@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={SUMMARY}, 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{chang_georgianna_heber_payne_muddiman_2010, title={Detection of alternative splice variants at the proteome level in Aspergillus flavus}, volume={9}, number={3}, journal={Journal of Proteome Research}, author={Chang, K. Y. and Georgianna, D. R. and Heber, S. and Payne, G. A. and Muddiman, D. C.}, year={2010}, pages={1209–1217} }
 @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{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{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{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={Abstract}, 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{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} }