Survival Analysis as a Basis for Testing Hypotheses when Using Quantitative Ordinal Scale Disease Severity Data.

Disease severity in plant pathology is often measured by the amount of a plant or plant part that exhibits disease symptoms. This is typically assessed using a numerical scale, which allows a standardized, convenient, and quick method of rating. These scales, known as quantitative ordinal scales (QOS), divide the percentage scale into a predetermined number of intervals. There are various ways to analyze these ordinal data, with traditional methods involving the use of midpoint conversion to represent the interval. However, this may not be precise enough, as it is only an estimate of the true value. In this case, the data may be considered interval-censored, meaning that we have some knowledge of the value but not an exact measurement. This type of uncertainty is known as censoring, and techniques that address censoring, such as survival analysis (SA), use all available information and account for this uncertainty. To investigate the pros and cons of using SA with QOS measurements, we conducted a simulation based on three pathosystems. The results showed that SA almost always outperformed midpoint conversion with data analyzed using a t test, particularly when data were not normally distributed. Midpoint conversion is currently a standard procedure. In certain cases, the midpoint approach required a 400% increase in sample size to achieve the same power as the SA method. However, as the mean severity increases, fewer additional samples are needed (approximately an additional 100%), regardless of the assessment method used. Based on these findings, we conclude that SA is a valuable method for enhancing the power of hypothesis testing when analyzing QOS severity data. Future research should investigate the wider use of survival analysis techniques in plant pathology and their potential applications in the discipline.

Fungicide Resistance in Venturia effusa, Cause of Pecan Scab: Current Status and Practical Implications.

Pecan scab, caused by Venturia effusa, is the most economically damaging disease of pecan in the southeastern United States, and annual epidemics are most effectively managed through multiple fungicide applications. The fungicide applications can be the single greatest operating cost for commercial growers and the return on that investment is impacted by fungicide resistance. V. effusa produces multiple generations of conidia per season, exhibits substantial genetic diversity, overwinters as stromata in the tree, and is under immense selection from the applied fungicides, all of which lead to a high risk for developing fungicide resistance. Since the mid-1970s, resistance or reduced sensitivity has been observed in isolates of V. effusa to the methyl benzimidazole carbamates, demethylation inhibitors, quinone outside inhibitors, organotin compounds, and the guanidines. Over the last 10 years, several studies have been conducted that have improved both scab management and fungicide resistance management in V. effusa. The aim of this review is to summarize recent developments in our understanding of fungicide resistance in V. effusa in the context of scab management in southeastern pecan orchards. The history, modes of action, general use of the labeled fungicides, and mechanisms and stability of fungicide resistance in V. effusa are discussed; conclusions and future research priorities are also presented.

Spatial Variation and Temporal Dynamics of Fungicide Sensitivity in Venturia effusa Within a Pecan Orchard.

An 18-ha commercial pecan orchard was sampled over 3 years to study the spatial and temporal variation in fungicide sensitivity of Venturia effusa, cause of pecan scab. The orchard was divided into a two-dimensional, 8 × 8 grid of 64 quadrats, each containing nine trees (unless there were missing trees), and samples were collected once per year from each quadrat to be tested for sensitivity to fentin hydroxide, propiconazole, and thiophanate-methyl. Averaged across the orchard, insensitivity to all three fungicides was significantly lower in 2016 compared with 2015, but significantly greater for fentin hydroxide and thiophanate-methyl in 2017. Although significant spatial autocorrelation was observed for sensitivity to propiconazole in 2017 and for thiophanate-methyl in 2015 and 2017, indicating clustering, all other fungicide-by-year combinations were not significant. Omnidirectional spatial dependence was observed for sensitivity to propiconazole and thiophanate-methyl in 2017. In both instances, the semivariance increased linearly with lag distance; however, the range of spatial dependence was >276.5 m and could not be estimated accurately. Additionally, a separate sampling was conducted in all 3 years to identify an appropriate sampling size and pattern for fungicide sensitivity screening. A leaflet sample size of 165 in 11 groups of 15 allowed for accurate sensitivity testing for the three fungicides in all 3 years; however, a sample size of 45 leaflets in three groups of 15 was sufficient for quantifying sensitivity for propiconazole and thiophanate-methyl, in most cases. These results indicate that considerable biological variation in fungicide sensitivity exists in orchard-scale populations of V. effusa and that the spatial characteristics of those populations may differ in two-dimensional space depending on the growing season.

Quantitative Ordinal Scale Estimates of Plant Disease Severity: Comparing Treatments Using a Proportional Odds Model.

