastern Atlantic. Although its populations are characterised by high morphological plasticity, neither congruent information about the morphological differentiation of S. abaster populations from the Mediterranean lagoons is available, nor population genetic surveys have been so far performed. In this context, the aims of our study were as follow: i) to describe the variation at nine meristic characters of S. abaster from two western Mediterranean brackish-water areas: the Tunis north lagoon (Tunisia) and the Mauguio lagoon (France); ii) to analyse sequences of four mitochondrial DNA regions in order to evaluate the occurrence of genetic variation between the two areas, if any. The morphological survey revealed a subdivision into two distinct groups: the first included the Tunisian specimens, the second the French ones. Genetic analysis evidenced the occurrence of a sharp genetic structuring with high levels of genetic differentiation between Tunisian and French S. abaster populations. Results suggest that the evolutionary forces driven by the different biogeographical and ecological conditions of the two Mediterranean brackish-water areas have boosted the morphological and genetic divergence of the populations here analysed. The scarce potential of long-distance dispersal of S. abaster may have also enhanced the divergence retrieved.     

Multimodal signals in male European treefrog (Hyla arborea) and the influence of population isolation on signal expression

In nocturnal treefrogs, mate choice implies the use of acoustic and visual signals. Multimodality is suspected to have evolved for either information redundancy or information complementariness. It is essential to explore multimodality in a natural context to understand the selection pressures operating on the signals. In the present study, we investigated calling and coloration in relation to male biometry and condition in four populations of European treefrog (Hyla arborea) varying in size and genetic isolation. We compared the signal intensity between core and satellite populations to estimate the impact of genetic diversity on male secondary sexual traits. The results obtained show important regional variations in both traits, likely as a result of local adaptations. Call and coloration are weakly correlated within an individual, implying that these traits likely convey different information about the signaller's identity or quality, thus supporting the hypothesis of complementariness of multiple messages. By contrast to the experimental evidence, we find that call and coloration are not related to male condition (as estimated by the residual of mass over size), suggesting that the condition‐dependence of these traits may be mediated by complex mechanisms not accurately reflected by the chosen estimator. Finally, male call and colour phenotypes present no robust pattern of variation with isolation status, probably because of variation in local selective pressures and in history of population dynamics. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 633–647.     

Identification of Mendelian inconsistencies between SNP and pedigree information of sibs

Background

Using SNP genotypes to apply genomic selection in breeding programs is becoming common practice. Tools to edit and check the quality of genotype data are required. Checking for Mendelian inconsistencies makes it possible to identify animals for which pedigree information and genotype information are not in agreement.

Methods

Straightforward tests to detect Mendelian inconsistencies exist that count the number of opposing homozygous marker (e.g. SNP) genotypes between parent and offspring (PAR-OFF). Here, we develop two tests to identify Mendelian inconsistencies between sibs. The first test counts SNP with opposing homozygous genotypes between sib pairs (SIBCOUNT). The second test compares pedigree and SNP-based relationships (SIBREL). All tests iteratively remove animals based on decreasing numbers of inconsistent parents and offspring or sibs. The PAR-OFF test, followed by either SIB test, was applied to a dataset comprising 2,078 genotyped cows and 211 genotyped sires. Theoretical expectations for distributions of test statistics of all three tests were calculated and compared to empirically derived values. Type I and II error rates were calculated after applying the tests to the edited data, while Mendelian inconsistencies were introduced by permuting pedigree against genotype data for various proportions of animals.

Results

Both SIB tests identified animal pairs for which pedigree and genomic relationships could be considered as inconsistent by visual inspection of a scatter plot of pairwise pedigree and SNP-based relationships. After removal of 235 animals with the PAR-OFF test, SIBCOUNT (SIBREL) identified 18 (22) additional inconsistent animals.Seventeen animals were identified by both methods. The numbers of incorrectly deleted animals (Type I error), were equally low for both methods, while the numbers of incorrectly non-deleted animals (Type II error), were considerably higher for SIBREL compared to SIBCOUNT.

Conclusions

Tests to remove Mendelian inconsistencies between sibs should be preceded by a test for parent-offspring inconsistencies. This parent-offspring test should not only consider parent-offspring pairs based on pedigree data, but also those based on SNP information. Both SIB tests could identify pairs of sibs with Mendelian inconsistencies. Based on type I and II error rates, counting opposing homozygotes between sibs (SIBCOUNT) appears slightly more precise than comparing genomic and pedigree relationships (SIBREL) to detect Mendelian inconsistencies between sibs.     

An in vitro evaluation of the effect of probiotics and prebiotics on the metabolic profile of human microbiota

In the current study, batch culture fermentations on fecal samples of 3 healthy individuals were performed to assess the effect of the addition of prebiotics (FOS), probiotics (Bifidobacterium longum Bar33 and Lactobacillus helveticus Bar13) and synbiotics (B. longum Bar33 + L. helveticus Bar13 + FOS) on the fecal metabolic profiles. A total of 84 different metabolites belonging to the families of sulfur compounds, nitrogen compounds, aldehydes, ketones, esters, alcohols, phenols, organic acids, and hydrocarbons were detected by GC-MS/SPME analysis. The highest number of metabolites varied in concentration in the models with added FOS and synbiotics, where several metabolic signatures were found in common. The increase of butyrate represented the greatest variation registered after the addition of FOS alone. Following the B. longum Bar33 addition, 2-methyl butyrate underwent the most evident variation. In the batch fermentation with added L. helveticus Bar13, the decrease of pyridine and butandiene was observed together with the increase of 2-methyl-5-ethyl-pyrazine, 2-butanone and butyrate. The modification of the fecal metabolic profiles induced by the simultaneous addition of B. longum Bar33 and L. helveticus Bar13 was very similar to that observed after the supplementation with L. helveticus Bar13, regarding mainly the decrease of pyridine and the increase of butyrate.