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TRANSCRIPT
Five Year Report
2006 – 2011
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Table of Contents
Introduction ..................................................................................................................................... 1
Mission ............................................................................................................................................ 1
Vision .............................................................................................................................................. 1
Objectives and Goals ...................................................................................................................... 2
CIFR Major Scientific Goals....................................................................................................... 2
CIFR Educational and Outreach Goals ....................................................................................... 3
Relevance to University mission .................................................................................................... 3
Impact on Instructional Programs ................................................................................................... 3
Center Administration and Organization ........................................................................................ 4
Dr. Ralph A. Dean – Center Director .......................................................................................... 4
Dr. Gary A. Payne – Associate Director ..................................................................................... 4
CIFR Scientific Advisory Committee Members............................................................................. 4
CIFR Organizational Chart ............................................................................................................. 5
CIFR External Grant Support ......................................................................................................... 6
CIFR Research Activities ............................................................................................................... 6
Ralph A. Dean ............................................................................................................................. 7
Gary A. Payne ............................................................................................................................. 8
Margaret E. Daub ........................................................................................................................ 9
Marc A. Cubeta ......................................................................................................................... 10
Ignazio Carbone ........................................................................................................................ 11
Paola Veronese .......................................................................................................................... 12
Peter Ojiambo ............................................................................................................................ 13
CIFR Sponsored Activities ........................................................................................................... 14
CIFR Outreach and Education. ..................................................................................................... 15
CIFR Training and Mentoring ...................................................................................................... 16
CIFR Collaborators ....................................................................................................................... 18
CIFR Invited Presentations ........................................................................................................... 25
CIFR Publications ......................................................................................................................... 29
CIFR Grant Support ...................................................................................................................... 39
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Introduction
The fungal kingdom represents an ecologically and genetically diverse group of eukaryotic
microorganisms that have an enormous impact on human–kind. Although originally thought to
be related to plants, contemporary molecular systematics has shown them to be the animal
kingdom‘s closest relatives and, consequently, the simplest life forms related to humans. Thus,
from a basic research perspective, fungi have been exploited to gain insight into more complex
biological processes including the molecular basis of human disease. Fungi provide nourishment,
are a rich source of numerous antibiotics and other valuable products, and are used extensively in
industrial fermentation processes. Fungi also cause devastating diseases, particularly of plants,
and continue to be responsible for enormous human suffering. It is noteworthy that a significant
number of plant pathogenic fungi also cause serious human and animal disease, for which there
are very few effective therapeutic agents. Further, many fungi elaborate toxins that make food
sources unsafe to eat. Over the next 25-30 years, world food production must be doubled. A
significant part of this requirement can be met by reducing losses caused by fungi, which are
responsible for the vast majority of disease and presently reduce yields by 20-35%. The cost of
these losses is estimated at over $200 billion annually. When losses of natural fibers, building
materials and ornamental plants are factored in, financial losses are magnified a further 10 fold.
It is widely recognized that fungal pathogens represent a major threat to global food security and
are considered potent biological weapons. Many of these fungi also have major impacts on
medicine and on the environment. The Center for Integrated Fungal Research (CIFR) was
conceived to address these pressing challenges.
Mission
The mission of CIFR is to most effectively work towards combating the threat of fungal disease
and to enhance industrial application of fungi through integration of a broad range of approaches
and expertise within a formal scientific framework, to improve genomic research techniques
through collaborative efforts with industry and technological partners, to disseminate related
educational information to the general public and to provide training and instruction for students,
post-doctoral fellows and visiting scientists in fungal biology and genomics.
Vision
CIFR‘s vision is to develop a holistic view, a consideration as a whole, of the interaction of
fungal pathogens and plants at different genetic scales from individuals to communities. In large
part the focus of genomic sciences to date has been reductionist, i.e. reducing a complex system,
in this case fungal pathogen-plant interactions, to its fundamental parts in the pursuit of
understanding. However, the properties of a given system (physical, genetic, biological, and
chemical, etc.) cannot be determined or explained by its components alone. Instead, the system
as a whole influences how the pieces behave; the whole is greater than the sum of its parts.
Putting the fundamental parts back together to understand the whole represents a significant
challenge that only now with the emerging tools and resources for fungal pathogens and plants
can be addressed.
Over the past few years, a number of large-scale genome initiatives on individuals and on
environmental samples have been undertaken with the aim of obtaining a more complete
understanding of biodiversity. The decoding of genomes has also proved invaluable to
understand how organisms and communities utilize resources within their environments, how
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they interact and how they adapt to environmental changes. Examination of genomes has
revealed immense variability of gene sets and of genomic structures between and within species.
Further, the analysis of the interaction of gene products has provided detailed pictures of the
structural and regulatory networks governing fungal development and responses to the
environment. Finally, these genomic sequences are providing novel insights on the evolutionary
history of organisms and communities as well as providing new opportunities to model fungal–
plant interactions through principles such as evolutionary game theory (predictions of ‗fitness‘).
Members of CIFR have and continue to be at the forefront in the analysis of genomes of fungal
pathogens, gaining knowledge of their underlying biological properties (gene expression, protein
networks etc), evolution and interactions with plants. This strength, coupled with the broad
expertise of CIFR faculty in population biology, mathematical epidemiology, host parasite
interactions and translation research position CIFR to be a leader in characterizing the interplay
among microbial communities and between these communities and plants to develop new
concepts in host-microbe interactions and to translate these concepts into sustainable control
strategies.
Objectives and Goals
CIFR will integrate a broad spectrum of approaches and expertise for investigating and analyzing
the fundamental biology of fungi of agronomic and industrial significance and their interaction
with plants and other community members. In addition to the advancement of basic knowledge
of biological processes, the data generated will provide practical applications for improvements
in quality of life and the environment. The Center will enhance NCSU‘s mission to strengthen
and expand Genomic Sciences and will take advantage of the University‘s research leadership in
agriculture, forestry and veterinary medicine, as well as newly emerged strengths in
Bioinformatics and Functional Genomics. The Center has its roots in the Department of Plant
Pathology, a department recognized nationally and internationally for research on the nature of
plant diseases, food safety and on improvement of plant health. Research at CIFR follows falls
under three thematic areas; Population Biology, Fungal Metabolism, and Molecular
Pathogenesis.
CIFR Major Scientific Goals
the discovery and analysis of complete gene sets from major plant pathogenic and
industrially important fungal species;
the understanding of genome organization, whole genome organization and comparative
analysis of economically important fungi
the understanding of growth and development of fungi including primary and secondary
metabolism;
comparative and global functional analyses of fungal-host interactions to decode the
molecular basis of disease caused by fungal pathogens; and
development and application of models to better understand the dynamics of host-pathogen
population biology, fungal ecology and microbial ecosystems.
