scholarly journals Modelling Inoculum Availability of Plurivorosphaerella nawae in Persimmon Leaf Litter with Bayesian Beta Regression

2019 ◽  
Author(s):  
Joaquín Martínez-Minaya ◽  
David Conesa ◽  
Antonio López-Quílez ◽  
José Luis Mira ◽  
Antonio Vicent
Keyword(s):  
Leaf Litter ◽  
Fixed Effects ◽  
Plant Pathogens ◽  
Random Effect ◽  
Beta Regression ◽  
Diospyros Kaki ◽  
Modelling Framework ◽  
Fungal Plant Pathogens ◽  
Serious Disease ◽  
Ascospore Production

AbstractCircular leaf spot (CLS), caused by Plurivorosphaerella nawae, is a serious disease of persimmon (Diospyros kaki) inducing necrotic lesions on leaves, defoliation and fruit drop. Under Mediter-ranean conditions, P. nawae forms pseudothecia in the leaf litter during winter and ascospores are released in spring infecting susceptible leaves. Persimmon growers are advised to apply fungicides for CLS control during the period of inoculum availability, which was defined based on ascospore counts under the microscope. A model of inoculum availability of P. nawae was developed and evaluated as an alternative to ascospore counts. Leaf litter samples were collected weekly in L’Alcúdia from 2010 to 2015. Leaves were soaked, placed in a wind tunnel, and released ascospores of P. nawae were counted. Hierarchical Bayesian beta regression methods were used to fit the dynamics of ascospore production in the leaf litter. The selected model, having the lowest values of DIC, WAIC and LCPO, included accumulated degree days (ADD) and ADD taking into account the vapor pressure deficit (ADDvpd) as fixed effects, and year as a random effect. This model had a MAE of 0.042 and RMSE of 0.062. The beta regression model was evaluated in four orchards for different years from 2010 to 2015. Higher accuracy was obtained at the beginning and the end of the ascospore production period, which are the events of interest to schedule fungicide sprays for CLS control in Spain. This same modelling framework can be extended to other fungal plant pathogens whose inoculum dynamics are expressed as proportion data.

scholarly journals Modelling Inoculum Availability of Plurivorosphaerella nawae in Persimmon Leaf Litter with Bayesian Beta Regression

2020 ◽  
Author(s):  
Joaquín Martínez-Minaya ◽  
David V Conesa ◽  
Antonio López-Quílez ◽  
Jose Luís Mira ◽  
Antonio Vicent
Keyword(s):  
Leaf Litter ◽  
Fixed Effects ◽  
Plant Pathogens ◽  
Random Effect ◽  
Absolute Error ◽  
Beta Regression ◽  
Diospyros Kaki ◽  
Modeling Framework ◽  
Fungal Plant Pathogens ◽  
Ascospore Production

Circular leaf spot (CLS), caused by Plurivorosphaerella nawae, is a serious disease affecting persimmon (Diospyros kaki) that induces necrotic lesions on leaves, defoliation and fruit drop. Under Mediterranean conditions, P. nawae forms pseudothecia in the leaf litter during winter and ascospores are released in spring infecting susceptible leaves. Persimmon growers are advised to apply fungicides for CLS control during the period of inoculum availability, which was defined based on ascospore counts under the microscope. A model of inoculum availability of P. nawae was developed and evaluated as an alternative to ascospore counts. Leaf litter samples were collected weekly in L’Alcúdia (Spain) from 2010 to 2015. Leaves were soaked, placed in a wind tunnel, and the ascospores of P. nawae released were counted. Hierarchical Bayesian beta regression methods were used to model the dynamics of ascospore production in the leaf litter. The selected model included accumulated degree days (ADD) and ADD taking into account the vapor pressure deficit (ADDvpd) as fixed effects, and year as random effect. This model had a mean absolute error of 0.042 and a root mean square error of 0.062. The beta regression model was evaluated in four orchards from 2010 to 2015. Higher accuracy was obtained at the beginning and the end of the ascospore production period, which are the events of interest to schedule fungicide sprays for CLS control in Spain. This same modeling framework can be extended to other fungal plant pathogens whose inoculum dynamics are expressed as proportion data.

scholarly journals A random effects population dynamics model based on proportions-at-age and removal data for estimating total mortality

