scholarly journals Detection of Phytophthora ramorum in Nurseries and Forest Lands in California in 2004 to 2009

Plant Disease ◽  
2016 ◽  
Vol 100 (1) ◽  
pp. 139-148 ◽  
Author(s):  
C. L. Blomquist ◽  
L. E. Yakabe ◽  
S. Rooney-Latham ◽  
N. McRoberts ◽  
C. Thomas
Keyword(s):  
Internal Control ◽  
False Negative ◽  
Sampling Strategy ◽  
Phytophthora Ramorum ◽  
Seasonal Effect ◽  
Enzyme Linked Immunosorbent Assay ◽  
Phytophthora Spp ◽  
Lithocarpus Densiflorus ◽  
Control Failure ◽  
Forest Lands

From December 2004 through May 2009, samples were collected from California nurseries and wild lands to survey for Phytophthora ramorum and comply with federal regulations of nursery stock. Samples were prescreened by an enzyme-linked immunosorbent assay (ELISA) that detects Phytophthora spp. and tested by culture, P. ramorum-specific real-time polymerase chain reaction (PCR), and nested PCR. Yearly percentages of infected samples ranged from 0.6 to 2.3%. Camellia spp., Rhododendron spp., Magnolia spp., Pieris spp., and Laurus nobilis tested positive the most frequently in the nurseries and Lithocarpus densiflorus, Umbellularia californica, and Quercus agrifolia tested positive most often from wild lands. Of the 118,410 samples isolated onto PARP media, 0.8% was identified as P. ramorum. Of 115,056 samples tested by ELISA, 5.9% tested positive for Phytophthora spp. Of the 6,520 samples tested by PCR, 12.4% tested positive for P. ramorum. The false-negative, positive, and internal control failure rates of the assays are discussed. After removing the seasonal effect of sampling strategy, isolation of the pathogen into culture was found to be seasonally dependent whereas detectability by PCR and ELISA was not. To our knowledge, this is the first evaluation of a regulatory testing program for a plant pathogen on this scale using standardized assays.

scholarly journals Development of Rapid Isothermal Amplification Assays for Detection of Phytophthora spp. in Plant Tissue

2015 ◽  
Vol 105 (2) ◽  
pp. 265-278 ◽  
Author(s):  
Timothy D. Miles ◽  
Frank N. Martin ◽  
Michael D. Coffey
Keyword(s):  
Real Time ◽  
Internal Control ◽  
Plant Tissue ◽  
Pathogen Detection ◽  
Phytophthora Ramorum ◽  
Isothermal Amplification ◽  
Sample Collection ◽  
Phytophthora Spp ◽  
Wide Range ◽  
Tissue Maceration

Several isothermal amplification techniques recently have been developed that are tolerant of inhibitors present in many plant extracts, which can reduce the need for obtaining purified DNA for running diagnostic assays. One such commercially available technique that has similarities with real-time polymerase chain reaction (PCR) for designing primers and a labeled probe is recombinase polymerase amplification (RPA). This technology was used to develop two simple and rapid approaches for detection of Phytophthora spp.: one genus-specific assay multiplexed with a plant internal control and the other species-specific assays for Phytophthora ramorum and P. kernoviae. All assays were tested for sensitivity (ranging from 3 ng to 1 fg of DNA) and specificity using DNA extracted from more than 136 Phytophthora taxa, 21 Pythium spp., 1 Phytopythium sp., and a wide range of plant species. The lower limit of linear detection using purified DNA was 200 to 300 fg of DNA in all pathogen RPA assays. Six different extraction buffers were tested for use during plant tissue maceration and the assays were validated in the field by collecting 222 symptomatic plant samples from over 50 different hosts. Only 56 samples were culture positive for Phytophthora spp. whereas 91 were positive using the Phytophthora genus-specific RPA test and a TaqMan real-time PCR assay. A technique for the generation of sequencing templates from positive RPA amplifications to confirm species identification was also developed. These RPA assays have added benefits over traditional technologies because they are rapid (results can be obtained in as little as 15 min), do not require DNA extraction or extensive training to complete, use less expensive portable equipment than PCR-based assays, and are significantly more specific than current immunologically based methods. This should provide a rapid, field-deployable capability for pathogen detection that will facilitate point-of-sample collection processing, thereby reducing the time necessary for accurate diagnostics and making management decisions.

