Biomedical subjects

C Lanave

Publications and source records attributed to C Lanave.

At least 19 recordsLinked to original sources

PubMed2005

Genomic organization of the sheep TRG1@ locus and comparative analyses of Bovidae and human variable genes.

gammadelta T cells commonly account for 0.5%-5% of human (gammadelta low species) circulating T cells, whereas they are very common in chickens, and they may account for >70% of peripheral cells in ruminants (gammadelta high species). We have previously reported the ovine TRG2@ locus structure, the first complete physical map of any ruminant animal TCR locus. Here we determined the TRG1@ locus organization in sheep, reported all variable (V) gamma gene segments in their germline configuration and included human and cattle sequences in a three species comparison. The TRG1@ locus spans about 140 kb and consists of three clusters named TRG5, TRG3, and TRG1 according to the constant (C) genes. The predicted tertiary structure of cattle and sheep V proteins showed a remarkably high degree of conservation between the experimentally determined human Vgamma9 and the proteins belonging to TRG5 Vgamma subgroup. However systematic comparison of primary and tertiary structure highligthed that in Bovidae the overall conformation of the gammadelta TCR, is more similar to the Fab fragment of an antibody than any TCR heterodimer. Phylogenetic analysis showed that the evolution of cattle and sheep V genes is related to the rearrangement process of V segments with the relevant C, and consequentely to the appartenence of the V genes to a given cluster. The TRG cluster evolution in cattle and sheep pointed out the existence of a TRG5 ancient cluster and the occurrence of duplications of its minimal structural scheme of one V, two joining (J), and one C.

Animals↗

PubMed2005

Comparative analyses of sheep and human TRG joining regions: evolution of J genes in Bovidae is driven by sequence conservation in their promoters for germline transcription.

The availability of genomic clones representative of the T cell receptor gamma (TRG1@ and TRG2@) ovine loci enabled us to compare the germline genomic organization and nucleotide diversity of joining (J) segments and reconstruct their evolutionary history by phylogenetic analysis of cattle, sheep and human expressed sequences. Expression profiling (RT-PCR data) in fetus and adult indicated that only the ovine J genes in which two or more of the key sequence features, such as recombination signal sequences (RSS), 3' splice sites, and core sequences, are missing or severely altered fail to be transcribed. Comparative genomic examination of the two human with the six sheep germline transcription promoters located at 5' of the relevant constant (C)-distal J segments showed a strong conservation of the redundant STAT consensus motifs, indicating that TRG1@ and TRG2@ loci are under the influence of IL-7 and STAT signalling. These findings support the phylogenetic analysis of human and Bovidae (cattle and sheep) that revealed a different grouping pattern of C-distal compared to C-proximal J segments. Likewise, the phylogenetic behaviour of either C-distal and C-proximal J segments is in accordance with the Bovidae TRG clusters evolution. Comparison of sheep and human structures of recombination signal sequences (RSS) has highlighted a greater conservation in sheep 12 RSS rather than 23 RSS thus suggesting that the initial recruitment of recombination activating genes (RAG) products requires at least one relatively high-affinity RSS per recombination event.

Animals↗

PubMed2005

Artiodactyl emergence is accompanied by the birth of an extensive pool of diverse germline TRDV1 genes.

Molecular cloning of cDNA from gamma/delta T cells has shown that in sheep, the variable domain of the delta chain is chiefly determined by the expression of the TRDV1 subgroup, apparently composed of a large number of genes. There are three other TRDV subgroups, but these include only one gene each. To evaluate the extent and the complexity of the genomic TRDV repertoire, we screened a sheep liver genomic library from a single individual of the Altamurana breed and sheep fibroblast genomic DNA from a single individual of the Gentile di Puglia breed. We identified a total of 22 TRDV1 genes and the TRDV4 gene. A sequence comparison between germline and the rearranged genes indicates that, in sheep, the TRDV repertoire is generated by the VDJ rearrangement of at least 40 distinct TRDV1 genes. All germline TRDV1 genes present a high degree of similarity in their coding as well as in 5' and 3' flanking regions. However, a systematic analysis of the translation products reveals that these genes present a broadly different and specific repertoire in the complementarity-determining regions or recognition loops, allowing us to organize the TRDV genes into sets. We assume that selection processes operating at the level of ligand recognition have shaped the sheep TRDV germline repertoire. A phylogenetic study based on a sequence analysis of the TRDV genes from different mammalian species shows that the diversification level of these genes is higher in artiodactyl species compared to humans and mice.

