Consulta: subjectFacets:"Pyrosequencing"
Registros recuperados: 12
Data/hora: 06/06/2024 15:33:29

High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses
Provedor de dados: 74
Autores: Yang,Seung Hak; Lim,Joung Soo; Khan,Modabber Ahmed; Kim,Bong Soo; Choi,Dong Yoon; Lee,Eun Young; Ahn,Hee Kwon.
The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses) and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3–6 weeks. The representation of phyla was restored...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Pig; Decomposition; Leachate; Bacterial community; Pyrosequencing.
Ano: 2015
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572015000300373

Constitutional and somatic methylation status of DMRH19 and KvDMR in Wilms tumor patients
Provedor de dados: 74
Autores: Cardoso,Leila C.A.; Castaño,Jair A. Tenorio; Pereira,Hanna S.; Lima,Maria Angélica de F.D.; Santos,Anna Cláudia E. dos; Faria,Paulo S. de; Ferman,Sima; Seuánez,Héctor N.; Nevado,Julián B.; Almeida,José Carlos Cabral de; Lapunzina,Pablo; Vargas,Fernando R.
The most frequent epigenetic alterations in Wilms tumor (WT) occur at WT2, assigned to 11p15. WT2 consists of two domains: telomeric domain 1 (DMRH19) that contains the IGF2 gene and an imprinted maternally expressed transcript (H19) and centromeric domain 2 (KvDMR) that contains the genes KCNQ1, KCNQ1OT1 and CDKN1C. In this work, we used pyrosequencing and MS-MLPA to compare the methylation patterns of DMRH19/KvDMR in blood and tumor samples from 40 WT patients. Normal constitutional KvDMR methylation indicated that most of the epigenetic alterations in WT occur at DMRH19. Constitutional DMRH19 hypermethylation (HM DMRH19) was observed in two patients with Beckwith-Wiedemann syndrome. Pyrosequencing and MS-MLPA showed HM DMRH19 in 28/34 tumor samples:...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Epigenetic; Histopathology; Methylation; MS-MLPA; Pyrosequencing.
Ano: 2012
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000500002

Caractérisation et quantification moléculaires de l’écosystème microbien d’altération du saumon cru et des crevettes cuites
Provedor de dados: 5
Autores: Mace, Sabrina.
Raw salmon and cooked shrimp sold in supermarket are usually found under vacuum or CO2 modified atmosphere packaging (MAP). This type of packaging inhibit growth of some bacteria, therefore, CO2 tolerant bacteria dominate spoilage microbiota of these products. The aim of this study is to improve knowledge about bacteria involved in spoilage. Spoilage microbial ecosystems of raw salmon and tropical cooked shrimp were described using classic miocrobiological and molecular methods like PCR-TTGE and pyrosequencing. Lactic acid bacteria, notably Lactococcus piscium, Carnobacterium maltaromaticum, Carnobacterium divergens, Lactobacillus sakei, and Gram negative bacteria like Photobacterium phosphoreum and Enterobacteriaceae (Serratia spp.) has been described as...
Tipo: Text
Palavras-chave: Produits de la mer; Microbiote; PCR-TTGE; Pyroséquençage; Potentiel d’altération; P. phosphoreum; PCR en temps-réel; Seafood products; Microbiota; PCR-TTGE; Pyrosequencing; Spoilage potential; P. phosphoreum; Real-time PCR.
Ano: 2013
URL: https://archimer.ifremer.fr/doc/00166/27773/25963.pdf

Small-scale variability of protistan planktonic communities relative to environmental pressures and biotic interactions at two adjacent coastal stations
Provedor de dados: 5
Autores: Genitsaris, Savvas; Monchy, Sebastien; Breton, Elsa; Lecuyer, Eric; Christaki, Urania.
The aim of this study was to analyze planktonic protistan assemblages under different environmental pressures at 2 adjacent coastal stations (inshore and offshore; similar to 6.4 km apart) in the eastern English Channel (EEC). Samples were collected between March 2012 and June 2013, and analyzed using bioinformatic analysis and tag pyrosequencing of the V2-V3 hypervariable region of the 18S rRNA gene. In addition to the taxonomic composition of the protistan communities, the detected operational taxonomic units (OTUs) were sorted into 6 major functional groups based on their trophic roles in marine systems. Comparisons of 13 environmental factors, including physical and chemical variables, indicated significant differences between the 2 stations. However,...
Tipo: Text
Palavras-chave: Unicellular eukaryotes; Community organization; Environmental parameters; Biotic interactions; 18S rRNA; Pyrosequencing; Bioinformatics; Ecological tools.
Ano: 2016
URL: https://archimer.ifremer.fr/doc/00373/48450/48765.pdf

