A Quantitative Trait Locus with a Major Effect on Root-Lesion Nematode Resistance in Barley.

Although the root-lesion nematode Pratylenchus thornei is known to affect barley (Hordeum vulgare L.), there have been no reports on the genetic control of P. thornei resistance in barley. In this research, P. thornei resistance was assessed for a panel of 46 barley mapping parents and for two mapping populations (Arapiles/Franklin and Denar/Baudin). With both populations, a highly significant quantitative trait locus (QTL) was mapped at the same position on the long arm of chromosome 7H. Single-nucleotide polymorphisms (SNPs) in this region were anchored to an RGT Planet pan-genome assembly and assayed on the mapping parents and other barley varieties. The results indicate that Arapiles, Denar, RGT Planet and several other varieties likely have the same resistance gene on chromosome 7H. Marker assays reported here could be used to select for P. thornei resistance in barley breeding. Analysis of existing barley pan-genomic and pan-transcriptomic data provided a list of candidate genes along with information on the expression and differential expression of some of those genes in barley root tissue. Further research is required to identify a specific barley gene that affects root-lesion nematode resistance.

A Multi-Study Exploration of Factors That Optimize Hardiness in Sport Coaches and the Role of Reflective Practice in Facilitating Hardy Attitudes.

Hardiness has been identified as a key personal characteristic that may moderate the ill-effects of stress on health and performance. However, little is known about how hardiness might be developed, particularly in sport coaches. To systematically address this gap, we present two linked studies. First, interviews were conducted with pre-determined high-hardy, elite coaches (n = 13) to explore how they had developed their hardy dispositions through the associated attitudinal sub-components of control, commitment, and challenge. Utilizing thematic analysis, we identified that hardiness was developed through experiential learning, external support, and the use of specific coping mechanisms. Key to all of these themes was the concept of reflective practice, which was thought to facilitate more meaningful learning from the participants' experiences and, subsequently, enhance the self-awareness and insight required to augment hardiness and its sub-components. To investigate further the potential relationship between coaches' reflective practices and their level of hardiness, we conducted a follow-up study. Specifically, a sample of 402 sports coaches completed the Dispositional Resilience Scale-15, the Self-Reflection and Insight Scale, and the Questionnaire for Reflective Thinking. Using latent profile analysis (LPA), we clustered participants into groups based on their reflective profiles (e.g., type of engagement, level of reflective thinking). We then examined differences in hardiness between the five latent sub-groups using multinomial regression. Findings revealed that the sub-group of highly engaged, intentionally critical reflective thinkers reported significantly higher levels of all three hardiness sub-components than all other sub-groups; these effect sizes were typically moderate-to-large in magnitude (standardized mean differences = -1.50 to -0.10). Conversely, the profile of highly disengaged, non-reflective, habitual actors reported the lowest level of all three dimensions. Collectively, our findings offer novel insights into the potential factors that may influence a coaches' level of hardiness. We provide particular support for the importance of reflective practice as a meta-cognitive strategy that helps coaches to develop hardy dispositions through augmenting its attitudinal sub-components. Consequently, our research makes a significant contribution by providing a comprehensive insight into how we might better train and support coaches to demonstrate the adaptive qualities required to thrive in demanding situations.

Fusaristatin A production negatively affects the growth and aggressiveness of the wheat pathogen Fusarium pseudograminearum.

Fusarium pseudograminearum (Fp), the causative fungal pathogen of the diseases Fusarium crown rot, is an important constraint to cereals production in many countries including Australia. Fp produces a number of secondary metabolites throughout its life cycle. One of these metabolites, the cyclic lipopeptide fusaristatin A, is encoded by a specific gene cluster containing a polyketide synthase and a three-module non-ribosomal peptide synthetase. However, a recent survey of Fp populations across Australia suggests that this cluster may only be present in a subset of isolates from Western Australia (WA). In this study, we screened 319 Fp isolates from WA and 110 Fp isolates from the Australian eastern states of New South Wales, Victoria, Queensland and South Australia to examine the distribution of this gene cluster among Australian Fp populations. The fusaristatin A gene cluster was found to be present in ~50% of Fp isolates from WA but completely absent in Fp isolates from eastern states. To determine its potential function, mutants of the fusaristatin A gene cluster were generated by disrupting the non-ribosomal peptide synthetase and polyketide synthase genes simultaneously in two different parental backgrounds. The mutants showed increased growth rates and were significantly more aggressive than their respective parental strains on wheat in crown rot pathogenicity assays. This suggested that fusaristatin A has a negative effect on fungal development and aggressiveness. The possible reasons for the geographically restricted presence of the fusaristatin A gene cluster and its role in fungal biology are discussed.

