@article{luis_carbone_mack_lebar_cary_gilbert_bhatnagar_wientjes_payne_moore_et al._2022, title={Dataset for transcriptomic profiles associated with development of sexual structures in Aspergillus flavus}, volume={42}, ISSN={["2352-3409"]}, DOI={10.1016/j.dib.2022.108033}, abstractNote={Information on the transcriptomic changes that occur within sclerotia of Aspergillus flavus during its sexual cycle is very limited and warrants further research. The findings will broaden our knowledge of the biology of A. flavus and can provide valuable insights in the development or deployment of non-toxigenic strains as biocontrol agents against aflatoxigenic strains. This article presents transcriptomic datasets included in our research article entitled, "Development of sexual structures influences metabolomic and transcriptomic profiles in Aspergillus flavus" [1], which utilized transcriptomics to identify possible genes and gene clusters associated with sexual reproduction and fertilization in A. flavus. RNA was extracted from sclerotia of a high fertility cross (Hi-Fert-Mated), a low fertility cross (Lo-Fert-Mated), and unmated strains (Hi-Fert-Unmated and Lo-Fert-Unmated) of A. flavus collected immediately after crossing and at every two weeks until eight weeks of incubation on mixed cereal agar at 30 °C in continuous darkness (n = 4 replicates from each treatment for each time point; 80 total). Raw sequencing reads obtained on an Illumina NovaSeq 6000 were deposited in NCBI's Sequence Read Archive (SRA) repository under BioProject accession number PRJNA789260. Reads were mapped to the A. flavus NRRL 3357 genome (assembly JCVI-afl1-v2.0; GCA_000006275.2) using STAR software. Differential gene expression analyses, functional analyses, and weighted gene co-expression network analysis were performed using DESeq2 R packages. The raw and analyzed data presented in this article could be reused for comparisons with other datasets to obtain transcriptional differences among strains of A. flavus or closely related species. The data can also be used for further investigation of the molecular basis of different processes involved in sexual reproduction and sclerotia fertility in A. flavus.}, journal={DATA IN BRIEF}, author={Luis, Jane Marian and Carbone, Ignazio and Mack, Brian M. and Lebar, Matthew D. and Cary, Jeffrey W. and Gilbert, Matthew K. and Bhatnagar, Deepak and Wientjes, Carol-Carter and Payne, Gary A. and Moore, Geromy G. and et al.}, year={2022}, month={Jun} }
 @article{luis_carbone_mack_lebar_cary_gilbert_bhatnagar_wientjes_payne_moore_et al._2022, title={Development of sexual structures influences metabolomic and transcriptomic profiles in Aspergillus flavus}, volume={126}, ISSN={["1878-6162"]}, DOI={10.1016/j.funbio.2022.01.001}, abstractNote={Sclerotium (female) fertility, the ability of a strain to produce ascocarps, influences internal morphological changes during sexual reproduction in Aspergillus flavus. Although sclerotial morphogenesis has been linked to secondary metabolite (SM) biosynthesis, metabolic and transcriptomic changes within A. flavus sclerotia during sexual development are not known. Successful mating between compatible strains may result in relatively high or low numbers of ascocarps being produced. Sclerotia from a high fertility cross (Hi-Fert-Mated), a low fertility cross (Lo-Fert-Mated), unmated strains (Hi-Fert-Unmated and Lo-Fert-Unmated) were harvested immediately after crosses were made and every two weeks until 8 weeks of incubation, then subjected to targeted metabolomics (n = 106) and transcriptomics analyses (n = 80). Aflatoxin B1 production varied between Hi-Fert-Mated and Hi-Fert-Unmated sclerotia, while it remained low or was undetected in Lo-Fert-Mated and Lo-Fert-Unmated sclerotia. Profiling of 14 SMs showed elevated production of an aflavazole analog, an aflavinine isomer, and hydroxyaflavinine in Hi-Fert-Mated sclerotia at 4 to 8 weeks. Similarly, genes ayg1, hxtA, MAT1, asd-3, preA and preB, and genes in uncharacterized SM gene clusters 30 and 44 showed increased expression in Hi-Fert-Mated sclerotia at these time points. These results broaden our knowledge of the biochemical and transcriptional processes during sexual development in A. flavus.}, number={3}, journal={FUNGAL BIOLOGY}, author={Luis, Jane Marian and Carbone, Ignazio and Mack, Brian M. and Lebar, Matthew D. and Cary, Jeffrey W. and Gilbert, Matthew K. and Bhatnagar, Deepak and Wientjes, Carol-Carter and Payne, Gary A. and Moore, Geromy G. and et al.}, year={2022}, month={Mar}, pages={187–200} }
 @article{antiga_la starza_miccoli_d'angeli_scala_zaccaria_shu_obrian_beccaccioli_payne_et al._2020, title={Aspergillus flavus Exploits Maize Kernels Using an "Orphan" Secondary Metabolite Cluster}, volume={21}, ISSN={["1422-0067"]}, DOI={10.3390/ijms21218213}, abstractNote={Aspergillus flavus is a saprophytic cosmopolitan fungus, capable of infecting crops both pre- and post-harvest and exploiting different secondary metabolites, including aflatoxins. Aflatoxins are known carcinogens to animals and humans, but display no clear effect in host plants such as maize. In a previous study, we mined the genome of A. flavus to identify secondary metabolite clusters putatively involving the pathogenesis process in maize. We now focus on cluster 32, encoding for fungal effectors such as salicylate hydroxylase (SalOH), and necrosis- and ethylene-inducing proteins (npp1 domain protein) whose expression is triggered upon kernel contact. In order to understand the role of this genetic cluster in maize kernel infection, mutants of A. flavus, impaired or enhanced in specific functions (e.g., cluster 32 overexpression), were studied for their ability to cause disease. Within this frame, we conducted histological and histochemical experiments to verify the expression of specific genes within the cluster (e.g., SalOH, npp1), the production of salicylate, and the presence of its dehydroxylated form. Results suggest that the initial phase of fungal infection (2 days) of the living tissues of maize kernels (e.g., aleuron) coincides with a significant increase of fungal effectors such as SalOH and Npp1 that appear to be instrumental in eluding host defences and colonising the starch-enriched tissues, and therefore suggest a role of cluster 32 to the onset of infection.}, number={21}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Antiga, Ludovica and La Starza, Sonia Roberta and Miccoli, Cecilia and D'Angeli, Simone and Scala, Valeria and Zaccaria, Marco and Shu, Xiaomei and Obrian, Gregory and Beccaccioli, Marzia and Payne, Gary A. and et al.}, year={2020}, month={Nov} }
 @article{luis_carbone_payne_bhatnagar_cary_moore_lebar_wei_mack_ojiambo_2020, title={Characterization of morphological changes within stromata during sexual reproduction inAspergillus flavus}, volume={112}, ISSN={["1557-2536"]}, DOI={10.1080/00275514.2020.1800361}, abstractNote={ABSTRACT Aspergillus flavus contaminates agricultural products worldwide with carcinogenic aflatoxins that pose a serious health risk to humans and animals. The fungus survives adverse environmental conditions through production of sclerotia. When fertilized by a compatible conidium of an opposite mating type, a sclerotium transforms into a stroma within which ascocarps, asci, and ascospores are formed. However, the transition from a sclerotium to a stroma during sexual reproduction in A. flavus is not well understood. Early events during the interaction between sexually compatible strains of A. flavus were visualized using conidia of a green fluorescent protein (GFP)-labeled MAT1-1 strain and sclerotia of an mCherry-labeled MAT1-2 strain. Both conidia and sclerotia of transformed strains germinated to produce hyphae within 24 h of incubation. Hyphal growth of these two strains produced what appeared to be a network of interlocking hyphal strands that were observed at the base of the mCherry-labeled sclerotia (i.e., region in contact with agar surface) after 72 h of incubation. At 5 wk following incubation, intracellular green-fluorescent hyphal strands were observed within the stromatal matrix of the mCherry-labeled strain. Scanning electron microscopy of stromata from a high- and low-fertility cross and unmated sclerotia was used to visualize the formation and development of sexual structures within the stromatal and sclerotial matrices, starting at the time of crossing and thereafter every 2 wk until 8 wk of incubation. Morphological differences between sclerotia and stromata became apparent at 4 wk of incubation. Internal hyphae and croziers were detected inside multiple ascocarps that developed within the stromatal matrix of the high-fertility cross but were not detected in the matrix of the low-fertility cross or the unmated sclerotia. At 6 to 8 wk of incubation, hyphal tips produced numerous asci, each containing one to eight ascospores that emerged out of an ascus following the breakdown of the ascus wall. These observations broaden our knowledge of early events during sexual reproduction and suggest that hyphae from the conidium-producing strain may be involved in the early stages of sexual reproduction in A. flavus. When combined with omics data, these findings could be useful in further exploration of the molecular and biochemical mechanisms underlying sexual reproduction in A. flavus.}, number={5}, journal={MYCOLOGIA}, author={Luis, Jane Marian and Carbone, Ignazio and Payne, Gary A. and Bhatnagar, Deepak and Cary, Jeffrey W. and Moore, Geromy G. and Lebar, Matthew D. and Wei, Qijian and Mack, Brian and Ojiambo, Peter S.}, year={2020}, month={Sep}, pages={908–920} }
 @article{musungu_bhatnagar_quiniou_brown_payne_o'brian_fakhoury_geisler_2020, title={Use of Dual RNA-seq for Systems Biology Analysis ofZea maysandAspergillus flavusInteraction}, volume={11}, ISBN={1664-302X}, DOI={10.3389/fmicb.2020.00853}, abstractNote={The interaction between Aspergillus flavus and Zea mays is complex, and the identification of plant genes and pathways conferring resistance to the fungus has been challenging. Therefore, the authors undertook a systems biology approach involving dual RNA-seq to determine the simultaneous response from the host and the pathogen. What was dramatically highlighted in the analysis is the uniformity in the development patterns of gene expression of the host and the pathogen during infection. This led to the development of a “stage of infection index” that was subsequently used to categorize the samples before down-stream system biology analysis. Additionally, we were able to ascertain that key maize genes in pathways such as the jasmonate, ethylene and ROS pathways, were up-regulated in the study. The stage of infection index used for the transcriptomic analysis revealed that A. flavus produces a relatively limited number of transcripts during the early stages (0 to 12 h) of infection. At later stages, in A. flavus, transcripts and pathways involved in endosomal transport, aflatoxin production, and carbohydrate metabolism were up-regulated. Multiple WRKY genes targeting the activation of the resistance pathways (i.e., jasmonate, phenylpropanoid, and ethylene) were detected using causal inference analysis. This analysis also revealed, for the first time, the activation of Z. mays resistance genes influencing the expression of specific A. flavus genes. Our results show that A. flavus seems to be reacting to a hostile environment resulting from the activation of resistance pathways in Z. mays. This study revealed the dynamic nature of the interaction between the two organisms.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Musungu, Bryan and Bhatnagar, Deepak and Quiniou, Sylvie and Brown, Robert L. and Payne, Gary A. and O'Brian, Greg and Fakhoury, Ahmad M. and Geisler, Matt}, year={2020} }
 @article{lewis_carbone_luis_payne_bowen_hagan_kemerait_heiniger_ojiambo_2019, title={Biocontrol Strains Differentially Shift the Genetic Structure of Indigenous Soil Populations of Aspergillus flavus}, volume={10}, ISSN={1664-302X}, url={http://dx.doi.org/10.3389/fmicb.2019.01738}, DOI={10.3389/fmicb.2019.01738}, abstractNote={Biocontrol using non-aflatoxigenic strains of Aspergillus flavus has the greatest potential to mitigate aflatoxin contamination in agricultural produce. However, factors that influence the efficacy of biocontrol agents in reducing aflatoxin accumulation under field conditions are not well-understood. Shifts in the genetic structure of indigenous soil populations of A. flavus following application of biocontrol products Afla-Guard and AF36 were investigated to determine how these changes can influence the efficacy of biocontrol strains in reducing aflatoxin contamination. Soil samples were collected from maize fields in Alabama, Georgia, and North Carolina in 2012 and 2013 to determine changes in the population genetic structure of A. flavus in the soil following application of the biocontrol strains. A. flavus L was the most dominant species of Aspergillus section Flavi with a frequency ranging from 61 to 100%, followed by Aspergillus parasiticus that had a frequency of <35%. The frequency of A. flavus L increased, while that of A. parasiticus decreased after application of biocontrol strains. A total of 112 multilocus haplotypes (MLHs) were inferred from 1,282 isolates of A. flavus L using multilocus sequence typing of the trpC, mfs, and AF17 loci. A. flavus individuals belonging to the Afla-Guard MLH in the IB lineage were the most dominant before and after application of biocontrol strains, while individuals of the AF36 MLH in the IC lineage were either recovered in very low frequencies or not recovered at harvest. There were no significant (P > 0.05) differences in the frequency of individuals with MAT1-1 and MAT1-2 for clone-corrected MLH data, an indication of a recombining population resulting from sexual reproduction. Population mean mutation rates were not different across temporal and spatial scales indicating that mutation alone is not a driving force in observed multilocus sequence diversity. Clustering based on principal component analysis identified two distinct evolutionary lineages (IB and IC) across all three states. Additionally, patristic distance analysis revealed phylogenetic incongruency among single locus phylogenies which suggests ongoing genetic exchange and recombination. Levels of aflatoxin accumulation were very low except in North Carolina in 2012, where aflatoxin levels were significantly (P < 0.05) lower in grain from treated compared to untreated plots. Phylogenetic analysis showed that Afla-Guard was more effective than AF36 in shifting the indigenous soil populations of A. flavus toward the non-toxigenic or low aflatoxin producing IB lineage. These results suggest that Afla-Guard, which matches the genetic and ecological structure of indigenous soil populations of A. flavus in Alabama, Georgia, and North Carolina, is likely to be more effective in reducing aflatoxin accumulation and will also persist longer in the soil than AF36 in the southeastern United States.}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Lewis, Mary H. and Carbone, Ignazio and Luis, Jane M. and Payne, Gary A. and Bowen, Kira L. and Hagan, Austin K. and Kemerait, Robert and Heiniger, Ron and Ojiambo, Peter S.}, year={2019}, month={Jul} }
