Hybridization and extensive mitochondrial introgression among fire salamanders in peninsular Italy

Discordance between mitochondrial and nuclear patterns of population genetic structure is providing key insights into the eco-evolutionary dynamics between and within species, and their assessment is highly relevant to biodiversity monitoring practices based on DNA barcoding approaches. Here, we investigate the population genetic structure of the fire salamander Salamandra salamandra in peninsular Italy. Both mitochondrial and nuclear markers clearly identified two main population groups. However, nuclear and mitochondrial zones of geographic transition between groups were located 600 km from one another. Recent population declines in central Italy partially erased the genetic imprints of past hybridization dynamics. However, the overall pattern of genetic variation, together with morphological and fossil data, suggest that a rampant mitochondrial introgression triggered the observed mitonuclear discordance, following a post-glacial secondary contact between lineages. Our results clearly show the major role played by reticulate evolution in shaping the structure of Salamandra salamandra populations and, together with similar findings in other regions of the species’ range, contribute to identify the fire salamander as a particularly intriguing case to investigate the complexity of mechanisms triggering patterns of mitonuclear discordance in animals

Natural hybridization and introgression between the Long-Spurred orchid, <i>Orchis longicornu</i> Poiret and the Green-Winged orchid, <i>O. morio</i> L. (Orchidaceae) in Corsica

Genetic studies have revealed in Southern Corsica, near Bonifacio, not only the existence of sporadic F1 hybrids between Orchis longicornu Poiret and O. morio L., but of a hybrid zone where both parental taxa are more or less introgressed. Our data indicate complete interfertility between the two taxa, which should therefore be considered as subspecies of the same biological species

<i>Orchis longicornu</i> Poiret in Sardinia: genetic, morphological and chorological data

Data are given on the genetic structure, morphology and chorology of the Long-Spurred orchid, Orchis longicornu Poiret (1789) from Sardinia and the occurrence in this island of the morphologically similar Orchis morio L. (1753), often recorded for Sardinia, is investigated. The genetic analysis of 27 enzyme lo ci in population samples from locations where both species had been recorded showed that: (i) in the population samples from Sardinia the polymorphic loci are in Hardy-Weinberg equilibrium; (ii) these samples are genetically poorly differentiated from each other (average Nei's D = 0.01): less than 2% of the overall genetic variation observed is attributable to differences between populations (GST = 0.015); (iii) a high rate of gene flow was estimated between Sardinian populations: Nm ≈ 4, possibly owing to seed dispersal by wind; (iv) when Sardinian samples are compared with O. morio from continental Italy, significant differences in genetic variation were observed: average He = 0.16 in the former, 0.12 in thc latter; (v) the genetic distance found between Sardinian populations and those of O. morio from continental ltaly is relatively high: average Nei's D = 0.18, average Rogers' D = 0.22; (vi) highly significant differences in allele frequencies were found at a number of loci (Mdh-2, Sod-3, Pgm-1, Gpi-1, Gpi-2) between populations from Sardinia and continental Italy, each giving a probability of correct identification that varies from 0.90 to 1 (diagnostic loci). These findings provide evidence that O. morio is not present in the material genetically analyzed from Sardinia, which includes a single species, apparently corresponding to O. longicornu. The slight heterogeneity observed at some loci in the Sardinian population samples can be attributed in some cases (e.g. Mdh-1, Adh, Est-6) to local differences, possibly adaptive; in others (e.g. Pgm-1 and Gpi-l) to genetic drift effects. The hypothesis that some alleles (Gpi-1100, Dia107, NADHdh-296) found in O. morio and recorded at low frequency in a few Sardinian populations reflect palaeointrogressive phenomena (owing to sporadical immigrant individuals of O. morio having diluted their genes in O. longicornu genome through multiple generations of backcrosses) is not sufficiently supported by the available data. The genetic data are in agreement with the results from morphological studies. These involved the examination of about 1500 specimens (both alive and dried) from all over Sardinia, and their comparison with herbarium specimens of O. longicornu from patria typica (Algeria) and of O. morio from continental Italy. The typification of O. longicornu is given. The specimens from Sardinia correspond well, on a morphological basis, to the Algerian ones and therefore were all assigned to O. longicornu. Several characters were considered, differentiating O. longicornu from O. morio both in fresh and dried specimens. However, some of them, currently used in diagnostic keys, show much overlap between the two species. This explains the quotations of O. morio from Sardinia, that appear to be misidentifications of O. longicornu. A description of O. longicornu from Sardinia is provided, and its distribution in the island is defined, on the basis of (i) a critical revision of literature rccords, and (ii) the examination of fresh and dried Sardinian specimens. O. longicornu is shown to be widespread throughout Sardinia, living in many different habitats from 0 to 1500 m a.s.l

