Standard area diagrams for pecan leaf scab: Effect of rater experience and location, and leaf size on reliability and accuracy of visual estimates.

Assessments of the severity of scab (Venturia effusa), an economically significant disease of pecan, are critical for determining pecan cultivar susceptibility, disease epidemiology, and integrated disease management approaches. We developed a standard area diagram (SAD) set to aid in assessments of pecan leaflet scab. Leaflets with scab lesions were harvested and scanned using a flatbed scanner at 600 dpi, and Fiji (ImageJ) was used to determine the actual percent disease severity. The SADs had 10 leaflets ranging in severity from 0.2 to 48.9%. Forty 'small' (1.34 - 7.43 cm2) and forty 'large' (7.67 - 25.9 cm2) leaflet images were randomized for rater assessments. The images were assessed twice by 36 raters, first without and then with the SADs as a guide. Data were subjected to analysis using Lin's Concordance Correlation Coefficient (LCC, pc) to determine the accuracy of ratings, and by Intra-class Correlation Coefficient analysis to determine inter-rater reliability. The effects of rater experience, rater location, and leaflet size were also determined. The SADs significantly improved the agreement between raters and the actual values (LCC, pc = 0.70 and 0.84 without and with the SADs, respectively). The reliability of estimates was improved (ICC = 0.54 and 0.82 without and with the SADs, respectively). The effect of rater location on overall concordance was significant without and with the SADs based on an analysis of variance (ANOVA) using a general linear model and lsmeans separation (P<0.05). A generalized linear mixed model analysis revealed that there was a significant interaction between rater location, experience, and the use of the SADs, with some raters having greater improvement in generalized bias and concordance. Raters had a significantly better accuracy when rating 'small' leaves (LCC, pc = 0.86) compared to 'large' leaves (LCC, pc = 0.82) when using the SADs, highlighting the impact of psychophysics on field evaluations of plant disease severity. The proposed SADs will serve as an improved tool for performing pecan leaflet scab assessments by the pecan research community.

A structure activity relationship study of 3,4'-dimethoxyflavone for ArlRS inhibition in Staphylococcus aureus.

Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are difficult to treat due to their resistance to many ß-lactam antibiotics, and their highly coordinated excretion of virulence factors. One way in which MRSA accomplishes this is by responding to environmental stimuli using two-component systems (TCS). The ArlRS TCS has been identified as having a key role in regulating virulence in both systemic and local infections caused by S. aureus. We recently disclosed 3,4'-dimethoxyflavone as a selective ArlRS inhibitor. In this study we explore the structure-activity relationship (SAR) of the flavone scaffold for ArlRS inhibition and identify several compounds with increased activity compared to the parent. Additionally, we identify a compound that suppresses oxacillin resistance in MRSA, and begin to probe the mechanism of action behind this activity.

Influence of Geographical Orchard Location on the Microbiome from the Progeny of a Pecan Controlled Cross.

Carya&nbsp;illinoinensis (Wangenh.) K.Koch production has expanded beyond the native distribution as the genetic diversity of the species, in part, has allowed the trees to grow under broad geographic and climatic ranges. Research in other plant species has demonstrated that the phytobiome enhances their ability to survive and thrive in specific environments and, conversely, is influenced by the prevailing environment and plant genetics, among other factors. We sought to analyze the microbiota of pecan seedlings from the controlled cross 'Lakota' × 'Oaxaca' that were made in Georgia and Texas, respectively, to determine if the maternal geographical origin influences the microbiome of the resulting progeny. No significant differences in bacterial communities were observed between the seeds obtained from the two different states (p = 0.081). However, seed origin did induce significant differences in leaf fungal composition (p = 0.012). Results suggest that, in addition to some environmental, epigenetics, or host genetic components, ecological processes, such as dispersal mechanisms of the host, differentially impact the pecan microbiome, which may have ramifications for the health of trees grown in different environments. Future studies on the role of the microbiome in plant health and productivity will aid in the development of sustainable agriculture for improved food security.

