Search results for "PHYLOGENY"
showing 10 items of 1398 documents
Nucleotide sequence of a ssRNA phage from Acinetobacter: kinship to coliphages.
2002
The complete nucleotide sequence of ssRNA phage AP205 propagating in Acinetobacter species is reported. The RNA has three large ORFs, which code for the following homologues of the RNA coliphage proteins: the maturation, coat and replicase proteins. Their gene order is the same as that in coliphages. RNA coliphages or Leviviridae fall into two genera: the alloleviviruses, like Qβ, which have a coat read-through protein, and the leviviruses, like MS2, which do not have this coat protein extension. AP205 has no read-through protein and may therefore be classified as a levivirus. A major digression from the known leviviruses is the apparent absence of a lysis gene in AP205 at the usual positio…
HSP70 gene expression in Mytilus galloprovincialis hemocytes is triggered by moderate heat shock and Vibrio anguillarum, but not by V. splendidus or …
2005
Complete sequence of HSP70 cDNA from the mussel, Mytilus galloprovincialis was established before quantifying its expression following moderate heat shock or injection of heat-killed bacteria. HSP70 cDNA is comprised of 2378 bp including one ORF of 654 aa, with a predicted 70 bp 5'-UTR and a 343 bp 3'-UTR (GenBank, 18 Jan 05, AY861684). Alignment identity ranged from 89% for Crassostrea ariakensis to 72% for C. virginica. Curiously, HSP70 gene and cDNA sequences from M. galloprovincialis, deposited later (03 and 27 May), show only 73% identity with the present sequence. Meanwhile, characteristic motifs of the HSP70 family were located in conserved positions. Expression of HSP70 gene was qua…
The pro-opiomelanocortin gene of the zebrafish (Danio rerio)
2003
The cDNA and the gene for pro-opiomelanocortin (POMC) in the zebrafish (Danio rerio) were isolated and analyzed. The gene consists of three exons and two short introns and has a similar overall structural organization as in Homo sapiens. Intron 1 (339 bp) divides the 5(') untranslated region from the coding region while intron 2 (1522 bp) is located between the signal peptide and the sequence encoding ACTH. Transcription starts 26 bp downstream of a TATA box and there is one polyadenylation signal in the 3(') untranslated region. The cDNA comprises of 964 bp with an open reading frame encoding a 222 amino acid hormone prepropeptide that is split into six putative hormones. Sequence comparis…
A method for determining the position and size of optimal sequence regions for phylogenetic analysis.
1995
The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optimize this kind of study, we suggest a heuristic procedure for detection of the shortest region whose informational content can be considered sufficient for significant phylogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of reference to those obtained for different windows of variable size and posit…
Characterisation of fascioliasis lymnaeid intermediate hosts from Chile by DNA sequencing, with emphasis on Lymnaea viator and Galba truncatula.
2011
In South America, Fasciola hepatica infection poses serious health problems in both humans and livestock. In Chile, the medical impact appears yearly stable and mainly concentrated in central regions, where the veterinary problem is highlighted by higher animal prevalences. Studies were undertaken by rDNA ITS-2 and ITS-1 and mtDNA cox1 sequencing to clarify the specific status of the lymnaeids, their geographical distribution and fascioliasis transmission capacity in Chile, by comparison with other American countries and continents. Results change the lymnaeid scenario known so far. The lymnaeid fauna of mainland Chile shows to be poor, including only two authochthonous species, Lymnaea via…
Extended-Spectrum ß-Lactamase, AmpC-Producing, and Fluoroquinolone-Resistant Escherichia coli in Retail Broiler Chicken Meat, Italy.
2015
Background: Globally, antimicrobial drug-resistant Escherichia coli is among the most common etiological agents of invasive disease in humans. In Europe, increasing proportions of infections due to third-generation cephalosporins and/or fluoroquinolone-resistant extraintestinal pathogenic E. coli (ExPEC) strains are reported. E. coli from poultry are those more closely linked to human E. coli, but lack of reliable data makes it difficult to assess the attributable risk of different food sources. In the present study, our objective was to investigate the antimicrobial resistance profile, phylogenetic background, and virulence factors of E. coli isolates from broiler chicken meat sold at reta…
Numerical Taxonomy of Vibrionaceae Isolated from Cultured Amberjack ( Seriola dumerili ) and Surrounding Water
2003
A numerical taxonomic study was performed on 148 isolates of Gram-negative, heterotrophic, facultative anaerobic bacteria isolated from amberjack (Seriola dumerili) and its surrounding culture water. The study included 30 type and reference strains belonging to genera Vibrio, Listonella, and Photobacterium. The strains were characterized by 109 morphological, biochemical, physiological, and nutritional tests. Cluster analysis of similarity matrices obtained with S(SM) and S(J) coefficients was carried out. UPGMA (unweighted pair group mathematical average) analysis defined 11 phena at S(SM) values > or = 86%. Nine phena were identified as Vibrio alginolyticus, V. fischeri, V. harveyi, V. ca…
Genetic relatedness among environmental, clinical, and diseased-eel Vibrio vulnificus isolates from different geographic regions by ribotyping and ra…
1998
ABSTRACT Genetic relationships among 132 strains of Vibrio vulnificus (clinical, environmental, and diseased-eel isolates from different geographic origins, as well as seawater and shellfish isolates from the western Mediterranean coast, including reference strains) were analyzed by random amplified polymorphic DNA (RAPD) PCR. Results were validated by ribotyping. For ribotyping, DNAs were digested with Kpn I and hybridized with an oligonucleotide probe complementary to a highly conserved sequence in the 23S rRNA gene. Random amplification of DNA was performed with M13 and T3 universal primers. The comparison between ribotyping and RAPD PCR revealed an overall agreement regarding the high l…
In-Depth Characterization of Viral Isolates from Plasma and Cells Compared with Plasma Circulating Quasispecies in Early HIV-1 Infection
2012
Background The use of in vitro models to unravel the phenotypic characteristics of circulating viral variants is key to understanding HIV-1 pathogenesis but limited by the availability of primary viral isolates from biological samples. However, overall in vivo genetic variability of HIV-1 within a subject may not be reflected in the viable viral population obtained after isolation. Although several studies have tried to determine whether viral populations expanded in vitro are representative of in vivo findings, the answer remains unclear due to the reduced number of clonal sequences analyzed or samples compared. In order to overcome previous experimental limitations, here we applied Deep P…
Volatile organic compounds in truffle (Tuber magnatum Pico): Comparison of samples from different regions of Italy and from different seasons
2015
AbstractIn this paper volatile organic compounds (VOCs) from Tuber magnatum fruiting bodies were analyzed using a PTR-TOF-MS instrument. The aim was to characterize the VOC's profile of the fruiting bodies and identify if any VOCs were specific to a season and geographical areas. Multiple factorial analysis (MFA) was carried out on the signals obtained by MS. Experiments using ITS region sequencing proved that the T. magnatum life cycle includes the formation of fruiting bodies at two different times of the year. The VOCs profiles diverge when different seasonal and geographical productions are considered. Using PTR-TOF-MS, compounds present at levels as low pptv were detected. This made it…