Studies in plant pathology, agronomy, and plant breeding requiring disease severity assessment often use quantitative ordinal scales (i.e., a special type of ordinal scale that uses defined numeric ranges); a frequently used example of such a scale is the Horsfall-Barratt scale. Parametric proportional odds models (POMs) may be used to analyze the ratings obtained from quantitative ordinal scales directly, without converting ratings to percent area affected using range midpoints of such scales (currently a standard procedure). Our aim was to evaluate the performance of the POM for comparing treatments using ordinal estimates of disease severity relative to two alternatives, the midpoint conversions (MCs) and nearest percent estimates (NPEs). A simulation method was implemented and the parameters of the simulation estimated using actual disease severity data from the field. The criterion for comparison of the three approaches was the power of the hypothesis test (the probability to reject the null hypothesis when it is false). Most often, NPEs had superior performance. The performance of the POM was never inferior to using the MC at severity <40%. Especially at low disease severity (≤10%), the POM was superior to using the MC method. Thus, for early onset of disease or for comparing treatments with severities <40%, the POM is preferable for analyzing disease severity data based on quantitative ordinal scales when comparing treatments and at severities >40% is equivalent to other methods.

Disease Severity Estimates-Effects of Rater Accuracy and Assessment Methods for Comparing Treatments.

Assessment of disease severity is required for several purposes in plant pathology; most often, the estimates are made visually. It is established that visual estimates can be inaccurate and unreliable. The ramifications of biased or imprecise estimates by raters have not been fully explored using empirical data, partly because of the logistical difficulties involved in different raters assessing the same leaves for which actual disease has been measured in a replicated experiment with multiple treatments. In this study, nearest percent estimates (NPEs) of Septoria leaf blotch (SLB) on leaves of winter wheat from nontreated and fungicide-treated plots were assessed in both 2006 and 2007 by four raters and compared with assumed actual values measured using image analysis. Lin's concordance correlation (LCC, ρc) was used to assess agreement between the two approaches. NPEs were converted to Horsfall-Barratt (HB) midpoints and were compared with actual values. The estimates of SLB severity from fungicide-treated and nontreated plots were analyzed using generalized linear mixed modeling to ascertain effects of rater using both the NPE and HB values. Rater 1 showed good accuracy (ρc = 0.986 to 0.999), while raters 3 and 4 were less accurate (ρc = 0.205 to 0.936). Conversion to the HB scale had little effect on bias but reduced numerically both precision and accuracy for most raters on most assessment dates (precision, r = -0.001 to -0.132; and accuracy, ρc = -0.003 to -0.468). Interrater reliability was also reduced slightly by conversion of estimates to HB midpoint values. Estimates of mean SLB severity were significantly different between image analysis and raters 2, 3, and 4, and there were frequently significant differences among raters (F = 151 to 1,260, P = 0.001 to P < 0.0001). Only on 26 June 2007 did conversion to the HB scale change the means separation ranking of rater estimates. Nonetheless, image analysis and all raters were able to differentiate control and treated-plot treatments (F = 116 to 1,952, P = 0.002 to P < 0.0001, depending on date and rater). Conversion of NPEs to the HB scale tended to reduce F values slightly (2006: NPEs, F = 116 to 276, P = 0.002 to 0.0005; and, for the HB-converted values, F = 101 to 270, P = 0.002 to 0.0005; 2007: NPEs, F = 164 to 1,952, P = 0.001 to P < 0.0001; and, for HB-converted values, F = 126 to 1,633, P = 0.002 to P < 0.0001). The results reaffirm the need for accurate and reliable disease assessment to minimize over- or underestimates compared with actual disease, and the data we present support the view that, where multiple raters are deployed, they should be assigned in a manner to reduce any potential effect of rater differences on the analysis.

Genetic Diversity and Population Structure of Fusicladium effusum on Pecan in the United States.

Fusicladium effusum causes pecan scab, which is the most destructive disease of pecan orchards in the United States. Conidia of the pathogen are spread by rain splash and wind. The fungus is pathogenically diverse; yet there is no information on its genetic diversity or population genetics. Universally primed polymerase chain reaction (UP-PCR) was used to investigate the genetic diversity and population structure on a hierarchical sample of 194 isolates collected from 11 orchard locations from Florida to Texas, consisting of three to four isolates from each of five to six trees at each location. Genetic variation was high throughout the region, with all but nine of the multilocus haplotypes being unique. Nei's average gene diversity ranged from 0.083 for a population from Mississippi to 0.160 for a population from Kansas. An analysis of molecular variance of the hierarchically sampled populations found that the majority of the genetic variability (82.6%) occurred at the scale of the individual tree and only relatively small amounts among populations in trees from an orchard (5.0%) or within groups (i.e., orchard location populations) (12.5%). The results suggest little population differentiation in F. effusum in the southeastern United States, although φpt values of genetic distance for pairwise comparisons indicated some populations could be differentiated from others. There was evidence of linkage disequilibrium in certain populations, and the common occurrence of asexual reproduction in F. effusum could lead to measurable linkage disequilibrium under certain circumstances. However, the degree of genetic diversity and the scale over which diversity is distributed is evidence that F. effusum undergoes regular recombination despite no known sexual stage.

