@article{cho_lee_dean_jeon_2023, title={Distinct dynamics of the nucleolus in response to nutrient availability and during development in the rice blast fungus}, volume={9}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.01844-23}, abstractNote={ABSTRACT The nucleolus has emerged as a central hub for nuclear functions in eukaryotes. Studies in mammals and the model yeast Saccharomyces cerevisiae showed that the nucleolus is pivotal to nuclear functions other than ribosome biogenesis. Importantly, rDNA transcription and ribosome assembly were shown to positively correlate with the size of the nucleolus. However, little is known about the nucleolus of filamentous fungi. Here, we investigated how the size and shape of nucleolus in the plant pathogenic filamentous fungus, Magnaporthe oryzae, respond to nutrient conditions and infection-related development by monitoring the nucleolar marker protein, MoNOP1 tagged with red fluorescent protein (MoNOP1-RFP). Our work revealed that in the hyphae of M. oryzae, the nucleolar size is decoupled from the nucleolar activity under low nutrient condition. A complete lack of carbon or nitrogen did not cause such decoupling. In conidia, no or faint RFP signals were initially observed, hinting at the absence of functional nucleoli. RFP signals only started to become visible in conidia within 2 hours of germination when the germ tube tip began to differentiate a specialized infection structure, the appressorium. RFP signals diminished thereafter. In contrast, in the appressorium, signals became concentrated after 6 hours as the appressorium matured. We propose that such nucleolar dynamics may reflect the strategy of filamentous fungi under low nutrient availability to forage for food resources as well as the roles of the nucleolus during fungal development. IMPORTANCE The nucleolus is a dynamic subnuclear structure that is involved in many fundamental processes of the nucleus. In higher eukaryotic cells, the size and shape of nucleoli correlate with nucleolar activities. For fungi, knowledge of the nucleolus and its functions is primarily gleaned from budding yeast. Whether such correlation is conserved and how nucleolar functions are regulated in filamentous fungi including important human and crop pathogens are largely unknown. Our observations reveal that the dynamics of nucleolus in a model plant pathogenic fungus, Magnaporthe oryzae, is distinct from those of animal and yeast nucleoli under low nutrient availability and during pathogenic development. Our data not only provide new insight into the nucleoli in filamentous fungi but also highlight the need for investigating how nucleolar dynamics is regulated in comparison to other eukaryotes. The nucleolus is a dynamic subnuclear structure that is involved in many fundamental processes of the nucleus. In higher eukaryotic cells, the size and shape of nucleoli correlate with nucleolar activities. For fungi, knowledge of the nucleolus and its functions is primarily gleaned from budding yeast. Whether such correlation is conserved and how nucleolar functions are regulated in filamentous fungi including important human and crop pathogens are largely unknown. Our observations reveal that the dynamics of nucleolus in a model plant pathogenic fungus, Magnaporthe oryzae, is distinct from those of animal and yeast nucleoli under low nutrient availability and during pathogenic development. Our data not only provide new insight into the nucleoli in filamentous fungi but also highlight the need for investigating how nucleolar dynamics is regulated in comparison to other eukaryotes.}, journal={MBIO}, author={Cho, Eunbyeol and Lee, Song Hee and Dean, Ralph A. and Jeon, Junhyun}, year={2023}, month={Sep} }
 @article{dean_2023, title={Issue Information}, volume={24}, ISSN={["1364-3703"]}, DOI={10.1111/mpp.13384}, abstractNote={dramatically attenuating virulence.(The strains shown in the image are, left to right, wild type, ∆ham2, ∆ham2-C, ∆ham3, ∆ham3-C.)See 24, pp.}, number={9}, journal={MOLECULAR PLANT PATHOLOGY}, author={Dean, Ralph}, year={2023}, month={Sep}, pages={1015–1016} }
 @article{sennik_kinoshita-millard_oh_kafer_dean_oralkan_2023, title={Plant Disease Detection Using an Electronic Nose}, ISSN={["1930-0395"]}, DOI={10.1109/SENSORS56945.2023.10325015}, abstractNote={This paper presents experimental results on differentiating between healthy wheat plants and plants infected with Fusarium Head Blight (FHB) based on sensing the ambient gases in the plant environment using a gravimetric electronic nose enabled by a functionalized capacitive micromachined ultrasonic transducer (CMUT) array and machine learning (ML) algorithms. The CMUT sensor array is functionalized with organic/inorganic materials to capture disease-related volatile signals. The sensor data is processed and analyzed using ML algorithms for accurate plant classification. Experimental results demonstrate the effectiveness of the proposed approach in achieving high accuracy for plant disease detection at the end of the 11th day after plant inoculation.}, journal={2023 IEEE SENSORS}, author={Sennik, Erdem and Kinoshita-Millard, Samuel and Oh, Yeonyee and Kafer, Christopher W. and Dean, Ralph A. and Oralkan, Omer}, year={2023} }
 @article{oh_ingram_shekasteband_adhikari_louws_dean_2023, title={Tissues and mechanisms associated with Verticillium wilt resistance in tomato using bi-grafted near-isogenic lines}, volume={5}, ISSN={["1460-2431"]}, url={https://doi.org/10.1093/jxb/erad182}, DOI={10.1093/jxb/erad182}, abstractNote={Abstract Host resistance is the primary means to control Verticillium dahliae, a soil-borne pathogen causing major losses on a broad range of plants, including tomato. The tissues and mechanisms responsible for resistance remain obscure. In the field, resistant tomato used as rootstocks does not confer resistance. Here, we created bi-grafted plants with near-isogenic lines (NILs) exhibiting (Ve1) or lacking (ve1) resistance to V. dahliae race 1. Ten days after inoculation, scion and rootstock tissues were subjected to differential gene expression and co-expression network analyses. Symptoms only developed in susceptible scions regardless of the rootstock. Infection caused more dramatic alteration of tomato gene expression in susceptible compared with resistant tissues, including pathogen receptor, signaling pathway, pathogenesis-related protein, and cell wall modification genes. Differences were observed between scions and rootstocks, primarily related to physiological processes in these tissues. Gene expression in scions was influenced by the rootstock genotype. A few genes were associated with the Ve1 genotype, which was independent of infection or tissue type. Several were physically clustered, some near the Ve1 locus on chromosome 9. Transcripts mapped to V. dahliae were dominated by secreted candidate effector proteins. These findings advance knowledge of molecular mechanisms underlying the tomato–V. dahliae interaction.}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Oh, Yeonyee and Ingram, Thomas and Shekasteband, Reza and Adhikari, Tika and Louws, Frank J. and Dean, Ralph A.}, editor={Höfte, MonicaEditor}, year={2023}, month={May} }
 @article{wang_dean_2022, title={Host induced gene silencing of Magnaporthe oryzae by targeting pathogenicity and development genes to control rice blast disease}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.959641}, abstractNote={Rice blast disease caused by the hemi-biotrophic fungus Magnaporthe oryzae is the most destructive disease of rice world-wide. Traditional disease resistance strategies for the control of rice blast disease have not proved durable. HIGS (host induced gene silencing) is being developed as an alternative strategy. Six genes (CRZ1, PMC1, MAGB, LHS1, CYP51A, CYP51B) that play important roles in pathogenicity and development of M. oryzae were chosen for HIGS. HIGS vectors were transformed into rice calli through Agrobacterium-mediated transformation and T0, T1 and T2 generations of transgenic rice plants were generated. Except for PMC1 and LHS1, HIGS transgenic rice plants challenged with M. oryzae showed significantly reduced disease compared with non-silenced control plants. Following infection with M. oryzae of HIGS transgenic plants, expression levels of target genes were reduced as demonstrated by Quantitative RT-PCR. In addition, treating M. oryzae with small RNA derived from the target genes inhibited fungal growth. These findings suggest RNA silencing signals can be transferred from host to an invasive fungus and that HIGS has potential to generate resistant rice against M. oryzae.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Wang, Mengying and Dean, Ralph A.}, year={2022}, month={Aug} }
 @article{sennik_erden_constantino_oh_dean_oralkan_2021, title={Electronic nose system based on a functionalized capacitive micromachined ultrasonic transducer (CMUT) array for selective detection of plant volatiles}, volume={341}, ISSN={["0925-4005"]}, url={https://doi.org/10.1016/j.snb.2021.130001}, DOI={10.1016/j.snb.2021.130001}, abstractNote={Here, a small, low-power, wireless gas sensor platform for selective detection of volatile organic compounds (VOCs) released from plants under different abiotic or biotic stress conditions is described. This sensor platform is implemented based on a capacitive micromachined ultrasonic transducer (CMUT) array, in which elements were functionalized with a variety of materials including polymers, phthalocyanines, and metals to improve selectivity. Input impedance measurements of the functionalized CMUT array were compared to pre-coating measurements to analyze the mechanical loading. The CMUT arrays were then exposed to VOCs known to be emitted by plants with different concentrations under dry air flow at room temperature. The results demonstrated that 1-Octanol created the strongest response across different channels and a resolution of 3-ppb was calculated for the CMUT element functionalized using silver ink when exposed to 1-Octanol. The relative responses of different channels to tested volatiles were observed to be different. The k-nearest neighbor (k-NN) algorithm was used for the gas classification by dividing the data to training and test groups. The k-NN results showed that the gases at low concentrations were successfully classified with better than 97 % accuracy. Finally, to emulate the ambient atmosphere for plants, the gas tests were repeated by adding different levels of humidity to the gas flow. With a minimum 98 % accuracy, the k-NN classifier demonstrated that the functionalized CMUT array can be used for selective detection of the group of plant VOCs used in this study, even at different relative humidity levels in the ambient atmosphere.}, journal={SENSORS AND ACTUATORS B-CHEMICAL}, publisher={Elsevier BV}, author={Sennik, Erdem and Erden, Fatih and Constantino, Nasie and Oh, YeonYee and Dean, Ralph A. and Oralkan, Omer}, year={2021}, month={Aug} }
 @article{constantino_oh_sennik_andersen_warden_oralkan_dean_2021, title={Soybean Cyst Nematodes Influence Aboveground Plant Volatile Signals Prior to Symptom Development}, volume={12}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2021.749014}, abstractNote={Soybean cyst nematode (SCN), Heterodera glycines, is one of the most destructive soybean pests worldwide. Unlike many diseases, SCN doesn't show above ground evidence of disease until several weeks after infestation. Knowledge of Volatile Organic Compounds (VOCs) related to pests and pathogens of foliar tissue is extensive, however, information related to above ground VOCs in response to root damage is lacking. In temporal studies, gas chromatography-mass spectrometry analysis of VOCs from the foliar tissues of SCN infested plants yielded 107 VOCs, referred to as Common Plant Volatiles (CPVs), 33 with confirmed identities. Plants showed no significant stunting until 10 days after infestation. Total CPVs increased over time and were significantly higher from SCN infested plants compared to mock infested plants post 7 days after infestation (DAI). Hierarchical clustering analysis of expression ratios (SCN: Mock) across all time points revealed 5 groups, with the largest group containing VOCs elevated in response to SCN infestation. Linear projection of Principal Component Analysis clearly separated SCN infested from mock infested plants at time points 5, 7, 10 and 14 DAI. Elevated Styrene (CPV11), D-Limonene (CPV32), Tetradecane (CPV65), 2,6-Di-T-butyl-4-methylene-2,5-cyclohexadiene-1-one (CPV74), Butylated Hydroxytoluene (CPV76) and suppressed Ethylhexyl benzoate (CPV87) levels, were associated with SCN infestation prior to stunting. Our findings demonstrate that SCN infestation elevates the release of certain VOCs from foliage and that some are evident prior to symptom development. VOCs associated with SCN infestations prior to symptom development may be valuable for innovative diagnostic approaches.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Constantino, Nasie and Oh, Yeonyee and Sennik, Erdem and Andersen, Brian and Warden, Michael and Oralkan, Omer and Dean, Ralph A.}, year={2021}, month={Sep} }
 @article{ingram_oh_adhikari_louws_dean_2020, title={Comparative Genome Analyses of 18 Verticillium dahliae Tomato Isolates Reveals Phylogenetic and Race Specific Signatures}, volume={11}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2020.573755}, abstractNote={Host resistance is one of the few strategies available to combat the soil borne pathogenic fungus Verticillium dahliae. Understanding pathogen diversity in populations is key to successfully deploying host resistance. In this study the genomes of 18 V. dahliae isolates of races 1 (n = 2), 2 (n = 4), and 3 (n = 12) from Japan, California, and North Carolina were sequenced and mapped to the reference genome of JR2 (from tomato). The genomes were analyzed for phylogenetic and pathogen specific signatures to classify specific strains or genes for future research. Four highly clonal lineages/groups were discovered, including a lineage unique to North Carolina isolates, which had the rare MAT1-1 mating type. No evidence for recombination between isolates of different mating types was observed, even in isolates of different mating types discovered in the same field. By mapping these 18 isolates genomes to the JR2 reference genome, 193 unique candidate effectors were found using SignalP and EffectorP. Within these effectors, 144 highly conserved effectors, 42 mutable effectors (truncated or present in some isolates but absent in others), and 7 effectors present in highly variable regions of the chromosomes were discovered. Of the 144 core effectors, 21 were highly conserved in V. alfalfae and V. longisporum, 7 of which have no known function. Within the non-core effectors 30 contained large numbers of non-synonymous mutations, while 15 of them contained indels, frameshift mutations, or were present on highly variable regions of the chromosome. Two of these highly variable region effectors (HVREs) were only present in race 2 isolates, but not in race 3 isolates. The race 1 effector Ave1 was also present in a highly variable region. These data may suggest that these highly variable regions are enriched in race determinant genes, consistent with the two-speed genome hypothesis.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Ingram, Thomas W. and Oh, Yeonyee and Adhikari, Tika B. and Louws, Frank J. and Dean, Ralph A.}, year={2020}, month={Nov} }
 @article{kalmar_oh_dean_muddiman_2020, title={Comparative Proteomic Analysis of Wild Type and Mutant Lacking an SCF E3 Ligase F-Box Protein in Magnaporthe oryzae}, volume={19}, ISBN={1535-3907}, DOI={10.1021/acs.jproteome.0c00294}, abstractNote={Magnaporthe oryzae (M. oryzae) is a pathogenic, filamentous fungus that is a primary cause of rice blast disease. The M. oryzae protein MGG_13065, SCF E3 Ubiquitin Ligase complex F-box protein has been identified as playing a crucial role in the infection process, specifically, as part of the ubiquitin mediated proteolysis pathway. Proteins targeted by MGG_13065 E3 ligase are first phosphorylated and then ubiquitinated by E3 ligase. In this study, we used a label-free quantitative global proteomics technique to probe the role of ubiquitination and phosphorylation in the mechanism of how E3 ligase regulates change in virulence of M. oryzae. To do this, we compared the WT M.oryzae 70-15 strain with a gene knock out (E3 ligase KO) strain. After applying a ≥ 5 normalized spectral count cut off, a total of 4,432 unique proteins were identified comprised of 4,360 and 4,372 in the WT and E3 ligase KO samples, respectively. Eighty proteins drastically increased in abundance while 65 proteins decreased in abundance in the E3 ligase KO strain. Fifty-nine proteins were identified only in the WT strain; 13 of which had both phosphorylation and ubiquitination post-translational modifications. Seventy-one proteins were revealed to be only in the E3 ligase KO strain; 23 having both phosphorylation and ubiquitination post-translational modifications. Several of these proteins were associated with key biological processes. These data greatly assist in the selection of future genes for functional studies and enabling mechanistic insight related to virulence.}, number={9}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Kalmar, Jaclyn Gowen and Oh, Yeonyee and Dean, Ralph A. and Muddiman, David C.}, year={2020}, pages={3761–3768} }
