In order to investigate the relationships between Italian wild boar and major pig breeds, we studied the genetic variability of four wild boar populations in Italy (Arezzo, Pisa, Parma, Bergamo) ...using a 533-bp fragment of the mitochondrial control region. Sixty-nine wild boar samples were analysed, allowing the identification of 10 distinct haplotypes, which involve a total of 15 single nucleotide polymorphisms. Phylogenetic and network analyses were performed also considering several sequences of wild and domesticated forms available in the databases. The Bayesian phylogenetic tree and the Median-Joining network analyses show three main groups: the Italian (IT), European (EU) and Asian (AS) clades. The IT clade corresponds to the Maremma endemic wild boar population and also includes Sardinian individuals, while the EU and AS groups include wild boars as well as domestic pig breeds. Only two individuals from Pisa cluster in the IT group, whereas two haplotypes from Bergamo cluster in the AS group and all other samples cluster in the EU clade. These findings suggest that in Italy wild boar populations have a mixed origin, both EU and AS, and that an interbreeding between wild and domesticated strains has probably occurred. Eight of the 10 wild boars coming from the Migliarino-San Rossore-Massaciuccoli Regional Park (Pisa) belong to H2 and H3 haplotypes, and cluster into the EU clade, suggesting that this regional park is not anymore exclusive of the endemic Maremma wild boar.
The availability of almost one thousand complete mitochondrial genome (mtDNA) sequences of chordates provides an almost unique opportunity to analyse the evolution of this genome in the phylum ...Chordata, and to identify possible divergent evolutionary trends followed by the three chordate subphyla: Vertebrata, Cephalochordata and Tunicata. Here, we review some genome-level features of mtDNA, such as genetic code, gene content, genome architecture and gene strand asymmetry, mostly focusing on differences existing between tunicates and remaining chordates. Indeed, tunicate mtDNAs show a surprisingly high variability in several genome-level features, even though the current tunicate taxon sampling is absolutely insufficient and is focused mainly on the class Ascidiacea. On the contrary, a stabilization of the mtDNA structural and evolutionary features is observed in both cephalochordates and vertebrates, where genome-level features are almost invariant. Thus, different evolutionary dynamics, probably related to divergent functional constraints, have modelled the overall mtDNA structure and organization of the three chordate subphyla.
Individual mitochondrial genes or genomic features are commonly used as phylogenetic markers at many taxonomic levels. We used a mitogenomics approach to demonstrate the existence of two cryptic ...species in the ascidian Ciona intestinalis , a model chordate whose status as a single species has recently been questioned. Comprehensive comparative analysis of the mitochondrial genome of the two cryptic species revealed significant differences in gene order, size and number of noncoding regions, compositional features and divergence of protein-coding genes.
A recently introduced neural networks architecture, 'adaptive spline neural networks' with FIR/IIR synapse, is used to define a general class of physical-like sound synthesis model. To reduce ...computational cost, use is made of power-of-two synapses followed by a CR-spline-based flexible activation function the shape of which can be modified through its control points. The learning phase is performed by an efficient combinatorial optimisation algorithm, Tabu Search, for both power-of-two weights and CR-spline control points.
Forum on Robert B. Pippin, "After the beautiful" ed. by M. Farina, with R.B. Pippin, M. Farina, F. Campana, F. Iannelli, T. Pinkard, I. Testa, L. Corti
Lebenswelt (Milano),
01/2016
7
Journal Article
PspC, also called SpsA, CbpA, PbcA, and Hic, is a surface protein of Streptococcus pneumoniae studied for its antigenic properties, its capability to bind secretory IgA, C3 and complement factor H, ...and its activity as an adhesin. In this work we characterized the pspC locus of 43 pneumococcal strains by DNA sequencing of PCR fragments. Using PCR primers designed on two unrelated open reading frames, flanking the pspC locus, it was possible to amplify the pspC locus of each of the 43 strains of S. pneumoniae. In 37 out of 43 strains there was a single copy of the pspC gene, while two tandem copies of pspC were found in the other six strains. The sequence of the pspC locus was different in each of the 43 strains. Insertion sequences were found in the pspC locus of 11 out of 43 strains. Analysis of the deduced amino acid sequence of the PspC variants showed a common organization of the molecules: (i) a 37 amino acid leader peptide which is conserved in all proteins, (ii) an N-terminal portion which is essentially alpha-helical, and is the result of assembly of eight major sequence blocks, (iii) a proline-rich region, and (iv) a C-terminal anchor responsible for the cell surface attachment. By sequence comparison we identified 11 major groups of PspC proteins. Proteins within one group displayed only minor variations of the amino acid sequence. An unexpected finding was that PspC variants could differ in the anchor sequence. While 32 of the PspC proteins displayed the typical choline binding domain of pneumococcal surface proteins, 17 other PspCs showed the LPXTG motif, which is typical of surface proteins of other gram-positive bacteria. This major difference in the anchor region was also observed in the adjacent proline-rich regions which differed considerably in size and composition.
The important human pathogen Streptococcus pneumoniae was found to absorb factor H, an inhibitor of complement, from human plasma. We identified the gene encoding a novel surface protein, factor ...H-binding inhibitor ofcomplement (Hic), in the pspC locus of type 3 pneumococci. Unlike PspC proteins in other serotypes, Hic is anchored to the cell wall by means of an LPXTG motif, and the overall sequence homology to various PspC proteins is low. However, the NH2-terminal region showed significant homology to the NH2-terminal region of several PspC proteins. A fragment of Hic, covering this homologous region, was expressed as a glutathioneS-transferase (GST) fusion protein. GST:Hic39–261 bound radiolabeled factor H and inhibited binding of factor H to pneumococci of different serotypes. Interaction kinetics between GST:Hic39–261 and factor H were studied with surface plasmon resonance and showed a high affinity binding (KA = 5 × 107,KD = 2.3 × 10−8). Mutant pneumococci lacking Hic showed no absorption of factor H in human plasma and no binding of radiolabeled factor H, suggesting that Hic is responsible for factor H-binding in type 3 pneumococci. Factor H-dependent inhibition of the alternative pathway was not diminished by the presence of GST:Hic39–261. In addition, an intrinsic inhibitory effect of Hic is suggested.
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