Some consequences of using the Horsfall-Barratt scale for hypothesis testing.

Comparing treatment effects by hypothesis testing is a common practice in plant pathology. Nearest percent estimates (NPEs) of disease severity were compared with Horsfall-Barratt (H-B) scale data to explore whether there was an effect of assessment method on hypothesis testing. A simulation model based on field-collected data using leaves with disease severity of 0 to 60% was used; the relationship between NPEs and actual severity was linear, a hyperbolic function described the relationship between the standard deviation of the rater mean NPE and actual disease, and a lognormal distribution was assumed to describe the frequency of NPEs of specific actual disease severities by raters. Results of the simulation showed standard deviations of mean NPEs were consistently similar to the original rater standard deviation from the field-collected data; however, the standard deviations of the H-B scale data deviated from that of the original rater standard deviation, particularly at 20 to 50% severity, over which H-B scale grade intervals are widest; thus, it is over this range that differences in hypothesis testing are most likely to occur. To explore this, two normally distributed, hypothetical severity populations were compared using a t test with NPEs and H-B midpoint data. NPE data had a higher probability to reject the null hypothesis (H0) when H0 was false but greater sample size increased the probability to reject H0 for both methods, with the H-B scale data requiring up to a 50% greater sample size to attain the same probability to reject the H0 as NPEs when H0 was false. The increase in sample size resolves the increased sample variance caused by inaccurate individual estimates due to H-B scale midpoint scaling. As expected, various population characteristics influenced the probability to reject H0, including the difference between the two severity distribution means, their variability, and the ability of the raters. Inaccurate raters showed a similar probability to reject H0 when H0 was false using either assessment method but average and accurate raters had a greater probability to reject H0 when H0 was false using NPEs compared with H-B scale data. Accurate raters had, on average, better resolving power for estimating disease compared with that offered by the H-B scale and, therefore, the resulting sample variability was more representative of the population when sample size was limiting. Thus, there are various circumstances under which H-B scale data has a greater risk of failing to reject H0 when H0 is false (a type II error) compared with NPEs.

Wind Speed Effects on the Quantity of Xanthomonas citri subsp. citri Dispersed Downwind from Canopies of Grapefruit Trees Infected with Citrus Canker.

The epidemic of citrus canker (Xanthomonas citri subsp. citri) in Florida continues to expand since termination of the eradication program in 2006. Storms are known to be associated with disease spread, but little information exists on the interaction of fundamental physical and biological processes involved in dispersal of this bacterium. To investigate the role of wind speed in dispersal, wind/rain events were simulated using a fan to generate wind up to 19 m·s-1 and spray nozzles to simulate rain. Funnels at ground level and panels at 1.3 m height and distances up to 5 m downwind collected wind-driven splash. Greater wind speeds consistently dispersed more bacteria, measured by concentration (colony forming units [CFU] ml-1) or number sampled (bacteria flux density [BFD] = bacteria cm-2 min-1), from the canopy in the splash. The CFU ml-1 of X. citri subsp. citri collected by panels 1 m downwind at the highest wind speed was up to 41-fold greater than that collected at the lowest wind speed. BFD at the highest wind speed was up to 884-fold higher than that collected at the lowest wind speed. Both panels at distances >1 m and funnels at distances >0 m collected many-fold more X. citri subsp. citri at higher wind speeds compared to no wind (up to 1.4 × 103-fold greater CFU ml-1 and 1.8 × 105-fold the BFD). The resulting relationship between wind speed up to 19 m·s-1 and the mean CFU ml-1 collected by panel collectors downwind was linear and highly significant. Likewise, the mean CFU ml-1 collected from the funnel collectors had a linear relationship with wind speed. The relationship between wind speed and BFD collected by panels was generally similar to that described for CFU ml-1 of X. citri subsp. citri collected. However, BFD collected by funnels was too inconsistent to determine a meaningful relationship with increasing wind speed. The quantity of bacteria collected by panels declined with distance, and the relationship was described by an inverse power model (R2 = 0.94 to 1.00). At higher wind speeds, more bacteria were dispersed to all distances. Windborne inoculum in splash in subtropical wet environments is likely to be epidemiologically significant, as both rain intensity and high wind speed can interact to provide conditions conducive for dispersing large quantities of bacteria from canker-infected citrus trees. Disease and crop management aimed at reducing sources of inoculum and wind speeds in a grove should help minimize disease spread by windborne inoculum.