 @article{wang_eyre_thon_oh_dean_2020, title={Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds}, volume={11}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2020.559728}, abstractNote={Microbes form close associations with host plants including rice as both surface (epiphytes) and internal (endophytes) inhabitants. Yet despite rice being one of the most important cereal crops agriculturally and economically, knowledge of its microbiome, particularly core inhabitants and any functional properties bestowed is limited. In this study, the microbiome in rice seedlings derived directly from seeds was identified, characterized and compared to the microbiome of the seed. Rice seeds were sourced from two different locations in Arkansas, USA of two different rice genotypes (Katy, M202) from two different harvest years (2013, 2014). Seeds were planted in sterile media and bacterial as well as fungal communities were identified through 16S and ITS sequencing, respectively, for four seedling compartments (root surface, root endosphere, shoot surface, shoot endosphere). Overall, 966 bacterial and 280 fungal ASVs were found in seedlings. Greater abundance and diversity were detected for the microbiome associated with roots compared to shoots and with more epiphytes than endophytes. The seedling compartments were the driving factor for microbial community composition rather than other factors such as rice genotype, location and harvest year. Comparison with datasets from seeds revealed that 91 (out of 296) bacterial and 11 (out of 341) fungal ASVs were shared with seedlings with the majority being retained within root tissues. Core bacterial and fungal microbiome shared across seedling samples were identified. Core bacteria genera identified in this study such as Rhizobium, Pantoea, Sphingomonas, and Paenibacillus have been reported as plant growth promoting bacteria while core fungi such as Pleosporales, Alternaria and Occultifur have potential as biocontrol agents.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Wang, Mengying and Eyre, Alexander W. and Thon, Michael R. and Oh, Yeonyee and Dean, Ralph A.}, year={2020}, month={Sep} }
 @article{kalmar_oh_dean_muddiman_2020, title={Investigating host-pathogen meta-metabolic interactions of Magnaporthe oryzae infected barley using infrared matrix-assisted laser desorption electrospray ionization mass spectrometry}, volume={412}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-019-02216-z}, abstractNote={Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging is a useful tool for identifying important meta-metabolomic features pertinent for enhancing our understanding of biological systems. Magnaporthe oryzae (M. oryzae) is a filamentous fungus that is the primary cause of rice blast disease. True to its name, M. oryzae primarily destroys rice crops and can also destroy other cereal crops as well. In a previous study, the F-box E3 ligase protein in M. oryzae was noted to be crucial for its growth and pathogenicity. In this study, we inoculated three separate sets of barley with wild-type M. oryzae, an F-box E3 ligase protein knock out of M. oryzae, and a control solution. Over the course of the infection (8 days), we imaged each treatment after development of an advanced polarity switching method, which allowed for the detection of low and high molecular weight compounds that ionize in positive or negative polarities. A set of features from initial experiments were chosen for another analysis using tandem mass spectrometry. Serotonin, a barley defense metabolite, was a compound identified in both positive and negative modes. Serotonin was putatively identified using MS1 data including carbon estimation and sulfur counting then confirmed based on tandem mass spectrometry fragmentation patterns. Metabolites in the melanin pathway, important for infection development of M. oryzae, were also identified using MS1 data but were unable to be confirmed with MS/MS due to their low abundances.}, number={1}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Kalmar, Jaclyn Gowen and Oh, Yeonyee and Dean, Ralph A. and Muddiman, David C.}, year={2020}, month={Jan}, pages={139–147} }
 @misc{wang_dean_2020, title={Movement of small RNAs in and between plants and fungi}, volume={21}, ISSN={["1364-3703"]}, DOI={10.1111/mpp.12911}, abstractNote={Abstract RNA interference is a biological process whereby small RNAs inhibit gene expression through neutralizing targeted mRNA molecules. This process is conserved in eukaryotes. Here, recent work regarding the mechanisms of how small RNAs move within and between organisms is examined. Small RNAs can move locally and systemically in plants through plasmodesmata and phloem, respectively. In fungi, transportation of small RNAs may also be achieved by septal pores and vesicles. Recent evidence also supports bidirectional cross‐kingdom communication of small RNAs between host plants and adapted fungal pathogens to affect the outcome of infection. We discuss several mechanisms for small RNA trafficking and describe evidence for transport through naked form, combined with RNA‐binding proteins or enclosed by vesicles.}, number={4}, journal={MOLECULAR PLANT PATHOLOGY}, author={Wang, Mengying and Dean, Ralph A.}, year={2020}, month={Apr}, pages={589–601} }
 @article{eyre_wang_oh_dean_2019, title={Identification and Characterization of the Core Rice Seed Microbiome}, volume={3}, ISSN={["2471-2906"]}, DOI={10.1094/PBIOMES-01-19-0009-R}, abstractNote={The use of microbes in agriculture for enhancing crop production is an emerging alternative to chemical fertilizers and pesticides; however, their effectiveness is often limited by factors such as host genotype and variability in geographic location. To address this issue, the microbiomes of six different rice (Oryza sativa) seeds, sourced from two locations in Arkansas, U.S.A. of two different genotypes and two harvest years, were characterized. The bacterial and fungal communities were identified in each of four seed compartments (grain, outer grain, husk, and outer husk) using high throughput Illumina MiSeq sequencing. More unique amplicon sequence variants were identified in the outer seed husk and least in the grain compartment for both the fungal and bacterial microbiomes, however this only resulted in a decrease in diversity for the fungal communities. Principal component analysis indicated that each tissue compartment harbored relatively distinct bacterial and fungal communities for the three innermost compartments. A bacterial and fungal core microbiome shared among the six seed types for each compartment was identified. Key bacterial genera in the core across all compartments were Sphingomonas, Methylobacterium, and taxa in the family Enterobacteriaceae, members of which have been reported to support rice growth. Compared with the bacterial core, more fungal taxa were identified, possibly resulting from the more abundant reads after filtering, and key genera identified were Alternaria, Hannaella, and members of the order Pleosporales. These core members represent valuable candidates for manipulating the rice microbiome, decreasing the use of chemicals while increasing plant performance.}, number={2}, journal={PHYTOBIOMES JOURNAL}, author={Eyre, Alexander W. and Wang, Mengying and Oh, Yeonyee and Dean, Ralph A.}, year={2019}, pages={148–157} }
 @article{raman_meyers_dean_donofrio_2018, title={Characterizing Small RNAs in Filamentous Fungi Using the Rice Blast Fungus, Magnaporthe oryzae, as an Example}, volume={1848}, ISBN={["978-1-4939-8723-8"]}, ISSN={["1940-6029"]}, DOI={10.1007/978-1-4939-8724-5_5}, abstractNote={The goal of this chapter is to provide a framework of sequential steps for small RNA (sRNA) analysis in filamentous fungi. Here, we present protocols for (1) comparative analysis of sRNAs in different conditions, (2) comparisons of sRNA libraries to RNAseq data and (3) identification and analysis of methylguanosine-capped and polyadenylated sRNAs (CPA-sRNAs). This species of small RNA is particularly interesting in Magnaporthe oryzae, as they map to transcription start and end sites of protein-coding genes. While we do not provide specific command lines for scripts, we provide a general framework for steps needed to carry out all three types of analyses, including relevant references, websites and free online tools. Screenshots are provided from our own customized interface using M. oryzae as an example, to assist the reader in visualizing many of the steps.}, journal={PLANT PATHOGENIC FUNGI AND OOMYCETES: METHODS AND PROTOCOLS}, author={Raman, Vidhyavathi and Meyers, Blake C. and Dean, Ralph A. and Donofrio, Nicole M.}, year={2018}, pages={53–66} }
 @article{dean_rouxel_2018, title={Host-Microbe Interactions: Fungi Vol 46}, volume={46}, ISSN={["1879-0364"]}, DOI={10.1016/j.mib.2018.11.009}, journal={CURRENT OPINION IN MICROBIOLOGY}, author={Dean, Ralph A. and Rouxel, Thierry}, year={2018}, month={Dec}, pages={III-V} }
 @article{oh_franck_dean_2018, title={Sequential Phosphopeptide Enrichment for Phosphoproteome Analysis of Filamentous Fungi: A Test Case Using Magnaporthe oryzae}, volume={1848}, ISBN={["978-1-4939-8723-8"]}, ISSN={["1940-6029"]}, DOI={10.1007/978-1-4939-8724-5_7}, abstractNote={A number of challenges have to be overcome to identify a complete complement of phosphorylated proteins, the phosphoproteome, from cells and tissues. Phosphorylated proteins are typically of low abundance and moreover, the proportion of phosphorylated sites on a given protein is generally low. The challenge is further compounded when the tissue from which protein can be recovered is limited. Global phosphoproteomics primarily relies on efficient enrichment methods for phosphopeptides involving affinity binding coupled with analysis by fast high-resolution mass spectrometry (MS) and subsequent identification using various software packages. Here, we describe an effective protocol for phosphopeptide enrichment using an Iron-IMAC resin in combination with titanium dioxide (TiO2) beads from trypsin digested protein samples of the filamentous fungus Magnaporthe oryzae. Representative protocols for LC-MS/MS analysis and phosphopeptide identification are also described.}, journal={PLANT PATHOGENIC FUNGI AND OOMYCETES: METHODS AND PROTOCOLS}, author={Oh, Yeonyee and Franck, William L. and Dean, Ralph A.}, year={2018}, pages={81–91} }
 @misc{soyer_balesdent_rouxel_dean_2018, title={To B or not to B: a tale of unorthodox chromosomes}, volume={46}, ISSN={["1879-0364"]}, DOI={10.1016/j.mib.2018.01.012}, abstractNote={• B chromosomes are dispensable parts of the karyotype of many eukaryotes. • Deemed genome parasites in plants and animals, provide advantage to pathogenic fungi. • Often enriched in repeats and in fast evolving pathogenicity-related genes. • B chromosomes are not a uniform class, share certain features with core chromosomes.}, journal={CURRENT OPINION IN MICROBIOLOGY}, author={Soyer, Jessica L. and Balesdent, Marie-Helene and Rouxel, Thierry and Dean, Ralph A.}, year={2018}, month={Dec}, pages={50–57} }
 @article{oh_robertson_parker_muddiman_dean_2017, title={Comparative proteomic analysis between nitrogen supplemented and starved conditions in Magnaporthe oryzae}, volume={15}, journal={Proteome Science}, author={Oh, Y. and Robertson, S. L. and Parker, J. and Muddiman, D. C. and Dean, R. A.}, year={2017} }
 @article{sharpee_oh_yi_franck_eyre_okagaki_valent_dean_2017, title={Identification and characterization of suppressors of plant cell death (SPD) effectors from Magnaporthe oryzae}, volume={18}, ISSN={["1364-3703"]}, DOI={10.1111/mpp.12449}, abstractNote={Summary}, number={6}, journal={MOLECULAR PLANT PATHOLOGY}, author={Sharpee, William and Oh, Yeonyee and Yi, Mihwa and Franck, William and Eyre, Alex and Okagaki, Laura H. and Valent, Barbara and Dean, Ralph A.}, year={2017}, month={Aug}, pages={850–863} }
 @article{okagaki_sailsbery_eyre_dean_2016, title={Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi}, volume={17}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-016-2491-y}, abstractNote={Magnaporthaceae, a family of ascomycetes, includes three fungi of great economic importance that cause disease in cereal and turf grasses: Magnaporthe oryzae (rice blast), Gaeumannomyces graminis var. tritici (take-all disease), and Magnaporthe poae (summer patch disease). Recently, the sequenced and assembled genomes for these three fungi were reported. Here, the genomes were compared for orthologous genes in order to identified genes that are unique to the Magnaporthaceae family of fungi. In addition, ortholog clustering was used to identify a core proteome for the Magnaporthaceae, which was examined for diversifying and purifying selection and evidence of two-speed genome evolution.A genome-scale comparative study was conducted across 74 fungal genomes to identify clusters of orthologous genes unique to the three Magnaporthaceae species as well as species specific genes. We found 1149 clusters that were unique to the Magnaporthaceae family of fungi with 295 of those containing genes from all three species. Gene clusters involved in metabolic and enzymatic activities were highly represented in the Magnaporthaceae specific clusters. Also highly represented in the Magnaporthaceae specific clusters as well as in the species specific genes were transcriptional regulators. In addition, we examined the relationship between gene evolution and distance to repetitive elements found in the genome. No correlations between diversifying or purifying selection and distance to repetitive elements or an increased rate of evolution in secreted and small secreted proteins were observed.Taken together, these data show that at the genome level, there is no evidence to suggest multi-speed genome evolution or that proximity to repetitive elements play a role in diversification of genes.}, journal={BMC GENOMICS}, author={Okagaki, Laura H. and Sailsbery, Joshua K. and Eyre, Alexander W. and Dean, Ralph A.}, year={2016}, month={Feb} }
 @article{parker_oh_moazami_pierce_loziuk_dean_muddiman_2016, title={Examining ubiquitinated peptide enrichment efficiency through an epitope labeled protein}, volume={512}, ISSN={["1096-0309"]}, DOI={10.1016/j.ab.2016.08.017}, abstractNote={Ubiquitination is a dynamic process that is responsible for regulation of cellular responses to stimuli in a number of biological systems. Previous efforts to study this post-translational modification have focused on protein enrichment; however, recent research utilizes the presence of the di-glycine (Gly-Gly) remnants following trypsin digestion to immuno-enrich ubiquitinated peptides. Monoclonal antibodies developed to the cleaved ubiquitin modification epitope, (tert-butoxycarbonyl) glycylglycine (Boc-Gly-Gly-NHS)1, are used to identify the Gly-Gly signature. Here, we have successfully generated the Boc-Gly-Gly-NHS modification and showed that when conjugated to a lysine containing protein, such as lysozyme, it can be applied as a standard protein to examine ubiquitinated peptide enrichment within a complex background.}, journal={ANALYTICAL BIOCHEMISTRY}, author={Parker, J. and Oh, Y. and Moazami, Y. and Pierce, J. G. and Loziuk, P. L. and Dean, R. A. and Muddiman, D. C.}, year={2016}, month={Nov}, pages={114–119} }
 @misc{sharpee_dean_2016, title={Form and function of fungal and oomycete effectors}, volume={30}, ISSN={["1878-0253"]}, DOI={10.1016/j.fbr.2016.04.001}, abstractNote={Plants are able to recognize conserved features of potential microbial invaders and mount an active defense in most cases. Over the course of evolution, a number of these microbes including plant pathogenic fungi and oomycetes have evolved means through the secretion of small molecules (effectors) to block these defenses and promote virulence. In recent years, research has uncovered a wealth of knowledge regarding how effectors function within the plant cell to promote disease. Function of effectors ranges from altering plant cellular metabolic pathways and signaling cascades, RNA silencing, anti-microbial inhibition, and interfering with recognition machinery. The importance of understanding effector function has given rise to a new area of research termed effectoromics, which in this review refers to high-throughput studies to elucidate the function of a large number of candidate effector genes. Effectoromics research has led to the identification of a number of effectors with redundant function, indicating that pathogenic fungi and oomycetes contain effectors that are individually dispensable but functionally redundant that act synergistically to promote disease.}, number={2}, journal={FUNGAL BIOLOGY REVIEWS}, author={Sharpee, William C. and Dean, Ralph A.}, year={2016}, month={Jun}, pages={62–73} }
 @article{okagaki_dean_2016, title={The influence of funding sources on the scientific method}, volume={17}, ISSN={["1364-3703"]}, DOI={10.1111/mpp.12380}, abstractNote={Funding for scientific research in the USA has become harder to obtain, especially for discovery‐based science, requiring the analysis of large datasets to find patterns and correlations. It is through such analysis that new hypotheses are formulated and dogma refuted, particularly as it pertains to science in the ‘‐omics’ era. The battle for funding has led to a change in the types of experiment that are being proposed by scientists. Grant panels are most commonly interested in proposals that are focused on solving problems, such as novel targets to prevent pathogen infection, or are guaranteed to be successful in the short term. Although it is understandable that grant panels would want to ensure that the money spent on projects will yield immediate results, targeting of virulence factors and drug targets has led to a narrowed view of pathogens and pathogenesis. 
