Genome-wide analysis of hybridization in wild boar populations reveals adaptive introgression from domestic pig.

The admixture of domestic pig into French wild boar populations has been monitored since the 1980s thanks to the existence of a cytogenetic difference between the two sub-species. The number of chromosomes is 2n = 36 in wild boar and 2n = 38 in pig, respectively. This difference makes it possible to assign the "hybrid" status to wild boar individuals controlled with 37 or 38 chromosomes. However, it does not make it possible to determine the timing of the hybridization(s), nor to guarantee the absence of domestic admixture in an animal with 2n = 36 chromosomes. In order to analyze hybridization in greater detail and to avoid the inherent limitations of the cytogenetic approach, 362 wild boars (WB) recently collected in different French geographical areas and in different environments (farms, free ranging in protected or unprotected areas, animals with 2n = 36, 37 or 38 chromosomes) were genotyped on a 70K SNP chip. Principal component analyses allowed the identification of 13 "outliers" (3.6%), for which the proportion of the genome of "domestic" origin was greater than 40% (Admixture analyses). These animals were probably recent hybrids, having Asian domestic pig ancestry for most of them. For the remaining 349 animals studied, the proportion of the genome of "wild" origin varied between 83% and 100% (median: 94%). This proportion varied significantly depending on how the wild boar populations were managed. Local ancestry analyses revealed adaptive introgression from domestic pig, suggesting a critical role of genetic admixture in improving the fitness and population growth of WB. Overall, our results show that the methods used to monitor the domestic genetic contributions to wild boar populations should evolve in order to limit the level of admixture between the two gene pools.

Genotyping data of French wild boar populations using porcine genome-wide genotyping array.

OBJECTIVE: The admixture of domestic pig into wild boar populations is controlled until now, by cytogenetic analysis. Even if a first-generation hybrid animal is discernable because of its 37-chromosome karyotype, the cytogenetic method is not applicable in the case of advanced intercrosses. The aim of this study is therefore to evaluate the use of SNP (Single Nucleotide Polymorphism) markers as an alternative technology to characterize recent or past hybridization between the two sub-species. The final goal would be to develop a molecular diagnostic tool. DATA DESCRIPTION: The Geneseek Genomic Profiler High-Density porcine beadchip (GGP70KHD, Illumina, USA), comprising 68,516 porcine SNPs, was used on a set of 362 wild boars with diverse chromosomal statuses collected from different areas and breeding environments in France. We generated approximately 62,192-64,046 genotypes per wild boar. The present dataset might be useful for the community (i) for developing molecular tools to evaluate the admixture of domestic pig into wild boar populations, and (ii) for genetic diversity studies including wild boar species or phylogeny analyses of Suidae populations. Raw data files and a processed matrix data file were deposited in the ArrayExpress at European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) data portal under accession number E-MTAB-10591.

Water Uptake in Epoxy Ionic Liquid Free Film Polymer by Gravimetric Analysis and Comparison with Nondestructive Dielectric Analysis.

Due to their high surface coverage, good adhesion to metal surfaces, and their excellent corrosion resistance, epoxy thermosets are widely used as protective coatings. However, anticorrosion protection of these coatings can be improved against water uptake and can be tuned by changing the chemical nature of the curing agents. In this work, a comparative study has been performed on the water uptake of an epoxy-amine based on bisphenol A diglycidyl ether (DGEBA) cured with an aliphatic amine and the same epoxy initiated with a phosphonium ionic liquid (IL). Thus, the epoxy networks were immersed in saline water solution in a controlled temperature environment. Gravimetric and electric impedance measurements were carried out for a maximum of 3 months. Results were analyzed in order to assess the water diffusion coefficients and water saturation limits. Two models, the Brasher-Kingsbury and a novel mixing rule, were applied on permittivity values. Results highlighted that epoxy-ionic liquid systems are less sensitive to water uptake than conventional epoxy-amine networks. Due to their higher hydrophobic properties the water diffusion coefficient of epoxy-ionic liquid systems are two times less compared to epoxy-amine samples and the water saturation limit is more than four times less. The analysis also shows that the novel mixing rule model proposed here is prone to better estimate the water uptake with accuracy from electrical impedance measurements.

