scholarly journals Use of Pyrosequencing to Quantify Incidence of a Specific Aspergillus flavus Strain Within Complex Fungal Communities Associated with Commercial Cotton Crops

2008 ◽  
Vol 98 (3) ◽  
pp. 282-288 ◽  
Author(s):  
Modan K. Das ◽  
Kenneth C. Ehrlich ◽  
Peter J. Cotty
Keyword(s):  
Aspergillus Flavus ◽  
Correlation Coefficients ◽  
Aflatoxin Contamination ◽  
South Texas ◽  
Wash Water ◽  
Nucleotide Polymorphisms ◽  
Management Tools ◽  
Good Correspondence ◽  
Single Nucleotide ◽  
Initial Polymerase Chain Reaction

Atoxigenic strains of Aspergillus flavus have been used as aflatoxin management tools on over 50,000 hectares of commercial crops since 2000. To assess treatment efficacy, atoxigenic strain incidence is routinely monitored by vegetative compatibility analyses (VCA) that require culturing, generation of auxotrophs, and complementation with tester mutants. Two pyrosequencing assays (PA) that require no culturing were developed for monitoring incidences of atoxigenic strains on ginned cottonseed. The assays, which quantify frequencies of characteristic single nucleotide polymorphisms (SNPs) in the aflR and pksA genes, were validated against standard VCA on cottonseed collected from commercial gins in South Texas, Arizona, and Southern California where the atoxigenic strain AF36 is used to manage aflatoxin contamination. Cottonseed washings were subjected to both VCA and PA. PA was performed directly on DNA isolated from particulates pelleted from the wash water by centrifugation. Addition of CaCl2 and diatomaceous earth prior to pelleting increased the amount of DNA isolated. Accuracy and reproducibility of the PA were contrasted with those for the VCA that has been used for over a decade. Correlation coefficients between VCA and PA indicated good correspondence between the results from the two assays (r = 0.91 for aflR assay and r = 0.80 for pksA assay). PAs were highly variable for samples with low incidences of A. flavus due to variability in the initial polymerase chain reaction step. This held for both DNA isolated from cottonseed washes and for mixtures of purified DNA. For samples yielding low quantities of A. flavus DNA, averaging of results from 4 to 5 replicates was required to achieve acceptable correlations with VCA. Pyrosequencing has the potential to become a powerful tool for monitoring atoxigenic strains within complex A. flavus communities without limitations imposed by traditional culturing methods.

scholarly journals Nutrient Environments Influence Competition among Aspergillus flavus Genotypes

2012 ◽  
Vol 79 (5) ◽  
pp. 1473-1480 ◽  
Author(s):  
Hillary L. Mehl ◽  
Peter J. Cotty
Keyword(s):  
Aspergillus Flavus ◽  
Mycelial Growth ◽  
Competitive Ability ◽  
Aflatoxin Contamination ◽  
Nucleotide Polymorphisms ◽  
Intraspecific Interactions ◽  
Single Nucleotide ◽  
Content Type ◽  
Agar Media ◽  
Nutrient Variability

ABSTRACTThe population dynamics ofAspergillus flavus, shaped in part by intraspecific competition, influence the likelihood and severity of crop aflatoxin contamination. Competition for nutrients may be one factor modulating intraspecific interactions, but the influences of specific types and concentrations of nutrients on competition between genotypes ofA. flavushave not been investigated. Competition between pairedA. flavusisolates on agar media was affected by varying concentrations of carbon (sucrose or asparagine) and nitrogen (nitrate or asparagine). Cocultivated isolate percentages from conidia and agar-embedded mycelia were quantified by measurements of isolate-specific single-nucleotide polymorphisms with quantitative pyrosequencing. Compositions and concentrations of nutrients influenced conidiation resulting from cocultivation, but the percentages of total conidia from each competing isolate were not predicted by sporulation of isolates grown individually. Success during sporulation did not reflect the outcomes of competition during mycelial growth, and the extents to which isolate percentages from conidia and mycelia differed varied among both isolate pairs and media. Whether varying concentrations of sucrose, nitrate, or asparagine increased, decreased, or had no influence on competitive ability was isolate dependent. Different responses ofA. flavusisolates to nutrient variability suggest genotypes are adapted to different nutrient environments that have the potential to influenceA. flavuspopulation structure and the epidemiology of aflatoxin contamination.

scholarly journals Single-nucleotide polymorphisms in FABP4 gene associated with growth traits in Egyptian sheep