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CIFR Educational and Outreach Goals
CIFR provides postdoctoral, undergraduate and graduate training, visiting scientist and pre-
college outreach designed to:
create and disseminate original knowledge to scientists, students, industry, and society
educate a new generation of scientists who recognize and understand the importance of
genomic research
increase the participation of underrepresented groups in the field of scientific research
increase scientific literacy in the K-12 classrooms
Relevance to University mission
CIFR complements and expands the reach of NCSU‘s mission as a research university. The
research conducted by CIFR provides direct benefits to human betterment by providing
information that can be applied in a variety of ways. CIFR research produces technological
changes that will benefit the social and economic well-being of the people of North Carolina, the
nation, and the world.
CIFR reflects NCSU‘s mission to teach, provide research and public service for undergraduates,
graduate students, the general public and industry. CIFR disseminates research information that
is current, relevant and vitally important locally, nationally and internationally. CIFR provides
opportunities for crossdisciplinary intellectual and critical foundations for understanding,
anticipating, and responding to public needs.
Through collaboration with the Center for Bioinformatics, the North Carolina Biotechnology
Center and other centers on campus and in the Research Triangle Park area, CIFR offers unique
undergraduate, graduate and post doctoral educational opportunities that are on the leading edge
of research.
Impact on Instructional Programs
CIFR as an academic research facility provides unique opportunities for learning for high school
through post-doctoral students. The quality of the research faculty and the facility enhances
NCSU‘s recruitment offerings for students in the biological sciences as well as bioinformatics,
statistics, physical and mathematical sciences, and business course offerings. CIFR actively
pursues collaborative projects and opportunities for interns across departments and colleges are
encouraged.
CIFR faculty have productive programs and have obtained significant competitive funding from
a variety of government, private and industrial sources. CIFR faculty have been awarded more
than $14 million and have published in excess of 120 papers in peer-reviewed journals over the
past five years. These successes coupled with state of the art research facilities serve to attract
high quality students and post docs to CIFR as well as to other instructional programs at NCSU.
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Center Administration and Organization
Dr. Ralph A. Dean – Center Director
Dr. Ralph A. Dean is the Center Director and a William Neal Reynolds Distinguished Professor
of Plant Pathology. Dr. Dean joined NCSU in 1999 after several years as Associate Director at
the Clemson University Genomics Institute. At NCSU, Dr Dean established the Fungal
Genomics Laboratory, which is currently supported by federal and industry research grants. In
2001, he and Dr. Gary A. Payne established the Center for Integrated Research. Dr. Dean‘s
research is focused on a comprehensive molecular dissection of the mechanisms regulating early
events of the host-pathogen recognition process, including the induction of a specialized
infection cell, the appressorium, in the rice blast fungus, Magnaporthe oryzae, a major threat to
food security worldwide. He also led the initiative to sequence the M. oryzae genome, the first
genome of a filamentous fungal plant pathogen to be publically available.
Dr. Gary A. Payne – Associate Director
The Associate Director of CIFR is Dr Gary Payne, William Neal Reynolds Distinguished
Professor of Plant Pathology. Dr. Payne is an internationally recognized expert in Aspergillus
flavus and mycotoxin biosynthesis. Dr. Payne led the A. flavus genome sequencing project and
is the director of AMPLIFY, a College of Agriculture and Life Sciences initiative for high yield
sustainable agriculture.
CIFR Scientific Advisory Committee Members
Steven Lommel, Professor, Assist VP for Research, Department of Plant Pathology, NC
State University
Steven Peretti, Associate Professor, Department of Chemical and Biomolecular
Engineering, NC State University
John R. Perfect, MD, Professor, Department of Medicine, Duke University
Allen Rodrigo, Director, NESCent (National Evolutionary Synthesis Center)
Mike Schwarz, Product Development Manager, Bayer CropScience
Allison Tally, Technical Manager, Syngenta Crop Protection
H. Vincent Morton, President, Viva Inc
Eric Ward, President, Two Blades Foundation
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CIFR Organizational Chart
Johnny C. Wynne
Dean - CALS
Scientific Advisory
Committee
Ralph A. Dean
Center Director,
William Neal Reynolds
Professor
Plant Pathology
CIFR Administrative
Assistant
Gary Payne
Associate Director,
William Neal Reynolds
Professor
Plant Pathology
Margaret Daub
Dept. Head,
William Neal
Reynolds Professor
Plant Biology
Marc Cubeta
Professor
Plant Pathology
Ignazio Carbone
Associate
Professor
Plant Pathology
Paola Veronese
Assistant
Professor
Plant Pathology
Peter Ojiambo
Assistant
Professor
Plant Pathology
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CIFR External Grant Support
CIFR faculty have obtained significant funding from a variety of sources including: National
Science Foundation, U.S. Department of Agriculture, National Institutes of Health, NCSU, and
corporate sponsors.
2006 2007 2008 2009 2010
Current
Support $8,023,415 $1,378,686 $705,748 $1,588,627 $1,639,727
Details of individual grants are provided at the end of this report (p. 39).
CIFR Research Activities
Research at CIFR falls under 3 programmatic themes: Population Biology, Fungal Metabolism
and Molecular Pathogenesis. As outlined in the following one page biographical sketches, the
research focus of Drs. Carbone, Cubeta and Ojiambo falls primarily within Population Biology.
Dr. Carbone‘s research emphasizes evolutionary and population genetic analysis of Aspergillus
species and community dynamics. The latter is a primary focus of the work ongoing in the
Cubeta lab, with an emphasis on soil borne fungi, particularly Rhizoctonia solani. Dr. Ojiambo
has a strong interest in modeling fungal plant pathogen populations, particularly downy mildew.
Under Fungal Metabolism, Drs. Daub and Payne research focuses on the biogenesis and role of
toxins, cercosporin and aflatoxin, respectively, in fungal disease. The research programs of Drs.
Dean and Veronese are primarily in Molecular Pathogenesis. Dr. Dean‘s program is aimed at
dissecting fungal pathogenesis using the rice blast pathosystem, whereas Dr. Veronese‘s program
exploits Arabidopisis as a model to elucidate the basis of disease caused by Verticillium wilt
pathogens. There is much overlap within these programmatic themes by CIFR faculty. Drs.
Cubeta, Dean, Payne and Veronese are all engaged in fungal genome projects and routinely share
their expertise. Dr. Carbone shares considerable expertise in phylogenetic analyses with several
CIFR faculty, such as exploring gene family expansion in fungal genomes with Dr. Dean. Dr.
Veronese provides valuable knowledge regarding plant defense mechanisms complementing
work done by Drs. Dean and Payne on identifying and characterizing disease resistance in rice
and corn, respectively. Dr. Ojiambo, the most recent addition to CIFR, is actively involved in
projects with Drs. Carbone, Payne and Cubeta. Many CIFR faculty are engaged in genetic
manipulation of fungi. Drs. Cubeta, Daub, Dean, and Payne routinely share advice between their
labs on current techniques and tools for functionally characterizing genes.