Meiotic Silencing in Pigs: A Case Study in a Translocated Azoospermic Boar.

Carriers of balanced constitutional reciprocal translocations usually present a normal phenotype, but often show reproductive disorders. For the first time in pigs, we analyzed the meiotic process of an autosome-autosome translocation associated with azoospermia. Meiotic process analysis revealed the presence of unpaired autosomal segments with histone γH2AX accumulation sometimes associated with the XY body. Additionally, γH2AX signals were observed on apparently synapsed autosomes other than the SSC1 or SSC15, as previously observed in Ataxia with oculomotor apraxia type 2 patients or knock-out mice for the Senataxin gene. Gene expression showed a downregulation of genes selected on chromosomes 1 and 15, but no upregulation of SSCX genes. We hypothesized that the total meiotic arrest observed in this boar might be due to the silencing of crucial autosomal genes by the mechanism referred to as meiotic silencing of unsynapsed chromatin (MSUC).

Routine Karyotyping Reveals Frequent Mosaic Reciprocal Chromosome Translocations in Swine: Prevalence, Pedigree, and Litter Size.

In the routine commercial karyotype analysis on 5,481 boars, we identified 32 carriers of mosaic reciprocal translocations, half of which were carrying a specific recurrent translocation, mos t(7;9). An additional 7 mosaic translocations were identified through lymphocyte karyotype analysis from parents and relatives of mosaic carriers (n = 45), a control group of non-carrier boars (n = 73), and a mitogen assessment study (n = 20), bringing the total number of mosaic carriers to 39 cases. Mosaic translocations in all carriers were recognized to be confined to hematopoietic cells as no translocations were identified in fibroblasts cells of the carriers. In addition, negative impact on reproduction was not observed as the fertility of the carriers and their relatives were comparable to breed averages, and cryptic mosaicism was not detected in the family tree. This paper presents the first study of mosaic reciprocal translocations identified in swine through routine screening practices on reproductively unproven breeding boars while presenting evidence that these type of chromosome abnormalities are not associated with any affected phenotype on the carrier animals. In addition, the detection of recurrent mosaic translocations in this study may emphasize the non-random nature of mosaic rearrangements in swine and the potential role of genomic elements in their formation.

Clinical evaluation of a dose management system-integrated 3D skin dose map by comparison with radiochromic films.

OBJECTIVES: To validate the performance of an automatic tool to estimate a patient's peak skin dose (PSD) and a skin dose map from data collected by a radiation dose management system (RDMS) during interventional procedures. METHODS: In total, 288 eligible consecutive patients undergoing abdominopelvic embolisation or planned coronary angioplasty using radiochromic films were screened between June 2018 and March 2019. For 98 included patients, PSD was measured using radiochromic films (PSDFilm) and computed by RDMS (PSDRDMS) using one flat and two anthropomorphic phantoms. Statistical concordance between PSDFilm and PSDRDMS was computed with Lin's concordance correlation coefficient and clinical concordance with the Bland and Altman graphic; values were compared using the paired Mann-Whitney-Wilcoxon test. RESULTS: In total, 190/288 patients were excluded and 98 patients were analysed (69 men, mean age 66 ± 14 years). The PSDFilm median (1st; 3rd quartile) was 0.59 Gy (0.40; 1.08). PSDRDMS was 0.62 Gy (0.43; 1.22) for the flat phantom and 0.62 Gy (0.42; 1.19) for anthropomorphic phantoms. The concordance between PSDFilm and PSDRDMS was good for both phantoms (flat: 0.94 [0.91; 0.95]; anthropomorphic 0.94 [0.91; 0.96]). Compared with the values of PSDFilm, the values of PSDRDMS were significantly increased by 5% (- 4%; 16%) for flat phantom (p = 0.001) and 7% (- 6%; 22%) for anthropomorphic phantoms (p = 0.002) for vascular procedures and 9% (- 4%; 26%, p = 0.01) and 6% (- 4%; 23%, p = 0.02) for cardiac procedures, respectively. Dose map representations matched for most patients. The gaps identified were due to table displacement during fluoroscopy events and the use of a wedge filter. CONCLUSIONS: The RDMS skin dose map tool allowed the computation of the PSD and skin dose distribution for all patients with fewer constraints than radiochromic films. However, the computed PSD was overestimated, increasing the number of patients requiring follow-up. KEY POINTS: • A good concordance correlation was identified between the peak skin dose (PSD) values measured with radiochromic films and estimated with the radiation dose management system (RDMS) skin dose map tool. • Differences were related to table displacement during fluoroscopy events and the use of a wedge filter, which are not accounted in the Digital Imaging and Communications in Medicine Radiation Dose Structured Reports. • For all procedures, the estimated PSDs were significantly higher than the measured PSDs by 5% (- 4%; 18%) for flat phantom (p < 0.001) and 6% (- 5%; 22%) for anthropomorphic phantoms (p < 0.001).