scholarly journals Essential properties and pitfalls of colorimetric Reverse Transcription Loop-mediated Isothermal Amplification as a point-of-care test for SARS-CoV-2 diagnosis

2021 ◽  
Vol 27 (1) ◽  
Author(s):  
Bruna de Oliveira Coelho ◽  
Heloisa Bruna Soligo Sanchuki ◽  
Dalila Luciola Zanette ◽  
Jeanine Marie Nardin ◽  
Hugo Manuel Paz Morales ◽  
...  
Keyword(s):  
Viral Load ◽  
Internal Control ◽  
Reverse Transcription ◽  
Color Change ◽  
Point Of Care ◽  
Colorimetric Detection ◽  
False Negative ◽  
Isothermal Amplification ◽  
Clinical Samples ◽  
Loop Mediated Isothermal Amplification

Abstract Background SARS-CoV-2 Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) colorimetric detection is a sensitive and specific point-of-care molecular biology technique used to detect the virus in only 30 min. In this manuscript we have described a few nuances of the technique still not properly described in the literature: the presence of three colors clusters; the correlation of the viral load with the color change; and the importance of using an internal control to avoid false-negative results. Methods To achieve these findings, we performed colorimetric RT-LAMP assays of 466 SARS-CoV-2 RT-qPCR validated clinical samples, with color quantification measured at 434 nm and 560 nm. Results First we determinate a sensitivity of 93.8% and specificity of 90.4%. In addition to the pink (negative) and yellow (positive) produced colors, we report for the first time the presence of an orange color cluster that may lead to wrong diagnosis. We also demonstrated using RT-qPCR and RT-LAMP that low viral loads are related to Ct values > 30, resulting in orange colors. We also demonstrated that the diagnosis of COVID-19 by colorimetric RT-LAMP is efficient until the fifth symptoms day when the viral load is still relatively high. Conclusion This study reports properties and indications for colorimetric RT-LAMP as point-of-care for SARS-CoV-2 diagnostic, reducing false results, interpretations and optimizing molecular diagnostics tests application.

scholarly journals Evaluation of Recombinant Proteins of Burkholderia mallei for Serodiagnosis of Glanders

2012 ◽  
Vol 19 (8) ◽  
pp. 1193-1198 ◽  
Author(s):  
Vijai Pal ◽  
Subodh Kumar ◽  
Praveen Malik ◽  
Ganga Prasad Rai
Keyword(s):  
Sensitivity And Specificity ◽  
Recombinant Proteins ◽  
False Negative ◽  
Enzyme Linked Immunosorbent Assay ◽  
Burkholderia Mallei ◽  
Content Type ◽  
Whole Cells ◽  
Negative Results ◽  
Elisa Format ◽  
Low Sensitivity

ABSTRACTGlanders is a contagious disease caused by the Gram-negative bacillusBurkholderia mallei. The number of equine glanders outbreaks has increased steadily during the last decade. The disease must be reported to the Office International des Epizooties, Paris, France. Glanders serodiagnosis is hampered by the considerable number of false positives and negatives of the internationally prescribed tests. The major problem leading to the low sensitivity and specificity of the complement fixation test (CFT) and enzyme-linked immunosorbent assay (ELISA) has been linked to the test antigens currently used, i.e., crude preparations of whole cells. False-positive results obtained from other diagnostic tests utilizing crude antigens lead to financial losses to animal owners, and false-negative results can turn a risk into a possible threat. In this study, we report on the identification of diagnostic targets using bioinformatics tools for serodiagnosis of glanders. The identified gene sequences were cloned and expressed as recombinant proteins. The purified recombinant proteins ofB. malleiwere used in an indirect ELISA format for serodiagnosis of glanders. Two recombinant proteins, 0375H and 0375TH, exhibited 100% sensitivity and specificity for glanders diagnosis. The proteins also did not cross-react with sera from patients with the closely related disease melioidosis. The results of this investigation highlight the potential of recombinant 0375H and 0375TH proteins in specific and sensitive diagnosis of glanders.