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Ralph A. Dean North Carolina State University
Center for Integrated Fungal Research
Department of Plant Pathology
Campus Box 7251, Raleigh, NC 27695-7251
Phone: (919) 513-0020 Fax: (919) 513-0024
Professional Preparation
University of London, England Botany B.S. (hons.) 1980
University of Kentucky Plant Pathology Ph.D 1986
University of Georgia Genetics Post Doctoral Associate 1986-1989
Appointments
July 2005-present William Neal Reynolds Professor of Plant Pathology
Sept 2001-present Director, Center for Integrated Fungal Research, North Carolina State University
June 2001-present Adjunct Professor, Dept. of Genetics, North Carolina State University
Sept 1999- present Professor and Director, Fungal Genomics, Dept. Plant Pathology, NCSU
Sept 1997-Aug 1999 Associate Director, Clemson University Genomics Institute
Aug 1996-July 1999 Chair, Interdisciplinary Program in Genetics
July 1995-July 1999 Associate Professor of Plant Pathology, Department of Plant Pathology &
Physiology, Clemson University
1990-1995 Assistant Professor of Plant Pathology, Department of Plant Pathology &
Physiology, Clemson University
Honors and Awards
2005 William Neal Reynolds Distinguished Professor
2004 Huxley Memorial Medal, Imperial College London
2004 USDA Group Honor Award for Excellence
Teaching
PP 790 Advances in Host-Microbe Interactions.
Research
Dr. Dean‘s research program has employed Magnaporthe oryzae as a model to understand the
mechanisms regulating host pathogen interactions for more than 20 years. Initial work focused on the
signaling pathways regulating the initiation and development of appressorium formation, a specialized
cell required by M. oryzae and many other pathogenic fungus for attachment to and penetration of host
tissues. Following the completion of the genome sequence, his lab currently focuses on:
1. Understanding the molecular basis of infection through comparative genome analyses of members of
the Magnaporthaceae.
2. Characterization of the transcription circuitry regulating infection.
3. Interrogation of post-translational protein modifications (phosphorylation and ubiquitination) during
infection.
4. Identification and characterization of effector proteins.
Synergistic Activities
Board member (2009- present) British Society of Plant Pathology
Editorial Board (2007-present) Fungal Biology Reviews
Member: (2008 – present) Postdoctoral Affairs Faculty Advisory Committee, NCSU
Senior Editor: (2002-present) Molecular Plant Pathology
Grant Review Panels: Served on USDA-NRI (2007) and NSF (2002, 2004, 2006)
Chair: (1998-present) International Rice Blast Genome Consortium
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Gary A. Payne North Carolina State University
Center for Integrated Fungal Research
Department of Plant Pathology
Campus Box 7567, Raleigh, NC 27695-7567
Phone: (919) 515-6994 Fax: (919) 513-0024
Professional Preparation
N.C. State University Agronomy B.S. 1970
Cornell University Plant Pathology Ph.D. 1977
University of Nebraska Research Assoc. Agric. Biochem. 1977-78
Appointments 2005-present William Neal Reynolds Professor of Plant Pathology
2001-present Associate Director, Center for Integrated Fungal Research
1990-Present Professor, Dept. Plant Pathology, North Carolina State University
1985-1990: Associate Professor, Dept. Plant Pathology, North Carolina State University
1978-1984: Assistant Professor, Dept. Plant Pathology, North Carolina State University
Honors and Awards
2005 William Neal Reynolds Distinguished Professor
1993 Fellow, American Phytopathological Society
Teaching
PP 707 Plant Microbe Interactions Co-taught with Ignazio Carbone
PP 730 Fungal Genetics and Physiology Co-taught with Marc Cubeta and Margo Daub
Research
Dr. Payne‘s laboratory conducts both basic and translational research directed at the control of
mycotoxins. Current research is focused in three areas:
1. Transcriptional analysis of Aspergillus flavus and maize during infection of developing seeds.
2. Histological examination of the infection process and tissue specific gene expression in maize in
response to infection.
3. Role of secondary metabolites during colonization of maize kernels.
4. Comparative analysis of pathogenesis by A. flavus and Fusarium verticillioides.
5. Nuclear condition in A. flavus and it role in the ecology of the fungus.
6. Selection for resistance to aflatoxin and fumonisin accumulation in maize.
7. Maize ribosome inhibiting protein (RIP) as a simulant for ricin.
Synergistic Activities
Co-Chair (2011-2013) Gordon Conference, Mycotoxins and Phycotoxins
Co-director (2009-Present) AMPLIFY, a College initiative for high yield sustainable agriculture
Program Chair (2007-2011) Aspergillus Genomics Research and Policy Committee
Chair (2004-2005) Division O, American Society for Microbiology
Co-chair (2000-2003) CAST Task Force on Mycotoxins.
Associate Editor Appl. Environ. Microbiol. (1993-2003; Phytopathology (1992-1993)
Grant Review Panels NSF (2007), USDA (1989, 90, 92, 93; Panel Manager 1995)
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Margaret E. Daub North Carolina State University
Center for Integrated Fungal Research
Department of Plant Biology
Campus Box 7612, Raleigh, NC 27695-7612
Phone: (919) 513-3807 Fax: (919) 515-6986
Professional Preparation
Undergraduate: College of Wooster, Wooster, Ohio Biology B.A., 1974
Graduate: University of Wisconsin-Madison Plant Pathology Ph.D., 1979
Postdoctoral: Michigan State University Plant Cell Biology 1979-1982
Appointments
1999-Present Professor and Head, Department of Plant Biology, NC State University
1994-Present Professor, Department of Plant Pathology, NC State University
1989-1994 Associate Professor, Department of Plant Pathology, NC State University
1983-1989 Assistant Professor, Department of Plant Pathology, NC State University
1979-1982 Postdoctoral Research Associate, Michigan State University
Honors and Awards 2007 William Neal Reynolds Distinguished Professorship
2002 Fellow, American Association for the Advancement of Science (AAAS)
2000 Fellow, American Phytopathological Society (APS)
1991 Ciba Geigy Award, APS
Teaching
PP (PB, MB, GN) 730, ―Fungal Genetics and Physiology‖, co-taught with Drs. Payne and Cubeta
BIT 815, ―Professionalism‖ (course for graduate students in NIH and GAANN Biotechnology
training grants), co-taught with Bob Kelly (Chemical Engineering)
[BIT 495/595, ―Manipulation of Eukaryotic Microbes‖ (Biotechnology Program lab course
reaching students in biology, agriculture, engineering) taught by Dr. Herrero from the Daub lab]
Research Margo Daub‘s research focuses on photoactivated, reactive-oxygen-generating toxins in fungal-plant
interactions and the engineering of plants for toxin resistance as a mechanism of disease control. Her
major area of focus has been on fungi in the genus Cercospora and the toxin cercosporin, including toxin
mode of action, role in disease, biosynthesis, and genes for resistance. Current efforts are directed at
testing putative toxin resistance genes from Cercospora for efficacy in engineering Cercospora-resistant
plants. In addition, she is investigating the possible production of photoactivated toxins by
Mycosphaerella fijiensis, causal agent of the Black Sigatoka disease of banana. Bioinformatics analysis
identified putative polyketide synthase toxin biosynthetic clusters in the M. fijiensis genome. Toxins and
their role in disease are being characterized by gene knock-out, gene expression and metabolite analysis.
