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Biomedical subjects

C Nesti

Publications and source records attributed to C Nesti.

10 recordsLinked to original sources

Isonymy and isolation by distance in Germany.

The isonymy structure of Germany was studied using the surname distributions of 5,150,310 private telephone users selected from 39,000,000 users registered in a 1996 commercial CD-ROM, which contains all telephone users in the country. The users were distributed in 106 towns selected on a geographic basis. Germany was subdivided into 50 adjacent rectangles, each 115 x 80 km, and at least the largest town in the rectangle was selected for study; the private telephone users in that district were downloaded from the CD-ROM and included in the analysis. The shortest distance between nearest neighbor towns was 10.7 km (Travemunde and Lübeck), and the largest distance was 69.8 km (Meppen and Osnabruck). The number of different surnames found in the whole analysis was 462,526. Lasker's distance, the negative value of the logarithm of isonymy between localities, was found to be linearly and significantly correlated with geographic distance (r = 0.51 +/- 0.010). A dendrogram was built with the matrix of isonymy distances, using UPGMA. This method separates the German towns into two main clusters, one in the southern half of the country and the other in the northern half. Within each cluster small subclusters with specific geographic distributions could be delimited. The two main clusters correspond fairly well to the north-south division of German sublanguages (Nieder- and Mitteldeutsch in the north vs. Frankisch-Alemannisch in the south). The other clusters are related to minor sublanguages. Comparisons with the results of a previous analysis of Switzerland's structure are given. From the present analysis isolation by distance emerges clearly, although it is less strong than in Switzerland and indicates that Germany has a fairly homogeneous isonymy structure. The random component of inbreeding estimated from isonymy indicates that eastern Germany is on average more inbred than western Germany.

CD-ROM

Clinical validity of the elbow flexion test for the diagnosis of ulnar nerve compression at the cubital tunnel.

We evaluated the elbow flexion test in 216 elbows without compression of the ulnar nerve at the cubital tunnel and without other neuropathies. We used Rayan's four positions as our test. The percentage of positive tests was only 3.6% at one minute, whereas evaluating the responses at three minutes we saw positive results in 16.2%. Therefore we find that if the test is performed for one minute it may be useful to help in diagnosing ulnar nerve compression at the cubital tunnel.

Adult

Correlation between age and DNA damage detected by FADU in human peripheral blood lymphocytes.

Fluorometric analysis of DNA unwinding (FADU) is a fast and reliable method for detecting single strand DNA breaks as an index of DNA damage induced by clastogenic agents. A study of damage detected by FADU was conducted on DNA extracted from peripheral blood lymphocytes of 128 healthy nonsmoking regular donors (ranging in age from 19 to 67 years) and from 5 umbilical cord blood samples. DNA damage was measured as percentage of unwound DNA after alkalinization. Statistical analyses, both parametric (Pearson r correlation coefficient, b regression coefficient, ANOVA) and nonparametric (Kruskal-Wallis H test, Spearman rs rank correlation coefficient), support a significant correlation between age of donors and amount of DNA damage. The same results are found when adult donors are divided in four age classes and the ANOVA test performed among the mean percentages of unwound DNA of each class. Furthermore, donors of the same age belonging to different blood groups (A, B, AB and O) do not show any difference in DNA damage detected by FADU.

Adult

Phylogeny inferred from codon usage pattern in 31 organisms.

We employed the Codonusage database to analyze the codon usage pattern in 31 organisms from all the main biological taxa. We tested the similarity in codon usage pattern between each organism and all the others by the Pearson linear correlation coefficient. The 465 values obtained were located in a 31 x 31 triangular matrix from which a correlation distance matrix was calculated. An evolutionary dendrogram was then constructed from these distances. The results showed a fair correlation between codon usage patterns and phylogenetic relationships, at least for organisms which diverged in rather recent times (end of Jurassic--beginning of Cretaceous).

Animals

Possible identity of transcription and translation signals in early vital systems.

The distribution of codons was analysed in three classes of eukaryote proteins having widely different evolutionary rates: 78 histones, 40 tubulins, and seven fibrinogens. In this set of genes, (i) it was confirmed that codons which are components of known transcription signals, like ATA, are used infrequently when a synonym is available, particularly in the more constrained proteins, and (ii) it was observed that the three codons which have an iso-accepting transfer with anticodon UAA, UAG or UGA are also suppressed. Then, the distribution of UAA, UAG and UGA trimers was studied in 498 tDNAs and 198 rDNAs. It was found that these trimers are weakly but significantly suppressed in tDNAs and to a lesser extent in rDNAs. It was advanced that the present suppression of ATA, which codes for Methionine in several mitochondria, and of the TAA, TAG and TGA trimers in tDNAs, might be an indication that at the very early stages of the evolution of translation and transcription the signals for initiation and termination were shared by the two processes.