scholarly journals Rapid Diagnosis of HIV-1 virus by Near Infrared Spectroscopy: based on Partial least squares regression

2021 ◽  
Vol 271 ◽  
pp. 03067
Author(s):  
Xiaohong He ◽  
Zhihong Song ◽  
Haifei Shang ◽  
Silang Yang ◽  
Lujing Wu ◽  
...  
Keyword(s):  
Infrared Spectroscopy ◽  
Near Infrared Spectroscopy ◽  
Near Infrared ◽  
False Negative ◽  
Cost Effective ◽  
Rapid Diagnosis ◽  
Enzyme Linked Immunosorbent Assay ◽  
Least Squares Regression ◽  
Early Screening ◽  
Hiv 1

Currently, the laboratory diagnostic tests available for HIV-1 viral infection are mainly based on serological testing which relies on enzyme-linked immunosorbent assay (ELISA) for blood HIV antigen detection and reverse transcription polymerase chain reaction (RT-PCR) for HIV specific RNA sequence identification. However, these methods are expensive and time-consuming, and suffer from false positive and/or false negative results. Thus, there is an urgent need for developing a cost effective, rapid and accurate diagnostic method for HIV-1 infection. In order to reduce the barriers for effective diagnosis, a near-infrared spectroscopy (NIR) method was used to detect the HIV-1 virus in human serum, specifically, three absorption peaks with dose-dependent at 1582nm, 1810nm and 2363nm were found by multiple FBiPLSR test analysis for HIV-nano and HIV-EGFP, but not for MLV. Therefore, we recommend the use of 1582nm, 1810nm and 2363nm as the characteristic spectrum peak, for early screening and rapid diagnosis of serum HIV.

scholarly journals Self-regulation and Locus of Control Predicting EFL Learners’ Willingness to Communicate

2018 ◽  
Vol 8 (8) ◽  
pp. 1094
Author(s):  
Shirin Arkavazi ◽  
Mania Nosratinia
Keyword(s):  
Locus Of Control ◽  
Internal Control ◽  
Quantitative Research ◽  
Self Regulation ◽  
Sampling Strategy ◽  
Willingness To Communicate ◽  
Efl Learners ◽  
Research Questions ◽  
Positive Correlations ◽  
Age Range

The purpose of this descriptive quantitative research was to systematically investigate the association among EFL learners' Self-Regulation (SR), Locus of Control (LC), and their Willingness to Communicate (WTC). To fulfill this purpose, 222 male and female EFL learners, within the age range of 20 to 32 (Mage = 26) were selected based on the convenience sampling strategy. These participants were asked to fill in three questionnaires, namely the English versions of the Motivated Strategies for Learning Questionnaire (Pintrich, Smith, Garcia, & McKeachie, 1991), the Internal Control Index (Duttweiler, 1984), and the WTC Scale (McCroskey, 1992). Since the assumptions of normality of distribution were partially violated, the research questions were answered using parametric and non-parametric tests. The obtained results led the researchers to conclude that significant and positive correlations exist between SR and WTC, SR and LC, and LC and WTC. Furthermore, considering WTC the predicted variable, a regression analysis revealed that LC is a better predictor of WTC than SR. The study finally presents a discussion on the results and provides some implications for those engaged in EFL learning and instruction.

scholarly journals Rapid Detection of Campylobacter coli, C. jejuni, and Salmonella enterica on Poultry Carcasses by Using PCR-Enzyme-Linked Immunosorbent Assay

2003 ◽  
Vol 69 (6) ◽  
pp. 3492-3499 ◽  
Author(s):  
Yang Hong ◽  
Mark E. Berrang ◽  
Tongrui Liu ◽  
Charles L. Hofacre ◽  
Susan Sanchez ◽  
...  
Keyword(s):  
Immunosorbent Assay ◽  
Salmonella Enterica ◽  
Rapid Detection ◽  
Diarrheal Disease ◽  
False Negative ◽  
Enzyme Linked Immunosorbent Assay ◽  
Campylobacter Coli ◽  
Culture Methods ◽  
Isolation And Identification ◽  
Serological Tests

