Barry M Pryor

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• Daines, M. O., Zhu, l., Pereira, R., Zhou, X., Bondy, C., Pryor, B. M., Zhou, J., & Chen, Y. (2021).

  Alternaria induces airway epithelial cytokine expression independent of protease-activated receptor

  . Respirology, 25(5), 502-510. doi:10.1111/resp.13675
• Pryor, B. M., & Daines, M. (2021). Novel Mouse Models of Fungal Asthma. Frontiers in Cellular and Infection Microbiology, section Fungal Pathogenesis. doi:https://doi.org/10.3389/fcimb.2021.683194
• Pryor, B. M., Chen, Y., Luo, Q., Liu, Y., Besselsen, D. G., Cunningham, A., Pereira, R. S., & Daines, M. O. (2021).

  Novel Mouse Models of Fungal Asthma

  . Frontiers in Cellular and Infection Microbiology. doi:10.3389/fcimb.2021.683194
• Pryor, B. M., Gervasio, D., & Evans, P. (2021).

  A Hybrid Microbial-Enzymatic Fuel Cell Cathode Overcomes Enzyme  Inactivation Limits in Biological Fuel Cells

  . Catalysts. doi:https://doi.org/10.3390/catal11020242
• Pryor, B. M., Waller, P. M., Davidowitz, G., & Gutierrez-Jaramillo, A. (2021). Bioregenerative Food Production System: Using integrated food production systems to feed the future. International Conference on Environmental Systems ICES, 2021-169.
• Pryor, B. M., & Gomez, B. A. (2020).

  First report of Fusarium wilt of queen palm in Arizona caused by Fusarium oxysporum f.sp. palmarum.

  . Plant Disease, 104(5), 1551-1551. doi:10.1094/pdis-03-19-0551-pdn
• Daines, M., Zhu, L., Pereira, R., Zhou, X., Bondy, C., Pryor, B. M., Zhou, J., & Chen, Y. (2019). Alternaria induces airway epithelial cytokine expression independent of protease-activated receptor. Respirology (Carlton, Vic.).
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  A novel fungal allergen, Alternaria (Alt), has been previously shown to associate with the pathogenesis of allergic rhinitis and bronchial asthma, particularly in arid and semi-arid regions. Airway epithelial cells are among the first to encounter Alt, and epithelial cytokine production and subsequent airway inflammation are early events in the response to Alt exposure. However, the underlying mechanism is unclear. As protease-activated receptor 2 (PAR2) has been implicated in most of the Alt-induced biological events, we investigated the regulation of airway inflammation and epithelial cytokine expression by PAR2.
• Pryor, B. M., & Rodriguez, B. (2018). Fusarium wilt of palm, a new disease of horticultural palms in Arizona. Plant Disease.
• Rotondo, F., Pryor, B. M., Peever, T. L., & Hong, S. G. (2018).

  Molecular diversity and allergenic profiles of Alternaria spp. from desert environments in Arizona.

  . Fungal biology, 122(1), 74-85. doi:10.1016/j.funbio.2017.10.010
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  This study examined the genetic diversity of small-spored Alternaria species in the southwest desert of the USA by sampling 552 isolates from different habitats (soil and plant debris) in different locations (urban and an undisturbed desert). To estimate the genetic diversity, Amplified Fragment Length Polymorphism (AFLP) fingerprinting analysis was performed for all isolates. Strains representative of the sampled genotypic diversity (n = 125) were further characterized according their sporulation pattern and the capability to produce allergens. Morphological characterization assigned the majority of the strains to the Alternaria alternata and Alternaria tenuissima morpho-groups with only two isolates assigned to the Alternaria arborescens morpho-group. AFLP fingerprinting differentiated the A. arborescens morpho-groups, but could not distinguish between the A. alternata and A. tenuissima morpho-groups. Western blot analysis showed that a large number of allergenic proteins were produced by strains. These proteins were not specific for any morpho-group nor source of isolation. A hierarchical analysis of molecular variance was performed on the AFLP data to quantify molecular variation and partition this variation among sampled locations and habitat. No statistically significant differentiation among locations and habitat was detected indicating a lack of population structure across environments.
• Rotondo, F., Pryor, B. M., Peever, T. L., & Ozkilinc, H. (2018).

  Contrasting species boundaries between sections Alternaria and Porri of the genus Alternaria

  . Plant Pathology, 67(2), 303-314. doi:10.1111/ppa.12749
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  College of Agricultural, Human, and Natural Resource Sciences, Washington State University; College of Agriculture and Life Sciences, University of Arizona; National Science Foundation [DEB 0918758]
• Koike, S., Smith, R., Pryor, B. M., & Cahn, M. (2017). Association of the carrot pathogen Alternaria dauci with new diseases, Alternaria leaf speck. Plant Health Progress, 18, 136-143.
• Pryor, B. M., & Jackson, L. W. (2017).

  Degradation of aflatoxin B1 from naturally contaminated maize using the edible fungus Pleurotus ostreatus

  . AMB Express. doi:10.1186/s13568-017-0415-0
• Pryor, B. M., & Jackson, L. W. (2017). Degradation of aflatoxin B1 from naturally contaminated maize using the edible fungus Pleurotus ostreatus. AMB Express, 7, 10. doi:10.1186/s13568-017-0415-0
• Pryor, B. M., Adaskaveg, J. E., Forster, H., & Lou, Y. (2017). Identification of Alternaria causing fruit rot of pomegranite in California. Plant Disease, 101, 421-427.
• Pryor, B. M., Adaskaveg, J. E., Förster, H., Hou, L., & Luo, Y. (2017).

  Identification of Alternaria Species Causing Heart Rot of Pomegranates in California

  . Plant Disease, 101(3), 421-427. doi:10.1094/pdis-08-16-1176-re
• Pryor, B. M., Cahn, M., Smith, R., & Koike, S. T. (2017).

  Association of the Carrot Pathogen Alternaria dauci With New Diseases, Alternaria Leaf Speck, of Lettuce and Celery in California

  . Plant Health Progress, 18(2), 136-143. doi:10.1094/php-12-16-0074-rs
• Pryor, B. M., Hong, S. G., Rotondo, F., & Peever, T. L. (2017). Allergen diversity among Alternaria species recovered from native desert in southern Arizona. Fungal Biology, 122:74-85., 74-85.
• Pryor, B. M., Ozkilinc, H., Rotondo, F., & Peever, T. L. (2017). Contrasting evolutionary patterns between sections Alternata and Porri of the genus Alternaria. Plant Pathology, 67, 303-314.
• Pryor, B. M., Porchas, M., & Matheron, M. E. (2017). Evaluation of conventional fungicides and biofungicides for managing Fusarium wilt of lettuce, 2016. Disease Management Reports, 11, V124.
• Dang, H. X., Pryor, B., Peever, T., & Lawrence, C. B. (2015). The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species. BMC genomics, 16, 239.
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  Alternaria is considered one of the most common saprophytic fungal genera on the planet. It is comprised of many species that exhibit a necrotrophic phytopathogenic lifestyle. Several species are clinically associated with allergic respiratory disorders although rarely found to cause invasive infections in humans. Finally, Alternaria spp. are among the most well known producers of diverse fungal secondary metabolites, especially toxins.
• Pryor, B. M., & Chitrampalam, P. (2015).

  Characterization of mating type (MAT) alleles differentiated by a natural inversion in Sclerotinia minor

  . Plant Pathology, 64(4), 911-920. doi:10.1111/ppa.12305
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  A recent study on fungal mating type genes revealed two MAT alleles within homothallic Sclerotinia sclerotiorum differentiated by an inversion, Inv− (inversion negative) and Inv+ (inversion positive). An analysis of mating type in closely related S. minor was conducted to shed light on the evolution of this MAT inversion. Inv− and Inv+ MAT alleles were identified in S. minor and were characterized. Both MAT alleles in S. minor were flanked by APN2 and SLA2, and consisted of two idiomorphs fused as in other homothallic ascomycetes. However, in the Inv+ MAT, the 3·6 kb MAT region was inverted relative to the Inv− MAT. Except for the inversion, both Inv− and Inv+ MAT in S. minor were equal in size and identical in nucleotide sequence. The MAT inversion in Inv+ S. minor was at exactly the same place as in Inv+ S. sclerotiorum and affected three of four MAT genes: MAT1-1-1 was truncated and MAT1-2-4 and MAT1-2-1 were inverted. Unlike S. sclerotiorum, expression of MAT genes did not differ between Inv− and Inv+ S. minor. The 250 bp inverted repeat motif that flanked the inverted MAT region in S. sclerotiorum and believed responsible for the MAT inversion was also found in S. minor, but was 256 bp. Depending on the MAT genes, 93–96% nucleotide identity was observed between Sclerotinia species. Both Inv+ and Inv− MAT S. minor and S. sclerotiorum isolates were commonly found in lettuce fields of Arizona along with MAT heterokaryons.
• Pryor, B. M., Lawrence, C. B., Peever, T. L., & Dang, H. X. (2015).

  The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species

  . BMC Genomics. doi:10.1186/s12864-015-1430-7
• Pryor, B. M., Maier, R. M., Soderlund, C., Nelson, W., & Vaughan, M. R. (2015).

  Assessing Fungal Community Structure from Mineral Surfaces in Kartchner Caverns Using Multiplexed 454 Pyrosequencing

  . Microbial Ecology. doi:10.1007/s00248-014-0560-9
• Vaughan, M. J., Nelson, W., Soderlund, C., Maier, R. M., & Pryor, B. M. (2015). Assessing Fungal Community Structure from Mineral Surfaces in Kartchner Caverns Using Multiplexed 454 Pyrosequencing. Microbial ecology.
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  Research on the distribution and structure of fungal communities in caves is lacking. Kartchner Caverns is a wet and mineralogically diverse carbonate cave located in an escarpment of Mississippian Escabrosa limestone in the Whetstone Mountains, Arizona, USA. Fungal diversity from speleothem and rock wall surfaces was examined with 454 FLX Titanium sequencing technology using the Internal Transcribed Spacer 1 as a fungal barcode marker. Fungal diversity was estimated and compared between speleothem and rock wall surfaces, and its variation with distance from the natural entrance of the cave was quantified. Effects of environmental factors and nutrient concentrations in speleothem drip water at different sample sites on fungal diversity were also examined. Sequencing revealed 2,219 fungal operational taxonomic units (OTUs) at the 95 % similarity level. Speleothems supported a higher fungal richness and diversity than rock walls. However, community membership and the taxonomic distribution of fungal OTUs at the class level did not differ significantly between speleothems and rock walls. Both OTU richness and diversity decreased significantly with increasing distance from the natural cave entrance. Community membership and taxonomic distribution of fungal OTUs also differed significantly between the sampling sites closest to the entrance and those furthest away. There was no significant effect of temperature, CO2 concentration, or drip water nutrient concentration on fungal community structure on either speleothems or rock walls. Together, these results suggest that proximity to the natural entrance is a critical factor in determining fungal community structure on mineral surfaces in Kartchner Caverns.
• Chitrampalam, P., & Pryor, B. M. (2014). Characterization of mating type (MAT) alleles differentiated by a natural inversion in Sclerotinia minor. Plant Pathology.
• Neilson, J. W., Pryor, B. M., Maier, R. M., Soderlund, C., Wing, R. A., Nelson, W., Fryslie, B., Legatzki, A., & Ortiz, M. (2014).

  Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave

  . The ISME Journal. doi:10.1038/ismej.2013.159
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  Carbonate caves represent subterranean ecosystems that are largely devoid of phototrophic primary production. In semiarid and arid regions, allochthonous organic carbon inputs entering caves with vadose-zone drip water are minimal, creating highly oligotrophic conditions; however, past research indicates that carbonate speleothem surfaces in these caves support diverse, predominantly heterotrophic prokaryotic communities. The current study applied a metagenomic approach to elucidate the community structure and potential energy dynamics of microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a speleothem metagenome revealed a community genetically adapted to low-nutrient conditions with indications that a nitrogen-based primary production strategy is probable, including contributions from both Archaea and Bacteria. Genes for all six known CO2-fixation pathways were detected in the metagenome and RuBisCo genes representative of the Calvin-Benson-Bassham cycle were over-represented in Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be significantly more abundant in the cave communities than in soils above the cave. MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads found Thaumarchaeota to be the third most abundant phylum in the community, and identified taxonomic associations to this phylum for indicator genes representative of multiple CO2-fixation pathways. The results revealed that this oligotrophic subterranean environment supports a unique chemoautotrophic microbial community with potentially novel nutrient cycling strategies. These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts.
• Pryor, B. M. (2014). Characterization of Alternaria isolates from the infectoria species-group and a new taxon from Arrhenatherum, Pseudoalternaria arrhenatheria sp. nov.. Mycological Progress.
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  Lawrence, D. P., Dugan, F. M., and Pryor, B. M. 2014. Characterization of Alternaria isolates from the infectoria species-group and a new taxon from Arrhenatherum, Pseudoalternaria arrhenatheria sp. nov. Mycological Progress 13:257-276.
• Pryor, B. M. (2014). Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave.. ISME Journal.
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  Marianyoly Ortiz, Antje Legatzki, Julia W. Neilson, Brandon Fryslie, William M. Nelson, Rod A. Wing, Carol A. Soderlund, Barry M. Pryor, and Raina M. Maier. 2014. Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave. The ISME Journal, 8:478–491.
• Pryor, B. M., Dugan, F. M., Gannibal, P. B., & Lawrence, D. A. (2014).

  Characterization of Alternaria isolates from the infectoria species-group and a new taxon from Arrhenatherum, Pseudoalternaria arrhenatheria sp. nov.

  . Mycological Progress. doi:10.1007/s11557-013-0910-x
• Pryor, B. M., Peever, T. L., Lawrence, C. B., Timmer, L. W., & Stewart, J. E. (2014).

  Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen

  . BMC Evolutionary Biology. doi:10.1186/1471-2148-14-38
• Stewart, J. E., Timmer, L. W., Lawrence, C. B., Pryor, B. M., & Peever, T. L. (2014). Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen. BMC Evolutionary Biology, 14(1), 38.
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  Traditional morphological and biological species concepts are difficult to apply to closely related, asexual taxa because of the lack of an active sexual phase and paucity of morphological characters. Phylogenetic species concepts such as genealogical concordance phylogenetic species recognition (GCPSR) have been extensively used; however, methods that incorporate gene tree uncertainty into species recognition may more accurately and objectively delineate species. Using a worldwide sample of Alternaria alternata sensu lato, causal agent of citrus brown spot, the evolutionary histories of four nuclear loci including an endo-polygalacturonase gene, two anonymous loci, and one microsatellite flanking region were estimated using the coalescent. Species boundaries were estimated using several approaches including those that incorporate uncertainty in gene genealogies when lineage sorting and non-reciprocal monophyly of gene trees is common.
• Chitrampalam, P., & Pryor, B. M. (2013). Population density and spatial pattern of sclerotia of Sclerotinia sclerotiorum in desert lettuce production fields. Canadian Journal of Plant Pathology, 35(4), 494-502.
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  Abstract: Soil population densities and spatial patterns of sclerotia produced by Sclerotinia sclerotiorum were determined in six commercial lettuce production fields with varying histories of lettuce drop in Yuma County, AZ. Each field was divided into eight approximate equal sections and in each section, a plot (10 × 20 m) was randomly selected for soil sampling. Soil cores were collected along both diagonals at 2 m intervals in each plot and sclerotia populations were determined by wet sieving. The average soil sclerotia population per plot ranged from 0.0 to 5.8/100 g soil. The highest and the lowest percent of individual soil samples with ≥ 1 sclerotia/100 g soil per plot were 63% and 7%, respectively. Three indices of dispersions-variance/mean, Morisitas index and Lloyds index-calculated for each of the six fields indicated that sclerotia distributions were aggregated. However, in none of the fields could the sclerotia distributions be adequately described by the Poisson, negative binomial or Neyman type A distributions. © 2013 The Canadian Phytopathological Society.
• Lawrence, D. P., Gannibal, P. B., Dugan, F. M., & Pryor, B. M. (2013). Characterization of Alternaria isolates from the infectoria species-group and a new taxon from Arrhenatherum, Pseudoalternaria arrhenatheria sp. nov.. Mycological Progress, 1-20.
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  Abstract: The infectoria species-group within the genus Alternaria was originally conceived by Simmons in 1993 and was based upon common morphological characteristics that included the development of conidial chains with primary, secondary, and tertiary branching resulting in substantial three-dimensional complexity. These characters can overlap to varying degrees with numerous taxa in another Alternaria group, the alternata species-group, making species-group differentiation difficult. However, members of the infectoria species-group are also distinguished from other small-spored Alternaria species based upon colony characteristics that typically include white or nearly white floccose colonies on DRYES medium and clumps of sporulation islands on low sugar media such as V8 agar, PCA, and weak PDA. In addition, the infectoria species-group contains representatives that are known to produce teleomorphs (Lewia), whereas the members of the alternata species-group and other Alternaria species-groups are strictly asexual. In this study, an assemblage of isolates recovered from varied hosts from the west coast of the United States were examined based upon morphological characters and compared to previously described members of the infectoria species-group. These isolates and members of the infectoria species-group typically produce arachnoid vegetative hyphae with multiple primary conidiophores, whereas other small-spored Alternaria species produce primary conidiophores predominately directly from the agar surface. Additionally, molecular phylogenetic analyses resolved these isolates and members of the infectoria species-group as distinctly nested amongst other sexual taxa in Allewia (Embellisia anamorph) and Macrospora (Nimbya anamorph) and phylogenetically distant to asexual lineages of Alternaria. One taxon among these isolates was novel and clustered with the asexual A. rosae in a distinct clade basal to all other members of the infectoria species-group. A new genus is proposed, Pseudoalternaria gen. nov. and a new taxon is described, Pseudoalternaria arrhenatheria sp. nov.. Moreover, a second taxon is reclassified, Pseudoalternaria rosae comb. nov. © 2013 German Mycological Society and Springer-Verlag Berlin Heidelberg.
• Lawrence, D. P., Gannibal, P. B., Peever, T. L., & Pryor, B. M. (2013). The sections of alternaria: Formalizing species-group concepts. Mycologia, 105(3), 530-546.
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  PMID: 23687125;Abstract: The systematics of Alternaria and allied genera traditionally has been based on the characteristics of conidia and the sporulation apparatus. This emphasis on morphology in the reconstruction of organismal relationships has resulted in taxonomic uncertainty and flux for a number of taxa in Alternaria and the related genera Stemphylium, Embellisia, Nimbya and Ulocladium. The present study used a molecular phylogenetic approach for systematic resolution and incorporated extensive taxon sampling (n 5 176 species) representing 10 genera and analyses of 10 protein-coding loci. Phylogenetic analyses based on five of these genes revealed eight distinct asexual lineages of Alternaria that cluster as the sister group to the asexual paraphyletic genus Ulocladium, while taxa with known teleomorphs currently circumscribed as Alternaria (the infectoria species group) cluster among genera that also have representatives with known teleomorphs. This work proposes to elevate the eight well supported asexual lineages of Alternaria to the taxonomic rank of section. Evolutionary relationships among Alternaria and closely related genera are discussed. © 2013 by The Mycological Society of America.
• Neilson, J. W., Pryor, B. M., Maier, R. M., Pierson, L. S., Soderlund, C., Wing, R. A., Yu, Y., Byrne, A., Legatzki, A., Nelson, W., & Ortiz, M. (2013).

  Profiling Bacterial Diversity and Taxonomic Composition on Speleothem Surfaces in Kartchner Caverns, AZ

  . Microbial Ecology. doi:10.1007/s00248-012-0143-6
• Ortiz, M., Neilson, J., Nelson, W., Legatzki, A., Byrne, A., Yu, Y., Soderlund, C., Pryor, B., Pierson, L., & Maier, R. (2013). Profiling bacterial diversity and taxonomic compostion on speleothem surfaces in Karchner Caversn, AZ. Microbial Ecology, 65, 371-383.
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  Ortiz, M., Neilson, J.W., Nelson, W.M., Legatzki, A., Byrne, A., Yu, Y., Soderlund, C.A., Pryor, B.M., Pierson, L.S., and Maier, R.M. 2013. Profiling bacterial diversity and taxonomic compostion on speleothem surfaces in Karchner Caversn, AZ. Microbial Ecology 65:371-383.
• Pryor, B. M. (2013). Characterization of Alternaria isolates from the infectoria species-group and a new taxon from Arrhenatherum, Pseudoalternaria arrhenatheria sp. nov. Mycological Progress.
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  Lawrence, D. P., Dugan, F. M., and Pryor, B. M. 2013. Characterization of Alternaria isolates from the infectoria species-group and a new taxon from Arrhenatherum, Pseudoalternaria arrhenatheria sp. nov.Mycological Progress, 10.1007/s11557-013-0910-x.
• Pryor, B. M. (2013). Population and spatial pattern of sclerotia of Sclerotinia sclerotiorum in desert lettuce production fields of Arizona and California. Canadian Journal of Plant Pathology.
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  Chitrampalam, P. and Pryor, B. M. 2013. Population and spatial pattern of sclerotia of Sclerotinia sclerotiorum in desert lettuce production fields of Arizona and California. Canadian Journal of Plant Pathology, 35:494-502.
• Pryor, B. M. (2013). Signatures of recombination in clonal lineages of the citrus brown spot pathogen, Alternaria alternata sensu lato.. Phytopathology, 741-749.
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  Stewart, J.E., K.A. Thomas, C.B. Lawrence, H. Dang, B.M. Pryor, L.M. Timmer and T.L. Peever. 2013. Signatures of recombination in clonal lineages of the citrus brown spot pathogen, Alternaria alternata sensu lato. Phytopathology 103:741-749.
• Pryor, B. M., & Chitrampalam, P. (2013).

  Population density and spatial pattern of sclerotia ofSclerotinia sclerotiorumin desert lettuce production fields

  . Canadian journal of plant pathology. doi:10.1080/07060661.2013.841758
• Pryor, B. M., Peever, T. L., Gannibal, P. B., & Lawrence, D. P. (2013).

  The sections ofAlternaria: formalizing species-group concepts

  . Mycologia. doi:10.3852/12-249
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  The systematics of Alternaria and allied genera traditionally has been based on the characteristics of conidia and the sporulation apparatus. This emphasis on morphology in the reconstruction of organismal relationships has resulted in taxonomic uncertainty and flux for a number of taxa in Alternaria and the related genera Stemphylium, Embellisia, Nimbya and Ulocladium. The present study used a molecular phylogenetic approach for systematic resolution and incorporated extensive taxon sampling (n = 176 species) representing 10 genera and analyses of 10 protein-coding loci. Phylogenetic analyses based on five of these genes revealed eight distinct asexual lineages of Alternaria that cluster as the sister group to the asexual paraphyletic genus Ulocladium, while taxa with known teleomorphs currently circumscribed as Alternaria (the infectoria species-group) cluster among genera that also have representatives with known teleomorphs. This work proposes to elevate the eight well supported asexual lineages of Alternaria to the taxonomic rank of section. Evolutionary relationships among Alternaria and closely related genera are discussed.
• Pryor, B. M., Peever, T. L., Timmer, L. M., Dang, H. X., Lawrence, C. B., Thomas, K. A., & Stewart, J. E. (2013).

  Signatures of Recombination in Clonal Lineages of the Citrus Brown Spot Pathogen, Alternaria alternata sensu lato

  . Phytopathology. doi:10.1094/phyto-08-12-0211-r
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  Most Alternaria spp. are considered asexual but recent molecular evolution analyses of Alternaria mating-type genes show that the mating locus is under strong purifying selection, indicating a possible role in sexual reproduction. The objective of this study was to determine the mode of reproduction of an Alternaria alternata sensu lato population causing citrus brown spot in central Florida. Mating type of each isolate was determined, and isolates were sequenced at six putatively unlinked loci. Three genetically distinct subpopulations (SH1, SH4A, and SH4B) were identified using network and Bayesian population structure analyses. Results demonstrate that most subpopulations of A. alternata associated with citrus are clonal but some have the ability to extensively recombine through a cryptic sexual cycle or parasexual cycle. Although isolates were sampled in close physical proximity (≈2,500-m 2 area), we were able to reject a random mating model using multilocus gametic disequilibrium tests for two subpopulations, SH1 and SH4B, suggesting that these subpopulations were predominantly asexual. However, three recombination events were identified in SH1 and SH4B and localized to individuals of opposite mating type, possibly indicating meiotic recombination. In contrast, in the third subpopulation (SH4A), where only one mating type was present, extensive reticulation was evident in network analyses, and multilocus gametic disequilibrium tests were consistent with recombination. Recombination among isolates of the same mating type suggests that a nonmeiotic mechanism of recombination such as the parasexual cycle may be operating in this subpopulation. The level of gene flow detected among subpopulations does not appear to be sufficient to prevent differentiation, and perhaps future speciation, of these A. alternata subpopulations.
• Pryor, B., Pryor, B. M., Lawrence, D. P., Gannibal, P. B., & Peever, T. L. (2013). The sections of Alternaria: formalizing species-group concepts. Mycologia, 105(3).
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  The systematics of Alternaria and allied genera traditionally has been based on the characteristics of conidia and the sporulation apparatus. This emphasis on morphology in the reconstruction of organismal relationships has resulted in taxonomic uncertainty and flux for a number of taxa in Alternaria and the related genera Stemphylium, Embellisia, Nimbya and Ulocladium. The present study used a molecular phylogenetic approach for systematic resolution and incorporated extensive taxon sampling (n = 176 species) representing 10 genera and analyses of 10 protein-coding loci. Phylogenetic analyses based on five of these genes revealed eight distinct asexual lineages of Alternaria that cluster as the sister group to the asexual paraphyletic genus Ulocladium, while taxa with known teleomorphs currently circumscribed as Alternaria (the infectoria species-group) cluster among genera that also have representatives with known teleomorphs. This work proposes to elevate the eight well supported asexual lineages of Alternaria to the taxonomic rank of section. Evolutionary relationships among Alternaria and closely related genera are discussed.
• Stewart, J. E., Thomas, K. A., Lawrence, C. B., Dang, H., Pryor, B. M., Timmer, L. M., & Peever, T. L. (2013). Signatures of recombination in clonal lineages of the citrus brown spot pathogen, Alternaria alternata sensu lato. Phytopathology, 103(7), 741-749.
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  PMID: 23441968;Abstract: Most Alternaria spp. are considered asexual but recent molecular evolution analyses of Alternaria mating-type genes show that the mating locus is under strong purifying selection, indicating a possible role in sexual reproduction. The objective of this study was to determine the mode of reproduction of an Alternaria alternata sensu lato population causing citrus brown spot in central Florida. Mating type of each isolate was determined, and isolates were sequenced at six putatively unlinked loci. Three genetically distinct subpopulations (SH1, SH4A, and SH4B) were identified using network and Bayesian population structure analyses. Results demonstrate that most subpopulations of A. alternata associated with citrus are clonal but some have the ability to extensively recombine through a cryptic sexual cycle or parasexual cycle. Although isolates were sampled in close physical proximity (≈2,500-m2 area), we were able to reject a random mating model using multilocus gametic disequilibrium tests for two subpopulations, SH1 and SH4B, suggesting that these subpopulations were predominantly asexual. However, three recombination events were identified in SH1 and SH4B and localized to individuals of opposite mating type, possibly indicating meiotic recombination. In contrast, in the third subpopulation (SH4A), where only one mating type was present, extensive reticulation was evident in network analyses, and multilocus gametic disequilibrium tests were consistent with recombination. Recombination among isolates of the same mating type suggests that a nonmeiotic mechanism of recombination such as the parasexual cycle may be operating in this subpopulation. The level of gene flow detected among subpopulations does not appear to be sufficient to prevent differentiation, and perhaps future speciation, of these A. alternata subpopulations. © 2013 The American Phytopathological Society.
• Troncoso-rojas, R., Tiznado-hernandez, M. E., Pryor, B. M., Garcia, H. S., & Baez-flores, M. E. (2013).

  Inter simple sequence repeat polymorphism in Alternaria genomic DNA exposed to lethal concentrations of isothiocyanates

  . African Journal of Microbiology Research, 7(10), 838-852. doi:10.5897/ajmr12.291
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  Isothiocyanates (ITCs) is a group of defense related compounds synthesized byBrassicas that have positive effects on human health which suggest that they are environmentally friendly compounds to control fungi infections. However, the development of ITC-resistant strains of fungi is a matter of concern.  The objective of the present work was to study the response of  Alternaria  alternata to allyl-isothiocyanate (AITC) and benzyl isothiocyanate (BITC) chronic exposure and the effect of the treatment on some of the inter simple sequence repeats (ISSR) regions. Five strains of A. alternata isolated from tomato and five isolated from cabbage were independently exposed in vitro to AITC and BITC. Concentrations were increased until it reached 0.08 and 0.6 mg/mL of AITC and BITC, respectively. Genomic DNA from both wild type and isogenic adapted strains to ITCs was isolated and five primers were used for ISSR amplification:  (GACA)4: 5´-GACAGACAGACAGACA-3´; M13:5´-GAGGGTGGCGGCGGTTCT-3´;(AAG)8:5´-AAGAAGAAGAAGAAGAAGAAGAAG-3´; (ACA)5: 5´-ACAACAACAACAACA-3´ and T3B: 5´-AGGTCGCGGGTTCGAATCC-3´. A lower degree of polymorphism was found to be induced by the treatment in the wild-type strains isolated from cabbage as compared with the wild-type strains isolated from tomato.  It can be concluded that ITCs exposure induced random mutations in different ISSR regions of the A. alternata genome which does not lead to the development of strains with a hereditable resistant phenotype.   Key words: Alternaria alternata, fungicide, allyl-isothiocyanate, benzyl-isothiocyanate, inter-simple sequence repeat
• Lawrence, D. P., Park, M. S., & Pryor, B. M. (2012). Nimbya and Embellisia revisited, with nov. comb for Alternaria celosiae and A. perpunctulata. Mycological Progress, 11(3), 799-815.
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  Abstract: Previous phylogenetic analyses revealed that species within the genera Nimbya and Embellisia reside within a large monophyletic clade that also includes the genera Alternaria, Ulocladium, Undifilum, Sinomyces, and Crivellia with Stemphylium as the sister taxon. This study expands upon previous work by including many contemporary species of each genus and utilizes molecular and morphological characters to further examine relationships. Maximum parsimony and Bayesian analysis reveals that Nimbya is not a monophyletic genus but is split into two phylogenetically distant clades, which have different and distinct conidial morphologies. One of these clades resides completely within Alternaria. Phylogenetic analyses also reveals that Embellisia does not form a monophyletic genus but is split into four monophyletic lineages. Moreover, several species of Embellisia cluster individually with clades that are predominantly Alternaria, Ulocladium, or Stemphylium, yet these Embellisia spp. possess morphological characters that are diagnostically Embellisia. Thus, these data reveal that both Nimbya and Embellisia are polyphyletic as currently defined and taxonomic restructuring is necessary in order to resolve conflict between historical morphological and contemporary molecular-based phylogenies. © 2011 German Mycological Society and Springer.
• Legatzki, A., Ortiz, M., Neilson, J., Casavant, R., Palmer, M., Rasmussen, C., Pryor, B., Pierson, I. L., & Maier, R. (2012). Factors influencing observed variations in the structure of bacterial communities on calcite formations in Kartchner Caverns, AZ, USA. Geomicrobiology Journal, 29, 422-434.
• Neilson, J. W., Pryor, B. M., Maier, R. M., Pierson, L. S., Rasmussen, C., Palmer, M. W., Casavant, R. R., Ortiz, M., & Legatzki, A. (2012).

