Population structure in the Mediterranean basin: a Y chromosome perspective

The Mediterranean region has been characterised by a number of pre-historical and historical demographic events whose legacy on the current genetic landscape is still a matter of debate. In order to investigate the degree of population structure across the Mediterranean, we have investigated Y chromosome variation in a large dataset of Mediterranean populations, 11 of which are first described here. Our analyses identify four main clusters in the Mediterranean that can be labelled as North Africa, Arab, Central-East and West Mediterranean. In particular, Near Eastern samples tend to separate according to the presence of Arab Y chromosome lineages, suggesting that the Arab expansion played a major role in shaping the current genetic structuring within the Fertile Crescent.

Y-chromosomal STR haplotypes in Sicily

Eight Y-chromosomal short tandem repeats (STRs)-DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393 and DYS385-were typed in a population sample (n=255) of unrelated Sicilian males from nine different towns on the main island and from the island of Pantelleria.

[Torture survivor asylum seekers in Italy: the experience of the humanitarian association "Doctors Against Torture"]

In recent years, the arrival in Italy of people who suffered torture in their countries led a group of volunteer doctors to set up a humanitarian association, "Doctors Against Torture", to provide care and treatment for torture survivors present in Rome. The paper describes the characteristics of 354 persons having at least one access from 1-1-1999 to 31-12-2001. About 51% of the victims came from the Middle East, 43% from Africa. Mean age was 29.6 (SD 7.0). The victims have suffered beatings and other forms of blunt trauma (64%), suspension and other positional torture (14%), psychological violence (28%), inhuman conditions of detention (10%), burns/electric shock (21%), wet asphyxiation and water jets (11%), sexual violence (15%), amputation/penetrating injuries (22%), dental torture and traumatic removal of nails (6%) and 58% suffered more than one type of torture. The types of violence observed require a thorough analysis of our knowledge in the field, in order to help victims on their way to rehabilitation, which is long and uncertain; at the same time, it is fundamental that public health begins to make itself responsible for these persons.

Pulmonary artery leiomyosarcoma with thyroid metastases

Primary pulmonary artery sarcomas are uncommon and usually fatal tumours. The diagnosis of these tumours is delayed in most cases as they are mistaken for pulmonary thromboembolism. We present a fatal case of a woman referred to us five months after a primary diagnosis of pulmonary thromboembolism, due to an increase in dyspnea and presence of hemoptysis despite having undergone anticoagulant treatment. On the basis of the findings obtained by computed tomography, echocardiogram and MRI, a mass arising from the pulmonary trunk was evidenced, that suggested other diagnostic hypotheses. The worsening of patient's conditions did not allow an endovascular catheter biopsy and diagnosis was made at autopsy. The mass was a leiomyosarcoma of the pulmonary artery with thyroid metastases, which is an uncommon findings.

Autosomal microsatellite and mtDNA genetic analysis in Sicily (Italy)

DNA samples from 465 blood donors living in 7 towns of Sicily, the largest island of Italy, have been collected according to well defined criteria, and their genetic heterogeneity tested on the basis of 9 autosomal microsatellite and mitochondrial DNA polymorphisms for a total of 85 microsatellite allele and 10 mtDNA haplogroup frequencies. A preliminary account of the results shows that: a) the samples are genetically heterogeneous; b) the first principal coordinates of the samples are correlated more with their longitude than with their latitude, and this result is even more remarkable when one outlier sample (Butera) is not considered; c) distances among samples calculated from allele and haplogroup frequencies and from the isonymy matrix are weakly correlated (r = 0.43, P = 0.06) but such correlation disappears (r = 0.16) if the mtDNA haplogroups alone are taken into account; d) mtDNA haplogroups and microsatellite distances suggest settlements of people occurred at different times: divergence times inferred from microsatellite data seem to describe a genetic composition of the town of Sciacca mainly derived from settlements after the Roman conquest of Sicily (First Punic war, 246 BC), while all other divergence times take root from the second to the first millennium BC, and therefore seem to backdate to the pre-Hellenistic period. A more reliable association of these diachronic genetic strata to different historical populations (e.g. Sicani, Elymi, Siculi), if possible, must be postponed to the analysis of more samples and hopefully more informative uniparental DNA markers such as the recently available DHPLC-SNP polymorphisms of the Y chromosome.