Glutathione S-transferase: a candidate gene for berry color in muscadine grapes (Vitis rotundifolia).

Muscadine grapes (Vitis rotundifolia Michx.) are a specialty crop cultivated in the southern United States. Muscadines (2n = 40) belong to the Muscadinia subgenus of Vitis, while other cultivated grape species belong to the subgenus Euvitis (2n = 38). The muscadine berry color locus was mapped to a 0.8 Mbp region syntenic with chromosome 4 of Vitis vinifera. In this study, we identified glutathione S-transferase4 as a likely candidate gene for anthocyanin transport within the berry color locus. PCR and Kompetitive allele-specific PCR genotyping identified a single intragenic SNP (C/T) marker corresponding to a proline to leucine mutation within the muscadine glutathione S-transferase4 (VrGST4) that differentiated black (CC and CT) from bronze (TT) muscadines in 126 breeding selections, 76 cultivars, and 359 progeny from 3 mapping populations. Anthocyanin profiling on a subset of the progeny indicated a dominant VrGST4 action. VrGST4 was expressed in skins of both black and bronze muscadines at similar levels. While nonsynonymous polymorphisms between black and bronze muscadines were discovered in VrGSTF12, another Type I GST-coding gene in the muscadine color locus, this gene was ruled out as a possible candidate for berry color because RNA sequencing indicated it is not expressed in berry skins at véraison from black or bronze genotypes. These results suggest that the bronze phenotype in muscadines is regulated by a mechanism distinct from the MybA gene cluster responsible for berry color variation in Vitis vinifera.

Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding.

Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence-absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the 'Pawnee' cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence-absence and functional annotation database among genomes and within the two outbred haplotypes of the 'Lakota' genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

High-density linkage maps and loci for berry color and flower sex in muscadine grape (Vitis rotundifolia).

KEY MESSAGE: Linkage maps of muscadine grape generated using genotyping-by-sequencing (GBS) provide insight into genome collinearity between Muscadinia and Euvitis subgenera and genetic control of flower sex and berry color. The muscadine grape, Vitis rotundifolia, is a specialty crop native to the southeastern USA. Muscadine vines can be male, female, or perfect-flowered, and berry color ranges from bronze to black. Genetic linkage maps were constructed using genotyping-by-sequencing in two F1 populations segregating for flower sex and berry color. The linkage maps consisted of 1244 and 2069 markers assigned to 20 linkage groups (LG) for the 'Black Beauty' × 'Nesbitt' and 'Supreme' × 'Nesbitt' populations, respectively. Data from both populations were used to generate a consensus map with 2346 markers across 20 LGs. A high degree of collinearity was observed between the genetic maps and the Vitis vinifera physical map. The higher chromosome number in muscadine (2n = 40) compared to V. vinifera (2n = 38) was accounted for by the behavior of V. vinifera chromosome 7 as two independently segregating LGs in muscadine. The muscadine sex locus mapped to an interval that aligned to 4.64-5.09 Mb on V. vinifera chromosome 2, a region which includes the previously described V. vinifera subsp. sylvestris sex locus. While the MYB transcription factor genes controlling fruit color in V. vinifera are located on chromosome 2, the muscadine berry color locus mapped to an interval aligning to 11.09-11.88 Mb on V. vinifera chromosome 4, suggesting that a mutation in a different gene in the anthocyanin biosynthesis pathway determines berry color in muscadine. These linkage maps lay the groundwork for marker-assisted breeding in muscadine and provide insight into the evolution of Vitis species.

Medical Monitoring for Occupational Asthma Among Toluene Diisocyanate Production Workers in the United States.

OBJECTIVE: The aim of this study was to describe a study of medical monitoring methods and lessons learned in detecting health outcomes in U.S. plants producing toluene diisocyanate (TDI). METHODS: A multidisciplinary team implemented a medical and environmental monitoring program in three TDI plants. RESULTS: Of 269 eligible workers, 197 (73%) participated and 42 (21%) met symptom and/or lung function criteria that would trigger evaluation for possible asthma over 5 years of data collection. Subsequent evaluation was delayed for most, and a web-based data collection system improved timeliness. CONCLUSION: Medical monitoring of TDI workers identified workers triggering further assessment per study protocol. Systems and/or personnel to ensure rapid follow-up are needed to highlight when triggering events represent potential cases of asthma needing further evaluation. Implementation of a research protocol requires resources and oversight beyond an occupational health program.