Comparison of Assessment of Citrus Canker Foliar Symptoms by Experienced and Inexperienced Raters.

Citrus canker (Xanthomonas citri subsp. citri) is destructive in many citrus production regions in tropical and subtropical parts of the world. Assessment of canker symptoms is required for diverse reasons, including monitoring epidemics, evaluating the efficacy of control strategies, and disease response in breeding material. The objectives were to compare the ability of experienced and inexperienced raters at assessing citrus canker, to identify factors that affect the quality of the assessment, to determine common sources of error, and to discern how error is related to actual disease magnitude. Two-hundred digital leaf images (0 to 37% area infected) were assessed once by 28 raters, five of whom were experienced plant pathologists (PPs), and 23 who had no experience in disease severity assessment (NPPs). True disease (lesion number [LN], % necrotic area [%N], and % chlorotic+necrotic area [%CN]) was measured using image analysis on a leaf-by-leaf basis, and each parameter was estimated by the 28 raters. LN was neither severely over- nor underestimated, while %N was greatly overestimated, with a lesser tendency to overestimate %CN over the true severity range of these two symptom types. A linear relationship existed between estimate of the disease and true disease for all measures of severity. Data were heteroscedastic and error was not constant with increasing true disease. Agreement between rater estimates and true disease was measured with Lin's concordance correlation coefficient (ρc). LN showed greatest agreement (ρc = 0.88 to 0.99), followed by %CN (ρc = 0.80 to 0.95) and %N (ρc = 0.19 to 0.84). Greater lesion number resulted in overestimation of area infected for both %N and %CN. Overestimation was particularly noticeable at low disease severities. There was a linear relationship between log variance and log true disease for LN (r2 = 0.71), %N (r2 = 0.85), and %CN (r2 = 0.88), and raters tended to estimate disease above 10% to the nearest 5 or 10%. GLM analysis showed differences between PP and NPP groups in assessing disease. For LN, precision of assessment for both groups was similar (r2 > 0.92 and 0.94, respectively), but for estimates of %N and %CN, the PPs were more precise (%N and %CN, r2 = 0.61 and 0.73, respectively) compared to NPPs (%N and %CN, r2 = 0.45 and 0.58, respectively). Absolute error for mean LN was low. The absolute error of %N and %CN showed overestimation to approximately 8% area infected. Above 8%, absolute error increased, but comprised both over- and underestimation. For %N and %CN, relative error was almost exclusively positive and dramatic at severity <8% (up to approximately 600%), but at severity >10% it was relatively small. Error in rater estimates of canker severity is ubiquitous. Understanding these sources of error will aid in the development of both appropriate training and relevant rating aids.

Automated Image Analysis of the Severity of Foliar Citrus Canker Symptoms.

Citrus canker (caused by Xanthomonas citri subsp. citri) is a destructive disease, reducing yield and rendering fruit unfit for fresh sale. Accurate assessment of citrus canker severity and other diseases is needed for several purposes, including monitoring epidemics and evaluation of germplasm. We compared measurements of citrus canker severity (percent area infected) from automated image analysis to visual estimates by raters and true values using images from five leaf samples (65, 123, 50, 50, and 200 leaves; disease severity from 0 to 60%). Severity on leaves was measured by automated image analysis by (i) basing threshold values on a presample of leaves, or (ii) replacing healthy leaf color on a leaf-by-leaf basis before automating image analysis. Samples 1 to 4 were assessed by three trained plant pathologists, and sample 5 was assessed by an additional 25 raters. Healthy leaf area color replacement gave the most consistent agreement with the true severity data. Using color replacement, agreement with true values based on Lin's concordance correlation coefficient (ρc) was 0.93, 0.79, 0.71, 0.85, and 0.89 for each of the samples, respectively. The range and consistency of agreement was generally less good for automated thresholds based on a presample (ρc = 0.35-0.90) or visual raters (ρc = 0.30-0.94). The constituents of agreement (precision and accuracy) showed similar trends. No one rater or method was best for every leaf sample, but replacing healthy color in each leaf with a standard color before automation of image analysis improved agreement, and was relatively quick (20 s per image). The accuracy and precision of automated image analysis of citrus canker severity can be comparable to unaided, direct visual estimation by many raters.