 @article{gilbert_medina_mack_lebar_rodriguez_bhatnagar_magan_obrian_payne_2018, title={Carbon Dioxide Mediates the Response to Temperature and Water Activity Levels in Aspergillus flavus during Infection of Maize Kernels}, volume={10}, ISSN={["2072-6651"]}, DOI={10.3390/toxins10010005}, abstractNote={Aspergillus flavus is a saprophytic fungus that may colonize several important crops, including cotton, maize, peanuts and tree nuts. Concomitant with A. flavus colonization is its potential to secrete mycotoxins, of which the most prominent is aflatoxin. Temperature, water activity (aw) and carbon dioxide (CO2) are three environmental factors shown to influence the fungus-plant interaction, which are predicted to undergo significant changes in the next century. In this study, we used RNA sequencing to better understand the transcriptomic response of the fungus to aw, temperature, and elevated CO2 levels. We demonstrate that aflatoxin (AFB1) production on maize grain was altered by water availability, temperature and CO2. RNA-Sequencing data indicated that several genes, and in particular those involved in the biosynthesis of secondary metabolites, exhibit different responses to water availability or temperature stress depending on the atmospheric CO2 content. Other gene categories affected by CO2 levels alone (350 ppm vs. 1000 ppm at 30 °C/0.99 aw), included amino acid metabolism and folate biosynthesis. Finally, we identified two gene networks significantly influenced by changes in CO2 levels that contain several genes related to cellular replication and transcription. These results demonstrate that changes in atmospheric CO2 under climate change scenarios greatly influences the response of A. flavus to water and temperature when colonizing maize grain.}, number={1}, journal={TOXINS}, author={Gilbert, Matthew K. and Medina, Angel and Mack, Brian M. and Lebar, Matthew D. and Rodriguez, Alicia and Bhatnagar, Deepak and Magan, Naresh and Obrian, Gregory and Payne, Gary}, year={2018}, month={Jan} }
 @article{jordan_brandenburg_payne_hoisington_magnan_rhoads_abudulai_adhikari_chen_akromah_et al._2018, title={Preventing mycotoxin contamination in groundnut cultivation}, volume={36}, ISBN={["978-1-78676-140-8"]}, ISSN={["2059-6944"]}, DOI={10.19103/AS.2017.0023.28}, journal={ACHIEVING SUSTAINABLE CULTIVATION OF GRAIN LEGUMES, VOL 2: IMPROVING CULTIVATION OF PARTICULAR GRAIN LEGUMES}, author={Jordan, David and Brandenburg, Rick and Payne, Gary and Hoisington, David and Magnan, Nick and Rhoads, James and Abudulai, Mumuni and Adhikari, Koushik and Chen, Jinru and Akromah, Richard and et al.}, year={2018}, pages={181–211} }
 @article{shu_livingston_woloshuk_payne_2017, title={Comparative Histological and Transcriptional Analysis of Maize Kernels Infected with Aspergillus flavus and Fusarium verticillioides}, volume={8}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2017.02075}, abstractNote={Aspergillus flavus and Fusarium verticillioides infect maize kernels and contaminate them with the mycotoxins aflatoxin, and fumonisin, respectively. Genetic resistance in maize to these fungi and to mycotoxin contamination has been difficult to achieve due to lack of identified resistance genes. The objective of this study was to identify new candidate resistance genes by characterizing their temporal expression in response to infection and comparing expression of these genes with genes known to be associated with plant defense. Fungal colonization and transcriptional changes in kernels inoculated with each fungus were monitored at 4, 12, 24, 48, and 72 h post inoculation (hpi). Maize kernels responded by differential gene expression to each fungus within 4 hpi, before the fungi could be observed visually, but more genes were differentially expressed between 48 and 72 hpi, when fungal colonization was more extensive. Two-way hierarchal clustering analysis grouped the temporal expression profiles of the 5,863 differentially expressed maize genes over all time points into 12 clusters. Many clusters were enriched for genes previously associated with defense responses to either A. flavus or F. verticillioides. Also within these expression clusters were genes that lacked either annotation or assignment to functional categories. This study provided a comprehensive analysis of gene expression of each A. flavus and F. verticillioides during infection of maize kernels, it identified genes expressed early and late in the infection process, and it provided a grouping of genes of unknown function with similarly expressed defense related genes that could inform selection of new genes as targets in breeding strategies.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Shu, Xiaomei and Livingston, David P., III and Woloshuk, Charles P. and Payne, Gary A.}, year={2017}, month={Dec} }
 @article{niu_payne_woloshuk_2017, title={Involvement of FST1 from Fusarium verticillioides in virulence and transport of inositol}, volume={18}, ISSN={["1364-3703"]}, DOI={10.1111/mpp.12430}, abstractNote={Fumonisin B1 (FB1), a polyketide mycotoxin produced by Fusarium verticillioides during the colonization of maize kernels, is detrimental to human and animal health. FST1 encodes a putative protein with 12 transmembrane domains; however, its function remains unknown. The FST1 gene is highly expressed by the fungus in the endosperm of maize kernels compared with the levels of expression in germ tissues. Previous research has shown that FST1 affects FB1 production, virulence, hydrogen peroxide resistance, hydrophobicity and macroconidia production. Here, we examine the phylogeny of FST1, its expression in a Saccharomyces cerevisiae strain lacking a functional myo-inositol transporter (ITR1) and the effect of amino acid changes in the central loop and C-terminus regions of FST1 on functionality. The results indicate that expression of FST1 in an ITR1 mutant strain restores growth on myo-inositol medium to wild-type levels and restores the inhibitory effects of FB1, suggesting that FST1 can transport both myo-inositol and FB1 into yeast cells. Our results with engineered FST1 also indicate that amino acids in the central loop and C-terminus regions are important for FST1 functionality in both S. cerevisiae and F. verticillioides. Overall, this research has established the first characterized inositol transporter in filamentous fungi and has advanced our knowledge about the global regulatory functions of FST1.}, number={5}, journal={MOLECULAR PLANT PATHOLOGY}, author={Niu, Chenxing and Payne, Gary A. and Woloshuk, Charles P.}, year={2017}, month={Jun}, pages={695–707} }
 @article{majumdar_rajasekaran_sickler_lebar_musungu_fakhoury_payne_geisler_carter-wientjes_wei_et al._2017, title={The Pathogenesis-Related Maize Seed (PRms) Gene Plays a Role in Resistance to Aspergillus flavus Infection and Aflatoxin Contamination}, volume={8}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2017.01758}, abstractNote={Aspergillus flavus is an opportunistic plant pathogen that colonizes and produces the toxic and carcinogenic secondary metabolites, aflatoxins, in oil-rich crops such as maize (Zea mays ssp. mays L.). Pathogenesis-related (PR) proteins serve as an important defense mechanism against invading pathogens by conferring systemic acquired resistance in plants. Among these, production of the PR maize seed protein, ZmPRms (AC205274.3_FG001), has been speculated to be involved in resistance to infection by A. flavus and other pathogens. To better understand the relative contribution of ZmPRms to A. flavus resistance and aflatoxin production, a seed-specific RNA interference (RNAi)-based gene silencing approach was used to develop transgenic maize lines expressing hairpin RNAs to target ZmPRms. Downregulation of ZmPRms in transgenic kernels resulted in a ∼250–350% increase in A. flavus infection accompanied by a ∼4.5–7.5-fold higher accumulation of aflatoxins than control plants. Gene co-expression network analysis of RNA-seq data during the A. flavus-maize interaction identified ZmPRms as a network hub possibly responsible for regulating several downstream candidate genes associated with disease resistance and other biochemical functions. Expression analysis of these candidate genes in the ZmPRms–RNAi lines demonstrated downregulation (vs. control) of a majority of these ZmPRms-regulated genes during A. flavus infection. These results are consistent with a key role of ZmPRms in resistance to A. flavus infection and aflatoxin accumulation in maize kernels.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Majumdar, Rajtilak and Rajasekaran, Kanniah and Sickler, Christine and Lebar, Matthew and Musungu, Bryan M. and Fakhoury, Ahmad M. and Payne, Gary A. and Geisler, Matt and Carter-Wientjes, Carol and Wei, Qijian and et al.}, year={2017}, month={Oct} }
 @article{musungu_bhatnagar_brown_payne_obrian_fakhoury_geisler_2016, title={A Network Approach of Gene Co-expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways}, volume={7}, ISSN={["1664-8021"]}, DOI={10.3389/fgene.2016.00206}, abstractNote={A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus, a link between aflatoxin production and vesicular transport was identified within the network. There was significant interspecies correlation of expression between Z. mays and A. flavus for a subset of 104 Z. mays, and 1942 A. flavus genes. This resulted in an interspecies subnetwork enriched in multiple Z. mays genes involved in the production of ROS. In addition to the ROS from Z. mays, there was enrichment in the vesicular transport pathways and the aflatoxin pathway for A. flavus. Included in these genes, a key aflatoxin cluster regulator, AflS, was found to be co-regulated with multiple Z. mays ROS producing genes within the network, suggesting AflS may be monitoring host ROS levels. The entire GEN for both host and pathogen, and the subset of interspecies correlations, is presented as a tool for hypothesis generation and discovery for events in the early stages of fungal infection of Z. mays by A. flavus.}, journal={FRONTIERS IN GENETICS}, author={Musungu, Bryan M. and Bhatnagar, Deepak and Brown, Robert L. and Payne, Gary A. and OBrian, Greg and Fakhoury, Ahmad M. and Geisler, Matt}, year={2016}, month={Nov} }
 @article{gilbert_mack_payne_bhatnagar_2016, title={Use of functional genomics to assess the climate change impact on Aspergillus flavus and aflatoxin production}, volume={9}, ISSN={["1875-0796"]}, DOI={10.3920/wmj2016.2049}, abstractNote={Aspergillus flavus is an opportunistic and pathogenic fungus that infects several crops of agricultural importance and under certain conditions may produce carcinogenic mycotoxins. Rising global temperatures, disrupted precipitation patterns and increased CO2 levels that are associated with future climate conditions are expected to impact the growth and toxigenic potential of A. flavus. Both laboratory and real world observations have demonstrated this potential, especially when examining the effects of water availability and temperature. Recent experiments have also established that CO2 may also be affecting toxin production. The application of current technologies in the field of functional genomics, including genomic sequencing, RNA-seq, microarray technologies and proteomics have revealed climate change-related, abiotic regulation of the aflatoxin cluster and influence on the plant-fungus interaction. Furthermore, elevated CO2 levels have been shown to impact expression of the aflatoxin biosynthetic r...}, number={5}, journal={WORLD MYCOTOXIN JOURNAL}, author={Gilbert, M. K. and Mack, B. M. and Payne, G. A. and Bhatnagar, D.}, year={2016}, pages={665–672} }
 @article{runa_carbone_bhatnagar_payne_2015, title={Nuclear heterogeneity in conidial populations of Aspergillus flavus}, volume={84}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2015.09.003}, abstractNote={Aspergillus flavus is a major producer of aflatoxin and an opportunistic pathogen for a wide range of hosts. Understanding genotypic and phenotypic variation within strains of A. flavus is important for controlling disease and reducing aflatoxin contamination. A. flavus is multinucleate and predominantly haploid (n) and homokaryotic. Although cryptic heterokaryosis may occur in nature, it is unclear how nuclei in A. flavus influence genetic heterogeneity and if nuclear condition plays a role in fungal ecology. A. flavus mainly reproduces asexually by producing conidia. In order to observe whether conidia are homokaryotic or heterokaryotic, we labeled nuclei of A. flavus using two different nuclear localized fluorescent reporters. The reporter constructs (pYH2A and pCH2B), encode histones HH2A and HH2B fused at the C terminus with either yellow (EYFP) or cyan (ECFP) fluorescent proteins, respectively. The constructs were transformed into the double auxotrophic strain AFC-1 (−pyrG, −argD) to generate a strain containing each reporter construct. By taking advantage of the nutritional requirement for each strain, we were able to generate fusants between FR36 (−argD) expressing yellow fluorescence, and FR46 (−pyr4) expressing cyan fluorescence. Conidia from fusants between FR36 and FR46 showed three types of fluorescence: only EYFP, only ECFP or both EYFP + ECFP. Conidia containing nuclei expressing EYFP + ECFP were separated by Fluorescence-Activated Cell sorting (FACS) and were found to contain both yellow and cyan fluorescent markers in the same nucleus. Further characterization of conidia having only one nucleus but expressing both EYFP + ECFP fluorescence were found to be diploid (2n). Our findings suggest that A. flavus maintains nuclear heterogeneity in conidial populations.}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Runa, Farhana and Carbone, Ignazio and Bhatnagar, Deepak and Payne, Gary A.}, year={2015}, month={Nov}, pages={62–72} }