ABSTRACT Contamination of retail poultry by Campylobacter spp. and Salmonella enterica is a significant source of human diarrheal disease. Isolation and identification of these microorganisms require a series of biochemical and serological tests. In this study, Campylobacter ceuE and Salmonella invA genes were used to design probes in PCR-enzyme-linked immunosorbent assay (ELISA), as an alternative to conventional bacteriological methodology, for the rapid detection of Campylobacter jejuni, Campylobacter coli, and S. enterica from poultry samples. With PCR-ELISA (40 cycles), the detection limits for Salmonella and Campylobacter were 2 � 102 and 4 � 101 CFU/ml, respectively. ELISA increased the sensitivity of the conventional PCR method by 100- to 1,000-fold. DNA was extracted from carcass rinses and tetrathionate enrichments and used in PCR-ELISA for the detection of Campylobacter and S. enterica, respectively. With PCR-ELISA, Salmonella was detected in 20 of 120 (17%) chicken carcass rinses examined, without the inclusion of an enrichment step. Significant correlation was observed between PCR-ELISA and cultural methods (kappa = 0.83; chi-square test, P < 0.001) with only one false negative (1.67%) and four false positives (6.67%) when PCR-ELISA was used to screen 60 tetrathionate enrichment cultures for Salmonella. With PCR-ELISA, we observed a positive correlation between the ELISA absorbance (optical density at 405 nm) and the campylobacter cell number in carcass rinse, as determined by standard culture methods. Overall, PCR-ELISA is a rapid and cost-effective approach for the detection and enumeration of Salmonella and Campylobacter bacteria on poultry.

Phytophthora ramorum. [Distribution map].

2006 ◽  
Author(s):  
Keyword(s):  
South Carolina ◽  
Phytophthora Ramorum ◽  
Distribution Map ◽  
Quercus Agrifolia ◽  
Quercus Kelloggii ◽  
Live Oak ◽  
Lithocarpus Densiflorus ◽  
Black Oak ◽  
New Distribution ◽  
Distribution In Europe

Abstract A new distribution map is provided for Phytophthora ramorum Werres, de Cock & Man in't Veld. Oomycota: Pythiales. Hosts include California black oak (Quercus kelloggii), California live oak (Quercus agrifolia), Rhododendron, shreve oak (Quercus parvula var. shrevei), tanoak (Lithocarpus densiflorus) and Viburnum. Information is given on the geographical distribution in Europe (Belgium, Denmark, France, Germany, Ireland, Italy, Netherlands, Norway, Poland, Slovenia, Spain, Sweden, Switzerland, UK) and North America (Canada (British Columbia), USA (California, Florida, Georgia, Louisiana, Oregon, South Carolina, Tennessee, Virginia, Washington)).

scholarly journals Proposal of De Novo Antigen Test for COVID-19: Ultrasensitive Detection of Spike Proteins of SARS-CoV-2

Diagnostics ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 594 ◽  
Author(s):  
Yuta Kyosei ◽  
Mayuri Namba ◽  
Sou Yamura ◽  
Rikiya Takeuchi ◽  
Noriko Aoki ◽  
...  
Keyword(s):  
De Novo ◽  
Limit Of Detection ◽  
False Negative ◽  
Cost Effective ◽  
Detection Sensitivity ◽  
Enzyme Linked Immunosorbent Assay ◽  
Antigen Test ◽  
Virus Rna ◽  
Antigen Tests ◽  
Spike Proteins

