The structure and migration patterns of the population of Uruguay through isonymy.

Surname distribution can be a useful tool for studying the genetic structure of a human population. In South America, the Uruguay population has traditionally been considered to be of European ancestry, despite its trihybrid origin, as proved through genetics. The aim of this study was to investigate the structure of the Uruguayan population, resulting from population movements and surname drift in the country. The distribution of the surnames of 2,501,774 people on the electoral register was studied in the nineteen departments of Uruguay. Multivariate approaches were used to estimate isonymic parameters. Isolation by Distance was measured by correlating isonymic and geographic distances. In the study sample, the most frequent surnames were consistently Spanish, reflecting the fact that the first immigration waves occurred before Uruguayan independence. Only a few surnames of Native origin were recorded. The effective surname number (α) for the entire country was 302, and the average for departments was 235.8 ± 19. Inbreeding estimates were lower in the south-west of the country and in the densely populated Montevideo area. Isonymic distances between departments were significantly correlated with linear geographic distance (p < 0.001) indicating continuously increasing surname distances up to 400 km. Surnames form clusters related to geographic regions affected by different historical processes. The isonymic structure of Uruguay shows a radiation towards the east and north, with short-range migration playing a major role, while the contribution of drift, considering the small variance of α, appears to be minor.

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

In Chile, the Hispanic dual surname system is used. To describe the isonymic structure of this country, the distribution of 16,277,255 surnames of 8,178,209 persons was studied in the 15 regions, the 54 provinces, and the 346 communes of the nation. The number of different surnames found was 72,667. Effective surname number (Fisher's α) for the entire country was 309.0, the average for regions was 240.8 ± 17.6, for provinces 209.2 ± 8.9, and for communes 178.7 ± 4.7. These values display a variation of inbreeding between administrative levels in the Chilean population, which can be attributed to the 'Prefecture effect' of Nei and Imaizumi. Matrices of isonymic distances between units within administrative levels were tested for correlation with geographic distance. The correlations were highest for provinces (r = 0.630 ± 0.019 for Euclidean distance) and lowest for communes (r = 0.366 ± 0.009 for Lasker's). The geographical distribution of the first three-dimensions of the Euclidean distance matrix suggests that population diffusion may have taken place from the north of the country toward the center and south. The prevalence of European plus European-Amerindian (95.4%) over Amerindian ethnicity (4.6%, CIA World Factbook) is compatible with diffusion of Caucasian groups over a low-density area populated by indigenous groups. The significant excess of maternal over paternal indigenous surnames indicates some asymmetric mating between nonAmerindian and Amerindian Chileans. The available studies of Y-markers and mt-markers are in agreement with this asymmetry. In the present work, we investigate the Chilean population with the aim of detecting its structure through the study of isonymy (Crow and Mange,1965) in the three administrative levels of the nation, namely 15 regions, 54 provinces, and 346 communes.

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, Nei's 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.

General preadaptation of viral infectors to their hosts.

We tested the hypothesis of optimal adaptation of viral infectors to eukaryotic hosts, using (1) correlation in codon and amino acid usage between organisms, and (2) canonical correlation between groups of hosts and infectors. The codon correlations between parasites and hosts vary, being low between swine and African swine fever virus (ASF; r = 0.18), and highest between potato and potato virus X (r = 0.60). The correlations might indicate different stages of evolution toward optimal adaptation of the parasite codon distribution to the host tRNA pools. The amino acid correlations vary from r = 0.71 between pig and ASF, to 0.88 between catfish and its herpesvirus. It was observed that both in virus and hosts, there is a negative correlation between frequency of an amino acid and molecular weight. Therefore, it was advanced that viral infectors might be preadapted to their hosts because of similarities of the tRNA pools of hosts, and that evolution toward optimization would be dependent on the size of the divergence between the codon distributions of infector and host. Preadaptation does not imply origin of the virus by lateral transfer from the present host, since the correlation of the molecular weight of amino acids with their abundance in proteins is a general phenomenon.

Amino acid and codon use: in two influenza viruses and three hosts.

OBJECTIVE: The aim of this study was to compare the use of amino acids and codons in influenza viruses A and B and in their common hosts, to highlight any relevant difference. METHODS: The frequency of the 20 amino acids and of the 61 codons was studied in influenza viruses A, B, and in man, pig, and chicken. The correlation in amino acid and codon use among these hosts was calculated. RESULTS: The correlation between the frequency of the 20 amino acids and the molecular weight was also calculated and it was very similar in all studied hosts, ranging from 0.506 to 0.595. The correlation of codon frequency among these organisms was highest between man and chicken (r=0.974), and lowest between pig and virus B (r=0.147). CONCLUSIONS: The important correlation in codon use among the three hosts and the two viruses suggests there was a remote lateral gene transfer among the three hosts and the two viruses. The higher use of alanine, leucine, and proline in man versus virus A is significant.