Amino Acid Sequence

Codon usage and evolutionary rates of proteins.

The 61 codons and the three terminators were counted in the coding sequences of 31 families of proteins of higher vertebrates. The protein families were ordered according to their evolutionary rate. In each family, the ratio between the Observed and Expected frequency of each codon was obtained (O/E ratio). A strong and significant positive correlation was observed between the O/E ratio of the eight codons AAC, TAT, ATA, GAA, ACA, AAT, ATG and CGA and the evolutionary rate of the protein. A negative and significant correlation was observed for codons AAG and GAG. It was advanced that the functional constraints of proteins can influence the usage of codons, particularly for those trimers which are components of signal sequences. It was also observed that the O/E ratios of the terminators are negatively correlated with the evolutionary rate of the protein they terminate, and the correlation is significant for TAA and TGA, which in vertebrates might be older than TAG.

Animals

A set of Alu-free frequent decamers from mammalian genomes enriched in transcription factor signals.

We have recently reported that the statistical analysis of the frequency distribution of short oligonucleotides within mammalian and viral genomes allows the production of sets of DNA sequences enriched in signals for transcription factors. Such statistical approaches could facilitate the identification of new promoter regions playing a role in the transcriptional regulation of gene expression. In the case of mammalian oligonucleotides, we found that the published set of frequent decamers enriched in transcriptional motifs is not suitable for studies on genes of Homo sapiens and evolutionarily related genomes, because it contains decameric sequences belonging to genomic repeats. We report here that most of the decameric sequences of DNA repeats belong to Alu repeats. Accordingly, we produced a subset of Alu-free frequent decamers. In addition, we eliminated from the subset of Alu-free frequent decamers those that are frequently present within other common human repeats, including (GT)n, (AT)n, (CA)n, (ATT)n, (CAA)n and (GTT)n. The Alu-free (repeats-free) subset of frequent mammalian decamers is enriched in signals for transcription factors and allows the identification of putative signals in genes, such as those coding for plasminogen activator, adenosine deaminase and p53, that contain a large number of Alu-like repeats interspersed within our genomic sequences. The newly generated compilation of frequent decamers described here might be used to locate genomic regions playing functional roles in the expression of genes of Homo sapiens and related primates.

Animals

Isonymy and the genetic structure of Switzerland. I. The distributions of surnames.

The surname distribution of the population of Switzerland was studied using a sample of 1,702,000 private users registered for the year 1994 in the Helvetic Telephone Directory. These users were distributed in four linguistic areas, in 26 Cantons and 271 Communes of the Confederation. Estimates of unbiased random isonymy, of Fisher's alpha, an indicator of abundance of surnames converging to the allele effective number in standard genetic polymorphisms, and of Karlin-McGregor's v, an indicator of immigration rates, were calculated for each Commune, each Canton, each linguistic area and for the whole Confederation. The Commune with the highest value of alpha was Geneva (alpha = 5312) followed by Versoix (3713) and by the Communes of Vaud on the north shore of Lake Leman, Chavannes (3381), Montreux (3200), Nyon (3114) and Lausanne (3109). The Italian-speaking Communes of the Ticino were next. The lowest value (alpha = 29) was observed in Poschiavo, south of the Berninapass; alpha = 39 was observed in Einsiedeln (Schwyz); then Mels and Widnau (62 and 67, Canton of St Gallen), Frutingen in Bern (72), and Appenzell (80). Accordingly, the highest consanguinity values were observed in the Grisons and in the nucleus of the founding Cantons, while the lowest were observed in the Cantons of Geneva and Vaud, preferential areas of immigration to Switzerland from abroad. The effect of subdivision on isonymy is large at the Commune level, and decreases in Cantons and linguistic groups. French and Italian languages indicate minor, German and Romanisch major inbreeding.

Data Collection

Isonymy and the genetic structure of Switzerland. II. Isolation by distance.

Isolation by distance in Switzerland was detected comparing the surname distributions between Cantons. The decay of isonymy with geographic distance between Cantons was consistent with Malecot's exponential decay of kinship. Lasker's distance was defined as the negative value of the logarithm of isonymy between localities, and it was found that it is linearly and significantly correlated with the log of geographic distance, both within and between languages. The peculiar geographic and linguistic structure of the Confederation, where mountain barriers exist at short distances separating different languages, might explain the rapid changes in surname similarity. It was predicted that the frequency of markers linked to the Y chromosome would show a similar association with distance in Switzerland.

Genetics, Population