Incidence of Occupational Asthma and Exposure to Toluene Diisocyanate in the United States Toluene Diisocyanate Production Industry.

OBJECTIVE: This study examines asthma risk in facilities producing toluene diisocyanate (TDI). METHODS: A total of 197 workers were monitored from 2007 to 2012. TDI air concentrations were used to estimate exposures. RESULTS: The incidence of cases consistent with TDI-induced asthma was 0.009 per person-years (seven cases) or consistent with TDI-induced asthma or asthma indeterminate regarding work-relatedness was 0.012 (nine cases). Increased risk of cases consistent with TDI asthma was observed for cumulative (odds ratio [OR] = 2.08, 95% confidence interval [CI] 1.07 to 4.05) per logarithm parts per billion-years and peak TDI exposures (OR = 1.18, 95% CI 1.06 to 1.32) (logarithm parts per billion). There was a weak association with cumulative and peak exposures for decline of short-term forced expiratory volume in one second (FEV1). Asthma symptoms were associated with workers noticing an odor of TDI (OR 6.02; 95% CI 1.36 to 26.68). CONCLUSIONS: There is evidence that cumulative and peak exposures are associated with TDI-induced asthma.

Longitudinal and Cross-sectional Analyses of Lung Function in Toluene Diisocyanate Production Workers.

OBJECTIVE: The aim of this study was to investigate lung function among toluene diisocyanate (TDI) production workers. METHODS: One hundred ninety-seven U.S workers performed spirometry from 2006 through 2012. Results were compared within the study cohort and with U.S. population measures. A mixed-effects model assessed factors affecting repeated forced expiratory volume in 1 second (FEV1) measurements. RESULTS: The cohort's mean FEV1 and forced vital capacity (FVC) percent reference values, although greater than 90%, were significantly lower and the prevalence of abnormal spirometry (predominantly restrictive pattern) was significantly higher than in the U.S. POPULATION: Differences in lung function among workers with higher cumulative TDI exposure were in the direction of an exposure effect, but not significant. CONCLUSION: We found little evidence of an adverse effect of TDI exposure on longitudinal spirometry in these workers. The association between TDI exposure and the increasing prevalence of a restrictive pattern needs further exploration.

Consumer Acceptability of Fresh-Market Muscadine Grapes.

The objective of this research was to investigate the acceptability of muscadine grape (Vitis rotundifolia) genotypes (cultivars and selections) and to correlate overall liking to other quality measurements to determine the main drivers of liking. Twenty-two genotypes grown at the Univ. of Georgia-Tifton Campus were evaluated. Four retail commercial grape genotypes (Vitis vinifera and "Concord") were also evaluated for comparison. Panelists familiar with muscadine grapes used the hedonic general labeled magnitude scale (HgLMS, -100 = strongest disliking of any kind ever experienced, +100 = strongest liking of any kind ever experienced) to rate overall liking and the liking of appearance, flavor, pulp texture, and skin texture. Puncture testing was done to assess grape berry texture, and compositional attributes soluble solids and pH were also measured. The sensory results indicated that the grapes were variable with overall liking scores from 12.2 to 39.6. The factors highly correlated with overall liking scores were muscadine flavor, pulp and skin liking, while a significant negative correlation was found between skin liking and skin texture and mechanical texture measures. The muscadine grapes with the highest overall liking scores were Ga. 5-1-34 and Ga. 2-8-21. Principal component analysis confirmed that grapes with a thinner skin and a higher pH tended to group around overall liking and flavor points. These results indicate that even among panelists familiar with muscadine grapes, skin thickness is a negative characteristic. Breeding for thinner skins may be a positive step in muscadines gaining a more widespread appeal in the fresh fruit market.