Visual Rating and the Use of Image Analysis for Assessing Different Symptoms of Citrus Canker on Grapefruit Leaves.

Citrus canker is caused by the bacterial pathogen Xanthomonas axonopodis pv. citri and infects several citrus species in wet tropical and subtropical citrus growing regions. Accurate, precise, and reproducible disease assessment is needed for monitoring epidemics and disease response in breeding material. The objective of this study was to assess reproducibility of image analysis (IA) for measuring severity of canker symptoms and to compare this to visual assessments made by three visual raters (VR1-3) for various symptom types (lesion numbers, % area necrotic, and % area necrotic+chlorotic), and to assess inter- and intra-VR reproducibility. Digital images of 210 citrus leaves with a range of symptom severity were assessed on two separate occasions. IA was more precise than VRs for all symptom types (inter-assessment correlation coefficients, r, for lesion numbers by IA = 0.99, by VRs = 0.89 to 0.94; for %, r for % area necrotic+chlorotic for IA = 0.97 and for VRs = 0.86 to 0.89; and r for % area necrotic for IA = 0.96 and for VRs = 0.74 to 0.85). Accuracy based on Lin's concordance coefficient also followed a similar pattern, with IA being most consistently accurate for all symptom types (bias correction factor, Cb = 0.99 to 1.00) compared to visual raters (Cb = 0.85 to 1.00). Lesion number was the most reproducible symptom assessment (Lin's concordance correlation coefficient, ρc, = 0.76 to 0.99), followed by % area necrotic+chlorotic (ρc = 0.85 to 0.97), and finally % area necrotic (ρc = 0.72 to 0.96). Based on the "true" value provided by IA, precision among VRs was reasonable for number of lesions per leaf (r = 0.88 to 0.94), slightly less precision for % area necrotic+chlorotic (r = 0.87 to 0.92), and poorest precision for % area necrotic (r = 0.77 to 0.83). Loss in accuracy was less, but showed a similar trend with counts of lesion numbers (Cb = 0.93 to 0.99) which was more consistently accurately reproduced by VRs than either % area necrotic (Cb = 0.85 to 0.99) or % area necrotic+chlorotic (Cb = 0.91 to 1.00). Thus, visual raters suffered losses in both precision and accuracy, with loss in precision estimating % area necrotic being the greatest. Indeed, only for % area necrotic was there a significant effect of rater (a two-way random effects model ANOVA returned a P < 0.001 and 0.016 for rater in assessments 1 and 2, respectively). VRs showed a marked preference for clustering of % area severity estimates, especially at severity >20% area (e.g., 25, 30, 35, 40, etc.), yet VRs were prepared to estimate disease of <1% area, and at 1% increments up to 20%. There was a linear relationship between actual disease (IA assessments) and VRs. IA appears to provide a highly reproducible way to assess canker-infected leaves for disease, but symptom characters (symptom heterogeneity, coalescence of lesions) could lead to discrepancies in results, and full automation of the system remains to be tested.

Characteristics of the Perception of Different Severity Measures of Citrus Canker and the Relationships Between the Various Symptom Types.

Citrus canker is a disease of citrus and is caused by the bacterial pathogen Xanthomonas citri subsp. citri. Ways of managing the disease are being sought, and accurate, precise, reproducible disease assessment is needed for monitoring epidemics. The objective of this study was to investigate the characteristics of visual assessment of citrus canker symptoms compared with actual disease measured using image analysis (IA). Images of 210 citrus leaves with a range of incidence and severity of citrus canker were assessed by three plant pathologists (VR1-3) and by IA. The number of lesions (L), % area necrotic (%AN), and % area necrotic+chlorotic (%ANC) were assessed. The best relationships were found between %AN and %ANC (r2 = 0.41 to 0.87), and the worst between L and %AN (r2 = 0.27 to 0.66). Bland-Altman plots showed various sources of rater error in assessments, including under- and over-estimation, proportional error, and heterogeneity of variation dependent on actual disease magnitude. There was a tendency to overestimate area diseased, but not lesion counts, and this tendency was pronounced at lower disease severity, with a leaf having more lesions tending to be assessed as having greater area infected compared with a leaf with fewer lesions but equal actual area infected. The rater estimations of disease were less accurate or precise with increasing actual disease severity as indicated by the fit of a normal probability density function-the incidence of extreme values increases with increasing actual disease. For example, for %ANC the kurtosis of the distribution ranged from 17.92 to 1.18, 0.51, and 0.22 in actual disease category ranges of 0 to 10, 11 to 20, 21 to 30, and 31 to 40% area infected, respectively. The log variance of the estimates plotted against log actual disease for all three raters over two assessment occasions gave a linear relationship for L, %AN, and %ANC (r2 = 0.74, 0.65, and 0.74, respectively). Training should improve the accuracy, precision, and reproducibility of raters, and knowledge of the characteristics of disease assessment should help develop and target the training more appropriately and address specific causes and sources of error.