Experimental evaluation of a radiation dose management system-integrated 3D skin dose map by comparison with XR-RV3 Gafchromic® films.

OBJECTIVE: To assess the interactive Skin Dose Map® tool (SDMTool) integrated to the radiation dose management system (RDMS) DoseWatch® with Gafchromic® films for implementation in routine practice. METHODS: A retrospective dose estimation software SDMTool was used to calculate Peak Skin Dose (PSD) and display the patient skin dose distribution. PSD was calculated with a triangle mesh of 0.055 cm2 resolution on ICRP 110 male anthropomorphic phantom and with a square ROI of 1 cm2 on flat phantom. The tool uses Radiation Dose Structured Reports (RDSR) data to model exposure events and calculate the PSD per event. The PSD and the skin dose distribution estimated with SDMTool were evaluated in comparison with Gafchromic® films positioned under the PMMA phantom (20 cm) for 13 configurations. Measurements were performed on a Philips system. Statistical analysis were carried out to compare PSDFilm and PSDSDM. RESULTS: Average differences between PSDFilm and PSDSDM were 6% ±â€¯6% (range from -3% to 22%) for flat phantom and 5% ±â€¯7% (range from -3% to 25%) for ICRP phantom. Concordance was good between the measured PSDFilm and the estimated PSDSDM with Lin's coefficient estimation and 95% Confidence Interval of 0.979 [0.875; 0.984] for flat phantom and 0.977 [0.877; 0.985] for ICRP phantom. Dose map representations are concordant for 11 of the 13 tests on PMMA phantom. Disparities arose from the limitations of the RSDR format: table displacement during fluoroscopy events and the use of wedge filter. CONCLUSION: The results found in this experimental evaluation show that the SDMTool is a suitable alternative to Gafchromic® film to calculate PSD.

Analysis of Meiotic Segregation Pattern and Interchromosomal Effects in a Bull Heterozygous for a 3/16 Robertsonian Translocation.

Robertsonian translocations are the most frequent chromosomal rearrangements detected in cattle. Here, we report on the detection of a new Robertsonian translocation between chromosomes BTA3 and BTA16. This rob(3;16) was dicentric, suggesting that its occurrence was recent. FISH analysis of decondensed sperm nuclei revealed a relatively low rate of unbalanced gametes produced by adjacent segregation (5.87%). In addition, and for the first time in bovines, a significant interchromosomal effect (ICE) was detected for 2 different autosomes: BTA17 (global disomy + nullisomy rate of 9%) and BTA20 (1.8%). These results suggest that ICE should be taken into consideration when assessing the putative effect of Robertsonian translocations on reproduction.

Meiotic Synapsis and Gene Expression Altered by a Balanced Y-Autosome Reciprocal Translocation in an Azoospermic Pig.