 
How does funding influence scientific ideas and hypotheses? It is common to design studies to examine genes already associated with virulence. Previous studies are the backbone of grant writing and help to solidify the logic of scientific studies. However, focusing on previously studied virulence traits and genes narrows our view of the biological processes that occur between host and pathogen. Experiments to find novel genes associated with virulence are often discouraged in grant writing, and such ‘fishing expeditions’ typically account for a very small proportion of proposed experiments. With the advent of novel algorithms for large‐scale in silico analysis of genes and genomes, it is possible to derive a great deal of information from RNAseq, genome sequencing and proteomics. Such large‐scale analyses go beyond ‘fishing expeditions’ and have shed light on biological functions that may or may not be involved in pathogenesis. Recent developments in bioinformatics have allowed scientists to test whether or not hypotheses derived from traditional experiments can be extrapolated to the whole genome. In addition, ‘‐omics’ studies can provide data that can be mined by an entire field for many years. Thus, large‐scale bioinformatics and ‘‐omics’ projects should be viewed as a ‘good investment’ during grant funding.}, number={5}, journal={MOLECULAR PLANT PATHOLOGY}, author={Okagaki, Laura H. and Dean, Ralph A.}, year={2016}, month={Jun}, pages={651–653} }
 @article{okagaki_nunes_sailsbery_clay_brown_john_oh_young_fitzgerald_haas_et al._2015, title={Genome sequences of three phytopathogenic species of the Magnaporthaceae family of fungi}, volume={5}, number={12}, journal={G3-Genes Genomes Genetics}, author={Okagaki, L. H. and Nunes, C. C. and Sailsbery, J. and Clay, B. and Brown, D. and John, T. and Oh, Y. and Young, N. and Fitzgerald, M. and Haas, B. J. and et al.}, year={2015}, pages={2539–2545} }
 @article{jeon_choi_lee_park_huh_dean_lee_2015, title={Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae}, volume={5}, ISSN={["2045-2322"]}, DOI={10.1038/srep08567}, abstractNote={Abstract}, journal={SCIENTIFIC REPORTS}, author={Jeon, Junhyun and Choi, Jaeyoung and Lee, Gir-Won and Park, Sook-Young and Huh, Aram and Dean, Ralph A. and Lee, Yong-Hwan}, year={2015}, month={Feb} }
 @article{franck_gokce_randall_oh_eyre_muddiman_dean_2015, title={Phosphoproteome Analysis Links Protein Phosphorylation to Cellular Remodeling and Metabolic Adaptation during Magnaporthe oryzae Appressorium Development}, volume={14}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/PR501064Q}, DOI={10.1021/pr501064q}, abstractNote={The rice pathogen, Magnaporthe oryzae, undergoes a complex developmental process leading to formation of an appressorium prior to plant infection. In an effort to better understand phosphoregulation during appressorium development, a mass spectrometry based phosphoproteomics study was undertaken. A total of 2924 class I phosphosites were identified from 1514 phosphoproteins from mycelia, conidia, germlings, and appressoria of the wild type and a protein kinase A (PKA) mutant. Phosphoregulation during appressorium development was observed for 448 phosphosites on 320 phosphoproteins. In addition, a set of candidate PKA targets was identified encompassing 253 phosphosites on 227 phosphoproteins. Network analysis incorporating regulation from transcriptomic, proteomic, and phosphoproteomic data revealed new insights into the regulation of the metabolism of conidial storage reserves and phospholipids, autophagy, actin dynamics, and cell wall metabolism during appressorium formation. In particular, protein phosphorylation appears to play a central role in the regulation of autophagic recycling and actin dynamics during appressorium formation. Changes in phosphorylation were observed in multiple components of the cell wall integrity pathway providing evidence that this pathway is highly active during appressorium development. Several transcription factors were phosphoregulated during appressorium formation including the bHLH domain transcription factor MGG_05709. Functional analysis of MGG_05709 provided further evidence for the role of protein phosphorylation in regulation of glycerol metabolism and the metabolic reprogramming characteristic of appressorium formation. The data presented here represent a comprehensive investigation of the M. oryzae phosphoproteome and provide key insights on the role of protein phosphorylation during infection-related development.}, number={6}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Franck, William L. and Gokce, Emine and Randall, Shan M. and Oh, Yeonyee and Eyre, Alex and Muddiman, David C. and Dean, Ralph A.}, year={2015}, month={May}, pages={2408–2424} }
 @article{losada_pakala_fedorova_joardar_shabalina_hostetler_pakala_zafar_thomas_rodriguez-carres_et al._2014, title={Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3}, volume={352}, ISSN={["1574-6968"]}, DOI={10.1111/1574-6968.12387}, abstractNote={The soil fungus Rhizoctonia solani is an economically important pathogen of agricultural and forestry crops. Here, we present the complete sequence and analysis of the mitochondrial genome of R. solani, field isolate Rhs1AP. The genome (235 849 bp) is the largest mitochondrial genome of a filamentous fungus sequenced to date and exhibits a rich accumulation of introns, novel repeat sequences, homing endonuclease genes, and hypothetical genes. Stable secondary structures exhibited by repeat sequences suggest that they comprise functional, possibly catalytic RNA elements. RNA-Seq expression profiling confirmed that the majority of homing endonuclease genes and hypothetical genes are transcriptionally active. Comparative analysis suggests that the mitochondrial genome of R. solani is an example of a dynamic history of expansion in filamentous fungi.}, number={2}, journal={FEMS MICROBIOLOGY LETTERS}, author={Losada, Liliana and Pakala, Suman B. and Fedorova, Natalie D. and Joardar, Vinita and Shabalina, Svetlana A. and Hostetler, Jessica and Pakala, Suchitra M. and Zafar, Nikhat and Thomas, Elizabeth and Rodriguez-Carres, Marianela and et al.}, year={2014}, month={Mar}, pages={165–173} }
 @article{jeon_choi_lee_dean_lee_2013, title={Experimental Evolution Reveals Genome-Wide Spectrum and Dynamics of Mutations in the Rice Blast Fungus, Magnaporthe oryzae}, volume={8}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0065416}, abstractNote={Knowledge on mutation processes is central to interpreting genetic analysis data as well as understanding the underlying nature of almost all evolutionary phenomena. However, studies on genome-wide mutational spectrum and dynamics in fungal pathogens are scarce, hindering our understanding of their evolution and biology. Here, we explored changes in the phenotypes and genome sequences of the rice blast fungus Magnaporthe oryzae during the forced in vitro evolution by weekly transfer of cultures on artificial media. Through combination of experimental evolution with high throughput sequencing technology, we found that mutations accumulate rapidly prior to visible phenotypic changes and that both genetic drift and selection seem to contribute to shaping mutational landscape, suggesting the buffering capacity of fungal genome against mutations. Inference of mutational effects on phenotypes through the use of T-DNA insertion mutants suggested that at least some of the DNA sequence mutations are likely associated with the observed phenotypic changes. Furthermore, our data suggest oxidative damages and UV as major sources of mutation during subcultures. Taken together, our work revealed important properties of original source of variation in the genome of the rice blast fungus. We believe that these results provide not only insights into stability of pathogenicity and genome evolution in plant pathogenic fungi but also a model in which evolution of fungal pathogens in natura can be comparatively investigated.}, number={5}, journal={PLOS ONE}, author={Jeon, Junhyun and Choi, Jaeyoung and Lee, Gir-Won and Dean, Ralph A. and Lee, Yong-Hwan}, year={2013}, month={May} }
 @article{franck_gokce_oh_muddiman_dean_2013, title={Temporal Analysis of theMagnaporthe OryzaeProteome During Conidial Germination and Cyclic AMP (cAMP)-mediated Appressorium Formation}, volume={12}, ISSN={1535-9476 1535-9484}, url={http://dx.doi.org/10.1074/MCP.M112.025874}, DOI={10.1074/mcp.m112.025874}, abstractNote={Rice blast disease caused by Magnaporthe oryzae is one of the most serious threats to global rice production. During the earliest stages of rice infection, M. oryzae conidia germinate on the leaf surface and form a specialized infection structure termed the appressorium. The development of the appressorium represents the first critical stage of infectious development. A total of 3200 unique proteins were identified by nanoLC-MS/MS in a temporal study of conidial germination and cAMP-induced appressorium formation in M. oryzae. Using spectral counting based label free quantification, observed changes in relative protein abundance during the developmental process revealed changes in the cell wall biosynthetic machinery, transport functions, and production of extracellular proteins in developing appressoria. One hundred and sixty-six up-regulated and 208 down-regulated proteins were identified in response to cAMP treatment. Proteomic analysis of a cAMP-dependent protein kinase A mutant that is compromised in the ability to form appressoria identified proteins whose developmental regulation is dependent on cAMP signaling. Selected reaction monitoring was used for absolute quantification of four regulated proteins to validate the global proteomics data and confirmed the germination or appressorium specific regulation of these proteins. Finally, a comparison of the proteome and transcriptome was performed and revealed little correlation between transcript and protein regulation. A subset of regulated proteins were identified whose transcripts show similar regulation patterns and include many of the most strongly regulated proteins indicating a central role in appressorium formation. A temporal quantitative RT-PCR analysis confirmed a strong correlation between transcript and protein abundance for some but not all genes. Collectively, the data presented here provide the first comprehensive view of the M. oryzae proteome during early infection-related development and highlight biological processes important for pathogenicity.}, number={8}, journal={Molecular & Cellular Proteomics}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={Franck, William L. and Gokce, Emine and Oh, Yeonyee and Muddiman, David C. and Dean, Ralph A.}, year={2013}, month={May}, pages={2249–2265} }
 @article{xue_yang_li_hu_yao_dean_zhao_shen_zhang_li_et al._2012, title={Comparative Analysis of the Genomes of Two Field Isolates of the Rice Blast Fungus Magnaporthe oryzae}, volume={8}, ISSN={["1553-7404"]}, DOI={10.1371/journal.pgen.1002869}, abstractNote={Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice worldwide. The fungal pathogen is notorious for its ability to overcome host resistance. To better understand its genetic variation in nature, we sequenced the genomes of two field isolates, Y34 and P131. In comparison with the previously sequenced laboratory strain 70-15, both field isolates had a similar genome size but slightly more genes. Sequences from the field isolates were used to improve genome assembly and gene prediction of 70-15. Although the overall genome structure is similar, a number of gene families that are likely involved in plant-fungal interactions are expanded in the field isolates. Genome-wide analysis on asynonymous to synonymous nucleotide substitution rates revealed that many infection-related genes underwent diversifying selection. The field isolates also have hundreds of isolate-specific genes and a number of isolate-specific gene duplication events. Functional characterization of randomly selected isolate-specific genes revealed that they play diverse roles, some of which affect virulence. Furthermore, each genome contains thousands of loci of transposon-like elements, but less than 30% of them are conserved among different isolates, suggesting active transposition events in M. oryzae. A total of approximately 200 genes were disrupted in these three strains by transposable elements. Interestingly, transposon-like elements tend to be associated with isolate-specific or duplicated sequences. Overall, our results indicate that gain or loss of unique genes, DNA duplication, gene family expansion, and frequent translocation of transposon-like elements are important factors in genome variation of the rice blast fungus.}, number={8}, journal={PLOS GENETICS}, author={Xue, Minfeng and Yang, Jun and Li, Zhigang and Hu, Songnian and Yao, Nan and Dean, Ralph A. and Zhao, Wensheng and Shen, Mi and Zhang, Haiwang and Li, Chao and et al.}, year={2012}, month={Aug} }
 @misc{nunes_dean_2012, title={Host-induced gene silencing: a tool for understanding fungal host interaction and for developing novel disease control strategies}, volume={13}, ISSN={["1364-3703"]}, DOI={10.1111/j.1364-3703.2011.00766.x}, abstractNote={SUMMARY}, number={5}, journal={MOLECULAR PLANT PATHOLOGY}, author={Nunes, Cristiano C. and Dean, Ralph A.}, year={2012}, month={Jun}, pages={519–529} }
 @article{gokce_franck_oh_dean_muddiman_2012, title={In-Depth Analysis of the Magnaporthe oryzae Conidial Proteome}, volume={11}, ISSN={["1535-3907"]}, DOI={10.1021/pr300604s}, abstractNote={The filamentous fungus Magnaporthe oryzae (M. oryzae) is the causative agent of rice blast disease and presents a significant threat to worldwide rice production. To establish the groundwork for future research on the pathogenic development of M. oryzae, a global proteomic study of conidia was performed. The filter aided sample preparation method (FASP) and anion StageTip fractionation combined with long, optimized shallow 210 min nanoLC gradients prior to mass spectrometry analysis on an Orbitrap XL was applied, which resulted in a doubling of protein identifications in comparison to our previous GeLC analysis. Herein, we report the identification of 2912 conidial proteins at a 1% protein false discovery rate (FDR) and we present the most extensive study performed on M. oryzae conidia to date. A similar distribution between identified proteins and the predicted proteome was observed when subcellular localization analysis was performed, suggesting the detected proteins build a representative portion of the predicted proteome. A higher percentage of cytoplasmic proteins (associated with translation, energy, and metabolism) were observed in the conidial proteome relative to the whole predicted proteome. Conversely, nuclear and extracellular proteins were less well represented in the conidial proteome. Further analysis by gene ontology revealed biological insights into identified proteins important for central metabolic processes and the physiology of conidia.}, number={12}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Gokce, Emine and Franck, William L. and Oh, Yeonyee and Dean, Ralph A. and Muddiman, David C.}, year={2012}, month={Dec}, pages={5827–5835} }
 @article{sailsbery_atchley_dean_2012, title={Phylogenetic Analysis and Classification of the Fungal bHLH Domain}, volume={29}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msr288}, abstractNote={The basic Helix-Loop-Helix (bHLH) domain is an essential highly conserved DNA-binding domain found in many transcription factors in all eukaryotic organisms. The bHLH domain has been well studied in the Animal and Plant Kingdoms but has yet to be characterized within Fungi. Herein, we obtained and evaluated the phylogenetic relationship of 490 fungal-specific bHLH containing proteins from 55 whole genome projects composed of 49 Ascomycota and 6 Basidiomycota organisms. We identified 12 major groupings within Fungi (F1-F12); identifying conserved motifs and functions specific to each group. Several classification models were built to distinguish the 12 groups and elucidate the most discerning sites in the domain. Performance testing on these models, for correct group classification, resulted in a maximum sensitivity and specificity of 98.5% and 99.8%, respectively. We identified 12 highly discerning sites and incorporated those into a set of rules (simplified model) to classify sequences into the correct group. Conservation of amino acid sites and phylogenetic analyses established that like plant bHLH proteins, fungal bHLH-containing proteins are most closely related to animal Group B. The models used in these analyses were incorporated into a software package, the source code for which is available at www.fungalgenomics.ncsu.edu.}, number={5}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Sailsbery, Joshua K. and Atchley, William R. and Dean, Ralph A.}, year={2012}, month={May}, pages={1301–1318} }
