SABIIA - Sistema Aberto e Integrado de Informação em Agricultura (Sabiia)

Paillard, Christine; Gausson, Sabrina; Nicolas, Jean-louis; Le Pennec, Jean Paul; Haras, Dominique.

Vibrio tapetis is the marine bacterium responsible for the brown ring disease (BRD) affecting die manila clam, Ruditapes philippinarum. Identification of V tapelis has been previously performed using biochemical criteria and serological procedures. All of these methods are time consuming and ill-adapted to individual screening. This study describes an oligonucleotidic probe (Vt446) and two PCR primers, deduced from the 16S rDNA sequence, allowing a fast and specific V tapetis identification using dot blot hybridisation and species-specific primed PCR (SSP-PCR). The probe and primers have been tested on 60 strains, including referenced Vibrio sp., Gram negative and positive bacteria, marine bacteria samples and isolated clam bacteria. For all the 19 V...

Tipo: Text

Palavras-chave: DOT BLOT hybridisation; SSP PCR; Vibriosis; Bivalve; Detection; Diagnostic.

Ano: 2006

URL: http://archimer.ifremer.fr/doc/2006/publication-1692.pdf

Observing and Studying Extreme Low Pressure Events with Altimetry

Occurrence of infectious Laryngotracheitis Virus (ILTV) in 2009-2013 in the State of São Paulo - Brazil

Carrere, Loren; Mertz, Francoise; Dorandeu, Joel; Quilfen, Yves; Patoux, Jerome.

The ability of altimetry to detect extreme low pressure events and the relationship between sea level pressure and sea level anomalies during extra-tropical depressions have been investigated. Specific altimeter treatments have been developed for tropical cyclones and applied to obtain a relevant along-track sea surface height (SSH) signal: the case of tropical cyclone Isabel is presented here. The S- and C-band measurements are used because they are less impacted by rain than the Ku-band, and new sea state bias (SSB) and wet troposphere corrections are proposed. More accurate strong altimeter wind speeds are computed thanks to the Young algorithm. Ocean signals not related to atmospheric pressure can be removed with accuracy, even within a Near Real Time...

Tipo: Text

Palavras-chave: Barotropic model; Sea level pressure; Extra tropical depressions; Tropical cyclones; Detection; Altimetry.

Ano: 2009

URL: http://archimer.ifremer.fr/doc/2009/publication-6350.pdf

Rev. Bras. Ciênc. Avic.

Parra,SHS; Nuñez,LFN; Astolfi-Ferreira,CS; Ferreira,JP.

Infectious laryngotracheitis is a very important respiratory disease because it causes significant economic losses in the poultry industry. The target of ILTV infections is the respiratory system, and the main organ in which the virus remains latent is the trigeminal ganglia. However, the virus has demonstrated tropism for other organs as well. The present study was conducted to determine the presence of Infectious Laryngotracheitis Virus (ILTV) in the state of São Paulo. Samples submitted to LABOR- USP during the last four years (2009-2013) analyzed by a nested/PCR technique. Out of the 682 samples from layers tested for LTIV, 12.46 % were positive, and derived from in both traditional (trachea and trigeminal ganglion) and untraditional (cecal tonsils,...

PCR-based sensitive detection of the edible fungus Boletus edulis from rDNA ITS sequences

Palavras-chave: Infectious Laryngotracheitis; PCR; Detection; Trachea; Trigeminal.

Ano: 2015

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-635X2015000100117

Electron. J. Biotechnol.

Lian,Bin; Zang,Jin-ping; Hou,Wei-guo; Yuan,Sheng; Smith,Donald L.

Identification of commercially important fungi, such as the valuable edible fungus Boletus edulis can be difficult considering visual or metabolic approaches. Based on phylogenetic analysis of the rDNA ITS sequence, a pair of specific primers was designed for differentiating B. edulis from other mushrooms by PCR. PCR was performed with total DNA as a template at an annealing temperature between 56-60ºC. Positive amplicons were obtained from B. edulis with all DNA templates from fruit bodies and cultured mycelium, but not from other fungal species at an annealing temperature of 60ºC. The result indicated that B. edulis could be clearly distinguished from other fungi by PCR, and there were no misidentifications under the reaction conditions used. The primers...

Tipo: Journal article

Palavras-chave: Boletus edulis; Detection; Edible fungi; Internal transcribed spacer; PCR; Specific primers.