Co-localization of rare oligonucleotides and regulatory elements in mammalian upstream gene regions.

In order to identify putative control signals of gene expression, 634 mammalian DNA sequences spanning 1.8 x 10(6) base-pairs were analysed and the frequencies of 1024 oligonucleotides five bases long (5-tuples) were determined. We defined as rare those 5-tuples having an observed frequency less than 50% of that expected by chance on the basis of base composition, and which had a reduction in frequency not attributable to CpG suppression or to coding constraints. Very few rare 5-tuples were identified; in addition, three oligonucleotides, reverse complements of rare 5-tuples, were found to have a frequency ranging between 0.582 and 0.671. The frequency of most of the rare 5-tuples was higher in 5' promoter regions as compared to exonic segments, so imitating the distribution pattern of known signals. Some of the rare 5-tuples identified by this strategy belonged to a portion of the nine base-pair binding site in promoters, which is also known as the octamer motif. In addition, three of the rare oligonucleotides were found to be located within other regulatory elements, previously identified by techniques of molecular biology. Two rare 5-tuples were found within sites of interaction between DNA and proteins, one of them being a transcriptional factor. The available data about known control sequences involved in gene expression in mammals therefore provide evidence for a role in gene regulation of the rare oligonucleotide selected.

Human HLA-DR alpha gene: a rare oligonucleotide (GTATA) identifies an upstream sequence required for nuclear protein binding.

Synthetic oligonucleotides containing putative regulatory sequences are currently employed to identify and isolate genes coding for nuclear binding factors. Upstream DNA sequences of eukaryotic genes required for transcriptional activity and tissue specificity can be identified by means of biochemical techniques as well as computer analysis using homology searching. An alternative approach has been recently proposed by our research group. Scanning DNA sequences 1.8 megabases in length from a Genetic Sequence Data Bank, we have identified rare oligonucleotides 5 base pairs (bp) long, which are localized within or close to regulatory segments in mammalian promoters. In this paper we demonstrate that the rare GTATA sequence identifies an upstream region of the HLA-DR alpha gene which operates in conjunction with the sequence AGAAGTCAG, homologous to a box found in many interferon-inducible genes, in binding nuclear proteins.

Chemical and mutagenic patterns of airborne particulate matter collected in 17 Italian towns.

The mutagenicity of airborne particulate matter collected in 17 towns of Italy in 1990 was assessed using the Ames test. The mutagenicity of crude extract correlated with amount of lead, suggesting the direct contribution of gasoline car exhausts. Moreover, the mutagenicity correlated with particulate matter amounts. An inverse correlation with temperature was observed. The crude extracts were fractionated in acid, basic, and neutral fractions. The latter was further separated into polycyclic aromatic hydrocarbon (PAH), polar, and nonpolar fractions. Acid and polar fractions showed the higher mutagenicity. Average recovery of mutagenicity was about 60%.

Monitoring human exposure to urban air pollutants.

A multidisciplinary study on a general population exposed to vehicle exhaust was undertaken in Pisa in 1991. Environmental factors such as air pollution and those associated with lifestyle were studied. Meanwhile, biological and medical indicators of health condition were investigated. Chromosomal aberrations, sister chromatid exchanges (SCEs), and micronuclei in lymphocytes were included for the assessment of the genotoxic risk. Because of the large number (3800) of subjects being investigated, standardization of protocols was compulsory. The results on data reproducibility are reported. To assess the reliability of the protocol on a large scale, the population of Porto Tolle, a village located in northeast Italy, was studied and compared to a subset of the Pisa population. Preliminary results showed that probable differences between the two populations and individuals were present in terms of SCE frequencies. The study was potentially able to detect the effects of several factors such as age, smoking, genetics, and environment. The in vitro treatment of lymphocytes with diepoxybutane confirmed the presence of more responsive individuals and permitted us to investigate the genetic predisposition to genetic damage. The possible influence of environmental factors was studied by correlation analyses with external exposure to air pollutants as well as with several lifestyle factors.

Assessment of prospective genetic counseling in the Ferrara area.

A group of 613 heterozygotes for beta thalassemia (267 married, 346 unmarried) who were screened mostly at elementary school age, were identified and interviewed at the average age of 23.7 years to assess their knowledge of the heterozygous state and its implications. It was found that 83% recalled some information about their heterozygous state; only 60% had some information about the meaning of being heterozygous, and only 26% said they knew of some relationship between Cooley's anemia and the heterozygous state for beta thalassemia. In the married group, the proportion of those having married another carrier was in agreement with random mating expectations. It was concluded that there is ample room for improvement in the procedures of delivery of prospective genetic counseling at the population level in this area.