Meiotic sex chromosome silencing (MSCS) has been argued as a prerequisite for normal meiotic cell division progression during the synaptic prophase I stage. Furthermore, irregular asynapsis of autosomal axes at meiosis may be encompassing the lack of transcriptional activity normally observed for the X and Y sex chromosomes. Therefore, any chromosomal rearrangement compromising the normal mechanism of MSCS and/or the contrary, the normal meiotic transcriptional activity of autosomal chromosomes, may be observed as a meiotic and concomitant spermatogenesis arrest. Previously, we have described a Y-autosome translocation t(Y;13)(p1.3;q3.3) in an azoospermic boar. Its chromosome synapsis behavior by synaptonemal complex immunostaining and FISH analyses is documented here. Histone γH2AX protein foci appeared to be located at unsynapsed chromosomal segments (e.g., X chromosome univalents or unpaired multivalent segments), although interestingly a high proportion of primary spermatocytes showed full paired synaptonemal complex-multivalent configurations which were devoid of a γH2AX focus signal, indicating meiotic chromosome silencing. RT-qPCR analysis of testicular expression showed downregulation of 3 SSC13 genes (MLH1, SOX2, UBE2B) and upregulation of SSCY genes (ZFY, SRY). The irregularity of the normal transcription pattern in case of these genes with proven roles in the testis is in agreement with the cytological observations and could contribute to the observed phenotype.

Intraindividual Variation of Meiotic Recombination Parameters in Pig Spermatocytes: A Preliminary Study.

Meiotic recombination parameters like crossover (CO) rate or synaptonemal complex (SC) length are known to vary strongly between individuals and between cells from the same individual. The origins of this variability remain elusive, and little is known about the variations that might occur between different samples and/or over time within the same individual. To document this question, pachytene cells from 3 boars of the Large White breed were analyzed twice, at a 1-year interval, using immunocytological techniques. CO rate, SC length, and MLH1 inter-foci distances varied significantly between the 3 individuals. CO rate and SC length differed significantly between the 2 sampling periods for 1 individual. However, no significant differences were observed between the 2 samples for CO distribution and inter-foci distances in the 3 boars studied.

Meiotic pairing and gene expression disturbance in germ cells from an infertile boar with a balanced reciprocal autosome-autosome translocation.

Individuals carrying balanced constitutional reciprocal translocations generally have a normal phenotype, but often present reproductive disorders. The aim of our research was to analyze the meiotic process in an oligoasthenoteratospermic boar carrying an asymmetric reciprocal translocation involving chromosomes 1 and 14. Different multivalent structures (quadrivalent and trivalent plus univalent) were identified during chromosome pairing analysis. Some of these multivalents were characterized by the presence of unpaired autosomal segments with histone γH2AX accumulation sometimes associated with the XY body. Gene expression in spermatocytes was studied by RNA-DNA-FISH and microarray-based testis transcriptome analysis. Our results revealed a decrease in gene expression for chromosomes 1 and 14 and an up-regulated expression of X-chromosome genes for the translocated boar compared with normal individuals. We hypothesized that the observed meiotic arrest and reproductive failure in this boar might be due to silencing of crucial autosomal genes (MSUC) and disturbance of meiotic sex chromosome inactivation (MSCI). Further analysis revealed abnormal meiotic recombination (frequency and distribution) and the production of a high rate of unbalanced spermatozoa.

Meiotic Recombination Analyses in Pigs Carrying Different Balanced Structural Chromosomal Rearrangements.