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing
Provedor de dados: 5
Autores: Logares, Ramiro; Audic, Stephane; Santini, Sebastien; Pernice, Massimo C.; De Vargas, Colomban; Massana, Ramon.
Flagellated heterotrophic microeukaryotes have key roles for the functioning of marine ecosystems as they channel large amounts of organic carbon to the upper trophic levels and control the population sizes of bacteria and archaea. Still, we know very little on the diversity patterns of most groups constituting this evolutionary heterogeneous assemblage. Here, we investigate 11 groups of uncultured flagellates known as MArine STramenopiles (MASTs). MASTs are ecologically very important and branch at the base of stramenopiles. We explored the diversity patterns of MASTs using pyrosequencing (18S rDNA) in coastal European waters. We found that MAST groups range from highly to lowly diversified. Pyrosequencing (hereafter '454') allowed us to approach to the...
Tipo: Text
Palavras-chave: Diversity; Heterotrophic-flagellates; MAST; Pyrosequencing; Stramenopiles.
Ano: 2012
URL: https://archimer.ifremer.fr/doc/00374/48501/48815.pdf

Selection of bioprotective cultures for preventing cold-smoked salmon spoilage
Provedor de dados: 5
Autores: Leroi, Francoise; Cornet, Josiane; Chevalier, Frederique; Cardinal, Mireille; Coeuret, Gwendoline; Chaillou, Stephane; Joffraud, Jean-jacques.
Biopreservation is a natural technology of food preservation, which consists of inoculating food with microorganisms selected for their antibacterial properties. The objective of this study was to select lactic acid bacteria (LAB) to improve the quality of cold-smoked salmon (CSS). In this work, different strains representative of the 4 dominant species, identified in a previous study by pyrosequencing the 16S rRNA gene, were isolated and their spoiling potential in CSS blocks, sterilized by ionization, was assessed by twelve trained panelists along the vacuum storage at 8 °C . Photobacterium phosphoreum, Brochothrix thermosphacta and Serratia proteamaculans released strong off-odors whereas the spoiling potential of Carnobacterium divergens was weaker....
Tipo: Text
Palavras-chave: Biopreservation; Lactic acid bacteria; Sensory analysis; Seafood products; Microbial ecosystem; Pyrosequencing.
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00268/37966/36045.pdf

Low Evolutionary Diversification in a Widespread and Abundant Uncultured Protist (MAST-4)
Provedor de dados: 5
Autores: Rodriguez-martinez, Raquel; Rocap, Gabrielle; Logares, Ramiro; Romac, Sarah; Massana, Ramon.
Recent culture-independent studies of marine planktonic protists have unveiled a large diversity at all phylogenetic scales and the existence of novel groups. MAST-4 represents one of these novel uncultured lineages, and it is composed of small (similar to 2 mu m) bacterivorous eukaryotes that are widely distributed in marine systems. MAST-4 accounts for a significant fraction of the marine heterotrophic flagellates at the global level, playing key roles in the marine ecological network. In this study, we investigated the diversity of MAST-4, aiming to assess its limits and structure. Using ribosomal DNA (rDNA) sequences obtained in this study (both pyrosequencing reads and clones with large rDNA operon coverage), complemented with GenBank sequences, we...
Tipo: Text
Palavras-chave: MAST-4; Low evolutionary diversification; Uncultured protist; Pyrosequencing; ITS secondary structure.
Ano: 2012
URL: https://archimer.ifremer.fr/doc/00374/48506/48778.pdf

Microbial communities associated with benthic faunal assemblages at cold seep sediments of the Sonora Margin, Guaymas Basin
Provedor de dados: 5
Autores: Cruaud, Perrine; Vigneron, Adrien; Pignet, Patricia; Caprais, Jean-claude; Lesongeur, Francoise; Toffin, Laurent; Godfroy, Anne; Cambon-bonavita, Marie-anne.
The Sonora Margin cold seeps present a seafloor mosaic pattern consisting of different faunal assemblages and microbial mats. To better understand if sedimentary microbial communities reflect this patchy distribution, all major habitats were investigated using four complementary approaches: 16S rRNA gene sequence 454 pyrosequencing, quantitative polymerase chain reaction, fluorescence in situ hybridization and geochemistry analyses. This study reveals that sediments populated by different surface assemblages show distinct porewater geochemistry features and are associated with distinct microbial communities. In the sediments underlying the microbial mat and the surrounding macrofauna, microbial communities were dominated by anaerobic methane oxidizers...
Tipo: Text
Palavras-chave: Microbial communities; Pyrosequencing; MBG-D; ANME; Faunal assemblages; Vesicomyidae; Siboglinidae; Microbial mat.
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00288/39889/38434.pdf