Genetic heterogeneity in five Italian regions: analysis of PAH mutations and minihaplotypes

Molecular analysis of 289 chromosomes has been performed in a cohort of phenylketonuria (PKU) patients whose ancestors lived in five Italian regions, Calabria, Campania, Piemonte, Puglia/Basilicata and Sicilia. Phenylalaninehydroxylase (PAH) gene mutations and minihaplotypes (combinations of PAH gene STR and VNTR systems) have been determined for 78.5 and 64%, respectively, of the chromosomes studied. 21 different minihaplotypes and 24 PKU mutations were found. Heterogeneity tests carried out for the frequencies of mutations and minihaplotypes show that the distribution of eight mutations and four minihaplotypes is statistically heterogeneous in the five Italian regions. Although the evolutionary rate of microsatellites or the age of these mutations is difficult to estimate with accuracy, our findings taken together show a genetic stratification of the Italian population. These results rule out allelic homogeneity of PKU at the molecular level between regions of Italy, yet minihaplotype data may be of practical use for a multistep approach to PAH gene genotyping.

PAH gene mutations in the Sicilian population: association with minihaplotypes and expression analysis

The molecular basis of PAH deficiency in the Sicilian population is characterized by a marked heterogeneity, with 44 mutations at a single locus identified by a "gene-scanning" approach and accounting for a detection rate of 91%. The remaining 9% of PAH alleles does not bear mutations in any of the 13 exons and 24 exon/intron junctions. Three mutations IVS10nt-11 G > A, R261Q, and A300S accounted for 30.5%, whereas the remaining mutations were found at relative frequencies of less than 5% and 20 mutations were observed once only. Five mutations have been detected only in Sicilians so far. By studying the association of mutations with intragenic STR-VNTR haplotypes ("minihaplotypes"), "identity by descent" has been established for 24 mutations also detected in other populations. This finding supports the hypothesis of a multipolar origin for a large proportion of PAH mutant alleles currently detected in Sicilians. In order to improve our understanding of the clinical heterogeneity of PAH deficiency in this population, we have for the first time analyzed three missense mutations L41F, T92I, and P211T in vitro by the pCDNA3/COS-7 eukaryotic expression system and found an activity of 10, 76, and 72%, respectively, compared to normal PAH. In two HPA patients with mild PKU and mild hyperphenylalaninemia (MHP), harboring respectively L41F/R261Q and T92I/P281L genotypes, the predicted biochemical effect of these genotypes appeared to be consistent with the metabolic phenotypes. In contrast, discordant metabolic phenotypes (mild PKU and MHP) were observed in two unrelated patients bearing the same R261Q/P211T genotype, a finding which underscores the complex relationship linking genotype to phenotype in PAH deficiency. Hypotheses on the possible mechanisms responsible for the observed discordance are discussed. The spectrum of PAH gene mutations in Sicily reflects the complex demographic history of this island at the crossroad of prehistoric and historical migrations in the Mediterranean sea. The data presented in this study also add to the present knowledge on the relationship between PAH genotypes and HPA phenotype and are expected to improve PAH genotyping among individuals with hyperphenylalaninemia.