Amino Acid Sequence↗

PubMed2004

Genetic characterization of Pompeii and Herculaneum Equidae buried by Vesuvius in 79 AD.

DNA extracted from the skeletons of five equids discovered in a Pompeii stable and of a horse found in Herculaneum was investigated. Amino acid racemization level was consistent with the presence of DNA. Post-mortem base modifications were excluded by sequencing a 146 bp fragment of the 16S rRNA mitochondrial gene. Sequencing of a 370 bp fragment of mitochondrial (mt)DNA control region allowed the construction of a phylogenetic tree that, along with sequencing of nuclear genes (epsilon globin, gamma interferon, and p53) fragments, gave us the possibility to address some questions puzzling archaeologists. What animals-donkeys, horses, or crossbreeds-were they? And, given they had been evidently assigned to one specific job, were they all akin or were they animals with different mitochondrial haplotypes? The conclusions provided by molecular analysis show that the Pompeii remains are those of horses and mules. Furthermore one of the equids (CAV5) seems to belong to a haplotype, which is either not yet documented in the GenBank or has since disappeared. As its characteristics closely recall those of donkeys, which is the out group chosen to construct the tree, that appears to have evolved within the Equidae family much earlier than horses, this assumption seems to be nearer the truth.

Animals↗

PubMed2003

Identification and isolation of lectin nucleotide sequences and species relationships in the genus Lens Miller.

Genes for lectin, a component of legume storage proteins, were identified and characterised in two lentil cultivars ( Lens culinaris ssp. culinaris) and six wild relatives. In each taxon no differences were found among the two or three lectin clones sequenced, while differences were observed among lectin genes isolated from the different taxa. All of the clones analysed contained an insert of 828 bp and showed a high similarity with the nucleotide sequence of Pisum sativum seed lectin, PSL1. The deduced amino acid lectin sequences in all taxa were 275 amino acids long, and their multiple alignment showed that most of the variation among them occurred in regions which are not important for metal- and sugar-binding. The data from Southern blot analysis indicated the presence of only one lectin gene in all Lens taxa except L. tomentosus. Phylogenetic analyses carried out on the lectin sequences showed the existence of two main clusters and clearly indicated that L. nigricans falls outside the two groups.

Base Sequence↗

PubMed2003

Lectin-related resistance factors against bruchids evolved through a number of duplication events.

Abundant lectin-related proteins found in common beans ( Phaseolus vulgaris L.) have been shown to confer resistance against the larvae of a number of bruchid species. Genes encoding for these proteins are members of the lectin multigene family, the most representative components being arcelins, phytohemagglutinins and alpha-amylase inhibitors. Arcelins have been described in seven variants, some of which are resistance factors against the Mexican bean weevil ( Zabrotes subfasciatus), a major bean predator. In this study the isolation and sequencing of arcelin genes from wild P. vulgaris genotypes, containing Arc3 and Arc7 variants, is reported, and similarities and evolutionary relationships among the seven known arcelins are described. The evolutionary analysis shows that arcelins 3 and 4 cluster together and are the most-ancient variants. A duplication event gave rise to two additional clusters, one comprising arcelins 1, 2 and 6 and separated from the cluster of arcelins 5 and 7. A multiple number of arcelin genes were found in arcelin 3 and 4 genotypes indicating that more than one type of arcelin gene may be present in the same locus. Some of these sequences are reminiscent of ancient duplication events in arcelin evolution demonstrating that arcelins have evolved through multiple duplications. A further aim of this paper was to better understand and describe the evolution of the entire lectin multigene family. Beside arcelins, a number of other types of sequences, such as putative lectins and sequences not easily classifiable, were found in genotypes containing Arc3 and Arc4. These results, together with the evolutionary analysis, indicate that lectin loci are quite complex and confirm their origin by multiple duplication events.

