scholarly journals Faster monitoring of the invasive alien species (IAS) Dreissena polymorpha in river basins through isothermal amplification

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Joana Carvalho ◽  
Alejandro Garrido-Maestu ◽  
Sarah Azinheiro ◽  
Pablo Fuciños ◽  
Jorge Barros-Velázquez ◽  
...  
Keyword(s):  
Real Time ◽  
Dreissena Polymorpha ◽  
Mitochondrial Gene ◽  
Environmental Dna ◽  
Isothermal Amplification ◽  
Detection Methods ◽  
Order Of Magnitude ◽  
Intercalating Dye ◽  
Time Required ◽  
Guadalquivir River

AbstractZebra mussel (Dreissena polymorpha) is considered as one of the 100 most harmful IAS in the world. Traditional detection methods have limitations, and PCR based environmental DNA detection has provided interesting results for early warning. However, in the last years, the development of isothermal amplification methods has received increasing attention. Among them, loop-mediated isothermal amplification (LAMP) has several advantages, including its higher tolerance to the presence of inhibitors and the possibility of naked-eye detection, which enables and simplifies its potential use in decentralized settings. In the current study, a real-time LAMP (qLAMP) method for the detection of Dreissena polymorpha was developed and tested with samples from the Guadalquivir River basin, together with two real-time PCR (qPCR) methods using different detection chemistries, targeting a specific region of the mitochondrial gene cytochrome C oxidase subunit I. All three developed approaches were evaluated regarding specificity, sensitivity and time required for detection. Regarding sensitivity, both qPCR approaches were more sensitive than qLAMP by one order of magnitude, however the qLAMP method proved to be as specific and much faster being performed in just 9 min versus 23 and 29 min for the qPCR methods based on hydrolysis probe and intercalating dye respectively.

Sensitive Detection of Soy (Glycine max) by Real-Time Polymerase Chain Reaction Targeting the Mitochondrial atpA Gene

2011 ◽  
Vol 94 (6) ◽  
pp. 1863-1873 ◽  
Author(s):  
Tobias Bauer ◽  
Katja Kirschbaum ◽  
Silvia Panter ◽  
Marion Kenk ◽  
Jörg Bergemann
Keyword(s):  
Mitochondrial Dna ◽  
Real Time ◽  
Nuclear Dna ◽  
Mitochondrial Gene ◽  
Soy Flour ◽  
Detection Methods ◽  
Minimal Amount ◽  
Food Matrix ◽  
Atpa Gene ◽  
Reporter Probe

Abstract Detection of trace amounts of allergens is essential for correct labeling of food products by the food industry. PCR-based detection methods currently used for this purpose are targeting sequences of DNA present in the cell nucleus. In addition to nuclear DNA, a substantial amount of mitochondrial DNA (mtDNA) copies are present in the cytoplasm of eukaryotic cells. The nuclear DNA usually consists of a set of DNA molecules present in two copies per cell, whereas mitochondrial DNA is present in a few hundred copies per cell. Thus, an increase in sensitivity can be expected when mtDNA is used as the target. In this study, we present a reporter probe-based real-time PCR method amplifying the mitochondrial gene of the alpha chain of adenosine triphosphate synthetase from soy. Increase in sensitivity was examined by determining the minimal amount of soy DNA detectable by mtDNA and nuclear DNA (nDNA) amplification. Additionally, the LOD of soy in a food matrix was determined for mtDNA amplification and compared to the LOD determined by nDNA amplification. As food matrix, a model spice spiked with soy flour was used. Sensitivity of PCR-based soy detection can be increased by using mtDNA as the target.

scholarly journals Rapid And Sensitive Detection Of Lawsonia Intracellularis In Pigs By Real-Time Loop-Mediated Isothermal Amplification

2015 ◽  
Vol 65 (1) ◽  
pp. 20-29 ◽  
Author(s):  
PARK Byung-Yong ◽  
SHIM Kwan-Seob ◽  
KIM Won-Il ◽  
HOSSAIN Md Mukter ◽  
KIM Bumseok ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Lamp Assay ◽  
Isothermal Amplification ◽  
Sensitive Detection ◽  
Detection Methods ◽  
Conventional Pcr ◽  
Fecal Samples ◽  
Loop Mediated Isothermal Amplification ◽  
Time Loop