 @article{shu_livingston_franks_boston_woloshuk_payne_2015, title={Tissue-specific gene expression in maize seeds during colonization by Aspergillus flavus and Fusarium verticillioides}, volume={16}, ISSN={["1364-3703"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84937630553&partnerID=MN8TOARS}, DOI={10.1111/mpp.12224}, abstractNote={Aspergillus flavus and Fusarium verticillioides are fungal pathogens that colonize maize kernels and produce the harmful mycotoxins aflatoxin and fumonisin, respectively. Management practice based on potential host resistance to reduce contamination by these mycotoxins has proven difficult, resulting in the need for a better understanding of the infection process by these fungi and the response of maize seeds to infection. In this study, we followed the colonization of seeds by histological methods and the transcriptional changes of two maize defence-related genes in specific seed tissues by RNA in situ hybridization. Maize kernels were inoculated with either A. flavus or F. verticillioides 21-22 days after pollination, and harvested at 4, 12, 24, 48, 72, 96 and 120 h post-inoculation. The fungi colonized all tissues of maize seed, but differed in their interactions with aleurone and germ tissues. RNA in situ hybridization showed the induction of the maize pathogenesis-related protein, maize seed (PRms) gene in the aleurone and scutellum on infection by either fungus. Transcripts of the maize sucrose synthase-encoding gene, shrunken-1 (Sh1), were observed in the embryo of non-infected kernels, but were induced on infection by each fungus in the aleurone and scutellum. By comparing histological and RNA in situ hybridization results from adjacent serial sections, we found that the transcripts of these two genes accumulated in tissue prior to the arrival of the advancing pathogens in the seeds. A knowledge of the patterns of colonization and tissue-specific gene expression in response to these fungi will be helpful in the development of resistance.}, number={7}, journal={MOLECULAR PLANT PATHOLOGY}, author={Shu, Xiaomei and Livingston, David P., III and Franks, Robert G. and Boston, Rebecca S. and Woloshuk, Charles P. and Payne, Gary A.}, year={2015}, month={Sep}, pages={662–674} }
 @article{niu_payne_woloshuk_2015, title={Transcriptome changes in Fusarium verticillioides caused by mutation in the transporter-like gene FST1}, volume={15}, DOI={10.1186/s12866-015-0427-3}, abstractNote={Fusarium verticillioides causes an important seed disease on maize and produces the fumonisin group of mycotoxins, which are toxic to humans and livestock. A previous study discovered that a gene (FST1) in the pathogen affects fumonisin production and virulence. Although the predicted amino acid sequence of FST1 is similar to hexose transporters, previous experimental evidence failed to prove function. Three new phenotypes were identified that are associated with the FST1 mutant of F. verticillioides (Δfst1), namely reduction in macroconidia production, increased sensitivity to hydrogen peroxide, and reduced mycelial hydrophobicity. A transcriptome comparison of the wild type and strain Δfst1 grown on autoclaved maize kernels for six days identified 2677 genes that were differentially expressed. Through gene ontology analysis, 961 genes were assigned to one of 12 molecular function categories. Sets of down-regulated genes in strain Δfst1 were identified that could account for each of the mutant phenotypes. The study provides evidence that disruption of FST1 causes several metabolic and developmental defects in F. verticillioides. FST1 appears to connect the expression of several gene networks, including those involved in secondary metabolism, cell wall structure, conidiogenesis, virulence, and resistance to reactive oxygen species. The results support our hypothesis that FST1 functions within the framework of environmental sensing.}, journal={BMC Microbiology}, author={Niu, C. X. and Payne, G. A. and Woloshuk, C. P.}, year={2015} }
 @article{reverberi_punelli_scala_scarpari_uva_mentzen_dolezal_woloshuk_pinzari_fabbri_et al._2013, title={Genotypic and Phenotypic Versatility of Aspergillus flavus during Maize Exploitation}, volume={8}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0068735}, abstractNote={Aspergillus flavus is a cosmopolitan fungus able to respond to external stimuli and to shift both its trophic behaviour and the production of secondary metabolites, including that of the carcinogen aflatoxin (AF). To better understand the adaptability of this fungus, we examined genetic and phenotypic responses within the fungus when grown under four conditions that mimic different ecological niches ranging from saprophytic growth to parasitism. Global transcription changes were observed in both primary and secondary metabolism in response to these conditions, particularly in secondary metabolism where transcription of nearly half of the predicted secondary metabolite clusters changed in response to the trophic states of the fungus. The greatest transcriptional change was found between saprophytic and parasitic growth, which resulted in expression changes in over 800 genes in A. flavus. The fungus also responded to growth conditions, putatively by adaptive changes in conidia, resulting in differences in their ability to utilize carbon sources. We also examined tolerance of A. flavus to oxidative stress and found that growth and secondary metabolism were altered in a superoxide dismutase (sod) mutant and an alkyl-hydroperoxide reductase (ahp) mutant of A. flavus. Data presented in this study show a multifaceted response of A. flavus to its environment and suggest that oxidative stress and secondary metabolism are important in the ecology of this fungus, notably in its interaction with host plant and in relation to changes in its lifestyle (i.e. saprobic to pathogenic).}, number={7}, journal={PLOS ONE}, author={Reverberi, Massimo and Punelli, Marta and Scala, Valeria and Scarpari, Marzia and Uva, Paolo and Mentzen, Wieslawa I. and Dolezal, Andrea L. and Woloshuk, Charles and Pinzari, Flavia and Fabbri, Anna A. and et al.}, year={2013}, month={Jul} }
 @article{reverberi_punelli_smith_zjalic_scarpari_scala_cardinali_aspite_pinzari_payne_et al._2012, title={How Peroxisomes Affect Aflatoxin Biosynthesis in Aspergillus Flavus}, volume={7}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0048097}, abstractNote={In filamentous fungi, peroxisomes are crucial for the primary metabolism and play a pivotal role in the formation of some secondary metabolites. Further, peroxisomes are important site for fatty acids β-oxidation, the formation of reactive oxygen species and for their scavenging through a complex of antioxidant activities. Oxidative stress is involved in different metabolic events in all organisms and it occurs during oxidative processes within the cell, including peroxisomal β-oxidation of fatty acids. In Aspergillus flavus, an unbalance towards an hyper-oxidant status into the cell is a prerequisite for the onset of aflatoxin biosynthesis. In our preliminary results, the use of bezafibrate, inducer of both peroxisomal β-oxidation and peroxisome proliferation in mammals, significantly enhanced the expression of pex11 and foxA and stimulated aflatoxin synthesis in A. flavus. This suggests the existence of a correlation among peroxisome proliferation, fatty acids β-oxidation and aflatoxin biosynthesis. To investigate this correlation, A. flavus was transformed with a vector containing P33, a gene from Cymbidium ringspot virus able to induce peroxisome proliferation, under the control of the promoter of the Cu,Zn-sod gene of A. flavus. This transcriptional control closely relates the onset of the antioxidant response to ROS increase, with the proliferation of peroxisomes in A. flavus. The AfP33 transformant strain show an up-regulation of lipid metabolism and an higher content of both intracellular ROS and some oxylipins. The combined presence of a higher amount of substrates (fatty acids-derived), an hyper-oxidant cell environment and of hormone-like signals (oxylipins) enhances the synthesis of aflatoxins in the AfP33 strain. The results obtained demonstrated a close link between peroxisome metabolism and aflatoxin synthesis.}, number={10}, journal={PLOS ONE}, author={Reverberi, Massimo and Punelli, Marta and Smith, Carrie A. and Zjalic, Slaven and Scarpari, Marzia and Scala, Valeria and Cardinali, Giorgia and Aspite, Nicaela and Pinzari, Flavia and Payne, Gary A. and et al.}, year={2012}, month={Oct} }
 @article{joardar_abrams_hostetler_paukstelis_pakala_pakala_zafar_abolude_payne_andrianopoulos_et al._2012, title={Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability}, volume={13}, ISSN={["1471-2164"]}, DOI={10.1186/1471-2164-13-698}, abstractNote={The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25–36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population studies. Despite the conservation of the core genes, the mitochondrial genomes of Aspergillus and Penicillium species examined here exhibit significant amount of interspecies variation. Most of this variation can be attributed to accessory genes and mobile introns, presumably acquired by horizontal gene transfer of mitochondrial plasmids and intron homing.}, journal={BMC GENOMICS}, author={Joardar, Vinita and Abrams, Natalie F. and Hostetler, Jessica and Paukstelis, Paul J. and Pakala, Suchitra and Pakala, Suman B. and Zafar, Nikhat and Abolude, Olukemi O. and Payne, Gary and Andrianopoulos, Alex and et al.}, year={2012}, month={Dec} }
 @article{wu_bhatnagar_bui-klimke_carbone_hellmich_munkvold_paul_payne_takle_2011, title={Climate change impacts on mycotoxin risks in US maize}, volume={4}, ISSN={1875-0710 1875-0796}, url={http://dx.doi.org/10.3920/wmj2010.1246}, DOI={10.3920/wmj2010.1246}, abstractNote={To ensure future food security, it is crucial to understand how potential climate change scenarios will affect agriculture. One key area of interest is how climatic factors, both in the near- and the long-term future, could affect fungal infection of crops and mycotoxin production by these fungi. The objective of this paper is to review the potential impact of climate change on three important mycotoxins that contaminate maize in the United States, and to highlight key research questions and approaches for understanding this impact. Recent climate change analyses that pertain to agriculture and in particular to mycotoxigenic fungi are discussed, with respect to the climatic factors – temperature and relative humidity – at which they thrive and cause severe damage. Additionally, we discuss how climate change will likely alter the life cycles and geographic distribution of insects that are known to facilitate fungal infection of crops.}, number={1}, journal={World Mycotoxin Journal}, publisher={Wageningen Academic Publishers}, author={Wu, F. and Bhatnagar, D. and Bui-Klimke, T. and Carbone, I. and Hellmich, R. and Munkvold, G. and Paul, P. and Payne, G. and Takle, E.}, year={2011}, month={Jan}, pages={79–93} }
 @article{reese_payne_nielsen_woloshuk_2011, title={Gene Expression profile and response to maize kernels by Aspergillus flavus}, volume={101}, ISSN={["1943-7684"]}, DOI={10.1094/phyto-09-10-0261}, abstractNote={Aspergillus flavus causes an ear rot of maize, often resulting in the production of aflatoxin, a potent liver toxin and carcinogen that impacts the health of humans and animals. Many aspects of kernel infection and aflatoxin biosynthesis have been studied but the precise effects of the kernel environment on A. flavus are poorly understood. The goal of this research was to study the fungal response to the kernel environment during colonization. Gene transcription in A. flavus was analyzed by microarrays after growth on kernels of the four developmental stages: blister (R2), milk (R3), dough (R4), and dent (R5). Five days after inoculation, total RNA was isolated from kernels and hybridized to Affymetrix Gene Chip arrays containing probes representing 12,834 A. flavus genes. Statistical comparisons of the expression profile data revealed significant differences that included unique sets of upregulated genes in each kernel stage and six patterns of expression over the four stages. Among the genes expressed in colonized dent kernels were a phytase gene and six putative genes involved in zinc acquisition. Disruption of the phytase gene phy1 resulted in reduced growth on medium containing phytate as the sole source of phosphate. Furthermore, growth of the mutant (Δphy1) was 20% of the wild-type strain when wound inoculated into maize ears. In contrast, no difference was detected in the amount of aflatoxin produced relative to fungal growth, indicating that phy1 does not affect aflatoxin production. The study revealed the genome-wide effects of immature maize kernels on A. flavus and suggest that phytase has a role in pathogenesis.}, number={7}, journal={Phytopathology}, author={Reese, B.N. and Payne, G.A. and Nielsen, D.M. and Woloshuk, C.P.}, year={2011}, pages={797–804} }