Synergistic Activities
Faculty mentor, NCSU NSF REU Synthetic Biology program, 2011 – present
Executive Board, NIH/GAANN Molecular Biotechnology Training Programs, 2000/2003 - present
Co-director (with J. Ristaino), Summer Research Program in Tropical Plant Pathology, 2011 - present
Co-PI, NSF/NCSU ADVANCE program to advance women faculty, 2008-present
Chair, American Phytopathological Society Publications Board, 2005-2010
Member, APS Strategic Planning Committee, 2009-2010
Member, American Phytopathological Society Honors and Awards Committee, 2003-2006
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Marc A. Cubeta North Carolina State University
Center for Integrated Fungal Research
Department of Plant Pathology
Campus Box 7567, Raleigh, NC 27695-7567
Phone: (919) 513-1227 Fax: (919) 513-0024
Professional Preparation
University of Delaware Plant and Soil Science BS 1980
University of Illinois Plant Pathology/Soil Microbiology MS 1983
North Carolina State University Plant Pathology PhD 1991
Appointments
2009 - present Professor Plant Pathology, North Carolina State University
2006 - present Member of Graduate Faculty, Biology, Duke University
2000 - 2008 Associate Professor, Plant Pathology, North Carolina State University
1994 - 2000 Assistant Professor, Plant Pathology, North Carolina State University
1992 - 1994 Post Doctoral Associate, Botany and Mycology, Duke University
Honors and Awards
2012 - Fulbright Scholar Award (Uppsala, Sweden)
1996 - Provost Award, North Carolina State University
Teaching
Advances in Evolutionary Ecology and Population Biology (PP562/762), Introduction to Mycology
(PP575), Fungal Genetics and Physiology (PP730), Emerging Issues in Agricultural Technology (PP590),
Biology of Plant Pathogens (PP501), Plant Disease Diagnosis (PP500).
Research
Dr. Cubeta‘s research is focused on understanding the disease ecology and population dynamics of the
soil fungus Rhizoctonia solani, an economically important pathogen of agricultural and forestry crops.
His research has provided a conceptual framework for understanding the genome organization, evolution,
population biology, and taxonomy of R. solani. Dr. Cubeta‘s laboratory is currently conducting studies
with closely related Rhizoctonia fungi that are associated with orchids and decayed wood, but do not
cause plant disease. This new area of research involves bioinformatics and ―omics-based‖ methods that
are providing new insight into many fundamental research questions related to the pathogenic and
saprobic behavior of the fungus. The goal of Dr. Cubeta‘s research program is to develop improved
management approaches to reduce economic losses to Rhizoctonia disease while promoting increased
productivity and sustainability.
Synergistic Activities
2012 Panel Chair, NP303 Panel 4 - Systematics USDA-ARS Crop Production and Protection
National Program, OSQR
2010 - 2013 Treasurer, Mycological Society of America
2006 - 2008 Ecology and Plant Pathology Councilor, Mycological Society of America
2005 - 2009 Program Committee (Chair 2009), Mycological Society of America
2002 - 2011 NSF, USDA, and Sigma Xi grant review panels
2001 - 2007 US National Committee of the Int'l Union for Microbiological Sciences
2001 - 2004 Phytopathology Committee (Chair 2004), Mycological Society of America
1998 - present International Rhizoctonia Committee, Int'l Society of Plant Pathology
1996 - 2001 Mycology Committee (Chair, 2001), American Phytopathological Society
1994 - 2004 Associate Editor Plant Pathology
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Ignazio Carbone North Carolina State University
Center for Integrated Fungal Research
Department of Plant Pathology
Campus Box 7244, Raleigh, NC 27695-7244
Phone: (919) 513-4866 Fax: (919) 513-0024
Professional Preparation
University of Toronto, Canada Toxicology and Pharmacology B.S. (hons.) 1992
University of Toronto, Canada Botany M.S 1994
University of Toronto, Canada Botany Ph.D 2000
Appointments
2008 – present Associate Professor, NC State University, Plant Pathology
2008 – present Graduate Recruitment and Admissions Coordinator, Plant Pathology
2002 – 2008 Assistant Professor, NC State University, Plant Pathology
2001 – 2002 Director of Biotech Group, Klisline Research & Consulting, Inc.
Honors and Awards
2009 Syngenta Award, American Phytopathological Society
2008 C. J. Alexopoulos Award, Mycological Society of America
2004 Faculty Center for Teaching and Learning Instructional Award
2004 Fulbright Award
Teaching
PP 715 Applied evolutionary and population genetic data analysis
PP 707 Plant-microbe interactions (co-taught with Dr. Gary Payne)
Research
Dr. Carbone‘s research focuses on the evolution of aflatoxigenicity. Aflatoxin is one of the most
carcinogenic compounds known and is responsible for major yield losses in oil seed crops worldwide.
The evolutionary processes that modulate aflatoxin biosynthesis in nature are poorly understood.
Currently, his lab is acquiring basic knowledge on the evolution of the aflatoxin gene cluster in
populations of agriculturally important aflatoxin-producing species. A long-term goal is the development
of novel biocontrol measures, ultimately fine-tuning these control strategies based on the population
genetic structure of these fungi.
Dr. Carbone‘s lab is also active in developing evolutionary and population genetic software that has
been applied broadly to:
1. Understand the underlying evolutionary processes shaping diversity in pathogen populations, which is
important for species delimitation and enumeration (collaborative NSF Dimensions of Biodiversity).
2. Understand the environmental factors that impact microbial community dynamics and species
distributions, which is essential in developing sustainable biological control agents (USDA-ARS).