Reproductive behavior of thalassemic couples segregating for Cooley anemia.

The reproductive behavior in 1984 of families segregating for Cooley anemia in Ferrara was compared with that of a control group of families, matched for some biological variables which affect fertility. At the resolution power of the sample, it was found that there is no significant difference in these variables due to segregation for Cooley anemia, and it appears that there is no longer significant reproductive compensation in thalassemic couples, although a tendency to compensate does still exist. The increased life span of children affected by Cooley anemia, due to improvements in treatment in the past decade, is probably the main reason why the compensatory reproductive behaviour of the past has almost disappeared.

Linkage of biopsy, cancer, and population records aimed at the estimation of family risks in neoplasia: a pilot study.

STUDY OBJECTIVE: The aim was to link individual demographic and medical records into sibships to obtain the sibling distribution of biopsies and cancers, and thereby calculate heritability and recurrence risks in families, thus aiding early diagnosis and prevention of cancers. DESIGN: The 157,823 individual records of the inhabitants of the town of Ferrara in Italy were automatically linked into 106,821 sibships. A 10% sample (10,842 sibships) was then extracted from the distribution of sibships and tabulated, for linkage to medical records. PATIENTS: The biopsy records at the Institute of Pathological Anatomy of the University of Ferrara were manually linked to cancer records and then to sibships. It was possible to construct the distribution of 2062 biopsies and of 829 cancers in sibships. RESULTS: From the distribution of biopsies and tumours in sibships, it was possible to estimate the incidence of tumours in the population (0.052) and in siblings of affected (0.083), and to apply to such distributions current methods for the estimate of heritability (h2 = 0.246) and of recurrence risks of tumours in sibships, age independent. CONCLUSIONS: The study shows that the procedure resulting in the estimation of incidences and recurrence risks for tumours could be completely automated, and extended to whole populations and homogeneous subgroups in post industrial cultures.

In vivo genotoxic interactions among three phenolic benzene metabolites.

Three benzene metabolites, hydroquinone (HQ), cathecol (CAT) and phenol (PHE) were studied to define their possible interaction in inducing micronuclei (Mn) in mouse bone marrow polychromatic erythrocytes (PCEs). HQ and CAT, administered separately, induced Mn while PHE showed no genotoxic effects. Binary and ternary mixtures of two or three metabolites gave different results, causing considerable increase or decrease in Mn induction. HQ and PHE, in binary mixtures, as well as PHE and CAT, increased Mn synergistically, while HQ and CAT interacted negatively. The genotoxicity of ternary mixtures was mainly the consequence of two metabolites: HQ and CAT. The maximal effect obtained is far below the induction of Mn consequent to benzene treatment. These data suggest that toxic and genotoxic effects of benzene alone could be the result of more complex interactions among these and other metabolites.

Correlations between 15 polycyclic aromatic hydrocarbons (PAH) and the mutagenicity of the total PAH fraction in ambient air particles in La Spezia (Italy).

Airborne particulate matter has been monitored 4 times a month for 1 year (1988) in the city of La Spezia (Italy). The polycyclic aromatic hydrocarbon (PAH) fractions were extracted, purified and characterized for the content of 15 individual PAH. In general when concentrations of individual PAH were compared statistical correlation was obtained. Mutagenicity studies were performed by the use of the Ames plate test with the Salmonella strains TA98, TA100, TA98NR and TA98DNP6 with and without metabolic activation (S9 mix). The TA98 strain was by far the most responsive and the S9 mix was absolutely required as expected when PAH are assayed. Besides mutagenicity, toxicity was also considered and it proved to be correlated with mutagenicity in TA98, +S9. The TA98NR and TA98DNP6 strains showed no appreciable differences from the parental strain TA98 indicating the absence of significant amounts of direct-acting nitro derivatives in our PAH samples. Of the 15 PAH considered in this study the amounts of cyclopental[c,d]pyrene (CPP) correlated best with mutagenicity. The role of CPP in contributing to the indirect mutagenicity of urban air PAH samples is discussed.

The analysis of the joint effect of substances on reversion systems and the assessment of antimutagenicity.

The statistical methods for the analysis of mutagenicity and carcinogenicity underwent considerable theoretical-practical development following the need for assessing the mutagenic and carcinogenic potential of substances. Antimutagenicity is investigated through the analysis of respondents in dose-response assays, when two different molecules are administered separately and as a mixture to a respondent system. When the number of respondent units is high, and doses are orthogonal, it is possible to apply simple models such as analysis of variance. This is not always possible or common, and alternative approaches have been developed, based on multiple regression and on tables of proportions. In this work, some of the most frequently used methods for the assessment of joint responses are reviewed, particularly those based on multiple regression, such as the method of Shaeffer et al. and the method of Hass et al. In order to illustrate these methods, joint responses of perylene and cyclopentapyrene, of N-acetylcysteine and dinitropyrene, and of N-acetylcysteine and extracts from diesel exhausts were analyzed. An antagonistic effect of perylene on the action of CPP was detected by the algorithm of Shaeffer et al. The effect is not multiplicative, i.e., it is not proportional to the product of doses. The antimutagenic effect of N-acetylcysteine on dinitropyrene is multiplicative, as detected by the method of Hass et al. The latter reveals that the inhibition by N-acetylcysteine on the mutagenic effect of extracts from diesel exhausts is also multiplicative.