Ano: 2008

URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582008000300011

Phylogenetic characterization of the first Ungulate tetraparvovirus 2 detected in pigs in Brazil

Souza,Carine Kunzler; Streck,André Felipe; Gonçalves,Karla Ratje; Pinto,Luciane Dubina; Ravazzolo,Ana Paula; Barcellos,David Emílio dos Santos Neves de; Canal,Cláudio Wageck.

Abstract Ungulate tetraparvovirus 2 (UTV2) , formerly known as porcine hokovirus due to its discovery in Hong Kong, is closely related to a Primate tetraparvovirus (human PARV-4) and Ungulate tetraparvovirus 1 (bovine hokovirus). Until now, UTV2 was detected in European, Asian and North American countries, but its occurrence in Latin America is still unknown. This study describes the first report of UTV2 in Brazil, as well as its phylogenetic characterization. Tissue samples (lymph node, lung, liver, spleen and kidney) of 240 piglets from eight different herds (30 animals each herd) were processed for DNA extraction. UTV2 DNA was detected by PCR and the entire VP1/VP2 gene was sequenced for phylogenetic analysis. All pigs from this study displayed...

Project ROMEO : E. C. n° FA-S2 9052 - Research objectives : Mortality in European Oysters - Final Report

Palavras-chave: Porcine; Tetraparvovirus; Phylogeny; Hokovirus; Detection; Ungulate.

Ano: 2016

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822016000200513

Renault, Tristan; Arzul, Isabelle.

Crassostrea gigas is increasingly being cultured in a great number of countries from animaIs originally introduced from Japan, and is one of the most exploited bivalve species in the EU (FAO, 1989). Although no serious pathogen was detected previously in Japanese oysters in Europe, mortalities have been observed since the introduction of this bivalve species into the EU. Thus, oyster cultivation may be endangered by the occurrence of epizootics, especially virus diseases, which are considered one of the maj or risks to production. Indeed, mortalities have been described among different species of ostreids and are associated with the presence of viruses belonging to various families. The first description of a virus was reported in adult Eastern oyters,...

Tipo: Text

Palavras-chave: Pathology; Virology; Herpes-like infection; Detection; Diagnosis; Herpesviridae; Oyster; Crassostrea gigas; Mortality.

Ano: 2000

URL: http://archimer.ifremer.fr/doc/00044/15536/12915.pdf

Quick adaptation of Ralstonia Solanacearum to copper stress to recover culturability and growth in water and soil

Ascarrunz,Sergio Daniel Moreira; Natsuaki,Tomohide; Honjo,Hitoshi; Fukui,Ryo.

Cells of Ralstonia solanacearum were exposed to Cu in distilled water, and the resulting Cu-stressed non-culturable cells were inoculated to natural (non-pasteurized) and pasteurized soils in order to examine their culturability and recovery. Exposing the cells to 20 µM CuSO4 produced transitory non-culturable cells, which exhibited a remarkable recovery in culturability after incubation in the solution for 36 h, reaching a density near the initial level by 108 h. To determine whether such non-culturable cells actually "resuscitated" or multiplied after adapting to Cu toxicity, growth curves were constructed in order to contrast the rates of increase in culturable cell numbers between Cu-stressed or non-stressed inocula. Additionally, fresh non-stressed...

Rapid and sensitive detection of ostreid Herpesvirus 1 in oyster samples by real-time PCR (Poster)

Palavras-chave: Ralstonia solanacearum; Non-culturable cells; Adaptation to copper; Survival; Detection.

Ano: 2011

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822011000200023

Pepin, Jean-francois; Riou, Antoine; Renault, Tristan.

Herpes and herpes-like virus infections have been reported in various marine mollusc species associated with high mortality rates. Following the characterisation and genome sequencing of ostreid herpesvirus 1 (OsHV-1), specific diagnostic tools have been developed based on conventional PCR techniques or in situ hybridisation. We have now developed a real-time PCR assay for rapid, sensitive and quantitative detection of OsHV-1, and compared it with a conventional PCR technique described previously. The new assay utilised SYBR® Green chemistry with specific primers C9/C10 targeting the C region, which is present in two copies in the OsHV-1 genome and encodes two proteins of unknown function. The assay was applied successfully to rapid diagnosis (100 minutes)...

Tipo: Text

Palavras-chave: Crassostrea gigas; PCR; Oyster; OsHV 1; Detection; Herpes virus 1.

