Search results for "sequence analysi"
showing 10 items of 1351 documents
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…
Hemoprotozoa of domestic animals in France: Prevalence and molecular characterization
2008
Very limited information is available on epizootiology of haematozoan infections in French domestic animals. In an attempt to address this issue, prevalence of piroplasmida was studied in carnivores and ruminants, whereas prevalence of Hepatozoon spp. was only investigated in carnivores. In total, 383 animals were included in the survey (namely 116 cats, 108 dogs, 91 sheep and 68 cows). Parasite diagnosis was carried out using molecular methods such as PCR and sequencing of the 18S rRNA gene. In addition, ruminant samples were analyzed with the reverse line blotting technique (RLB). Results of RLB and PCR plus sequencing were in total agreement. In carnivores, haematozoan prevalence was clo…
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…
Pyrosequencing vs. culture-dependent approaches to analyze lactic acid bacteria associated to chicha, a traditional maize-based fermented beverage fr…
2015
The diversity of lactic acid bacteria (LAB) associated with chicha, a traditional maize-based fermented alcoholicbeverage from Northwestern Argentina, was analyzed using culture-dependent and culture-independent approaches.Samples corresponding to 10 production steps were obtained from two local producers at Maimará(chicha M) and Tumbaya (chicha T). Whereas by culture-dependent approach a few number of species(Lactobacillus plantarum and Weissella viridescens in chicha M, and Enterococcus faecium and Leuconostocmesenteroides in chicha T) were identified, a higher quantitative distribution of taxa was found in both beveragesby pyrosequencing. The relative abundance of OTUs was higher in chic…
Complete Genome Sequence of the Enterobacter cancerogenus Bacteriophage Enc34
2012
ABSTRACT Enterobacter cancerogenus is widely distributed in nature and is generally recovered from environmental or vegetal sources. In some cases, it has also been associated with human infections. In this study, the complete genomic sequence of virulent E. cancerogenus bacteriophage Enc34 was determined. The Enc34 genome is 60,364 bp in length and contains 80 open reading frames. To our knowledge, this is the first report of a bacteriophage infecting E. cancerogenus .
Wickerhamomyces sylviae f.a., sp. nov., an ascomycetous yeast species isolated from migratory birds.
2013
In the present work, we investigated the phylogenetic position and phenotypic characteristics of eight yeast isolates collected from migratory birds on the island of Ustica, Italy. A phylogenetic analysis based on the D1/D2 region of the large-subunit rRNA gene showed that all isolates clustered as a single separate lineage within the Wickerhamomyces clade. They exhibited distinct morphological and physiological characteristics and were clearly separated from their closest relatives, Wickerhamomyces lynferdii, Wickerhamomyces anomalus and Wickerhamomyces subpelliculosus, in blastn searches. On the basis of the isolation source, physiological features and molecular strain typing carried out …
A sequence motif enriched in regions bound by the Drosophila dosage compensation complex
2010
Abstract Background In Drosophila melanogaster, dosage compensation is mediated by the action of the dosage compensation complex (DCC). How the DCC recognizes the fly X chromosome is still poorly understood. Characteristic sequence signatures at all DCC binding sites have not hitherto been found. Results In this study, we compare the known binding sites of the DCC with oligonucleotide profiles that measure the specificity of the sequences of the D. melanogaster X chromosome. We show that the X chromosome regions bound by the DCC are enriched for a particular type of short, repetitive sequences. Their distribution suggests that these sequences contribute to chromosome recognition, the genera…
Assessing the root of bilaterian animals with scalable phylogenomic methods.
2009
A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however, has been inconsistent in phylogenetic studies using one or several genes. Furthermore, Acoela has been among the least stable taxa in recent animal phylogenomic analyses, which simultaneously examine many genes from many species, while Nemertodermatida has not been sampled in any phylogenomic study. New sequence data are presented here from org…
Expression of the human XPB/ERCC-3 excision repair gene-homolog in the sponge Geodia cydonium after exposure to ultraviolet radiation.
1998
Abstract The marine demosponge Geodia cydonium encodes a gene, termed GCXPB , which displays 62% identity to the human XPB/ERCC-3 gene that specifically corrects the repair defect in xeroderma pigmentosum and in Cockayne's syndrome. The cDNA was isolated and characterized the deduced aa sequence, XPB_GEOCY, with the calculated size of 91,541 Da comprises the characteristic domains found in the related helicases. Phylogenetic tree analysis revealed that the sponge sequence is grouped to the metazoan related XPB/ERCC-3 polypeptides. Northern Blot analyses have been performed with sponge samples collected at different depths, thus exposed to different intensities of UV sunlight in the field. T…
Acyl-homoserine lactone production is more common among plant-associated Pseudomonas spp. than among soilborne Pseudomonas spp.
2001
ABSTRACT A total of 137 soilborne and plant-associated bacterial strains belonging to different Pseudomonas species were tested for their ability to synthesize N -acyl-homoserine lactones (NAHL). Fifty-four strains synthesized NAHL. Interestingly, NAHL production appears to be more common among plant-associated than among soilborne Pseudomonas spp. Indeed, 40% of the analyzed Pseudomonas syringae strains produced NAHL which were identified most often as the short-chain NAHL, N -hexanoyl- l -homoserine lactone, N -(3-oxo-hexanoyl)-homoserine lactone, and N -(3-oxo-octanoyl)- l -homoserine lactone (no absolute correlation between genomospecies of P. syringae and their ability to produce NAHL …