Amino Acid Sequence↗

PubMed2003

Evolution of TRG clusters in cattle and sheep genomes as drawn from the structural analysis of the ovine TRG2@ locus.

The availability of genomic clones representative of the T-cell receptor constant gamma (TRGC) ovine genes enabled us to demonstrate, by fluorescent in situ hybridization (FISH) on cattle and sheep metaphases, the presence of two T-cell receptor gamma (TRG1@ and TRG2@) paralogous loci separated by at least five chromosomal bands on chromosome 4. Only TRG1@ is included within a region of homology with human TRG locus on chromosome 7, thus TRG2@ locus appears to be peculiar to ruminants. The structure of the entire TRG2@ locus, the first complete physical map of any ruminant animal TCR gamma locus, is reported here. The TRG2@ spans about 90 kb and consists of three clusters that we named TRG6, TRG2, and TRG4, according to the constant genes name. Phylogenetic analysis has highlighted the correlation between the grouping pattern of cattle and sheep variable gamma (TRGV) genes and the relevant TRGC; variable (V), joining (J), and constant (C) rearrange to be found together in mature transcripts. The simultaneous results on the TRG2@ locus molecular organization in sheep and on the phylogenetic analysis of cattle and sheep V expressed sequences indicate that at least six TRG clusters distributed in the two loci are present in these ruminant animals. The inferred evolution of TRG clusters in cattle and sheep genomes is consistent with a scenario where a minimal ancient cluster, containing the basic structural scheme of one V, one J, and one C gene, has undergone a process of duplication and intrachromosomal transposition.

Animals↗

PubMed2001

Exon-intron organization of TRGC genes in sheep.

A series of genomic clones derived from a sheep library were used to determine the germline configuration and the exon-intron organization of TRGC2, TRGC3, and TRGC4 genes. Based on the outcomes of molecular analysis, we compared and aligned the genomic sequences with the known complete cDNA sequences of sheep and deduced the exon-intron organization of TRGC genes in this ruminant animal, EX1, corresponding to the disulfide-linked constant domain, and EX3, corresponding to the transmembrane and cytoplasmatic domains, are similar in length in all genes. Conversely, the hinge-encoding EX2A, EX2B, and EX2C exons differ in number and length between genes, and EX2A contains the TTKPP motif irrespective of whether it occurs in single or triplicate form. The molecular data also indicate that at least one additional gene is present in sheep. Phylogenetic analysis grouped the ruminant TRGC genes in two clusters that could have emerged from two ancestral forms that underwent a series of duplications giving rise to the new sequences that were selected and then fixed in the ruminant lineages. A correlation between the cluster distribution in the phylogenetic tree of TRGC genes and their expression during fetal development is discussed.

Amino Acid Sequence↗

PubMed2001

Lectin and lectin-related proteins in lima bean (Phaseolus lunatus L.) seeds: biochemical and evolutionary studies.

Lectin-related polypeptides are a class of defence proteins found in seeds of Phaseolus species. In Lima bean (P. lunatus), these proteins and their genes have been well characterized in the Andean morphotype, which represents one of the two gene pools of this species. To study the molecular evolution of the lectin family in Lima bean we characterized the polypeptides belonging to this multigene family and cloned the genes belonging to the Mesoamerican gene pool. The latter gene pool contains components similar to those of the Andean pool, namely: an amylase inhibitor-like (AIL), an arcelin-like (ARL) lectin and the less abundant Lima bean lectin (LBL). These proteins originate from an ancestor gene of the lectin type which duplicated to yield the lectin gene and the progenitor of ARL and AIL. In this species. ARL represents an evolutionary intermediate form that precedes AIL. Phylogenetic analysis supports an Andean origin for Lima bean. The molecular evolutionary studies were extended to the genes of common bean and demonstrated that true lectin genes and the ancestor of lectin-related genes are the result of a duplication event that occurred before speciation. Lima and common bean followed different evolutionary pathways and in the latter species a second duplication event occurred that gave rise, in Mesoamerican wild genotypes, to arcelin genes.