  Factors Influencing Observed Variations in the Structure of Bacterial Communities On Calcite Formations in Kartchner Caverns, AZ, USA

  . Geomicrobiology Journal. doi:10.1080/01490451.2011.581326
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  Kartchner Caverns is an oligotrophic subterranean environment that hosts a wide diversity of actively growing calcite speleothems (secondary mineral deposits). In a previous study, we demonstrated that bacterial communities extracted from these surfaces are quite complex and vary between formations. In the current study, we evaluated the influence of several environmental variables on the superficial bacterial community structure of 10 active formations located in close proximity to one another in a small room of Kartchner Caverns State Park, Arizona, USA. Physical (color, dimensions) and chemical (elemental profile and organic carbon concentration) properties, as well as the DGGE-based bacterial community structure of the formations were analyzed. While elemental concentration was found to vary among the formations, the differences in the community structure could not be correlated with concentrations of either organic carbon or any of the elements evaluated. In contrast, the locations of formations with...
• Pryor, B. M., Brunelli, A., Collina, M., & Rotondo, F. (2012).

  Comparison of Alternaria spp. Collected in Italy from Apple with A. mali and Other AM-Toxin Producing Strains

  . Phytopathology. doi:10.1094/phyto-04-12-0076-r
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  Since 1999, a disease of apple caused by an Alternaria sp. has been affecting orchards in northern Italy resulting in necrotic spots on leaves and on fruit. Forty-four single-spored isolates were obtained from diseased plant materials to investigate the diversity of this fungus in Italy and to compare these isolates to isolates of Alternaria associated with apple disease in previous studies, including A. mali, causal agent of apple blotch. All isolates, including the reference strains, were tested for pathogenicity utilizing in vitro bioassays on detached leaf or on fruit (‘Golden Delicious’). In addition, morphological characterizations were conducted describing both the three-dimensional sporulation pattern and the colony morphology of each isolate. In order to assess the genetic diversity within the Italian Alternaria population, sequence characterization of specific loci and anonymous regions (endoPG, OPA1-3, OPA2-1, and OPA10-2) and genetic fingerprinting based on amplified fragment length polymorphism and inter simple sequence repeat markers were performed. The single spore isolates exhibited differential pathogenicity, which did not correlate with the morphological groupings or to groupings defined by molecular approaches. Moreover, 10 pathogenic isolates out of the 44 single-spored tested were positive for the host-specific AM-toxin gene based upon polymerase chain reaction amplification using specific primers for the AM-toxin gene. This suggests that the production of the AM-toxin may be involved in pathogenesis by some of the Italian isolates of A. alternata from apple. However, this research also suggests that a number of different Alternaria genotypes and morphotypes may be responsible for the apple disease in Italy and that a single taxon cannot be defined as the sole causal agent.
• Pryor, B. M., Park, M. S., & Lawrence, D. A. (2012).

  Nimbya and Embellisia revisited, with nov. comb for Alternaria celosiae and A. perpunctulata

  . Mycological Progress. doi:10.1007/s11557-011-0793-7
• Rotondo, F., Brunelli, A., & Pryor, B. (2012). Comparison of Alternaria collected in Italy from apple with A. mali and other AM-toxin producing strains. Phytopathology, 203, 1130-1142.
• Rotondo, F., Collina, M., Brunelli, A., & Pryor, B. M. (2012). Comparison of Alternaria spp. Collected in Italy from apple with A. mali and other AM-toxin producing strains. Phytopathology, 102(12), 1130-1142.
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  PMID: 22934716;Abstract: Since 1999, a disease of apple caused by an Alternaria sp. has been affecting orchards in northern Italy resulting in necrotic spots on leaves and on fruit. Forty-four single-spored isolates were obtained from diseased plant materials to investigate the diversity of this fungus in Italy and to compare these isolates to isolates of Alternaria associated with apple disease in previous studies, including A. mali, causal agent of apple blotch. All isolates, including the reference strains, were tested for pathogenicity utilizing in vitro bioassays on detached leaf or on fruit ('Golden Delicious'). In addition, morphological characterizations were conducted describing both the three-dimensional sporulation pattern and the colony morphology of each isolate. In order to assess the genetic diversity within the Italian Alternaria population, sequence characterization of specific loci and anonymous regions (endoPG, OPA1-3, OPA2-1, and OPA10-2) and genetic fingerprinting based on amplified fragment length polymorphism and inter simple sequence repeat markers were performed. The single spore isolates exhibited differential pathogenicity, which did not correlate with the morphological groupings or to groupings defined by molecular approaches. Moreover, 10 pathogenic isolates out of the 44 single-spored tested were positive for the host-specific AM-toxin gene based upon polymerase chain reaction amplification using specific primers for the AM-toxin gene. This suggests that the production of the AM-toxin may be involved in pathogenesis by some of the Italian isolates of A. alternata from apple. However, this research also suggests that a number of different Alternaria genotypes and morphotypes may be responsible for the apple disease in Italy and that a single taxon cannot be defined as the sole causal agent. © 2012 The American Phytopathological Society.
• Baez-Flores, M., Troncoso-Rojas, R., Islas-Osuna, M., Dominguez, M., Pryor, B., & Tiznado-Hernandez, M. (2011). Differentially expressed cDNAs in Alternaria alternata treated with 2-propenyl isothiocyanate. Microbiology Research, 166, 566-577.
• Báez-Flores, M. E., Troncoso-Rojas, R., A., M., Domínguez, M. R., Pryor, B., & Tiznado-Hernández, M. E. (2011). Differentially expressed cDNAs in Alternaria alternata treated with 2-propenyl isothiocyanate. Microbiological Research, 166(7), 566-577.
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  PMID: 21257298;Abstract: The molecular mechanism of the fungal tolerance phenotype to fungicides is not completely understood. This knowledge would allow for the development of environmentally friendly strategies for the control of fungal infection. With the goal of determining genes induced by 2p-ITC, a forward suppressive subtractive hybridization was performed using cDNAs from ITC-treated Alternaria alternata as a " tester" and from untreated fungus as a " driver." Using this approach, a library containing 102 ESTs was generated that resulted in 50 sequences after sequence assembly (17 contigs and 33 singletons). Blastx analysis revealed that 38% and 40% of the sequences showed significant similarity with known and hypothetical proteins, respectively, whereas 18% were not similar to known genes. These last sequences could represent novel genes that play an unknown role in the molecular responses of fungi during adaptation to 2p-ITC. Clones similar to opsins, ABC transporters, calmodulin, ATPases and SNOG proteins were identified. Using real-time RT-PCR analysis, significant inductions of an ABC transporter and a Ca ++ ATPase during 2p-ITC treatment were discovered. These results suggest that the fungal resistance phenotype to 2p-ITC involves calcium ions and 2p-ITC efflux via an ABC transporter. © 2010 Elsevier GmbH.
• Lawrence, D., Kroken, S., Pryor, B., & Arnold, A. (2011). Interkingdom Gene Transfer of a Hybrid NPS/PKS from Bacteria to Filamentous Ascomycota. PLoS ONE, 6(11).
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  e28231. doi:10.1371/journal.pone.0028231
• Lawrence, D., Park, M., & Pryor, B. (2011). Nimbya and Embellisia revisited, with nov. comb for Alternaria celosiae and A. perpunctulata. Mycological Progress.
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  DOI 10.1007/s11557-011-0793-7
• Legatzki, A., Ortiz, M., Neilson, J., Doninguez, S., Andersen, G., Toomey, R., Pryor, B., Pierson, I. L., & Maier, R. (2011). Bacterial and archaeal community structure of two adjacent calcite speleothems in Kartchner Caverns, Arizona, USA. Geomicrobiology Journal, 28, 99-117.
• Maier, R. M., Pryor, B. M., & Vaughan, M. R. (2011).

  Fungal communities on speleothem surfaces in Kartchner Caverns, Arizona, USA

  . International Journal of Speleology. doi:10.5038/1827-806x.40.1.8
• Neilson, J. W., Pryor, B. M., Maier, R. M., Pierson, L. S., Toomey, R. S., Andersen, G. L., Dominguez, S., Ortiz, M., & Legatzki, A. (2011).

  Bacterial and Archaeal Community Structure of Two Adjacent Calcite Speleothems in Kartchner Caverns, Arizona, USA

  . Geomicrobiology Journal. doi:10.1080/01490451003738465
• Pryor, B. M., Arnold, A. E., Kroken, S., & Lawrence, D. A. (2011).

  Interkingdom Gene Transfer of a Hybrid NPS/PKS from Bacteria to Filamentous Ascomycota

  . PLOS ONE. doi:10.1371/journal.pone.0028231
• Pryor, B. M., Barnard, K., Schlecht, J., & Taralova, E. H. (2011).

  Modelling and visualizing morphology in the fungus Alternaria

  . Fungal Biology. doi:10.1016/j.funbio.2011.08.002
• Pryor, B. M., Tiznado-Hernández, M. E., Domínguez, M. R., Osuna, M. A., Troncoso-Rojas, R., & Báez-Flores, M. E. (2011).

  Differentially expressed cDNAs in Alternaria alternata treated with 2-propenyl isothiocyanate

  . Microbiological Research. doi:10.1016/j.micres.2010.11.004
• Pryor, B., Taralova, E. H., Schlecht, J., Barnard, K., & Pryor, B. M. (2011). Modelling and visualizing morphology in the fungus Alternaria. Fungal biology, 115(11).
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  Alternaria is one of the most cosmopolitan fungal genera encountered and impacts humans and human activities in areas of material degradation, phytopathology, food toxicology, and respiratory disease. Contemporary methods of taxon identification rely on assessments of morphology related to sporulation, which are critical for accurate diagnostics. However, the morphology of Alternaria is quite complex, and precise characterization can be laborious, time-consuming, and often restricted to experts in this field. To make morphology characterization easier and more broadly accessible, a generalized statistical model was developed for the three-dimensional geometric structure of the sporulation apparatus. The model is inspired by the widely used grammar-based models for plants, Lindenmayer-systems, which build structure by repeated application of rules for growth. Adjusting the parameters of the underlying probability distributions yields variations in the morphology, and thus the approach provides an excellent tool for exploring the morphology of Alternaria under different assumptions, as well as understanding how it is largely the consequence of local rules for growth. Further, different choices of parameters lead to different model groups, which can then be visually compared to published descriptions or microscopy images to validate parameters for species-specific models. The approach supports automated analysis, as the models can be fit to image data using statistical inference, and the explicit representation of the geometry allows the accurate computation of any morphological quantity. Furthermore, because the model can encode the statistical variation of geometric parameters for different species, it will allow automated species identification from microscopy images using statistical inference. In summary, the approach supports visualization of morphology, automated quantification of phenotype structure, and identification based on form.
• Taralova, E., Schlecht, J., Barnard, K., & Pryor, B. (2011). Modeling and visualizing morphology in the fungus Alternaria. Fungal Biology, 115, 1163-1173.
• Vaughan, M., Maier, R., & Pryor, B. (2011). Fungal communities on speleothem surfaces in Kartchner Caverns, Arizona, USA. International Journal of Speleology, 40, 65-77.
• Chia, G., & Pryor, B. M. (2010). A PCR-based assay for detection of fusarium oxysporum f. Sp. lactucae in lettuce seed. Plant Disease, 94(7), 860-866.
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  Abstract: A nested polymerase chain reaction-based (nPCR) assay was developed and evaluated for the rapid detection of Fusarium oxysporum f. sp. lactucae in seed of lettuce. Three primers were designed from sequences of the intergenic spacer region of the rDNA and were used in the PCR amplifications. The first amplification employed the primer pair GYCF1 and GYCR4C and produced a product of 2,270 bp. The second amplification employed the forward primer GYCF1 and the nested primer R943 and produced a single 936-bp PCR product. The nPCR protocol developed successfully detected the target sequence in genomic DNA at 1 fg/œl. A seed assay was tested that included a 4-day incubation step in which seed were maintained under high humidity conditions to increase fungal biomass for DNA extraction. In seed lots prepared by mixing known amounts of F. oxysporum f. sp. Lactucae-infested seed with noninfested seed, this assay permitted the detection of the pathogen from lots with infestation rates as low as 0.1%. Samples of lettuce seed obtained from 88 commercial lettuce seed lots were assayed for the pathogen by direct plating and by using the nPCR assay. The pathogen was not detected by either diagnostic method, suggesting the seed lots were pathogen free or the level was below detection limits. © 2010 The American Phytopathological Society.
• Chitrampalam, P., Cox, C. A., Turini, T. A., & Pryor, B. M. (2010). Efficacy of Coniothyrium minitans on lettuce drop caused by Sclerotinia minor in desert agroecosystem. Biological Control, 55(2), 92-96.
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  Abstract: Field experiments were conducted over 2years in Yuma County, Arizona and Imperial County, California, to evaluate if increased application rates of a commercial formulation of Coniothyrium minitans (Contans) were effective against lettuce drop caused by Sclerotinia minor. The efficacy of C. minitans at varied application rates were compared to two field isolates of Paenibacillus polymyxa and the chemical fungicide Boscolid (Endura). Two applications of manufacture recommended rate of Contans (2.2kg/ha) did not significantly reduce the incidence of lettuce drop caused by S. minor, even though applications at this rate have been shown to be very effective in controlling lettuce drop caused by Sclerotinia sclerotiorum. However, two applications of high rates of Contans (6.6, 8.8, or 11kg/ha), one at planting and one at post-thinning, significantly reduced the incidence of lettuce drop in most trials. Two isolates of P. polymyxa each applied at a rate of 9.4L/ha (109cfu/ml) were not effective in reducing the incidence of lettuce drop. Two applications of Endura, one at thinning and one at 4weeks post-thinning, significantly reduced the incidence of lettuce drop in Yuma County, AZ, but not in Imperial County, CA. In summary, successful management of lettuce drop caused by S. minor in desert ecosystem could best be achieved with high application rates of C. minitans. © 2010 Elsevier Inc.
• Hayes, R. J., Wu, B. M., Pryor, B. M., Chitrampalam, P., & Subbarao, K. V. (2010). Assessment of resistance in lettuce (Lactuca sativa L.) to mycelial and ascospore infection by Sclerotinia minor Jagger and S. sclerotiorum (Lib.) de Bary. HortScience, 45(3), 333-341.
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  Abstract: Lettuce drop caused by Sclerotinia spp. is an economically important disease of lettuce (Lactuca sativa L.), and cultivars with resistance to mycelial infection by Sclerotinia sclerotiorum (Lib.) de Bary and S. minor Jagger as well as to S. sclerotiorum ascospores are needed. Assessing resistance in field experiments can be complicated by fast bolting or small stature lettuce lines that may escape rather than resist the pathogens. Therefore, methods to select resistant lines from morphologically variable populations are needed. We used S. sclerotiorum and S. minor-infested field experiments, regression analysis, field experiments with artificially high plant densities, and S. sclerotiorum ascospore inoculations to identify lettuce lines with resistance to both pathogens. Three replicated experiments in S. sclerotiorum-infested fields were conducted in Yuma, AZ, and three replicated experiments in a S. minor-infested field were conducted in Salinas, CA, using diverse populations of iceberg, romaine, leaf, butterhead, Latin, oilseed lettuce, and wild relatives of lettuces; and genetic variation for the incidence of lettuce drop from mycelial infections was identified. In two S. minor field experiments, a quadratic regression model was developed that related rapid bolting with reduced lettuce drop. Regression residuals were calculated, and eight cultivars or PIs had negative residuals in two independent field experiments, indicating higher resistance than predicted by their rate of bolting. Eruption, a small-statured Latin cultivar, had significantly lower disease levels than susceptible cultivars in experiments with high plant densities, indicating that its small size did not facilitate disease escape. Ascospore inoculations confirmed resistance in 'Eruption' and L. virosa SAL012, whereas the oilseed lettuce PI 251246 may have partial resistance to infection. These lines will likely be useful for development of Sclerotinia spp.-resistant lettuce cultivars.
• Pryor, B. M., & Mbofung, G. Y. (2010).