 @article{georgianna_fedorova_burroughs_dolezal_bok_horowitz-brown_woloshuk_yu_keller_payne_2010, title={Beyond aflatoxin: four distinct expression patterns and functional roles associated with Aspergillus flavus secondary metabolism gene clusters}, volume={11}, ISSN={["1364-3703"]}, DOI={10.1111/J.1364-3703.2009.00594.X}, abstractNote={Species of Aspergillus produce a diverse array of secondary metabolites, and recent genomic analysis has predicted that these species have the capacity to synthesize many more compounds. It has been possible to infer the presence of 55 gene clusters associated with secondary metabolism in Aspergillus flavus; however, only three metabolic pathways-aflatoxin, cyclopiazonic acid (CPA) and aflatrem-have been assigned to these clusters. To gain an insight into the regulation of and to infer the ecological significance of the 55 secondary metabolite gene clusters predicted in A. flavus, we examined their expression over 28 diverse conditions. Variables included culture medium and temperature, fungal development, colonization of developing maize seeds and misexpression of laeA, a global regulator of secondary metabolism. Hierarchical clustering analysis of expression profiles allowed us to categorize the gene clusters into four distinct clades. Gene clusters for the production of aflatoxins, CPA and seven other unknown compound(s) were identified as belonging to one clade. To further explore the relationships found by gene expression analysis, aflatoxin and CPA production were quantified under five different cell culture environments known to be conducive or nonconducive for aflatoxin biosynthesis and during the colonization of developing maize seeds. Results from these studies showed that secondary metabolism gene clusters have distinctive gene expression profiles. Aflatoxin and CPA were found to have unique regulation, but are sufficiently similar that they would be expected to co-occur in substrates colonized with A. flavus.}, number={2}, journal={MOLECULAR PLANT PATHOLOGY}, author={Georgianna, D. Ryan and Fedorova, Natalie D. and Burroughs, James L. and Dolezal, Andrea L. and Bok, Jin Woo and Horowitz-Brown, Sigal and Woloshuk, Charles P. and Yu, Jiujiang and Keller, Nancy P. and Payne, Gary A.}, year={2010}, month={Mar}, pages={213–226} }
 @article{eller_payne_holland_2010, title={Selection for Reduced Fusarium Ear Rot and Fumonisin Content in Advanced Backcross Maize Lines and Their Topeross Hybrids}, volume={50}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-78650082599&partnerID=MN8TOARS}, DOI={10.2135/cropsci2009.11.0683}, abstractNote={Backcross breeding is an important method to improve elite cultivars for traits controlled by a small number of loci but has been used less frequently to improve quantitatively controlled traits. Resistances to Fusarium ear rot (caused by Fusarium verticillioides (Sacc.) Nirenberg (teleomorph Gibberella moniliformis Wineland)) and contamination by the associated mycotoxin fumonisin in maize (Zea mays L.) are quanti- tatively inherited. We backcrossed the more resistant but unadapted inbred GE440 for four generations to the susceptible but agronomi- cally elite commercial inbred FR1064. A selected set of 19 BC 4 F 1:3 lines had greater resistance to ear rot and fumonisin content than their recur- rent parent FR1064. Topcrosses of the selected lines had greater resistance to Fusarium ear rot and similar grain yield compared to the topcross of the recurrent parent FR1064. We also geno- typed selected lines at DNA markers linked to ear rot and fumonisin resistance quantitative trait loci (QTL) identifi ed in the BC 1 generation of this cross to determine which QTL demon- strated allele frequency shifts due to selection. Markers linked to QTL on chromosomes 1 and 4 inherited the GE440 allele signifi cantly more often than expected by random chance.}, number={6}, journal={CROP SCIENCE}, author={Eller, Magen S. and Payne, Gary A. and Holland, James B.}, year={2010}, pages={2249–2260} }
 @misc{georgianna_payne_2009, title={Genetic regulation of aflatoxin biosynthesis: From gene to genome}, volume={46}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2008.10.011}, abstractNote={Aflatoxins are notorious toxic secondary metabolites known for their impacts on human and animal health, and their effects on the marketability of key grain and nut crops. Understanding aflatoxin biosynthesis is the focus of a large and diverse research community. Concerted efforts by this community have led not only to a well-characterized biosynthetic pathway, but also to the discovery of novel regulatory mechanisms. Common to secondary metabolism is the clustering of biosynthetic genes and their regulation by pathway specific as well as global regulators. Recent data show that arrangement of secondary metabolite genes in clusters may allow for an important global regulation of secondary metabolism based on physical location along the chromosome. Available genomic and proteomic tools are now allowing us to examine aflatoxin biosynthesis more broadly and to put its regulation in context with fungal development and fungal ecology. This review covers our current understanding of the biosynthesis and regulation of aflatoxin and highlights new and emerging information garnered from structural and functional genomics. The focus of this review will be on studies in Aspergillus flavus and Aspergillus parasiticus, the two agronomically important species that produce aflatoxin. Also covered will be the important contributions gained by studies on production of the aflatoxin precursor sterigmatocystin in Aspergillus nidulans.}, number={2}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Georgianna, D. Ryan and Payne, Gary A.}, year={2009}, month={Feb}, pages={113–125} }
 @article{nicholson_koulman_monahan_pritchard_payne_scott_2009, title={Identification of Two Aflatrem Biosynthesis Gene Loci in Aspergillus flavus and Metabolic Engineering of Penicillium paxilli To Elucidate Their Function}, volume={75}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.02146-08}, abstractNote={ABSTRACT Aflatrem is a potent tremorgenic toxin produced by the soil fungus Aspergillus flavus, and a member of a structurally diverse group of fungal secondary metabolites known as indole-diterpenes. Gene clusters for indole-diterpene biosynthesis have recently been described in several species of filamentous fungi. A search of Aspergillus complete genome sequence data identified putative aflatrem gene clusters in the genomes of A. flavus and Aspergillus oryzae. In both species the genes for aflatrem biosynthesis cluster at two discrete loci; the first, ATM1, is telomere proximal on chromosome 5 and contains a cluster of three genes, atmG, atmC, and atmM, and the second, ATM2, is telomere distal on chromosome 7 and contains five genes, atmD, atmQ, atmB, atmA, and atmP. Reverse transcriptase PCR in A. flavus demonstrated that aflatrem biosynthesis transcript levels increased with the onset of aflatrem production. Transfer of atmP and atmQ into Penicillium paxilli paxP and paxQ deletion mutants, known to accumulate paxilline intermediates paspaline and 13-desoxypaxilline, respectively, showed that AtmP is a functional homolog of PaxP and that AtmQ utilizes 13-desoxypaxilline as a substrate to synthesize aflatrem pathway-specific intermediates, paspalicine and paspalinine. We propose a scheme for aflatrem biosynthesis in A. flavus based on these reconstitution experiments in P. paxilli and identification of putative intermediates in wild-type cultures of A. flavus.}, number={23}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Nicholson, Matthew J. and Koulman, Albert and Monahan, Brendon J. and Pritchard, Beth L. and Payne, Gary A. and Scott, Barry}, year={2009}, month={Dec}, pages={7469–7481} }
 @misc{cleveland_yu_fedorova_bhatnagar_payne_nierman_bennett_2009, title={Potential of Aspergillus flavus genomics for applications in biotechnology}, volume={27}, ISSN={["1879-3096"]}, DOI={10.1016/j.tibtech.2008.11.008}, abstractNote={Aspergillus flavus is a common saprophyte and opportunistic pathogen that produces numerous secondary metabolites. The primary objectives of the A. flavus genomics program are to reduce and eliminate aflatoxin contamination in food and feed and to discover genetic factors that contribute to plant and animal pathogenicity. A. flavus expressed sequence tags (ESTs) and whole-genome sequencing have been completed. Annotation of the A. flavus genome has revealed numerous genes and gene clusters that are potentially involved in the formation of aflatoxin and other secondary metabolites, as well as in the degradation of complex carbohydrate polymers. Analysis of putative secondary metabolism pathways might facilitate the discovery of new compounds with pharmaceutical properties, as well as new enzymes for biomass degradation.}, number={3}, journal={TRENDS IN BIOTECHNOLOGY}, author={Cleveland, Thomas E. and Yu, Jiujiang and Fedorova, Natalie and Bhatnagar, Deepak and Payne, Gary A. and Nierman, William C. and Bennett, Joan W.}, year={2009}, month={Mar}, pages={151–157} }
 @article{yu_payne_nierman_machida_bennett_campbell_robens_bhatnagar_dean_cleveland_2008, title={Aspergillus flavus genomics as a tool for studying the mechanism of aflatoxin formation}, volume={25}, ISSN={["1944-0057"]}, DOI={10.1080/02652030802213375}, abstractNote={Aspergillus flavus is a weak pathogen that infects plants, animals and humans. When it infects agricultural crops, however, it produces one of the most potent carcinogens known (aflatoxins). To devise strategies to control aflatoxin contamination of pre-harvest agricultural crops and post-harvest grains during storage, we launched the A. flavus genomics program. The major objective of this program is the identification of genes involved in aflatoxin biosynthesis and regulation, as well as in pathogenicity, to gain a better understanding of the mechanism of aflatoxin formation. The sequencing of A. flavus whole genome has been completed. Initial annotation of the sequence revealed that there are about 13,071 genes in the A. flavus genome. Genes which potentially encode for enzymes involved in secondary metabolite production in the A. flavus genome have been identified. Preliminary comparative genome analysis of A. flavus with A. oryzae is summarized here.}, number={9}, journal={FOOD ADDITIVES AND CONTAMINANTS PART A-CHEMISTRY ANALYSIS CONTROL EXPOSURE & RISK ASSESSMENT}, author={Yu, Jiujiang and Payne, Gary A. and Nierman, William C. and Machida, Masayuki and Bennett, Joan W. and Campbell, Bruce C. and Robens, Jane F. and Bhatnagar, Deepak and Dean, Ralph A. and Cleveland, Thomas E.}, year={2008}, pages={1152–1157} }
 @article{eller_holland_payne_2008, title={BREEDING FOR IMPROVED RESISTANCE TO FUMONISIN CONTAMINATION IN MAIZE}, volume={27}, ISSN={["1556-9551"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77956939673&partnerID=MN8TOARS}, DOI={10.1080/15569540802450326}, abstractNote={Maize grain infected by Fusarium verticillioides may contain the mycotoxin fumonisin, which is associated with livestock and human diseases. To reduce levels of fumonisin in grain, efforts are under way to identify sources of maize with increased resistance to fungal infection and fumonisin contamination. Field and laboratory techniques have been developed to measure both Fusarium ear rot and fumonisin contamination. Application of these techniques has led to the identification of resistant maize lines and facilitated genetic analysis of resistance to ear rot and fumonisin accumulation. Maize genetics and breeding studies are guiding strategies to improve resistance to fumonisin accumulation.}, number={3-4}, journal={TOXIN REVIEWS}, author={Eller, Magen S. and Holland, James B. and Payne, Gary A.}, year={2008}, pages={371–389} }
 @misc{holmes_boston_payne_2008, title={Diverse inhibitors of aflatoxin biosynthesis}, volume={78}, ISSN={["1432-0614"]}, DOI={10.1007/s00253-008-1362-0}, number={4}, journal={APPLIED MICROBIOLOGY AND BIOTECHNOLOGY}, author={Holmes, Robert A. and Boston, Rebecca S. and Payne, Gary A.}, year={2008}, month={Mar}, pages={559–572} }
 @article{machida_terabayashi_sano_yamane_tamano_payne_yu_cleveland_nierman_2008, title={Genomics of industrial Aspergilli and comparison with toxigenic relatives}, volume={25}, ISSN={["0265-203X"]}, DOI={10.1080/02652030802273114}, abstractNote={Aspergillus oryzae has been used in Japanese fermentation industries for more than a thousand years. The species produces large amounts of various hydrolytic enzymes and has been successfully applied to modern biotechnology. The size of the A. oryzae genome (37.5 Mb) is very close to that of A. flavus and A. niger, and 20–30% larger than that of either A. nidulans or A. fumigatus. A. oryzae and A. flavus have exactly the same number of aspartic proteinase genes, of which each orthologous pair shares highly conserved amino acid sequences. Synteny analysis with A. fumigatus and A. nidulans showed that the A. oryzae genome has a mosaic structure consisting of syntenic and non-syntenic blocks. In the microorganisms to be compared, the density of the genes having homologs was obviously higher on the syntenic than on the non-syntenic blocks. Expression analysis by the DNA microarray supported the significantly lower expression of genes on the non-syntenic than on the syntenic blocks.}, number={9}, journal={FOOD ADDITIVES AND CONTAMINANTS PART A-CHEMISTRY ANALYSIS CONTROL EXPOSURE & RISK ASSESSMENT}, author={Machida, Masayuki and Terabayashi, Yoshinobu and Sano, Motoaki and Yamane, Noriko and Tamano, Koichi and Payne, Gary A. and Yu, Jiujiang and Cleveland, Thomas E. and Nierman, William C.}, year={2008}, pages={1147–1151} }
 @article{eller_robertson-hoyt_payne_holland_2008, title={Grain yield and fusarium ear rot of maize hybrids developed from lines with varying levels of resistance}, volume={53}, number={3-4}, journal={Maydica}, author={Eller, M. S. and Robertson-Hoyt, L. A. and Payne, G. A. and Holland, J. B.}, year={2008}, pages={231–237} }