Combinations of cytochrome P-450 genotypes and risk of early-onset lung cancer in Caucasians and African Americans: a population-based study.

Polymorphisms in CYP1A1 and CYP1B1 genes in humans are associated with reduction of enzymatic activity towards several substrates, including those found in tobacco smoke. To investigate the potential role these polymorphisms have as modulators of early-onset lung cancer risk, a population-based case-control study involving early-onset lung cancer cases was performed. Biological samples were available for 383 individuals diagnosed prior to 50 years of age identified from the metropolitan Detroit Surveillance, Epidemiology and End Results (SEER) program and 449 age, race and sex-matched controls ascertained through random digit dialing. Genotype frequencies varied significantly by race for CYP1A1 Ile(462)Val and CYP1B1 Leu(432)Val genotypes, so all analyses were stratified by race. No association was seen between lung cancer risk and polymorphisms in CYP1A1 Msp1 or CYP1B1 Leu(432)Val for Caucasians or African Americans, after adjusting for age at diagnosis, sex, pack years of smoking and family history of lung cancer. In Caucasians, those with the IIe/Val genotype at CYP1A1 Ile(462)Val locus were at decreased risk of having lung cancer compared to those with the lle/lle genotype, after adjusting for age at diagnosis, sex, pack years of smoking and family history of cancer (OR=0.41 95% Cl 0.19-0.90). These results were not replicated among the African American population, nor were they modified by amount of smoking.

CYP1A1 and CYP1B1 polymorphisms and risk of lung cancer among never smokers: a population-based study.

The cytochrome P450 (CYP) superfamily of enzymes catalyse one of the first steps in the metabolism of carcinogens such as polycyclic aromatic hydrocarbons, nitroaromatics and arylamines. Polymorphisms within the CYP1A1 gene have been shown to be associated with lung cancer risk, predominantly among Asian populations. Despite functional evidence of a possible role of CYP1B1 in lung cancer susceptibility, only a few studies have evaluated polymorphisms in this gene in relation to lung cancer susceptibility. This population-based study evaluates polymorphisms in both of these CYP genes within never smokers, most of whom had environmental tobacco smoke (ETS) exposure. Cases (n = 160) were identified through the metropolitan Detroit Surveillance, Epidemiology and End Results program, and age, sex and race-matched population-based controls (n = 181) were identified using random digit dialing. Neither CYP1A1 MspI nor CYP1A1 Ile(462)Val was associated with lung cancer susceptibility among Caucasians or African-Americans. Among Caucasians, however, CYP1B1 Leu(432)Val was significantly associated with lung cancer susceptibility odds ratio (OR) for at least one valine allele = 2.87 [95% confidence interval (CI) 1.63-5.07]. Combinations of this Phase I enzyme polymorphism along with selected Phase II enzyme polymorphisms (GSTM1 null, GSTP1 Ile(105)Val and NQO1 C(609)T) were evaluated. The combination of CYP1B1 Leu(432)Val and NQO1 C(609)T appeared to be associated with the highest risk of lung cancer (OR = 4.14, 95% CI 1.60-10.74), although no combinations differed significantly from the risk associated with CYP1B1 Leu(432)Val alone. When individuals were stratified by household ETS exposure (yes/no), CYP1B1 Leu(432)Val alone and in combination with Phase II enzyme polymorphisms was more strongly associated with increased lung cancer susceptibility among those with at least some household ETS exposure. Additional studies will be required to further validate these findings among never smokers and to evaluate the effects of this polymorphism among smoking populations as well.

Comparison of Techniques to Sample Xanthomonas axonopodis pv. citri in Windblown Spray.