Amino Acid Sequence↗

PubMed2000

Evolution of the mitochondrial genetic system: an overview.

Mitochondria, semi-autonomous organelles possessing their own genetic system, are commonly accepted to descend from free-living eubacteria, namely hydrogen-producing alpha-proteobacteria. The progressive loss of genes from the primitive eubacterium to the nucleus of the eukaryotic cell is strongly justified by the Muller rachet principle, which postulates that asexual genomes, like mitochondrial ones, accumulate deleterious and sublethal mutations faster than sexual genomes, like the nucleus. According to this principle, the mitochondrial genome would be doomed to death; instead, we observe that the mitochondrial genome has a variable size and structure in the different organisms, though it contains more or less the same set of genes. This is an example of genetic conservation versus structural diversity. From an evolutionary point of view the genetic system of organelles is clearly under strong selective pressure and for its survival it needs to utilize strategies to slow down or halt the ratchet. Anyway, the mitochondrial genome changes with time, and the rate of evolution is different for both diverse regions of the mtDNA and between lineages, as demonstrated in the case of mammalian mt genomes. We report here our data on the evolution of the mitochondrial DNA in mammals which demonstrate the suitability of mtDNA as a molecular tool for evolutionary analyses.

Animals↗

PubMed2000

The complete Tirant transposable element in Drosophila melanogaster shows a structural relationship with retrovirus-like retrotransposons.

We have determined the structure and organization of Tirant, a retrotransposon of Drosophila melanogaster reported in literature to be responsible for four independent mutations. Tirant is a long terminal repeat (LTR) retrotransposon 8527bp long. It possesses three open reading frames (ORF) encoding Gag, Pol and Env proteins with a strong similarity with ZAM, a recently identified member of the gypsy class of retrovirus-like mobile elements. Molecular analysis of the Tirant genomic copies present in four D. melanogaster strains revealed that most of them are defective, non-autonomous elements that differ in the position and extension of the conserved internal portion. Defective elements lacking the Gag ORF but retaining the Env ORF are abundant in heterochromatin. Four discrete Tirant transcripts are observed during embryogenesis in the strain Oregon-R, the smaller of which, 1.8kb in size, originates from the splicing of a primary transcript and leads to a subgenomic RNA coding for the Env product.

Amino Acid Sequence↗

PubMed2000

MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status.

MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces cerevisiae. MitBASE reports all available information from different organisms and from intraspecies variants and mutants. Data have been drawn from the primary databases and from the literature; value adding information has been structured, e.g., editing information on protist mtDNA genomes, pathological information for human mtDNA variants, etc. The different databases, some of which are structured using commercial packages (Microsoft Access, File Maker Pro) while others use a flat-file format, have been integrated under ORACLE. Ad hoc retrieval systems have been devised for some of the above listed databases keeping into account their peculiarities. The database is resident at the EBI and is available at the following site: http://www3.ebi.ac.uk/Research/Mitbase/mitbas e.pl. The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecies diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme.

Animals↗

PubMed2000

Update of AMmtDB: a database of multi-aligned metazoa mitochondrial DNA sequences.

The AMmtDB database (http://bio-www.ba.cnr.it:8000/srs6/ ) has been updated by collecting the multi-aligned sequences of Chordata mitochondrial genes coding for proteins and tRNAs. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB data selected through SRS can be viewed and managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALW and PILEUP programs and then carefully optimized manually.

Animals↗

PubMed2000

Genomic organization of sheep TRDJ segments and their expression in the delta-chain repertoire in thymus.

cDNA sequences obtained from polymerase chain reaction products of reverse-transcribed RNA from sheep thymus showed the presence of a large number of members of the TRDV1 gene family. Some are TRDV1 genes also found in peripheral blood lymphocytes, while four genes had not been described so far. The cDNA sequences also showed extensive junctional diversity and a preferential usage of the three TRDJ elements. We characterized the genomic organization of the sheep TRDJ locus and detected a correlation between the nonrandom usage of TRDJ elements during development and their chromosomal order.