Ano: 2007

URL: http://archimer.ifremer.fr/doc/2007/acte-3653.pdf

Rapid detection and quantification of the marine toxic algae, Alexandrium minutum, using a super-paramagnetic immunochromatographic strip test

Rapid detection of food-borne Salmonella contamination using IMBs-qPCR method based on pagC gene

Gas, Fabienne; Baus, Beatrice; Quere, Julien; Chapelle, Annie; Dreanno, Catherine.

The dinoflagellates of Alexandrium genus are known to be producers of paralytic shellfish toxins that regularly impact the shellfish aquaculture industry and fisheries. Accurate detection of Alexandrium including A. minutum is crucial for environmental monitoring and sanitary issues. In this study, we firstly developed a quantitative lateral flow immunoassay (LFIA) using super-paramagnetic nanobeads for A. minutum whole cells. This dipstick assay relies on two distinct monoclonal antibodies used in a sandwich format and directed against surface antigens of this organism. No sample preparation is required. Either frozen or live cells can be detected and quantified. The specificity and sensitivity are assessed by using phytoplankton culture and field samples...

Tipo: Text

Palavras-chave: Alexandrium minutum; Detection; Quantification; Dipstick lateral flow immunoassay; Super-paramagnetic.

Ano: 2016

URL: http://archimer.ifremer.fr/doc/00286/39695/38152.pdf

Wang,Jiashun; Li,Yi; Chen,Jia; Hua,Deping; Li,Yi; Deng,Hui; Li,Ying; Liang,Zhixuan; Huang,Jinhai.

Abstract Detection of Salmonella is very important to minimize the food safety risk. In this study, the recombinant PagC protein and PagC antibody were prepared and coupled with immunomagnetic beads (IMBs) to capture Salmonella cells from pork and milk samples. And then the SYBR Green qualitative PCR was developed to detect the pathogenic Salmonella. The results showed that the PagC polyclonal antiserum is of good specificity and the capture rate of 0.1 mg IMBs for Salmonella tended to be stable at the range of 70-74% corresponding to the concentrations between 101 and 104 CFU/mL. The method developed demonstrated high specificity for the positive Salmonella samples when compared to non-specific DNA samples, such as Escherichia coli, Staphylococcus aureus,...

Rapid identification of Mycobacterium tuberculosis complex by a novel hybridization signal amplification method based on self-assembly of DNA-streptavidin nanoparticles

Palavras-chave: Salmonella; IMBs-qPCR; PagC gene; Detection.

Ano: 2018

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822018000200320

Wang,Haihe; Zhao,Chunyan; Li,Fan.

Rapid detection of Mycobacterium tuberculosis complex (MTBC) is a critical step in controlling tuberculosis (TB). In this study, we used IS6110 as the specific identification target to develop a novel hybridization signal amplification method (HSAM) for the rapid and direct detection of MTBC from clinical sputum specimens. This system consists of magnetic bead-linked capture probes for target isolation, dextranbased nanoparticles for amplifying the reporter molecule (biotinylated-FITC), and detection probes (2B-DNA) for binding the nanoparticles. Both the capture and detection probes were specific to the IS6110 target sequence. Our results determined that as few as 10 copies of the IS6110 sequence or 10 M. tuberculosis bacteria could be detected,...

Rhinovirus detection using different PCR-based strategies

Palavras-chave: Mycobacterium tuberculosis complex (MTBC); Detection; Diagnosis; Rapid methods; Identification.

Ano: 2011

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822011000300016

Silva,E.R.M.; Watanabe,A.S.A.; Carraro,E.; Perosa,A.H.S.; Granato,C.F.H.; Bellei,N.C.J..

Human rhinoviruses (HRVs) are the major cause of the common cold. HRVs were recently reclassified into the Enterovirus genus (HEV) in the Picornaviridae family. HRVs and other members of the HEV genus share many common features, including sense RNA genomes and partial nucleotide sequence identity. The aim of this study was to evaluate different HRV detection strategies. Samples from adults with acute respiratory infection (n = 291) who were treated in Sao Paulo Hospital (2001-2003) were tested using three assays. The first assay detected picornaviruses by RT-PCR and hybridization, the second detected rhinoviruses using RT-PCR/sequencing, and the third differentiated HRV from HEV using duplex semi-nested-RT-PCR. Analysis of the results obtained from the...