Polymerase chain reaction (PCR)-based antigen tests are technically difficult, time-consuming, and expensive, and may produce false negative results requiring follow-up confirmation with computed tomography. The global coronavirus disease 2019 (COVID-19) pandemic has increased the demand for accurate, easy-to-use, rapid, and cost-effective antigen tests for clinical application. We propose a de novo antigen test for diagnosing COVID-19 using the combination of sandwich enzyme-linked immunosorbent assay and thio-nicotinamide adenine dinucleotide (thio-NAD) cycling. Our test takes advantage of the spike proteins specific to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The limit of detection of our test was 2.3 × 10−18 moles/assay. If the virus has ~25 spike proteins on its surface, our method should detect on the order of 10−20 moles of virus/assay, corresponding to ~104 copies of the virus RNA/assay. The detection sensitivity approaches that of PCR-based assays because the average virus RNA load used for PCR-based assays is ~105 copies per oro- or naso-pharyngeal swab specimen. To our knowledge, this is the first ultrasensitive antigen test for SARS-CoV-2 spike proteins that can be performed with an easy-to-use microplate reader. Sufficient sensitivity can be achieved within 10 min of thio-NAD cycling. Our antigen test allows for rapid, cost-effective, specific, ultrasensitive, and simultaneous multiple measurements of SARS-CoV-2, and has broad application for the diagnosis for COVID-19.

scholarly journals Sensitivity and specificity of indirect ELISA for the detection of antibody titers against BVDV from beef cattle raised in Pará State

2017 ◽  
Vol 38 (5) ◽  
pp. 3049
Author(s):  
Rinaldo Batista Viana ◽  
Aline do Socorro Lima Kzam ◽  
Bruno Moura Monteiro ◽  
Cláudio Cabral Campello ◽  
Eliomar De Moura Sousa ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Predictive Value ◽  
False Negative ◽  
Foot And Mouth Disease ◽  
Metropolitan Region ◽  
Enzyme Linked Immunosorbent Assay ◽  
Significance Level ◽  
Bovine Kidney ◽  
Diarrhea Virus ◽  
Positive Diagnosis

The aims of this study were to establish the prevalence of anti-bovine viral diarrhea virus (BVDV) antibodies (Ab) in beef cattle raised in Pará state, to compare the prevalence of seropositive animals to BVDV using a commercial indirect enzyme-linked immunosorbent assay kit (iELISA) and the virus neutralization (VN) test, and finally, to determine the sensitivity (Se) and specificity (Sp) of the iELISA for the detection of anti-BVDV Ab using VN as a gold standard. A total of 400 serum blood samples from Nelore cows aged at least 24 months from five farms in the Pará state from two mesoregions (Metropolitan Region of Belem and Northeast of Pará) were analyzed. All animals were vaccinated against brucellosis and foot-and-mouth disease. The examination of anti-BVDV Ab with VN was performed in the Laboratory of Bovine Viruses of the Biological Institute of Sao Paulo as described in the Manual of Diagnostic Tests and Vaccines for Terrestrial Animals. For VN, bovine kidney epithelial cells from the Madin Darby Bovine Kidney (MDBK) strain were used. The determinations of anti-BVDV Ab were performed with the iELISA test at the Laboratory of Immunology and Microbiology of the Federal Rural University of Amazonia according to the manufacturer's recommendations. The results were classified as follows: (a) correct positive diagnosis, (b) incorrect positive diagnosis, (c) correct negative diagnosis, and (d) incorrect negative diagnosis, according to the results obtained from VN. From the values obtained from VN and iELISA, Se [(a ÷ a + d) × 100], Sp [(c ÷ c + b) × 100], positive predictive value [(a ÷ a + B) × 100], and negative predictive value [(c ÷ c + d) × 100] were calculated for iELISA. The frequencies (%) of seropositive animals were determined and compared both between the different tests (iELISA and VN) and between the different farms (1, 2, 3, 4, and 5). The statistical analysis was performed with a significance level of 5%. The prevalence of seropositive animals was found to be different (P < 0.0001) using VN (39.25% [157/400]) and iELISA (54.50% [218/400]). It was observed that the Se and Sp of the iELISA assay were 98.72% and 74.07%, respectively. Of the total, 25.93% (63/243) of the samples were considered false-positive and 1.27% false-negative (2/157). It was concluded that the BVDV infection is present in beef cattle herds of the state of Para. Based on the speed of execution, ease of handling, and high Se of the iELISA, it is suggested that this assay can be used as a screening test for the detection of anti-BVDV Ab with the aim of eliminating infected animals from large herds of beef cattle.

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