A report on the clinical-pathological correlations of 788 gingival lesion

The diagnosis and treatment of a variety of non-plaque related gingival diseases have become an integrated aspect of everyday dentistry. The aim of this study was to analyse the relationship between clinical appearance and histopathological features of gingival lesions in a large Northern Italian population. A retrospective study of 788 cases of gingival and alveolar mucosal biopsies was set up. Statistical analysis was performed by calculating the odds ratio and 95% confidence interval (C.I.), in order to assess the degree of association between the clinical parameters considered (primary lesions) and the single pathologies, statistically evaluated by Mantel-Haenszel tests. The correlation between clinical and histological diagnosis was classified as follow: 1) expected data (ED): provisional clinical diagnosis; 2) real data (RD): final histopathology diagnosis; 3) concordant data (CD): correspondence between the expected data and real data. The correlation was calculated as follow: CC (complete concordance) = CD x 100 / ED, this expressing the percentage in which the clinical and the histological diagnosis overlapped. The most frequently observed and biopsied primary lesions resulted to be exophytic, followed by mucosal colour changes and finally by losses of substance. The statistically significant association between primary lesion and their manifestation in gingival pathologies was reported. Volume increases, for instance, were positively correlated to plasma cell epulis, pyogenic granuloma, fibrous reactive hyperplasia and hemangioma. Verrucous-papillary lesions were most often seen in verrucous carcinoma, verrucous leukoplakia and mild dysplasia. White lesion resulted to be related to leukoplakia or oral lichen planus. Red lesions resulted to be related only oral lichen planus. Erosive vesicle-bullous lesions were linked to disimmune pathologies. Ulcerative lesions were positively associated to oral squamous cell cancer. Finally, potentially malignant disorders have the most percentage high concordance. Among the malignant lesions, the correlation increased up to the squamous cell carcinoma and leukaemia. This article presented the frequency and the clinico-pathological concordance of all primary lesions and the histopathological diagnosis of gingival lesions. For every primary lesion, it is possible to correlate a specific histopathological diagnosis in a statistical manner. This can be a valuable aid for not specialist clinicians who daily observe mucosae and have the opportunity to intercept major diseases

HLA-C dysregulation as a possible mechanism of immune evasion in SARS-CoV-2 and other RNA-virus infections

One of the mechanisms by which viruses can evade the host's immune system is to modify the host's DNA methylation pattern. This work aims to investigate the DNA methylation and gene expression profile of COVID-19 patients, divided into symptomatic and asymptomatic, and healthy controls, focusing on genes involved in the immune response. In this study, changes in the methylome of COVID-19 patients' upper airways cells, the first barrier against respiratory infections and the first cells presenting viral antigens, are shown for the first time. Our results showed alterations in the methylation pattern of genes encoding proteins implicated in the response against pathogens, in particular the HLA-C gene, also important for the T-cell mediated memory response. HLA-C expression significantly decreases in COVID-19 patients, especially in those with a more severe prognosis and without other possibly confounding co-morbidities. Moreover, our bionformatic analysis revealed that the identified methylation alteration overlaps with enhancers regulating HLA-C expression, suggesting an additional mechanism exploited by SARS-CoV-2 to inhibit this fundamental player in the host's immune response. HLA-C could therefore represent both a prognostic marker and an excellent therapeutic target, also suggesting a preventive intervention that conjugate a virus-specific antigenic stimulation with an adjuvant increasing the T-cell mediated memory response

PRENOLIN project. Results of the validation phase at sendai site

One of the objectives of the PRENOLIN project is the assessment of uncertainties associated with non-linear simulation of 1D site effects. An international benchmark is underway to test several numerical codes, including various non-linear soil constitutive models, to compute the non-linear seismic site response. The preliminary verification phase (i.e. comparison between numerical codes on simple, idealistic cases) is now followed by the validation phase, which compares predictions of such numerical estimations with actual strong motion data recorded from well-known sites. The benchmark presently involves 21 teams and 21 different non-linear computations. Extensive site characterization was performed at three sites of the Japanese KiK-net and PARI networks. This paper focuses on SENDAI site. The first results indicate that a careful analysis of the data for the lab measurement is required. The linear site response is overestimated while the non-linear effects are underestimated in the first iteration. According to these observations, a first set of recommendations for defining the non-linear soil parameters from lab measurements is proposed. PRENOLIN is part of two larger projects: SINAPS@, funded by the ANR (French National Research Agency) and SIGMA, funded by a consortium of nuclear operators (EDF, CEA, AREVA, ENL)

Breakthroughs in Medicinal Chemistry: New Targets and Mechanisms, New Drugs, New Hopes-7

Breakthroughs in Medicinal Chemistry: New Targets and Mechanisms, New Drugs, New Hopes is a series of editorials which is published on a biannual basis by the Editorial Board of the Medicinal Chemistry section of the journal Molecules. In these editorials, we highlight in brief reports (of about one hundred words) a number of recently published articles that describe crucial findings, such as the discovery of novel drug targets and mechanisms of action or novel classes of drugs, which may inspire future medicinal chemistry endeavors devoted to addressing prime unmet medical needs