  A PCR-Based Assay for Detection of Fusarium oxysporum f. sp. lactucae in Lettuce Seed

  . Plant Disease, 94(7), 860-866. doi:10.1094/pdis-94-7-0860
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  A nested polymerase chain reaction-based (nPCR) assay was developed and evaluated for the rapid detection of Fusarium oxysporum f. sp. lactucae in seed of lettuce. Three primers were designed from sequences of the intergenic spacer region of the rDNA and were used in the PCR amplifications. The first amplification employed the primer pair GYCF1 and GYCR4C and produced a product of 2,270 bp. The second amplification employed the forward primer GYCF1 and the nested primer R943 and produced a single 936-bp PCR product. The nPCR protocol developed successfully detected the target sequence in genomic DNA at 1 fg/μl. A seed assay was tested that included a 4-day incubation step in which seed were maintained under high humidity conditions to increase fungal biomass for DNA extraction. In seed lots prepared by mixing known amounts of F. oxysporum f. sp. lactucae–infested seed with noninfested seed, this assay permitted the detection of the pathogen from lots with infestation rates as low as 0.1%. Samples of lettuce seed obtained from 88 commercial lettuce seed lots were assayed for the pathogen by direct plating and by using the nPCR assay. The pathogen was not detected by either diagnostic method, suggesting the seed lots were pathogen free or the level was below detection limits.
• Pryor, B. M., Subbarao, K. V., Chitrampalam, P., Wu, B. M., & Hayes, R. J. (2010).

  Assessment of Resistance in Lettuce (Lactuca sativa L.) to Mycelial and Ascospore Infection by Sclerotinia minor Jagger and S. sclerotiorum (Lib.) de Bary

  . Hortscience. doi:10.21273/hortsci.45.3.333
• Pryor, B. M., Turini, T. A., Cox, C., & Chitrampalam, P. (2010).

  Efficacy of Coniothyrium minitans on lettuce drop caused by Sclerotinia minor in desert agroecosystem

  . Biological Control. doi:10.1016/j.biocontrol.2010.07.003
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  Abstract Field experiments were conducted over 2 years in Yuma County, Arizona and Imperial County, California, to evaluate if increased application rates of a commercial formulation of Coniothyrium minitans (Contans) were effective against lettuce drop caused by Sclerotinia minor. The efficacy of C. minitans at varied application rates were compared to two field isolates of Paenibacillus polymyxa and the chemical fungicide Boscolid (Endura). Two applications of manufacture recommended rate of Contans (2.2 kg/ha) did not significantly reduce the incidence of lettuce drop caused by S. minor, even though applications at this rate have been shown to be very effective in controlling lettuce drop caused by Sclerotinia sclerotiorum. However, two applications of high rates of Contans (6.6, 8.8, or 11 kg/ha), one at planting and one at post-thinning, significantly reduced the incidence of lettuce drop in most trials. Two isolates of P. polymyxa each applied at a rate of 9.4 L/ha (109 cfu/ml) were not effective in reducing the incidence of lettuce drop. Two applications of Endura, one at thinning and one at 4 weeks post-thinning, significantly reduced the incidence of lettuce drop in Yuma County, AZ, but not in Imperial County, CA. In summary, successful management of lettuce drop caused by S. minor in desert ecosystem could best be achieved with high application rates of C. minitans.
• Andrew, M., Peever, T. L., & Pryor, B. M. (2009). An expanded multilocus phylogeny does not resolve morphological species within the small-spored Alternaria species complex. Mycologia, 101(1), 95-109.
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  PMID: 19271672;Abstract: Small-spored Alternaria species are a taxo-nomically challenging group of fungi with few morphological or molecular characters that allow unambiguous discrimination among taxa. The protein-coding genes most commonly employed in fungal systematics are invariant among these taxa, so noncoding, anonymous regions of the genome were developed to assess evolutionary relationships among these organisms. Nineteen sequence-characterized amplified regions (SCAR) were screened for phylogenetic utility by comparing sequences among reference isolates of small-spored Alternaria species. Five of nineteen loci were consistently amplifiable and had sufficient phylogenetic signal. Phylogenetic analyses were performed with 150 small-spored Alternaria isolates using sequence data from an endopolygalac-turonase gene and two anonymous loci. Associations among phylogenetic lineage, morphological classification, geography and host were evaluated for use as practical taxonomic characters. Samples included isolates from citrus in Florida, pistachio in California, desert plants in Arizona, walnuts in France/Italy and apples in South Africa. No associations were found between host or geographic associations and phylogenetic lineage, indicating that these characters were not useful for cladistic classification of small-spored Alternaria. Similarly strict congruence between morphology and phylogenetic lineage was not found among isolates grouped morphologically with A. alternata or A. tenuissima. In contrast 34 isolates grouped morphologically with A. arborescens fell into discrete clades for all datasets. Although 5-9 well supported clades were evident among isolates, it is currently unclear if these clades should be considered phylogenetic species or emerging evolutionary line-ages within the phylogenetically defined alternata species-group. © 2009 by The Mycological Society of America.
• Pryor, B. M., Creamer, R., Shoemaker, R. A., McLain-Romero, J., & Hambleton, S. (2009). Undifilum, a new genus for endophytic Embellisia oxytropis and parasitic Helminthosporium bornmuelleri on legumes. Botany, 87(2), 178-194.
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  Abstract: Fungal endophytes of Oxytropis kansuensis Bunge from China, previously described as Embellisia oxytropis Q. Wang, Nagao & Kakish, and endophytes of Oxytropis sericea Nutt. and Oxytropis lambertii Pursh from the United States were compared and are reported here as conspecific members of a new genus in the Pleosporaceae, Undifilum, based on morphological and molecular analyses. Morphological comparisons revealed characters that are similar to those of the genus Embellisia including conidia ovate to obclavate to long ellipsoid, straight or slightly to decidedly inequilateral with occasionally one or two cells distinctly swollen, and transepta occasionally thickened, dark, and rigid in comparison with the exterior conidium wall. However, upon germination, conidia produced unique and diagnostic germ tubes that were wavy or undulating in their growth until branching. Moreover, all isolates were found to produce the toxic alkaloid swainsonine. Parsimony analysis of sequences from ITS1-5.8S-ITS2, glyceraldehyde-3-phosphate dehydrogenase gene, and mitochondrial small subunit rDNA data sets revealed that the Oxytropis endophytes formed a clade distinct from other Embellisia species and species in the genera Alternaria, Ulocladium, Nimbya, and Crivellia. A second taxon, Helmintho-sporium bornmuelleri P. Magnus, was reexamined and found to possess similar morphological features to those of the Oxytropis isolates, but lacked swainsonine production. Sequence analysis placed this second taxon in the same clade with high bootstrap support. The distinct morphology and genetics of these taxa demonstrates that these fungi, both recovered from legumes, represent a new genus, hereinafter described as Undifilum. The two species now placed in this genus are redescribed as Undifilium oxytropis and Undifilium bornmuelleri. © 2009 NRC Canada.
• Pryor, B. M., Lee, H. K., Hong, S. G., & Choi, J. Y. (2009).

  An efficient method to prepare PCR cloning vectors.

  . Mycobiology, 37(3), 240-2. doi:10.4489/myco.2009.37.3.240
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  An improved procedure for preparing PCR cloning vectors was developed. This procedure includes the incorporation of adapters to create XcmI restriction enzyme sites in pBluescript II SK(+) vectors, digestion with XcmI followed by further digestion of the small fragment produced by XcmI digestion with additional enzymes, and purification with PCR purification kits. Using this procedure, PCR cloning vectors with high ligation efficiencies and low blue or false-positive colonies were obtained.
• Pryor, B. M., Maier, R. M., Pierson, L. S., Neilson, J. W., Legatzki, A., & Ortiz, M. (2009).

  Intra- and inter- speleothem variability of bacterial communities in Kartchner Caverns

  . Geochimica et Cosmochimica Acta Supplement.
• Pryor, B. M., Maier, R. M., Pierson, L. S., Neilson, J. W., Ortiz, M., & Legatzki, A. (2009).

  Bacterial and archaeal diversity in Kartchner Caverns, a carbonate cave in southwestern USA

  . Geochimica et Cosmochimica Acta Supplement.
• Pryor, B. M., Park, M. S., & Runa, F. (2009).

  Ulocladium systematics revisited: phylogeny and taxonomic status

  . Mycological Progress. doi:10.1007/s11557-008-0576-y
• Pryor, B. M., Peever, T. L., & Andrew, M. (2009).

  An expanded multilocus phylogeny does not resolve morphological species within the small-sporedAlternariaspecies complex

  . Mycologia. doi:10.3852/08-135
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  Small-spored Alternaria species are a taxonomically challenging group of fungi with few morphological or molecular characters that allow unambiguous discrimination among taxa. The protein-coding genes most commonly employed in fungal systematics are invariant among these taxa, so noncoding, anonymous regions of the genome were developed to assess evolutionary relationships among these organisms. Nineteen sequence-characterized amplified regions (SCAR) were screened for phylogenetic utility by comparing sequences among reference isolates of small-spored Alternaria species. Five of nineteen loci were consistently amplifiable and had sufficient phylogenetic signal. Phylogenetic analyses were performed with 150 small-spored Alternaria isolates using sequence data from an endopolygalacturonase gene and two anonymous loci. Associations among phylogenetic lineage, morphological classification, geography and host were evaluated for use as practical taxonomic characters. Samples included isolates from citrus in Florida, pistachio in California, desert plants in Arizona, walnuts in France/Italy and apples in South Africa. No associations were found between host or geographic associations and phylogenetic lineage, indicating that these characters were not useful for cladistic classification of small-spored Alternaria. Similarly strict congruence between morphology and phylogenetic lineage was not found among isolates grouped morphologically with A. alternata or A. tenuissima. In contrast 34 isolates grouped morphologically with A. arborescens fell into discrete clades for all datasets. Although 5-9 well supported clades were evident among isolates, it is currently unclear if these clades should be considered phylogenetic species or emerging evolutionary lineages within the phylogenetically defined alternata species-group.
• Runa, F., Park, M. S., & Pryor, B. M. (2009). Ulocladium systematics revisited: Phylogeny and taxonomic status. Mycological Progress, 8(1), 35-47.
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  Abstract: The genus Ulocladium represents phaeodictyosporic Hyphomycetes that produce conidia that are essentially obovoid in shape. Previous molecular studies that included Ulocladium and related taxa in Alternaria, Embellisia, and Stemphylium revealed a conflict between morphology and phylogeny, and Ulocladium was supported as polyphyletic with a paraphyletic core group. Moreover, the genus consistently resolved within a larger Alternaria/Ulocladium clade, resulting in paraphyly of Alternaria and questions as to the taxonomic status of Ulocladium. In the present study, 13 Ulocladium species and three genetic loci were included for a more comprehensive systematic analysis of the genus than had previously been conducted. Total genomic DNA was extracted from representative taxa and sequences were determined for the nuclear internal transcribed spacer region, including the 5.8S rDNA gene, and the protein-coding genes glyceraldehyde-3- phosphate dehydrogenase and Alt a1. Subsequent phylogenetic analyses based on maximum parsimony and Bayesian methods included related Alternaria, Embellisia, and Stemphylium spp. Results supported previous findings of polyphyletic and paraphyletic relationships of Ulocladium among other taxa. Ten Ulocladium species clustered into a core Ulocladium clade and all taxa possessed the key diagnostic feature of Ulocladium, namely, conidia essentially obovoid in shape. However, A. cheiranthi and E. indefessa also clustered within this group with high bootstrap support but did not posses this diagnostic feature. This paraphyletic clade resolved basal to the core Alternaria clade with high bootstrap support, unlike previous studies in which its position was imbedded within the primary Alternaria clade. Thus, the status of the genus as an independent lineage and a unique taxon is strongly supported. As previously reported, U. alternariae and U. oudemansii, which posses the key conidium characteristics of Ulocladium, clustered as a separate clade sister to the core Ulocladium clade. Further studies are necessary to determine if these taxa represent an independent lineage or share a common ancestor with other Ulocladium species. Obovoid conidia were poorly represented in the isolate of U. lanuginosum that was included in these analyses (the only U. lanuginosum isolate currently available), and the isolate resolved as A. radicina based upon all three loci sequenced. Based upon these data and the origin of the isolate, which was originally deposited as A. malvae, a reassessment of its identity is supported. © 2008 German Mycological Society and Springer.
• Shoemaker, R. A., Pryor, B. M., Creamer, R., McLain-Romero, J., & Hambleton, S. (2009).

