Comments Regarding the Binary Power Law for Heterogeneity of Disease Incidence

The binary power law (BPL) has been successfully used to characterize heterogeneity (overdispersion or small-scale aggregation) of disease incidence for many plant pathosystems. With the BPL, the log of the observed variance is a linear function of the log of the theoretical variance for a binomial distribution over the range of incidence values, and the estimated scale (kappa) and slope (b) parameters provide information on the characteristics of aggregation. When b == 1, the interpretation is that the degree of aggregation remains constant over the range of incidence values observed; otherwise, aggregation is variable. In two articles published in this journal in 2009, Gosme and Lucas used their stochastic simulation model, Cascade, to show a multiphasic (split-line) relationship of the variances, with straight-line (linear) relationships on a log-log scale within each phase. In particular, they showed a strong break point in the lines at very low incidence, with b considerably > 1 in the first line segment (corresponding to a range of incidence values usually not observed in the field), and b being approximate to a parts per thousand 1 in the next segment (corresponding to the range of incidence values usually observed). We evaluated their findings by utilizing a general spatially explicit stochastic simulator developed by Xu and Ridout in 1998, with a wide range of median dispersal distances for the contact distribution and number of plants in the sampling units (quadrats), and through an assessment of published BPL results. The simulation results showed that the split-line phenomenon can occur, with a break point at incidence values of approximate to a parts per thousand 0.01; however, the split is most obvious for short median dispersal distances and large quadrat sizes. However, values of b in the second phase were almost always > 1, and only approached 1 with extremely short median dispersal distances and small quadrat sizes. An appraisal of published results showed no evidence of multiple phases (although the minimum incidence may generally be too high to observe the break), and estimates of b were almost always > 1. Thus, it appears that the results from the Cascade simulation model represent a special epidemiological case, corresponding primarily to a roughly nearest-neighbor population-dynamic process. Implications of a multiphasic BPL property may be important and are discussed.Keywords: Citrus sudden death, Spore dispersal gradient, Hierarchy, Temporal analyses, Epidemics, Bacterial blight, Leaf blight, Multiple scales, Hop powdery mildew, Spatial pattern analysi

Development of a grower-conducted inoculum detection assay for management of grape powdery mildew

Management of grape powdery mildew (Erysiphe necator) and other polycyclic diseases often relies on calendar-based pesticide application schedules that assume the presence of inoculum. An inexpensive, loop-mediated isothermal amplification (LAMP) assay was designed to quickly detect airborne inoculum of E. necator to determine when to initiate a fungicide application programme. Field efficacy was tested in 2010 and 2011 in several commercial and research vineyards in the Willamette Valley of Oregon from pre-bud break to v eraison. In each vineyard, three impaction spore traps were placed adjacent to the trunk. One trap was maintained and used by the grower to conduct the LAMP assay (G-LAMP) on-site and the other two traps were used for laboratory-conducted LAMP (L-LAMP) and quantitative PCR assay (qPCR). Using the qPCR as a gold standard, L-LAMP was comparable with qPCR in both years, and G-LAMP was comparable to qPCR in 2011. Latent class analysis indicated that qPCR had a true positive proportion of 98% in 2010 and 89% in 2011 and true negative proportion of 96% in 2010 and 64% in 2011. An average of 3 3 fewer fungicide applications were used when they were initiated based on spore detection relative to the grower standard practice. There were no significant differences in berry or leaf incidence between plots with fungicides initiated at detection or grower standard practice plots, suggesting that growers using LAMP to initiate fungicide applications can use fewer fungicide applications to manage powdery mildew compared to standard practices

Redefining IPM for Strawberry Production under the Emerging Threat of Anthracnose and Strawberry Sap Beetle

A sampling survey of strawberry acreage in New York was conducted to determine the distribution of two pests of increasing concern to strawberry growers in New York: strawberry sap beetle, Stelidota geminata (Say), and anthracnose, Colletotrichum acutatum. The 2002 sampling for both pests was conducted in a total of 37 strawberry fields at 14 farms, with farms distributed throughout four agricultural regions of New York

A Loop-Mediated Isothermal Amplification Assay and Sample Preparation Procedure for Sensitive Detection of Xanthomonas fragariae in Strawberry.