2012 ◽  
Vol 69 (11) ◽  
pp. 1881-1893 ◽  
Author(s):  
Verena M. Trenkel ◽  
Mark V. Bravington ◽  
Pascal Lorance
Keyword(s):  
Population Dynamics ◽  
Random Effects ◽  
Fixed Effects ◽  
Random Effect ◽  
Total Mortality ◽  
Estimation Bias ◽  
Effective Sample Size ◽  
Dynamics Model ◽  
Population Dynamics Model ◽  
Study Parameter

Catch curves are widely used to estimate total mortality for exploited marine populations. The usual population dynamics model assumes constant recruitment across years and constant total mortality. We extend this to include annual recruitment and annual total mortality. Recruitment is treated as an uncorrelated random effect, while total mortality is modelled by a random walk. Data requirements are minimal as only proportions-at-age and total catches are needed. We obtain the effective sample size for aggregated proportion-at-age data based on fitting Dirichlet-multinomial distributions to the raw sampling data. Parameter estimation is carried out by approximate likelihood. We use simulations to study parameter estimability and estimation bias of four model versions, including models treating mortality as fixed effects and misspecified models. All model versions were, in general, estimable, though for certain parameter values or replicate runs they were not. Relative estimation bias of final year total mortalities and depletion rates were lower for the proposed random effects model compared with the fixed effects version for total mortality. The model is demonstrated for the case of blue ling (Molva dypterygia) to the west of the British Isles for the period 1988 to 2011.

Morphological, biochemical and molecular identification of rhizobacteria isolates with potential for biocontrol of fungal plant pathogens

2021 ◽  
pp. 1-14
Author(s):  
Stephen Larbi-Koranteng ◽  
Richard Tuyee Awuah ◽  
Fredrick Kankam ◽  
Muntala Abdulai ◽  
Marian Dorcas Quain ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Plant Pathogens ◽  
Fungal Plant Pathogens

scholarly journals The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marta Matuszewska ◽  
Tomasz Maciąg ◽  
Magdalena Rajewska ◽  
Aldona Wierzbicka ◽  
Sylwia Jafra
Keyword(s):  
Gene Expression ◽  
Antimicrobial Activity ◽  
Carbon Source ◽  
Reference Genes ◽  
Plant Pathogens ◽  
Plant Protection ◽  
Carbon Sources ◽  
Unknown Compound ◽  
Fungal Plant Pathogens ◽  
The Impact

AbstractPseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound (“cluster 17”) and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.

Determining the Rate of Ergot-alkaloid Degradation in Toxic Endophyte-infected Tall Fescue Hay and Haylage During Long Term Storage

2021 ◽  
Vol 99 (Supplement_2) ◽  
pp. 22-22
Author(s):  
Charles A Zumbaugh ◽  
Susannah A Gonia ◽  
Kathryn M Payne ◽  
Thomas B Wilson
Keyword(s):  
Tall Fescue ◽  
Ergot Alkaloid ◽  
Fixed Effects ◽  
High Performance ◽  
Nutritive Value ◽  
Day Treatment ◽  
Random Effect ◽  
Storage Period ◽  
Neutral Detergent Fiber ◽  
Experimental Unit

Abstract The objectives of this experiment were to determine changes in the nutritive value and ergot alkaloid concentrations of endophyte-infected tall fescue hay and haylage during a 180-d storage period. Forage from a single field of Kentucky-31 tall fescue was cut for hay in late June and allowed to dry in the field. The dry matter (DM) of the windrow of cut forage was measured every 2 h after clipping. Forage was sampled from the windrow in 6 location blocks once forage DM reached target levels for haylage and hay treatments. Haylage and hay samples were taken when the DM of the windrow reached 50% and 80%, respectively. Seven subsamples of each treatment within block were chopped to 1.91 cm in length with a lettuce chopper and vacuum sealed in oxygen-excluding bags. Sample bags were stored indoors and opened at 30 d intervals over the 180-d storage period. Samples were analyzed for pH, nutritive value, and individual ergot alkaloid concentrations using high-performance liquid chromatography. Within each storage day, treatment within block was considered the experimental unit. Data were analyzed in SAS using the MIXED procedure with fixed effects of treatment, day, and the treatment by day interaction. Location block was considered a random effect. As expected, pH was decreased for haylage compared to hay at all time points (P < 0.01) and DM was greater (P < 0.01) for hay compared to haylage. Neutral detergent fiber values were greater (P < 0.01) for hay compared to haylage and declined during storage (P < 0.01). Total ergot alkaloid concentrations did not differ by treatment (P = 0.61), but ergovaline concentrations declined (P < 0.01) during storage. Collectively, these results indicate minimal differences in nutritive value and ergot alkaloid concentrations between hay and haylage during storage, and that ergovaline concentrations decline during storage.