  Undifilum, a new genus for endophytic Embellisia oxytropis and parasitic Helminthosporium bornmuelleri on legumes

  . Botany, 87(2), 178-194. doi:10.1139/b08-130
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  Fungal endophytes of Oxytropis kansuensis Bunge from China, previously described as Embellisia oxytropis Q. Wang, Nagao & Kakish, and endophytes of Oxytropis sericea Nutt. and Oxytropis lambertii Pursh from the United States were compared and are reported here as conspecific members of a new genus in the Pleosporaceae, Undifilum, based on morphological and molecular analyses. Morphological comparisons revealed characters that are similar to those of the genus Embellisia including conidia ovate to obclavate to long ellipsoid, straight or slightly to decidedly inequilateral with occasionally one or two cells distinctly swollen, and transepta occasionally thickened, dark, and rigid in comparison with the exterior conidium wall. However, upon germination, conidia produced unique and diagnostic germ tubes that were wavy or undulating in their growth until branching. Moreover, all isolates were found to produce the toxic alkaloid swainsonine. Parsimony analysis of sequences from ITS1–5.8S–ITS2, glyceraldehyde-3-phosphate dehydrogenase gene, and mitochondrial small subunit rDNA data sets revealed that the Oxytropis endophytes formed a clade distinct from other Embellisia species and species in the genera Alternaria , Ulocladium , Nimbya , and Crivellia . A second taxon, Helminthosporium bornmuelleri P. Magnus, was reexamined and found to possess similar morphological features to those of the Oxytropis isolates, but lacked swainsonine production. Sequence analysis placed this second taxon in the same clade with high bootstrap support. The distinct morphology and genetics of these taxa demonstrates that these fungi, both recovered from legumes, represent a new genus, hereinafter described as Undifilum . The two species now placed in this genus are redescribed as Undifilium oxytropis and Undifilium bornmuelleri .
• Andersen, B., Dongo, A., & Pryor, B. M. (2008). Secondary metabolite profiling of Alternaria dauci, A. porri, A. solani, and A. tomatophila. Mycological Research, 112(2), 241-250.
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  PMID: 18262401;Abstract: Chemotaxonomy (secondary metabolite profiling) has been shown to be of great value in the classification and differentiation in Ascomycota. However, few studies have investigated the use of metabolite production for classification and identification purposes of plant pathogenic Alternaria species. The purpose of the present study was to describe the methodology behind metabolite profiling in chemotaxonomy using A. dauci, A. porri, A. solani, and A. tomatophila strains as examples of the group. The results confirmed that A. dauci, A. solani, and A. tomatophila are three distinct species each with their own specific metabolite profiles, and that A. solani and A. tomatophila both produce altersolanol A, altertoxin I, and macrosporin. By using automated chemical image analysis and other multivariate statistic analyses, three sets of species-specific metabolites could be selected, one each for A. dauci, A. solani, and A. tomatophila. © 2007 The British Mycological Society.
• Park, M. S., Romanoski, C. E., & Pryor, B. M. (2008). A re-examination of the phylogenetic relationship between the causal agents of carrot black rot, Alternaria radicina and A. carotiincultae. Mycologia, 100(3), 511-527.
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  PMID: 18751557;Abstract: The phylogenetic relationship between Alternaria radicina and A. carotiincultae was re-examined based on morphology, sequence analysis of rDNA (ITS and mitochondrial small subunit [mtSSU]), protein coding genes (actin [ACT], β-tubulin, chitin synthase [CHS], translation elongation factor [EF-1a], Alternaria allergen a1 [Alt a1], and glyceraldehyde-3-phosphate dehydrogenase [gpd]), and RAPD and ISSR analysis of total genomic DNA. Although some morphological characters overlapped to a degree, with A. radicina isolates expressing moderate variation and A. carotiincultae isolates being highly uniform, A. carotiincultae could be differentiated from A. radicina based on significantly greater growth rate on potato dextrose agar (PDA) or acidified PDA (APDA) and average number of transverse septa per conidium. Sequence of rDNA and two protein coding genes, ACT and CHS, were invariant between species. However polymorphism with the EF-1a, β-tubulin, and Alt a1 gene strictly separated the population of A. radicina and A. carotiincultae as distinct lineages, as did RAPD and ISSR analysis. The polymorphic gpd gene did not strictly separate the two species. However isolates of A. radicina encompassed several haplotypes, one of which was the exclusive haplotype possessed by A. carotiincultae isolates, suggesting evidence of incomplete lineage sorting. The results suggest that A. carotiincultae is closely related to A. radicina but is a recently divergent and distinct lineage, which supports its status as a separate species. © 2008 by The Mycological Society of America.
• Pryor, B. M., Dongo, A., & Andersen, B. (2008).

  Secondary metabolite profiling of Alternaria dauci, A. porri, A. solani, and A. tomatophila

  . Mycological research. doi:10.1016/j.mycres.2007.09.004
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  Chemotaxonomy (secondary metabolite profiling) has been shown to be of great value in the classification and differentiation in Ascomycota. However, few studies have investigated the use of metabolite production for classification and identification purposes of plant pathogenic Alternaria species. The purpose of the present study was to describe the methodology behind metabolite profiling in chemotaxonomy using A. dauci, A. porri, A. solani, and A. tomatophila strains as examples of the group. The results confirmed that A. dauci, A. solani, and A. tomatophila are three distinct species each with their own specific metabolite profiles, and that A. solani and A. tomatophila both produce altersolanol A, altertoxin I, and macrosporin. By using automated chemical image analysis and other multivariate statistic analyses, three sets of species-specific metabolites could be selected, one each for A. dauci, A. solani, and A. tomatophila.
• Romanoski, C. E., Pryor, B. M., & Park, M. S. (2008).

  A re-examination of the phylogenetic relationship between the causal agents of carrot black rot,Alternaria radicinaandA. carotiincultae

  . Mycologia. doi:10.3852/07-186r1
• Cho, Y., Cramer Jr., R. A., Kim, K., Davis, J., Mitchell, T. K., Figuli, P., Pryor, B. M., Lemasters, E., & Lawrence, C. B. (2007). The Fus3/Kss1 MAP kinase homolog Amk1 regulates the expression of genes encoding hydrolytic enzymes in Alternaria brassicicola. Fungal Genetics and Biology, 44(6), 543-553.
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  PMID: 17280842;Abstract: Mitogen-activated protein (MAP) kinases have been shown to be required for virulence in diverse phytopathogenic fungi. To study its role in pathogenicity, we disrupted the Amk1 MAP kinase gene, a homolog of the Fus3/Kss1 MAP kinases in Saccharomyces cerevisiae, in the necrotrophic Brassica pathogen, Alternaria brassicicola. The amk1 disruption mutants showed null pathogenicity on intact host plants. However, amk1 mutants were able to colonize host plants when they were inoculated on a physically damaged host surface, or when they were inoculated along with nutrient supplements. On intact plants, mutants expressed extremely low amounts of several hydrolytic enzyme genes that were induced over 10-fold in the wild-type during infection. These genes were also dramatically induced in the mutants on wounded plants. These results imply a correlation between virulence and the expression level of specific hydrolytic enzyme genes plus the presence of an unidentified pathway controlling these genes in addition to or in conjunction with the Amk1 pathway.
• Mbofung, G. Y., Hong, S. G., & Pryor, B. M. (2007). Phylogeny of Fusarium oxysporum f. sp. lactucae inferred from mitochondrial small subunit, elongation factor 1-α, and nuclear ribosomal intergenic spacer sequence data. Phytopathology, 97(1), 87-98.
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  PMID: 18942941;Abstract: Fusarium oxysporum f. sp. lactucae, causal agent of Fusarium wilt of lettuce, is a serious pathogen recently reported in Arizona. Sequence analysis of the mitochondrial small subunit (mtSSU), translation elongation factor 1-α (EF-1α) gene, and the nuclear ribosomal DNA intergenic spacer (IGS) region was conducted to resolve relationships among f. sp. lactucae isolates, F. oxysporum isolates from other hosts, and local non-pathogenic isolates. Analysis of mtSSU sequences provided limited phylogenetic resolution and did not differentiate the lactucae isolates from 13 other F. oxysporum isolates. Analysis of EF-1α sequences resulted in moderate resolution, grouping seven formae speciales with the lactucae isolates. Analysis of the IGS region revealed numerous sequence polymorphisms among F. oxysporum formae speciales consisting of insertions, deletions, and single nucleotide transitions and substitutions. Repeat sequence analysis revealed several duplicated subrepeat units that were distributed across much of the region. Based on analysis of the IGS sequence data, lactucae race 1 isolates resolved as a monophyletic group with three other formae speciales of F. oxysporum. In all analyses, lactucae race 2 isolates composed a separate lineage that was phylogenetically distinct and distantly related to the lactucae race 1 isolates. © 2007 The American Phytopathological Society.
• Pryor, B. M., & Asma, M. (2007).

  First Report of Seedling Damping-Off of Fennel Caused by Alternaria petroselini in the Netherlands.

  . Plant disease, 91(12), 1688. doi:10.1094/pdis-91-12-1688a
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  In April 2005, serious seedling damping-off was noted on fennel (Foeniculum vulgare Mill. cv. Rondo) in a transplant greenhouse facility in Maasdijk, the Netherlands. Symptoms appeared 3 to 4 weeks after sowing and included black, sunken lesions aboveground on the stem and belowground on the hypocotyls. Mortality of seedlings was 6 to 10% (10 to 15 seedlings per 150-plant tray). Following removal of diseased seedlings, further transplant mortality in the field was not evident. Samples of diseased tissue were collected, surface disinfested, and placed in petri dishes containing water agar. After 7 to 10 days of incubation at 25°C under fluorescent lights, an Alternaria sp. was growing from each sample. Single conidium cultures were obtained from representative colonies and cultured on potato dextrose agar (PDA) and potato carrot agar (PCA) for morphological examination. On PDA, colonies were dark olive brown, cottony, subsurface microsclerotia production abundant, and no production of pigments in the medium. On PCA, conidia were darkly pigmented, broadly ellipsoidal to subsphaerical, and produced singly. Mature conidia were 28 to 45 × 20 to 25 μm with two to four transepta and one to three longisepta. Characteristics were consistent with those of Alternaria petroselini (2,3). In subsequent freezer-blotter assays (ISTA blotter method; www.seedtest.org ) of seed lot used in the original planting, the same fungus was recovered at an infestation level of 30%, confirming that it was seedborne. To confirm pathogenicity on fennel, pathogenicity tests were conducted on a common fennel cultivar (Floro F1) in the greenhouse and on fennel stalks in the laboratory. Fennel seeds were soaked in a conidia suspension (106/ml in sterile H2O) for 10 min. Control seeds were soaked in sterile H2O. Seeds were dried on paper, sown in soil plugs, and grown in the greenhouse at 16 to 20°C. After 4 weeks, black lesions were observed on the fennel stems and symptoms were similar to those observed on the original infected material. Control plants remained healthy. A fungus was reisolated from the lesions of symptomatic plants and was identical to the fungus isolated from the original infected material. For the fennel stalk assay, two surface-sterilized fennel stalks were sliced longitudinally and three 4-mm plugs from a 10-day-old culture of each isolate were placed along the fennel stalks. Sterile agar plugs were used as negative controls. After 7 to 10 days of incubation at 25°C in plastic boxes, test isolates grew extensively from agar plugs and resulted in extensive black necrosis of the fennel stalks. No necrosis resulted from control plugs. DNA was extracted from field isolates, and the nuclear internal transcribed spacer region was sequenced using protocol previously described (1). A representative sequence was deposited in GenBank (Accession No. EF636901). A BLAST search of the NCBI database revealed A. petroselini Accession No. AY154685 as the closest match (total score = 1,014, 100% coverage, 99% sequence identity). The next closest match was A. radicina Accession No. DQ394074 (total score 987, 100% coverage, 98% sequence identity). To our knowledge, this is the first report of A. petroselini causing disease of fennel and the fungus being seedborne on fennel seed. An isolate has been deposited at the Centraalbureau voor Schimmelcultures (Accession No. 118228). References: (1) B. M. Pryor and D. M. Bigelow. Mycologia 95:1141, 2003. (2) B. M. Pryor and R. L. Gilbertson. Mycologia 94:49, 2002. (3) E. G. Simmons. Mycotaxon 55:55, 1995.
• Pryor, B. M., Belisario, A., Figuli, P. J., Maccaroni, M., & Hong, S. G. (2007).

  Characterization of Alternaria species-groups associated with disease complexes of walnut and hazelnut.

  . Plant Disease.
• Pryor, B. M., Hong, S. G., & Mbofung, G. Y. (2007).

  Phylogeny of Fusarium oxysporum f. sp. lactucae Inferred from Mitochondrial Small Subunit, Elongation Factor 1-α, and Nuclear Ribosomal Intergenic Spacer Sequence Data

  . Phytopathology. doi:10.1094/phyto-97-0087
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  Fusarium oxysporum f. sp. lactucae, causal agent of Fusarium wilt of lettuce, is a serious pathogen recently reported in Arizona. Sequence analysis of the mitochondrial small subunit (mtSSU), translation elongation factor 1-α (EF-1α) gene, and the nuclear ribosomal DNA intergenic spacer (IGS) region was conducted to resolve relationships among f. sp. lactucae isolates, F. oxysporum isolates from other hosts, and local non-pathogenic isolates. Analysis of mtSSU sequences provided limited phylogenetic resolution and did not differentiate the lactucae isolates from 13 other F. oxysporum isolates. Analysis of EF-1α sequences resulted in moderate resolution, grouping seven formae speciales with the lactucae isolates. Analysis of the IGS region revealed numerous sequence polymorphisms among F. oxysporum formae speciales consisting of insertions, deletions, and single nucleotide transitions and substitutions. Repeat sequence analysis revealed several duplicated subrepeat units that were distributed across much of the region. Based on analysis of the IGS sequence data, lactucae race 1 isolates resolved as a monophyletic group with three other formae speciales of F. oxysporum. In all analyses, lactucae race 2 isolates composed a separate lineage that was phylo-genetically distinct and distantly related to the lactucae race 1 isolates.
• Pryor, B. M., Lawrence, C. B., Lemasters, E., Figuli, P. J., Mitchell, T. K., Davis, J., Kim, K. H., Cramer, R. A., & Cho, Y. (2007).

  The Fus3/Kss1 MAP kinase homolog Amk1 regulates the expression of genes encoding hydrolytic enzymes in Alternaria brassicicola☆

  . Fungal Genetics and Biology. doi:10.1016/j.fgb.2006.11.015
• Hong, S. G., Maccaroni, M., Figuli, P. J., Pryor, B. M., & Belisario, A. (2006). Polyphasic classification of Alternaria isolated from hazelnut and walnut fruit in Europe. Mycological Research, 110(11), 1290-1300.
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  PMID: 17077026;Abstract: Brown apical necrosis of English walnut and grey necrosis of hazelnut are destructive fruit diseases caused by a complex of opportunistic fungi including several small-spored catenulate Alternaria taxa. Thirty Alternaria isolates recovered from walnut and hazelnut fruit that were pathogenic on their respective host were compared along with type or representative isolates of A. alternata, A. tenuissima, A. arborescens, and A. infectoria using morphological and molecular criteria. Morphological examination using standardized procedures separated the walnut and hazelnut isolates into three morphological groups: the A. alternata group, the A. tenuissima group, and the A. arborescens group based upon common characteristics of the conidium and the sporulation apparatus. To evaluate genetic relationships among these groups, AFLP markers, inter simple sequence repeat (ISSR) markers, and histone gene sequence data were compared. Based upon AFLP data, the A. alternata and A. tenuissima groups comprised a single lineage, and the A. arborescens group comprised a separate lineage. ISSR data supported the grouping by AFLP data except for three isolates of the A. alternata group that clustered with the A. arborescens group. Base substitution of the H4 gene supported the discrimination of the A. arborescens group from the A. alternata and A. tenuissima groups. Tests of hypotheses based upon groupings derived from the various data sets supported the discrimination of the A. arborescens group but did not support the discrimination of the A. alternata group from the A. tenuissima group. © 2006 The British Mycological Society.
• Pryor, B. M., Belisario, A., Figuli, P. J., Maccaroni, M., & Hong, S. G. (2006).

  Polyphasic classification of Alternaria spp. isolated from hazelnut and walnut in Europe

  . Plant Disease.
• Pryor, B. M., Belisario, A., Figuli, P. J., Maccaroni, M., & Hong, S. H. (2006).

  Polyphasic classification of Alternaria isolated from hazelnut and walnut fruit in Europe

  . Mycological research. doi:10.1016/j.mycres.2006.08.005
• Pryor, B. M., Schumaker, K. S., Lawrence, C. B., Cramer, R. A., Kim, Y., & Hong, S. G. (2006).