3. Identify the genetic reservoirs for emerging and reemerging plant pathogens (Duke collaboration).
Synergistic Activities
Bioinformatics Workshops: South Africa (2010), Mexico (2009) and Yale (2008)
Grant Review Panels: NSF (2007, 2008) and NIH (2005)
Member: (2009 – present) CALS Research Committee
Member: (2012 – 2014) MSA Councilor in Genetics/Molecular Biology
Chair: (2010 – 2011) MSA Genetics and Cell Biology Committee
Page | 12
Paola Veronese North Carolina State University
Center for Integrated Fungal Research
Department of Plant Pathology
Campus Box 7251, Raleigh, NC 27695-7251
Phone: (919) 513-8219 Fax: (919) 513-0024
Professional Preparation
Sapienza University of Rome, Italy Biology B.S. 1990
Tuscia University of Viterbo, Italy Horticulture Ph.D 1998
Appointments
Assistant Professor, Jul 2005-present, Plant Pathology Department, NC State University
Postdoctoral Fellow, 2002-2005, Botany & Plant Pathology Department, Purdue University
Postdoctoral Fellow, 1998-2002, Horticulture & Landscape Architecture Dept., Purdue University
Ph D Student, 1995-1998, Crop Production Department, Tuscia University
Research Associate, 1991-1994, ENEA Research Center, Rome, Italy
Teaching (3 credit graduate courses)
Molecular Genetics of Plant Stress Responses
Advances in Host-Microbe Interactions
Plant-Microbe Interactions/Concepts, guest lectures
Research
Dr. Veronese is interested in identifying molecular genetic mechanisms governing compatible and
incompatible plant interactions with microbial pathogens. Her lab is conducting studies on model
systems, which are amenable to functional genomics approaches, with the goal of translating methods and
knowledge developed to crop systems. Dr. Veronese is Co-PI of an NSF-funded project to study the role
of alternative splicing (AS) in controlling the innate immune response of the model plant Arabidopsis
thaliana. The research has uncovered, for the first time, the extent of the defense transcriptome regulated
at the isoform level, indicating that AS is an important and so far uninvestigated layer of the plant defense
machinery. Dr. Veronese is also actively involved in generating tools for functional analysis of microbial
pathogenicity. She is Co-PI of an NSF&CSREES/USDA project for sequencing and comparative analysis
of phytopathogenic Verticillium spp. genomes, which has revealed fundamental aspects of the pathogen
biology underpinning its broad host range and worldwide distribution. Dr. Veronese values the
importance of collaborative research and plan to continue to participate in multidisciplinary projects
involving NC State Departments as well as the broader scientific community.
Synergistic activities
Faculty of the NC State Biotechnology Program, Genomics Science Graduate Program, Environmental
Science Academic Program
Member of APS Host Resistance, Women in Plant Pathology and Diversity and Genetics Committees,
Genetics Chair (2008-2009)
Associate Editor of ―Molecular Plant-Microbe Interactions‖ (MPMI), 2007-2009
Ad hoc reviewer for: PLoS Genetics, The Plant Journal, Plant Physiology, Journal of Experimental
Botany, Molecular Plant Pathology, Plant Science, Gene, Phytopathology, Botany, Physiological and
Molecular Plant Pathology, ―Fruit, Vegetables and Cereal Science and Biotechnology‖
Panelist of the NSF-IOS program ―Symbiosis, Defense & Self-recognition‖, 2010
External reviewer of the Department of Plant Sciences, University of Milan, Italy, 2011
Ad hoc proposal reviewer for the Natural Sciences and Engineering Council of Canada, 2009 and 2010
Ad hoc proposal reviewer for the Dutch Technology Foundation STW, 2006 and 2008
Page | 13
Peter Ojiambo North Carolina State University
Center for Integrated Fungal Research
Department of Plant Pathology
Campus Box 7567, Raleigh, NC 27695-7567
Phone: (919) 513-2188 Fax: (919) 513-0024
Professional Preparation
University of Georgia Plant Pathology Ph.D. 2004
University of Nairobi, Kenya Plant Pathology M.S. 1997
University of Nairobi, Kenya Agriculture B.S. (hons.) 1994
Appointments
2008-present Assistant Professor, Plant Pathology, NC State University
2006-2007 Post Doctoral Fellow, Plant Pathology, International Institute for Tropical
Agriculture, Ibadan, Nigeria
2005 Post Doctoral Research Associate, Plant Pathology, University of Georgia
Honors and Awards
5th I.E. Melhus Graduate Student Symposium Speaker, American Phytopathological Society (2005)
Broadus E. Browne Award for the Outstanding PhD Candidate, College of Agriculture and
Environmental Sciences, University of Georgia (2004)
Kenneth E. Papa Award for the Outstanding PhD Candidate, Department of Plant Pathology, The
University of Georgia (2004)
Outstanding Graduate Teaching Assistant, The University of Georgia (2004)
Outstanding Academic Achievement, Sigma-Xi Honor Society of Agriculture, The University of
Georgia Chapter (2004)
Outstanding Graduate Research Paper, Georgia Association of Plant Pathologists (2004)
Teaching
PP 790-004: Advances in Evolutionary Ecology & Population Biology (Spring semester)
PP 790A: Epidemiology: Theory & Application (Fall semester)
Research Projects
Theoretical aspects of adaptive cluster sampling for assessing plant disease incidence
Quantitative and applied epidemiology on wheat (Septoria nodorum blotch), blueberry (Mummy
berry disease), cucurbits (Cucurbit downy mildew)
Quantitative aspects of spread of cucurbit downy mildew in eastern U.S.
Incorporation of models of pathogen biology in cucurbit downy mildew forecasting
Biological control of aflatoxin contamination in corn
CIFR Collaborative Projects
Host resistance and bio-control of A. flavus (with Gary Payne and Ignazio Carbone)
Modeling caporgenic germination blueberry mummies (with Marc Cubeta)
Ecology and population biology of P. cubensis (with Ignazio Carbone)
Synergistic Activities
Immediate Past Chair, Epidemiology Committee, American Phytopathological Society
Section Chair, Annual Meeting Board, American Phytopathological Society
Organizer, 11th I.E. Melhus Graduate Student Symposium, American Phytopathological Society
Editor, Plant Pathology, British Society for Plant Pathology
Page | 14
CIFR Sponsored Activities
Over the past 5 years CIFR has sponsored seminar speakers, a distinguished lecture series and
held an annual retreat. All faculty, staff and students are invited to attend this 2-day retreat,
which includes chalk talks and a presentation from an invited guest.
CIFR Retreat:
- Heung Zhu, Institute for Basic Biomedical Sciences, Johns Hopkins University, 2006
- Linda Cohen, Department of Cell & Systems Biology, University of Toronto, 2007
- Nancy Keller, Dept. of Medical Microbiology and Immunology, University of
Wisconsin, 2008
Distinguished Lecture Series:
- Kenneth H. Wolfe, Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland, 2006
- Jeffrey L. Bennetzen, Department of Genetics, University of Georgia, 2006
Seminar Series (Co-sponsored/Co-invited)
- Xiannian Dong, Department of Biology, Duke University, 2007
- Shauna Somerville, Department of Plant & Microbial Biology, University of California,
Berkeley, 2008
- David Geiser, Department of Plant Pathology, Penn State University, 2008
- Scott Gold, Department of Plant Pathology, University of Georgia, 2008
- Harald Scherm, Department of Plant Pathology, University of Georgia, 2009
- Nick Grunwald, USDA ARS, Corvallis, OR, 2010
- Allan Collmer, Department of Plant Pathology, Cornell University, 2010
- Adam Bogdanove, Department of Plant Pathology, Iowa State University, 2010
- Brett Tyler, Virginia Bioinformatics Institute, Virginia Tech, 2010
Page | 15
CIFR Outreach and Education.
CIFR faculty are actively engaged in a number of outreach and education programs.
Dr. Dean developed the Summer College in Biotechnology and Life Sciences (SCIBLS) to
provide an opportunity for high school students needing a pre-college experience.
Disadvantaged students are highly targeted. The four-week summer session provides an
introduction to college life and the university environment with the goal of easing the transition
between high school and college. SCIBLS is first and foremost an academic experience. Three-
credit hour coursework is designed to be a challenging experience for college bound students
interested in a science, technology, engineering, or mathematics college major affording the
academically advanced students the opportunity to participate in science coursework not
available at most high schools. Currently three 3-credict classes are offered each summer.