 @article{oh_franck_han_shows_gokce_muddiman_dean_2012, title={Polyubiquitin Is Required for Growth, Development and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae}, volume={7}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0042868}, DOI={10.1371/journal.pone.0042868}, abstractNote={Protein ubiquitination, which is highly selective, regulates many important biological processes including cellular differentiation and pathogenesis in eukaryotic cells. Here, we integrated pharmacological, molecular and proteomic approaches to explore the role of ubiquitination in Magnaporthe oryzae, the leading fungal disease of rice world-wide. Inhibition of ubiquitin-mediated proteolysis using the 26S proteasome inhibitor, Bortezomib, significantly attenuated conidia germination, appressorium formation and pathogenicity in M. oryzae. Gene expression analysis revealed that many genes associated with protein ubiquitination were developmentally regulated during conidia germination. Only a few, including a polyubiquitin encoding gene, MGG_01282, were more abundantly expressed during appressorium formation and under nitrogen starvation. Targeted gene deletion of MGG_01282, in addition to a significant reduction in protein ubiquitination as determined by immuno blot assays, resulted in pleiotropic effects on M. oryzae including reduced growth and sporulation, abnormal conidia morphology, reduced germination and appressorium formation, and the inability to cause disease. Mutants were also defective in sexual development and were female sterile. Using mass spectrometry, we identified 63 candidate polyubiquitinated proteins under nitrogen starvation, which included overrepresentation of proteins involved in translation, transport and protein modification. Our study suggests that ubiquitination of target proteins plays an important role in nutrient assimilation, development and pathogenicity of M. oryzae.}, number={8}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Oh, Yeonyee and Franck, William L. and Han, Sang-Oh and Shows, Angela and Gokce, Emine and Muddiman, David C. and Dean, Ralph A.}, editor={Nielsen, KirstenEditor}, year={2012}, month={Aug}, pages={e42868} }
 @misc{dean_van kan_pretorius_hammond-kosack_di pietro_spanu_rudd_dickman_kahmann_ellis_et al._2012, title={The Top 10 fungal pathogens in molecular plant pathology}, volume={13}, ISSN={["1364-3703"]}, DOI={10.1111/j.1364-3703.2011.00783.x}, abstractNote={SUMMARY}, number={4}, journal={MOLECULAR PLANT PATHOLOGY}, author={Dean, Ralph and Van Kan, Jan A. L. and Pretorius, Zacharias A. and Hammond-Kosack, Kim E. and Di Pietro, Antonio and Spanu, Pietro D. and Rudd, Jason J. and Dickman, Marty and Kahmann, Regine and Ellis, Jeff and et al.}, year={2012}, month={May}, pages={414–430} }
 @article{nunes_sailsbery_dean_2011, title={Characterization and application of small RNAs and RNA silencing mechanisms in fungi}, volume={25}, ISSN={1749-4613}, url={http://dx.doi.org/10.1016/j.fbr.2011.10.001}, DOI={10.1016/j.fbr.2011.10.001}, abstractNote={Although extensively cataloged and functionally diverse in plants and animals, the role and targets of small RNAs remain mostly uncharacterized in filamentous fungi. To date, much of the knowledge of small RNAs in filamentous fungi has been derived from studies of a limited group of fungi, most notably in Neurospora crassa. While most of the recently discovered classes of small RNAs appear to be unique to fungi some are commonly found in eukaryotes. It is noteworthy that the RNA silencing protein machinery involved in small RNA biogenesis has also diverged greatly, particularly within filamentous fungi, and may explain the diversity of small RNA classes. In this review, we summarize important classes of eukaryotic small RNAs and provide a current analysis of the RNA silencing machinery based on available fungal genome sequences. Finally, we discuss opportunities for exploiting knowledge of small RNAs and RNA silencing for practical application such as engineering plants resistant to fungal pathogens.}, number={4}, journal={Fungal Biology Reviews}, publisher={Elsevier BV}, author={Nunes, Cristiano C. and Sailsbery, Joshua K. and Dean, Ralph A.}, year={2011}, month={Dec}, pages={172–180} }
 @article{collier_randall_sarkar_rao_dean_muddiman_2011, title={Comparison of stable-isotope labeling with amino acids in cell culture and spectral counting for relative quantification of protein expression}, volume={25}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.5151}, abstractNote={Protein quantification is one of the principal goals of mass spectrometry (MS)‐based proteomics, and many strategies exist to achieve it. Several approaches involve the incorporation of a stable‐isotope label using either chemical derivatization, enzymatically catalyzed incorporation of 18O, or metabolic labeling in a cell or tissue culture. These techniques can be cost or time prohibitive or not amenable to the biological system of interest. Label‐free techniques including those utilizing integrated ion abundance and spectral counting offer an alternative to stable‐isotope‐based methodologies. Herein, we present the comparison of stable‐isotope labeling of amino acids in cell culture (SILAC) with spectral counting for the quantification of human embryonic stem cells as they differentiate toward the trophectoderm at three time points. Our spectral counting experimental strategy resulted in the identification of 2641 protein groups across three time points with an average sequence coverage of 30.3%, of which 1837 could be quantified with more than five spectral counts. SILAC quantification was able to identify 1369 protein groups with an average coverage of 24.7%, of which 1027 could be quantified across all time points. Within this context we further explore the capacity of each strategy for proteome coverage, variation in quantification, and the relative sensitivity of each technique to the detection of change in relative protein expression. Copyright © 2011 John Wiley & Sons, Ltd.}, number={17}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Collier, Timothy S. and Randall, Shan M. and Sarkar, Prasenjit and Rao, Balaji M. and Dean, Ralph A. and Muddiman, David C.}, year={2011}, month={Sep}, pages={2524–2532} }
 @article{nunes_gowda_sailsbery_xue_chen_brown_oh_mitchell_dean_2011, title={Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae}, volume={12}, DOI={10.1186/1471-2164-12-288}, abstractNote={Abstract}, journal={BMC Genomics}, author={Nunes, C. C. and Gowda, M. and Sailsbery, J. and Xue, M. F. and Chen, F. and Brown, D. E. and Oh, Y. and Mitchell, T. K. and Dean, Ralph}, year={2011} }
 @article{gokce_shuford_franck_dean_muddiman_2011, title={Evaluation of Normalization Methods on GeLC-MS/MS Label-Free Spectral Counting Data to Correct for Variation during Proteomic Workflows}, volume={22}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-011-0237-2}, abstractNote={Normalization of spectral counts (SpCs) in label-free shotgun proteomic approaches is important to achieve reliable relative quantification. Three different SpC normalization methods, total spectral count (TSpC) normalization, normalized spectral abundance factor (NSAF) normalization, and normalization to selected proteins (NSP) were evaluated based on their ability to correct for day-to-day variation between gel-based sample preparation and chromatographic performance. Three spectral counting data sets obtained from the same biological conidia sample of the rice blast fungus Magnaporthe oryzae were analyzed by 1D gel and liquid chromatography-tandem mass spectrometry (GeLC-MS/MS). Equine myoglobin and chicken ovalbumin were spiked into the protein extracts prior to 1D-SDS- PAGE as internal protein standards for NSP. The correlation between SpCs of the same proteins across the different data sets was investigated. We report that TSpC normalization and NSAF normalization yielded almost ideal slopes of unity for normalized SpC versus average normalized SpC plots, while NSP did not afford effective corrections of the unnormalized data. Furthermore, when utilizing TSpC normalization prior to relative protein quantification, t-testing and fold-change revealed the cutoff limits for determining real biological change to be a function of the absolute number of SpCs. For instance, we observed the variance decreased as the number of SpCs increased, which resulted in a higher propensity for detecting statistically significant, yet artificial, change for highly abundant proteins. Thus, we suggest applying higher confidence level and lower fold-change cutoffs for proteins with higher SpCs, rather than using a single criterion for the entire data set. By choosing appropriate cutoff values to maintain a constant false positive rate across different protein levels (i.e., SpC levels), it is expected this will reduce the overall false negative rate, particularly for proteins with higher SpCs.}, number={12}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Gokce, Emine and Shuford, Christopher M. and Franck, William L. and Dean, Ralph A. and Muddiman, David C.}, year={2011}, month={Dec}, pages={2199–2208} }
 @article{andrews_dean_hawkridge_muddiman_2011, title={Improving Proteome Coverage on a LTQ-Orbitrap Using Design of Experiments}, volume={22}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-011-0075-2}, abstractNote={Design of experiments (DOE) was used to determine improved settings for a LTQ-Orbitrap XL to maximize proteome coverage of Saccharomyces cerevisiae. A total of nine instrument parameters were evaluated with the best values affording an increase of approximately 60% in proteome coverage. Utilizing JMP software, 2 DOE screening design tables were generated and used to specify parameter values for instrument methods. DOE 1, a fractional factorial design, required 32 methods fully resolving the investigation of six instrument parameters involving only half the time necessary for a full factorial design of the same resolution. It was advantageous to complete a full factorial design for the analysis of three additional instrument parameters. Measured with a maximum of 1% false discovery rate, protein groups, unique peptides, and spectral counts gauged instrument performance. Randomized triplicate nanoLC-LTQ-Orbitrap XL MS/MS analysis of the S. cerevisiae digest demonstrated that the following five parameters significantly influenced proteome coverage of the sample: (1) maximum ion trap ionization time; (2) monoisotopic precursor selection; (3) number of MS/MS events; (4) capillary temperature; and (5) tube lens voltage. Minimal influence on the proteome coverage was observed for the remaining four parameters (dynamic exclusion duration, resolving power, minimum count threshold to trigger a MS/MS event, and normalized collision energy). The DOE approach represents a time- and cost-effective method for empirically optimizing MS-based proteomics workflows including sample preparation, LC conditions, and multiple instrument platforms.}, number={4}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Andrews, Genna L. and Dean, Ralph A. and Hawkridge, Adam M. and Muddiman, David C.}, year={2011}, month={Apr}, pages={773–783} }
 @article{gokce_andrews_dean_muddiman_2011, title={Increasing proteome coverage with offline RP HPLC coupled to online RP nanoLC-MS}, volume={879}, ISSN={["1873-376X"]}, DOI={10.1016/j.jchromb.2011.01.032}, abstractNote={Fractionation prior to mass spectrometry is an indispensable step in proteomics. In this paper we report the success of performing offline reversed phase high pressure liquid chromatography (HPLC) fractionation on a C18 2.0 mm×150 mm column at the peptide level with microliter per minute flow rates prior to online nano-flow reversed phase liquid chromatography mass spectrometry (nanoLC-MS) using the well-studied fungus Saccharomyces cerevisiae. A C18 75 μm×150 mm column was used online and the online elution gradients for each fraction were adjusted in order to obtain well resolved separation. Comparing this method directly to only performing nanoLC-MS we observed a 61.6% increase in the number of identified proteins. At a 1% false discovery rate 1028 proteins were identified using two dimensions of RPLC versus 636 proteins identified in a single nano-flow separation. The majority of proteins identified by one dimension of nano-LC were present in the proteins identified in our two dimensional strategy. Although increasing analysis time, this non-orthogonal and facile pre-fractionation method affords a more comprehensive examination of the proteome.}, number={9-10}, journal={JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES}, author={Gokce, Emine and Andrews, Genna L. and Dean, Ralph A. and Muddiman, David C.}, year={2011}, month={Mar}, pages={610–614} }
 @article{li_zhou_kong_wang_zhang_zhu_mitchell_dean_xu_2011, title={MoSfl1 Is Important for Virulence and Heat Tolerance in Magnaporthe oryzae}, volume={6}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0019951}, abstractNote={The formation of appressoria, specialized plant penetration structures of Magnaporthe oryzae, is regulated by the MST11-MST7-PMK1 MAP kinase cascade. One of its downstream transcription factor, MST12, is important for penetration and invasive growth but dispensable for appressorium formation. To identify additional downstream targets that are regulated by Pmk1, in this study we performed phosphorylation assays with a protein microarray composed of 573 M. oryzae transcription factor (TF) genes. Three of the TF genes phosphorylated by Pmk1 in vitro were further analyzed by coimmunoprecipitation assays. One of them, MoSFL1, was found to interact with Pmk1 in vivo. Like other Sfl1 orthologs, the MoSfl1 protein has the HSF-like domain. When expressed in yeast, MoSFL1 functionally complemented the flocculation defects of the sfl1 mutant. In M. oryzae, deletion of MoSFl1 resulted in a significant reduction in virulence on rice and barley seedlings. Consistent with this observation, the Mosfl1 mutant was defective in invasive growth in penetration assays with rice leaf sheaths. In comparison with that of vegetative hyphae, the expression level of MoSFL1 was increased in appressoria and infected rice leaves. The Mosfl1 mutant also had increased sensitivity to elevated temperatures. In CM cultures of the Mosfl1 and pmk1 mutants grown at 30°C, the production of aerial hyphae and melanization were reduced but their growth rate was not altered. When assayed by qRT-PCR, the transcription levels of the MoHSP30 and MoHSP98 genes were reduced 10- and 3-fold, respectively, in the Mosfl1 mutant. SFL1 orthologs are conserved in filamentous ascomycetes but none of them have been functionally characterized in non-Saccharomycetales fungi. MoSfl1 has one putative MAPK docking site and three putative MAPK phosphorylation sites. Therefore, it may be functionally related to Pmk1 in the regulation of invasive growth and stress responses in M. oryzae.}, number={5}, journal={PLOS ONE}, author={Li, Guotian and Zhou, Xiaoying and Kong, Lingan and Wang, Yuling and Zhang, Haifeng and Zhu, Heng and Mitchell, Thomas K. and Dean, Ralph A. and Xu, Jin-Rong}, year={2011}, month={May} }
 @article{mathioni_belo_rizzo_dean_donofrio_2011, title={Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses}, volume={12}, ISSN={["1471-2164"]}, DOI={10.1186/1471-2164-12-49}, abstractNote={Abstract}, journal={BMC GENOMICS}, author={Mathioni, Sandra M. and Belo, Andre and Rizzo, Christopher J. and Dean, Ralph A. and Donofrio, Nicole M.}, year={2011}, month={Jan} }
 @article{kim_hu_oh_park_choi_lee_dean_mitchell_2010, title={Combining ChIP-chip and Expression Profiling to Model the MoCRZ1 Mediated Circuit for Ca2+/Calcineurin Signaling in the Rice Blast Fungus}, volume={6}, ISSN={["1553-7374"]}, DOI={10.1371/journal.ppat.1000909}, abstractNote={Significant progress has been made in defining the central signaling networks in many organisms, but collectively we know little about the downstream targets of these networks and the genes they regulate. To reconstruct the regulatory circuit of calcineurin signal transduction via MoCRZ1, a Magnaporthe oryzae C2H2 transcription factor activated by calcineurin dephosphorylation, we used a combined approach of chromatin immunoprecipitation - chip (ChIP-chip), coupled with microarray expression studies. One hundred forty genes were identified as being both a direct target of MoCRZ1 and having expression concurrently differentially regulated in a calcium/calcineurin/MoCRZ1 dependent manner. Highly represented were genes involved in calcium signaling, small molecule transport, ion homeostasis, cell wall synthesis/maintenance, and fungal virulence. Of particular note, genes involved in vesicle mediated secretion necessary for establishing host associations, were also found. MoCRZ1 itself was a target, suggesting a previously unreported autoregulation control point. The data also implicated a previously unreported feedback regulation mechanism of calcineurin activity. We propose that calcium/calcineurin regulated signal transduction circuits controlling development and pathogenicity manifest through multiple layers of regulation. We present results from the ChIP-chip and expression analysis along with a refined model of calcium/calcineurin signaling in this important plant pathogen.}, number={5}, journal={PLOS PATHOGENS}, author={Kim, Soonok and Hu, Jinnan and Oh, Yeonyee and Park, Jongsun and Choi, Jinhee and Lee, Yong-Hwan and Dean, Ralph A. and Mitchell, Thomas K.}, year={2010}, month={May} }
 @article{collier_sarkar_franck_rao_dean_muddiman_2010, title={Direct Comparison of Stable Isotope Labeling by Amino Acids in Cell Culture and Spectral Counting for Quantitative Proteomics}, volume={82}, ISSN={["1520-6882"]}, DOI={10.1021/ac101978b}, abstractNote={Numerous experimental strategies exist for relative protein quantification, one of the primary objectives of mass spectrometry based proteomics analysis. These strategies mostly involve the incorporation of a stable isotope label via either metabolic incorporation in cell or tissue culture (¹⁵N/¹⁴N metabolic labeling, stable isotope labeling by amino acids in cell culture (SILAC)), chemical derivatization (ICAT, iTRAQ, TMT), or enzymatically catalyzed incorporation (¹⁸O labeling). Also, these techniques can be cost or time prohibitive or not amenable to the biological system of interest (i.e., metabolic labeling of clinical samples, most animals, or fungi). This is the case with the quantification of fungal proteomes, which often require auxotroph mutants to fully metabolically label. Alternatively, label-free strategies for protein quantification such as using integrated ion abundance and spectral counting have been demonstrated for quantification affording over 2 orders of magnitude of dynamic range which is comparable to metabolic labeling strategies. Direct comparisons of these quantitative techniques are largely lacking in the literature but are highly warranted in order to evaluate the capabilities, limitations, and analytical variability of available quantitative strategies. Here, we present the direct comparison of SILAC to label-free quantification by spectral counting of an identical set of data from the bottom-up proteomic analysis of human embryonic stem cells, which are readily able to be quantified using both strategies, finding that both strategies result in a similar number of protein identifications. We also discuss necessary constraints for accurate quantification using spectral counting and assess the potential of this label-free strategy as a viable alternative for quantitative proteomics.}, number={20}, journal={ANALYTICAL CHEMISTRY}, author={Collier, Timothy S. and Sarkar, Prasenjit and Franck, William L. and Rao, Balaji M. and Dean, Ralph A. and Muddiman, David C.}, year={2010}, month={Oct}, pages={8696–8702} }