Pratylenchus thornei: The Relationship Between Presowing Nematode Density and Yield Loss in Wheat and Barley.

The root lesion nematode Pratylenchus thornei causes economic losses in wheat and barley internationally through both reduced grain yield and grain quality. This study investigated the relationships between the presowing P. thornei density and grain yield and the postharvest nematode densities. Four field experiments were conducted at the same site between 2010 and 2014. A range of presowing P. thornei densities was established in the first year by growing three cereal cultivars that ranged from resistant to susceptible. In the following year, plots were sown with the five same cereal cultivars. A linear relationship was observed between the natural log of the presowing P. thornei density and grain yield across all seasons. The results showed that grain yield losses varied between cultivars and seasons. The importance of season was significant, with this study conducted over several seasons, and it highlighted the variability in yield losses between seasons, which will need further investigation. The greatest yield losses observed were 25 to 28% when the maximum presowing P. thornei densities ranged between 150 and 250 P. thornei g of soil-1. An analysis of the relationship between the presowing and postharvest nematode densities revealed that increased presowing nematode densities resulted in decreased multiplication rates in all seasons and in all cultivars. Nematode multiplication rates also varied between seasons. These results explain why it is difficult to predict nematode levels based on cropping history, and additionally, they highlight the importance of growing resistant cultivars to maintain low levels of P. thornei to minimize risk of yield losses.

Age-related environmental gradients influence invertebrate distribution in the Prince Charles Mountains, East Antarctica.

The potential impact of environmental change on terrestrial Antarctic ecosystems can be explored by inspecting biodiversity patterns across large-scale gradients. Unfortunately, morphology-based surveys of Antarctic invertebrates are time-consuming and limited by the cryptic nature of many taxa. We used biodiversity information derived from high-throughput sequencing (HTS) to elucidate the relationship between soil properties and invertebrate biodiversity in the Prince Charles Mountains, East Antarctica. Across 136 analysed soil samples collected from Mount Menzies, Mawson Escarpment and Lake Terrasovoje, we found invertebrate distribution in the Prince Charles Mountains significantly influenced by soil salinity and/or sulfur content. Phyla Tardigrada and Arachnida occurred predominantly in low-salinity substrates with abundant nutrients, whereas Bdelloidea (Rotifera) and Chromadorea (Nematoda) were more common in highly saline substrates. A significant correlation between invertebrate occurrence, soil salinity and time since deglaciation indicates that terrain age indirectly influences Antarctic terrestrial biodiversity, with more recently deglaciated areas supporting greater diversity. Our study demonstrates the value of HTS metabarcoding to investigate environmental constraints on inconspicuous soil biodiversity across large spatial scales.

Modeling Pathogen DNA Content and Visual Disease Assessment in Seed Tubers to Inform Disease in Potato Progeny Root, Stolon, and Tubers.

Measurement of pathogens on seed tubers is essential for informing likelihood of subsequent potato disease. Here we utilized quantitative PCR assessment of pathogen DNA and visual assessment of disease to measure seed tuber inoculum and used this to model development of disease in potato grown in pathogen-free soil. Analysis by recursive partitioning and modeling using receiver operating curves indicated both abundance of Rhizoctonia solani AG3 and Streptomyces scabies DNA, and disease symptoms associated with these pathogens on seed tubers could predict subsequent disease in progeny tubers and for R. solani, stolons. In contrast, abundance of Spongospora subterranea DNA and disease symptoms on seed tubers were not consistently associated with powdery scab in progeny tubers. The relationship between S. subterranea DNA and seed tuber symptoms on root galling was stronger. Symptomless seed tubers that carried high levels of S. subterranea DNA were also associated with greater root galling than those with low pathogen DNA levels. There was a modest association between root galling and powdery scab in progeny tubers. These results highlight the importance of using certified seed tubers, and demonstrate a statistical tool for measuring the impact of seed tuber-borne inoculum.