  Phylogeny of Alternaria and Evolution of Pathogenicity on Arabidopsis

  . 한국미생물학회 학술대회논문집.
• Hong, S. G., Cramer, R. A., Lawrence, C. B., & Pryor, B. M. (2005). Alt a 1 allergen homologs from Alternaria and related taxa: Analysis of phylogenetic content and secondary structure. Fungal Genetics and Biology, 42(2), 119-129.
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  PMID: 15670710;Abstract: A gene for the Alternaria major allergen, Alt a 1, was amplified from 52 species of Alternaria and related genera, and sequence information was used for phylogenetic study. Alt a 1 gene sequences evolved 3.8 times faster and contained 3.5 times more parsimony-informative sites than glyceraldehyde-3- phosphate dehydrogenase (gpd) sequences. Analyses of Alt a 1 gene and gpd exon sequences strongly supported grouping of Alternaria spp. and related taxa into several species-groups described in previous studies, especially the infectoria, alternata, porri, brassicicola, and radicina species-groups and the Embellisia group. The sonchi species-group was newly suggested in this study. Monophyly of the Nimbya group was moderately supported, and monophyly of the Ulocladium group was weakly supported. Relationships among species-groups and among closely related species of the same species-group were not fully resolved. However, higher resolution could be obtained using Alt a 1 sequences or a combined dataset than using gpd sequences alone. Despite high levels of variation in amino acid sequences, results of in silico prediction of protein secondary structure for Alt a 1 demonstrated a high degree of structural similarity for most of the species suggesting a conservation of function. © 2004 Elsevier Inc. All rights reserved.
• Hong, S. G., Liu, D., & Pryor, B. M. (2005). Restriction mapping of the IGS region in Alternaria spp. reveals variable and conserved domains. Mycological Research, 109(1), 87-95.
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  PMID: 15736866;Abstract: Accurate identification of Alternaria spp. is dependent upon the production of diagnostic morphological characters under defined cultural conditions and the proper assessment of character variation. This process is often compromised by variation in laboratory facilities and technical expertise. To assist taxon identification and phylogenetic studies, restriction site information from the intergenic spacer (IGS) region of nuclear rDNA was evaluated. Restriction maps were constructed from 15 species of Alternaria and Stemphylium botryosum (telemorph Pleospora herbarum) for 11 restriction enzymes using a new method for restriction mapping based on differential priming of IGS amplicons. IGS fragment size varied among species from 2.2-3.9 kb. Based upon restriction site homology among closely-related and more distantly related species, the IGS region could be divided into conserved and variable domains. The conserved domain was approximately 0.75 kb in size and was located at the 3′ end of the IGS region. Restriction site homology within this region was very high, especially among closely related taxa. The remainder of the region comprised the variable domain, which encompassed considerable differences in size and restriction sites among taxa. The presence or absence of restriction sites among taxa was analyzed using methods of neighbor-joining. Phylogenetic relationships based on this method were concordant with those previously resolved based upon other methods and other genomic regions.
• Pryor, B. M., Lawrence, C. B., Cramer, R. J., & Hong, S. H. (2005).

  Alt a 1 allergen homologs from Alternaria and related taxa: analysis of phylogenetic content and secondary structure

  . Fungal Genetics and Biology. doi:10.1016/j.fgb.2004.10.009
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  A gene for the Alternaria major allergen, Alt a 1, was amplified from 52 species of Alternaria and related genera, and sequence information was used for phylogenetic study. Alt a 1 gene sequences evolved 3.8 times faster and contained 3.5 times more parsimony-informative sites than glyceraldehyde-3-phosphate dehydrogenase (gpd) sequences. Analyses of Alt a 1 gene and gpd exon sequences strongly supported grouping of Alternaria spp. and related taxa into several species-groups described in previous studies, especially the infectoria, alternata, porri, brassicicola, and radicina species-groups and the Embellisia group. The sonchi species-group was newly suggested in this study. Monophyly of the Nimbya group was moderately supported, and monophyly of the Ulocladium group was weakly supported. Relationships among species-groups and among closely related species of the same species-group were not fully resolved. However, higher resolution could be obtained using Alt a 1 sequences or a combined dataset than using gpd sequences alone. Despite high levels of variation in amino acid sequences, results of in silico prediction of protein secondary structure for Alt a 1 demonstrated a high degree of structural similarity for most of the species suggesting a conservation of function.
• Pryor, B. M., Liu, D., & Hong, S. H. (2005).

  Restriction mapping of the IGS region in Alternaria spp. reveals variable and conserved domains

  . Mycological research. doi:10.1017/s0953756204001388
• Pryor, B., Hong, S. G., Cramer, R. A., Lawrence, C. B., & Pryor, B. M. (2005). Alt a 1 allergen homologs from Alternaria and related taxa: analysis of phylogenetic content and secondary structure. Fungal genetics and biology : FG & B, 42(2).
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  A gene for the Alternaria major allergen, Alt a 1, was amplified from 52 species of Alternaria and related genera, and sequence information was used for phylogenetic study. Alt a 1 gene sequences evolved 3.8 times faster and contained 3.5 times more parsimony-informative sites than glyceraldehyde-3-phosphate dehydrogenase (gpd) sequences. Analyses of Alt a 1 gene and gpd exon sequences strongly supported grouping of Alternaria spp. and related taxa into several species-groups described in previous studies, especially the infectoria, alternata, porri, brassicicola, and radicina species-groups and the Embellisia group. The sonchi species-group was newly suggested in this study. Monophyly of the Nimbya group was moderately supported, and monophyly of the Ulocladium group was weakly supported. Relationships among species-groups and among closely related species of the same species-group were not fully resolved. However, higher resolution could be obtained using Alt a 1 sequences or a combined dataset than using gpd sequences alone. Despite high levels of variation in amino acid sequences, results of in silico prediction of protein secondary structure for Alt a 1 demonstrated a high degree of structural similarity for most of the species suggesting a conservation of function.
• Pryor, B., Hong, S. G., Liu, D., & Pryor, B. M. (2005). Restriction mapping of the IGS region in Alternaria spp. reveals variable and conserved domains. Mycological research, 109(Pt 1).
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  Accurate identification of Alternaria spp. is dependent upon the production of diagnostic morphological characters under defined cultural conditions and the proper assessment of character variation. This process is often compromised by variation in laboratory facilities and technical expertise. To assist taxon identification and phylogenetic studies, restriction site information from the intergenic spacer (IGS) region of nuclear rDNA was evaluated. Restriction maps were constructed from 15 species of Alternaria and Stemphylium botryosum (telemorph Pleospora herbarum) for 11 restriction enzymes using a new method for restriction mapping based on differential priming of IGS amplicons. IGS fragment size varied among species from 2.2-3.9 kb. Based upon restriction site homology among closely-related and more distantly related species, the IGS region could be divided into conserved and variable domains. The conserved domain was approximately 0.75 kb in size and was located at the 3' end of the IGS region. Restriction site homology within this region was very high, especially among closely related taxa. The remainder of the region comprised the variable domain, which encompassed considerable differences in size and restriction sites among taxa. The presence or absence of restriction sites among taxa was analyzed using methods of neighbor-joining. Phylogenetic relationships based on this method were concordant with those previously resolved based upon other methods and other genomic regions.
• Belisario, A., Pryor, B. M., Maccaroni, M., Figuli, P. J., Corazza, L., Coramusi, A., & Belisario, A. (2004).

  First Report of Alternaria Species Groups Involved in Disease Complexes of Hazelnut and Walnut Fruit.

  . Plant disease, 88(4), 426. doi:10.1094/pdis.2004.88.4.426a
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  During the last 5 years, two new diseases, brown apical necrosis (BAN) and gray necrosis (GN), were observed on English walnut (Juglans regia) and hazelnut (Corylus avellana), respectively (2,3). Both diseases caused severe fruit drop resulting in yield loss often exceeding 30%. Previous work demonstrated that BAN and GN are disease complexes caused by several fungi (Alternaria spp., Fusarium spp., and a Phomopsis sp.) (2,3). In both diseases, preliminary identification of Alternaria spp. revealed they were a complex of small-spored catenulate taxa related to A. alternata. To further characterize these taxa, additional pathogenicity tests and morphological examinations were conducted with isolates obtained from each host. Single-spored isolates were prescreened for pathogenicity by inoculating detached, surface-disinfested hazelnut leaves or walnut leaflets (1). Only isolates that produced foliar lesions after 5 days were used in subsequent fruit inoculations. From this screening, 35 isolates were selected (19 from walnut and 16 from hazelnut). For each isolate, attached fruit of respective hosts were inoculated at bloom by placing 10 μl of a conidial suspension (1 × 106 conidia per ml of H2O + 0.26% agar) onto the stigmas (150 fruit per isolate). Controls (150 fruit) were treated with agar solution only. After 15 days, fruit were examined for development of disease symptoms, and examination continued until fruit maturation (late July). Approximately 20 to 50% of the inoculated fruit displayed discoloration or necrosis of internal tissue, particularly the pericarp and the embryo, although symptoms were more limited than those typically seen in fully expressed BAN and GN. No differences in symptoms were evident among the isolates tested. The controls showed no symptom development initially, although 5% began to develop discoloration at fruit maturity. Fungal isolates used as inoculum were reisolated from all symptomatic fruit by surface disinfesting tissue from the margins of necrotic lesions. For each isolate, the conidial characteristics were described from cultures grown under defined conditions (4). Three distinct groups of isolates were identified. Alternata sp. group isolates produced conidial chains (8 to 20 spores) with numerous secondary and occasionally tertiary chains branching from apical and median cells. Conidia were typically ovate and often possessed a one-celled apical extension. Tenuissima sp. group isolates developed conidial chains (10 to 22 spores) with occasional branching forming secondary chains from apical and median cells. Conidia were ovate to obclavate, often with long apical extensions (10 to 35 μm). Arborescens sp. group isolates developed conidial chains (5 to 12 spores) with numerous secondary, tertiary, and quaternary short chains branching from apical cells. Conidia were typically ovate with minimal apical extensions. Of the walnut isolates, 12, 4, and 3 were from the arborescens, alternata, and tenuissima sp. groups, respectively. Of the hazelnut isolates, 7, 6, and 3 were from the arborescens, alternata, and tenuissima sp. groups, respectively. The finding that Alternaria from several distinct sp. groups can cause similar disease on a single host is consistent with previous work on pistachio, almond, and pear (4). References: (1) A. Belisario et al. Plant Dis. 83:696, 1999. (2) A. Belisario et al. Plant Dis. 86:599, 2002. (3) A. Belisario et al. Inf. Agrario 59:71, 2003. (4) B. M. Pryor et al. Phytopathology 92:406, 2002.
• Farrar, J. J., Pryor, B. A., & Davis, R. M. (2004). Alternaria diseases of carrot. Plant Disease, 88(8), 776-784.
• Hong, S. G., & Pryor, B. M. (2004). Development of selective media for the isolation and enumeration of Alternaria species from soil and plant debris. Canadian Journal of Microbiology, 50(7), 461-468.
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  PMID: 15381969;Abstract: A new semi-selective medium, acidified weak potato-dextrose agar (AWPDA) with Mertect (active ingredient: thiabendazole), was developed for the isolation and enumeration of Alternaria species from samples of soil and plant debris. The medium was selected based on growth inhibition tests against Alternaria and several other commonly encountered saprobic fungi utilizing three antifungal agents, Botran (active ingredient: dichloran), Bayleton (active ingredient: triadimefon), and Mertect, and two basal media, acidified potato-dextrose agar (APDA) and AWPDA. Botran inhibited growth of Rhizopus stolonifer moderately, but had little effect on Cladosporium cladosporoides, Fusarium oxysporum, Penicillium chrysogenum, or Trichoderma harzianum. Bayleton inhibited growth of R. stolonifer and C. cladosporoides severely, and inhibited growth of F. oxysporum, P. chrysogenum, and T. harzianum moderately. Mertect inhibited growth of C. cladosporoides, F. oxysporum, P. chrysogenum, and T. harzianum completely, but had little or moderate effect on R. stolonifer. All three antifungal agents inhibited growth of Alternaria species slightly or moderately. The combination of Bayleton and Mertect inhibited growth of all fungi severely. A comparison of recovery rates of Alternaria from soil and plant debris samples on AWPDA with Mertect and weak potato-dextrose agar (WPDA) revealed that Alternaria spp. accounted for 63.6%-81.0% of recovered fungal isolates on AWPDA with Mertect as compared to 0.6%-2.7% of recovered isolates on WPDA. The AWPDA medium with Mertect exhibited superior selective growth of Alternaria species from samples of soil and plant debris, and will be useful in studies where the recovery and enumeration of Alternaria species is necessary.
• Pryor, B. M., & Hong, S. G. (2004).

  Development of selective media for the isolation and enumeration of Alternaria species from soil and plant debris

  . Canadian Journal of Microbiology. doi:10.1139/w04-036
• Pryor, B. M., Davis, R. M., & Farrar, J. J. (2004).

  Alternaria Diseases of Carrot

  . Plant Disease, 88(8), 776-784. doi:10.1094/pdis.2004.88.8.776
• Pryor, B., Hong, S. G., & Pryor, B. M. (2004). Development of selective media for the isolation and enumeration of Alternaria species from soil and plant debris. Canadian journal of microbiology, 50(7).
  More info

  A new semi-selective medium, acidified weak potato-dextrose agar (AWPDA) with Mertect (active ingredient: thiabendazole), was developed for the isolation and enumeration of Alternaria species from samples of soil and plant debris. The medium was selected based on growth inhibition tests against Alternaria and several other commonly encountered saprobic fungi utilizing three antifungal agents, Botran (active ingredient: dichloran), Bayleton (active ingredient: triadimefon), and Mertect, and two basal media, acidified potato-dextrose agar (APDA) and AWPDA. Botran inhibited growth of Rhizopus stolonifer moderately, but had little effect on Cladosporium cladosporoides, Fusarium oxysporum, Penicillium chrysogenum, or Trichoderma harzianum. Bayleton inhibited growth of R. stolonifer and C. cladosporoides severely, and inhibited growth of F. oxysporum, P. chrysogenum, and T. harzianum moderately. Mertect inhibited growth of C. cladosporoides, F. oxysporum, P. chrysogenum, and T. harzianum completely, but had little or moderate effect on R. stolonifer. All three antifungal agents inhibited growth of Alternaria species slightly or moderately. The combination of Bayleton and Mertect inhibited growth of all fungi severely. A comparison of recovery rates of Alternaria from soil and plant debris samples on AWPDA with Mertect and weak potato-dextrose agar (WPDA) revealed that Alternaria spp. accounted for 63.6%-81.0% of recovered fungal isolates on AWPDA with Mertect as compared to 0.6%-2.7% of recovered isolates on WPDA. The AWPDA medium with Mertect exhibited superior selective growth of Alternaria species from samples of soil and plant debris, and will be useful in studies where the recovery and enumeration of Alternaria species is necessary.
• Pryor, B. M., & Bigelow, D. M. (2003).