Abstract A simple and rapid real-time loop-mediated isothermal amplification (LAMP) assay designed to detect Lawsonia (L.) intracellularis, an important bacteria causing proliferative enteropathy in pigs. A set of four primers targeting the ubiquinone/menaquinone biosynthesis methylase (ubiE) gene was designed for the LAMP reaction. Additionally, serial 10-fold dilutions of cultured L. intracellularis and spiked feces were also used for the optimization of real-time LAMP. The lower limit of the linear range of the assay in L. intracellularis was 1.0 × 100 L. intracellularis. Real-time LAMP was 10 and 100 times more sensitive than real-time PCR and conventional PCR detection methods, respectively. Based on testing of 213 porcine fecal samples using real-time LAMP, realtime PCR and PCR, the agreement quotients of real-time LAMP with conventional PCR and with real-time PCR were 0.77 and 0.95, respectively. This study demonstrated that real-time LAMP was a powerful tool for the rapid and sensitive detection of L. intracellularis in porcine fecal samples.

scholarly journals Influence of Features on Accuracy of Anomaly Detection for an Energy Trading System

Sensors ◽  
2021 ◽  
Vol 21 (12) ◽  
pp. 4237
Author(s):  
Hoon Ko ◽  
Kwangcheol Rim ◽  
Isabel Praça
Keyword(s):  
Anomaly Detection ◽  
Real Time ◽  
Feature Detection ◽  
Trading System ◽  
Judgment Accuracy ◽  
Energy Trading ◽  
Real Time Processing ◽  
Detection Model ◽  
Time Required ◽  
The Relationship

The biggest problem with conventional anomaly signal detection using features was that it was difficult to use it in real time and it requires processing of network signals. Furthermore, analyzing network signals in real-time required vast amounts of processing for each signal, as each protocol contained various pieces of information. This paper suggests anomaly detection by analyzing the relationship among each feature to the anomaly detection model. The model analyzes the anomaly of network signals based on anomaly feature detection. The selected feature for anomaly detection does not require constant network signal updates and real-time processing of these signals. When the selected features are found in the received signal, the signal is registered as a potential anomaly signal and is then steadily monitored until it is determined as either an anomaly or normal signal. In terms of the results, it determined the anomaly with 99.7% (0.997) accuracy in f(4)(S0) and in case f(4)(REJ) received 11,233 signals with a normal or 171anomaly judgment accuracy of 98.7% (0.987).

scholarly journals Near-surface real-time seismic imaging using parsimonious interferometry

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sherif M. Hanafy ◽  
Hussein Hoteit ◽  
Jing Li ◽  
Gerard T. Schuster
Keyword(s):  
Fluid Flow ◽  
Real Time ◽  
Temporal Resolution ◽  
Seismic Imaging ◽  
Time Lapse ◽  
Rock Properties ◽  
Recording Time ◽  
Near Surface ◽  
Arrival Times ◽  
Order Of Magnitude

AbstractResults are presented for real-time seismic imaging of subsurface fluid flow by parsimonious refraction and surface-wave interferometry. Each subsurface velocity image inverted from time-lapse seismic data only requires several minutes of recording time, which is less than the time-scale of the fluid-induced changes in the rock properties. In this sense this is real-time imaging. The images are P-velocity tomograms inverted from the first-arrival times and the S-velocity tomograms inverted from dispersion curves. Compared to conventional seismic imaging, parsimonious interferometry reduces the recording time and increases the temporal resolution of time-lapse seismic images by more than an order-of-magnitude. In our seismic experiment, we recorded 90 sparse data sets over 4.5 h while injecting 12-tons of water into a sand dune. Results show that the percolation of water is mostly along layered boundaries down to a depth of a few meters, which is consistent with our 3D computational fluid flow simulations and laboratory experiments. The significance of parsimonious interferometry is that it provides more than an order-of-magnitude increase of temporal resolution in time-lapse seismic imaging. We believe that real-time seismic imaging will have important applications for non-destructive characterization in environmental, biomedical, and subsurface imaging.

