Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds.

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states.

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30-35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.

Signatures of de-domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution.

Autochthonous pig breeds are usually reared in extensive or semi-extensive production systems that might facilitate contact with wild boars and, thus, reciprocal genetic exchanges. In this study, we analysed variants in the melanocortin 1 receptor (MC1R) gene (which cause different coat colour phenotypes) and in the nuclear receptor subfamily 6 group A member 1 (NR6A1) gene (associated with increased vertebral number) in 712 pigs of 12 local pig breeds raised in Italy (Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano and Sarda) and south-eastern European countries (Krskopolje from Slovenia, Black Slavonian and Turopolje from Croatia, Mangalitsa and Moravka from Serbia and East Balkan Swine from Bulgaria) and compared the data with the genetic variability at these loci investigated in 229 wild boars from populations spread in the same macro-geographic areas. None of the autochthonous pig breeds or wild boar populations were fixed for one allele at both loci. Domestic and wild-type alleles at these two genes were present in both domestic and wild populations. Findings of the distribution of MC1R alleles might be useful for tracing back the complex genetic history of autochthonous breeds. Altogether, these results indirectly demonstrate that bidirectional introgression of wild and domestic alleles is derived and affected by the human and naturally driven evolutionary forces that are shaping the Sus scrofa genome: autochthonous breeds are experiencing a sort of 'de-domestication' process, and wild resources are challenged by a 'domestication' drift. Both need to be further investigated and managed.

Ligulate inflorescence of Helianthus × multiflorus, cv. Soleil d'Or, correlates with a mis-regulation of a CYCLOIDEA gene characterised by insertion of a transposable element.

Members of CYCLOIDEA (CYC)/TEOSINTE BRANCHED1 (TB1) transcription factor family are essential to control flower symmetry and inflorescence architecture. In the Helianthus annuus genome, ten CYC/TB1 genes have been identified. Studies performed on mutants recognised HaCYC2c as one of the key players controlling zygomorphism in sunflower. We identified CYC2c genes in the diploid Helianthus decapetalus (HdCYC2c) and in the interspecific hybrid Helianthus × multiflorus (H × mCYC2cA and H × mCYC2cB), a triploid (2n = 3× = 51), originated from unreduced eggs of H. decapetalus fertilised by reduced H. annuus male gametes. Phylogenetic analysis showed that HdCYC2c and H × mCYC2c were placed within a CYC2 subclade together with HaCYC2c but distinct from it. The present data showed that in H. × multiflorus the allele derived from H. annuus is deleted or highly modified. The H. × multiflorus taxon exists as radiate and ligulate inflorescence types. We analysed CYC2c expression in H. decapetalus and in the cultivar 'Soleil d'Or' of H. × multiflorus, a ligulate inflorescence type with actinomorphic corolla of disk flowers transformed into a zygomorphic ray-like corolla. In H. decapetalus, the HdCYC2c gene showed differential expression between developing flower types, being up-regulated in the corolla of ray flowers in comparison to the disk flower corolla. In H. × multiflorus, an insertion of 865 bp, which is part of a CACTA transposable element, was found in the 5'-untranslated region (5'-UTR) of H × mCYC2cB. This insertion could promote, even with epigenetic mechanisms, ectopic expression of the gene throughout the inflorescence, resulting in the observed loss of actinomorphy and originating a ligulate head.

Genome-wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds.

Italy counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north-south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sardinian breeds diverged more from other breeds, a probable consequence of the combined effect of ancient sporadic introgression of feral mouflon and long-lasting genetic isolation from continental sheep populations. The study allowed the detection of previously undocumented episodes of recent introgression (Delle Langhe into the endangered Altamurana breed) as well as signatures of known, or claimed, historical introgression (Merino into Sopravissana and Gentile di Puglia; Bergamasca into Fabrianese, Appenninica and, to a lesser extent, Leccese). Arguments that would question, from a genomic point of view, the current breed classification of Bergamasca and Biellese into two separate breeds are presented. Finally, a role for traditional transhumance practices in shaping the genetic makeup of Alpine sheep breeds is proposed. The study represents the first exhaustive analysis of Italian sheep diversity in an European context, and it bridges the gap in the previous HapMap panel between Western Mediterranean and Swiss breeds.

First results on angular distributions of thermal dileptons in nuclear collisions.

The NA60 experiment at the CERN Super Proton Synchrotron has studied dimuon production in 158A GeV In-In collisions. The strong excess of pairs above the known sources found in the complete mass region 0.2

Four novel mutations of the coproporphyrinogen III oxidase gene.

