Alberto Carrieri

Detection of xanthine oxidase activity products by EPR and HPLC in bronchoalveolar lavage fluid from patients with chronic obstructive pulmonary disease

Xanthine oxidase (xanthine: oxygen oxidoreductase, EC 1.1.3.22), a molybdenum-containing hydroxylase that produces superoxide and uric acid from purine substrates and molecular oxygen, is involved in the oxidative stress underlying several human pathologies including lung diseases. An enzymatic activity similar to xanthine oxidase was previously reported in bronchoalveolar lavage fluid of patients with chronic obstructive pulmonary disease (COPD-BAL), by fluorometric analysis of DNA unwinding and cytochrome c reduction kinetics. Here we report the detection of xanthine oxidase activity products by electron paramagnetic resonance (EPR) in presence of the spin-trap 5,5-dimethyl-1-pyrroline N-oxide (DMPO) and reversed-phase high-performance liquid chromatography (RP-HPLC) in COPD-BAL (n = 14, average age of patients 65 years, range 38-81) and BAL from healthy nonsmoker controls (n = 6, average age 64 years, range 44-73). Superoxide DMPO adducts were detected in COPD-BAL and in an in vitro system containing xanthine and xanthine oxidase (XA/XO), but not in BAL controls and when superoxide dismutase (SOD, 1000 I.U./ml) was added to COPD-BAL. The HPLC analyses after addition of xanthine showed production of uric acid in COPD-BAL and in the XA/XO system but not in BAL controls. These results support the involvement of xanthine oxidase in the mechanisms of superoxide production by BAL supernatant, which increases oxidative stress in chronic obstructive pulmonary disease.

Interleukin-1β levels in gingival crevicular fluid and serum under naturally occurring and experimentally induced gingivitis

AIMS To evaluate the interleukin-1 beta (IL-1 beta) levels in gingival crevicular fluid (GCF) and serum in either naturally occurring (N-O) or experimentally induced (E-I) plaque-associated gingivitis. MATERIAL AND METHODS Thirty-seven periodontally healthy subjects were evaluated in real life conditions (N-O gingivitis) as well as after 21 days of experimental gingivitis trial (E-I gingivitis). During the experimental gingivitis trial, in one maxillary quadrant (test quadrant), gingival inflammation was induced by oral hygiene abstention, while in the contralateral (control) quadrant, oral hygiene was routinely continued. IL-1 beta concentrations in N-O and E-I gingivitis were investigated for IL-1B(+3954) and IL-1B(-511) gene polymorphisms. RESULTS (i) GCF IL-1 beta concentrations in E-I gingivitis were significantly higher compared with N-O gingivitis; (ii) an intra-individual correlation between GCF concentrations of IL-1 beta detected in N-O and E-I gingivitis was observed in control quadrants, but not in test quadrants; (iii) IL-1 beta concentration in GCF was associated with IL-1B(+3954) genotype only at test quadrants; (iv) IL-1 beta was detectable in serum only at low levels in a limited number of subjects, without difference between gingivitis conditions. CONCLUSIONS Aspects of the bacterial challenge to the gingival tissues, such as the amount of plaque deposits and plaque accumulation rate, appear to affect the IL-1 beta levels in GCF in subjects with a specific IL-1B genotype.

Age-related treatment response following non-surgical periodontal therapy

BACKGROUND To date, no studies have evaluated the effect of patient age on the treatment response following non-surgical periodontal therapy (NSPT). AIM To evaluate the outcomes of NSPT in two cohorts of patients with a substantial age difference. MATERIALS AND METHODS Two groups of periodontitis patients with a substantial age difference (younger group, Y, and older group, O) were retrospectively selected. The effectiveness of NSPT was assessed by evaluating the changes in the prevalence of sites with different pocket probing depths (PPD) as well as the changes in patient- and site-specific bleeding on probing (BoP) scores. RESULTS Y group comprised 57 patients, mean age: 34.7 +/- 4.4 years, and O group comprised 60 patients, mean age: 58.9 +/- 5.3 years (p<0.0001). NSPT resulted in a significant improvement of PPD and BoP in both age groups. No statistically significant inter-group differences were observed in the investigated clinical parameters as well as their changes with respect to pre-treatment. However, multiple regression analysis showed a significantly higher risk of showing residual pockets following treatment in group O. CONCLUSIONS The results of the present study seem to indicate that age has a limited effect on treatment response following NSPT in periodontitis patients.