Human Y-chromosome variation in the western Mediterranean area: implications for the peopling of the region

Y-chromosome variation was analyzed in a sample of 1127 males from the Western Mediterranean area by surveying 16 biallelic and 4 multiallelic sites. Some populations from Northeastern Europe and the Middle East were also studied for comparison. All Y-chromosome haplotypes were included in a parsimonious genealogic tree consisting of 17 haplogroups, several of which displayed distinct geographic specificities. One of the haplogroups, HG9.2, has some features that are compatible with a spread into Europe from the Near East during the Neolithic period. However, the current distribution of this haplogroup would suggest that the Neolithic gene pool had a major impact in the eastern and central part of the Mediterranean basin, but very limited consequences in Iberia and Northwestern Europe. Two other haplogroups, HG25.2 and HG2.2, were found to have much more restricted geographic distributions. The first most likely originated in the Berbers within the last few thousand years, and allows the detection of gene flow to Iberia and Southern Europe. The latter haplogroup is common only in Sardinia, which confirms the genetic peculiarity and isolation of the Sardinians. Overall, this study demonstrates that the dissection of Y-chromosome variation into haplogroups with a more restricted geographic distribution can reveal important differences even between populations that live at short distances, and provides new clues to their past interactions.

Molecular evidence of Bartonella spp. in questing adult Ixodes pacificus ticks in California

Ticks are the vectors of many zoonotic diseases in the United States, including Lyme disease, human monocytic and granulocytic ehrlichioses, and Rocky Mountain spotted fever. Most known Bartonella species are arthropod borne. Therefore, it is important to determine if some Bartonella species, which are emerging pathogens, could be carried or transmitted by ticks. In this study, adult Ixodes pacificus ticks were collected by flagging vegetation in three sites in Santa Clara County, Calif. PCR-restriction fragment length polymorphism and partial sequencing of 273 bp of the gltA gene were applied for Bartonella identification. Twenty-nine (19.2%) of 151 individually tested ticks were PCR positive for Bartonella. Male ticks were more likely to be infected with Bartonella than female ticks (26 versus 12%, P = 0.05). None of the nine ticks collected at Baird Ranch was PCR positive for Bartonella. However, 7 (50%) of 14 ticks from Red Fern Ranch and 22 (17%) of 128 ticks from the Windy Hill Open Space Reserve were infected with Bartonella. In these infected ticks, molecular analysis showed a variety of Bartonella strains, which were closely related to a cattle Bartonella strain and to several known human-pathogenic Bartonella species and subspecies: Bartonella henselae, B. quintana, B. washoensis, and B. vinsonii subsp. berkhoffii. These findings indicate that I. pacificus ticks may play an important role in Bartonella transmission among animals and humans.

MtDNA control region and RFLP data for Sicily and France

The forensic application of mtDNA typing requires large databases which are regionally well defined. To further this aim, we have typed mtDNA in a sample of 111 French and 106 Sicilians. The French were typed for both hypervariable segments (HVR1 and HVR2) of the mtDNA control region, whereas the Sicilians were only typed for HVR1, but in addition for the coding region RFLP markers for mtDNA groups H, I, J, K, L, M, T, U, V and X. In both samples, the predominant sequence type by far was the Cambridge reference sequence. Comparing HVR1 sequences, we found that the French sample was twice as diverse as the Sicilian sample as measured by sequence matches. A further set of sequence match comparisons including the French, Sicilian, and the published British mtDNA samples, demonstrate that sequence matching probabilities within samples differ by less than a factor of 2 from the matching probabilities between samples.

Relation between growth dynamics and diffusional limitations in Saccharomyces cerevisiae cells growing as entrapped in an insolubilised gelatin gel

Flow-cytometric analysis was employed to investigate growth dynamics of a yeast cell population immobilised in an insolubilised gelatin gel by means of the quantitative determination of the average protein content per cell. This analysis was carried out on both the immobilised cell population considered as a whole and the subpopulations colonising the gelatin matrix at different depths. The results show that growth of the gelatin-immobilised yeast population was affected by the existence of a gradient of nutrient concentrations through the matrix and are in agreement with the unsteady-state diffusion model employed for the description of glucose transfer in the gel.

