Biomedical subjects

F Caldara

Publications and source records attributed to F Caldara.

5 recordsLinked to original sources

PubMed2001

Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate.

The public availability of numerous microbial genomes is enabling the analysis of bacterial biology in great detail and with an unprecedented, organism-wide and taxon-wide, broad scope. Streptococcus pneumoniae is one of the most important bacterial pathogens throughout the world. We present here sequences and functional annotations for 2.1-Mbp of pneumococcal DNA, covering more than 90% of the total estimated size of the genome. The sequenced strain is a clinical isolate resistant to macrolides and tetracycline. It carries a type 19F capsular locus, but multilocus sequence typing for several conserved genetic loci suggests that the strain sequenced belongs to a pneumococcal lineage that most often expresses a serotype 15 capsular polysaccharide. A total of 2,046 putative open reading frames (ORFs) longer than 100 amino acids were identified (average of 1,009 bp per ORF), including all described two-component systems and aminoacyl tRNA synthetases. Comparisons to other complete, or nearly complete, bacterial genomes were made and are presented in a graphical form for all the predicted proteins.

DNA, Bacterial↗

PubMed1996

Molecular phylogeny of grey mullets based on mitochondrial DNA sequence analysis: evidence of a differential rate of evolution at the intrafamily level.

The phylogeny of the grey mullets is considered problematic both at the intra- and interfamily level. Such a difficulty arises from the highly homogeneous morphology displayed by this group of fish and, consequently, from the paucity of the key morphological characters suitable to address their phylogeny and evolution. In the present work, we have approached the phylogenetic and evolutionary relationships of seven species of Mugilidae, six of which from the Mediterranean Sea, on the basis of the DNA sequences of two mitochondrial genes (cytochrome b and 12S rRNA). Despite the morphological homogeneity exhibited by the taxa considered, the two species of the genus Mugil (M. cephalus and M. curema) showed a remarkable genetic divergence compared to all the other members of the family. The relative rate test revealed a significantly higher rate of evolution along the Mugil lineage.

Animals↗

PubMed1996

Identification of 4370 expressed sequence tags from a 3'-end-specific cDNA library of human skeletal muscle by DNA sequencing and filter hybridization.

A systematic study on the mRNA species expressed in the human skeletal muscle is presented in this paper. To carry on this study, a new method has been developed for the construction of unbiased cDNA libraries specially designed for the production of ESTs corresponding to the 3'-end portion of the mRNAs. The method has been applied to human skeletal muscle, where the analysis of the transcription profile is particularly difficult for the presence of several very abundant transcripts. To detect and quantify high-level mRNAs, the first 1054 ESTs were obtained from randomly selected clones. The 10 most abundant transcripts accounted for > 45% of the clones. Subsequently, these transcripts were identified by filter hybridization, thus making DNA sequencing more productive. Overall, 4370 clones were identified: 3372 by DNA sequencing and 998 by filter hybridization. The number of groups of sequences identifying individual transcripts was relatively low compared with other tissues, resulting in a total of 934 groups out of 4370 ESTs. Of these, 719 groups were represented by only one sequence.

Cloning, Molecular↗

PubMed1994

Cytochrome b and 16S rRNA sequence variation in the Salmo trutta (Salmonidae, Teleostei) species complex.

PCR amplification and direct sequencing of regions of the cytochrome b and 16S rRNA mitochondrial genes was carried out on Italian and Irish populations of the brown trout (Salmo trutta) species complex. These included S. t. marmoratus, S. t. macrostigma, Salmo carpio, and Salmo fibreni collected in Italy, and S. t. trutta morpha fario, from both Italy and Ireland. Samples of Atlantic salmon (Salmo salar) were also examined and used as an outgroup in the phylogenetic analysis. Results based on 592 bp indicated differentiation between fario morphs from Italy and Ireland. Despite the large phenotypic differences within Italian salmonids, very low genetic variation was found. On the basis of the mtDNA sequences studied, S. carpio and S. fibreni, which have been described as good species, are genetically undifferentiated from the other Italian taxa. The finding of a haplotype from Ireland in the Brenta River in Italy stresses the importance of conservation genetics studies aimed at identifying and preserving native genotypes.

Animals↗

PubMed1993

Mitochondrial DNA sequence variation in the European sea bass, Dicentrarchus labrax L. (Serranidae): evidence of differential haplotype distribution in natural and farmed populations.

PCR and direct sequencing of 300 to 377-bp fragments of the cytochrome b mitochondrial gene were carried out in 40 specimens of European sea bass, Dicentrarchus labrax L., collected at different sites in the Mediterranean basin and representing wild and farmed populations. Sequence analysis revealed 6 transitional changes, which generated 5 different haplotypes (A-E). Only one mutation was nonsynonymous because it occurred in the first position of a codon leading to the replacement of valine by isoleucine. The genotypic distribution revealed that haplotype B was not present in the farm samples, whereas its frequency in the wild samples exceeded 30%. In contrast, haplotypes D and E were found in farmed populations but not in the wild populations. The comparison among wild populations showed a nonhomogeneous distribution of the two most frequent haplotypes, A and B.

Amino Acid Sequence↗