Search results for "real-time PCR"
showing 10 items of 39 documents
All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing.
2013
Background DNA-based methods like PCR efficiently identify and quantify the taxon composition of complex biological materials, but are limited to detecting species targeted by the choice of the primer assay. We show here how untargeted deep sequencing of foodstuff total genomic DNA, followed by bioinformatic analysis of sequence reads, facilitates highly accurate identification of species from all kingdoms of life, at the same time enabling quantitative measurement of the main ingredients and detection of unanticipated food components. Results Sequence data simulation and real-case Illumina sequencing of DNA from reference sausages composed of mammalian (pig, cow, horse, sheep) and avian (c…
Nation-wide study of the occurrence of Listeria monocytogenes in French soils using culture-based and molecular detection methods
2013
Identifiant HAL : hal-01120618; International audience; Soil is a potential reservoir of human pathogens and a possible source of contamination of animals, crops and water. In order to study the distribution of Listeria monocytogenes in French soils, a real-time PCR TaqMan assay targeting the phosphoribosylpyrophosphate synthetase (prs) gene of L. monocytogenes was developed for the specific detection and quantification of this bacterium within a collection of 1315 soil DNAs originated from the French Soil Quality Monitoring Network. The prs real-time PCR TaqMan assay was specific for L. monocytogenes and could quantify accurately down to 104L. monocytogenes per gram of dry soil. Among the …
Detection of Fusarium Species in Clinical Specimens by Probe-Based Real-Time PCR
2019
The mold Fusarium is a ubiquitous fungus causing plant, animal and human infections. In humans, Fusarium spp. are the major cause of eye infections in patients wearing contact lenses or after local trauma. Systemic infections by Fusarium spp. mainly occur in immunosuppressed patients and can disseminate throughout the human body. Due to high levels of resistance to antifungals a fast identification of the causative agent is an urgent need. By using a probe-based real-time PCR assay specific for the genus Fusarium we analysed several different clinical specimens detecting Fusarium spp. commonly found in clinical samples in Germany. Also, a large collection of lung fluid samples of haematolog…
SCAR-based real time PCR to identify a biocontrol strain (T1) of Trichoderma atroviride and study its population dynamics in soils.
2006
Strains of Trichoderma spp. are known for their antagonistic properties against plant pathogens, some are already on the market, others are under development. In order to launch a strain on the market its perfect identification at the species and strain levels is needed. The aim of this study is to (i) design a SCAR marker for specific identification of strain T1 of Trichoderma atroviride and (ii) monitor population dynamics of this strain in soil by real time PCR. A primer pair targeting a 141-bp fragment enabled specific detection of this strain without cross detection of autochthonous populations of Trichoderma in several field soils. In two soils, population dynamics assessed by real ti…
Freezing and storage at -20 °C provides adequate preservation of Toxoplasma gondii DNA for retrospective molecular analysis.
2014
Equipe EA MERS; International audience; Nucleic acid-based testing has become crucial for toxoplasmosis diagnosis. For retrospective (forensic or scientific) studies, optimal methods must be employed for DNA long-term storage. We compared Toxoplasma gondii detection before and after DNA storage using real-time PCR. No significant differences were found depending on duration or storage conditions at -20 °C or -80 °C.
Local response of bacterial densities and enzyme activities to elevated atmospheric CO2 and different N supply in the rhizosphere of Phaseolus vulgar…
2008
Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; Altered flux of labile C from plant roots into soil is thought to influence growth and maintenance of microbial communities under elevated atmospheric CO2 concentrations. We studied the abundance and function of the soil microbial community at two levels of spatial resolution to assess the response of microorganisms in the rhizosphere of the whole root system and of apical root zones of Phaseolus vulgaris L. to elevated CO2 and high or low N supply. At the coarser resolution, microb…
Real-time PCR based procedures for detection and quantification of Aspergillus carbonarius in wine grapes
2008
9 pages, 4 tables, 1 figure.
Environmental DNA analysis indicates that migration barriers are decreasing the occurrence of European eel (Anguilla anguilla) in distance from the s…
2020
Abstract The European eel (Anguilla L.) is considered critically endangered by the IUCN Red List, and recruitment remains low. One of the challenges for the species today is migration barriers that limit their habitat. Along the Norwegian coast, like in other countries, the abundance of eels appears to decrease with distance from the sea. This pattern may be a result of factors like water temperature, water quality, competition, and habitat suitability and availability. This study aims to use environmental DNA (eDNA) analysis to investigate the potential relationship between migration barriers and the decreasing occurrence of eels in distance from the sea by the coast of southern Norway. Si…
Preliminary evaluation of a zinc-copper-citric acid biocomplex for the control of Plenodomus tracheiphilus causal agent of citrus mal secco disease
2022
In this study we evaluated a zinc copper-citric acid biocomplex (Dentamet®) for the effect on citrus mal secco disease caused by Plenodomus tracheiphilus. In vitro tests highlighted an inhibitory activity of the compound on mycelial growth and phialoconidia germination. Independent in vivo trials were performed in a growth chamber inoculating a virulent fungal isolate on sour orange seedlings and young plants of two lines of Femminello lemon, namely ‘Zagara bianca’ and ‘2Kr’, grafted on sour orange and grown in pots. The compound was leaf sprayed three days before the inoculation by wounds with phialoconidia. Overall, disease index and disease progress curve in plants inoculated with P. tra…
The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM–SIAPEC-IAP–SIBioC–SIC–SIF Italian Scientific Societies
2021
The term liquid biopsy (LB) refers to the use of various biological fluids as a surrogate for neoplastic tissue to achieve information for diagnostic, prognostic and predictive purposes. In the current clinical practice, LB is used for the identification of driver mutations in circulating tumor DNA derived from both tumor tissue and circulating neoplastic cells. As suggested by a growing body of evidence, however, there are several clinical settings where biological samples other than tissue could be used in the routine practice to identify potentially predictive biomarkers of either response or resistance to targeted treatments. New applications are emerging as useful clinical tools, and o…