Gene--gene interaction among cytokine polymorphisms influence susceptibility to aggressive periodontitis.

Aggressive periodontitis (AgP) is a multifactorial disease. The distinctive aspect of periodontitis is that this disease must deal with a large number of genes interacting with one another and forming complex networks. Thus, it is reasonable to expect that gene–gene interaction may have a crucial role. Therefore, we carried out a pilot case-control study to identify the association of candidate epistatic interactions between genetic risk factors and susceptibility to AgP, by using both conventional parametric analyses and a higher order interactions model, based on the nonparametric Multifactor Dimensionality Reduction algorithm. We analyzed 122 AgP patients and 246 appropriate periodontally healthy individuals, and genotyped 28 polymorphisms, located within 14 candidate genes, chosen among the principal genetic variants pointed out from literature and having a role in inflammation and immunity. Our analyses provided significant evidence for gene–gene interactions in the development of AgP, in particular, present results: (a) indicate a possible role of two new polymorphisms, within SEPS1 and TNFRSF1B genes, in determining host individual susceptibility to AgP; (b) confirm the potential association between of IL-6 and Fc γ- receptor polymorphisms and the disease; (c) exclude an essential contribution of IL-1 cluster gene polymorphisms to AgP in our Caucasian-Italian population.

Surnames in Siberia: A study of the population of Yakutia through isonymy

We studied the isonymic structure of the Republic of Sakha (Yakutia), in the Russian Federation, using the surname distributions of 491,259 citizens above 18 years registered as residents in 2002. These were distributed in 35 districts and 497 towns and settlements of the Republic. The number of different surnames was 44,625. Matrices of isonymic distances between the 35 districts were tested for correlation with the geographic distance between the population centers of gravity of the districts. We found that, for the whole of Yakutia, Neis distance was correlated with geographic distance (r = 0.693 +/- 0.027). A dendrogram of the 35 districts was built from the distance matrix, using the UPGMA method. The clusters identified by the dendrogram correlate with the geographic position of the districts. The correlation of random inbreeding calculated from isonymy, F(ST), with latitude was positive and highly significant but weak (r = 0.23). So, inbreeding was highest in the Arctic districts, and lowest in the South. Average alpha for 497 towns was 107, for 35 districts it was 311, and for the Republic 433. The value of alpha was higher for Russian than for the local languages. The geographical distribution of alpha, high in the Center and South-East and lower in the North-West, is compatible with the settlement of groups of migrants moving from the South-East toward the center and the North of Yakutia. It is proposed that low-density demic diffusion of human populations results in high inbreeding and may have been a general phenomenon in the early phases of human radiations.

Surnames in Bolivia: A study of the population of Bolivia through isonymy

In Bolivia, the Hispanic dual surname system is used. To describe the isonymic structure of Bolivia, the surname distribution of 12,139,448 persons registered in the 2006 census data was studied in 9 districts and 112 provinces of the nation, for a total of 23,244,064 surnames. The number of different surnames found was 174,922. Matrices of isonymic distances between the administrative units (districts and provinces) were constructed and tested for correlation with geographic distance. In the 112 provinces, isonymic distances were correlated with geographic distance (r = 0.545 ± 0.011 for Euclidean, 0.501 ± 0.012 for Neis, and 0.556 ± 0.010 for Laskers distance). The multiple regression of the surname effective number (α), equivalent to the allele effective number in a genetic system, was nonsignificant on latitude and longitude; however, it was highly significant and negative on altitude (r = -0.72). Because the Andes extend from north to south in west-central Bolivia, random inbreeding was lowest in the eastern districts, and highest in mountainous western Bolivia. Average α for the provinces was 122 ± 2; for the districts, it was 216 ± 29, and for the whole of Bolivia it was 213. The geographical distribution of α in the provinces is compatible with the settlement of subsequent groups of migrants moving from east and north toward the center and south of Bolivia. The relative frequency of indigenous surnames is correlated positively with altitude. This suggests that the country was populated by recent low-density demic diffusion over a low-density indigenous population. This may have been a common phenomenon in the immigration to tropical South America.