Scab Susceptibility of a Provenance Collection of Pecan in Three Different Seasons in the Southeastern United States.

Pecan scab (caused by Fusicladium effusum) is the most economically destructive disease of pecan in the Southeast United States. Wet, humid conditions typical of the Southeast are known to provide conditions conducive to epidemics. A provenance collection of pecan from 19 locations representing the native range of the tree is located in Byron, Georgia, and was assessed for pecan scab severity in 1998, 2013, and 2014. There were significant differences among the 19 provenances (F = 5.6 to 62.5, P < 0.0001). Provenances from wetter locations (generally north of Texas) had the greatest proportion of scab resistant trees, while provenances from the drier southern areas (Texas and Mexico) tended to be the most susceptible to scab. The association with rainfall was borne out by correlation analysis (r = -0.625 to -0.823 [P < 0.0001 to 0.004]). Other factors consistently associated with scab severity included leaflet tilt and droop angle (r = -0.533 to -0.883 [P < 0.0001 to 0.02]). Multiple regression analysis demonstrated that leaflet droop angle was a particularly good predictor of provenance susceptibility. Leaflet characteristics vary with provenance location, and whether there is a direct relationship between scab severity and leaflet characteristics is not established. Estimates of heritability were not entirely consistent among years, but different methods were used to assess scab severity in 1998 (a 1 to 5 category scale) compared with 2013 and 2014 (the percent ratio scale). Despite using different methods, there was generally good agreement among years in regard to severity of disease on individual trees. In conclusion, trees from more northern populations (in areas with greater annual rainfall) are most likely to provide valuable and diverse sources of resistance to scab. The provenance collection contains a range of scab-resistant genotypes from diverse locations that can contribute to genetic improvement regarding scab resistance.

Developing a registry of workers involved in nanotechnology: BASF experiences.

OBJECTIVE: To assist BASF in the establishment of a registry of workers involved in nanotechnology. METHODS: The initial step was a complete inventory of nanomaterials and sites of use. Guidance was developed to clarify which particulate nanomaterials were to be included in the survey. Site management was then contacted by the medical department to obtain a list of workers. RESULTS: The time line for collecting data ranged from several months to a year, depending on the information needed, and presented challenges based on the lack of global definition and labeling of nanomaterials. Less than 50 nanomaterials are used as raw materials in less than 10% of the sites globally. In North America, less than 5% of sites and 5% workers use nanomaterials. CONCLUSIONS: Further work is required to integrate the inventory, registry, and exposure assessments.

Effect of intensive glycemic lowering on health-related quality of life in type 2 diabetes: ACCORD trial.

OBJECTIVE: To compare the effect of intensive versus standard glycemic control strategies on health-related quality of life (HRQL) in a substudy of the Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial. RESEARCH DESIGN AND METHODS: A randomly selected subsample of 2,053 ACCORD participants enrolled in the HRQL substudy was assessed at baseline and 12-, 36-, and 48-month visits. HRQL assessment included general health status (the 36-Item Short Form Health Survey [SF-36]), diabetes symptoms (the Diabetes Symptom Distress Checklist), depression (Patient Health Questionnaire [PHQ]-9), and treatment satisfaction (Diabetes Treatment Satisfaction Questionnaire [DTSQ]). Repeated-measures ANOVA models were used to estimate change in HRQL outcomes by treatment group over 48 months adjusting for model covariates. The effects of early discontinuation of the ACCORD intensive glycemic control arm on study results were explored. RESULTS: A total of 1,956 (95%) completed the self-report HRQL instrument(s) at baseline. The intensive arm had a larger decrease in SF-36 physical health component score than the standard arm (-1.6 vs. -1.1, P = 0.0345). Treatment satisfaction (DTSQ) showed larger improvement with intensive than standard (P = 0.0004). There were no differences in mean scores of the Diabetes Symptom Checklist and PHQ-9. Effects of participant transition following discontinuation of the intensive arm on HRQL were not significant. CONCLUSIONS: The ACCORD trial strategy of intensive glycemic control did not lead to benefits in HRQL and was associated with modest improvement in diabetes treatment satisfaction. Thus patient acceptability was apparently not compromised with intensive and complex interventions such as those used in ACCORD.