Contributions of Fusarium virguliforme and Heterodera glycines to the disease complex of sudden death syndrome of soybean.

BACKGROUND: Sudden death syndrome (SDS) of soybean caused by Fusarium virguliforme spreads and reduces soybean yields through the North Central region of the U.S. The fungal pathogen and Heterodera glycines are difficult to manage. METHODOLOGY/PRINCIPAL FINDINGS: The objective was to determine the contributions of H. glycines and F. virguliforme to SDS severity and effects on soybean yield. To quantify DNA of F. virguliforme in soybean roots and soil, a specific real time qPCR assay was developed. The assay was used on materials from soybean field microplots that contained in a four-factor factorial-design: (i) untreated or methyl bromide-fumigated; (ii) non-infested or infested with F. virguliforme; (iii) non-infested or infested with H. glycines; (iv) natural precipitation or additional weekly watering. In years 2 and 3 of the trial, soil and watering treatments were maintained. Roots of soybean 'Williams 82' were collected for necrosis ratings at the full seed growth stage R6. Foliar symptoms of SDS (area under the disease progress curve, AUDPC), root necrosis, and seed yield parameters were related to population densities of H. glycines and the relative DNA concentrations of F. virguliforme in the roots and soil. The specific and sensitive real time qPCR was used. Data from microplots were introduced into models of AUDPC, root necrosis, and seed yield parameters with the frequency of H. glycines and F. virguliforme, and among each other. The models confirmed the close interrelationship of H. glycines with the development of SDS, and allowed for predictions of disease risk based on populations of these two pathogens in soil. CONCLUSIONS/SIGNIFICANCE: The results modeled the synergistic interaction between H. glycines and F. virguliforme quantitatively in previously infested field plots and explained previous findings of their interaction. Under these conditions, F. virguliforme was mildly aggressive and depended on infection of H. glycines to cause highly severe SDS.

A DNA-based method for studying root responses to drought in field-grown wheat genotypes.

Root systems are critical for water and nutrient acquisition by crops. Current methods measuring root biomass and length are slow and labour-intensive for studying root responses to environmental stresses in the field. Here, we report the development of a method that measures changes in the root DNA concentration in soil and detects root responses to drought in controlled environment and field trials. To allow comparison of soil DNA concentrations from different wheat genotypes, we also developed a procedure for correcting genotypic differences in the copy number of the target DNA sequence. The new method eliminates the need for separation of roots from soil and permits large-scale phenotyping of root responses to drought or other environmental and disease stresses in the field.

Genetic mapping and marker development for resistance of wheat against the root lesion nematode Pratylenchus neglectus.

BACKGROUND: The Rlnn1 locus, which resides on chromosome 7A of bread wheat (Triticum aestivum L.) confers moderate resistance against the root lesion nematode Pratylenchus neglectus. Prior to this research, the exact linkage relationships of Rlnn1 with other loci on chromosome 7A were not clear and there were no simple codominant markers available for selection of Rlnn1 in wheat breeding. The objectives of the research reported here were to (1) develop an improved genetic map of the Rlnn1 region of chromosome 7A and (2) develop molecular markers that could be used in marker-assisted selection to improve resistance of wheat against P. neglectus. RESULTS: A large-effect quantitative trait locus (QTL) for resistance against P. neglectus was genetically mapped using a population of Excalibur/Kukri doubled haploid lines. This QTL coincides in position with the rust resistance gene(s) Lr20/Sr15, the phytoene synthase gene Psy-A1 and 10 molecular markers, including five new markers designed using wheat-rice comparative genomics and wheat expressed sequence tags. Two of the new markers are suitable for use as molecular diagnostic tools to distinguish plants that carry Rlnn1 and Lr20/Sr15 from those that do not carry these resistance genes. CONCLUSIONS: The genomic location of Rlnn1 was confirmed to be in the terminal region of the long arm of chromosome 7A. Molecular markers were developed that provide simple alternatives to costly phenotypic assessment of resistance against P. neglectus in wheat breeding. In Excalibur, genetic recombination seems to be completely suppressed in the Rlnn1 region.

