Search results for "sequence data"
showing 10 items of 1952 documents
Nucleotide variation in the VP7 gene affects PCR genotyping of G9 rotaviruses identified in Italy
2003
A modified (aFT9m) and a degenerate (aFT9d) version of the rotavirus G9-specific primer (aFT9) allowed strains that were previously untypable, because of point mutations accumulating at the primer binding site, to be G typed by reverse transcription-polymerase chain reaction. The strains were collected during 2001-2002 in Italy in hospitals of the Apulia region, from children affected by severe rotavirus-associated enteritis. Using a wide selection of G9 rotaviruses detected worldwide, sequencing of the G9 untypable strains, sequence comparison, and phylogenetic analysis showed that the Italian strains have strong genetic similarity (< or =99.4%) to G9 rotaviruses identified recently in man…
Genomic characterization of a novel group A lamb rotavirus isolated in Zaragoza, Spain.
2008
An ovine rotavirus (OVR) strain, 762, was isolated from a 30-day-old lamb affected with severe gastroenteritis, in Zaragoza, Spain, and the VP4, VP7, VP6, NSP4, and NSP5/NSP6 genes were subsequently characterized molecularly. Strain OVR762 was classified as a P[14] rotavirus, as the VP4 and VP8* trypsin-cleavage product of the VP4 protein revealed the highest amino acid (aa) identity (94% and 97%, respectively) with that of the P11[14] human rotavirus (HRV) strain PA169, isolated in Italy. Analysis of the VP7 gene product revealed that OVR762 possessed G8 serotype specificity, a type common in ruminants, with the highest degree of aa identity (95–98%) shared with serotype G8 HRV, bovine rot…
A comparative analysis of the products of GROEL-1 gene fromChlamydia trachomatisserovar D and the HSP60 var1 transcript fromHomo sapienssuggests a po…
2009
Summary Chlamydia trachomatis serovar D produces large quantities of HSP60-1 during infections, which accumulate inside the host cell inducing autoimmunity. We compare the aminoacid sequences of the human HSP60 with the bacterial counterpart to better elucidate how CTHSP60 may simulate HSP60 from human origin during infection and may induce an autoimmune response. As a result of the comparison we suggest several possible epitopes of the CTHSP60, which may induce autoimmunity.
Characterization of the first extended-spectrum beta-lactamase-producing nontyphoidal Salmonella strains isolated in Tehran, Iran.
2009
The infections caused by Salmonella remain a significant public health problem throughout the world. beta-Lactams and fluoroquinolones are generally used to treat invasive Salmonella infections, but emergence and spread of antibiotic-resistant strains are being increasingly notified in many countries. In particular, detection of extended-spectrum beta-lactamases (ESBLs) in Salmonella spp. is a newly emerging threat worldwide. This study was carried out to characterize beta-lactamase-producing Salmonella strains identified in Tehran, Iran. Over the 2-year period from 2007 to 2008, 6 of 136 Salmonella isolates recovered from pediatrics patients, including three Salmonella enterica serotypes E…
Pythium perplexum isolated from soil in France: morphology, molecular characterisation and biological control.
2001
Pythium perplexum (F-926) was isolated from a soil sample taken in the Burgundy region in France. In 1907, it was mistakenly described by Bulter as P. vexans. Despite morphological resemblance, the comparison between the internal transcribed spacer 1 regions of the ribosomal DNA of the two fungi leaves no doubt of their different identities. P. perplexum was found to be highly pathogenic to cucumber seedlings. Damping-off disease of cucumber caused by P. perplexum can effectively be controlled by using the soil bacterium Serratia plymuthica (B-781). The details of the morphology and the molecular characterisation of P. perplexum and its biological control with S. plymuthica are described he…
Isolation and characterization of a fish F-type lectin from gilt head bream (Sparus aurata) serum.
2007
A novel fucose-binding lectin, designated SauFBP32, was purified by affinity chromatography on fucose-agarose, from the serum of the gilt head bream Sparus aurata. Electrophoretic mobility of the subunit revealed apparent molecular weights of 35 and 30 kDa under reducing and non-reducing conditions, respectively. Size exclusion analysis suggests that the native lectin is a monomer under the selected experimental conditions. Agglutinating activity towards rabbit erythrocytes was not significantly modified by addition of calcium or EDTA; activity was optimal at 37 degrees C, retained partial activity by treatment at 70 degrees C, and was fully inactivated at 90 degrees C. On western blot anal…
Transfer, composition and technological characterization of the lactic acid bacterial populations of the wooden vats used to produce traditional stre…
2015
The biofilms of 12 wooden vats used for the production of the traditional stretched cheeses Caciocavallo Palermitano and PDO Vastedda della valle del Belìce were investigated. Salmonella spp. and Listeria monocytogenes were never detected. Total coliforms were at low numbers with Escherichia coli found only in three vats. Coagulase-positive staphylococci (CPS) were below the enumeration limit, whereas lactic acid bacteria (LAB) dominated the surfaces of all vats. In general, the dominance was showed by coccus LAB. Enterococci were estimated at high numbers, but usually between 1 and 2 Log cycles lower than other LAB. LAB populations were investigated at species and strain level and for thei…
Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic div…
2015
Ecological and evolutionary studies largely assume that island populations display low levels of neutral genetic variation. However, this notion has only been formally tested in a few cases involving plant taxa, and the confounding effect of selection on genetic diversity (GD) estimates based on putatively neutral markers has typically been overlooked. Here, we generated nuclear microsatellite and plastid DNA sequence data in Periploca laevigata, a plant taxon with an island–mainland distribution area, to (i) investigate whether selection affects GD estimates of populations across contrasting habitats; and (ii) test the long-standing idea that island populations have lower GD than their mai…
Analysis of early strains of the norovirus pandemic variant GII.4 Sydney 2012 identifies mutations in adaptive sites of the capsid protein.
2014
AbstractGlobal surveillance for norovirus identified in 2012 the emergence of a novel pandemic GII.4 variant, termed Sydney 2012. In Italy, the novel pandemic variant was identified as early as November 2011 but became predominant only in the winter season 2012–2013. Upon sequencing and comparison with strains of global origin, the early Sydney 2012 strains were found to differ from those spreading in 2012–2013 in the capsid (ORF2) putative epitopes B, C and D, segregating into a distinct phylogenetic clade. At least three residues (333, 340 and 393, in epitopes B, C and D, respectively) of the VP1 varied among Sydney 2012 strains of different clades. These findings suggest that the spread …
Epidemiological dynamics of norovirus GII.4 variant New Orleans 2009.
2015
Norovirus (NoV) is one of the major causes of diarrhoeal disease with epidemic, outbreak and sporadic patterns in humans of all ages worldwide. NoVs of genotype GII.4 cause nearly 80–90 % of all NoV infections in humans. Periodically, some GII.4 strains become predominant, generating major pandemic variants. Retrospective analysis of the GII.4 NoV strains detected in Italy between 2007 and 2013 indicated that the pandemic variant New Orleans 2009 emerged in Italy in the late 2009, became predominant in 2010–2011 and continued to circulate in a sporadic fashion until April 2013. Upon phylogenetic analysis based on the small diagnostic regions A and C, the late New Orleans 2009 NoVs circulati…