  Molecular characterization ofEmbellisiaandNimbyaspecies and their relationship toAlternaria,UlocladiumandStemphylium

  . Mycologia. doi:10.1080/15572536.2004.11833024
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  DNA sequences from rDNA and protein-coding regions were determined for six Embellisia and two Nimbya spp. and were compared to those from Alternaria, Ulocladium and Stemphylium spp. Sequences determined included rDNA from the nuclear internal transcribed-spacer region (ITS1/5.8S/ITS2) and the mitochondrial small-subunit (mt SSU) and a portion of the glyceraldehyde-3-phosphate dehydrogenase (gpd) gene. Phylogenetic analyses were performed on each dataset separately and then combined for total evidence analysis using methods of maximum parsimony and maximum likelihood. Results revealed that Embellisia and Nimbya clustered within a large monophyletic Alternaria-Nimbya-Embellisia-Ulocladium clade with Stemphylium as the sister taxon. Members of the infectoria species-group were the most basal group in this large polygeneric clade. Embellisia and Nimbya were sister taxa of the remaining Alternaria and Ulocladium spp. and were related more closely to Alternaria than was Stemphylium. Four Embellisia spp. formed a monophyletic clade. However, E. allii clustered with the two Nimbya spp. and E. indefessa clustered with Alternaria and Ulocladium spp., revealing that Embellisia, as currently circumscribed, is polyphyletic. Potential revisions of taxonomy for all genera are discussed.
• Pryor, B. M., & Bigelow, D. M. (2003). Molecular characterization of Embellisia and Nimbya species and their relationship to Alternaria, Ulocladium and Stemphylium. Mycologia, 95(6), 1141-1154.
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  PMID: 21149017;Abstract: DNA sequences from rDNA and protein-coding regions were determined for six Embellisia and two Nimbya spp. and were compared to those from Alternaria, Ulocladium and Stemphylium spp. Sequences determined included rDNA from the nuclear internal transcribed-spacer region (ITS1/5.8S/ ITS2) and the mitochondrial small-subunit (mt SSU) and a portion of the glyceraldehyde-3- phosphate dehydrogenase (gpd) gene. Phylogenetic analyses were performed on each dataset separately and then combined for total evidence analysis using methods of maximum parsimony and maximum likelihood. Results revealed that Embellisia and Nimbya clustered within a large monophyletic Alternaria-Nimbya- Embellisia-Ulocladium clade with Stemphylium as the sister taxon. Members of the infectoria species-group were the most basal group in this large polygeneric clade. Embellisia and Nimbya were sister taxa of the remaining Alternaria and Ulocladium spp. and were related more closely to Alternaria than was Stemphylium. Four Embellisia spp. formed a monophyletic clade. However, E. allii clustered with the two Nimbya spp. and E. indefessa clustered with Alternaria and Ulocladium spp., revealing that Embellisia, as currently circumscribed, is polyphyletic. Potential revisions of taxonomy for all genera are discussed.
• Pryor, B. M., & Gilbertson, R. L. (2002).

  Relationships and taxonomic status ofAlternaria radicina,A. carotiincultae, andA. petroselinibased upon morphological, biochemical, and molecular characteristics

  . Mycologia. doi:10.1080/15572536.2003.11833248
• Pryor, B. M., & Gilbertson, R. L. (2002). Relationships and taxonomic status of Alternaria radicina, A. carotiincultae, and A. petroselini based upon morphological, biochemical, and molecular characteristics. Mycologia, 94(1), 49-61.
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  PMID: 21156477;Abstract: Alternaria radicina, A. carotiincultae, and A. petroselini are closely related pathogens of umbelliferous crops. Relationships among these fungi were determined based on growth rate, spore morphology, cultural characteristics, toxin production, and host range. Random amplified polymorphic DNA (RAPD) analysis of these species, other species of Alternaria, and closely related fungi was also performed. A. petroselini was readily differentiated from A. radicina and A. carotiincultae on the basis of spore morphology, production of microsclerotia, host range, and RAPD analysis. Alternaria radicina and A. carotiincultae were considerably more similar to each other than to A. petroselini, but could be differentiated on the basis of growth rate, spore morphology, colony morphology, and, to a limited extent, RAPD analysis. When grown on media having a high nutritional content, A. radicina produced a diffusible yellow pigment and crystals of the fungal metabolite radicinin. In contrast, A. carotiincultae produced little or no radicinin. However, when A. carotiincultae was grown on the same medium amended with radicinin, growth rate and colony and conidial morphology were more similar to those of A. radicina. These results suggest that the morphological differences between A. radicina and A. carotiincultae are due, at least in part, to radicinin production, and that these fungi are conspecific. Therefore, we propose that A. carotiincultae be considered a synonym of A. radicina.
• Pryor, B. M., & Michailides, T. J. (2002).

  Morphological, Pathogenic, and Molecular Characterization of Alternaria Isolates Associated with Alternaria Late Blight of Pistachio

  . Phytopathology. doi:10.1094/phyto.2002.92.4.406
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  Alternaria isolates were obtained from various pistachio tissues collected in five orchards in California. For all isolates, morphological characteristics of the colony and sporulation apparatus were determined and compared with those of representative isolates of A. alternata, A. tenuissima, A. arborescens, and A. infectoria. A selection of the pistachio isolates and the representative Alternaria isolates were evaluated for pathogenicity to pistachio. Molecular characteristics of these isolates were determined using random amplified polymorphism DNA (RAPD) analysis, polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis of nuclear intergenic spacer rDNA, and sequence analysis of nuclear internal transcribed spacer (ITS) rDNA. Based on morphological characteristics, the pistachio isolates were grouped as identical or very similar to either A. alternata, A. tenuissima, A. arborescens, or A. infectoria. Isolates from the alternata, tenuissima, and arborescens species-groups were pathogenic to pistachio and no significant differences in pathogenicity were observed. Isolates from the infectoria species-group were only weakly pathogenic to pistachio. Based on cluster analysis of RAPD and PCR-RFLP data, three distinct clusters were evident; the infectoria cluster, the arborescens cluster, and a combined alternata/tenuissima cluster. Based on analysis of ITS sequence data, the infectoria species-group was phylogenetically distinct from the other species-groups. Isolates of the alternata, tenuissima, and arborescens species-groups comprised a monophyletic clade in which the three species-groups could not be further resolved.
• Pryor, B. M., & Michailides, T. J. (2002). Morphological, pathogenic, and molecular characterization of Alternaria isolates associated with alternaria late blight of pistachio. Phytopathology, 92(4), 406-416.
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  PMID: 18942954;Abstract: Alternaria isolates were obtained from various pistachio tissues collected in five orchards in California. For all isolates, morphological characteristics of the colony and sporulation apparatus were determined and compared with those of representative isolates of A. alternata, A. tenuissima, A. arborescens, and A. infectoria. A selection of the pistachio isolates and the representative Alternaria isolates were evaluated for pathogenicity to pistachio. Molecular characteristics of these isolates were determined using random amplified polymorphism DNA (RAPD) analysis, polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis of nuclear intergenic spacer rDNA, and sequence analysis of nuclear internal transcribed spacer (ITS) rDNA. Based on morphological characteristics, the pistachio isolates were grouped as identical or very similar to either A. alternata, A. tenuissima, A. arborescens, or A. infectoria. Isolates from the alternata, tenuissima, and arborescens species-groups were pathogenic to pistachio and no significant differences in pathogenicity were observed. Isolates from the infectoria species-group were only weakly pathogenic to pistachio. Based on cluster analysis of RAPD and PCR-RFLP data, three distinct clusters were evident; the infectoria cluster, the arborescens cluster, and a combined alternata/tenuissima cluster. Based on analysis of ITS sequence data, the infectoria species-group was phylogenetically distinct from the other species-groups. Isolates of the alternata, tenuissima, and arborescens species-groups comprised a monophyletic clade in which the three species-groups could not be further resolved.
• Pryor, B. M., Gilbertson, R. L., Nunez, J. J., Davis, R. M., & Strandberg, J. O. (2002).

  Survival and Persistence of Alternaria dauci in Carrot Cropping Systems

  . Plant Disease. doi:10.1094/pdis.2002.86.10.1115
• Pryor, B. M., Strandberg, J. O., Davis, R. M., Nunez, J. J., & Gilbertson, R. L. (2002). Survival and persistence of Alternaria dauci in carrot cropping systems. Plant Disease, 86(10), 1115-1122.
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  Abstract: Alternaria dauci was recovered in California from carrot crop residue and from volunteer carrot plants in fallow carrot fields. The fungus was not recovered from common weeds surrounding fallow fields. To evaluate further the survival of A. dauci on carrot crop residue, infected carrot leaf tissue was placed in fields or in soil in greenhouse pots, and recovered over time. In California, A. dauci was recovered from infected leaf tissue in both fallow and irrigated fields for as long as 1 year. In Florida, A. dauci was recovered from infected leaf tissue in fallow fields for up to 30 weeks. In greenhouse experiments, A. dauci was recovered from infected leaf tissue for as long as 1 year in dry soil, but only up to 30 weeks in soil that was watered weekly. To determine the infectivity of A. dauci borne on carrot crop residue, infected carrot crops were incorporated into organic and mineral field soils, and soil samples were collected over time. Carrot seed were planted in collected soil, and seedling infection by A. dauci was recorded. Seedling infection was detected up to 13 and 14 weeks after crop incorporation in organic and mineral soil, respectively. Seedling infection was detected for up to 5 weeks in soil that remained dry compared with 3 weeks in flooded soil.
• Pryor, B. M., & Gilbertson, R. L. (2001).

  A PCR-based Assay for Detection of Alternaria radicina on Carrot Seed

  . Plant Disease. doi:10.1094/pdis.2001.85.1.18
• Pryor, B. M., & Gilbertson, R. L. (2001). A PCR-based assay for detection of Alternaria radicina on carrot seed. Plant Disease, 85(1), 18-23.
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  Abstract: Pryor, B. M., and Gilbertson, R. L. 2001. A PCR-based assay for detection of Alternaria radicina on carrot seed. Plant Dis. 85:18-23. A pair of polymerase chain reaction (PCR) primers was developed based upon the sequence of a cloned random amplified polymorphic DNA (RAPD) fragment of Alternaria radicina, and a PCR-based seed assay was developed for the detection of A. radicina from infested carrot seed. The seed assay involved a 5-day incubation step, in which seed was maintained under high humidity conditions in order to increase fungal biomass. Seed was then incubated with lysis buffer, extracted with phenol-chloroform, and DNA was recovered using a silica matrix. PCR amplification of the target A. radicina DNA sequence was enhanced by the addition of skim milk to the PCR reaction mixture. With this PCR-based seed assay, A. radicina was detected from carrot seed lots with natural infestation rates as low as 0.3%. In seed lots prepared by mixing known amounts of A. radicina-infested seed with noninfested seed, this assay allowed for the detection of the pathogen from lots with infestation rates as low as 0.1%.
• Viveros, M., Teviotdale, B. L., Pryor, B. M., & Adaskaveg, J. E. (2001).

  First Report of Alternaria Leaf Spot of Almond Caused by Species in the Alternaria alternata Complex in California.

  . Plant disease, 85(5), 558. doi:10.1094/pdis.2001.85.5.558b
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  A new leaf spot disease of almond (Prunus dulcis [Mill.] D. Webb) was observed in California in the late 1980s and was first associated with severe defoliation in the mid-1990s (1). Orchards in areas with frequent summer dews, high humidity, and little air movement sustained severe defoliation, resulting in yield losses often exceeding 50%. Symptoms occur only on leaf blades in late spring and summer. Lesions develop as small, circular, tan spots 1 to 3 mm in diameter that may enlarge to 5 to 20 mm in size. Semicircular lesions frequently develop along the leaf margins and tips. The centers of mature lesions become black with fungal sporulation. The fungi isolated from the margins of sporulating and non-sporulating lesions were identified as three species in the Alternaria alternata complex: A. alternata, A. arborescens, and A. tenuissima (2,3). Cultures grown in the dark on potato dextrose (PDA) or potato-carrot agar are grayish white to olivacious green in the former two species and dark gray and wooly in the latter species. On 5% PDA, cultures of all three species produced catenulate dictyospores that were granular to punctate (-verrucose), pale yellowish to brown or black, and had visible apical and basal pores. Conidial morphology depended on chain position; apical conidia ranged from ovoid to ellipsoid, whereas basal conidia were elliptical to obclavate. Average conidial dimensions of A. alternata and A. arborescens ranged from 20 to 28 × 8 to 10 μm. Conidia of A. alternata were produced in acropetal succession in branching chains on single, short suberect conidiophores. A. arborescens produced conidia similarly but mostly in dichotomously branching chains on short to long conidiophores. Average conidial dimensions of A. tenuissima ranged from 20 to 34 × 8 to 12 μm and they were produced in simple chains with one or two branches forming occasionally. In preliminary studies, the optimum temperature for mycelial growth on PDA for all three species ranged from 24 to 28°C. Fifty mature leaves on each of four 7- or 8-year-old almond cv. Butte trees were inoculated at 2- to 3-week intervals from mid-spring through summer in 1999 and 2000. Leaves were sprayed with aqueous suspensions containing 105 conidia per milliliter for one isolate each of A. alternata and A. arborescens and two isolates of A. tenuissima or with sterile distilled water. The shoots were covered for 72 h with plastic-lined brown paper bags containing wet paper towels. Leaves were examined for infection after 7 and 14 days. All isolates were pathogenic and produced non-sporulating lesions similar to those observed in natural infections. No symptoms were observed on noninoculated control plants. Disease incidence was low (
• Pryor, B. M., & Gilbertson, R. L. (2000).

  Molecular phylogenetic relationships amongst Alternaria species and related fungi based upon analysis of nuclear ITS and mt SSU rDNA sequences

  . Mycological research. doi:10.1017/s0953756200003002
  More info

  To elucidate relationships among Alternaria, Ulocladium, and Stemphylium species, nuclear internal transcribed spacer (ITS) and mitochondrial small subunit (SSU) ribosomal DNA (rDNA) sequences from 18 Alternaria, four Ulocladium and four Stemphylium spp. were determined and compared. Phylogenetic analysis of the ITS and SSU rDNA sequences, performed by the neighbour joining and maximum parsimony methods, revealed that the Stemphylium spp. were phylogenetically distinct from the Alternaria and Ulocladium spp. Most Alternaria spp. and the Ulocladium spp. were placed together in a large Alternaria/Ulocladium clade. Within this large clade, the Alternaria spp. clustered into several distinct species-clades, most of which correlated with species-groups previously established based upon morphological characteristics. The Ulocladium spp. were placed into two species-clades, each of which also included Alternaria spp. A. longissima was distantly related to the other Alternaria spp., as well as the Ulocladium and Stemphylium spp. Based upon ITS and nuclear 18S rDNA sequence identities, A. longissima was most closely related to Leptosphaeria .
• Pryor, B. M., & Gilbertson, R. L. (2000). Molecular phylogenetic relationships amongst Alternaria species and related fungi based upon analysis of nuclear ITS and mt SSU rDNA sequences. Mycological Research, 104(11), 1312-1321.
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  Abstract: To elucidate relationships among Alternaria, Ulocladium, and Stemphylium species, nuclear internal transcribed spacer (ITS) and mitochondrial small subunit (SSU) ribosomal DNA (rDNA) sequences from 18 Alternaria, four Ulocladium and four Stemphylium spp. were determined and compared. Phylogenetic analysis of the ITS and SSU rDNA sequences, performed by the neighbour joining and maximum parsimony methods, revealed that the Stemphylium spp. were phylogenetically distinct from the Alternaria and Ulocladium spp. Most Alternaria spp. and the Ulocladium spp. were placed together in a large Alternaria/Ulocladium clade. Within this large clade, the Alternaria spp. clustered into several distinct species-clades, most of which correlated with species-groups previously established based upon morphological characteristics. The Ulocladium spp. were placed into two species-clades, each of which also included Alternaria spp. A. longissima was distantly related to the other Alternaria spp., as well as the Ulocladium and Stemphylium spp. Based upon ITS and nuclear 18S rDNA sequence identities, A. longissima was most closely related to Leptosphaeria.
• Pryor, B. M., Davis, R. M., & Gilbertson, R. L. (2000). A toothpick inoculation method for evaluating carrot cultivars for resistance to Alternaria radicina. HortScience, 35(6), 1099-1102.
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  Abstract: The susceptibility of 46 carrot cultivars to infection by Alternaria radicina Meier, Drechsler, and Eddy, causal agent of black rot disease, was evaluated in field trials with a toothpick inoculation method. Toothpicks infested with A. radicina were inserted into the shoulders of 10- to 12-week-old carrots (Daucus carota L.) and lesion areas were measured 9 to 10 weeks later. There were significant differences in lesion size among cultivars. Relatively resistant cultivars included 'Panther' and 'Caro-pak', and susceptible cultivars included 'Royal Chantenay' and 'Nogales'. Nine of the cultivars were inoculated with A. radicina-infested toothpicks and maintained in cold-storage for 10 weeks. Lesion development was greater in cold-storage than in the field, but the relative ranking of cultivars in terms of resistance to A. radicina was similar.
• Pryor, B. M., Gilbertson, R. L., & Davis, R. M. (2000).