Correct pairing, synapsis and recombination between homologous chromosomes are essential for normal meiosis. All these events are strongly regulated, and our knowledge of the mechanisms involved in this regulation is increasing rapidly. Chromosomal rearrangements are known to disturb these processes. In the present paper, synapsis and recombination (number and distribution of MLH1 foci) were studied in three boars (Sus scrofa domestica) carrying different chromosomal rearrangements. One (T34he) was heterozygote for the t(3;4)(p1.3;q1.5) reciprocal translocation, one (T34ho) was homozygote for that translocation, while the third (T34Inv) was heterozygote for both the translocation and a pericentric inversion inv(4)(p1.4;q2.3). All three boars were normal for synapsis and sperm production. This particular situation allowed us to rigorously study the impact of rearrangements on recombination. Overall, the rearrangements induced only minor modifications of the number of MLH1 foci (per spermatocyte or per chromosome) and of the length of synaptonemal complexes for chromosomes 3 and 4. The distribution of MLH1 foci in T34he was comparable to that of the controls. Conversely, the distributions of MLH1 foci on chromosome 4 were strongly modified in boar T34Inv (lack of crossover in the heterosynaptic region of the quadrivalent, and crossover displaced to the chromosome extremities), and also in boar T34ho (two recombination peaks on the q-arms compared with one of higher magnitude in the controls). Analyses of boars T34he and T34Inv showed that the interference was propagated through the breakpoints. A different result was obtained for boar T34ho, in which the breakpoints (transition between SSC3 and SSC4 chromatin on the bivalents) seemed to alter the transmission of the interference signal. Our results suggest that the number of crossovers and crossover interference could be regulated by partially different mechanisms.

Soft chemical control of superconductivity in lithium iron selenide hydroxides Li(1-x)Fe(x)(OH)Fe(1-y)Se.

Hydrothermal synthesis is described of layered lithium iron selenide hydroxides Li(1-x)Fe(x)(OH)Fe(1-y)Se (x ∼ 0.2; 0.02 < y < 0.15) with a wide range of iron site vacancy concentrations in the iron selenide layers. This iron vacancy concentration is revealed as the only significant compositional variable and as the key parameter controlling the crystal structure and the electronic properties. Single crystal X-ray diffraction, neutron powder diffraction, and X-ray absorption spectroscopy measurements are used to demonstrate that superconductivity at temperatures as high as 40 K is observed in the hydrothermally synthesized samples when the iron vacancy concentration is low (y < 0.05) and when the iron oxidation state is reduced slightly below +2, while samples with a higher vacancy concentration and a correspondingly higher iron oxidation state are not superconducting. The importance of combining a low iron oxidation state with a low vacancy concentration in the iron selenide layers is emphasized by the demonstration that reductive postsynthetic lithiation of the samples turns on superconductivity with critical temperatures exceeding 40 K by displacing iron atoms from the Li(1-x)Fe(x)(OH) reservoir layer to fill vacancies in the selenide layer.

Meiotic recombination analyses of individual chromosomes in male domestic pigs (Sus scrofa domestica).

For the first time in the domestic pig, meiotic recombination along the 18 porcine autosomes was directly studied by immunolocalization of MLH1 protein. In total, 7,848 synaptonemal complexes from 436 spermatocytes were analyzed, and 13,969 recombination sites were mapped. Individual chromosomes for 113 of the 436 cells (representing 2,034 synaptonemal complexes) were identified by immunostaining and fluorescence in situ hybridization (FISH). The average total length of autosomal synaptonemal complexes per cell was 190.3 µm, with 32.0 recombination sites (crossovers), on average, per cell. The number of crossovers and the lengths of the autosomal synaptonemal complexes showed significant intra- (i.e. between cells) and inter-individual variations. The distributions of recombination sites within each chromosomal category were similar: crossovers in metacentric and submetacentric chromosomes were concentrated in the telomeric regions of the p- and q-arms, whereas two hotspots were located near the centromere and in the telomeric region of acrocentrics. Lack of MLH1 foci was mainly observed in the smaller chromosomes, particularly chromosome 18 (SSC18) and the sex chromosomes. All autosomes displayed positive interference, with a large variability between the chromosomes.

γ-Al2O3 nanoparticles synthesised by pulsed laser ablation in liquids: a plasma analysis.

Pulsed laser ablation has proved its reliability for the synthesis of nano-particles and nano-structured materials, including metastable phases and complex stoichiometries. The possible nucleation of the nanoparticles in the gas phase and their growth has been little investigated, due to the difficulty of following the gas composition as well as the thermodynamic parameters. We show that such information can be obtained from the optically active plasma during its short lifetime, only a few microseconds for each laser pulse, as a result of a quick quenching due to the liquid environment. For this purpose, we follow the laser ablation of an α-Al2O3 target (corindon) in water, which leads to the synthesis of nanoparticles of γ-Al2O3. The AlO blue-green emission and the Al(I) (2)P(0)-(2)S doublet emission provide the electron density, the density ratio between the Al atoms and AlO molecules, and the rotational and vibrational temperatures of the AlO molecules. These diagnostic considerations are discussed in the framework of theoretical studies from the literature (density functional theory). We have found that starting from a hot atomized gas, the nucleation cannot occur in the first microseconds. We also raise the question of the influence of water on the control of the stoichiometry.