A Study of the Population of Paraguay through Isonymy

In order to describe the isonymic structure of Paraguay, the distribution of 4,843,868 surnames of 2,882,163 persons was studied in the 18 departments and 237 districts of the nation. The correlations between isonymic and geographic distances for departments were r = 0.713 ± 0.052 for Euclidean distance, 0.597 ± 0.074 for Neis and 0.582 ± 0.076 for Laskers, and for districts r = 0.320 ± 0.007, 0.235 ± 0.009 and 0.422 ± 0.008, respectively. Average α was 151 for the entire country, 140.6 ± 6.5 for departments and 108.2 ± 2.7 for districts. The geographical distribution of districts’α is compatible with the settlement of subsequent groups of migrants moving from South towards the Centre and North of Paraguay. The geographical analysis of the first three components of Laskers isonymy distance matrix is in agreement with such a process. The prevalence of Spanish–Amerindian ethnic groups and the relative absence of indigenous surnames (absence due mainly to the forced surname change of 1848) is in agreement with the diffusion of Spanish speaking males over a low‐density area populated by indigenous groups. The present distribution of Y‐markers and mt‐markers in the available studies in most Latin American populations is compatible with this process.

Surnames in Albania: a study of the population of Albania through isonymy.

In order to describe the isonymic structure of Albania, the distribution of 3,068,447 surnames was studied in the 12 prefectures and their administrative subdivisions: the 36 districts and 321 communes. The number of different surnames found was 37,184. Effective surname number for the entire country was 1327, the average for prefectures was 653.3 ± 84.3, for districts 365.9 ± 42.0 and for communes 122.6 ± 8.7. These values display a variation of inbreeding between administrative levels in the Albanian population, which can be attributed to the previously published “Prefecture effect”.

Surnames in Honduras: A Study of the Population of Honduras through Isonymy

In this work, we investigated surname distribution in 4,348,021 Honduran electors with the aim of detecting population structure through the study of isonymy in three administrative levels: the whole nation, the 18 departments, and the 298 municipalities. For each administrative level, we studied the surname effective number, α, the total inbreeding, FIT, the random inbreeding, FST, and the local inbreeding, FIS. Principal components analysis, multidimensional scaling, and cluster analysis were performed on Laskers distance matrix to detect the direction of surname diffusion and for a graphic representation of the surname relationship between different locations. The values of FIT, FST, and FIS display a variation of random inbreeding between the administrative levels in the Honduras population, which is attributed to the “Prefecture effect.” Multivariate analyses of department data identified two main clusters, one south‐western and the second north‐eastern, with the Bay Islands and the eastern Gracias a Dios out of the main clusters.

Codon and Aminoacid Usage Patterns in Mycobacteria

The large number of organisms and of genes sequenced at the present time permits now to study molecular evolution in such lower clades as genera, species, and subspecies. Here, we focus our attention on the genus Mycobacterium, in which we examined codon and aminoacid usage in 13 species, and in 12 subspecies for a total of 8,836,513 codons from 26,755 sequences. Within the genus Mycobacterium, frequencies of codon and aminoacid usage correlate between species and between subspecies. In the groups studied, aminoacid molecular weight and codon degeneracy influence correlations between frequencies, while GC content is the main factor influencing the effective number of codons. The coding GC, which is highly correlated with total genomic GC content, seems to be the main factor influencing present synonymous codon usage in the genus. In particular, the GC content at the 3rd base position seems to shape heavily the effective number of codons, giving indication that here mutational bias dominates over translational selection. Evolutionary trees based on codon and aminoacid usage are consistent with traditional phylogenies of species within the genus.