2020 ◽  
Vol 13 (6) ◽  
pp. 1126-1132
Author(s):  
Heba Ibrahim Shafey ◽  
Karima Fathy Mahrous ◽  
Amal Ahmed Mohamed Hassan ◽  
Hossam Eldin Rushdi ◽  
Mohamed Abd El-Aziz Mohamed Ibrahim
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Correlation Coefficients ◽  
Nucleotide Polymorphisms ◽  
Negative Effects ◽  
Single Nucleotide ◽  
Fatty Acid Binding ◽  
Sheep Breeds ◽  
Intron 1

Aim: The present study was performed to assess the association of single-nucleotide polymorphisms (SNPs) in the fatty acid-binding protein 4 (FABP4) gene with birth weight (BW), final weight (FW), and average daily gain (ADG) in three Egyptian sheep breeds. Materials and Methods: Genomic DNA was extracted from the blood samples of 50 male and female individuals representing Ossimi, Rahmani, and Barki sheep breeds. A 407 bp nucleotide (nt) segment from the first intron of FABP4 was amplified by polymerase chain reaction, sequenced, and analyzed in the different samples. Results: Sequence analysis of the determined segment (407 bp) revealed four SNPs (all transition types) at nt position 372 (CP011894.1:g.57605471) A>G, nt position 211 (CP011894.1:g.57605632) A>G, nt position 143 (CP011894.1:g.57605700) T>C, and nt position 111 (CP011894.1:g.57605732) T>C. The allelic and genotypic frequencies for the identified SNPs in the sheep breeds were calculated. At nt positions 372 and 211, two alleles were identified (A and G). Only two genotypes were present at nt position 372 (AA and AG), while three genotypes were present at nt position 211 (AA, AG, and GG). Two alleles (T and C) and three identified genotypes (TT, TC, and CC) were detected at nt positions 143 and 111. Analysis of the results revealed that AA genotype at nt position 372 is associated with higher estimates for BW, FW, and ADG when compared to all the other genotypes. Very high correlation coefficients were found between the genotypes 143-TT and 111-TT and also between 143-TC and 111-TC. The genotypes 372-AG, 211-GG, 211-AA, 143-TT, 143-CC, 111-TT, 111-TC, and 111-CC were associated with negative effects on BW, FW, and ADG. Conclusion: The detection of four SNPs in a partial sequence of the Egyptian ovine FABP4 gene intron 1 reflected that this gene harbors substantial diversity. In addition, a novel SNP at nt position 372 (CP011894.1:g.57605471) A>G was associated with higher estimates for BW, FW, and ADG.

scholarly journals Variation in Competitive Ability Among Isolates of Aspergillus flavus from Different Vegetative Compatibility Groups During Maize Infection

2010 ◽  
Vol 100 (2) ◽  
pp. 150-159 ◽  
Author(s):  
H. L. Mehl ◽  
P. J. Cotty
Keyword(s):  
Aspergillus Flavus ◽  
Competitive Ability ◽  
Aflatoxin Contamination ◽  
Vegetative Compatibility ◽  
Life Strategy ◽  
Nucleotide Polymorphisms ◽  
Vegetative Compatibility Groups ◽  
Kernel Infection ◽  
Aflatoxin B ◽  
Maize Kernels

Aspergillus flavus, the primary causal agent of aflatoxin contamination, includes many genetically diverse vegetative compatibility groups (VCGs). Competitive ability during infection of living maize kernels was quantified for isolates from 38 VCGs. Kernels were inoculated with both a common VCG, CG136, and another VCG; after 7 days (31°C), conidia were washed from kernels, and aflatoxins and DNA were extracted from kernels and conidia separately. CG136-specific single-nucleotide polymorphisms were quantified by pyrosequencing; VCGs co-inoculated with CG136 produced 46 to 85 and 51 to 84% of A. flavus DNA from kernels and conidia, respectively. Co-inoculation with atoxigenic isolates reduced aflatoxin up to 90% and, in some cases, more than predicted by competitive exclusion alone. Conidia contained up to 42 ppm aflatoxin B1, indicating airborne conidia as potentially important sources of environmental exposure. Aflatoxin-producing potential and sporulation were negatively correlated. For some VCGs, sporulation during co-infection was greater than that predicted by kernel infection, suggesting that some VCGs increase dispersal while sacrificing competitive ability during host tissue colonization. The results indicate both life strategy and adaptive differences among A. flavus isolates and provide a basis for selection of biocontrol strains with improved competitive ability, sporulation, and aflatoxin reduction on target hosts.

scholarly journals Aspergillus flavus in Soils and Corncobs in South Texas: Implications for Management of Aflatoxins in Corn-Cotton Rotations

Plant Disease ◽  
2004 ◽  
Vol 88 (12) ◽  
pp. 1366-1371 ◽  
Author(s):  
Ramon Jaime-Garcia ◽  
Peter J. Cotty
Keyword(s):  
Aspergillus Flavus ◽  
Rio Grande Valley ◽  
Aflatoxin Contamination ◽  
Soil Samples ◽  
South Texas ◽  
Reduced Tillage ◽  
The North ◽  
Previous Season ◽  
Significant Difference