The effect of high hydrostatic pressure on the microbiological quality and safety of carrot juice during refrigerated storage.

The microbial quality of untreated and pressure-treated carrot juice was compared during storage at 4, 8 and 12 °C. High pressure treatment at 500 MPa and 600 MPa (1 min/20 °C) reduced the total counts by approximately 4 log CFU ml⁻¹ and there was very little growth of the survivors during storage at 4 °C for up to 22 days. Total counts increased during storage of pressure-treated juice at 8 °C and 12 °C but took significantly longer to reach maximum levels compared to the untreated juice. The microflora in the untreated juice consisted predominantly of Gram-negative bacteria, identified as mostly Pantoea spp., Erwinia spp. and Pseudomonas spp. Initially the pressure-treated juice contained low numbers of spore-forming bacteria (Bacillus spp. and Paenibacillus spp.) and Gram-positive cocci; the spore-formers continued to dominate during storage. When irradiation-sterilised juice was inoculated with a cocktail of Listeria monocytogenes, numbers decreased during storage at 4 °C and 8 °C by 1.50 and 0.56 log CFU ml⁻¹ respectively. When the inoculated carrot juice was pressure treated (500 MPa/1 min/20 °C) no L. monocytogenes were found immediately after pressure treatment or during storage at 4, 8 and 12 °C (>6 log inactivation). In contrast, pressure treatment in TSBYE only resulted in 1.65 log inactivation and survivors grew rapidly. This suggests that the antilisterial effect of carrot juice is enhanced by HPP.

Predicting Take-All Severity in Second-Year Wheat Using Soil DNA Concentrations of Gaeumannomyces graminis var. tritici Determined with qPCR.

The lack of accurate detection of Gaeumannomyces graminis var. tritici inoculum in soil has hampered efforts to predict the risk of severe take-all for wheat growers. The current study used a molecular method to quantify soil G. graminis var. tritici concentrations in commercial wheat fields in New Zealand and to compare them with the proportion of crops surpassing the thresholds for visible and moderate to severe take-all over three growing seasons. The study evaluated a soil G. graminis var. tritici DNA-based take-all prediction system developed in Australia, with four take-all risk categories. These categories were found to be useful for predicting disease severity in second wheat but did not clearly separate risk between fields in medium- and high-risk categories. A sigmoidal relationship was identified between inoculum concentration and the proportion of fields exceeding the two disease thresholds. A logistic response curve was used to further examine this relationship and evaluate the boundaries between take-all risk categories. G. graminis var. tritici boundaries between medium- and high-risk categories were clustered near or within the upper plateau of the relationship. Alternative G. graminis var. tritici boundaries for a three-category system were identified that provided better separation of take-all risk between categories. This information could improve prediction of the risk of severe take-all.

A comparative study of changes in the microbiota of apple juice treated by high hydrostatic pressure (HHP) or high pressure homogenisation (HPH).

The objective of this study was to assess the effect of High Pressure Homogenisation (HPH) compared with High Hydrostatic Pressure (HHP) on the microbiological quality of raw apple juice during storage at ideal (4 °C) and abuse (12 °C) temperatures. In the case of HPH, only low numbers of micro-organisms were detected after treatment at 300 MPa (typically between 2 and 3 log.ml⁻¹). These were identified as Streptomyces spp., and numbers did not increase during storage of the juice for 35 days, irrespective of storage temperature. In the case of HHP, the total aerobic counts were also reduced significantly (p < 0.05) after treatment for 1 min at 500 and 600 MPa and the numbers did not increase significantly during storage at 4 °C. However, during storage at 12 °C the counts did increase significantly (p < 0.05) and by day 14 counts at 500 MPa were not significantly different from the control juice. This confirms that good temperature control is important if the full benefits of HHP treatment are to be realised. Frateuria aurantia dominated the microbiota of the HHP apple juice stored at 12 °C along with low levels of Bacillus and Streptomyces spp. The HPH and HHP juices both turned brown during storage indicating that neither treatment was sufficient to inactivate polyphenol oxidase. The enzyme is known to be pressure resistant and this discolouration was controlled by a heat treatment (70 °C for 1 min) used in commercial practice and given prior to HP treatment.