 @misc{torto-alalibo_collmer_gwinn-giglio_lindeberg_meng_chibucos_tseng_lomax_biehl_ireland_et al._2010, title={Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology}, volume={74}, ISSN={["1098-5557"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-78650086447&partnerID=MN8TOARS}, DOI={10.1128/mmbr.00017-10}, abstractNote={SUMMARYMicrobes form intimate relationships with hosts (symbioses) that range from mutualism to parasitism. Common microbial mechanisms involved in a successful host association include adhesion, entry of the microbe or its effector proteins into the host cell, mitigation of host defenses, and nutrient acquisition. Genes associated with these microbial mechanisms are known for a broad range of symbioses, revealing both divergent and convergent strategies. Effective comparisons among these symbioses, however, are hampered by inconsistent descriptive terms in the literature for functionally similar genes. Bioinformatic approaches that use homology-based tools are limited to identifying functionally similar genes based on similarities in their sequences. An effective solution to these limitations is provided by the Gene Ontology (GO), which provides a standardized language to describe gene products from all organisms. The GO comprises three ontologies that enable one to describe the molecular function(s) of gene products, the biological processes to which they contribute, and their cellular locations. Beginning in 2004, the Plant-Associated Microbe Gene Ontology (PAMGO) interest group collaborated with the GO consortium to extend the GO to accommodate terms for describing gene products associated with microbe-host interactions. Currently, over 900 terms that describe biological processes common to diverse plant- and animal-associated microbes are incorporated into the GO database. Here we review some unifying themes common to diverse host-microbe associations and illustrate how the new GO terms facilitate a standardized description of the gene products involved. We also highlight areas where new terms need to be developed, an ongoing process that should involve the whole community.}, number={4}, journal={MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS}, author={Torto-Alalibo, Trudy and Collmer, Candace W. and Gwinn-Giglio, Michelle and Lindeberg, Magdalen and Meng, Shaowu and Chibucos, Marcus C. and Tseng, Tsai-Tien and Lomax, Jane and Biehl, Bryan and Ireland, Amelia and et al.}, year={2010}, month={Dec}, pages={479–503} }
 @misc{meng_torto-alalibo_chibucos_tyler_dean_2009, title={Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology terms}, volume={9}, ISSN={["1471-2180"]}, DOI={10.1186/1471-2180-9-s1-s7}, abstractNote={Abstract}, journal={BMC MICROBIOLOGY}, author={Meng, Shaowu and Torto-Alalibo, Trudy and Chibucos, Marcus C. and Tyler, Brett M. and Dean, Ralph A.}, year={2009}, month={Feb} }
 @misc{meng_brown_ebbole_torto-alalibo_oh_deng_mitchell_dean_2009, title={Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae}, volume={9}, ISSN={["1471-2180"]}, DOI={10.1186/1471-2180-9-s1-s8}, abstractNote={Abstract}, journal={BMC MICROBIOLOGY}, author={Meng, Shaowu and Brown, Douglas E. and Ebbole, Daniel J. and Torto-Alalibo, Trudy and Oh, Yeon Yee and Deng, Jixin and Mitchell, Thomas K. and Dean, Ralph A.}, year={2009}, month={Feb} }
 @misc{torto-alalibo_meng_dean_2009, title={Infection strategies of filamentous microbes described with the Gene Ontology}, volume={17}, ISSN={["1878-4380"]}, DOI={10.1016/j.tim.2009.05.003}, abstractNote={Filamentous microbes that form highly developed symbiotic associations (ranging from pathogenesis to mutualism) with their hosts include fungi, oomycetes and actinomycete bacteria. These organisms share many common features in growth, development and infection and have evolved similar strategies for neutralizing host defense responses to establish symbioses. Recent advances in sequencing technologies have led to a remarkable increase in the number of sequenced genomes of filamentous organisms. Analysis of the available genomes has provided useful information about genes that might be important for host infection and colonization. However, because many functional similarities among these organisms have arisen by convergent evolution, sequence-based genomic comparisons will miss many genes that are functionally analogous. In the absence of sequence similarity, annotating genes with standardized terms from the Gene Ontology (GO) can facilitate functional comparisons. Here, we review common strategies employed by filamentous organisms during colonization of their hosts, with reference to GO terms that best describe the processes involved. Filamentous microbes that form highly developed symbiotic associations (ranging from pathogenesis to mutualism) with their hosts include fungi, oomycetes and actinomycete bacteria. These organisms share many common features in growth, development and infection and have evolved similar strategies for neutralizing host defense responses to establish symbioses. Recent advances in sequencing technologies have led to a remarkable increase in the number of sequenced genomes of filamentous organisms. Analysis of the available genomes has provided useful information about genes that might be important for host infection and colonization. However, because many functional similarities among these organisms have arisen by convergent evolution, sequence-based genomic comparisons will miss many genes that are functionally analogous. In the absence of sequence similarity, annotating genes with standardized terms from the Gene Ontology (GO) can facilitate functional comparisons. Here, we review common strategies employed by filamentous organisms during colonization of their hosts, with reference to GO terms that best describe the processes involved. filamentous or rod-shaped bacteria of the order Actinomycetales. extracellular component around mesophyll cells in a plant. swollen dome-shaped structure differentiated from germ tube to facilitate penetration of the host plant. symbionts that depend entirely on their host for their nutrients and as such preserve the viability of their host. a class of mostly aquatic fungi. non-motile asexual spores that develop off conidiophores in certain oomycetes and fungi. fungi that live asymptomatically within a plant tissue for part of its life. germination hypha, which emerges from a spore and often penetrates the host tissue. specialized branch of a hypha formed inside a host cell by certain fungi and oomycetes in order to obtain nourishment from their host. symbionts that initially inhabit living host cells and as infection proceeds, actively kill the host to obtain nutrients from dead tissues. a class of cysteine-rich proteins that form hydrophobic coating on surfaces. fungi that form mutualistic association with the roots of plants. symbiont that kills host tissues during colonization and obtains nutrients from the dead matter. organisms that resemble filamentous fungi but are evolutionarily related to heterokont biflagellate algae in the kingdom Stramenopila. molecules that are found in microorganisms but not in the host. a serine protease similar to subtilisin and characterized by a catalytic triad of amino acids that include aspartate, histidine and serine. a spherical vesicle found in the cytoplasm of zoospores. asexual spores which use flagella for locomotion.}, number={7}, journal={TRENDS IN MICROBIOLOGY}, author={Torto-Alalibo, Trudy and Meng, Shaowu and Dean, Ralph A.}, year={2009}, month={Jul}, pages={320–327} }
 @article{powell_conant_brown_carbone_dean_2008, title={Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens}, volume={9}, ISSN={["1471-2164"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-42549135491&partnerID=MN8TOARS}, DOI={10.1186/1471-2164-9-147}, abstractNote={Abstract}, journal={BMC GENOMICS}, author={Powell, Amy J. and Conant, Gavin C. and Brown, Douglas E. and Carbone, Ignazio and Dean, Ralph A.}, year={2008}, month={Mar} }
 @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{shao_wang_dean_lin_gao_hu_2008, title={Expression of a harpin-encoding gene in rice confers durable nonspecific resistance to Magnaporthe grisea}, volume={6}, ISSN={["1467-7644"]}, DOI={10.1111/j.1467-7652.2007.00304.x}, abstractNote={Summary}, number={1}, journal={PLANT BIOTECHNOLOGY JOURNAL}, author={Shao, Min and Wang, Jinsheng and Dean, Ralph A. and Lin, Yongjun and Gao, Xuewen and Hu, Shuijin}, year={2008}, month={Jan}, pages={73–81} }
 @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}, abstractNote={Naturally occurring Antisense Transcripts (NATs) compose an emerging group of regulatory RNAs. These regulatory elements appear in all organisms examined, but little is known about global expression of NATs in fungi. Analysis of currently available EST sequences suggests that 352 cis NATs are present in Aspergillus flavus. An Affymetrix GeneChip microarray containing probes for these cis NATs, as well as all predicted genes in A. flavus, allowed a whole genome expression analysis of these elements in response to two ecologically important temperatures for the fungus. RNA expression analysis showed that 32 NATs and 2,709 genes were differentially expressed between 37 degrees C, the optimum temperature for growth, and 28 degrees C, the conducive temperature for the biosynthesis of aflatoxin (AF) and many other secondary metabolites. These NATs correspond to sense genes with diverse functions including transcription initiation, carbohydrate processing and binding, temperature sensitive morphogenesis, and secondary metabolism. This is the first report of a whole genome transcriptional analysis of NAT expression in a fungus.}, 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} }
 @misc{oh_donofrio_pan_coughlan_brown_meng_mitchell_dean_2008, title={Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae}, volume={9}, ISSN={["1474-760X"]}, DOI={10.1186/gb-2008-9-5-r85}, abstractNote={Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood.We analyzed genome-wide gene expression changes during spore germination and appressorium formation on a hydrophobic surface compared to induction by cAMP. During spore germination, 2,154 (approximately 21%) genes showed differential expression, with the majority being up-regulated. During appressorium formation, 357 genes were differentially expressed in response to both stimuli. These genes, which we refer to as appressorium consensus genes, were functionally grouped into Gene Ontology categories. Overall, we found a significant decrease in expression of genes involved in protein synthesis. Conversely, expression of genes associated with protein and amino acid degradation, lipid metabolism, secondary metabolism and cellular transportation exhibited a dramatic increase. We functionally characterized several differentially regulated genes, including a subtilisin protease (SPM1) and a NAD specific glutamate dehydrogenase (Mgd1), by targeted gene disruption. These studies revealed hitherto unknown findings that protein degradation and amino acid metabolism are essential for appressorium formation and subsequent infection.We present the first comprehensive genome-wide transcript profile study and functional analysis of infection structure formation by a fungal plant pathogen. Our data provide novel insight into the underlying molecular mechanisms that will directly benefit efforts to identify fungal pathogenicity factors and aid the development of new disease management strategies.}, number={5}, journal={GENOME BIOLOGY}, author={Oh, Yeonyee and Donofrio, Nicole and Pan, Huaqin and Coughlan, Sean and Brown, Douglas E. and Meng, Shaowu and Mitchell, Thomas and Dean, Ralph A.}, year={2008} }
 @article{meng_patel_heist_betts_tucker_galadima_donofrio_brown_mitchell_li_et al._2007, title={A systematic analysis of T-DNA insertion events in Magnaporthe oryzae}, volume={44}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2007.04.002}, abstractNote={We describe here the analysis of random T-DNA insertions that were generated as part of a large-scale insertional mutagenesis project for Magnaporthe oryzae. Chromosomal regions flanking T-DNA insertions were rescued by inverse PCR, sequenced and used to search the M. oryzae genome assembly. Among the 175 insertions for which at least one flank was rescued, 137 had integrated in single-copy regions of the genome, 17 were in repeated sequences, one had no match to the genome, and the remainder were unassigned due to illegitimate T-DNA integration events. These included in order of abundance: head-to-tail tandem insertions, right border excision failures, left border excision failures and insertion of one T-DNA into another. The left borders of the T-DNA were frequently truncated and inserted in sequences with micro-homology to the left terminus. By contrast the right borders were less prone to degradation and appeared to have been integrated in a homology-independent manner. Gross genome rearrangements rarely occurred when the T-DNAs integrated in single-copy regions, although most insertions did cause small deletions at the target site. Significant insertion bias was detected, with promoters receiving two times more T-DNA hits than expected, and open reading frames receiving three times fewer. In addition, we found that the distribution of T-DNA inserts among the M. oryzae chromosomes was not random. The implications of these findings with regard to saturation mutagenesis of the M. oryzae genome are discussed.}, number={10}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Meng, Yan and Patel, Gayatri and Heist, Melanie and Betts, Melania F. and Tucker, Sara L. and Galadima, Natalia and Donofrio, Nicole M. and Brown, Doug and Mitchell, Thomas K. and Li, Lei and et al.}, year={2007}, month={Oct}, pages={1050–1064} }
 @article{shi_sharma-shivappa_chinn_dean_shivappa_2007, title={Challenges in quantification of ligninolytic enzymes from Phanerochaete chrysosporium cultivation for pretreatment of cotton stalks}, volume={50}, DOI={10.13031/2013.24071}, abstractNote={Enzymes play an important role in the breakdown of lignin during microbial pretreatment of lignocellulosic feedstocks. However, quantification of the various enzyme activities with assays developed for enzyme extracts from pure cultures can be challenging. In this study, spectrophotometric assays used for the quantification of peroxidases in enzyme extracts from submerged (SmC) and solid-state (SSC) cultivation of P. chrysosporium on cotton stalks during 14 days pretreatment failed to detect lignin peroxidase (LiP) and manganese peroxidase (MnP) activities. However, results from sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) suggested presence of protein bands with molecular weights corresponding to MnP and LiP in the enzyme extracts from fungal pretreatment cultures. Addition of crude enzyme extracts from SmC and SSC treated samples to fresh cotton stalks showed 3.42% and 7.45% increase in lignin content, respectively. This slight increase may be attributed to components within crude extracts that polymerize the phenolic compounds instead of resulting in delignification. It can be inferred from this study that although qualitative methods for ligninolytic enzyme estimation provide useful information, it is essential to investigate alternative approaches to quantify ligninolytic enzymes during cultivation on natural lignocellulosic materials to overcome the limitations of existing assays.}, number={6}, journal={Transactions of the ASABE}, author={Shi, J. and Sharma-Shivappa, R. R. and Chinn, Mari and Dean, Ralph and Shivappa, R. B.}, year={2007}, pages={2347–2354} }
 @article{betts_tucker_galadima_meng_patel_li_donofrio_floyd_nolin_brown_et al._2007, title={Development of a high throughput transformation system for insertional mutagenesis in Magnaporthe oryzae}, volume={44}, ISSN={["1087-1845"]}, DOI={10.1016/j.fgb.2007.05.001}, abstractNote={Towards the goal of disrupting all genes in the genome of Magnaporthe oryzae and identifying their function, a collection of >55,000 random insertion lines of M. oryzae strain 70-15 were generated. All strains were screened to identify genes involved in growth rate, conidiation, pigmentation, auxotrophy, and pathogenicity. Here, we provide a description of the high throughput transformation and analysis pipeline used to create our library. Transformed lines were generated either by CaCl2/PEG treatment of protoplasts with DNA or by Agrobacterium tumefaciens-mediated transformation (ATMT). We describe the optimization of both approaches and compare their efficiency. ATMT was found to be a more reproducible method, resulting in predominantly single copy insertions, and its efficiency was high with up to 0.3% of conidia being transformed. The phenotypic data is accessible via a public database called MGOS and all strains are publicly available. This represents the most comprehensive insertional mutagenesis analysis of a fungal pathogen.}, number={10}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Betts, Melania F. and Tucker, Sara L. and Galadima, Natalia and Meng, Yan and Patel, Gayatri and Li, Lei and Donofrio, Nicole and Floyd, Anna and Nolin, Shelly and Brown, Doug and et al.}, year={2007}, month={Oct}, pages={1035–1049} }