SCIBLS has been funded primarily through program fees and grants from the NSF and the
Burroughs Wellcome Fund. SCIBLS is currently supported by CIFR and North Carolina State
University's College of Agriculture and Life Sciences Academic Programs.
Dr. Cubeta has developed a number of educational outreach and engagement workshops for high
school students and biology teachers in North Carolina with financial support from NSF and
USDA. Workshop titles include: Exploring fungi: educators and students as co-investigators of
the ecology and biogeography of wood-decay fungi; fungi growing on the tree of life and
searching for Rhizoctonia fungi on archaeological specimens of potato from Peru. The primary
objective of these workshops is to develop collaborative, inquiry-based assignments for high
school students to foster a better understanding of the biogeography, diversity and ecology of
fungi. A total of 21 and 84 high school biology teachers and students, respectively, have
participated in the workshops.
Several CIFR faculty have provided research experiences for undergraduate students and visiting
graduate students. With support form the NSF, Dr. Dean has provided REUs (Research
Experience for Undergraduates) for numerous students over the past 5 years. Likewise, Drs.
Daub and Payne have hosted REUs through an NSF program in Synthetic Biology. Dr. Veronese
has hosted five undergraduates in her lab through the Kelman Scholars Program. All students
are engaged in a 10-week full-time training program and present a poster on their activities at the
NCSU Undergraduate Summer Research Symposium. Dr. Payne has hosted several visiting
graduate students over the past 5 years including students from Trinity College, Dublin in
Ireland, La Spienza University in Rome, Universidad de Concepción (UdeC) in Chile, Università
―La Sapienza‖ in Italy, and Misión Biológica de Galicia – CSIC in Spain. Dr. Daub is also co-
director (with Jean Ristaino, Plant Pathology) of a summer research experience for students in
Tropical Plant Pathology in cooperation with the University of Costa Rica. In addition, she
coordinates an annual exchange program for botany students with Zhejiang University, and is a
co-PI and member of the leadership team for the NSF-funded ADVANCE program, focused on
advancing opportunities for women faculty at NCSU.
Dr. Carbone and his lab provide valuable software resources to CIFR as well as to the broader
research community with the continued development of the SNAP evolutionary toolkit for
analyzing molecular sequence variation. SNAP Workbench is a comprehensive package of
population genetic tools for comprehensive analyses of evolutionary processes on different
temporal and spatial scales. The SNAP tools are now available online through the NCSU SNAP
portal, analogous to the cloud computing services provided by Amazon. In addition to the tools,
Dr. Carbone routinely provides training to faculty and students and offers numerous hands on
workshops at national and international conferences.
Page | 16
CIFR Training and Mentoring
CIFR faculty have trained and mentored 40 graduate students, 60 undergraduate students and 31
post-doctoral fellows/senior researchers in the past 5 years. In addition they have hosted 20
international scholars.
Post Doc/Senior personnel Graduate Undergradute Visiting Scholar
Name Year Name Year Name Year Name Year
Ralph A. Dean
Tom Mitchell 2003-2007 Mine Altunay 2004-2007 Paige Birdsall 2006 Yong Hwan
Lee
2009
Nicole Donofrio 2003-2006 Jixin Deng 2002-2008 Leethaniel Brumsfield
2008 Min-feng Xue 2008-2009
William Franck 2010-present Stephen Diener 2001-2005 Brent Clay 2011 Bjorn Sode 2009
Malali Gowda 2006-2009 Gregory Bernard 2006-2011 Robyn Hicks 2007
Tarek Joobeur 1999-2006 Jixin Deng 2002-2008 Alisha
Holtzhausen
2008
Junichiro Marui 2004-2006 Jun-Seop Jeong 2000-2006 Donte' Jackson 2009
Shaowu Meng 2006-2008 Yeon Yee Oh 2003-2007 April Johnson 2008
Yeon Yee Oh 2008-present Junhyun Jeon 2008-present Yana Lagrand 2007
Amy Powell 2004-2008 Cristiano Nunes 2006-present Jonas Michel 2010
Abdelaty Saleh 2007-2010 Joshua Sailsbery 2008-present Ca Adrian Norman
2007
Doug Brown 2000-2010 William Sharpee 2010-present La Toya Poole 2006
Helen Pan 2000-2006 Gabrielle Riesner 2008
Yvonne Rossario 2007
Angela Shows 2009
Julianne Tajuba 2006
Stewart Young 2007
Hey Min Kim 2006
Gary A. Payne
Greg Obrian 2000-2011 Xiaomei Shu 2009-present Rufus Vandezande 2011 Ana Cavo 2011
Zhengyu He 2004-2007 Farhana Runa 2009-present Cary Jackson 2009-2011 Marta Punelli 2009
Beth Prichard 2004–2006 A. L. Dolezal 2006-2010 Jonathan
Vandezande
2009-2010 Liz Janice
Hernandez Borrero
2009
D. R. Georgiana 2005–2009 Lucy Liu 2008 Giancarlo
Perrone
2008
M. R. Starr
(Eller)
2004-2009 Kyle Gazdeck 2007 Salomé Zaldúa 2008
R.A. Holmes 2002–2008 Marta Punelli 2007-2009
C.A. Jacobus 2002–2007 Nora Kaldi 2007
Margaret Daub
Alongkorn Amnuaykanjanasin
2006-2007 Elizabeth Rueschhoff
2003 – 2009 Shante Bryant 2009-present Nafisa Ibrahim 2007-2009
Eugenia Gonzalez 2004-2007 Aydin Beseli 2008-present Morgan Carter 2011-present Andre de Souza 2009-2010
Sonia Herrero 2001-present Roslyn Noar 2010 – present Catherine
Hammond
2008
Heriberto Velez 2007 Andrew Mealin 2009-2010
Zhenghua Zhang 2008
Marc Cubeta
Marianela Rodriguez-Carres
2009-present Meghan McCormick
2010-present Juan Austarius 2009 Warren Copes 2006 and 2009
Elizabeth Thomas 2008-present Kathleen
Burchhardt
2009-present Meagan Clark 2010 Ayman Esh 2009
Takeshi Toda 2005-2007 Faith Bartz 2005-2010 Shah Fiza 2007-2008 Suha Jabaji 2009 and
Page | 17
2011
Zhi Zhang 2008-2009 Amanda Kaye 2004-2009 Moises Figueroa 2009-2010 Loukas Kanetis 2008
Suman Pakala 2009-2010 Nikki Charlton 2002-2007 DeMonica Gentry 2009-present Paul Bayman 2006
Luci Liu 2008
Katie Neufeld 2009
Max Sherar 2010-present
Nick Taylor 2008-2010
Shari Thomas 2009
Carmen Cubilla 2011-present
Ignazio Carbone
Ryoko Oono 2011-present Trent Monacell 2008–present Mary Lewis 2011-present Erica Goss 2007
Jorge H. Ramirez-
Prado
2005-2008 Rodrigo Olarte 2008–present Stephen Tourigny 2011-present Valdir
Lourenco Jr.