Amino Acid Sequence↗

PubMed2000

Evidence for two distinct subgroups of alfalfa mosaic virus (AMV) from france and italy and their relationships with other AMV strains Brief report.

The nucleotide sequence of the putative coat protein open reading frame of seven previously uncharacterized AMV strains from Italy and France was determined and aligned with comparable sequences of other AMV strains (425 L, 425 M, YSMV, S, VRU, 15/64 and Da). The data set of AMV sequences was used to determine phylogenetic relationships by both a stochastic (stationary Markov model) and a deterministic method (maximum-parsimony) of analysis. The topology of the trees obtained with the two methods was essentially the same showing that all AMV strains clustered in two monophyletic groups. Close clustering of Italian strains in subgroup I and of French strains in subgroup II seems to suggests the effect of geographic distinctiveness of evolutionary dynamics of these AMV strains. This separation did not correlate with differences in host range or symptoms (necrotic or non necrotic) induced in tomato but rather it reflected variations in the amino acid sequence of their CP, which might be related to structural properties of virus particles. A simple and rapid procedure based on the reverse transcriptase-polymerase chain reaction (RT-PCR) followed by ezymatic digestion (RFLP) was developed to identify and classify AMV isolates into the two subgroups. The method applied to a number of other AMV isolates from Italy and France supported their division in two distinct subgroups. This RT-PCR RFLP method may be useful way to investigate the dynamics of AMV populations in nature.

Alfalfa mosaic virus↗

PubMed1999

MitBASE: a comprehensive and integrated mitochondrial DNA database.

MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects all available information from different organisms and from intraspecie variants and mutants. Research institutions from different countries are involved, each in charge of developing, collecting and annotating data for the organisms they are specialised in. The design of the actual structure of the database and its implementation in a user-friendly format are the care of the European Bioinformatics Institute. The database can be accessed on the Web at the following address: http://www.ebi.ac. uk/htbin/Mitbase/mitbase.pl. The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecie diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme.

Animals↗

PubMed1999

Update of AMmtDB: a database of multi-aligned metazoa mitochondrial DNA sequences.

The present paper describes AMmtDB, a database collecting the multi-aligned sequences of vertebrate mitochondrial genes coding for proteins and tRNAs, as well as the multiple alignment of the mammalian mtDNA main regulatory region (D-loop) sequences. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. As far as the genes coding for tRNAs are concerned, the multi-alignments based on the primary and the secondary structures are both provided; for the mammalian D-loop multi-alignments we report the conserved regions of the entire D-loop (CSB1, CSB2, CSB3, the central region, ETAS1 and ETAS2) as defined by Sbisà et al. [ Gene (1997), 205, 125-140). A flatfile format for AMmtDB has been designed allowing its implementation in SRS (http://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB ). Data selected through SRS can be managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALV and PILEUP programs and then carefully optimized manually.

Animals↗

PubMed1998

Update of MmtDB: a Metazoa mitochondrial DNA variants database.

The present paper describes the improvements in MmtDB, a specialised database designed to collect Metazoa mitochondrial DNA variants. Priority in the data collection has been given to Metazoa for which a large amount of variants is available, e.g., for humans. Starting from the sequences available in the Nucleotide Sequence Databases, the redundant sequences have been removed and new sequences from other sources have been added. Value-added information is associated to each variant sequence, e.g., analysed region, experimental method, tissue and cell lines, population data, sex, age, family code and information about the variation events (nucleotide position, involved gene, restriction site gain or loss). Cross-references are introduced to the EMBL Data Library, as well as an internal cross-referencing among MmtDB entries according to tissual, heteroplasmic, familiar and aplotypical correlation. Furthermore MmtDB has a new section, AMmtDB: Aligned Metazoan mitochondrial biosequences. MmtDB can be accessed through the World Wide Web at URL http://WWW.ba.cnr.it/[symbol: see text]areamt08/MmtDBWWW.htm

Animals↗