Skin cytogenetic assay for the detection of clastogens-carcinogens topically administered to mice.

A method for assessing the effect of clastogens on mouse skin epidermal cells was devised and applied. Toxic and mutagenic responses in epidermal cells were tested using two known mutagens and carcinogens, urethane (URE) and 7,12-dimethylbenz[a]anthracene (DMBA). Cell generation time, sister-chromatid exchanges (SCE) and chromosomal aberrations (CA) after topical and intraperitoneal (i.p.) treatment were measured in epidermal and bone marrow cells. After topical administration both tissues responded similarly, whereas after i.p. treatment skin cells were less responsive than bone marrow cells. However, the results indicate the validity of this new cytogenetic approach for the assessment of the genotoxicity of compounds applied directly to skin.

Cytogenetic effects of benzimidazoles in mouse bone marrow.

The cytogenetic effects of three benzimidazoles, i.e., benomyl, methyl thiophanate and methyl 2-benzimidazolecarbamate (MBC), were studied in mouse bone marrow cells by analyzing three genetic endpoints: micronuclei, structural chromosome aberrations plus or minus gaps, and aneugenic effects (hyperdiploidy or polyploidy). In general, the effects were small, but it was observed that benomyl and MBC significantly induced micronuclei as well as aneugenic effects, hyperdiploidy (no metaphases with more than one or two extra chromosomes, 2n + 1 or 2n + 2, were observed) and polyploidy (4n). The induction of chromosome gaps and breaks was less evident. Methyl thiophanate significantly induced micronuclei, but it was less effective than benomyl and MBC. Our results showed that micronuclei are a good indicator of aneugenic effects in mouse bone marrow cells. A curvilinear trend test has been devised to fit the curves originating from the time-dependent responses.

Genotoxicity of two metabolites of benzene: phenol and hydroquinone show strong synergistic effects in vivo.

Possible interactions between hydroquinone (HQ) and phenol (PHE), 2 known benzene metabolites, in inducing micronuclei in mouse bone marrow cells were investigated. HQ and PHE administered alone gave weak and negative results, respectively, at the doses tested. However, simultaneous administration of both compounds caused a considerable increase in the induction of micronuclei as well as an increase in bone marrow toxicity. Using 3 different statistical methods, it was shown that the observed joint effect was significantly higher than additive interaction, and was close to multiplicative interaction. These findings bring further support to the hypothesis that the toxic and genotoxic effects of benzene are produced by several metabolites acting synergistically.

Two years' air mutagenesis monitoring in a northwestern rural area of Italy with an industrial plant.

The mutagenicity of organic extracts from inhalable airborne particles, collected in a northwestern rural area of Italy in which an industrial plant producing chemical intermediates is present, was assessed during the years 1989 and 1990. The Ames plate test with Salmonella strains TA98 and TA100 with and without metabolic activation was used. Eight sites in the first and three sites in the second year were monitored once and twice a month respectively. Results show that the mutagenicity of air particulate matter reaches maximum values in the cold months and is not dependent on plant activities. In addition, a correlation analysis between mutagenicity data and number of vehicles seems to indicate traffic emissions as the main source of mutagens.

Allele and genotype frequencies for D1S80 and 3'APOB in Recanati, Central Italy.

The VNTR 3'APOB and D1S80 loci were studied in a sample of 179 individuals living in the Recanati Area (Central Italy). For 3'APOB, we found 34 genotypes and 11 alleles. The system was in Hardy-Weinberg equilibrium. The observed and expected heterozygosity were 0.788 and 0.798 respectively. The discrimination power was 0.96, the a-priori paternity exclusion power was 0.619 and the polymorphism information content was 0.773. For D1S80, we found 45 genotypes and 18 alleles. The system deviated significantly from Hardy-Weinberg equilibrium. The observed and expected heterozygosity were 0.696 and 0.790 respectively. The discrimination power was 0.96, the a-priori paternity exclusion power was 0.617 and PIC was 0.767. The Recanati sample was compared with the general Italian frequencies for the 3'APOB locus. A difference of borderline significance was detected (P = 0.04). For D1S80, the sample was compared with a sample from Southern Italy and no significant difference was detected.