Detection by real-time quaking-induced conversion (RT-QuIC), ELISA, and IHC of chronic wasting disease prion in lymph nodes from Pennsylvania white-tailed deer with specific PRNP genotypes

2021 ◽  
pp. 104063872110214
Author(s):  
Deepanker Tewari ◽  
David Steward ◽  
Melinda Fasnacht ◽  
Julia Livengood
Keyword(s):  
Real Time ◽  
Disease Susceptibility ◽  
Chronic Wasting Disease ◽  
Low Frequency ◽  
The United States ◽  
Detection Methods ◽  
Spongiform Encephalopathy ◽  
Wasting Disease ◽  
Diagnostic Laboratory ◽  
Highly Sensitive

Chronic wasting disease (CWD) is a prion-mediated, transmissible disease of cervids, including deer ( Odocoileus spp.), which is characterized by spongiform encephalopathy and death of the prion-infected animals. Official surveillance in the United States using immunohistochemistry (IHC) and ELISA entails the laborious collection of lymphoid and/or brainstem tissue after death. New, highly sensitive prion detection methods, such as real-time quaking-induced conversion (RT-QuIC), have shown promise in detecting abnormal prions from both antemortem and postmortem specimens. We compared RT-QuIC with ELISA and IHC for CWD detection utilizing deer retropharyngeal lymph node (RLN) tissues in a diagnostic laboratory setting. The RLNs were collected postmortem from hunter-harvested animals. RT-QuIC showed 100% sensitivity and specificity for 50 deer RLN (35 positive by both IHC and ELISA, 15 negative) included in our study. All deer were also genotyped for PRNP polymorphism. Most deer were homozygous at codons 95, 96, 116, and 226 (QQ/GG/AA/QQ genotype, with frequency 0.86), which are the codons implicated in disease susceptibility. Heterozygosity was noticed in Pennsylvania deer, albeit at a very low frequency, for codons 95GS (0.06) and 96QH (0.08), but deer with these genotypes were still found to be CWD prion-infected.

scholarly journals Statistical Uncertainty of DNS in Geometries without Homogeneous Directions

2021 ◽  
Vol 11 (4) ◽  
pp. 1399
Author(s):  
Jure Oder ◽  
Cédric Flageul ◽  
Iztok Tiselj
Keyword(s):  
Channel Flow ◽  
A Priori ◽  
Time Integration ◽  
Navier Stokes ◽  
Statistical Uncertainty ◽  
Time Step ◽  
Order Of Magnitude ◽  
Averaging Time ◽  
The Individual ◽  
Time Required

In this paper, we present uncertainties of statistical quantities of direct numerical simulations (DNS) with small numerical errors. The uncertainties are analysed for channel flow and a flow separation case in a confined backward facing step (BFS) geometry. The infinite channel flow case has two homogeneous directions and this is usually exploited to speed-up the convergence of the results. As we show, such a procedure reduces statistical uncertainties of the results by up to an order of magnitude. This effect is strongest in the near wall regions. In the case of flow over a confined BFS, there are no such directions and thus very long integration times are required. The individual statistical quantities converge with the square root of time integration so, in order to improve the uncertainty by a factor of two, the simulation has to be prolonged by a factor of four. We provide an estimator that can be used to evaluate a priori the DNS relative statistical uncertainties from results obtained with a Reynolds Averaged Navier Stokes simulation. In the DNS, the estimator can be used to predict the averaging time and with it the simulation time required to achieve a certain relative statistical uncertainty of results. For accurate evaluation of averages and their uncertainties, it is not required to use every time step of the DNS. We observe that statistical uncertainty of the results is uninfluenced by reducing the number of samples to the point where the period between two consecutive samples measured in Courant–Friedrichss–Levy (CFL) condition units is below one. Nevertheless, crossing this limit, the estimates of uncertainties start to exhibit significant growth.

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