First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus):a collaborative approach

Additional file 8: Table S7. Allelic patterns in 2000–2010 (pop1 - pre-arctos) and 2011–2017 (pop2 - arctos & post arctos). Na number of different alleles, Na Freq. ≥5% number of alleles with a frequency ≥ 5%, Ne number of effective alleles, I Shannon Information Index, No. Private Alleles number of private alleles, Ho observed heterozygosity and He expected heterozygosity

Dysregulation of oncogenic factors by GFI1B p32: investigation of a novel GFI1B germline mutation

GFI1B is a transcription factor essential for the regulation of erythropoiesis and megakaryopoiesis, and pathogenic variants have been associated with thrombocytopenia and bleeding. Analysing thrombocytopenic families by whole exome sequencing, we identified a novel GFI1B variant (c.648+5G>A), which causes exon 9 skipping and overexpression of a shorter p32 isoform. We report the clinical data of our patients and critically review the phenotype observed in individuals with different GFI1B variants leading to the same effect on the p32 expression. Since p32 is increased in acute and chronic leukemia cells, we tested the expression level of genes playing a role in various type of cancers, including hematological tumors and found that they are significantly dysregulated, suggesting a potential role for GFI1B in carcinogenesis regulation. Increasing the number of individuals with GFI1B variants will allow us to better characterize this rare disease and determine whether it is associated with an increased risk of developing malignancies

Performance of SNP markers for parentage analysis in the Italian Alpine brown bear using non-invasive samples

Determination of parentage provides valuable information for the conservation of wild populations, for instance, by allowing the monitoring of breeding success and inbreeding. Between 1999 and 2002, nine brown bears (Ursus arctos) were translocated to augment the remnant population of a few surviving individuals in the Italian Alps, but only part of them reproduced, with a higher inbreeding risk occurrence in the long-time. Currently, in the Alpine population, parentage tests are assessed through the analysis of 15 microsatellite loci (STRs), but the reduction of genetic variability in future generations will need the use of additional informative markers. Single nucleotide polymorphisms (SNPs) have been proven to be useful and reliable in individual identification and family reconstruction; moreover, they can perform well on low-quality samples. In this study, we analysed 51 SNPs to generate a SNP multilocus genotype dataset of 54 Alpine brown bears (Ursus arctos) and compared its performance in parentage analysis with the validated STR dataset. We found that SNPs alone are not sufficient to determine parentage relationships, but the combination of SNPs and STRs provided unambiguous parentage assignments. The combined panel also performed better than STRs when true parents were not present in the dataset and, consequently, showed higher values of assignment probabilities

Real time contrast enhanced ultrasonography in detection of liver metastases from gastrointestinal cancer

Background: Contrast enhanced ultrasound (CEUS) is an imaging technique which appeared on the market around the year 2000 and proposed for the detection of liver metastases in gastrointestinal cancer patients, a setting in which accurate staging plays a significant role in the choice of treatment. Methods: A total of 109 patients with colorectal (n = 92)or gastric cancer prospectively underwent computed tomography (CT) scan and conventional US evaluation followed by real time CEUS. A diagnosis of metastases was made by CT or, for lesions not visibile at CT, the diagnosis was achieved by histopathology or by a malignant behavior during follow-up. Results: Of 109 patients, 65 were found to have metastases at presentation. CEUS improved sensitivity in metastatic livers from 76.9% of patients (US) to 95.4% (p < 0.01), while CT scan reached 90.8% (p = n.s. vs CEUS, p < 0.01 vs US). CEUS and CT were more sensitive than US also for detection of single lesions (87 with US, 122 with CEUS, 113 with CT). In 15 patients (13.8%), CEUS revealed more metastases than CT, while CT revealed more metastases than CEUS in 9 patients (8.2%) (p = n.s.). Conclusion: CEUS is more sensitive than conventional US in the detection of liver metastases and could be usefully employed in the staging of patients with gastrointestinal cancer. Findings at CEUS and CT appear to be complementary in achieving maximum sensitivity. © 2007 Piscaglia et al; licensee BioMed Central Ltd

Challenging the loss of genetic variability in Italian brown bears (Ursus arctos) - A genome-wide approach