2006-2007
Alex Putman 2009–present Kate Lester 2011
Farhana Runa 2010–present Lauryn Collier 2011
Carolyn
Worthington
2010–present Tiara Washington 2010
Geromy Moore 2006–2010 Jacalyn Elliott 2006-2009
Elizabeth Schoenbaum
2005–2008 Prashant Baronia 2007
Troy Taylor 2007–2010 Lloyd Bowden 2007
Eric Price 2006-2007
Thomas Shelby 2006
Paola Veronese
Nobuaki Suzuki 2006-2007 Manan Chandra 2011-present Kayla Pennerman 2010
Selvakumar Veluchami
2008-2009 Robson Ferreira de Almeida
2007-2009 Amarpreet Kaur 2008
Xiaoping Tan 2009-2010 Lindsey
Montefiori
2008
Monica Borghi 2011-present Olivia Campbel 2007
Crystall Phelps 2007
Colette Williams 2010
Peter Ojiambo
Loukas Kanetis 2008 Ashley Zearfoss 2008-2010 Rob Kautz 2009-present Luis Felipe
Arauz
2009
Katie Neufeld 2009-present Brittany Perrish 2009
Lucky Mehra 2011-present Courtney Wade 2010
Anna Thomas 2011–present Charles Shew 2010
Rebecca Echerd 2011-present
Sydney Jarrett 2011
Page | 18
CIFR Collaborators
CIFR faculty have developed extensive research collaborations with scientists in the USA and
around the world. The table below highlights these collaborations and identifies shared
publications and grants. The numbers indicate publication and grant number listed under CIFR
Publications and CIFR Grants at the end of the report (p.29 and p. 39).
Institution Publication # Grant #
Ralph Dean
CALS
Ignazio Carbone CIFR 12, 28, 88 36-40
Marc Cubeta CIFR 5, 36-40
Margo Daub CIFR 36
Gary Payne CIFR 87, 97, 102, 120 23, 36-40
Paola Veronese CIFR 36
NCSU
David Muddiman Chemistry 6, 23, 38 17
Ratna Sharma-Shivappa Ag. Engineering 100
Todd Wehner Horticulture 56
USA
Dan Ebbole Texas A&M 11, 103 15
Mark Farman Univ. Kentucky 11, 70, 92, 103
Lijun Ma Broad Institute 16
Tom Mitchell Ohio State Univ 11, 32, 43, 53, 61, 68, 70,
75, 78, 103, 107
12, 15, 16, 36
Bill Neirman J Craig Venter Inst. 87, 97
Brett Tyler Virginia Tech 69, 109 13
Marc Orbach Univ Arizona 11, 70, 103
Jin-rong Xu Purdue Univ. 11, 70, 103 12
Yinong Yang Penn State Univ. 15
Guo-liang Wang Ohio State Univ 103 15
Heng Zhu Johns Hopkins 12
International
Fred Asiebbu SLU, Sweden 2
Yong-Hwan Lee Seoul Natl Univ. Korea 61
Gary Payne
CALS Institution Publication # Grant #
Ralph Dean CIFR 87, 97, 102,120 36-40
Marc Cubeta CIFR 129 36-40
Page | 19
Peter Ojiambo CIFR 31
Ignazio Carbone CIFR 36-40
James Holland Crop Science 34, 94, 95, 96,104 21, 25
Dahlia Nielsen Statistics 15, 36,102 19
NCSU
David Muddiman Chemistry 17, 22, 37
USA
Bill Neirman J Craig Venter Inst. 15, 77, 87, 89, 97,120,121
Nataiie Federova J Craig Venter Inst. 36, 97
Charles Woloshuk Purdue University 36, 91, 101 20, 24
Deepak Bhatnagar USDA/ARS/SRRC
15, 77, 87, 89, 97, 118,
120, 121 22
Jeffrey Cary USDA/ARS/SRRC 15, 87, 97 22
Jiujiang Yu USDA/ARS/SRRC
15, 36, 77, 89, 97, 120,
121 24
Thomas Cleveland USDA/ARS/SRRC
15, 77, 87, 89, 97, 120,
121
John Groopman Johns Hopkins 55
International
Massimo Reverberi
Università ―La Sapienza‖,
Rome, Italy submitted
Giancarlo Perrone ISPA-CNR, Bari, Italy In preparation
Margo Daub
CALS
Jean Ristaino Plant Pathology 7.3, 8
Ignazio Carbone CIFR 36
Marc Cubeta CIFR 36
Ralph Dean CIFR 36
Gary Payne CIFR 36
Paola Veronese CIFR 36
NCSU
Marcia Gumpertz Provost Office 9
Laura Severin English 9
Daniel Solomon College of PAMS 9
Mary Wyer Psychology 9
Page | 20
USA
Kuang-Ren Chung Univ. Florida 20,25
International
Alongkorn Amnuaykanjanasin Natl. Cntr Biotech. Gen.