 @article{johnson_egner_obrian_glassbrook_roebuck_sutter_payne_kensler_groopman_2008, title={Quantification of urinary aflatoxin B-1 dialdehyde metabolites formed by aflatoxin aldehyde reductase using isotope dilution tandem mass spectrometry}, volume={21}, ISSN={["0893-228X"]}, DOI={10.1021/tx700397n}, abstractNote={The aflatoxin B 1 aldehyde reductases (AFARs), inducible members of the aldo-keto reductase superfamily, convert aflatoxin B 1 dialdehyde derived from the exo- and endo-8,9-epoxides into a number of reduced alcohol products that might be less capable of forming covalent adducts with proteins. An isotope dilution tandem mass spectrometry method for quantification of the metabolites, C-8 monoalcohol, dialcohol, and C-6a monoalcohol, was developed to ascertain their possible role as urinary biomarkers for application to chemoprevention investigations. This method uses a novel (13)C 17-aflatoxin B 1 dialcohol internal standard, synthesized from (13)C 17-aflatoxin B 1 biologically produced by Aspergillus flavus. Chromatographic standards of the alcohols were generated through sodium borohydride reduction of the aflatoxin B 1 dialdehyde. This method was then explored for sensitivity and specificity in urine samples of aflatoxin B 1-dosed rats that were pretreated with 3 H-1,2-dithiole-3-thione to induce the expression of AKR7A1, a rat isoform of AFAR. One of the two known monoalcohols and the dialcohol metabolite were detected in all urine samples. The concentrations were 203.5 +/- 39.0 ng of monoalcohol C-6a/mg of urinary creatinine and 10.0 +/- 1.0 ng of dialcohol/mg of creatinine (mean +/- standard error). These levels represented about 8.0 and 0.4% of the administered aflatoxin B 1 dose that was found in the urine at 24 h, respectively. Thus, this highly sensitive and specific isotope dilution method is applicable to in vivo quantification of urinary alcohol products produced by AFAR. Heretofore, the metabolic fate of the 8,9-epoxides that are critical for aflatoxin toxicities has been measured by biomarkers of lysine-albumin adducts, hepatic and urinary DNA adducts, and urinary mercapturic acids. This urinary detection of the alcohol products directly contributes to the goal of mass balancing the fate of the bioreactive 8,9-epoxides of AFB 1 in vivo.}, number={3}, journal={CHEMICAL RESEARCH IN TOXICOLOGY}, author={Johnson, Denise N. and Egner, Patricia A. and OBrian, Greg and Glassbrook, Norman and Roebuck, Bill D. and Sutter, Thomas R. and Payne, Gary A. and Kensler, Thomas W. and Groopman, John D.}, year={2008}, month={Mar}, pages={752–760} }
 @article{georgianna_hawkridge_muddiman_payne_2008, title={Temperature-dependent regulation of proteins in Aspergillus flavus: Whole organism stable isotope labeling by amino acids}, volume={7}, ISSN={["1535-3907"]}, DOI={10.1021/pr8001047}, abstractNote={Stable isotope labeling by amino acids in cell culture (SILAC) has been used in many different organisms including yeast, mammalian cells, and Arabidopsis cell culture. We present an adaptation of this method to quickly quantify protein changes in response to environmental stimuli regulating biosynthesis of the carcinogen aflatoxin in the fungus Aspergillus flavus. Changes in relative protein concentrations in response to temperature were quantified and compared to changes in aflatoxin biosynthesis and the transcription of the aflatoxin biosynthetic genes. In a comparison between conducive (28 degrees C) and nonconducive (37 degrees C) temperatures for aflatoxin biosynthesis, 31 proteins were found to be more abundant at 37 degrees C and 18 more abundant at 28 degrees C. The change in expression of the aflatoxin pathway enzymes closely followed the strong repression of both aflatoxin biosynthesis and transcription of the aflatoxin pathway genes observed at 37 degrees C. Transcripts corresponding to the 379 proteins quantified by SILAC were analyzed using microarrays, but their expression did not always correlate well with transcript levels of encoding genes. This is the first reported labeling of a multicellular free-living prototroph using the SILAC procedure to compare (13)C(6)-arginine-labeled samples to (12)C(6)-arginine-labeled samples for quantitative proteomics. The data presented shows the utility of this procedure in quantifying changes in protein expression in response to environmental stimuli.}, number={7}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Georgianna, D. Ryan and Hawkridge, Adam M. and Muddiman, David C. and Payne, Gary A.}, year={2008}, month={Jul}, pages={2973–2979} }
 @article{smith_robertson_yates_nielsen_brown_dean_payne_2008, title={The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus}, volume={54}, ISSN={0172-8083 1432-0983}, url={http://dx.doi.org/10.1007/s00294-008-0215-9}, DOI={10.1007/s00294-008-0215-9}, number={5}, journal={Current Genetics}, publisher={Springer Science and Business Media LLC}, author={Smith, Carrie A. and Robertson, Dominique and Yates, Bethan and Nielsen, Dahlia M. and Brown, Doug and Dean, Ralph A. and Payne, Gary A.}, year={2008}, month={Sep}, pages={241–269} }
 @article{collier_hawkridge_georgianna_payne_muddiman_2008, title={Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer}, volume={80}, ISSN={["1520-6882"]}, DOI={10.1021/ac800254z}, abstractNote={Online liquid chromatography-mass spectrometric (LC-MS) analysis of intact proteins (i.e., top-down proteomics) is a growing area of research in the mass spectrometry community. A major advantage of top-down MS characterization of proteins is that the information of the intact protein is retained over the vastly more common bottom-up approach that uses protease-generated peptides to search genomic databases for protein identification. Concurrent to the emergence of top-down MS characterization of proteins has been the development and implementation of the stable isotope labeling of amino acids in cell culture (SILAC) method for relative quantification of proteins by LC-MS. Herein we describe the qualitative and quantitative top-down characterization of proteins derived from SILAC-labeled Aspergillus flavus using nanoflow reversed-phase liquid chromatography directly coupled to a linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (nLC-LTQ-FTICR-MS). A. flavus is a toxic filamentous fungus that significantly impacts the agricultural economy and human health. SILAC labeling improved the confidence of protein identification, and we observed 1318 unique protein masses corresponding to 659 SILAC pairs, of which 22 were confidently identified. However, we have observed some limiting issues with regard to protein quantification using top-down MS/MS analyses of SILAC-labeled proteins. The role of SILAC labeling in the presence of competing endogenously produced amino acid residues and its impact on quantification of intact species are discussed in detail.}, number={13}, journal={ANALYTICAL CHEMISTRY}, author={Collier, Timothy S. and Hawkridge, Adam M. and Georgianna, D. Ryan and Payne, Gary A. and Muddiman, David C.}, year={2008}, month={Jul}, pages={4994–5001} }
 @article{cary_obrian_nielsen_nierman_harris-coward_yu_bhatnagar_cleveland_payne_calvo_2007, title={Elucidation of veA-dependent genes associated with aflatoxin and sclerotial production in Aspergillus flavus by functional genomics}, volume={76}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/s00253-007-1081-y}, DOI={10.1007/s00253-007-1081-y}, number={5}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Cary, J. W. and OBrian, G. R. and Nielsen, D. M. and Nierman, W. and Harris-Coward, P. and Yu, J. and Bhatnagar, D. and Cleveland, T. E. and Payne, G. A. and Calvo, A. M.}, year={2007}, month={Jul}, pages={1107–1118} }
 @article{du_obrian_payne_2007, title={Function and regulation of aflJ in the accumulation of aflatoxin early pathway intermediate in Aspergillus flavus}, volume={24}, ISSN={["0265-203X"]}, DOI={10.1080/02652030701513826}, abstractNote={aflJ resides within the aflatoxin biosynthetic gene cluster adjacent to the pathway regulatory gene aflR and is involved in aflatoxin production, but its function is unknown. Over-expression of aflJ in the aflatoxin-producing strain 86-10 resulted in increased aflatoxin. In an effort to study the function and regulation of aflJ, strain 649-1 lacking the entire biosynthetic cluster was transformed with either reporter constructs, expression constructs, or cosmid clones and analysed for gene expression or metabolite accumulation. Over-expression of aflJ did not result in elevated transcription of ver-1, omtA or aflR. To determine if over-expression of aflJ leads to an increase in early pathway intermediates, strain 649-1 was transformed with cosmid 5E6 and either gpdA::aflJ alone, gpdA::aflR alone, or aflJ and aflR together. Cosmid 5E6 contains the genes pksA, nor-1, fas-1, and fas-2, which are required for the biosynthesis of the early pathway intermediate averantin. 649-1 transformants containing 5E6 alone produced no detectable averantin. In contrast, 5E6 transformants with gpdA::aflR produced averantin, but only half as much as those transformants containing both aflR and aflJ. Northern blot analysis showed that 5E6 transformants containing both aflR and aflJ had five times more pksA transcripts and four times more nor-1 transcripts than 5E6 transformants containing gpdA::aflR alone. Further, aflJ transcription was regulated by aflR. Over-expression of aflR resulted in elevated aflJ transcription. aflJ appears to modulate the regulation of early genes in aflatoxin biosynthesis.}, number={10}, journal={FOOD ADDITIVES AND CONTAMINANTS}, author={Du, W. and Obrian, G. R. and Payne, G. A.}, year={2007}, pages={1043–1050} }
 @article{yuy_ronningy_wilkinsony_campbell_payne_bhatnagar_cleveland_nierman_2007, title={Gene profiling for studying the mechanism of aflatoxin biosynthesis in Aspergillus flavus and A-parasiticus}, volume={24}, ISSN={["1944-0057"]}, DOI={10.1080/02652030701513800}, abstractNote={Aflatoxins are toxic and carcinogenic polyketide metabolites produced by certain fungal species, including Aspergillus flavus and A. parasiticus. Many internal and external factors, such as nutrition and environment affect aflatoxin biosynthesis; therefore, we analyzed the transcriptome of A. flavus using expressed sequence tags (ESTs) from a normalized cDNA expression library constructed from mycelia harvested under several conditions. A total of 7218 unique ESTs were identified from 26 110 sequenced cDNA clones. Functional classifications were assigned to these ESTs and genes, potentially involved in the aflatoxin contamination process, were identified. Based on this EST sequence information, a genomic DNA amplicon microarray was constructed at The Institute for Genomic Research (TIGR). To identify potential regulatory networks controlling aflatoxin contamination in food and feeds, gene expression profiles in aflatoxin-supportive media versus non-aflatoxin-supportive media were evaluated in A. flavus and A. parasiticus. Genes consistently expressed in several aflatoxin-supportive media are reported. †Yu, Ronning and Wilkinson contributed equally to this work.}, number={10}, journal={FOOD ADDITIVES AND CONTAMINANTS PART A-CHEMISTRY ANALYSIS CONTROL EXPOSURE & RISK ASSESSMENT}, author={Yuy, Jiujiang and Ronningy, Catherine M. and Wilkinsony, Jeffery R. and Campbell, Bruce C. and Payne, Gary A. and Bhatnagar, Deepak and Cleveland, Thomas E. and Nierman, William C.}, year={2007}, pages={1035–1042} }
 @article{he_price_obrian_georgianna_payne_2007, title={Improved protocols for functional analysis in the pathogenic fungus Aspergillus flavus}, volume={7}, ISSN={["1471-2180"]}, DOI={10.1186/1471-2180-7-104}, abstractNote={An available whole genome sequence for Aspergillus flavus provides the opportunity to characterize factors involved in pathogenicity and to elucidate the regulatory networks involved in aflatoxin biosynthesis. Functional analysis of genes within the genome is greatly facilitated by the ability to disrupt or mis-express target genes and then evaluate their result on the phenotype of the fungus. Large-scale functional analysis requires an efficient genetic transformation system and the ability to readily select transformants with altered expression, and usually requires generation of double (or multi) gene deletion strains or the use of prototrophic strains. However, dominant selectable markers, an efficient transformation system and an efficient screening system for transformants in A. flavus are absent.The efficiency of the genetic transformation system for A. flavus based on uracil auxotrophy was improved. In addition, A. flavus was shown to be sensitive to the antibiotic, phleomycin. Transformation of A. flavus with the ble gene for resistance to phleomycin resulted in stable transformants when selected on 100 mug/ml phleomycin. We also compared the phleomycin system with one based on complementation for uracil auxotrophy which was confirmed by uracil and 5-fluoroorotic acid selection and via transformation with the pyr4 gene from Neurospora crassa and pyrG gene from A. nidulans in A. flavus NRRL 3357. A transformation protocol using pyr4 as a selectable marker resulted in site specific disruption of a target gene. A rapid and convenient colony PCR method for screening genetically altered transformants was also developed in this study.We employed phleomycin resistance as a new positive selectable marker for genetic transformation of A. flavus. The experiments outlined herein constitute the first report of the use of the antibiotic phleomycin for transformation of A. flavus. Further, we demonstrated that this transformation protocol could be used for directed gene disruption in A. flavus. The significance of this is twofold. First, it allows strains to be transformed without having to generate an auxotrophic mutation, which is time consuming and may result in undesirable mutations. Second, this protocol allows for double gene knockouts when used in conjunction with existing strains with auxotrophic mutations. To further facilitate functional analysis in this strain we developed a colony PCR-based method that is a rapid and convenient method for screening genetically altered transformants. This work will be of interest to those working on molecular biology of aflatoxin metabolism in A. flavus, especially for functional analysis using gene deletion and gene expression.}, journal={BMC MICROBIOLOGY}, author={He, Zhu-Mei and Price, Michael S. and OBrian, Gregory R. and Georgianna, D. Ryan and Payne, Gary A.}, year={2007}, month={Nov} }