 @article{torto-alalibo_tripathy_smith_arredondo_zhou_li_chibucos_qutob_gijzen_mao_et al._2007, title={Expressed sequence tags from Phytophthora sojae reveal genes specific to development and infection}, volume={20}, ISSN={["1943-7706"]}, DOI={10.1094/MPMI-20-7-0781}, abstractNote={ Six unique expressed sequence tag (EST) libraries were generated from four developmental stages of Phytophthora sojae P6497. RNA was extracted from mycelia, swimming zoospores, germinating cysts, and soybean (Glycine max (L.) Merr.) cv. Harosoy tissues heavily infected with P. sojae. Three libraries were created from mycelia growing on defined medium, complex medium, and nutrient-limited medium. The 26,943 high-quality sequences obtained clustered into 7,863 unigenes composed of 2,845 contigs and 5,018 singletons. The total number of P. sojae unigenes matching sequences in the genome assembly was 7,412 (94%). Of these unigenes, 7,088 (90%) matched gene models predicted from the P. sojae sequence assembly, but only 2,047 (26%) matched P. ramorum gene models. Analysis of EST frequency from different growth conditions and morphological stages revealed genes that were specific to or highly represented in particular growth conditions and life stages. Additionally, our results indicate that, during infection, the pathogen derives most of its carbon and energy via glycolysis of sugars in the plant. Sequences identified with putative roles in pathogenesis included avirulence homologs possessing the RxLR motif, elicitins, and hydrolytic enzymes. This large collection of P. sojae ESTs will serve as a valuable public genomic resource. }, number={7}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Torto-Alalibo, Trudy A. and Tripathy, Sucheta and Smith, Brian M. and Arredondo, Felipe D. and Zhou, Lecong and Li, Hua and Chibucos, Marcus C. and Qutob, Dinah and Gijzen, Mark and Mao, Chunhong and et al.}, year={2007}, month={Jul}, pages={781–793} }
 @misc{xu_zhao_dean_2007, title={From genes to genomes: A new paradigm for studying fungal pathogenesis in magnaporthe oryzae}, volume={57}, journal={Fungal genomics}, author={Xu, J. R. and Zhao, X. H. and Dean, R. A.}, year={2007}, pages={175–218} }
 @article{dean_2007, title={Fungal gene clusters}, volume={25}, ISSN={["1087-0156"]}, DOI={10.1038/nbt0107-67}, abstractNote={The genome of the fungus that causes corn smut disease has been sequenced.}, number={1}, journal={NATURE BIOTECHNOLOGY}, author={Dean, Ralph A.}, year={2007}, month={Jan}, pages={67–67} }
 @article{gowda_venu_li_jantasuriyarat_chen_bellizzi_pampanwar_kim_dean_stahlberg_et al._2007, title={Magnaporthe grisea infection triggers RNA variation and antisense transcript expression in rice}, volume={144}, ISSN={["1532-2548"]}, DOI={10.1104/pp.107.095653}, abstractNote={Abstract}, number={1}, journal={PLANT PHYSIOLOGY}, author={Gowda, Malali and Venu, R.-C. and Li, Huameng and Jantasuriyarat, Chatchawan and Chen, Songbiao and Bellizzi, Maria and Pampanwar, Vishal and Kim, HyeRan and Dean, Ralph A. and Stahlberg, Eric and et al.}, year={2007}, month={May}, pages={524–533} }
 @article{jeong_mitchell_dean_2007, title={The Magnaporthe grisea snodprot1 homolog, MSPI, is required for virulence}, volume={273}, ISSN={["1574-6968"]}, DOI={10.1111/j.1574-6968.2007.00796.x}, abstractNote={Secreted proteins play central roles in plant-microbe interactions acting as signals, toxins, and effectors. One important group of small secreted proteins is the snodprot1 family, members of which have demonstrated phytotoxic properties. A split-marker transformation system was applied for gene deletion of the snodprot1 homolog, MSP1, in the rice blast fungus Magnaporthe grisea. msp1 mutants were phenotypically indistinguishable from wild type and elaborated apparently normal appressoria. However, the deletion mutants were greatly reduced in virulence primarily due to impaired growth in planta. Western blot analysis showed that the protein was secreted and not associated with the fungal cell wall. When purified MSP1 protein was applied to wounded leaf tissue, no apparent phytotoxic effects were noted. This is the first report to the authors' knowledge that directly implicates a snodprot1 protein as a virulence factor.}, number={2}, journal={FEMS MICROBIOLOGY LETTERS}, author={Jeong, Jun Seop and Mitchell, Thomas K. and Dean, Ralph A.}, year={2007}, month={Aug}, pages={157–165} }
 @article{deng_carbone_dean_2007, title={The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes}, volume={7}, ISSN={["1471-2148"]}, DOI={10.1186/1471-2148-7-30}, abstractNote={Abstract}, journal={BMC EVOLUTIONARY BIOLOGY}, author={Deng, Jixin and Carbone, Ignazio and Dean, Ralph A.}, year={2007}, month={Feb} }
 @article{adomas_heller_li_olson_chu_osborne_craig_van zyl_wolfinger_sederoff_et al._2007, title={Trranscript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasion}, volume={27}, ISSN={["1758-4469"]}, DOI={10.1093/treephys/27.10.1441}, abstractNote={The mechanisms underlying defence reactions to a pathogen attack, though well studied in crop plants, are poorly understood in conifers. To analyze changes in gene transcript abundance in Pinus sylvestris L. root tissues infected by Heterobasidion annosum (Fr.) Bref. s.l., a cDNA microarray containing 2109 ESTs from P. taeda L. was used. Mixed model statistical analysis identified 179 expressed sequence tags differentially expressed at 1, 5 or 15 days post inoculation. In general, the total number of genes differentially expressed during the infection increased over time. The most abundant group of genes up-regulated upon infection coded for enzymes involved in metabolism (phenylpropanoid pathway) and defence-related proteins with antimicrobial properties. A class III peroxidase responsible for lignin biosynthesis and cell wall thickening had increased transcript abundance at all measurement times. Real-time RT-PCR verified the microarray results with high reproducibility. The similarity of the expression profiling pattern observed in this pathosystem to those documented in crop pathology suggests that angiosperms and gymnosperms use similar genetic programs in responding to invasive growth by microbial pathogens.}, number={10}, journal={TREE PHYSIOLOGY}, author={Adomas, Aleksandra and Heller, Gregory and Li, Guosheng and Olson, Ake and Chu, Tzu-Ming and Osborne, Jason and Craig, Deborah and Van Zyl, Len and Wolfinger, Russ and Sederoff, Ron and et al.}, year={2007}, month={Oct}, pages={1441–1458} }
 @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{joobeur_gusmini_zhang_levi_xu_wehner_oliver_dean_2006, title={Construction of a watermelon BAC library and identification of SSRs anchored to melon or Arabidopsis genomes}, volume={112}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-006-0258-6}, abstractNote={A bacterial artificial chromosome (BAC) library was constructed for watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus) with an average insert-size of 106 kb, providing 21 haploid genome equivalents. The library was used to identify BAC clones that are anchored to probes evenly distributed on the genomes of melon or Arabidopsis. Twenty eight probes (representing 66% of the tested probes) from melon and 30 probes (65%) from Arabidopsis identified positive BAC clones. Two methods were implemented to identify SSRs from the positively hybridizing BAC clones. First, analysis of BAC end sequences revealed 37 SSRs. For the second method, pooled DNA of BACs identified by the melon probes was used to develop a shotgun library. The library was then screened with synthetic SSR oligonucleotides by hybridization. Sequence analysis of positively hybridizing shotgun clones revealed 142 different SSRs. Thirty eight SSRs were characterized using three watermelon cultivars, five plant introduction (PI) accessions of C. lanatus var lanatus and four PIs of C. lanatus var citroides. Of these, 36 (95%) were found to be polymorphic with up to six alleles per marker. Polymorphism information content values for polymorphic markers varied between 0.22 and 0.79 with an average of 0.53. The methods described herein will be valuable for the construction of a watermelon linkage map with SSRs evenly distributed on its genome that is anchored to the genomes of melon and Arabidopsis.}, number={8}, journal={THEORETICAL AND APPLIED GENETICS}, author={Joobeur, T. and Gusmini, G. and Zhang, X. and Levi, A. and Xu, Y. and Wehner, T. C. and Oliver, M. and Dean, R. A.}, year={2006}, month={May}, pages={1553–1562} }
 @article{gowda_venu_raghupathy_nobuta_li_wing_stahlberg_couglan_haudenschild_dean_et al._2006, title={Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods}, volume={7}, journal={BMC Genomics}, author={Gowda, M. and Venu, R. C. and Raghupathy, M. B. and Nobuta, K. and Li, H. M. and Wing, R. and Stahlberg, E. and Couglan, S. and Haudenschild, C. D. and Dean, R. and et al.}, year={2006} }
 @article{donofrio_oh_lundy_pan_brown_jeong_coughlan_mitchell_dean_2006, title={Global gene expression during nitrogen starvation in the rice blast fungus, Magnaporthe grisea}, volume={43}, ISSN={["1087-1845"]}, DOI={10.1016/j.fgb.2006.03.005}, abstractNote={Efficient regulation of nitrogen metabolism likely plays a role in the ability of fungi to exploit ecological niches. To learn about regulation of nitrogen metabolism in the rice blast pathogen Magnaporthe grisea, we undertook a genome-wide analysis of gene expression under nitrogen-limiting conditions. Five hundred and twenty genes showed increased transcript levels at 12 and 48 h after shifting the fungus to media lacking nitrate as a nitrogen source. Thirty-nine of these genes have putative functions in amino acid metabolism and uptake, and include the global nitrogen regulator in M. grisea, NUT1. Evaluation of seven nitrogen starvation-induced genes revealed that all were expressed during rice infection. Targeted gene replacement on one such gene, the vacuolar serine protease, SPM1, resulted in decreased sporulation and appressorial development as well as a greatly attenuated ability to cause disease. Data are discussed in the context of nitrogen metabolism under starvation conditions, as well as conditions potentially encountered during invasive growth in planta.}, number={9}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Donofrio, N. M. and Oh, Y. and Lundy, R. and Pan, H. and Brown, D. E. and Jeong, J. S. and Coughlan, S. and Mitchell, T. K. and Dean, R. A.}, year={2006}, month={Sep}, pages={605–617} }
 @article{soderlund_haller_pampanwar_ebbole_farman_orbach_wang_wing_xu_brown_et al._2006, title={MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions}, volume={19}, ISSN={["1943-7706"]}, DOI={10.1094/MPMI-19-1055}, abstractNote={ The MGOS (Magnaporthe grisea Oryza sativa) web-based database contains data from Oryza sativa and Magnaporthe grisea interaction experiments in which M. grisea is the fungal pathogen that causes the rice blast disease. In order to study the interactions, a consortium of fungal and rice geneticists was formed to construct a comprehensive set of experiments that would elucidate information about the gene expression of both rice and M. grisea during the infection cycle. These experiments included constructing and sequencing cDNA and robust long-serial analysis gene expression libraries from both host and pathogen during different stages of infection in both resistant and susceptible interactions, generating >50,000 M. grisea mutants and applying them to susceptible rice strains to test for pathogenicity, and constructing a dual O. sativa-M. grisea microarray. MGOS was developed as a central web-based repository for all the experimental data along with the rice and M. grisea genomic sequence. Community-based annotation is available for the M. grisea genes to aid in the study of the interactions. }, number={10}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Soderlund, Carol and Haller, Karl and Pampanwar, Vishal and Ebbole, Daniel and Farman, Mark and Orbach, Marc J. and Wang, Guo-Liang and Wing, Rod and Xu, Jin-Rong and Brown, Doug and et al.}, year={2006}, month={Oct}, pages={1055–1061} }
 @misc{rehmeyer_li_kusaba_kim_brown_staben_dean_farman_2006, title={Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae}, volume={34}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkl588}, abstractNote={Eukaryotic pathogens of humans often evade the immune system by switching the expression of surface proteins encoded by subtelomeric gene families. To determine if plant pathogenic fungi use a similar mechanism to avoid host defenses, we sequenced the 14 chromosome ends of the rice blast pathogen, Magnaporthe oryzae. One telomere is directly joined to ribosomal RNA-encoding genes, at the end of the ∼2 Mb rDNA array. Two are attached to chromosome-unique sequences, and the remainder adjoin a distinct subtelomere region, consisting of a telomere-linked RecQ-helicase (TLH) gene flanked by several blocks of tandem repeats. Unlike other microbes, M.oryzae exhibits very little gene amplification in the subtelomere regions—out of 261 predicted genes found within 100 kb of the telomeres, only four were present at more than one chromosome end. Therefore, it seems unlikely that M.oryzae uses switching mechanisms to evade host defenses. Instead, the M.oryzae telomeres have undergone frequent terminal truncation, and there is evidence of extensive ectopic recombination among transposons in these regions. We propose that the M.oryzae chromosome termini play more subtle roles in host adaptation by promoting the loss of terminally-positioned genes that tend to trigger host defenses.}, number={17}, journal={NUCLEIC ACIDS RESEARCH}, author={Rehmeyer, Cathryn and Li, Weixi and Kusaba, Motoaki and Kim, Yun-Sik and Brown, Doug and Staben, Chuck and Dean, Ralph and Farman, Mark}, year={2006}, month={Oct}, pages={4685–4701} }
 @article{thon_pan_diener_papalas_taro_mitchell_dean_2006, title={The  role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae}, volume={7}, number={2}, journal={Genome Biology}, author={Thon, M. R. and Pan, H. Q. and Diener, S. and Papalas, J. and Taro, A. and Mitchell, T. K. and Dean, R. A.}, year={2006} }
 @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{diener_houfek_kalat_windham_burke_opperman_dean_2005, title={Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system}, volume={6}, journal={BMC Bioinformatics}, author={Diener, S. E. and Houfek, T. D. and Kalat, S. E. and Windham, D. E. and Burke, M. and Opperman, C. and Dean, R. A.}, year={2005} }
 @article{li_martin_jeffers_dean_camberato_2005, title={Genetic variation among Rhizoctonia solani isolates from warm-season turfgrasses}, volume={10}, journal={International Turfgrass Society Research Journal}, author={Li, J. F. and Martin, S. B. and Jeffers, S. N. and Dean, R. A. and Camberato, J. J.}, year={2005}, pages={230} }
 @article{jantasuriyarat_gowda_haller_hatfield_lu_stahlberg_zhou_li_kim_yu_et al._2005, title={Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction}, volume={138}, ISSN={["1532-2548"]}, DOI={10.1104/pp.104.055624}, abstractNote={Abstract}, number={1}, journal={PLANT PHYSIOLOGY}, author={Jantasuriyarat, C and Gowda, M and Haller, K and Hatfield, J and Lu, GD and Stahlberg, E and Zhou, B and Li, HM and Kim, HR and Yu, YS and et al.}, year={2005}, month={May}, pages={105–115} }
 @article{kulkarni_thon_pan_dean_2005, title={Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea}, volume={6}, number={3}, journal={Genome Biology}, author={Kulkarni, R. D. and Thon, M. R. and Pan, H. Q. and Dean, R. A.}, year={2005} }
 @article{donofrio_rajagopalon_brown_diener_windham_nolin_floyd_mitchell_galadima_tucker_et al._2005, title={PACLIMS: A component LIM system for high-throughput functional genomic analysis}, volume={6}, journal={BMC Bioinformatics}, author={Donofrio, N. and Rajagopalon, R. and Brown, D. and Diener, S. and Windham, D. and Nolin, S. and Floyd, A. and Mitchell, T. and Galadima, N. and Tucker, S. and et al.}, year={2005} }
 @article{dean_talbot_ebbole_farman_mitchell_orbach_thon_kulkarni_xu_pan_et al._2005, title={The genome sequence of the rice blast fungus Magnaporthe grisea}, volume={434}, ISSN={["1476-4687"]}, DOI={10.1038/nature03449}, abstractNote={Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.}, number={7036}, journal={NATURE}, author={Dean, RA and Talbot, NJ and Ebbole, DJ and Farman, ML and Mitchell, TK and Orbach, MJ and Thon, M and Kulkarni, R and Xu, JR and Pan, HQ and et al.}, year={2005}, month={Apr}, pages={980–986} }
 @inbook{altunay_brown_byrd_dean_2005, series={Lecture Notes in Computer Science}, title={Trust-Based Secure Workflow Path Construction}, volume={3826}, ISBN={9783540749738 9783540749745}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/11596141_29}, DOI={10.1007/11596141_29}, abstractNote={Security and trust relationships between services significantly govern their willingness to collaborate and participate in a workflow. Existing workflow tools do not consider such relationships as an integral part of their planning logic: rather, they approach security as a run-time issue. We present a workflow management framework that fully integrates trust and security into the workflow planning logic. It considers not only trust relationships between the workflow requestor and individual services, but also trust relationships among the services themselves. It allows each service owner to define an upper layer of collaboration policies (rules that specify the terms under which participation in a workflow is allowed) and integrates them into the planning logic. Services that are unfit for collaboration due to security violations are replaced at the planning stage. This approach increases the services owners’ control over the workflow path, their willingness for collaboration, and avoids run-time security failures.}, booktitle={Service-Oriented Computing – ICSOC 2007}, publisher={Springer Berlin Heidelberg}, author={Altunay, M. and Brown, D. and Byrd, G. and Dean, R.}, editor={Benatallah, B. and Casati, F. and Traverso, P.Editors}, year={2005}, pages={382–395}, collection={Lecture Notes in Computer Science} }