Establishment of microbiota in larval culture of Pacific oyster, Crassostrea gigas
Provedor de dados: 5
Autores: Asmani, Katia; Petton, Bruno; Le Grand, Jacqueline; Mounier, Jerome; Robert, Rene; Nicolas, Jean-louis.
This study has two main objectives: (1) to implement a recycling aquaculture system (RS) for the larvae of the oyster Crassostrea gigas, and (2) to characterise the bacterial communities established in different compartments of this system. An RS with 25% fresh seawater addition per hour and another with no addition (0%) were compared with a flow-through system (FT). Larval survival was equivalent in RS and FT, but growth rate was 17% slower in RS than in FT. The physical chemical parameters remained stable, except for pH that decreased to 7.75 and salinity that increased to 37.5‰ in the RS 0%. In both systems, the cultivable bacteria were present in similar numbers in seawater (around 105 ml− 1) and in larvae (103 larva− 1) on day 15.  Bacterial...
Tipo: Text
Palavras-chave: RAS; Bivalve larvae; Microbiota; Pyrosequencing; Hatchery.
Ano: 2016
URL: https://archimer.ifremer.fr/doc/00346/45691/45311.pdf

The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories
Provedor de dados: 5
Autores: Gatesoupe, Francois-joel; Huelvan, Christine; Le Bayon, Nicolas; Le Delliou, Herve; Madec, Lauriane; Mouchel, Olivier; Quazuguel, Patrick; Mazurais, David; Zambonino-infante, Jose-luis.
Background  The better understanding of how intestinal microbiota interacts with fish health is one of the key to sustainable aquaculture development. The present experiment aimed at correlating active microbiota associated to intestinal mucosa with Specific Growth Rate (SGR) and Hypoxia Resistance Time (HRT) in European sea bass individuals submitted to different nutritional histories: the fish were fed either standard or unbalanced diets at first feeding, and then mixed before repeating the dietary challenge in a common garden approach at the juvenile stage. Results  A diet deficient in essential fatty acids (LH) lowered both SGR and HRT in sea bass, especially when the deficiency was already applied at first feeding. A protein-deficient diet with high...
Tipo: Text
Palavras-chave: Host-microbe interaction; 16S rRNA; Pyrosequencing; Autochthonous bacteria; Alternative feed ingredients; Physiological status.
Ano: 2016
URL: https://archimer.ifremer.fr/doc/00356/46719/46590.pdf

Development of typing methods based on pyrosequencing technology fot the analysis of six bovine genes related to marbling
Provedor de dados: 46
Autores: Ripoli,M.V; Rogberg-Muñoz,A; Liron,J.P; Giovambattista,G.
Several methods such as PCR-RFLP, OLA, DNA sequencing, PCR-SSCP and ARMS-PCR have been developed to detect the allelic variation at substitutions K232A of DGAT1, GH6.1 of GH, F279Y of GHR, R4C of LEP, I74V of FABP4, and at the transition in the TG 5´ leader sequence. Most of these methods are manual processes and therefore increase the time spent on the assay and limit the number of animals analyzed. Herein, we describe the development of pyrosequencing-based methods for the bovine DGAT1, GH, GHR, LEP, FABP4 and TG genes, whose polymorphisms have been associated with variation in carcass composition. This method was validated by analyzing DNA samples belonging to the Aberdeen Angus and Hereford breeds previously typed by PCR-SSCP, PCR-RFLP and/or DNA...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bovine molecular markers; Polymorphism; Pyrosequencing; Marbling.
Ano: 2013
URL: http://www.scielo.org.ar/scielo.php?script=sci_arttext&pid=S1852-62332013000300005

COMPOSITION AND FUNCTION OF THE MICROBIAL COMMUNITY RELATED WITH THE NITROGEN CYCLING ON THE POTATO RHIZOSPHERE
Provedor de dados: 37
Autores: FLÓREZ-ZAPATA,NATHALIA; GARCÍA,JUAN CARLOS; DEL PORTILLO,PATRICIA; RESTREPO,SILVIA; URIBE-VELEZ,DANIEL.
In the S. tuberosum group phureja crops, mineral fertilizer and organic amendments are applied to meet the plants´ nutritional demands, however the effect of such practices on the associated rizospheric microbial communities are still unknown. Nitrogen plays an important role in agricultural production, and a great diversity of microorganisms regulates its transformation in the soil, affecting its availability for the plant. The aim of this study was to assess the structure of microbial communities related with the N cycle of S. tuberosum group phureja rizospheric soil samples, with contrasting physical-chemical properties and fertilization strategy. Few significant differences between the community composition at the phylum level were found, only...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Nitrogen cycle; Nitrification; Nitrogenase; Pyrosequencing; Solanum phureja.
Ano: 2013
URL: http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0120-548X2013000300004