Here we report the characterization of four novel mutations and a previously described one of the coproporphyrinogen III oxidase (CPO) gene in five Italian patients affected by Hereditary Coproporphyria (HCP). Three of the novel genetic variants are missense mutations (p.Gly242Cys; p.Leu398Pro; p.Ser245Phe) and one is a frameshift mutation (p.Gly188TrpfsX45).

Evidence for radial flow of thermal dileptons in high-energy nuclear collisions.

The NA60 experiment at the CERN SPS has studied low-mass dimuon production in 158A GeV In-In collisions. An excess of pairs above the known meson decays has been reported before. We now present precision results on the associated transverse momentum spectra. The slope parameter Teff extracted from the spectra rises with dimuon mass up to the rho, followed by a sudden decline above. While the initial rise is consistent with the expectations for radial flow of a hadronic decay source, the decline signals a transition to an emission source with much smaller flow. This may well represent the first direct evidence for thermal radiation of partonic origin in nuclear collisions.

J/psi production in Indium-Indium collisions at 158 GeV/nucleon.

The NA60 experiment studies muon pair production at the CERN Super Proton Synchrotron. In this Letter we report on a precision measurement of J/psi in In-In collisions. We have studied the J/psi centrality distribution, and we have compared it with the one expected if absorption in cold nuclear matter were the only active suppression mechanism. For collisions involving more than approximately 80 participant nucleons, we find that an extra suppression is present. This result is in qualitative agreement with previous Pb-Pb measurements by the NA50 experiment, but no theoretical explanation is presently able to coherently describe both results.

First measurement of the rho spectral function in high-energy nuclear collisions.

We report on a precision measurement of low-mass muon pairs in 158 AGeV indium-indium collisions at the CERN SPS. A significant excess of pairs is observed above the yield expected from neutral meson decays. The unprecedented sample size of 360,000 dimuons and the good mass resolution of about 2% allow us to isolate the excess by subtraction of the decay sources. The shape of the resulting mass spectrum is consistent with a dominant contribution from pi+pi- -->rho -->mu+mu- annihilation. The associated space-time averaged spectral function shows a strong broadening, but essentially no shift in mass. This may rule out theoretical models linking hadron masses directly to the chiral condensate.

Serum antibodies to capsular polysaccharide vaccine of group A and C Neisseria meningitidis in military recruits in Italy.

In this study we evaluated, by a standard bactericidal assay, the antibody response to the meningococcal group A and C polysaccharide vaccine used for the immunization programme of the Italian military recruits, compulsory by law since 1987. The percentage of responders, those who developed a four-fold increase in the bactericidal titre to polysaccharide A and C, was 96% and 98%, respectively. No significant side effects were observed after vaccination.

Meningococcal carriage and vaccination in army recruits in Italy.

The effect of Neisseria meningitidis group A and C polysaccharide vaccine on nasopharyngeal carriage was studied in the training center for army medical officers in Florence. Nasopharyngeal swabs were cultured for N. meningitidis at the time of vaccination (one week after entry to service) and again seven weeks later in a follow-up cohort of 171 men. During the two surveys the overall carriage did not showed significant difference (respectively 16% and 12%); while the percentage of isolates belonging to the serogroup C showed a significant reduction from 6% to 0.6% (P less than 0.01). No increased prevalence of meningococci belonging serogroups other than A or C was observed during the two surveys. The cumulative carriage was 20%. Out of the 35 carriers during the whole study period, only 5 (14%) belonged to the same serogroup. These findings show that meningococcal vaccine may inhibit the nasopharyngeal carriage of group specific meningococci in army recruits.

[Urinary microbial load evaluation: comparison of an agar-colony count method and a colorimetric method]. / Valutazione della carica microbica urinaria: confronto tra metodo della conta in agar e metodo colorimetrico.

The quantity of bacteria of 500 urocultures was analyzed in the Laboratory of Clinical Pathology of the "Regina Elena" Institute of Rome (Italy). These evaluations were carried out both by the classic agar colony-count method (CC) and by a new colorimetric system (Dye test, Dt), recently introduced on the market. Using the CC system, 142 (28.6%) positive and 358 (71.8%) negative samples were found, considering the usual 100,000 CFU/ml to be the limit. The results of the colorimetric test were read on a graduated scale of red color. By means of a concordance analysis, a correct relationship between the color grade and the positivity of the samples was established. For this equivalence a more intense color than that suggested by the manufacturer was found. Furthermore an 89.7% rate of concordant and a 10.2% of discordant results were observed. These latter may be divided into two fractions: the first (4.6%) was Dt-positive and CC-negative (these samples are characterized by the presence of residual antibiotics in 78.3% of the cases); the second fraction (5.6%) was Dt-negative and CC-positive (characterized by a 67.9% of Pseudomonas sp. isolation frequency).