Comparative analysis of genomic inbreeding parameters and runs of homozygosity islands in several fancy and meat rabbit breeds

Runs of homozygosity (ROH) are defined as long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROH and their length are indicators of the level and origin of inbreeding. In this study, we analysed SNP chip datasets (obtained using the Axiom OrcunSNP Array) of a total of 702 rabbits from 12 fancy breeds and four meat breeds to identify ROH with different approaches and calculate several genomic inbreeding parameters. The highest average number of ROH per animal was detected in Belgian Hare (~150) and the lowest in Italian Silver (~106). The average length of ROH ranged from 4.001 ± 0.556 Mb in Italian White to 6.268 ± 1.355 Mb in Ermine. The same two breeds had the lowest (427.9 ± 86.4 Mb, Italian White) and the highest (921.3 ± 179.8 Mb, Ermine) average values of the sum of all ROH segments. More fancy breeds had a higher level of genomic inbreeding (as defined by ROH) than meat breeds. Several ROH islands contain genes involved in body size, body length, pigmentation processes, carcass traits, growth, and reproduction traits (e.g.: AOX1, GPX5, IFRD1, ITGB8, NELL1, NR3C1, OCA2, TRIB1, TRIB2). Genomic inbreeding parameters can be useful to overcome the lack of information in the management of rabbit genetic resources. ROH provided information to understand, to some extent, the genetic history of rabbit breeds and to identify signatures of selection in the rabbit genome

Precise tests of low energy QCD from Ke4 decay properties

We report results from the analysis of the K\ub1 \u2192 pi+ pi 12 e\ub1 \u3bd (Ke4 ) decay by the NA48/2 collaboration at the CERN SPS, based on the total statistics of 1.13 million decays collected in 2003\u20132004. The hadronic form factors in the S- and P-wave and their variation with energy are obtained. The phase difference between the S- and P-wave states of the pion pion system is accurately measured and allows a precise determination of a00 and a02 , the I = 0 and I = 2 S-wave pion pion scattering lengths: a00 = 0.2220 \ub1 0.0128stat \ub1 0.0050syst \ub1 0.0037th , a02 = 120.0432 \ub1 0.0086stat \ub1 0.0034syst \ub1 0.0028th . Combination of this result with the other NA48/2 measurement obtained in the study of K\ub1 \u2192 pi0 pi0 pi\ub1 decays brings an improved determination of a00 and the first precise experimental measurement of a02, providing a stringent test ofChiral Perturbation Theory predictions and lattice QCD calculations. Using constraints based on analyticity and chiral symmetry, even more precise values are obtained: a00 = 0.2196 \ub1 0.0028stat \ub1 0.0020syst and a02 = 120.0444 \ub10.0007stat \ub1 0.0005syst \ub1 0.0008ChPT

A measurement of the transverse polarization of Lambda-hyperons produced in inelastic pN-reactions at 450 GeV proton energy

A study of the polarization of Λ hyperons produced in inelastic pN reactions induced by the 450 GeV proton beam from the CERN SPS has been performed with the NA48 detector. The Λ hyperons were detected at a fixed angle of 4.2 mrad in the momentum range from 50 GeV/c to 200 GeV/c. The polarization changes from −0.053 ± 0.034 to −0.298 ± 0.074 for a transverse momentum range of the Λ between 0.28 GeV/c and 0.86 GeV/c. The antiΛ polarization is consistent with zero

Measurement of K0e3 form factors

The semileptonic decay of the neutral K meson, K0L → π± e∓ ν (Ke3 ), was used to study the strangeness-changing weak interaction of hadrons. A sample of 5.6 million reconstructed events recorded by the NA48 experiment was used to measure the Dalitz plot density. Admitting all possible Lorentz-covariant couplings, the form factors for vector (f+(q2)), scalar (fS) and tensor (fT) interactions were measured. The linear slope of the vector form factor λ+ = 0.0284 ± 0.0007 ± 0.0013 and values for the ratios |fS/f+(0)| = 0.015 +0.007-0.010 ± 0.012 and |fT/f+(0)| = 0.05 +0.03-0.04 ± 0.03 were obtained. The values for fS and fT are consistent with zero. Assuming only vector–axial-vector couplings, λ+ = 0.0288 ± 0.0004 ± 0.0011 and a good fit consistent with pure V–A couplings were obtained. Alternatively, a fit to a dipole form factor yields a pole mass of M = 859 ± 18 MeV, consistent with the K∗(892) mass

Measurement of the radiative Ke3 branching ratio

We present a measurement of the relative branching ratio of the decay K0 → π± e± νγ (Ke3γ) with respect to K0 → π± e± ν (Ke3 + Ke3γ ) decay. The result is based on observation of 19 000 Ke3γ and 5.6 × 10^6 Ke3 decays. The value of the branching ratio is BR(K0e3γ , E∗γ > 30 MeV, θ∗eγ > 20◦)/ Br(K0e3 ) = (0.964 ± 0.008+0.011-0.009)%. This result agrees with theoretical predictions but is at variance with a recently published result

A new measurement of direct CP violation in two pion decays of the neutral kaon

The NA48 experiment at CERN has performed a new measurement of direct CP violation, based on data taken in 1997 by simultaneously collecting KL and KS decays into pi0 pi0 and pi+ pi-. The result for the CP violating parameter Re(epsilon'/epsilon) is (18.5 +- 4.5(stat.) +- 5.8(syst.)) x 10^-4