The first part of this PhD thesis is devoted to the application of molecular genetics to describe demographic trends, geographic distribution patterns and genetic status of the Alpine population 15 years after the reintroduction program. In order to achieve the first objective we a) increased the number of STR markers (from 10 to 15 loci) in the Alpine population to raise the informativity content for population genetics studies, and possibly resolve uncertain parentage assignments; b) presented an annual overview of the demographic status of the Alpine population for a long-term monitoring program; c) measured the genetic diversity over generations, highlighting possible trends d) identified parentage relationships and provided a pedigree reconstruction, showing if there is an increase of inbreeding events over generations; e) estimated the effective population size; f) verified whether or not a connection between the reintroduced population in the central Alps and the Dinaric population was established. We furthermore provided considerations for conservation and management of this species in the Alps, taking into account the emerged demographic, spatial and genetic aspects. The second part is methodological and is about developing a new set of SNP markers to enhance the resolution power for population genetics analysis of the Alpine and Apennine populations. In order to identify reliable and informative SNPs we a) tested the effectiveness of an existing SNP panel, developed for the Scandinavian brown bear populations, on the two Italian brown bear subspecies, identifying a set of SNPs that has potential for a SNP-based individual and sex identification system. I took into consideration the ascertainment bias that arises when transferring SNP markers across populations; and b) tested the selected subset of SNPs for parentage assignments in the Alpine population, comparing its resolution power with that derived from STRs

Testing a new SNP-chip on the Alpine and Apennine brown bear (Ursus arctos) populations using non-invasive samples

Brown bears in Italy persist in two isolated populations, one in the Alpine and the other in the Apennine mountain range. Both are threatened and elusive. Non-invasive genetics provides a good way to monitor the populations. Microsatellites (STRs) have been the marker of choice for non-invasive genetic monitoring, but due to non-invasive bad quality samples, these analyses were plagued by low amplification rates and genotyping errors. Moreover, to compare microsatellite genotypes, allele calibration is needed between laboratories, leading to difficulties in individual identification. In contrast, SNP genotyping is directly comparable between laboratories, and more sensitive and accurate. Here we test a 96-marker SNP chip developed for the Scandinavian brown bear population on the Italian populations. A subset of these SNPs was found informative and could reliable confirm species, sex and, only in the Alpine population, distinguish individuals. A total of 51 informative SNPs provided better resolution power than 15 STRs, used in the routine monitoring of the Alpine population in Italy. In contrast, only 15 SNPs were found to be informative for the Apennine population, which did not have enough resolution to discriminate individuals and were less informative than 11 STRs. While highly useful in the Alpine population, additional SNP markers must be included to reach the same level of resolution in the Apennine population

Cross-Amplification in Strigiformes: A New STR Panel for Forensic Purposes

Strigiformes are affected by a substantial decline mainly caused by habitat loss and destruction, poaching, and trapping. Moreover, the increasing trend in bird trade and the growing interest in wild-caught rather than captive-bred birds are expected to encourage illegal trade. The biomolecular investigation represents a valuable tool to track illegal trade and to explore the genetic variability to preserving biodiversity. Microsatellite loci (STRs) are the most used markers to study genetic variability. Despite the availability of species-specific microsatellite loci in Strigiformes, a unique panel permitting the description of the genetic variability across species has not been identified yet. We tested 32 highly polymorphic microsatellite markers to evaluate the reliability of a unique microsatellite panel in different species of Strigiformes and its use for conservation and forensic purposes. We included in the study 84 individuals belonging to 28 parental groups and 11 species of Strigiformes. After screening polymorphic microsatellite loci, the description of genetic variability, and the kinship assessment, we characterized a final panel of 12 microsatellite loci able to identify individuals in 9 Strigiformes species. This STR panel might support the authorities in the forensic investigation for suspected smugglers and false parental claims; moreover, it can be useful to evaluate relatedness among individuals in captive-bred populations and to implement research projects finalized to the description of the genetic variability in wild populations

A new form of inherited thrombocytopenia due to monoallelic loss of function mutation in the thrombopoietin gene

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A new form of inherited thrombocytopenia due to monoallelic loss of function mutation in the thrombopoietin gene

Thrombopoietin (THPO) is an essential regulator of haemopoiesis that is required for the maintenance of haemopoietic progenitors and their differentiation into megakaryocytes (Mks). Moreover, it modulates the events that drive Mk maturation and allows the release of platelets into bone marrow sinusoids. THPO plays these roles by binding the MPL receptor, which is expressed in bone marrow stem cells, Mks, platelets and many other human cells. Until recently, no inherited THPO defect was known to cause thrombocytopenia or bone marrow aplasia. However, it was recently shown that microdeletions encompassing the THPO gene in chromosome 3 result in a complex clinical picture, including mild congenital thrombocytopenia. Moreover, a Micronesian family carrying the homozygous c.112C>T (p.Arg38Cys or p.Arg17Cys in the mature protein) missense mutation in THPO presents inherited bone marrow aplasia. No THPO mutation associated with isolated thrombocytopenia has been reported to date, but the application of whole exome sequencing (WES) in a cohort of patients with inherited thrombocytopenias (ITs) of unknown origin revealed that monoallelic changes in this gene identify a new form of IT. In fact, WES identified two unrelated individuals carrying the heterozygous variant c.91C>T (p. Arg31*), which is expected to result in mutant protein degradation and THPO haploinsufficiency