Aspergillus flavus causes aflatoxin contamination in both cottonseed and corn. Corn-cotton rotations are common in South Texas, where reduced tillage frequently results in long-term residence of corncobs on soil surfaces. Corncobs are colonized by A. flavus either prior to harvest or while in the soil. This study sought to determine the potential of corncobs as sources of inoculum for cotton and corn in South Texas. A. flavus communities in corncob and soil samples were collected during the planting seasons of 2001 to 2003 from 29 fields extending from Calhoun and Victoria Counties in the north to the Rio Grande Valley. In order to assess persistence of A. flavus in corncobs, A. flavus communities in corncobs and soil were contrasted every 2 to 3 months in four fields throughout the 3-year study. To assess seasonal variation, similar contrasts were performed in two fields on a biweekly basis. The results indicate that corncobs are major sources of A. flavus inoculum. Corncobs from the previous season contained, on average, over 190 times more A. flavus propagules than soil from the same field, and 2-year-old corncobs still retained 45 times more propagules than soil. There was no significant difference in the incidence of A. flavus strain S on corncobs and soil. The quantity of A. flavus in corncobs decreased with corncob age (r 2 = 0.54; P = 0.002).

scholarly journals Spatial Relationships of Soil Texture and Crop Rotation to Aspergillus flavus Community Structure in South Texas

2006 ◽  
Vol 96 (6) ◽  
pp. 599-607 ◽  
Author(s):  
Ramon Jaime-Garcia ◽  
Peter J. Cotty
Keyword(s):  
Aspergillus Flavus ◽  
Rio Grande Valley ◽  
Clay Content ◽  
Rio Grande ◽  
Aflatoxin Contamination ◽  
Soil Samples ◽  
South Texas ◽  
The West ◽  
The North ◽  
Coast Region

Aspergillus flavus, the causal agent of aflatoxin contamination of cottonseed, is a natural inhabitant of soils. A. flavus can be divided into the S and L strains, of which the S-strain isolates, on average, produce greater quantities of aflatoxins than the L-strain isolates. Aflatoxin contamination can be severe in several crops in South Texas. The structure of A. flavus communities residing in soils of South Texas was determined from 326 soil samples collected from 152 fields located from the Rio Grande Valley in the south to Fort Bend County in the north from 2001 through 2003. Analysis of variance indicated significant differences in the incidence of A. flavus isolates belonging to the S strain (percent S) among regions. The Coastal Bend (30.7%) and Upper Coast (25.5%) regions had significantly higher percent S incidence than the Rio Grande Valley (4.8%). No significant differences in percent S among years were detected. The CFU per gram of soil were not significantly different among regions. Strain S incidence was positively correlated with clay content and negatively correlated with sand content. Fields cropped to cotton the previous year had a higher S-strain incidence, whereas fields cropped to corn had greater total quantities of A. flavus propagules. Maps of S-strain patterns show that the S strain constitutes >30% of the overall A. flavus community in the area extending from the central Coastal Bend region to the central Upper Coast region. The west Rio Grande Valley had the lowest S-strain incidence (<10%). Geographic variation in S-strain incidence may influence the distribution of aflatoxin contamination in South Texas.

scholarly journals Identification of Atoxigenic Aspergillus flavus Isolates to Reduce Aflatoxin Contamination of Maize in Kenya

Plant Disease ◽  
2011 ◽  
Vol 95 (2) ◽  
pp. 212-218 ◽  
Author(s):  
C. Probst ◽  
R. Bandyopadhyay ◽  
L. E. Price ◽  
P. J. Cotty
Keyword(s):  
Biological Control ◽  
Aspergillus Flavus ◽  
Aflatoxin Contamination ◽  
Fungal Communities ◽  
Management Tools ◽  
Maize Production ◽  
Vegetative Compatibility Groups ◽  
Potential Value ◽  
Maize Sample ◽  
Maize Kernels