Four techniques were evaluated to sample windblown splash from canker-infected citrus plants. Two volumetric cyclone samplers (PAS450 and Burkard Cyclone) and two passive samplers (funnels and panels) were evaluated. The PAS450 collected no detectable bacteria in any trial. The Burkard cyclone consistently collected spray, but was found to do so even when the power was turned off. Thus, the Burkard cyclone essentially functioned passively, negating the advantage of a volumetric sampler for this application. Panels collected the greatest volume of splash followed by funnel samplers. CFU of Xanthomonas axonopodis pv. citri per ml collected were significantly different between Burkards and panel samplers, but panels and funnels collected similar concentrations (Burkards, funnels, and panels collected 1,182, 1,426, and 2,667 CFU per ml, respectively). Positive correlations were found between the volume and the total X. axonopodis pv. citri collected, and between CFU per ml and total collected for panel and funnel samples. However, there was no correlation between CFU per ml and volume collected for either sampler. The Burkard sample showed a strong positive correlation (P < 0.01) between volume collected, total number of X. axonopodis pv. citri collected, and CFU per ml. The CFU per ml collected by the panels and funnels were similar (coefficient of determination, R2 = 0.97), compared with the relationship between the Burkard and panel catches (R2 = 0.68), or between the Burkard and funnel catches (R2 = 0.62). Panels collected the greatest volume, and effectively collected bacteria-laden windblown splash. The greater sampling area of the panels allowed a more representative sample than the other methods tested.

Effect of Simulated Wind-Driven Rain on Duration and Distance of Dispersal of Xanthomonas axonopodis pv. citri from Canker-Infected Citrus Trees.

Dynamics of dispersal of the bacteria that causes citrus canker (Xanthomonas axonopodis pv. citri) were assessed in simulated wind-driven rain splash. The wind/rain-splash events were simulated using electric blowers to generate turbulent wind (15 to 20 m s-1) and sprayer nozzles to produce water droplets entrained in the wind flow. The splash was blown at an inoculum source of canker-infected trees 1 m downwind. The splash downwind of the source of the infected trees was collected by vertical panel samplers and funnel samplers. The duration over which bacteria were dispersed in spray was assessed in continuous wind at intervals from 0 to 52 h after commencing the simulated rain splash event. In one experiment on 11 February 2003, a total of 1.48 × 106 bacteria were collected by panels 1 m downwind from the inoculum source during the first 10 min of dispersal, but the numbers declined to 3.60 × 105 bacteria after 1 h and ranged between 1.42 × 105 and 1.93 × 104 up to 52 h. In a more detailed study (15 July 2003) of dispersal duration over 4 h, the greatest quantity of bacteria collected by panel samplers were dispersed in the first 5-min period (1.01 × 108 bacteria collected). By 10 min after initiation of dispersal, approximately one-third (3.09 × 107 bacteria collected) of the initial number was being dispersed, and by the end of the first hour, only one-tenth (1.31 × 107 bacteria collected) of the initial quantity was dispersed. Funnel samplers placed at ground level under the trees showed a similar trend. The distance to which bacteria were dispersed in wind-blown splash was also tested under simulated conditions: on 18 September 2003, bacteria were collected by panel samplers at all distances sampled (1, 2, 4, 6, 8, 10, and 12 m) with the greatest number of bacteria deposited at 1 m (4.93 × 106 bacteria collected), while 2.22 × 103 bacteria were deposited over a 10-min period 12 m from the inoculum source. Wind speed declined from 19.5 m s-1 upwind of the trees to 2.8 m s-1 1 m downwind, and by 4 m downwind from the inoculum source, movement was similar to the surrounding air. The data on duration and distance of dispersal were best described by power law regression models compared to exponential models. Citrus canker is readily dispersed in wind-driven rain and is dispersed in large quantities immediately after the stimulus occurs, upon which wind-driven splash can disperse inoculum over a prolonged period and over a substantial distance.

NQO1 T allele associated with decreased risk of later age at diagnosis lung cancer among never smokers: results from a population-based study.

The NAD(P)H:quinone oxidoreductase 1 gene, NQO1, contains a C to T transition at amino acid codon 187, which results in very low enzymatic activity. Previous studies of the association between NQO1 genotype and lung cancer have had mixed findings. This population-based case control study examines the association between NQO1 genotype and lung cancer in the largest sample of never smokers (<100 cigarettes, lifetime) to date. Cases (n = 161) were identified through the metropolitan Detroit Surveillance, Epidemiology and End Results (SEER) program, and 5-year age- and race-matched population-based controls (n = 173) were identified using random digit dialing. Allele frequencies of C and T, respectively, were 0.79 and 0.21 in Caucasians, and 0.84 and 0.16 in African Americans. Among those diagnosed aged >/=50 years, C/T and T/T genotyped individuals had 0.48 times lower lung cancer risk than individuals with C/C genotype (95% CI: 0.27-0.87). There was a non-significant suggestion of a protective effect associated with the T allele among those with a history of environmental tobacco smoke exposure (OR = 0.57, 95% CI: 0.32-1.03) but not among those without (OR = 0.98, 95% CI: 0.41-2.38). Sex, race, family history of lung cancer and histologic type did not modify the effect of NQO1 genotype on lung cancer risk. The observed risk reductions may be attributable to the greatly reduced procarcinogen activating of NAD(P)H:quinone oxidoreductase 1 in individuals with at least one copy of the T allele.