  A Toothpick Inoculation Method for Evaluating Carrot Cultivars for Resistance to Alternaria radicina

  . Hortscience. doi:10.21273/hortsci.35.6.1099
  More info

  The susceptibility of 46 carrot cultivars to infection by Alternaria radicina Meier, Drechsler, and Eddy, causal agent of black rot disease, was evaluated in field trials with a toothpick inoculation method. Toothpicks infested with A. radicina were inserted into the shoulders of 10- to 12-week-old carrots ( Daucus carota L.) and lesion areas were measured 9 to 10 weeks later. There were significant differences in lesion size among cultivars. Relatively resistant cultivars included `Panther' and `Caro-pak', and susceptible cultivars included `Royal Chantenay' and `Nogales'. Nine of the cultivars were inoculated with A. radicina -infested toothpicks and maintained in cold-storage for 10 weeks. Lesion development was greater in cold-storage than in the field, but the relative ranking of cultivars in terms of resistance to A. radicina was similar.
• Stock, S. P., Pryor, B. M., & Kaya, H. K. (1999). Distribution of entomopathogenic nematodes (Steinernematidae and Heterorhabditidae) in natural habitats in California, USA. Biodiversity and Conservation, 8(4), 535-549.
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  Abstract: A total of 270 soil samples from 30 different habitats in 10 geographic regions of California were evaluated for the presence of rhabditid entomopathogenic nematodes. Nematodes were isolated from 26.3% of the samples. The recovered isolates were identified as Steinernema carpocapsae, S. feltiae, S. kraussei, S. longicaudum, S. oregonense, Heterorhabditis marelatus and H. bacteriophora. Among the steinernematids, S. kraussei and S. feltiae were the most commonly encountered species, generally occurring in acidic soils high in organic matter. Among the heterorhabditids, H. bacteriophora was isolated along the southern coast, whereas H. marelatus was recovered along the northern coast of California. Steinernematids were recovered from coniferous forests, oak woodlands and grasslands whereas heterorhabditids were isolated from coastal marshes.
• Pryor, B. M., Davis, R. M., & Gilbertson, R. L. (1998). Detection of soilborne Alternaria radicina and its occurrence in california carrot fields. Plant Disease, 82(8), 891-895.
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  Abstract: Alternaria radicina, causal agent of black rot disease of carrot, was recovered from soil by plating dilutions on a semi-selective medium, A. radicina semi-selective agar. The efficiency of this soil assay was 93% based on recovery of the fungus from non-infested field soil amended with A. radicina conidia. Soilborne A. radicina was recovered from five of six carrot-growing areas in California, but was only commonly found in the Cuyama Valley, where the fungus was detected in 83% of sampled fields. Over a 3-year period of sampling, A. radicina soil populations in Cuyama Valley fields prior to carrot planting ranged from 0 to 317 CFU/g. There was a positive correlation between A. radicina soil populations in these fields and the incidence of black rot disease at harvest. A. radicina was recovered from dry soil after 4 years of storage, and the fungus survived in this soil as solitary conidia or as conidia associated with organic debris.
• Pryor, B. M., Gilbertson, R. L., & Davis, R. M. (1998).

  Detection of Soilborne Alternaria radicina and Its Occurrence in California Carrot Fields

  . Plant Disease. doi:10.1094/pdis.1998.82.8.891
• Pryor, B. M., Davis, R. M., & Gilbertson, R. L. (1994). Detection and eradication of Alternaria radicina on carrot seed. Plant Disease, 78(5), 452-456.
• Pryor, B. M., Gilbertson, R. L., & Davis, R. M. (1994).

  Detection and Eradicationof Alternaria radicinaon Carrot Seed

  . Plant Disease. doi:10.1094/pd-78-0452

Proceedings Publications

• Gallenbeck, S., Giacomelli, G. A., & Pryor, B. M. (2019, July). Mushrooms on Mars: A Subsystem for Human Life Support. In 49th International Conference on Environmental Systems ICES-2019, 1-11.
• Giacomelli, G. A., Pryor, B. M., & Gellenbeck, S. (2019).

  Mushrooms on Mars: A Subsystem for Human Life Support

  . In ICES-2021conference 12-15 July 2021..
• Spriggs, E., Schlecht, J., Pryor, B. M., & Barnard, K. (2007).

  Inferring Grammar-based Structure Models from 3D Microscopy Data

  . In 2007 IEEE Conference on Computer Vision and Pattern Recognition, 1-8.
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  We present a new method to fit grammar-based stochastic models for biological structure to stacks of microscopic images captured at incremental focal lengths. Providing the ability to quantitatively represent structure and automatically fit it to image data enables important biological research. We consider the case where individuals can be represented as an instance of a stochastic grammar, similar to L-systems used in graphics to produce realistic plant models. In particular, we construct a stochastic grammar of Alternaria, a genus of fungus, and fit instances of it to microscopic image stacks. We express the image data as the result of a generative process composed of the underlying probabilistic structure model together with the parameters of the imaging system. Fitting the model then becomes probabilistic inference. For this we create a reversible-jump MCMC sampler to traverse the parameter space. We observe that incorporating spatial structure helps fit the model parts, and that simultaneously fitting the imaging system is also very helpful.
• Schlecht, J., Pryor, B. M., & Barnard, K. (2006).

  Statistical Inference of Biological Structure and Point Spread Functions in 3D Microscopy

  . In Third International Symposium on 3D Data Processing, Visualization, and Transmission (3DPVT'06), 373-380.
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  We present a novel method for detecting and quantifying 3D structure in stacks of microscopic images captured at incremental focal lengths. We express the image data as stochastically generated by an underlying model for biological specimen and the effects of the imaging system. The method simultaneously fits a model for proposed structure and the imaging system's parameters, which include a model of the point spread function. We demonstrate our approach by detecting spores in image stacks of Alternaria, a microscopic genus of fungus. The spores are modeled as opaque ellipsoids and fit to the data using statistical inference. Since the number of spores in the data is not known, model selection is incorporated into the fitting process. Thus, we develop a reversible jump Markov chain Monte Carlo sampler to explore the parameter space. Our results show that simultaneous statistical inference of specimen and imaging models is useful for quantifying biological structures in 3D microscopic images. In addition, we show that inferring a model of the imaging system improves the overall fit of the specimen model to the data.

Presentations

• Pryor, B. M., Giacomelli, G. A., & Gellenbeck, S. (2019, October). Mushrooms on Mars. MBR Space Settlement Challenge. Dubai, UAE: UN Office for Outer Space Affairs, UAE Space Agency and the MBR Space Center.
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  MBR Space Settlement Challenge at conference we will be holding on 13-15th November. The purpose of the conference will be to discuss 7 of the projects done for the Challenge that focus specifically on Space Research & Technologies for Food and Water Security on Earth. Of course we will be happy to cover the associated expenses of course, including airfare and a 3-4 day hotel stay of your visit. The event will be held with the support of the UN Office for Outer Space Affairs and our national stakeholders including the UAE Space Agency and the MBR Space Center.
• Pryor, B. M. (2018, March). Optimizing specialty mushroom production: impacts of substrate, temperature, and CO2 on bioefficiency. CEAC Short Course in Controlled Environment Systems. Tucson Marriott: Controlled Environment Agriculture Center.
• Pryor, B. M. (2018, November). Current Management of Fursarium Wilt of Lettuce. Yuma Center of Excellence Research Conference. Yuma Agricultural Center: Yuma Center for Excellence in Desert Agriculture.
• Pryor, B. M. (2018, Novermber). Optimizing specialty mushroom production: impacts of culture parameters on bioefficiency and nutrition. WSU Plant Pathology Seminar Series. Pullman, WA: Dept of Plant Pathology, Washington State University.
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  Invited Speaker
• Pryor, B. M. (2017, fall). Commercial mushroom production in the southwest deserts. Aquaponics Fall Seminar Series. Tucson, AZ: Arizona Aquaponics Club.
• Pryor, B. M. (2017, fall). Rapid Detection of Fusarium oxysporum in infected lettuce tissue. YCEDA Annual Stateholder Meeting. Yuma, AZ: Yuma Center for Excellence in Desert Agriculture.
• Pryor, B. M. (2017, fall). Sustainable mushroom production in the Southwest deserts. Tohono O'odham Sustainability Seminar Series. San Xavier Mission, Tucson, AZ: Tohono O'odham Nation.
• Pryor, B. M. (2017, spring). Common and uncommon tree diseases of the Southwest. Cooperative Extension Tree Health workshop. Phoenix, AZ: Maricopa County Cooperative Extension.
• Pryor, B. M. (2017, spring). Improved management of Fusarium wilt of lettuce with advanced diagnostics. YCEDA Research Updates 2017. Yuma, Arizona: Yuma Center for Excellence in Desert Agriculture.
• Pryor, B. M. (2017, spring). Management of Fusarium wilt of palm, a new disease of horticultural palms in Arizona. Cooperative Extension Palm and Citrus workshop. Phoenix, AZ: Maricopa County Cooperative Extension.
• Pryor, B. M. (2017, spring). Plant disease in native Arizona ecosystems. Spring seminar series Arizona Native Plant Society. Tucson, AZ: Arizona Native Plant Society.
• Pryor, B. M. (2017, spring). Specialty mushroom production: Arizona's new specialty crop. Tucson's 1st Annual Gourmet Mushrooms and Wine Tasting. Feast Restaurant, Tucson, AZ: Slow Food, Arizona.
• Pryor, B. M. (2017, spring). The effects of substrate composition and environment on mushroom yields. CEAC seminar series. University of Arizona: Controlled Environment Agriculture Center.
• Pryor, B. M. (2017, summer). Commecial mushroom production in Arizona. Benson Rotary Spring Seminar Series. Benson, AZ: Rotary Club of Benson.
• Pryor, B. M. (2016, spring). Desert mushroom production: lessons in sustainability. UA College of Ag and Life Sciences Faculty Luncheon. Tucson, AZ: UA College of Ag and Life Sciences.
• Pryor, B. M. (2016, spring). Mushrooms and engineering: innovative applications for sustainable living. The Arizona Section of the American Society of Agricultural and Biological Engineers Annual Dinner. Tucson, AZ: The Arizona Section of the American Society of Agricultural and Biological Engineers.
• Pryor, B. M. (2016, spring). The MycoCats: recycling with mushrooms on the UA campus. UA Controlled Environment Agricultural Center Seminar Series. Tucson: UA Controlled Environment Agricultural Center.
• Pryor, B. M. (2016, spring). The MycoCats: sustainable mushroom production. UA Green Talks. Tucson, AZ: UA Solar Cats.
• Pryor, B. M. (2016, summer). Management of plant parasitic seed plants. 2016 Desert Horticulture Conference. Tucson, AZ: UA Cooperative Extension.
• Pryor, B. M. (2014, April). Fungi for food and fuel. Plant Sciences Faculty Forum.
• Pryor, B. M., & Jackson, L. (2014, March). Sustaining decay: toward closing food system loops by integrating fungi. Arizona Higher Education Sustainability Conference.
• Pryor, B. M. (2012, August). Using comparative genomics for species resolution in Alternaria. special symposium at the 2012 Annual Meeting of the APS. Providence, RI.
• Pryor, B. M. (2012, May). Diseases and parasites of tress in southwest landscaping. Desert Horticulture Conference. Tucson, AZ.

Poster Presentations

• Pryor, B. M., & Evans, J. P. (2014, Jan). Recycling mesquite pods with fungi. 2014 Undergraduate Biology Research Program.

Others

• Pryor, B. M., & Plasse, T. (2018, January). Advanced Production of Specialty Mushrooms in Arizona.
  More info

  Created and delivered a new 4 part, 4 hour workshop (the first workshop was developed in 2016) on advanced concepts of commercial mushroom production. Subjects include specifics of production for 10 species of the most commonly produced specialty mushrooms, techniques in pasteurization of substrate, spawn production, impact of environmental parameters, and regulatory aspects of GHP/GAP certification through USDA. Delivered this workshop, complete with a mobile mushroom shed, at Cooperative Extension office across Arizona. Tucson, 2/21; Kingman, 4/11: Sierra Vista, 5/9; Navajo Nation, 5/23; Phoenix, 6/20; Flagstaff, 6/27; Tucson, 9/7. http://www.azmushroomgrowers.org/
• Pryor, B. M. (2017, summer). Arizona Illustrated Spotlight. Public Television.
  More info

  https://tv.azpm.org/p/originals-azill-sci/2017/2/15/106296-expanding-the-palate/
• Pryor, B. M. (2016, spring). Arizona Mushroom Growers Association. web.
  More info

  Organized the Arizona Mushroom Growers Association (currently 45 members) and developed a website as a focus and center for the organization. Information and news on local mushroom production is posted, along with digital presentations of the 2016 AZ Mushroom Production Workshop. A newsletter is periodically sent out to all members as well. http://www.azmushroomgrowers.org/
• Pryor, B. M., & Plasse, T. (2016, spring). Small-scale Commercial Mushroom Production Workshop.
  More info

  Created and delivered a 4 part, 4 hour workshop on multiple aspects of commercial mushroom production. Subjects include a mycology primer, nutritional properties of mushroom, beginning to end specifics of small scale specialty mushroom production, and the economics of the commercial mushroom industry. Delivered this workshop, complete with a mobile mushroom shed, at Cooperative Extension office across Arizona. Tucson, 1/10; Phoenix, 1/24; Yuma, 4/20; Phoenix, 4/27; Sho Lo, 6/1; Flagstaff, 7/6; Prescott, 8/8; Tucson, 8/31
• Pryor, B. M. (2012, Fall). 3-D Alternaria Generator website. http://kobus.ca/alternaria
• Pryor, B. M. (2011, Fall). Lettuce Disease Management website.
• Pryor, B. M. (2010, Fall). 3-D Alternaria Generator website. http://kobus.ca/alternaria/
• Pryor, B. M. (2010, Fall). Alternaria On-line website. http://ag.arizona.edu/plp/alternaria/online.htm
• Pryor, B. M. (2010, Fall). Interactive kiosk for education in microbiology. Kartchner Caverns Interpretive Center.
  More info

  NSF Microbial Observatory project