 @article{robertson-hoyt_betran_payne_white_isakeit_maragos_molnar_holland_2007, title={Relationships among resistances to Fusarium and Aspergillus ear rots and contamination by fumonisin and aflatoxin in maize}, volume={97}, ISSN={["1943-7684"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33847337945&partnerID=MN8TOARS}, DOI={10.1094/PHYTO-97-3-0311}, abstractNote={ABSTRACT Fusarium verticillioides, F. proliferatum, and Aspergillus flavus cause ear rots of maize and contaminate the grain with mycotoxins (fumonisin or aflatoxin). The objective of this study was to investigate the relationships between resistance to Fusarium and Aspergillus ear rots and fumonisin and aflatoxin contamination. Based on a previous study of 143 recombinant inbred lines from the cross NC300 x B104, 24 lines with the highest and 24 lines with the lowest mean fumonisin concentration were selected for further evaluation. Paired plots of each line were inoculated with F. verticillioides and F. proliferatum or with A. flavus in replicated trials in 2004 and 2005 in Clayton, NC, and College Station, TX. The low-fumonisin group had significantly lower levels of fumonisin, aflatoxin, and Fusarium and Aspergillus ear rots. Across year-location environments, all four traits were significantly correlated; the genotypic correlation (r(G)) ranged from r(G) = 0.88 (aflatoxin and Aspergillus ear rot) to r(G) = 0.99 (Fusarium and Aspergillus ear rots). Quantitative trait loci (QTLs) were identified and their effects estimated. Two QTLs affected both toxin concentrations, one QTL affected both ear rots, and one QTL affected Aspergillus and Fusarium rots and fumonisin. These results suggest that at least some of the genes involved in resistance to ear rots and mycotoxin contamination are identical or genetically linked.}, number={3}, journal={PHYTOPATHOLOGY}, author={Robertson-Hoyt, Leilani A. and Betran, Javier and Payne, Gary A. and White, Don G. and Isakeit, Thomas and Maragos, Chris M. and Molnar, Terence L. and Holland, James B.}, year={2007}, month={Mar}, pages={311–317} }
 @article{robertson-hoyt_kleinschmidt_white_payne_maragos_holland_2007, title={Relationships of resistance to Fusarium ear rot and fumonisin contamination with agronomic performance of maize}, volume={47}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-35348855713&partnerID=MN8TOARS}, DOI={10.2135/cropsci2006.10.0676}, abstractNote={Resistance to Fusarium ear rot [caused by Fusarium verticillioides (Sacc.) Nirenberg (synonym F. moniliforme Sheldon) (teleomorph: Gibberella moniliformis) and F. proliferatum (Matsushima) Nirenberg (teleomorph: G. intermedia)] and fumonisin contamination is heritable and controlled by at least 11 gene regions in a maize (Zea mays L.) population created by backcrossing the highly resistant donor line, GE440, to the susceptible but commercially successful recurrent parent line, FR1064. The relationship between resistances to Fusarium ear rot and fumonisin contamination and agronomic performance has not been reported. Therefore, the objective of this study was to examine the relationship between disease resistance and agronomic utility in this population by measuring resistances to Fusarium ear rot and fumonisin contamination in BC 1 F 1:2 lines, and yield and agronomic performance in topcrosses of these lines. Fumonisin contamination was not correlated with yield, but two fumonisin quantitative trait loci (QTL) mapped to similar positions as yield QTL. Fusarium ear rot had a small positive correlation with topcross yield (r = 0.29), but QTL for the two traits mapped to distinct genomic positions. Similar results for other traits indicate that QTL can contribute in opposite directions to the overall genetic correlations between traits and that some trait correlations arise in the absence of detectable QTL effects on both traits. In general, no strong relationships were observed between disease resistance traits and agronomic traits, thus selection for increased resistance should not unduly affect agronomic performance.}, number={5}, journal={CROP SCIENCE}, author={Robertson-Hoyt, Leilani A. and Kleinschmidt, Craig E. and White, Don G. and Payne, Gary A. and Maragos, Chris M. and Holland, James B.}, year={2007}, pages={1770–1778} }
 @article{smith_woloshuk_robertson_payne_2007, title={Silencing of the aflatoxin gene cluster in a diploid strain of Aspergillus flavus is suppressed by ectopic aflR expression}, volume={176}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.107.073460}, abstractNote={Aflatoxins are toxic secondary metabolites produced by a 70-kb cluster of genes in Aspergillus flavus. The cluster genes are coordinately regulated and reside as a single copy within the genome. Diploids between a wild-type strain and a mutant (649) lacking the aflatoxin gene cluster fail to produce aflatoxin or transcripts of the aflatoxin pathway genes. This dominant phenotype is rescued in diploids between a wild-type strain and a transformant of the mutant containing an ectopic copy of aflR, the transcriptional regulator of the aflatoxin biosynthetic gene cluster. Further characterization of the mutant showed that it is missing 317 kb of chromosome III, including the known genes for aflatoxin biosynthesis. In addition, 939 kb of chromosome II is present as a duplication on chromosome III in the region previously containing the aflatoxin gene cluster. The lack of aflatoxin production in the diploid was not due to a unique or a mis-expressed repressor of aflR. Instead a form of reversible silencing based on the position of aflR is likely preventing the aflatoxin genes from being expressed in 649 × wild-type diploids. Gene expression analysis revealed the silencing effect is specific to the aflatoxin gene cluster.}, number={4}, journal={GENETICS}, author={Smith, Carrie A. and Woloshuk, Charles P. and Robertson, Dominique and Payne, Gary A.}, year={2007}, month={Aug}, pages={2077–2086} }
 @article{obrian_georgianna_wilkinson_yu_abbas_bhatnagar_cleveland_nierman_payne_2007, title={The effect of elevated temperature on gene transcription and aflatoxin biosynthesis}, volume={99}, ISSN={["0027-5514"]}, DOI={10.3852/mycologia.99.2.232}, abstractNote={The molecular regulation of aflatoxin biosynthesis is complex and influenced by several environmental conditions; one of these is temperature. Aflatoxins are produced optimally at 28-30 C, and production decreases as temperatures approach 37 C, the optimum temperature for fungal growth. To better characterize the influence of temperature on aflatoxin biosynthesis, we monitored the accumulation of aflatoxin and the expression of more than 5000 genes in Aspergillus flavus at 28 C and 37 C. A total of 144 genes were expressed differentially (P < 0.001) between the two temperatures. Among the 103 genes more highly expressed at 28 C, approximately 25% were involved in secondary metabolism and about 30% were classified as hypothetical. Genes encoding a catalase and superoxide dismutase were among those more highly expressed at 37 C. As anticipated we also found that all the aflatoxin biosynthetic genes were much more highly expressed at 28 C relative to 37 C. To our surprise expression of the pathway regulatory genes aflR and aflS, as well as aflR antisense, did not differ between the two temperatures. These data indicate that the failure of A. flavus to produce aflatoxin at 37 C is not due to lack of transcription of aflR or aflS. One explanation is that AFLR is nonfunctional at high temperatures. Regardless, the factor(s) sensing the elevated temperatures must be acute. When aflatoxin-producing cultures are transferred to 37 C they immediately stop producing aflatoxin.}, number={2}, journal={MYCOLOGIA}, author={OBrian, G. R. and Georgianna, D. R. and Wilkinson, J. R. and Yu, J. and Abbas, H. K. and Bhatnagar, D. and Cleveland, T. E. and Nierman, W. and Payne, G. A.}, year={2007}, pages={232–239} }
 @article{rokas_payne_fedorova_baker_machida_yu_georgianna_dean_bhatnagar_cleveland_et al._2007, title={What can comparative genomics tell us about species concepts in the genus Aspergillus?}, ISSN={["1872-9797"]}, DOI={10.3114/sim.2007.59.02}, abstractNote={Understanding the nature of species” boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intraspecific comparisons, whereas the other two deal with interspecific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus - N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species.}, number={59}, journal={STUDIES IN MYCOLOGY}, author={Rokas, A. and Payne, G. and Fedorova, N. D. and Baker, S. E. and Machida, M. and Yu, J. and Georgianna, D. Ryan and Dean, Ralph A. and Bhatnagar, Deepak and Cleveland, T. E. and et al.}, year={2007}, pages={11–17} }
 @article{robertson_kleinschmidt_white_payne_maragos_holland_2006, title={Heritabilities and correlations of fusarium ear rot resistance and fumonisin contamination resistance in two maize populations}, volume={46}, ISSN={["1435-0653"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-32344440659&partnerID=MN8TOARS}, DOI={10.2135/cropsci2005.0139}, abstractNote={Fusarium verticillioides (Sacc.) Nirenberg (synonym F. moniliforme Sheldon) (teleomorph: Gibberella moniliformis )a ndF. proliferatum (Matsushima)Nirenberg (teleomorph:G. intermedia) are fungalpathogens of maize (Zea mays L.) that cause ear rot and contaminate grain with fumonisins, a family of mycotoxins that adversely affect animal and human health. The objective of this study was to estimate heritabilities of and genotypic and phenotypic correlations between fumonisin concentration, ear rot, and flowering time in two maize populations. In the (GE440 3 FR1064) 3 FR1064 backcross population, the genotypic and phenotypic correlations between ear rot and fumonisin concentration were0.96and0.40,respectively.Heritabilityestimatedonanentrymean basis was 0.75 for fumonisin concentration and 0.47 for ear rot resistance. In the NC300 3 B104 recombinant inbred line population, the genotypic and phenotypic correlations between ear rot and fumonisin concentration were 0.87 and 0.64, respectively. Heritability estimated on an entry mean basis was 0.86 for fumonisin concentration and 0.80 for ear rot resistance. Correlations between fumonisin concentration and silking date were not significant in either population, and correlations between ear rot resistance and silking date were small (less than 0.30) in both populations. Moderate to high heritabilities and strong genetic correlations between ear rot and fumonisin concentration suggest that selection for reduced ear rot should frequently identify lines with reduced fumonisin concentration. Ear rot can be screened visually and so is less costly and less time-consuming to evaluate than laboratory assays for fumonisin concentration.}, number={1}, journal={CROP SCIENCE}, author={Robertson, LA and Kleinschmidt, CE and White, DG and Payne, GA and Maragos, CM and Holland, JB}, year={2006}, pages={353–361} }
 @article{johansson_whitaker_hagler_bowman_slate_payne_2006, title={Predicting aflatoxin and fumonisin in shelled corn lots sing poor-quality grade components}, volume={89}, number={2}, journal={Journal of AOAC International}, author={Johansson, A. S. and Whitaker, T. B. and Hagler, W. M. and Bowman, D. T. and Slate, A. B. and Payne, G.}, year={2006}, pages={433–440} }
 @article{robertson-hoyt_jines_balint-kurti_kleinschmidt_white_payne_maragos_molnar_holland_2006, title={QTL mapping for fusarium ear rot and fumonisin contamination resistance in two maize populations}, volume={46}, DOI={10.2135/cropsci205.12-0450}, number={4}, journal={Crop Science}, author={Robertson-Hoyt, L. A. and Jines, M. P. and Balint-Kurti, Peter and Kleinschmidt, C. E. and White, D. G. and Payne, G. A. and Maragos, C. M. and Molnar, T. L. and Holland, J. B.}, year={2006}, pages={1734–1743} }
 @article{price_yu_nierman_kim_pritchard_jacobus_bhatnagar_cleveland_payne_2006, title={The aflatoxin pathway regulator AfIR induces gene transcription inside and outside of the aflatoxin biosynthetic cluster}, volume={255}, ISSN={["1574-6968"]}, DOI={10.1111/j.1574-6968.2005.00084.x}, abstractNote={Aflatoxin contamination of food and feed is a major concern due to the carcinogenic properties of this mycotoxin. Previous studies using classical approaches have identified a cluster of genes responsible for aflatoxin production under the control of the pathway-specific transcriptional regulator aflR, but it is unknown whether aflR controls expression of other genes within the genome. Transcription profiling comparing wild type and DeltaaflR strains of Aspergillus parasiticus grown under conditions conducive for aflatoxin production identified only 23 upregulated genes in the wild type. These included 20 genes in the aflatoxin biosynthetic cluster, and three additional genes outside the aflatoxin biosynthetic cluster (nadA, hlyC, and niiA), all with AflR binding sites. This report is the first to demonstrate genes outside the biosynthetic cluster as being associated with aflR expression.}, number={2}, journal={FEMS MICROBIOLOGY LETTERS}, author={Price, MS and Yu, JJ and Nierman, WC and Kim, HS and Pritchard, B and Jacobus, CA and Bhatnagar, D and Cleveland, TE and Payne, GA}, year={2006}, month={Feb}, pages={275–279} }
 @article{payne_nierman_wortman_pritchard_brown_dean_bhatnagar_cleveland_machida_yu_2006, title={Whole genome comparison of Aspergillus flavus and A-oryzae}, volume={44}, ISSN={["1369-3786"]}, DOI={10.1080/13693780600835716}, abstractNote={Aspergillus flavus is a plant and animal pathogen that also produces the potent carcinogen aflatoxin. Aspergillus oryzae is a closely related species that has been used for centuries in the food fermentation industry and is Generally Regarded As Safe (GRAS). Whole genome sequences for these two fungi are now complete, providing us with the opportunity to examine any genomic differences that may explain the different ecological niches of these two fungi, and perhaps to identify pathogenicity factors in A. flavus. These two fungi are very similar in genome size and number of predicted genes. The estimated genome size (36·8 Mb) and predicted number of genes (12 197) for A. flavus is similar to that of A. oryzae (36·7 Mb and 12 079, respectively). These two fungi have significantly larger genomes than Aspergillus nidulans (30·1) and Aspergillus fumigatus (29·4). The A. flavus and A. oryzae genomes are enriched in genes for secondary metabolism, but do not differ greatly from one another in the predicted number of polyketide synthases, nonribosomal peptide synthases or the number of genes coding for cytochrome P450 enzymes. A micro-scale analysis of the two fungi did show differences in DNA correspondence between the two species and in the number of transposable elements. Each species has approximately 350 unique genes. The high degree of sequence similarity between the two fungi suggests that they may be ecotypes of the same species and that A. oryzae has resulted from the domestication of A. flavus.}, journal={MEDICAL MYCOLOGY}, author={Payne, G. A. and Nierman, W. C. and Wortman, J. R. and Pritchard, B. L. and Brown, D. and Dean, R. A. and Bhatnagar, D. and Cleveland, T. E. and Machida, Masayuki and Yu, J.}, year={2006}, month={Sep}, pages={S9–S11} }