GSTM1, GSTT1 and GSTP1 polymorphisms, environmental tobacco smoke exposure and risk of lung cancer among never smokers: a population-based study.

Glutathione S-transferases detoxify polycyclic aromatic hydrocarbons found in tobacco smoke by glutathione conjugation. Polymorphisms within the GSTM1, GSTT1 and GSTP1 genes, coding for enzymes with deficient or reduced activity, have been studied as potential modifiers of lung cancer risk. It is hypothesized that risk associated with potential susceptibility gene polymorphisms might be most evident at low levels of exposure. Never smokers developing lung cancer represent a highly susceptible subset of the population, exposed to tobacco carcinogens only through environmental tobacco smoke. This population-based case-control study examines the association between GSTM1, GSTT1 and GSTP1 genotypes and lung cancer in one of the largest samples of never smokers to date. Cases (n = 166) were identified through the metropolitan Detroit Surveillance, Epidemiology and End Results (SEER) program and age- and race-matched population-based controls (n = 181) were identified using random digit dialing. Overall, there was no significant association between single or combinations of genotypes at GSTM1, GSTT1 or GSTP1 and lung cancer risk after adjustment for age, race, sex and household ETS exposure in years. However, in never smokers exposed to 20 or more years of household ETS, carrying the GSTM1 null genotype was associated with a 2.3-fold increase in risk [95% confidence interval (CI) 1.05-5.13]. Individuals in this high ETS exposure category carrying the GSTM1 null and the GSTP1 Val allele were at over 4-fold increased risk of developing lung cancer (OR = 4.56, 95% CI: 1.21-17.21). These findings suggest that in the presence of ETS, the GSTM1 genotype both alone and in combination with the GSTP1 genotype alters the risk of developing lung cancer among never smokers.

Analysis of the prostate cancer-susceptibility locus HPC20 in 172 families affected by prostate cancer.

A recent study of hereditary prostate cancer has provided evidence for a prostate cancer-susceptibility locus, HPC20, which maps to 20q13. To assess further the potential contribution of this locus to prostate cancer susceptibility, we studied 172 unrelated families affected by prostate cancer, using 17 polymorphic markers across a 98.5-cM segment of chromosome 20 that contains the candidate region. Parametric analysis, allowing for heterogeneity, resulted in an overall HLOD score of 0.09 (P=.39) at D20S171, under the assumption of linkage in 6% of families. Mode-of-inheritance-free analysis of the entire data set resulted in a maximal Zlr score of 0.76 (LOD 0.13; P=.22) at the same location. The strongest evidence for linkage was seen in the subset of 16 black families (LOD 0.86; Zlr=1.99; P=.023) between markers D20S893 and D20S120, near the putative location of HPC20. Although some positive results were observed, our linkage study does not provide statistically significant support for the existence of a prostate cancer-susceptibility locus HPC20 at 20q13.

The Blau syndrome gene is not a major risk factor for sarcoidosis.

BACKGROUND: A genetic predisposition to sarcoidosis has long been postulated, although no specific susceptibility genes are known. Candidate genes for the two granulomatous inflammatory disorders with clinical similarities to sarcoidosis, Blau syndrome and Crohn's disease, have been localized to a 40 centimorgan region spanning the chromosome 16 centromere. PATIENTS AND METHODS: Using a sample of 35 African-American sibling pairs, who both had clinically confirmed sarcoidosis, we tested for genetic linkage between the 16p12-q21 interval (the likely location of the Blau syndrome gene) and sarcoidosis. RESULTS: We found no evidence for linkage to any of the eight markers we tested in the 16p12-q21 interval. Ninety percent of the 16p12-q21 region had a LOD score < -2 for a dominant gene conferring a relative risk of 3 or greater for sarcoidosis. One hundred percent of the region had a LOD score < -2 for a dominant gene with a relative risk of 3.5 or greater or recessive gene with relative risk of 2.5 or greater. Based on simulation results we could not exclude a dominant gene with relative risk < 5 at the 0.05 significance level, nor a recessive gene with relative risk < 3, over the entire 16p12-q21 interval. CONCLUSIONS: While the clinical similarities between Blau Syndrome and sarcoidosis suggest genetic homogeneity between the disorders, we found no evidence for linkage of sarcoidosis to the Blau syndrome locus. Our exclusion results suggest that the Blau Syndrome gene does not have a major effect on sarcoidosis susceptibility.