Aspergillus flavus has two morphotypes, the S strain and the L strain, that differ in aflatoxin-producing ability and other characteristics. Fungal communities on maize dominated by the S strain of A. flavus have repeatedly been associated with acute aflatoxin poisonings in Kenya, where management tools to reduce aflatoxin levels in maize are needed urgently. A. flavus isolates (n = 290) originating from maize produced in Kenya and belonging to the L strain morphotype were tested for aflatoxin-producing potential. A total of 96 atoxigenic isolates was identified from four provinces sampled. The 96 atoxigenic isolates were placed into 53 vegetative compatibility groups (VCGs) through complementation of nitrate non-utilizing mutants. Isolates from each of 11 VCGs were obtained from more than one maize sample, isolates from 10 of the VCGs were detected in multiple districts, and isolates of four VCGs were found in multiple provinces. Atoxigenic isolates were tested for potential to reduce aflatoxin concentrations in viable maize kernels that were co-inoculated with highly toxigenic S strain isolates. The 12 most effective isolates reduced aflatoxin levels by >80%. Reductions in aflatoxin levels caused by the most effective Kenyan isolates were comparable with those achieved with a United States isolate (NRRL-21882) used commercially for aflatoxin management. This study identified atoxigenic isolates of A. flavus with potential value for biological control within highly toxic Aspergillus communities associated with maize production in Kenya. These atoxigenic isolates have potential value in mitigating aflatoxin outbreaks in Kenya, and should be evaluated under field conditions.

scholarly journals Identifying diagnosis-specific genotype–phenotype associations via joint multitask sparse canonical correlation analysis and classification

2020 ◽  
Vol 36 (Supplement_1) ◽  
pp. i371-i379 ◽  
Author(s):  
Lei Du ◽  
Fang Liu ◽  
Kefei Liu ◽  
Xiaohui Yao ◽  
Shannon L Risacher ◽  
...  
Keyword(s):  
Correlation Analysis ◽  
Canonical Correlation Analysis ◽  
Canonical Correlation ◽  
Correlation Coefficients ◽  
Imaging Genetics ◽  
Supplementary Information ◽  
Local Optimum ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Sparse Canonical Correlation Analysis

Abstract Motivation Brain imaging genetics studies the complex associations between genotypic data such as single nucleotide polymorphisms (SNPs) and imaging quantitative traits (QTs). The neurodegenerative disorders usually exhibit the diversity and heterogeneity, originating from which different diagnostic groups might carry distinct imaging QTs, SNPs and their interactions. Sparse canonical correlation analysis (SCCA) is widely used to identify bi-multivariate genotype–phenotype associations. However, most existing SCCA methods are unsupervised, leading to an inability to identify diagnosis-specific genotype–phenotype associations. Results In this article, we propose a new joint multitask learning method, named MT–SCCALR, which absorbs the merits of both SCCA and logistic regression. MT–SCCALR learns genotype–phenotype associations of multiple tasks jointly, with each task focusing on identifying one diagnosis-specific genotype–phenotype pattern. Meanwhile, MT–SCCALR cannot only select relevant SNPs and imaging QTs for each diagnostic group alone, but also allows the selection of those shared by multiple diagnostic groups. We derive an efficient optimization algorithm whose convergence to a local optimum is guaranteed. Compared with two state-of-the-art methods, MT–SCCALR yields better or similar canonical correlation coefficients and classification performances. In addition, it owns much better discriminative canonical weight patterns of great interest than competitors. This demonstrates the power and capability of MTSCCAR in identifying diagnostically heterogeneous genotype–phenotype patterns, which would be helpful to understand the pathophysiology of brain disorders. Availability and implementation The software is publicly available at https://github.com/dulei323/MTSCCALR. Supplementary information Supplementary data are available at Bioinformatics online.

Nuclear receptors in disease: the oestrogen receptors

2004 ◽  
Vol 40 ◽  
pp. 157-167 ◽  
Author(s):  
Maria Nilsson ◽  
Karin Dahlman-Wright ◽  
Jan-Åke Gustafsson
Keyword(s):  
Nuclear Receptors ◽  
Target Genes ◽  
Receptor Subtype ◽  
Target Tissue ◽  
Oestrogen Receptors ◽  
Nucleotide Polymorphisms ◽  
Cell Type ◽  
Single Nucleotide ◽  
Beneficial Effects ◽  
The Family

For several decades, it has been known that oestrogens are essential for human health. The discovery that there are two oestrogen receptors (ERs), ERalpha and ERbeta, has facilitated our understanding of how the hormone exerts its physiological effects. The ERs belong to the family of ligand-activated nuclear receptors, which act by modulating the expression of target genes. Studies of ER-knockout (ERKO) mice have been instrumental in defining the relevance of a given receptor subtype in a certain tissue. Phenotypes displayed by ERKO mice suggest diseases in which dysfunctional ERs might be involved in aetiology and pathology. Association between single-nucleotide polymorphisms (SNPs) in ER genes and disease have been demonstrated in several cases. Selective ER modulators (SERMs), which are selective with regard to their effects in a certain cell type, already exist. Since oestrogen has effects in many tissues, the goal with a SERM is to provide beneficial effects in one target tissue while avoiding side effects in others. Refined SERMs will, in the future, provide improved therapeutic strategies for existing and novel indications.

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