scholarly journals Effect of hay type on cecal and fecal microbiome and fermentation parameters in horses

2020 ◽  
Author(s):  
Rachel J Sorensen ◽  
James S Drouillard ◽  
Teresa L Douthit ◽  
Qinghong Ran ◽  
Douglas G Marthaler ◽  
...  
Keyword(s):  
Fixed Effects ◽  
Volatile Fatty Acids ◽  
Random Effect ◽  
Alpha Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Fecal Microbiome ◽  
Β Diversity ◽  
Fermentation Parameters

Abstract The effect of hay type on the microbiome of the equine gastrointestinal tract is relatively unexplored. Our objective was to characterize the cecal and fecal microbiome of mature horses consuming alfalfa or Smooth Bromegrass (brome) hay. Six cecally cannulated horses were used in a split plot design run as a crossover in 2 periods. Whole plot treatment was ad libitum access to brome or alfalfa hay fed over two 21-d acclimation periods with subplots of sampling location (cecum and rectum) and sampling hour. Each acclimation period was followed by a 24-h collection period where cecal and fecal samples were collected every 3 h for analysis of pH and volatile fatty acids (VFA). Fecal and cecal samples were pooled and sent to a commercial lab (MR DNA, Shallowater, TX) for amplification of the V4 region of the 16S rRNA gene and sequenced using Illumina HiSeq. Main effects of hay on VFA, pH, and taxonomic abundances were analyzed using the MIXED procedure of SAS 9.4 with fixed effects of hay, hour, location, period, all possible interactions and random effect of horse. Alpha and β diversity were analyzed using the R Dame package. Horses fed alfalfa had greater fecal than cecal pH (P ≤ 0.05) whereas horses fed brome had greater cecal than fecal pH (P ≤ 0.05). Regardless of hay type, total volatile fatty acid (VFA) concentrations were greater (P ≤ 0.05) in the cecum than in feces, and alfalfa resulted in greater (P ≤ 0.05) VFA concentrations than brome in both sampling locations. Alpha diversity was greater (P ≤ 0.05) in fecal compared to cecal samples. Microbial community structure within each sampling location and hay type differed from one another (P ≤ 0.05). Bacteroidetes were greater (P ≤ 0.05) in the cecum compared to the rectum, regardless of hay type. Firmicutes and Firmicutes:Bacteroidetes were greater (P ≤ 0.05) in the feces compared to cecal samples of alfalfa-fed horses. In all, fermentation parameters and bacterial abundances were impacted by hay type and sampling location in the hindgut.

scholarly journals Stress-Activated Protein Kinase Signalling Regulates Mycoparasitic Hyphal-Hyphal Interactions in Trichoderma atroviride

2021 ◽  
Vol 7 (5) ◽  
pp. 365
Author(s):  
Dubraska Moreno-Ruiz ◽  
Linda Salzmann ◽  
Mark D. Fricker ◽  
Susanne Zeilinger ◽  
Alexander Lichius
Keyword(s):  
Protein Kinase ◽  
Map Kinases ◽  
Plant Pathogens ◽  
Tip Growth ◽  
Mitogen Activated Protein Kinase ◽  
Trichoderma Atroviride ◽  
Contact Phase ◽  
Fungal Plant Pathogens ◽  
Signalling Network ◽  
Mapk Signalling

Trichoderma atroviride is a mycoparasitic fungus used as biological control agent against fungal plant pathogens. The recognition and appropriate morphogenetic responses to prey-derived signals are essential for successful mycoparasitism. We established microcolony confrontation assays using T. atroviride strains expressing cell division cycle 42 (Cdc42) and Ras-related C3 botulinum toxin substrate 1 (Rac1) interactive binding (CRIB) reporters to analyse morphogenetic changes and the dynamic displacement of localized GTPase activity during polarized tip growth. Microscopic analyses showed that Trichoderma experiences significant polarity stress when approaching its fungal preys. The perception of prey-derived signals is integrated via the guanosine triphosphatase (GTPase) and mitogen-activated protein kinase (MAPK) signalling network, and deletion of the MAP kinases Trichoderma MAPK 1 (Tmk1) and Tmk3 affected T. atroviride tip polarization, chemotropic growth, and contact-induced morphogenesis so severely that the establishment of mycoparasitism was highly inefficient to impossible. The responses varied depending on the prey species and the interaction stage, reflecting the high selectivity of the signalling process. Our data suggest that Tmk3 affects the polarity-stress adaptation process especially during the pre-contact phase, whereas Tmk1 regulates contact-induced morphogenesis at the early-contact phase. Neither Tmk1 nor Tmk3 loss-of-function could be fully compensated within the GTPase/MAPK signalling network underscoring the crucial importance of a sensitive polarized tip growth apparatus for successful mycoparasitism.