Investigation of cancer occurrences associated with an herbicide manufacturing facility.

This study evaluated cancer incidence and mortality among 251 employees of a facility that synthesized a benzothiadiazin herbicide between 1979-1987. It was initiated in response to a perceived cancer cluster. Cancers were identified mainly by review of occupational medical records and personal interviews. Standardized incidence ratios (SIRs) were computed using comparison data provided by the Louisiana Tumor Registry. Overall mortality was less than expected and did not vary by job type or duration of assignment in the facility. Total cancer incidence was marginally elevated [SIR = 1.4; 95% Confidence Interval (CI): 0.9-1.9] and was highest among men assigned to the unit during 1979 [SIR = 2.1; 95% CI: 1.3-3.3]. Thirteen of 20 cancers among these men were either prostate (9) or digestive system (4) cancers. Increased medical examinations and cancer awareness may have contributed to the detection of cancers at earlier ages than would be seen in a general population. No specific workplace agents were identified to account for the findings although a workplace role cannot be ruled out.

A first linkage map of pecan cultivars based on RAPD and AFLP markers.

We report here the first genetic linkage maps of pecan [Carya illinoinensis (Wangenh.) K. Koch], using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers. Independent maps were constructed for the cultivars 'Pawnee' and 'Elliot' using the double pseudo-testcross mapping strategy and 120 F1 seedlings from a full-sib family. A total of 477 markers, including 217 RAPD, 258 AFLP, and two morphological markers were used in linkage analysis. The 'Pawnee' linkage map has 218 markers, comprising 176 testcross and 42 intercross markers placed in 16 major and 13 minor (doublets and triplets) linkage groups. The 'Pawnee' linkage map covered 2,227 cM with an average map distance of 12.7 cM between adjacent markers. The 'Elliot' linkage map has 174 markers comprising 150 testcross and 22 intercross markers placed in 17 major and nine minor linkage groups. The 'Elliot' map covered 1,698 cM with an average map distance of 11.2 cM between adjacent markers. Segregation ratios for dichogamy type and stigma color were not significantly different from 1:1, suggesting that both traits are controlled by single loci with protogyny and green stigmas dominant to protandry and red stigmas. These loci were tightly linked (1.9 cM) and were placed in 'Elliot' linkage group 16. These linkage maps are an important first step towards the detection of genes controlling horticulturally important traits such as nut size, nut maturity date, kernel quality, and disease resistance.

Experience with early detection of toluene diisocyanate-associated occupational asthma.

There is good reason to expect that regular respiratory surveillance and early removal of workers who develop toluene diisocyanate (TDI)-associated occupational asthma can effectively protect these workers from accelerated pulmonary function decline. Application of this simple principle in operating industrial workplaces presents numerous challenges. The experience of one corporation is presented. One approach is to remove from future diisocyanate work, all workers who develop symptoms consistent with occupational asthma. However, the experience within this one corporation concurs with earlier, more carefully controlled investigations that such a strategy would be unduly restrictive of workers' occupational options. Fewer than half of the workers, who might have triggered such a practice, have required removal after more thorough occupational medical evaluation. Diisocyanates are such well known occupational asthmagens that other exposures tend to be ignored when considering respiratory health problems in a workplace. A small series of workers with work-related respiratory symptoms will be discussed. The usual industrial hygiene air monitoring demonstrated excellent control of the polyisocyanate hazard. Further investigation demonstrated poor control of a mold-release solution. Control of that exposure has allowed previously restricted workers to return to their former work making polyurethane parts. The number of cases available for analysis and discussion from this single, albeit large, corporation is small. Significant advances in understanding whether time-weighted average (TWA), task-specific, or dermal exposures to TDI and other polyisocyanates are most hazardous will require either many more years of experience within one corporation, or pooling of experience across the industry.