 @article{thon_martin_goff_wing_dean_2004, title={BAC end sequences and a physical map reveal transposable element content and clustering patterns in the genome of Magnaporthe grisea}, volume={41}, ISSN={["1087-1845"]}, DOI={10.1016/j.fgb.2004.02.003}, abstractNote={Transposable elements (TEs) are viewed as major contributors to the evolution of fungal genomes. Genomic resources such as BAC libraries are an underutilized resource for studying genome-wide TE distribution. Using the BAC end sequences and physical map that are available for the rice blast fungus, Magnaporthe grisea, we describe a likelihood ratio test designed to identify clustering of TEs in the genome. A significant variation in the distribution of three TEs, MAGGY, MGL, and Pot2 was observed among the fingerprint contigs of the physical map. We utilized a draft sequence of M. grisea chromosome 7 to validate our results and found a similar pattern of clustering. By examining individual BAC end sequences, we found evidence for 11 unique integrations of MAGGY or MGL into Pot2 but no evidence for the reciprocal integration of Pot2 into another TE. This suggests that: (a) the presence of Pot2 in the genome predates that of the other TEs, (b) Pot2 was less transpositionally active than other TEs, or (c) that MAGGY and MGL have integration site preference for Pot2. High transition/transversion mutation ratios as well as bias in transition site context was observed in MAGGY and MGL elements, but not in Pot2 elements. These features are consistent with the effects of a Repeat-Induced Point (RIP) mutation-like process occurring in MAGGY and MGL elements. This study illustrates the general utility of a physical map and BAC end sequences for the study of genome-wide repetitive DNA content and organization. Index Descriptors: Transposon; Transposable element; Rice blast; Magnaporthe grisea; Pyricularia grisea; BAC library; Physical map}, number={7}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Thon, MR and Martin, SL and Goff, S and Wing, RA and Dean, RA}, year={2004}, month={Jul}, pages={657–666} }
 @article{diener_dunn-coleman_foreman_houfek_teunissen_solingen_dankmeyer_mitchell_ward_dean_2004, title={Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei}, volume={230}, ISSN={["1574-6968"]}, DOI={10.1016/S0378-1097(03)00916-9}, abstractNote={Trichoderma reesei is a filamentous fungus widely used as an efficient protein producer and known to secrete large quantities of biomass degrading enzymes. Much work has been done aimed at improving the secretion efficiency of this fungus. It is generally accepted that the major bottlenecks in secretion are protein folding and ornamentation steps in this pathway. In an attempt to identify genes involved in these steps, the 5' ends of 21888 cDNA clones were sequenced from which a unique set of over 5000 were also 3' sequenced. Using annotation tools Gene Ontology terms were assigned to 2732 of the sequences. Homologs to the majority of Aspergillus niger's Srg genes as well as a number of homologs to genes involved in protein folding and ornamentation pathways were identified.}, number={2}, journal={FEMS MICROBIOLOGY LETTERS}, author={Diener, SE and Dunn-Coleman, N and Foreman, P and Houfek, TD and Teunissen, PJM and Solingen, P and Dankmeyer, L and Mitchell, TK and Ward, M and Dean, RA}, year={2004}, month={Jan}, pages={275–282} }
 @article{diener_dunn-coleman_foreman_houfek_teunissen_solingen_dankmeyer_mitchell_ward_dean_2004, title={Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei (vol 230, pg 275, 2004)}, volume={235}, DOI={10.1111/j.1574-6968.2004.tb09588.x}, number={1}, journal={FEMS Microbiology Letters}, author={Diener, S. E. and Dunn-Coleman, N. and Foreman, P. and Houfek, T. D. and Teunissen, P. J. M. and Solingen, P. Van and Dankmeyer, L. and Mitchell, T. K. and Ward, M. and Dean, Ralph}, year={2004}, pages={209} }
 @article{asiegbu_choi_jeong_dean_2004, title={Cloning, sequencing and functional analysis of Magnaporthe grisea MVP1 gene, a hex-1 homolog encoding a putative 'woronin body' protein}, volume={230}, DOI={10.1016/S0378-1097(03)0858-9}, number={1}, journal={FEMS Microbiology Letters}, author={Asiegbu, F. O. and Choi, W. and Jeong, J. S. and Dean, Ralph}, year={2004}, pages={85–90} }
 @article{asiegbu_choi_jeong_dean_2004, title={Cloning, sequencing and functional analysis of Magnaporthe grisea MVP1 gene, a hex-1 homolog encoding a putative ‘woronin body’ protein}, volume={230}, ISSN={0378-1097 1574-6968}, url={http://dx.doi.org/10.1016/S0378-1097(03)00858-9}, DOI={10.1016/S0378-1097(03)00858-9}, abstractNote={A hex-1 homolog named MVP1 was isolated from an appressoria cDNA library of the rice blast fungus Magnaporthe grisea. The transcript of approximately 1.6 kb contains 546 bp of coding sequence with a 3' untranslated region about 168 bp long and a 5' untranslated region about 870 bp long. Southern gel blot analysis of genomic DNA following digestion with three restriction enzymes (BamHI, EcoRI, HindIII) indicated that the gene exists as a single copy in M. grisea genome. RNA gel blot analyses showed that MVP1 was highly expressed in germinating conidia and the mycelial stage compared to appressoria or non-germinated conidia. MVP1 showed a high degree of homology to the hex-1 gene recently described to encode a major protein in the woronin bodies of Neurospora crassa. Double homologous recombination was used to replace MVP1 with the hyg(R) gene. MVP1 knockout mutants showed apical swellings when grown on agar plates containing 2% sorbose but they were not impaired in any other vegetative or pathogenic properties evaluated. The pathological and other phenotypic consequences of gene disruption are discussed.}, number={1}, journal={FEMS Microbiology Letters}, publisher={Oxford University Press (OUP)}, author={Asiegbu, Frederick O. and Choi, Woobong and Jeong, Jun Seop and Dean, Ralph A.}, year={2004}, month={Jan}, pages={85–90} }
 @article{ebbole_jin_thon_pan_bhattarai_thomas_dean_2004, title={Gene discovery and gene expression in the rice blast fungus, Magnaporthe grisea: Analysis of expressed sequence tags}, volume={17}, ISSN={["0894-0282"]}, DOI={10.1094/MPMI.2004.17.12.1337}, abstractNote={ Over 28,000 expressed sequence tags (ESTs) were produced from cDNA libraries representing a variety of growth conditions and cell types. Several Magnaporthe grisea strains were used to produce the libraries, including a nonpathogenic strain bearing a mutation in the PMK1 mitogen-activated protein kinase. Approximately 23,000 of the ESTs could be clustered into 3,050 contigs, leaving 5,127 singleton sequences. The estimate of 8,177 unique sequences indicates that over half of the genes of the fungus are represented in the ESTs. Analysis of EST frequency reveals growth and cell type-specific patterns of gene expression. This analysis establishes criteria for identification of fungal genes involved in pathogenesis. A large fraction of the genes represented by ESTs have no known function or described homologs. Manual annotation of the most abundant cDNAs with no known homologs allowed us to identify a family of metallothionein proteins present in M. grisea, Neurospora crassa, and Fusarium graminearum. In addition, multiply represented ESTs permitted the identification of alternatively spliced mRNA species. Alternative splicing was rare, and in most cases, the alternate mRNA forms were unspliced, although alternative 5′ splice sites were also observed. }, number={12}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Ebbole, DJ and Jin, Y and Thon, M and Pan, HQ and Bhattarai, E and Thomas, T and Dean, R}, year={2004}, month={Dec}, pages={1337–1347} }
 @article{kulkarni_dean_2004, title={Identification of proteins that interact with two regulators of appressorium development, adenylate cyclase and cAMP-dependent protein kinase A, in the rice blast fungus Magnaporthe grisea}, volume={270}, DOI={10.1007/s00438-003-0935-y}, abstractNote={Adenylate cyclase (MAC1) and the catalytic subunit of cAMP-dependent protein kinase A (CPKA) are required for appressorium development and pathogenesis in the rice blast pathogen Magnaporthe grisea. To identify new components in the cAMP signal transduction pathway, we used the yeast two-hybrid system to screen MAC1 and CPKA against an appressorium cDNA library. The cDNA library was constructed by GATEWAY recombinational cloning, enabling transfer of the library to various alternative vectors. The protein phosphatase domain in MAC1, which is unique to fungal adenylate cyclases, interacted with a MAP kinase kinase and a Ser/Thr kinase. Interactions of MAC1 with the kinases may prove to be part of feedback loops between the corresponding signaling pathways. A predicted membrane protein, ACI1, which is highly expressed under conditions that are conducive to appressorium formation, also interacted with MAC1. ACI1 has an extracellular domain containing eight-cysteines, which is also present in other fungal proteins implicated in pathogenesis. The N-terminal half of CPKA, which includes a glutamine-rich sequence unique to a group of fungal sequences, interacted with a putative transcriptional regulator and two different glycosyl hydrolases. Phosphorylation motifs in these sequences suggest that they could be CPKA substrates. The protein interaction assay employed here can now be scaled up to identify interactions between a larger set of proteins in the M. grisea interactome.}, number={6}, journal={Molecular Genetics and Genomics}, author={Kulkarni, R. D. and Dean, Ralph}, year={2004}, pages={497–508} }
 @article{diener_chellappan_mitchell_dunn-coleman_ward_dean_2004, title={Insight into Trichoderma reesei's genome content, organization and evolution revealed through BAC library characterization}, volume={41}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2004.08.007}, abstractNote={Trichoderma reesei is an important industrial fungus known for its ability to efficiently secrete large quantities of protein as well as its wide variety of biomass degrading enzymes. Past research on this fungus has primarily focused on extending its protein production capabilities, leaving the structure of its 33 Mb genome essentially a mystery. To begin to address these deficiencies and further our knowledge of T. reesei's secretion and cellulolytic potential, we have created a genomic framework for this fungus. We constructed a BAC library containing 9216 clones with an average insert size of 125 kb which provides a coverage of 28 genome equivalents. BAC ends were sequenced and annotated using publicly available software which identified a number of genes not seen in previously sequenced EST datasets. Little evidence was found for repetitive sequence in T. reesei with the exception of several copies of an element with similarity to the Podospora anserina transposon, PAT. Hybridization of 34 genes involved in biomass degradation revealed five groups of co-located genes in the genome. BAC clones were fingerprinted and analyzed using fingerprinted contigs (FPC) software resulting in 334 contigs covering 28 megabases of the genome. The assembly of these FPC contigs was verified by congruence with hybridization results.}, number={12}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Diener, SE and Chellappan, MK and Mitchell, TK and Dunn-Coleman, N and Ward, M and Dean, RA}, year={2004}, month={Dec}, pages={1077–1087} }
 @article{gusmini_wehner_joobeur_dean_levi_2004, title={Protocol for DNA extraction from watermelon leaves for SSR marker studies}, ISBN={1064-5594}, number={27}, journal={Report (Cucurbit Genetics Cooperative)}, author={Gusmini, G. and Wehner, T. C. and Joobeur, T. and Dean, R. A. and Levi, A.}, year={2004}, pages={25} }
 @article{gowda_jantasuriyarat_dean_wang_2004, title={Robust-LongSAGE (RL-SAGE): A substantially improved LongSAGE method for gene discovery and transcriptome analysis}, volume={134}, ISSN={["1532-2548"]}, DOI={10.1104/pp.103.034496}, abstractNote={Abstract}, number={3}, journal={PLANT PHYSIOLOGY}, author={Gowda, M and Jantasuriyarat, C and Dean, RA and Wang, GL}, year={2004}, month={Mar}, pages={890–897} }
 @article{joobeur_king_nolin_thomas_dean_2004, title={The fusarium wilt resistance locus Fom-2 of melon contains a single resistance gene with complex features}, volume={39}, ISSN={["1365-313X"]}, DOI={10.1111/j.1365-313X.2004.02134.x}, abstractNote={Summary}, number={3}, journal={PLANT JOURNAL}, author={Joobeur, T and King, JJ and Nolin, SJ and Thomas, CE and Dean, RA}, year={2004}, month={Aug}, pages={283–297} }
 @article{kothera_keinath_dean_farnham_2003, title={AFLP analysis of a worldwide collection of Didymella bryoniae}, volume={107}, ISSN={["0953-7562"]}, DOI={10.1017/S0953756203007470}, abstractNote={Didymella bryoniae (anamorph Phoma cucurbitacearum) is an ascomycete that causes gummy stem blight, a foliar disease that occurs on cucurbits in greenhouses and fields throughout the world. In a previous study using RAPD analysis, little genetic diversity was found among isolates of D. bryoniae from New York and South Carolina, USA. Here we report the use of amplified fragment length polymorphism (AFLP) analysis to assess the genetic variation within a worldwide collection of D. bryoniae, 102 field and greenhouse isolates from ten states in the USA (California, Delaware, Florida, Georgia, Indiana, Maryland, Michigan, Oklahoma, South Carolina, and Texas) and seven other countries (Australia, Canada, China, Greece, Israel, Sweden, and The Netherlands) were examined. Seven different AFLP primer-pair combinations generated 450 bands, of which 134 were polymorphic (30%). Using cluster analysis, two groups and a total of seven subgroups were delineated. Representative isolates varied in their virulence on muskmelon and watermelon seedlings, but the degree of virulence was not strongly associated with AFLP groupings. However, isolates from the northern USA grouped separately from isolates originating from the southern USA.}, journal={MYCOLOGICAL RESEARCH}, author={Kothera, RT and Keinath, AP and Dean, RA and Farnham, MW}, year={2003}, month={Mar}, pages={297–304} }
 @article{kulkarni_kelkar_dean_2003, title={An eight-cysteine-containing CFEM domain unique to a group of fungal membrane proteins}, volume={28}, ISSN={["1362-4326"]}, DOI={10.1016/S0968-0004(03)00025-2}, abstractNote={CFEM, an eight cysteine-containing domain, has been identified by analyzing over 25 fungal sequences selected from database sequence searches. Features of CFEM suggest that it is a novel domain with characteristics distinct from known cysteine-rich domains. Some CFEM-containing proteins (e.g. Pth11 from Magnaporthe grisea) are proposed to have important roles in fungal pathogenesis.}, number={3}, journal={TRENDS IN BIOCHEMICAL SCIENCES}, author={Kulkarni, RD and Kelkar, HS and Dean, RA}, year={2003}, month={Mar}, pages={118–121} }
 @article{in-depth view of structure, activity, and evolution of rice chromosome 10_2003, volume={300}, number={5625}, journal={Science}, year={2003}, pages={1566–1569} }
 @article{asiegbu_choi_li_nahalkova_dean_2003, title={Isolation of a novel antimicrobial peptide gene (Sp-AMP) homologue from Pinus sylvestris (Scots pine) following infection with the root rot fungus Heterobasidion annosum}, volume={228}, ISSN={["1574-6968"]}, DOI={10.1016/S0378-1097(03)00697-9}, abstractNote={A new family of antimicrobial peptide homologues termed Sp-Amp has been discovered in Pinus sylvestris (Scots pine). This is the first report of such proteins to be characterized in a conifer species. Sp-AMP1 was identified in a substructured cDNA library of root tissue infected with the root rot fungus Heterobasidion annosum and encodes a mature peptide of 79 amino acid residues. Three additional members of the Sp-AMP family (Sp-AMPs 2-4) encode cysteine-rich proteins of 105 amino acids, each containing an N-terminal region with a probable cleavage signal sequence. Northern analysis confirmed that Sp-AMP expression is elevated in Scots pine roots upon infection with H. annosum. These peptides share 64% amino acid identity with a mature protein from Macadamia integrifolia (MiAMP1), which allowed us to build a homology model for preliminary analysis. Southern analyses further confirmed that several copies of the gene are present in the Scots pine genome. The potential significance of Sp-AMP in the H. annosum-conifer pathosystem is discussed.}, number={1}, journal={FEMS MICROBIOLOGY LETTERS}, author={Asiegbu, FO and Choi, WB and Li, GS and Nahalkova, J and Dean, RA}, year={2003}, month={Nov}, pages={27–31} }
 @article{takano_choi_mitchell_okuno_dean_2003, title={Large scale parallel analysis of gene expression during infection-related morphogenesis of Magnaporthe grisea}, volume={4}, ISSN={["1464-6722"]}, DOI={10.1046/J.1364-3703.2003.00182.X}, abstractNote={SUMMARY}, number={5}, journal={MOLECULAR PLANT PATHOLOGY}, author={Takano, Y and Choi, WB and Mitchell, TK and Okuno, T and Dean, RA}, year={2003}, month={Sep}, pages={337–346} }