Toward routine, DNA-based detection methods for marine pests.

Marine pest incursions can cause significant ongoing damage to aquaculture, biodiversity, fisheries habitat, infrastructure and social amenity. They represent a significant and ongoing economic burden. Marine pests can be introduced by several vectors including aquaculture, aquarium trading, commercial shipping, fishing, floating debris, mining activities and recreational boating. Despite the inherent risks, there is currently relatively little routine surveillance of marine pest species conducted in the majority of countries worldwide. Accurate and rapid identification of marine pest species is central to early detection and management. Traditional techniques (e.g. physical sampling and sorting), have limitations, which has motivated some progress towards the development of molecular diagnostic tools. This review provides a brief account of the techniques traditionally used for detection and describes developments in molecular-based methods for the detection and surveillance of marine pest species. Recent advances provide a platform for the development of practical, specific, sensitive and rapid diagnosis and surveillance tools for marine pests for use in effective prevention and control strategies.

Pharmacogenomics in the curricula of colleges and schools of pharmacy in the United States.

OBJECTIVES: To assess the breadth, depth, and perceived importance of pharmacogenomics instruction and level of faculty development in this area in schools and colleges of pharmacy in the United States. METHODS: A questionnaire used and published previously was further developed and sent to individuals at all US schools and colleges of pharmacy. Multiple approaches were used to enhance response. RESULTS: Seventy-five (83.3%) questionnaires were returned. Sixty-nine colleges (89.3%) included pharmacogenomics in their PharmD curriculum compared to 16 (39.0%) as reported in a 2005 study. Topic coverage was <10 hours for 28 (40.6%), 10-30 hours for 29 (42.0%), and 31-60 hours for 10 (14.5%) colleges and schools of pharmacy. Fewer than half (46.7%) were planning to increase course work over the next 3 years and 54.7% had no plans for faculty development related to pharmacogenomics. CONCLUSIONS: Most US colleges of pharmacy include pharmacogenomics content in their curriculum, however, the depth may be limited. The majority did not have plans for faculty development in the area of pharmacogenomic content expertise.

Effect of high pressure on the microbiological quality of cooked chicken during storage at normal and abuse refrigeration temperatures.

Vacuum-packaged cooked poultry meat was treated at a range of pressures (400-600 MPa) and hold times (1, 2 and 10 min), followed by storage at 4 degrees , 8 degrees or 12 degrees C for up to 35 days. Weissella viridescens was found to be the dominant microorganism in the pressure-treated meat, constituting 100% of the microflora identified at 500 and 600 MPa. None of the pressure-treated samples had obvious signs of spoilage during the 35 day storage period, even when the Weissella count was >7 log(10) cfu/g. Studies on a typical W. viridescens isolate showed it to be relatively pressure-resistant in poultry meat, with <1 log reduction in numbers after a treatment of 2 min at 600 MPa. Agar diffusion assays showed that the isolate also caused the inhibition of a number of Gram-positive and Gram-negative pathogens, including strains of Clostridium botulinum, Listeria monocytogenes, Bacillus cereus and Escherichia coli. The selection of a pressure-resistant organism, such as this Weissella sp. could be advantageous in extending the shelf-life, and also microbiological safety, of the cooked meat, as it could give protection in addition to the pressure treatment itself.

Inactivation of fungal spores in apple juice by high pressure homogenization.

High pressure homogenization (HPH) at 300 MPa in apple juice provides more than 5-log kill of ascospores of Saccharomyces cerevisiae, conidiospores of filamentous fungi, and sporulated black yeasts. HPH and heat treatment were more effective against vegetative cells than against the spores of yeasts used in this study. Ascospores of Talaromyces macrosporus and Neosartorya spinosa were resistant to HPH at 300 MPa. HPH of ascospores of T. macrosporus may result in activation.

Vascular stiffness is related to superoxide generation in the vessel wall.