A methodological strategy for PAH genotyping in populations with a marked molecular heterogeneity of hyperphenylalaninemia

The elucidation of the molecular basis of hyperphenylalaninemia in various world populations (PKU Consortium Database: http://www.mcgill/ca/pahdb/) has revealed a remarkable molecular heterogeneity at the locus encoding for phenylalanine hydroxylase. As a consequence, genotyping of HPA patients has prompted the establishment of an impressive number of mutatIon detection protocols. In spite of the large variety of methods proposed so far, no comprehensive strategy has been yet developed for the detection of PAH gene mutations. Therefore, new approaches, combining the advantages of individual methods are required, especially in populations with a high number of PAH gene mutations. In this study, we propose the use of Reverse Dot Blot Analysis within a general mutation protocol to simplify the genotyping of hyperphenylalaninemics in the very heterogeneous population of Sicily (Italy).

Patterns of male-specific inter-population divergence in Europe, West Asia and North Africa

We typed 1801 males from 55 locations for the Y-specific binary markers YAP, DYZ3, SRY10831 and the (CA)n microsatellites YCAII and DYS413. Phylogenetic relationships of chromosomes with the same binary haplotype were condensed in seven large one-step networks, which accounted for 95% of all chromosomes. Their coalescence ages were estimated based on microsatellite diversity. The three largest and oldest networks undergo sharp frequency changes in three areas. The more recent network 3.1A clearly discriminates between Western and Eastern European populations. Pairwise Fst showed an overall increment with increasing geographic distance but with a slope greatly reduced when compared to previous reports. By sectioning the entire data set according to geographic and linguistic criteria, we found higher Fst-on-distance slopes within Europe than in West Asia or across the two continents.

Eight new mutations of the phenylalanine hydroxylase gene in Italian patients with hyperphenylalaninemia

This report identifies eight new mutations of the phenylalanine hydroxylase gene detected in Italian patients with hyperphenylalaninemia. The trivial name of the mutations, predicted phenotypic effect, and population of origin (Italian region) are as follows: F55L (nonconservative change: classic, moderate, mild PKU ?; Sicily), IVS2nt-13 (splicing defect, classic PKU; Tuscany), I65N (nonconservative change classic, moderate, mild PKU ?; Sicily), H201Y (non-PKU HPA; Sicily), I269L (non-PKU HPA, or polymorphism; Sicily), IVS7nt3 (splicing defect or polymorphism; Sicily), I283N (classic PKU; Sicily), IVS12nt2 (splicing defect, classic PKU; Sicily and Apulia). In Sicily, the relative frequency of mutations F55L, I65N, H201Y, I269L, IVS7nt3, I283N, IVS12nt2 is < 1%. The seven new mutations identified in the Sicilian population increase the remarkable genetic heterogeneity typical of this population with an estimated homozygosity value at the PAH locus of 0.041.

Dramatic brain aminergic deficit in a genetic mouse model of phenylketonuria

Clinical data suggest that brain catecholamines and serotonin are deficient in phenylketonuria (PKU), an inherited metabolic disorder that causes severe mental retardation and neurological disturbances. To test this hypothesis, brain tissue levels of dopamine (DA), norepinephrine (NE), 5-hydroxytryptamine (5-HT) and their metabolites were evaluated in the genetic mouse model of PKU (Pah(enu2)). Results indicated a significant reduction of 5-HT levels and metabolism in prefrontal cortex (pFC), cingulate cortex (Cg), nucleus accumbens (NAc), caudate putamen (CP), hippocampus (HIP) and amygdala (AMY). NE content and metabolism were reduced in pFC, Cg, AMY and HIP. Finally, significantly reduced DA content and metabolism was observed in pFC, NAc, CP and AMY. In pFC, NAc and CP there was also a marked reduction of DA release.

Bloodstream infections can develop late (after day 100) and/or in the absence of neutropenia in children receiving allogeneic bone marrow transplantation

