Search results for "genetic analysi"
showing 10 items of 150 documents
Evolution of fitness in experimental populations of vesicular stomatitis virus
1996
Abstract The evolution of fitness in experimental clonal populations of vesicular stomatitis virus (VSV) has been compared under different genetic (fitness of initial clone) and demographic (population dynamics) regimes. In spite of the high genetic heterogeneity among replicates within experiments, there is a clear effect of population dynamics on the evolution of fitness. Those populations that went through strong periodic bottlenecks showed a decreased fitness in competition experiments with wild type. Conversely, mutant populations that were transferred under the dynamics of continuous population expansions increased their fitness when compared with the same wild type. The magnitude of …
Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family.
2016
Reconstructing the transition from a single compartment bacterium to a highly compartmentalized eukaryotic cell is one of the most studied problems of evolutionary cell biology. However, timing and details of the establishment of compartmentalization are unclear and difficult to assess. Here, we propose the use of molecular markers specific to cellular compartments to set up a framework to advance the understanding of this complex intracellular process. Specifically, we use a protein family related to ribosome biogenesis, YRG (YlqF related GTPases), whose evolution is linked to the establishment of cellular compartments, leveraging the current genomic data. We analyzed orthologous proteins …
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…
Complete genome analysis of contemporary G12P[8] rotaviruses reveals heterogeneity within Wa-like genomic constellation
2016
G12 rotaviruses are globally emergent rotaviruses causing severe childhood gastroenteritis. Little is known about the evolution and diversity of G12P[8] rotaviruses and the possible role that widespread vaccine use, globally, has had on their emergence. In Sicily, Italy, surveillance activity for rotaviruses has been conducted uninterruptedly since 1985, thus representing a unique observatory for the study of human rotaviruses in the pre- and post-vaccine era. G12 rotaviruses were first detected only in 2012 and between 2012 and 2014 they accounted for 8.7% of all rotavirus-associated infections among children, with peaks of 27.8% in 2012/2013 and 21% in 2014. We determined and analyzed the…
Full-genome sequencing of a Hungarian canine G3P[3] Rotavirus A strain reveals high genetic relatedness with a historic Italian human strain
2015
A canine Rotavirus A strain was identified in the fecal specimen of a young dog during 2012 in Hungary. The strain RVA/Dog-wt/HUN/135/2012/G3P[3] shared complete genotype constellation (G3-P[3]-I3-R3-C3-M3-A15-N2-T3-E3-H6) and high genome sequence similarity (nt, 98.8 %) with a historic human strain, RVA/Human-tc/ITA/PA260-97/1997/G3P[3]. This study provides evidence for the canine origin of the unusual NSP1 genotype, A15, and reinforces the hypothesis of direct interspecies transmission of canine rotaviruses to humans.
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…