Review of Kaon Physics at CERN and in Europe

The Kaon physics program at CERN and in Europe will be presented. I will first give a short review of recent results form the NA48/2 and NA62 experiments, with special emphasis to the measurement of RK , the ratio of Kaon leptonic decays rates, K → eν and K → μν, using the full minimum bias data sample collected in 2007-2008. The main subject of the talk will be the study of the highly suppressed decay K → πνν. While its rate can be predicted with minimal theoretical uncertainty in the Standard Model (BR ∼ 8 × 10−11), the smallness of BR and the challenging experimental signature make it very difficult to measure. The branching ratio for this decay is thus a sensitive probe of the flavour sector of the SM. The aim of NA62 is the measurement of the K → πνν BR with ∼ 10% precision in two years of data taking. This will require the observation of 10K decays in the experiment's fiducial volume, as well as the use of high-performance systems for precision tracking, particle identification, and photon vetoing. These aspects of the experiment will also allow NA62 to carry out a rich program of searches for lepton flavour and/or number violating K decays. Data taking will start in October 2014. The physics prospects and the status of the construction and commissioning of the NA62 experiment will be presented. In the last part of the talk I will report on Kaon physics results and prospects from other experiments at CERN (e.g. LHCb) and in Europe (e.g. KLOE and KLOE-2) and briefly mention the status in US

Effect of does parity order on litter homogeneity parameters

In rabbits’ reproductive performance, litter size, birth weight, growth, and mortality rate are among the most important indicators to define the productive potential and they are associated with parity order. Birth weight and little size are valuable parameters as related to mortality and weaning weight. Thus, it is important to study individual newborn and intra-litter homogeneity parameters. This trial aimed to consider the litter homogeneity weight at birth, both within each litter and in the whole population, in order to suggest new proper within-litter homogenisation parameters. In this study, the 1st and 6th parity order had, respectively, the lowest and highest values in litter size (8.96 vs 12.39, n), born-alive (8.36 vs 12.22, n), litter weight (456.4 g vs 719.8, g), born-alive weight, and quartiles’ homogeneity. These parameters decreased in greater parity orders. No significant effects on still-born numbers and mortality rates were evidenced. All these litter homogeneity evaluation parameters appeared interesting in describing differences between parity orders. The results confirmed that does parity order influences litter size and born-alive weight, but also the intra- and inter-litter homogenisation. Litter homogenisation is crucial to ensure a proportionate share of milk, more equal growth, and better productive performances. Based on these results, we suggest for the commercial genetic centres to equalise the litters according to the birth weight, by dividing the population into quartiles and rearing kits with light birth weight in smaller litters and those with heavier birth weight in larger litters.HIGHLIGHTS Does parity order influences litter size and born-alive weight Kit’s quartiles distribution is a useful tool for equalisation practic

Sex-Specific Transcriptome Differences in Substantia Nigra Tissue: A Meta-Analysis of Parkinson’s Disease Data

Parkinson’s disease (PD) is one of the most common progressive neurodegenerative diseases. Clinical and epidemiological studies indicate that sex differences, as well as genetic components and ageing, can influence the prevalence, age at onset and symptomatology of PD. This study undertook a systematic meta-analysis of substantia nigra microarray data using the Transcriptome Mapper (TRAM) software to integrate and normalize a total of 10 suitable datasets from multiple sources. Four different analyses were performed according to default parameters, to better define the segments differentially expressed between PD patients and healthy controls, when comparing men and women data sets. The results suggest a possible regulation of specific sex-biased systems in PD susceptibility. TRAM software allowed us to highlight the different activation of some genomic regions and loci involved in molecular pathways related to neurodegeneration and neuroinflammatory mechanisms

Meta-Analysis of Parkinson's Disease Transcriptome Data Using TRAM Software: Whole Substantia Nigra Tissue and Single Dopamine Neuron Differential Gene Expression

<div><p>The understanding of the genetic basis of the Parkinson's disease (PD) and the correlation between genotype and phenotype has revolutionized our knowledge about the pathogenetic mechanisms of neurodegeneration, opening up exciting new therapeutic and neuroprotective perspectives. Genomic knowledge of PD is still in its early stages and can provide a good start for studies of the molecular mechanisms that underlie the gene expression variations and the epigenetic mechanisms that may contribute to the complex and characteristic phenotype of PD. In this study we used the software TRAM (Transcriptome Mapper) to analyse publicly available microarray data of a total of 151 PD patients and 130 healthy controls substantia nigra (SN) samples, to identify chromosomal segments and gene loci differential expression. In particular, we separately analyzed PD patients and controls data from post-mortem snap-frozen SN whole tissue and from laser microdissected midbrain dopamine (DA) neurons, to better characterize the specific DA neuronal expression profile associated with the late-stage Parkinson's condition. The default "Map" mode analysis resulted in 10 significantly over/under-expressed segments, mapping on 8 different chromosomes for SN whole tissue and in 4 segments mapping on 4 different chromosomes for DA neurons. In conclusion, TRAM software allowed us to confirm the deregulation of some genomic regions and loci involved in key molecular pathways related to neurodegeneration, as well as to provide new insights about genes and non-coding RNA transcripts not yet associated with the disease.</p></div