Search results for "Genetic Analysis"

Genotyping of the genus Proteus by rpoB sequence analysis

2005

Background. The genetic relationship among different species within the genus Proteus has still not been clarified and previous studies by rRNA gene restriction patterns (ribotypes) suggested a high genetic variability in the presently recognised nomenspecies. Methods. The usefulness of rpoB sequencing for inter- and intraspecies discrimination in the genus Proteus was evaluated on 11 type and clinical strains belonging to the four described species: P. penneri, P. vulgaris, P. mirabilis, and P. myxofaciens. Results. The rpoB sequencing proved able to characterise the different species, showing six well defined rpoB sequence groups in the 1153 bp region analysed. P. myxofaciens and P. mirab…

An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides

2018

Infection with human BK polyomavirus, a small double-stranded DNA virus, potentially results in severe complications in immunocompromised patients. Here, we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing. Our data reveal the highest genomic evolutionary rate described in double-stranded DNA viruses, i.e., 10−3–10−5 substitutions per nucleotide site per year. High mutation rates in viruses allow their escape from immune surveillance and adaptation to new hosts. By combining mutational landscapes across viral genomes with in silico prediction of viral peptides, we demonstrate the presence of significantly more coding substitutions within predicted cog…

Comparative cytogenetics of human chromosome 3q21.3 reveals a hot spot for ectopic recombination in hominoid evolution

2004

Fluorescence in situ hybridization mapping of fully integrated human BAC clones to primate chromosomes, combined with precise breakpoint localization by PCR analysis of flow-sorted chromosomes, was used to analyze the evolutionary rearrangements of the human 3q21.3-syntenic region in orangutan, siamang gibbon, and silvered-leaf monkey. Three independent evolutionary breakpoints were localized within a 230-kb segment contained in BACs RP11-93K22 and RP11-77P16. Approximately 200 kb of the human 3q21.3 sequence was not present on the homologous orangutan, siamang, and Old World monkey chromosomes, suggesting a genomic DNA insertion into the breakpoint region in the lineage leading to humans a…

G2 rotavirus infections in an infantile population of the South of Italy: variability of viral strains over time.

2005

Rotavirus positive samples collected in Palermo, Italy, during 2002–2004 did not react with the G2 type-specific RV5:3 monoclonal antibodies (MAbs) and could be identified as G2 only by RT-PCR genotyping. The genetic variation of VP7 and VP4 antigenic proteins was studied in 14 G2 samples including a selection of both those successfully characterized by serotyping and those failing to be serotyped. The phylogenetic analysis performed on partial VP7 sequences showed a temporal clustering of these strains, with those isolated in Palermo in 2003 belonging to the same lineage of G2 MAbs-unreactive strains identified in UK in 1996–1997 and in Bari, Italy, in 2003–2004. A single amino acid substi…

Genetic diversity and phylogenetic relationships among four breeds reared in Sicily using β-lactoglobulin promoter region polymorphisms

2011

The aim of this work was to analyze the genetic diversity and the phylogenetic relationships among the Valle del Belice (VDB) breed and the other sheep breeds considered as ancestors, using -lactoglobulin (BLG) promoter region polymorphisms. The BLG promoter region of 50 randomly chosen animals from the four breeds (VDB n=20; Comisana (COM) n=10; Pinzirita (PIN) n=10; Sarda (SAR) n=10) were sequenced and aligned, and results showed the presence of 36 single nucleotide polymorphisms (SNPs) and one deletion. The number of polymorphic sites identified showed high variability within breeds. Nucleotide (π) and haplotype (Hd) diversity were estimated with DnaSP software, whereas PHASE software w…

Application of molecular markers to investigate genetic diversity in Sicilian livestock

2014

La diversità genetica delle specie e razze di interesse zootecnico, rappresenta un’importante risorsa in tutti i sistemi di allevamento . Per lo studio della diversità genetica, nel corso dei decenni sono stati sviluppati diversi metodi che si basano su informazioni del pedigree o su dati molecolari (microsatelliti e SNPs, Single Nucleotide Polymorphisms). Con l’aumento della disponibilità di marcatori molecolari per la maggior parte delle specie di interesse zootecnico, e con lo sviluppo di sofisticate tecniche analitiche, sta crescendo la capacità di caratterizzare la variabilità genetica delle razze. Inoltre, ad oggi, poche sono le informazioni sulla diversità genetica delle razze e dell…

Phylogenetic analysis of the Sicilian Hieracium taxa (Asteraceae) using "DNA barcoding": preliminary data

2014

Phylogenetic analysis in the clinical risk management of an outbreak of hepatitis C virus infection among transfused thalassaemia patients in Italy

2021

Background: Occurrence of hepatitis C virus (HCV) infection is reduced by effective risk management procedures, but patient-to-patient transmission continues to be reported in healthcare settings. Aim: To report the use of phylogenetic analysis in the clinical risk management of an HCV outbreak among 128 thalassaemia outpatients followed at a thalassaemia centre of an Italian hospital. Methods: Epidemiological investigation and root-cause analysis were performed. All patients with acute hepatitis and known chronic infection were tested for HCV RNA, HCV genotyping, and NS3, NS5A, and NS5B HCV genomic region sequencing. To identify transmission clusters, phylogenetic trees were built for each…

One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.

2020

Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species…

A novel S379A TARDBP mutation associated to late-onset sporadic ALS

2019

Since 2008, several groups have reported a lot of dominant mutations in TARDBP gene as a primary cause of Amyotrophic lateral sclerosis (ALS). Mutations in TARDBP gene are responsible for 4–5% of familial ALS (fALS) and nearly 1% of sporadic ALS (sALS). To date, over 50 dominant mutations were found in TDP-43 in both familial and sporadic ALS patients, most of which were missense mutations in the C-terminal glycine-rich region. Herein, we describe the clinical and genetic analysis of an Italian non-familial ALS patient with a late onset and a rapid disease progression, which led to the discovery of a novel TARDBP mutation. After neurological evaluation, molecular investigation highlighted t…