OBJECTIVES: Oxidative stress causes endothelial dysfunction and plays a major role in the pathogenesis of cardiovascular disease. Increased vascular stiffness is an intermediate phenotype in the development of cardiovascular disease. We hypothesized that vascular stiffness is partially determined by oxidative stress. METHODS: We examined 163 participants out of whom 80 had coronary artery disease. Vascular stiffness was assessed by pulse wave analysis, pulse wave velocity and measurement of aortic compliance by cardiac MRI. Circulating markers of oxidative stress and vascular superoxide generation in saphenous vein were measured. RESULTS: After adjustment for age, sex, BMI, heart rate, blood pressure and lipids only carotid-femoral pulse wave velocity and aortic compliance were different between patients and control group. Aortic compliance was reduced (11.4 +/- 6.3 vs. 13.9 +/- 7.3 ml x 10(-3) per mmHg; P = 0.035) and vascular superoxide generation increased (1.01 +/- 0.45 vs. 0.76 +/- 0.44 nmol/mg per min; P = 0.035) in patients with coronary artery disease compared with those without. In a multiple stepwise regression analysis, aortic compliance was determined by age (P < 0.001) and vascular superoxide production (P = 0.033). CYBA C242T and NOS3 G894T polymorphisms had additive effects on vascular superoxide generation (P = 0.026) and xanthine oxidase activity was increased in patients with CAD (P = 0.043). Genetic factors (P = 0.033) and xanthine oxidase activity (P < 0.001) were also related to aortic compliance. CONCLUSION: By measuring vascular superoxide generation and aortic compliance using cardiac MRI, we demonstrated a functional relationship between oxidative stress and vascular stiffness. Patients identified with high levels of vascular stiffness are most likely to benefit from strategies to reduce vascular oxidative stress.

Antimicrobial resistance and heat sensitivity of oxacillin-resistant, mecA-positive Staphylococcus spp. from unpasteurized milk.

Eight Staphylococcus spp. carrying the mecA gene were isolated from oxacillin enrichments of 70 unpasteurized milk samples. The isolates were identified as five Staphylococcus epidermidis, two Staphylococcus lentus, and one Staphylococcus haemolyticus. No mecA-positive Staphylococcus aureus were isolated. All isolates carried genes for other antibiotic resistances in addition to mecA. The results establish that mecA-carrying coagulase-negative Staphylococcus spp. in unpasteurized milk have the potential to be a reservoir of other genes encoding antimicrobial resistance. Two S. epidermidis isolates with qacA/B genes were resistant to benzalkonium chloride. Decimal reduction times (D-values) for the mecA-Staphylococcus spp. at 56 degrees C in whole milk ranged from 1.46 to 2.82 min. D-values at 56 degrees C for nine S. aureus milk isolates ranged from 10.8 to 20.1 min. Heat treatments intended to control S. aureus may be an effective means to protect consumers of milk and dairy products. Contact with or consumption of milk and dairy products that have not been heat treated may lead to the spread of antimicrobial resistance genes in Staphylococcus spp. to animals and humans.

Developing and testing a diagnostic probe for grape phylloxera applicable to soil samples.

Grape phylloxera, Daktulosphaira vitifoliae (Fitch) (Hemiptera Phylloxeridae) is a damaging pest of grapevines (Vitis spp.) around the world, and the management of this pest requires early detection of infestations. Here, we describe the development and validation of a sensitive DNA test for grape phylloxera that can be applied to soil. Species-specific primers were developed for grape phylloxera in the internal transcribed space region 2, and their specificity was confirmed after thorough screening by using a wide range of vineyard organisms and aphid genera. Preliminary testing of the detection limits of the grape phylloxera-specific primers was conducted using field-sourced soil types spiked with a known number of grape phylloxera. The assay was converted to a real-time polymerase chain reaction format (TaqMan MGB). This assay, in combination with DNA extraction from soil, can detect phylloxera crawlers added to soil. The assay was evaluated in the field at a recently detected grape phylloxera infestation site from the Yarra Valley in Victoria, Australia. The DNA assay proved to be substantially more sensitive than a standard ground survey for detecting grape phylloxera presence on vine roots in the infested vineyard. Moreover, unlike the ground survey, the assay provided quantitative information on grape phylloxera infestations, because grape phylloxera DNA concentrations in samples from vines closely matched the numbers of grape phylloxera crawlers collected with emergence traps placed at the base of vines. Unlike other detection techniques, the method can be applied at any time of the year, and it can be potentially modified to provide specific information on the virulence levels of the particular grape phylloxera genotypes responsible for any new infestations.