Corporate Ownership Structure and Its Effect on Capital Structure: Evidence from BSE Listed Manufacturing Companies in India

2021 ◽  
pp. 227797522096830
Author(s):  
Palaniappan Gurusamy
Keyword(s):  
Capital Structure ◽  
Ownership Structure ◽  
Fixed Effects ◽  
Random Effect ◽  
Corporate Ownership ◽  
Manufacturing Companies ◽  
Hausman Test ◽  
Lm Test ◽  
Corporate Ownership Structure ◽  
The Capital Structure

The study aims to examine the relationship between corporate ownership structure and capital structure of BSE listed manufacturing firms in India. The study has included the sample of 357 companies which covers 16 major sectors during the period of 2006–2015. Considering the dynamic panel nature of the data relating to the capital structure and the ownership structure variables. The analysis undertakes a novel approach of examining the determinants both single equation and reduced equation models. In order to determine the most appropriate model, based on the F test, the Breusch Pagan LM test and finally the Hausman Test is conducted. The Hausman test result has been estimated by the fixed effect model is better than the other two models such as pooled OLS and random effect estimation. Based on the fixed effects results, size, risk and profitability have a highly significant relationship with leverage. Meanwhile, the growth opportunities and tangibility represent insignificant values. The study found that the explanatory variables of the promoters’ ownership and the institutional ownership have a negative impact on leverage, while the corporate ownership has a positive influence on the capital structure decision. The individual or public ownership has a negative and significantly related to the capital structure, whereas the effect of the foreign ownership inversely related to the firm’s leverage.

scholarly journals 251 Evaluation of Condensed Algal Residue Solubles as an Ingredient in Cattle Finishing Diets

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 137-138
Author(s):  
Calvin Gibbons ◽  
Andrea K Watson ◽  
Galen E Erickson ◽  
Bradley M Boyd ◽  
Levi J McPhillips ◽  
...  
Keyword(s):  
Great Plains ◽  
Fixed Effects ◽  
Block Design ◽  
Random Effect ◽  
Distillers Grains ◽  
Experimental Unit ◽  
Omega 3 ◽  
Finishing Diets ◽  
Randomized Block Design ◽  
Algae Oil

Abstract Algae oil production for Omega-3 fatty acid supplementation yields a byproduct called Condensed Algal Residue Solubles (CARS; 25.4% DM, 19.3% CP, 8.3% Fat, 9.96% Na on DM basis), de-oiled algae cells with residual fermentation substrates. This study evaluated the use of CARS in feedlot finishing diets. Crossbreed steers, (n=480) were blocked and stratified by initial body weight (BW) into 4 blocks, and assigned randomly to treatments. Treatments were designed as a 2 x 3 factorial with 3 inclusions of CARS (0, 2.5, 5% of diet DM) and 2 different base diets representing Northern and Southern Great Plains diets. The Southern diets contained steam flaked corn and dry distillers grains while the Northern diets had dry rolled and high moisture corn with wet distillers grains. CARS replaced corn in both diets. All blocks were harvested after 148 days on feed. Performance data were analyzed as a randomized block design with CARS inclusion, base diet, and interactions as fixed effects, BW block as a random effect and pen (n=48) as the experimental unit. Orthogonal contrasts were used to test linear and quadratic effects of CARS inclusion. There were no significant interactions between CARS inclusion and diet type (P ≥ 0.49). Main effects of CARS indicated positive quadratic responses for carcass adjusted ADG, G:F, 12th rib back fat, yield grade (P < 0.01; increasing to 2.5% inclusion, decreasing at 5%) and hot carcass weight was both linear and quadratic (P ≤ 0.01 and P ≥ 0.06 respectively; 969, 977, 935 as CARS increased). Linear decrease in DMI, final adjusted BW and ribeye area (P ≤ 0.01) as CARS increased. Cattle fed the Southern diets had greater ADG and G:F compared to Northern diets (P < 0.01). Including 2.5% CARS in the diet improved feed efficiency in both Northern and Southern based feedlot diets.

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