Use of cardiopulmonary exercise testing to assess early ventilatory changes related to occupational particulate matter

Palavras-chave: Rhinovirus; Enterovirus; Detection; Differentiation.

Ano: 2012

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822012000200038

BJMBR

Chao,T.P.; Sperandio,E.F.; Ostolin,T.L.V.P.; Almeida,V.R.; Romiti,M.; Gagliardi,A.R.T.; Arantes,R.L.; Dourado,V.Z..

Spirometry has been used as the main strategy for assessing ventilatory changes related to occupational exposure to particulate matter (OEPM). However, in some cases, as one of its limitations, it may not be sensitive enough to show abnormalities before extensive damage, as seen in restrictive lung diseases. Therefore, we hypothesized that cardiopulmonary exercise testing (CPET) may be better than spirometry to detect early ventilatory impairment caused by OEPM. We selected 135 male workers with at least one year of exposure. After collection of self-reported socioeconomic status, educational level, and cardiovascular risk data, participants underwent spirometry, CPET, body composition assessment (bioelectrical impedance), and triaxial accelerometry (for...

Use of ROV's in operation of EAN underwater installation in the North Sea.

Palavras-chave: Occupational exposure to particulate matter; Cardiopulmonary exercise testing; Detection; Spirometry; Ventilatory impairment.

Ano: 2018

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2018000500612

Vibrio nigripulchritudo monitoring and strain dynamics in shrimp pond sediments

Ricci, F.

The purpose of the paper is to present the state of the Art in use of ROV for assistance in offshore operations. This is done through a review of operations and gained experience during East Frigg Field diverless installation in 1988 and 10 years or under water Inspection, Maintenance and Repair (IMR) on all Fields operated by Elf Aquitaine Norge A/S (EAN). Basic requirements to the types of ROVs are given and the cost-efficiency of the operations are discussed. The potential for further development of the ROVs to replace divers for a large part of annual IMR tasks below water is addressed.

Tipo: Text

Palavras-chave: Steel structures; Detection; Cracks; Surveillance and enforcement; Pipelines; Offshore structures; Underwater inspection; Offshore operations; Marine technology; Offshore; Unmanned vehicles.

Ano: 1990

URL: http://archimer.ifremer.fr/doc/1990/acte-1164.pdf

Zika detection: comparison of methodologies

Walling, Emilie; Vourey, Elodie; Ansquer, Dominique; Beliaeff, Benoit; Goarant, C..

Aims: A description of bacterial pathogens in shrimp ponds is necessary to understand their pathogenesis. Vibrio nigripulchritudo was shown to contain saprophytic and pathogenic strains among New Caledonian isolates. We established a method to map the development of V. nigripulchritudo in pond sediments at three different genetic levels: the species level, then at the pathogenic cluster level and finally at the plasmid level, present only in all highly pathogenic isolates. Methods and Results: PCR methods were applied to shrimp pond sediments both before and after a mortality outbreak. Using crude samples, the species V. nigripulchritudo is not detected at first (0/42 samples at day 56 post stocking) but appears frequently in the sediments after the...

Tipo: Text

Palavras-chave: Detection; Diagnosis; Diseases; Ecology; PCR; Plasmids; Soil; Virulence.

Ano: 2010

URL: http://archimer.ifremer.fr/doc/00004/11484/8177.pdf

Colombo,Tatiana Elias; Terzian,Ana Carolina Bernardes; Araújo Júnior,João Pessoa; Parreira,Ricardo; Cabrera,Eliana Márcia Sotello; Santos,Izalco Nuremberg Penha dos; Reis,Andréia Francesli Negri; Costa,Fabiana Rodrigues; Cruz,Lilian Elisa Arão Antônio; Rombola,Patrícia Lopes; Nogueira,Maurício Lacerda.

ABSTRACT Many countries in the Americas have detected local transmission of multiple arboviruses that cause febrile illnesses. Therefore, laboratory testing has become an important tool for confirming the etiology of these diseases. The present study aimed to compare the sensitivity and specificity of three different Zika virus detection assays. One hundred serum samples from patients presenting with acute febrile symptoms were tested using a previously reported TaqMan® RT-qPCR assay. We used a SYBR® Green RT-qPCR and a conventional PCR methodologies to compare the results. Of the samples that were determined to be negative by the TaqMan® RT-qPCR assay, 100% (Kappa = 0.670) were also found to be negative by SYBR® Green RT-qPCR based on Tm comparison;...