 @article{price_shannon_sabrina_robert_payne_2005, title={Aflatoxin conducive and non-conducive growth conditions reveal new gene associations with aflatoxin production}, volume={42}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2005.03.009}, abstractNote={Research on aflatoxin (AF) production has traditionally focused on defining the AF biosynthetic pathway with the goal of identifying potential targets for intervention. To understand the effect of nitrogen source, carbon source, temperature, and pH on the regulation of AF biosynthesis, a targeted cDNA microarray consisting of genes associated with AF production over time was employed. Expression profiles for genes involved in AF biosynthesis grouped into five clades. A putative regulon was identified consisting of 20 genes that were induced in the conducive nitrogen and pH treatments and the non-conducive carbon and temperature treatments, as well as four other putative regulons corresponding to each of the four variables studied. Seventeen genes exhibited consistent induction/repression profiles across all the experiments. One of these genes was consistently downregulated with AF production. Overexpression of this gene resulted in repression of AF biosynthesis. The cellular function of this gene is currently unresolved.}, number={6}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Price, MS and Shannon, BCB and Sabrina, TB and Robert, AKB and Payne, GA}, year={2005}, month={Jun}, pages={506–518} }
 @article{xue_isleib_payne_novitzky_obrian_2005, title={Aflatoxin production in peanut lines selected to represent a range of linoleic acid concentrations}, volume={68}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028X-68.1.126}, abstractNote={To determine whether concentrations of linoleate in peanut (Arachis hypogaea L.) seed oil could be used to predict an ability to support aflatoxin production, seeds of genotypes representing a range of linoleate content were inoculated with Aspergillus flavus Link ex Fries and assayed for aflatoxin content. Seeds were blanched and quartered, inoculated with conidia of A. flavus, placed on moistened filter paper in petri dishes, and incubated for 8 days at 28 degrees C. Multiple regression analysis was used to account for the variation among lines with the use of fatty acid concentrations as independent variables. In test 1, linoleate accounted for 39 to 44% of the variation among lines for aflatoxin B1 and B2 and total aflatoxin (26 to 27% after log transformation). Oleate accounted for substantial additional variation (27 to 29%) among lines (20 to 23% after log transformation). Other fatty acids accounted for small fractions of among-line variation. In test 2, linoleate accounted for about 35 to 44% of the variation among entries across traits (29 to 37% for log-transformed data); arachidate accounted for 19 to 29% (27 to 33% after log transformation). Eicosenoate accounted for a small part of the total entry variation. In both experiments, residual variation among entries was significant. Low-linoleate lines consistently contained more aflatoxin, whereas normal- to high-linoleate lines contained variable amounts. Although fatty acid concentrations accounted for significant portions of genetic variation, it is not practical to use them as predictors for susceptibility to aflatoxin contamination, especially for lines in the normal range for oleate and linoleate.}, number={1}, journal={JOURNAL OF FOOD PROTECTION}, author={Xue, HQ and Isleib, TG and Payne, GA and Novitzky, WF and Obrian, G}, year={2005}, month={Jan}, pages={126–132} }
 @article{moore_price_boston_weissinger_payne_2004, title={A chitinase from Tex6 maize kernels inhibits growth of Aspergillus flavus}, volume={94}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO.2004.94.1.82}, abstractNote={ABSTRACT The maize inbred Tex6 has resistance to colonization and aflatoxin accumulation by Aspergillus flavus. A protein inhibitory to growth of A. flavus has been identified from aqueous extracts of mature Tex6 seeds. This study reports the purification of a chitinase associated with this inhibitory activity to electrophoretic homogeneity and the further characterization of its properties. The inhibitory protein, which has an M(r) of 29,000, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, is an endochitinase that is also capable of exochitinase activity. The enzyme has an optimal pH of 5.5 and a temperature optimum of 45 degrees C. Chitinase activity in maize kernels peaked approximately 36 days after pollination. The Tex6 chitinase purified in this study is capable of inhibiting the growth of A. flavus by 50% at a concentration of 20 mug/ml. Our data indicate that chitinase activity in Tex6 kernels makes a major contribution to the antifungal activity in this maize genotype. Partial peptide sequence of the chitinase showed it to differ from previously reported chitinases.}, number={1}, journal={PHYTOPATHOLOGY}, author={Moore, KG and Price, MS and Boston, RS and Weissinger, AK and Payne, GA}, year={2004}, month={Jan}, pages={82–87} }
 @misc{yu_chang_ehrlich_cary_bhatnagar_cleveland_payne_linz_woloshuk_bennett_2004, title={Clustered pathway genes in aflatoxin biosynthesis}, volume={70}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.70.3.1253-1262.2004}, abstractNote={Aflatoxins, a group of polyketide-derived furanocoumarins (Fig. [1][1]), are the most toxic and carcinogenic compounds among the known mycotoxins. Among the at least 16 structurally related aflatoxins characterized, however, there are only four major aflatoxins, B1, B2, G1, and G2 (AFB1, AFG1, AFB2}, number={3}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Yu, JJ and Chang, PK and Ehrlich, KC and Cary, JW and Bhatnagar, D and Cleveland, TE and Payne, GA and Linz, JE and Woloshuk, CP and Bennett, JW}, year={2004}, month={Mar}, pages={1253–1262} }
 @article{pirttila_mcintyre_payne_woloshuk_2004, title={Expression profile analysis of wild-type and fec1 mutant strains of Fusarium verticillioides during fumonisin biosynthesis}, volume={41}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2004.02.001}, abstractNote={Fusarium verticillioides produces a group of mycotoxins known as fumonisins that are associated with a variety of mycotoxicoses in humans and animals. In this study, DNA microarrays were constructed with expressed sequence tags (ESTs) from F. verticillioides. To identify genes with patterns of expression similar to the fumonisin biosynthetic (FUM) genes, the microarray was probed with labeled cDNAs originating from a wild-type strain and a fcc1 mutant grown on maize and in a defined medium adjusted to either pH 3 or pH 8. The comparative analyses revealed differential expression of genes corresponding to 116 ESTs when the fungal strains were grown on maize. Under different pH conditions, 166 ESTs were differentially expressed, and 19 ESTs were identified that displayed expression patterns similar to the FUM ESTs. These results provide candidate genes with potential roles in fumonisin biosynthesis.}, number={6}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Pirttila, AM and McIntyre, LM and Payne, GA and Woloshuk, CP}, year={2004}, month={Jun}, pages={647–656} }
 @article{bush_carson_cubeta_hagler_payne_2004, title={Infection and fumonisin production by Fusarium verticillioides in developing maize kernels}, volume={94}, ISSN={["0031-949X"]}, DOI={10.1094/PHYTO.2004.94.1.88}, abstractNote={ABSTRACT Fusarium ear rot and fumonisin contamination are serious problems for maize growers, particularly in the southeastern United States. The lack of maize genotypes highly resistant to infection by Fusarium verticillioides or to fumonisin contamination emphasizes the need for management strategies to prevent contamination by this mycotoxin. Information on the initial appearance of infection and fumonisin contamination of kernels and their increase over time is needed to determine if early harvest may be an appropriate control strategy. Maize ears from replicated studies at two locations in eastern North Carolina were harvested weekly, starting 2 weeks after pollination and continuing for 14 weeks. The percentage of kernels infected with F. verticillioides and the fumonisin contamination in the harvested samples were determined. Kernel infection by F. verticillioides and fumonisin contamination appeared as kernels neared physiological maturity and increased up to the average harvest date for maize in North Carolina. Beyond this date, the concentrations of fumonisin fluctuated. Under years conducive for fumonisin contamination, early harvest (greater than 25% grain moisture) may help reduce the level of contamination.}, number={1}, journal={PHYTOPATHOLOGY}, author={Bush, BJ and Carson, ML and Cubeta, MA and Hagler, WM and Payne, GA}, year={2004}, month={Jan}, pages={88–93} }
 @article{xue_isleib_payne_wilson_novitzky_g o'brian_2003, title={Comparison of aflatoxin production in normal- and high-oleic backeross-derived peanut lines}, volume={87}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS.2003.87.11.1360}, abstractNote={The effect of the high-oleate trait of peanut on aflatoxin production was tested by comparing normal oleic lines with high-oleic backcross-derived lines. Seeds were blanched, quartered, and inoculated with Aspergillus flavus conidia, placed on moistened filter paper in petri dishes, and incubated for 8 days. In one experiment, dishes were stacked in plastic bags in a Latin square design with bags and positions in stacks as blocking variables. High-oleic lines averaged nearly twice as much aflatoxin as normal lines. Background genotype had no significant effect on aflatoxin content, and interaction between background genotype and oleate level was not detected. In a second experiment, dishes were arranged on plastic trays enclosed in plastic bags and stacked with PVC spacers between trays. Fungal growth and aflatoxin production were greater than in the first experiment. Background genotype, oleate level, and their interaction were significant. The mean of high-oleic lines was almost twice that of normal lines, but the magnitude of the difference varied with background genotype. Special care should be taken with high-oleic lines to prevent growth of Aspergillus spp. and concomitant development of aflatoxin contamination.}, number={11}, journal={PLANT DISEASE}, author={Xue, HQ and Isleib, TG and Payne, GA and Wilson, RF and Novitzky, WP and G O'Brian}, year={2003}, month={Nov}, pages={1360–1365} }
 @article{brown_brown-jenco_bhatnagar_payne_2003, title={Construction and preliminary evaluation of an Aspergillus flavus reporter gene construct as a potential tool for screening aflatoxin resistance}, volume={66}, ISSN={["0362-028X"]}, DOI={10.4315/0362-028X-66.10.1927}, abstractNote={Effective preharvest strategies to eliminate aflatoxin accumulation in crops are not presently available. The molecular biology of aflatoxin biosynthesis has been extensively studied, and genetic and molecular tools such as reporter gene systems for the measurement of fungal growth have been developed. A reporter construct containing the Aspergillus flavus beta-tubulin gene promoter fused to Escherichia coli beta-glucuronidase (GUS) has been shown to be a reliable tool for the indirect measurement of fungal growth in maize kernels. Since cost-saving alternative methods for the direct measurement of aflatoxin levels are needed to facilitate more widespread field and laboratory screening of maize lines, a new reporter gene construct involving the promoter region of the omtA gene of the aflatoxin biosynthetic pathway was constructed and tested. Expression of GUS activity by this construct (omtA::GUS) was correlated with aflatoxin accumulation in culture. In the fungal transformant GAP26-1, which harbors this construct, aflatoxin production and GUS expression on sucrose-containing medium showed the same temporal pattern of toxin induction. Furthermore, GUS expression by GAP26-1 was shown to be associated with aflatoxin accumulation in maize kernels inoculated with this strain. Our results suggest that this and other reporter gene pathway promoter constructs may provide superior alternatives to direct aflatoxin quantification with respect to time, labor, and materials for the screening of maize lines for resistance to aflatoxin accumulation.}, number={10}, journal={JOURNAL OF FOOD PROTECTION}, author={Brown, RL and Brown-Jenco, CS and Bhatnagar, D and Payne, GA}, year={2003}, month={Oct}, pages={1927–1931} }
 @article{obrian_fakhoury_payne_2003, title={Identification of genes differentially expressed during aflatoxin biosynthesis in Aspergillus flavus and Aspergillus parasiticus}, volume={39}, ISSN={["1087-1845"]}, DOI={10.1016/S1087-1845(03)00014-8}, abstractNote={A complex regulatory network governs the biosynthesis of aflatoxin. While several genes involved in aflatoxin production are known, their action alone cannot account for its regulation. Arrays of clones from an Aspergillus flavus cDNA library and glass slide microarrays of ESTs were screened to identify additional genes. An initial screen of the cDNA clone arrays lead to the identification of 753 unique ESTs. Many showed sequence similarity to known metabolic and regulatory genes; however, no function could be ascribed to over 50% of the ESTs. Gene expression analysis of Aspergillus parasiticus grown under conditions conducive and non-conductive for aflatoxin production was evaluated using glass slide microarrays containing the 753 ESTs. Twenty-four genes were more highly expressed during aflatoxin biosynthesis and 18 genes were more highly expressed prior to aflatoxin biosynthesis. No predicted function could be ascribed to 18 of the 24 genes whose elevated expression was associated with aflatoxin biosynthesis.}, number={2}, journal={FUNGAL GENETICS AND BIOLOGY}, author={OBrian, GR and Fakhoury, AM and Payne, GA}, year={2003}, month={Jul}, pages={118–127} }