 @article{little_dean_young_mckane_martin_jones_blikslager_2003, title={PI3K signaling is required for prostaglandin-induced  mucosal recovery in ischemia-injured porcine ileum}, volume={284}, ISSN={0193-1857 1522-1547}, url={http://dx.doi.org/10.1152/ajpgi.00121.2002}, DOI={10.1152/ajpgi.00121.2002}, abstractNote={ We have previously shown that PGE2 and PGI2 induce recovery of transepithelial resistance (TER) in ischemia-injured porcine ileal mucosa, associated with initial increases in Cl−secretion. We believe that the latter generates an osmotic gradient that stimulates resealing of tight junctions. Because of evidence implicating phosphatidylinositol 3-kinase (PI3K) in regulating tight junction assembly, we postulated that this signaling pathway is involved in PG-induced mucosal recovery. Porcine ileum was subjected to 45 min of ischemia, after which TER was monitored for a 180-min recovery period. Endogenous PG production was inhibited with indomethacin (5 μM). PGE2 (1 μM) and PGI2(1 μM) stimulated recovery of TER, which was inhibited by serosal application of the osmotic agent urea (300 mosmol/kgH2O). The PI3K inhibitor wortmannin (10 nM) blocked recovery of TER in response to PGs or mucosal urea. Immunofluorescence imaging of recovering epithelium revealed that PGs restored occludin and zonula occludens-1 distribution to interepithelial junctions, and this pattern was disrupted by pretreatment with wortmannin. These experiments suggest that PGs stimulate recovery of paracellular resistance via a mechanism involving transepithelial osmotic gradients and PI3K-dependent restoration of tight junction protein distribution. }, number={1}, journal={American Journal of Physiology-Gastrointestinal and Liver Physiology}, publisher={American Physiological Society}, author={Little, Dianne and Dean, Rebecca A. and Young, Karen M. and McKane, Shaun A. and Martin, Linda D. and Jones, Samuel L. and Blikslager, Anthony T.}, year={2003}, month={Jan}, pages={G46–G56} }
 @misc{mitchell_thon_jeong_brown_deng_dean_2003, title={The rice blast pathosystem as a case study for the development of new tools and raw materials for genome analysis of fungal plant pathogens}, volume={159}, ISSN={["0028-646X"]}, DOI={10.1046/j.1469-8137.2003.00787.x}, abstractNote={Summary}, number={1}, journal={NEW PHYTOLOGIST}, author={Mitchell, TK and Thon, MR and Jeong, JS and Brown, D and Deng, JX and Dean, RA}, year={2003}, month={Jul}, pages={53–61} }
 @article{foreman_brown_dankmeyer_dean_diener_dunn-coleman_goedegebuur_houfek_england_kelley_et al._2003, title={Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reesei}, volume={278}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.M304750200}, abstractNote={The filamentous fungus Trichoderma reesei produces and secretes profuse quantities of enzymes that act synergistically to degrade cellulase and related biomass components. We partially sequenced over 5100 random T. reesei cDNA clones. Among the sequences whose predicted gene products had significant similarity to known proteins, 12 were identified that encode previously unknown enzymes that likely function in biomass degradation. Microarrays were used to query the expression levels of each of the sequences under different conditions known to induce cellulolytic enzyme synthesis. Most of the genes encoding known and putative biomass-degrading enzymes were transcriptionally co-regulated. Moreover, despite the fact that several of these enzymes are not thought to degrade cellulase directly, they were coordinately overexpressed in a cellulase overproducing strain. A variety of additional sequences whose function could not be ascribed using the limited sequence available displayed analogous behavior and may also play a role in biomass degradation or in the synthesis of biomass-degrading enzymes. Sequences exhibiting additional regulatory patterns were observed that might reflect roles in regulation of cellulase biosynthesis. However, genes whose products are involved in protein processing and secretion were not highly regulated during cellulase induction.}, number={34}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Foreman, PK and Brown, D and Dankmeyer, L and Dean, R and Diener, S and Dunn-Coleman, NS and Goedegebuur, F and Houfek, TD and England, GJ and Kelley, AS and et al.}, year={2003}, month={Aug}, pages={31988–31997} }
 @article{wang_choi_thomas_dean_2002, title={Cloning of disease-resistance homologues in end sequences of BAC clones linked to Fom-2, a gene conferring resistance to Fusarium wilt in melon (Cucumis melo L.)}, volume={45}, ISSN={["0831-2796"]}, DOI={10.1139/G02-005}, abstractNote={Disease resistance has not yet been characterized at the molecular level in cucurbits, a group of high-value, nutritious, horticultural plants. Previously, we genetically mapped the Fom-2 gene that confers resistance to Fusarium wilt races 0 and 1 of melon. In this paper, two cosegregating codominant markers (AM, AFLP marker; FM, Fusarium marker) were used to screen a melon bacterial artificial chromosome (BAC) library. Identified clones were fingerprinted and end sequenced. Fingerprinting analysis showed that clones identified by each marker assembled into two separate contigs at high stringency. GenBank searches produced matches to leucine-rich repeats (LRRs) of resistance genes (R genes); to retroelements and to cellulose synthase in clones identified by FM; and to nucleotide-binding sites (NBSs) of R genes, retroelements, and cytochrome P-450 in clones identified by AM. A 6.5-kb fragment containing both NBS and LRR sequences was found to share high homology to TIR (Toll-interleukin-1 receptor)–NBS–LRR R genes, such as N, with 42% identity and 58% similarity in the TIR–NBS and LRR regions. The sequence information may be useful for identifying NBS–LRR class of R genes in other cucurbits.Key words: BAC end sequencing, Cucumis melo L., Fusarium wilt, R gene.}, number={3}, journal={GENOME}, author={Wang, YH and Choi, WB and Thomas, CE and Dean, RA}, year={2002}, month={Jun}, pages={473–480} }
 @article{somai_keinath_dean_2002, title={Development of PCR-ELISA for detection and differentiation of Didymella bryoniae from related Phoma species}, volume={86}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS.2002.86.7.710}, abstractNote={The causal agent of gummy stem blight, Didymella bryoniae, often is isolated from infected cucurbits together with other Phoma spp. Polymerase chain reaction (PCR) primers specific to D. bryoniae and Phoma were used to develop and evaluate a microtiter-based PCR-enzyme-linked immunosorbent assay (ELISA) technique. Primers were modified by addition of a fluorescein and a biotin label to the 5′ ends of the forward and reverse primers, respectively. After amplification, PCR products were detected in an ELISA using horseradish peroxidase-conjugated antifluorescein antibody and three substrates that yielded three colored products, one for each fungal group. The most sensitive substrate (highest signal:noise ratio) was 2,2′ -azino-bis[3-ethylbenz-thiazoline-6-sulfonic acid]. PCR-ELISA successfully detected 45 of 46 D. bryoniae and all 13 Phoma isolates that were used. Results were comparable to those obtained with gel electrophoresis. Only one D. bryoniae isolate could not be detected with PCR-ELISA; this isolate also produced a fragment larger than other D. bryoniae isolates on agarose gels. PCR-ELISA was used successfully on crude extracts of “blind” fungal samples and identified seven of seven isolates as D. bryoniae or Phoma. Although less sensitive than gel electrophoresis, PCR-ELISA was a highly specific, yet simple, rapid and convenient assay for detection of D. bryoniae and Phoma sp.}, number={7}, journal={PLANT DISEASE}, author={Somai, BM and Keinath, AP and Dean, RA}, year={2002}, month={Jul}, pages={710–716} }
 @article{somai_dean_farnham_zitter_keinath_2002, title={Internal transcribed spacer regions 1 and 2 and random amplified polymorphic DNA analysis of Didymella bryoniae and related Phoma species isolated from cucurbits}, volume={92}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO.2002.92.9.997}, abstractNote={Didymella bryoniae (anamorph Phoma cucurbitacearum) is the causal agent of gummy stem blight, although other Phoma species are often isolated from cucurbit plants exhibiting symptoms of the disease. The molecular and phylogenetic relationships between D. bryoniae and these Phoma species are unknown. Isolates of D. bryoniae and Phoma obtained from cucurbits grown at various geographical locations in the United States were subjected to random amplified polymorphic DNA (RAPD) analysis and internal transcribed spacer (ITS) sequence analysis (ITS-1 and ITS-2) to determine the molecular and phylogenetic relationships within and between these fungi. Using RAPD fingerprinting, 59 isolates were placed into four phylogenetic groups, designated RAPD group (RG) I, RG II, RG III, and RG IV. D. bryoniae isolates clustered in either RG I (33 isolates), RG II (12 isolates), or RG IV (one isolate), whereas all 13 Phoma isolates clustered to RG III. There was greater than 99% sequence identity in the ITS-1 and ITS-2 regions between isolates in RG I and RG II, whereas isolates in RG III, P. medicaginis ATCC 64481, and P. exigua ATCC 14728 clustered separately. On muskmelon seedlings, a subset of RG I isolates were highly virulent (mean disease severity was 71%), RG II and RG IV isolates were slightly virulent (mean disease severity was 4%), and RG III isolates were nonpathogenic (disease severity was 0% for all isolates). The ITS sequences indicate that RG I and RG II are both D. bryoniae, but RAPD fingerprints and pathogenicity indicate that they represent two different molecular and virulence subgroups.}, number={9}, journal={PHYTOPATHOLOGY}, author={Somai, BM and Dean, RA and Farnham, MW and Zitter, TA and Keinath, AP}, year={2002}, month={Sep}, pages={997–1004} }
 @article{martin_blackmon_rajagopalan_houfek_sceeles_denn_mitchell_brown_wing_dean_2002, title={MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea}, volume={30}, ISSN={["0305-1048"]}, DOI={10.1093/nar/30.1.121}, abstractNote={We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.}, number={1}, journal={NUCLEIC ACIDS RESEARCH}, author={Martin, SL and Blackmon, BP and Rajagopalan, R and Houfek, TD and Sceeles, RG and Denn, SO and Mitchell, TK and Brown, DE and Wing, RA and Dean, RA}, year={2002}, month={Jan}, pages={121–124} }
 @article{xue_park_choi_zheng_dean_xu_2002, title={Two novel fungal virulence genes specifically expressed in appressoria of the rice blast fungus}, volume={14}, ISSN={["1040-4651"]}, DOI={10.1105/tpc.003426}, abstractNote={The PMK1 mitogen-activated protein kinase gene regulates appressorium formation and infectious hyphae growth in the rice blast fungus. To further characterize this mitogen-activated protein kinase pathway, we constructed a subtraction library enriched for genes regulated by PMK1. Two genes identified in this library, GAS1 and GAS2, encode small proteins that are homologous with gEgh16 of the powdery mildew fungus. Both were expressed specifically during appressorium formation in the wild-type strains, but neither was expressed in the pmk1 mutant. Mutants deleted in GAS1 and GAS2 had no defect in vegetative growth, conidiation, or appressoria formation, but they were reduced in appressorial penetration and lesion development. Interestingly, deletion of both GAS1 and GAS2 did not have an additive effect on appressorial penetration and lesion formation. The GAS1–green fluorescent protein and GAS2–green fluorescent protein fusion proteins were expressed only in appressoria and localized in the cytoplasm. These two genes may belong to a class of proteins specific for filamentous fungi and function as novel virulence factors in fungal pathogens.}, number={9}, journal={PLANT CELL}, author={Xue, CY and Park, G and Choi, WB and Zheng, L and Dean, RA and Xu, JR}, year={2002}, month={Sep}, pages={2107–2119} }
 @article{levi_thomas_zhang_joobeur_dean_wehner_carle_2001, title={A genetic linkage map for watermelon based on randomly amplified polymorphic DNA markers}, volume={126}, ISSN={["2327-9788"]}, DOI={10.21273/jashs.126.6.730}, abstractNote={A genetic linkage [randomly amplified polymorphic DNA (RAPD)-based] map was constructed for watermelon [Citrullus lanatus (Thunb.) Matsum and Nakai] using a BC1 population [PI 296341-fusarium wilt resistant × New Hampshire Midget (fusarium susceptible)] × `New Hampshire Midget'. The map contains 155 RAPD markers, and a 700-base pair sequenced characterized amplified region (SCAR) marker that corresponds to a fragment produced by the RAPD primer GTAGCACTCC. This marker was reported previously as linked (1.6 cM) to race 1 fusarium wilt resistance in watermelon. The markers segregated to 17 linkage groups. Of these, 10 groups included nine to 19 markers, and seven groups included two to four markers. The map covers a genetic linkage distance of 1295 cM. Nine of the 10 large linkage groups contained segments with low (or no) level of recombination (0 to 2.6 cM) among markers, indicating that the watermelon genome may contain large chromosomal regions that are deficient in recombination events. The map should be useful for identification of markers linked closely to genes that control fruit quality and fusarium wilt (races 1 and 2) resistance in watermelon.}, number={6}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE}, author={Levi, A and Thomas, CE and Zhang, XP and Joobeur, T and Dean, RA and Wehner, TC and Carle, BR}, year={2001}, month={Nov}, pages={730–737} }
 @article{zhu_bilgin_bangham_hall_casamayor_bertone_lan_jansen_bidlingmaier_houfek_et al._2001, title={Global analysis of protein activities using proteome chips}, volume={293}, ISSN={["1095-9203"]}, DOI={10.1126/science.1062191}, abstractNote={To facilitate studies of the yeast proteome, we cloned 5800 open reading frames and overexpressed and purified their corresponding proteins. The proteins were printed onto slides at high spatial density to form a yeast proteome microarray and screened for their ability to interact with proteins and phospholipids. We identified many new calmodulin- and phospholipid-interacting proteins; a common potential binding motif was identified for many of the calmodulin-binding proteins. Thus, microarrays of an entire eukaryotic proteome can be prepared and screened for diverse biochemical activities. The microarrays can also be used to screen protein-drug interactions and to detect posttranslational modifications.}, number={5537}, journal={SCIENCE}, author={Zhu, H and Bilgin, M and Bangham, R and Hall, D and Casamayor, A and Bertone, P and Lan, N and Jansen, R and Bidlingmaier, S and Houfek, T and et al.}, year={2001}, month={Sep}, pages={2101–2105} }
 @article{luo_wang_frisch_joobeur_wing_dean_2001, title={Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2)}, volume={44}, ISSN={["0831-2796"]}, DOI={10.1139/gen-44-2-154}, abstractNote={Utilizing improved methods, two bacterial artificial chromosome (BAC) libraries were constructed for the multidisease-resistant line of melon MR-1. The HindIII library consists of 177 microtiter plates in a 384-well format, while the EcoRI library consists of 222 microtiter plates. Approximately 95.6% of the HindIII library clones contain nuclear DNA inserts with an average size of 118 kb, providing a coverage of 15.4 genome equivalents. Similarly, 96% of the EcoRI library clones contain nuclear DNA inserts with an average size of 114 kb, providing a coverage of 18.7 genome equivalents. Both libraries were evaluated for contamination with high-copy vector, empty pIndigoBac536 vector, and organellar DNA sequences. High-density filters were screened with two genetic markers FM and AM that co-segregate with Fom-2, a gene conferring resistance to races 0 and 1 of Fusarium wilt. Fourteen and 18 candidate BAC clones were identified for the FM and AM probes, respectively, from the HindIII library, while 34 were identified for the AM probe from filters A, B, and C of the EcoRI library.}, number={2}, journal={GENOME}, author={Luo, MZ and Wang, YH and Frisch, D and Joobeur, T and Wing, RA and Dean, RA}, year={2001}, month={Apr}, pages={154–162} }
 @article{wang_thomas_dean_2000, title={Genetic mapping of a fusarium wilt resistance gene (Fom-2) in melon (Cucumis melo L.)}, volume={6}, ISSN={["1380-3743"]}, DOI={10.1023/A:1009671925793}, number={4}, journal={MOLECULAR BREEDING}, author={Wang, YH and Thomas, CE and Dean, RA}, year={2000}, month={Aug}, pages={379–389} }
 @article{fang_dean_2000, title={Site-directed mutagenesis of the magB gene affects growth and development in Magnaporthe grisea}, volume={13}, ISSN={["0894-0282"]}, DOI={10.1094/MPMI.2000.13.11.1214}, abstractNote={ G protein signaling is commonly involved in regulating growth and differentiation of eukaryotic cells. We previously identified MAGB, encoding a Gα subunit, from Magnaporthe grisea, and disruption of MAGB led to defects in a number of cellular responses, including appres-sorium formation, conidiation, sexual development, mycelial growth, and surface sensing. In this study, site-directed mutagenesis was used to further dissect the pleiotropic effects controlled by MAGB. Conversion of glycine 42 to arginine was predicted to abolish GTPase activity, which in turn would constitutively activate G protein signaling in magBG42R. This dominant mutation caused autolysis of aged colonies, misscheduled melanization, reduction in both sexual and asexual reproduction, and reduced virulence. Furthermore, magBG42R mutants were able to produce appressoria on both hydrophobic and hydrophilic surfaces, although development on the hydrophilic surface was delayed. A second dominant mutation, magBG203R (glycine 203 converted to arginine), was expected to block dissociation of the Gβγ from the Gα subunit, thus producing a constitutively inactive G protein complex. This mutation did not cause drastic phenotypic changes in the wild-type genetic background, other than increased sensitivity to repression of conidiation by osmotic stress. However, magBG203R is able to complement phenotypic defects in magB mutants. Comparative analyses of the phenotypical effects of different magB mutations are consistent with the involvement of the Gβγ subunit in the signaling pathways regulating cellular development in M. grisea. }, number={11}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Fang, EGC and Dean, RA}, year={2000}, month={Nov}, pages={1214–1227} }