Xanthomonas fragariae is a bacterium that causes angular leaf spot of strawberry. Asymptomatic infection is common and contributes to the difficulties in disease management. The aim of this study was to develop a loop-mediated isothermal amplification (LAMP) assay as an efficient method for detection of asymptomatic infections of X. fragariae. In addition, a new method of sample preparation was developed that allows sampling of a larger amount of plant tissue, hence increasing the detection rate in real-life samples. The sample preparation procedure includes an overnight incubation of strawberry tissues in phosphate-buffered saline (PBS), followed by a quick sample concentration and a boiling step to extract DNA for amplification. The detection limit of the LAMP assay was approximately 2×10(3) CFU/mL for pure bacteria culture and 300 CFU/mL for bacteria spiked strawberry leaf and petiole samples. LAMP provided a 2-3 fold lower detection limit than the standard qPCR assay but was faster, and more user-friendly. The LAMP assay should serve as a rapid, sensitive and cost-effective tool for detecting asymptomatic infections of X. fragariae in strawberry nursery stock and contribute to improved disease management

Pulse evolution in CO₂ lasers

Explicit formulas are examined for the development of optical pulses in gain‐switched or Q‐switched laser oscillators and for the distortion of such pulses in succeeding stages of laser amplification. The results are compared to data obtained with a TEA CO₂ oscillator‐amplifier system

Evaluation of a Viable-Cell Detection Assay for Xanthomonas fragariae with Latent Class Analysis

Most molecular diagnostic assays are designed to detect the simple presence of a protein or nucleic acid without regard to whether that protein or nucleic acid originated from a viable and presumably pathogenic organism at the time of isolation. We recently developed a viable-cell detection assay (propidium monoazide [PMA]-qPCR) for specific detection of viable (living) cells of Xanthomonas fragariae, the pathogen causing angular leaf spot of strawberry, and herein describe a unique set of statistical analyses for validation of this assay. For any detection assay or test, calculation of its sensitivity and specificity is essential for determining its diagnostic capabilities, particularly when evaluating competing assays or tests. This is often achieved by running competing tests concurrently on a set of samples with known pathogen density or disease status and cross-tabulating results. However, the PMA-qPCR assay is unique among PCR-based diagnostics because it is designed specifically to detect DNA from living cells only, whereas most traditional PCR assays are designed to detect DNA from the target organism regardless of its state of viability. Thus, one cannot directly compare the results from a cell-viability assay with those from a general assay to gauge the performance of either assay because the assays target two different but overlapping populations (i.e., the viable-cell population and the viable- plus nonviable-cell population). To address this challenge, two standard statistical approaches to diagnostic test evaluation were used jointly to estimate the test performance of the PMA-qPCR assay relative to two common assays for detection of X. fragariae. In both analyses, the PMA-qPCR outperformed the qPCR for detection of viable cells under a range of conditions. Viability testing is extremely useful in certification and disease management applications, and with the information on test performance generated here, the test can be put to practical use to design sampling strategies to account for the errors in testing. [Graphic: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023

Youden’s index for the LAMP assay.

<p>The sensitivities and specificities used to calculate the index were estimated through latent class analyses for each combination of LAMP reaction times and qPCR C_t threshold values.</p

Reaction curves for qPCR and real-time LAMP.

<p>(A) qPCR and (B) LAMP amplification curves of pure bacterial DNA. (C) DNA melting curves for the LAMP assay in (B). (D) Gel electrophoresis results of the same samples processed in (B). Samples were run in 1.5% agarose gel with 100 bp DNA ladder and stained with ethidium bromide. (E) End product-detection with HNB dye of the same samples processed in (D). Samples 1–10 in (D) and (E) had the same concentration of <i>X</i>. <i>fragariae</i> as shown in the legend of (A) from top to bottom. (F) qPCR and (G) LAMP amplification curve of <i>X</i>. <i>fragariae-</i>spiked leaf samples processed through the sample preparation procedure.</p

qPCR sensitivities (A, B) and specificities (C, D) relative to LAMP assay results.

<p>The sensitivities and specificities were estimated through latent class analyses for each combination of qPCR C_t and LAMP T_t threshold values. Error bars are standard errors of the means and are shown for a select series in each plot to avoid clutter. The series with the largest error was typically chosen as the representative series. Data points lacking error bars for that series were either too small or were not estimable by the MLE procedure.</p

LAMP sensitivity (A, B) and specificity (C, D) relative to qPCR assay results.

<p>The sensitivities and specificities were estimated through latent class analyses for each combination of LAMP T_t and qPCR C_t threshold values. Error bars are standard errors of the means and are shown for a select series in each plot to avoid clutter. The series with the largest error was typically chosen as the representative series. Data points lacking error bars for that series were either too small or were not estimable by the MLE procedure.</p