 @misc{scheidegger_payne_2003, title={Unlocking the secrets behind secondary metabolism: A review of Aspergillus flavus from pathogenicity to functional genomics}, volume={22}, ISSN={["0731-3837"]}, DOI={10.1081/TXR-120024100}, abstractNote={Aspergillus flavus has received a considerable amount of attention due to its ability to produce aflatoxin, a secondary metabolite that is both immunosuppressive and carcinogenic to animals and humans. Research on aflatoxin over the last 40 years has made it one of the best studied fungal secondary metabolites. In spite of the large volume of research in this area, many unanswered questions remain concerning the genetic regulation of aflatoxin production and the molecular signals that intimately associate the synthesis of aflatoxin with specific environmental and nutritional conditions. It is anticipated that the tools now available in the field of genomics will build upon our existing knowledge and provide answers to some of these questions. Complete genome sequences are now available for a number of fungal species that are closely related to A. flavus. This information can be used along with current genomic analyses in A. flavus to more closely examine the biosynthesis and regulation of secondary metabolism. The intent of this review is to summarize the large body of knowledge that exists from many years of research on A. flavus, with the hope that this information in the light of new genomic studies may bring scientists closer to unraveling the web of regulatory circuits that govern aflatoxin biosynthesis. Specifically, scientific findings in the following areas will be presented: classification and phylogenetic analyses of A. flavus, population biology, ecology and pathogenicity in agricultural environments, classical genetics including linkage group and mutant analyses, gene clusters, regulation of aflatoxin biosynthesis, and genomics.}, number={2-3}, journal={JOURNAL OF TOXICOLOGY-TOXIN REVIEWS}, author={Scheidegger, KA and Payne, GA}, year={2003}, pages={423–459} }
 @article{price_classen_payne_2001, title={Aspergillus niger absorbs copper and zinc from swine wastewater}, volume={77}, ISSN={["1873-2976"]}, DOI={10.1016/S0960-8524(00)00135-8}, abstractNote={Wastewater from swine confined-housing operations contains elevated levels of copper and zinc due to their abundance in feed. These metals may accumulate to phytotoxic levels in some agricultural soils of North Carolina due to land application of treated swine effluent. We evaluated fungi for their ability to remove these metals from wastewater and found Aspergillus niger best suited for this purpose. A. niger was able to grow on plates amended with copper at a level five times that inhibitory to the growth of Saccharomyces cerevisiae. We also found evidence for internal absorption as the mechanism used by A. niger to detoxify its environment of copper, a property of the fungus that has not been previously exploited for metal bioremediation. In this report, we show that A. niger is capable of removing 91% of the copper and 70% of the zinc from treated swine effluent.}, number={1}, journal={BIORESOURCE TECHNOLOGY}, author={Price, MS and Classen, JJ and Payne, GA}, year={2001}, month={Mar}, pages={41–49} }
 @article{brown_cleveland_woloshuk_payne_bhatnagar_2001, title={Growth inhibition of a Fusarium verticillioides GUS strain in corn kernels of aflatoxin-resistant genotypes}, volume={57}, ISSN={["0175-7598"]}, DOI={10.1007/s00253-001-0838-y}, number={5-6}, journal={APPLIED MICROBIOLOGY AND BIOTECHNOLOGY}, author={Brown, RL and Cleveland, TE and Woloshuk, CP and Payne, GA and Bhatnagar, D}, year={2001}, month={Dec}, pages={708–711} }
 @article{nielsen_payne_boston_2001, title={Maize ribosome-inactivating protein inhibits normal development of Aspergillus nidulans and Aspergillus flavus}, volume={14}, ISSN={["0894-0282"]}, DOI={10.1094/mpmi.2001.14.2.164}, abstractNote={The abundant maize kernel ribosome-inactivating protein 1 (RIP1) was tested for antifungal activity against Aspergillus nidulans and Aspergillus flavus. A microculture assay was developed to monitor fungal growth and development after treatment of conidia with RIP1 or control proteins. A striking decrease in hyphal proliferation was observed when conidia of A. nidulans, a genetically well-characterized nonpathogenic species, were treated with RIP1 protein. Treatment with a RIP1 mutant protein that lacked enzymatic ribosome-inactivating activity caused no observable effects. RIP1 treatment of conidia from the maize pathogen A. flavus resulted in increased hyphal branching. Examination of the branched hyphae after Congo red staining revealed only one growing hyphal tip per conidium. These results indicate that both fungi were affected by RIP1 treatment, but the lysis seen with treatment of A. nidulans was apparently avoided by A. flavus. A developmental time course revealed that both fungal species were affected by RIP1 at the postdivisional growth stage. The inhibitory activity of RIP1 against normal fungal growth is consistent with a biological function to protect the seed from fungal invasion.}, number={2}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Nielsen, K and Payne, GA and Boston, RS}, year={2001}, month={Feb}, pages={164–172} }
 @misc{brown_brown-jenco_payne_1999, title={Genetic and molecular analysis of aflatoxin biosynthesis}, volume={26}, ISSN={["1096-0937"]}, DOI={10.1006/fgbi.1998.1114}, abstractNote={The aflatoxin biosynthetic pathway represents one of the est studied pathways of fungal secondary metabolism. Its lucidation is the result of over 30 years of study by cientists in many disciplines. For recent reviews on the hemistry of the pathway see articles by Bhatnagar et al. 1992) Minto and Townsend (1997), and Woloshuk and rieto (1997). Concern over the toxicity and carcinogenicty of aflatoxin has been the prime force driving research in his area. Aflatoxin B1 (AFB1) is the most potent naturally ccurring carcinogen known (Squire, 1989), and epidemioogical data implicate aflatoxin as a component of liver ancer in humans in certain parts of the world (Hall and ild, 1994). Although aflatoxins are not extremely toxic, onsumption of aflatoxin contaminated food by animals can ead to decreased weight gain, hemorrhaging, and suppression f the immune system (Miller and Wilson, 1994). Aflatoxins are produced by four species of Aspergillus: . flavus, A. parasiticus, A. nomius, and A. tamarii (Payne, 998; Kurtzman et al., 1986; Goto et al., 1996). From an gricultural standpoint, the two most significant fungi are}, number={2}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Brown, MP and Brown-Jenco, CS and Payne, GA}, year={1999}, month={Mar}, pages={81–98} }
 @article{du_huang_flaherty_wells_payne_1999, title={Green fluorescent protein as a reporter to monitor gene expression and food colonization by Aspergillus flavus}, volume={65}, number={2}, journal={Applied and Environmental Microbiology}, author={Du, W. L. and Huang, Z. Y. and Flaherty, J. E. and Wells, K. and Payne, G. A.}, year={1999}, pages={834–836} }
 @article{meyers_o'brian_du_bhatnagar_payne_1998, title={Characterization of aflj, a gene required for conversion of pathway intermediates to aflatoxin}, volume={64}, number={10}, journal={Applied and Environmental Microbiology}, author={Meyers, D. M. and O'Brian, G. and Du, W. L. and Bhatnagar, D. and Payne, G. A.}, year={1998}, pages={3713–3717} }
 @misc{payne_brown_1998, title={Genetics and physiology of aflatoxin biosynthesis}, volume={36}, ISSN={["1545-2107"]}, DOI={10.1146/annurev.phyto.36.1.329}, abstractNote={Aflatoxins are the most thoroughly studied mycotoxins. Elegant early research on the biosynthetic scheme of the pathway has allowed a molecular characterization of aflatoxin biosynthesis and its regulation. Genetic studies on aflatoxin biosynthesis in Aspergillus flavus and A. parasiticus, and sterigmatocystin biosynthesis in A. nidulans, led to the cloning of 17 genes responsible for 12 enzymatic conversions in the AF/ST pathways. Pathway-specific regulation is by a Zn(II)2Cys6 DNA-binding protein that regulates the transcription of all pathway genes. Less is known about the global factors that regulate aflatoxin biosynthesis, but there is a clear link between development and aflatoxin biosynthesis. There is also a large body of information on physiological factors involved in aflatoxin biosynthesis, but it has been difficult to understand their role in the regulation of this pathway. This chapter discusses current knowledge on the molecular biology and genetics of the pathway, and provides a summary of the physiological factors known to influence aflatoxin formation.}, journal={ANNUAL REVIEW OF PHYTOPATHOLOGY}, author={Payne, GA and Brown, MP}, year={1998}, pages={329–362} }
 @article{huang_white_payne_1997, title={Corn seed proteins inhibitory to Aspergillus flavus and aflatoxin biosynthesis}, volume={87}, ISSN={["0031-949X"]}, DOI={10.1094/PHYTO.1997.87.6.622}, abstractNote={ABSTRACT This study reports the presence of two fractions from corn seeds inhibitory to aflatoxin formation. Using a sensitive laboratory assay that can measure both inhibition of fungal growth and inhibition of aflatoxin biosynthesis, we examined aqueous extracts from seeds of Tex6, a corn inbred shown to be highly resistant to aflatoxin accumulation in field and laboratory evaluations. In these extracts, we identified two biologically active fractions. One inhibited growth of Aspergillus flavus and, thus, aflatoxin accumulation, and the other inhibited aflatoxin formation with little effect on fungal growth. The compounds responsible for these activities appear to be proteaceous, as they are water soluble, heat labile, and sensitive to proteinase K treatment. The compounds were partially purified by ultrafiltration and chromatography. The estimated molecular mass of the growth inhibitor is approximately 28 kDa, and that of the aflatoxin biosynthesis inhibitor appears to be greater than 100 kDa. Partially purified preparations of the growth inhibitor and aflatoxin biosynthesis inhibitor cause 50% inhibition at 26 and 75 mug of protein/ml, respectively. The presence of these compounds in Tex6 may explain its resistance to aflatoxin accumulation.}, number={6}, journal={PHYTOPATHOLOGY}, author={Huang, ZY and White, DG and Payne, GA}, year={1997}, month={Jun}, pages={622–627} }
 @article{liu_brewer_flaherty_payne_bhatnagar_chu_1997, title={Immunochemical identification of AFLR, a regulatory protein, involved in aflatoxin biosynthesis}, volume={9}, ISSN={["1465-3443"]}, DOI={10.1080/09540109709354959}, abstractNote={Polyclonal antibodies against AFLR, the aflR gene product of Aspergillus flavus and A. parasiticus, were generated by immunizing a rabbit with the Escherichia coli‐expressed recombinant AFLR protein of A. flavus. Immunoblot analysis revealed that the antibodies not only reacted with the recombinant AFLR protein of A. flavus or A. parasiticus but also with native 47‐kDa AFLR in A. flavus and A. parasiticus. Immunoblot analysis revealed that accumulation of the 47‐kDa AFLR in cultures of A. flavus and A. parasiticus correlated well with the production of aflatoxin under various culture conditions that regulate aflatoxin formation. Neither AFLR nor aflatoxin was found when A. parasiticus NRRL 2999 was grown in peptone mineral salts (PMS) medium; however, both were detected after the culture was transferred to glucose mineral salts (GMS) medium. The AFLR protein was absent in the non‐aflatoxigenic Penicillium and Fusarium species grown in GMS medium. The data indicate that the antibodies obtained in the prese...}, number={4}, journal={FOOD AND AGRICULTURAL IMMUNOLOGY}, author={Liu, BH and Brewer, JF and Flaherty, JE and Payne, G and Bhatnagar, D and Chu, FS}, year={1997}, month={Dec}, pages={289–298} }
 @article{flaherty_payne_1997, title={Overexpression of aflR leads to upregulation of pathway gene transcription and increased aflatoxin production in Aspergillus flavus}, volume={63}, number={10}, journal={Applied and Environmental Microbiology}, author={Flaherty, J. E. and Payne, G. A.}, year={1997}, pages={3995–4000} }
 @article{payne_nystrom_bhatnagar_cleveland_woloshuk_1993, title={Cloning of the afl-2 gene involved in aflatoxin biosynthesis from Aspergillus flavus}, volume={59}, number={1}, journal={Applied and Environmental Microbiology}, author={Payne, G. A. and Nystrom, G. J. and Bhatnagar, D. and Cleveland, T. E. and Woloshuk, C. P.}, year={1993}, pages={156} }
 @misc{payne_1992, title={AFLATOXIN IN MAIZE}, volume={10}, ISSN={["1549-7836"]}, DOI={10.1080/07352689209382320}, abstractNote={Abstract Aflatoxin B1 is a potent hepatacarcinogen that occurs in corn worldwide. The aflatoxin‐producing fungus Aspergillus flavus can grow and produce aflatoxin on corn preharvest and in storage. Within the U.S., aflatoxin contamination of preharvest corn has been reported in 23 states, and contamination is chronic in the southeastern U.S. where hot, drought conditions often favor the fungus and the production of aflatoxin. Management practices have been developed to reduce aflatoxin contamination, but in years when environmental conditions are extremely favorable for the fungus, no control strategy is effective. Resistance to aflatoxin accumulation appears to be heritable, but no commercial hybrids are available with adequate resistance. This review covers the epidemiology of A. flavus in preharvest corn from the infection process to the factors that influence aflatoxin formation. Also discussed are the problems associated with the development of resistant varieties and new strategies that are being de...}, number={5}, journal={CRITICAL REVIEWS IN PLANT SCIENCES}, author={PAYNE, GA}, year={1992}, pages={423–440} }
 @inbook{payne_1991, title={Molecular approaches for studying aflatoxin biosynthesis}, booktitle={Aflatoxin in corn : new perspectives}, publisher={Ames, Iowa : Iowa Agriculture and Home Economics Experiment Station, Iowa State University}, author={Payne, G. A.}, editor={O.L. Shotwell and Hurburgh, C.R., Jr.Editors}, year={1991} }