Cytogenetic analysis of somatic and germinal cells from 38,XX/38,XY phenotypically normal boars.

Many chromosomal abnormalities have been reported to date in pigs. Most of them have been balanced structural rearrangements, especially reciprocal translocations. A few cases of XY/XX chimerism have also been diagnosed within the national systematic chromosomal control program of young purebred boars carried out in France. Until now, this kind of chromosomal abnormality has been mainly reported in intersex individuals. We investigated 38,XY/38,XX boars presenting apparently normal phenotypes to evaluate the potential effects of this particular chromosomal constitution on their reproductive performance. To do this, we analyzed (1) the chromosomal constitution of cells from different organs in one boar; (2) the aneuploidy rates for chromosomes X, Y, and 13 in sperm nuclei sampled from seven XY/XX boars. 2n = 38,XX cells were identified in different nonhematopoietic tissues including testis (frequency, <8%). Similar aneuploidy rates were observed in the sperm nuclei of XY/XX and normal individuals (controls). Altogether, these results suggest that the presence of XX cells had no or only a very limited effect on the reproduction abilities of the analyzed boars.

Studies of male and female meiosis in inv(4)(p1.4;q2.3) pig carriers.

Inversions are well-known structural chromosomal rearrangements in humans and pigs. Such rearrangements generally have no effect on the carrier's phenotype. However, the presence of an inversion may impair spermatogenesis and lead to the production of recombinant gametes, responsible for early miscarriages, stillbirth, or congenital abnormalities. This is the first report on meiotic segregation and pairing behavior of the inv(4)(p1.4;q2.3) pericentric inversion in pigs. Despite the very large size of the inverted fragment (76% of the chromosome), SpermFISH results showed that only 4.08% of the gametes produced by male heterozygotes were unbalanced. This low proportion could be explained by the particular behavior of normal and inverted SSC4 chromosomes during the initial stages of meiosis. Indeed, immunohistochemistry analyses revealed that heterosynapsis occurred in 92% of the cells, whereas synaptic adjustment was detected in a few spermatocytes only. Unexpectedly, the proportion of unbalanced gametes produced by female heterozygotes, estimated by FISH on metaphase II oocytes, was also very low (3.69%) and comparable to that in males. According to previous results for male and female meiotic processes, different proportions of recombinant gametes in the two genders would have been expected. Complementary studies should be carried out to further document the meiotic behavior of inversions in pigs.

Chromosomal control of pig populations in France: 2002-2006 survey.

The chromosomal control of pig populations has been widely developed in France over the last ten years. By December 31st, 2006, 13,765 individuals had been karyotyped in our laboratory, 62% of these since 2002. Ninety percent were young purebred boars controlled before service in artificial insemination centres, and 3% were hypoprolific boars. So far, 102 constitutional structural chromosomal rearrangements (67 since 2002) have been described. Fifty-six were reciprocal translocations and 8 peri- or paracentric inversions. For the first time since the beginning of the programme and after more than 11,000 pigs had been karyotyped, one Robertsonian translocation was identified in 2005 and two others in 2006. The estimated prevalence of balanced structural chromosomal rearrangements in a sample of more than 7,700 young boars controlled before service was 0.47%. Twenty-one of the 67 rearrangements described since 2002 were identified in hypoprolific boars. All were reciprocal translocations. Twelve mosaics (XX/XY in 11 individuals, XY/XXY in one individual) were also diagnosed. Two corresponded to hypoprolific boars, and three to intersexed animals. The results presented in this communication would justify an intensification of the chromosomal control of French and, on a broader scale, European and North-American pig populations.