We retrospectively evaluated the incidence and time from transplantation of bloodstream infections occurring in children receiving bone marrow transplant (BMT) at G Gaslini Children's Hospital between September 1984 and December 1997. During this period the incidence was 35% after allogeneic and 26% after autologous BMT (P=0.08). Among these episodes, 38% after allogeneic BMT and 90% after autologous BMT were detected in the presence of neutropenia within the first 30 days from reinfusion (P < 0.001). Incidence of catheter-related bloodstream infections was 40% after allogeneic and 8% after autologous BMT (P < 0.001). Bloodstream infections in the absence of neutropenia were 55% after allogeneic BMT vs 10% after autologous BMT (P < 0.001) and occurred later after reinfusion (mean 199 vs 41 days, P <0.001). Among the episodes occurring after allogeneic BMT and in the absence of neutropenia, 61% were related to the presence of a central venous catheter, 15% were related to the presence of GVHD, but 23% were not associated with any of major risk factors for infection. Finally, 38% of episodes following allogeneic BMT were detected after day 100 vs 1% after autologous BMT. We concluded that patients receiving allogeneic BMT experience a high incidence of bloodstream infections in the absence of neutropenia and that a significant proportion of these episodes is not clearly associated with well known risk factors such as GVHD or central venous catheters. Moreover, many episodes develop a long time after the transplantation procedure. Therefore, any febrile episode following allogeneic BMT even late and/or in the absence of neutropenia should be intensively managed.

A European multicenter study of phenylalanine hydroxylase deficiency: classification of 105 mutations and a general system for genotype-based prediction of metabolic phenotype

Phenylketonuria (PKU) and mild hyperphenylalaninemia (MHP) are allelic disorders caused by mutations in the gene encoding phenylalanine hydroxylase (PAH). Previous studies have suggested that the highly variable metabolic phenotypes of PAH deficiency correlate with PAH genotypes. We identified both causative mutations in 686 patients from seven European centers. On the basis of the phenotypic characteristics of 297 functionally hemizygous patients, 105 of the mutations were assigned to one of four arbitrary phenotype categories. We proposed and tested a simple model for correlation between genotype and phenotypic outcome. The observed phenotype matched the predicted phenotype in 79% of the cases, and in only 5 of 184 patients was the observed phenotype more than one category away from that expected. Among the seven contributing centers, the proportion of patients for whom the observed phenotype did not match the predicted phenotype was 4%-23% (P<.0001), suggesting that differences in methods used for mutation detection or phenotype classification may account for a considerable proportion of genotype-phenotype inconsistencies. Our data indicate that the PAH-mutation genotype is the main determinant of metabolic phenotype in most patients with PAH deficiency. In the present study, the classification of 105 PAH mutations may allow the prediction of the biochemical phenotype in >10,000 genotypes, which may be useful for the management of hyperphenylalaninemia in newborns.

The STR252-IVS10nt546-VNTR7 phenylalanine hydroxylase minihaplotype in five Mediterranean samples

IVS10nt546 (IVS10nt-11g-->a) is the most common molecular defect of the phenylalanine hydroxylase gene causing phenylketonuria in Mediterranean populations. Previous studies have proposed various and alternative hypotheses concerning the geographical origin and pattern of diffusion of this mutation in this area. In this study, this issue was re-examined on a large sample (149) of "Mediterranean" IVS10nt546 mutant alleles analysed with multiallelic intragenic polymorphisms. The analysis of intragenic microsatellite (STR) and minisatellite (VNTR) polymorphisms shows allelic heterogeneity of the IVS10nt546 mutation. Eight STR and three VNTR alleles were found in association with the splicing defect. Of the ten detected STR-VNTR combinations ("minihaplotypes"), we identified a predominant allelic association (VNTR7-STR252) embedded in a RFLP-haplotype 6 background, which seems to correspond to the ancestral gene originating in the Turkey-Israel area. Analysis of both absolute and relative gene frequencies of the STR252-IVS10nt546-VNTR7 minihaplotypes, shows statistically significant (P < 0.02) variations and may suggest gene flow from Turkey and/or Israel to Italy and Spain. The associated migratory events need not be unique in time (and people) but seem to suggest they may be traced back to the expansion of the Neolithic culture and people, thus allowing dating of the origin of this mutation to at least 5000-10000 years ago. Alternative hypotheses are discussed to explain, in light of the available historical and pre-historical evidence, the pattern of diffusion of the IVS10nt546 mutation in the Mediterranean basin.