Engineering, Thailand
5,46
Nafisa Ibrahim Fayoum Univ. Egypt 7.1
Maffia Luis Univ. Viscosa, Brazil
de Souza Andre Univ. Viscosa, Brazil
Marc Cubeta
NCSU
Ignazio Carbone CIFR 18,60 39-42
Margo Daub CIFR 38
Ralph Dean CIFR 5, 39-42
Peter Ojiambo CIFR 58 6
Tom Mitchell CIFR 38
Gary Payne CIFR 129 39-42
Paola Veronese CIFR 38
Jonathan Baros CALS 6
Larry Grand CALS 4
Rod Gurganus CALS 6
Kelly Ivors CALS 9, 126
David Marshall CALS 9
James Moyer CALS 60, 105
Elizabeth Parks CALS 60, 105
Barbara Shew CALS
David Shew CALS 60, 105
Becky Boston CALS
David Danehower CALS 10
George Kennedy CALS
USA
Mike Newnam Bayer Crop Sciences
Jim Clark Duke
Tom Mitchell Duke
Rytas Vilgalys Duke University 16, 41
Nataiie Federova JCVI
William Nierman JCVI 5
Ven Subbiah PhytoMyco Research Co. 9
Allison Talley Syngenta
Page | 21
Tim Brenneman University of Georgia 119
Phil Nolte University of Idaho
Stellos Tavantzis University of Maine 18, 124
Tim James University of Michigan 16
Robert Trigiano University of Tenensee 59
Gary Samuels
USDA Systematic
Mycology Lab 98
Carl Strausbaugh USDA-ARS Idaho 108
Warren Copes USDA-ARS Poplarville 24, 93
International
Peter Guest Australia 98
Stephen Neate Australia
Rosario Ferrucho Columbia 35
Rita Grosch Germany
Ewald Langer Germany
Gitta Langer Germany
Takeshi Toda Japan, Akita Univ. 9,24,93,108
Shigeo Naito Japan, Hokkaido 9
Kostas Aliferis McGill 3
Suha Jabaji McGill 3
Dolores Gonzalez Mexico 41
Paul Bayman Puerto Rico
Paulo Ceresini Sao Paulo State 16, 35
Alison Lees Scotland
Nils Hallenberg Sweden
Jan Stenlid Sweden
Teun Boukhout The Netherlands
James Woodhall UK 117
Martin Bidartindo UK, Kew
Ignazio Carbone
CALS
Ralph Dean CIFR 12, 28, 88 36-40
Marc Cubeta CIFR 18, 60 36-40
Margo Daub CIFR 36
Gary Payne CIFR 118 36-40
Paola Veronese CIFR 36
NCSU
Greg Gibson Genetics 72
Page | 22
Preema Arasu Veterinary Medicine 72
Christina Cowger Plant Pathology 85, 86
Mike Benson Plant Pathology 84
Jean Ristaino Plant Pathology 39 3
USA
Bruce Horn USDA-ARS, Georgia
1, 13, 14, 49, 50, 51, 52,
71, 90 2
Nik Grunwald USDA-ARS, Oregon 42, 66
Elizabeth Arnold Univ of Arizona 1
Francois Lutzoni Duke Univ 1
Georgiana May Univ of Minnesota 1
International
Eduardo Mizubuti Brazil 64
Paola Veronese
CALS
Ignazio Carbone CIFR 36
Marc Cubeta CIFR 36
Margo Daub CIFR 36
Ralph Dean CIFR 36
Gary Payne CIFR 36
George Allen Horticulture 35
Wendy Boss Plant Biology 35
John Dole Horticulture 35
William Fonteno Horticulture 35
Dominique Robertson Plant Biology 35
Bryon Sosinski Horticulture 35
Brian Whipker Horticulture 35
John Williamson Horticulture 35
NCSU
Steffen Heber Computer Science and BRC 33
USA
Burton Bluhm University of Arkansas 116
Robert Dietrich Syngenta 116
Scott Gold University of Georgia 62 34
Seogchan Kang PennState University 62 34
Page | 23
Steven Klosterman USDA-ARS, Salinas (CA) 62 34
Li-jun Ma Univ. of Massachusetts,
Amherst
62 34
Tesfaye Mengiste Purdue University 65, 116
John Salmeron Syngenta 116
Johannes Stratmann University of South
Carolina
48
Krishna Subbarao UC Davis 62 34
International
Dez Barbara University of Warwick,
UK
62
Kathy Dobinson Agricultre & Agri-Food,
Canada
62 34
Bart Thomma Wageningen University 62
Peter Ojiambo
CALS
Gary Payne CIFR 31
Marc Cubeta CIFR 58 6
Ignazio Carbone CIFR
William Cline CALS 6
Frank Louws CALS 27
NCSU
Mark Brooks NCSU 81 27
Ryan Boyles NCSU 81 27
Alan Lloyd NCSU 7
Sujit Ghosh NCSU
Christina Cowger NCSU 123 32
USA
Scott Isard Penn State 27
Mahomad Babadoost Univ. of IL 81 27
Steve Bost Univ. of KY 81 27
John Damicone Univ. of OK 81 27
Dan Egel Purdue Univ. 81 27
Katherine Everts Univ. of MD 81 27
Don Ferrin LSU 81 27
Amanda Gevens Univ. of WI 81 27
Mary Hausbeck MI State Univ. 81 27
Dan Ingram Univ. of TN 81 27
Page | 24
Tom Isakeit Texas A&M 81 27
Beth Gugino Penn State 81 27
Antony Keinath Clemson Univ. 81 27
Steve Koike UC Davis 81 27
David Langston Univ. of GA 81 27
Margaret McGrath Cornell Univ. 81 27
Sally Miller Ohio State Univ 81 27
Robert Mulrooney Univ. of Delaware 81 27
Ed Sikora Auburn Univ. 81 27
Robert Wick Univ. of MA 81 27
Steve Rideout VirginiaTech 81 27
Kenny Seebold Univ. of KY 81 27
Andy Wyenandt Rutgers Univ. 81 27
Shouan Zhang Univ. FL 81 27
Page | 25
CIFR Invited Presentations
CIFR faculty have given 117 invited research presentations over the past 5 years. Of these 53 were
invited international presentations as listed below.
Ralph Dean
Dr. Dean has given 43 invited presentations on his research over the past 5 years, of which 15 were
invited international talks. As highlighted below, many of these presentations were in Asia and Europe.
1. BGI International Plant Pathogenomics Conference, ―Next generation biology: examination
of the transciptome and proteome reveals novel insights into fungal pathogenicity of the rice
blast fungus Magnaporthe oryzae.‖ Shenzhen, China, January 24 -26, 2011.
2. Seoul National University, ―The next step, where do we go with the rice blast genome
project‖. Seoul, Korea, Jan 28th 2011.
3. Plant and Crop Sciences Seminar, ―Beyond the Genome: What Can Be Learned About Rice
Blast Infection From the Transcriptome and Proteome.‖ School of Biosciences, University of
Nottingham, United Kingdom, December 8 – 9, 2010.
4. John Innes Center Seminar, ―Next generation biology: insights into pathogenesis of the rice
blast fungus‖, Norwich, United Kingdom, May 18, 2010.
5. Plant and Microbial Sciences Seminar, ―Next generation biology: novel insights into fungal
pathogenicity.‖ Imperial College London, England, February 17, 2010.
6. 7th Hangzhou International Symposium on Plant Pathology and Biotechnology, Beyond the
genome sequence: the complex biology of Magnaporthe oryzae. Institute of Biotechnology,
Zhejiang University, Hangzhou, People‘s Republic of China. October 22‐25, 2009.
7. US‐China Relations Conference, Rice blast, a global disease: opportunities for US-China
partnerships. Renaissance Beijing Capital Hotel, Beijing, China. October, 21‐23, 2009.
8. 4th International Rice Blast Conference (IRBC), An ‗omics‘ interrogation of pathogenesis by
the rice blast fungus. Changsha, China, October 9‐14, 2007.
9. BSPP Presidential Meeting 2007—Attack and Defense in Plant Disease, An ‗Omics‘
perspective on fungal pathogenesis. University of Bath, United Kingdom. September 12‐14,
2007.
10. Department of Plant Pathology Seminar, Genome analysis of the rice blast fungus. Nanjing
Agricultural University. Nanjing, China. June 4, 2007.
11. 6th Hangzhou International Symposium on Plant Pathology and Biotechnology, An ‗omics‘
perspective on fungal pathogenicity. Zhejiang University. Hangzhou, China. May 31‐June 3,
2007.
12. Max Planck Institute for Plant Breeding Research Seminar, An ‗omics‘ approach to
understanding fungal pathogenesis. Cologne, Germany. May 30, 2007.
13. 3rd International Rauischholzhausen Conference, An ‗omics‘ perspective on fungal
pathogenicity. Rauischholzhausen, Germany. March 4‐6, 2007.
14. College of Life Science International Programs Delegation, Opportunities for research
collaboration in genomic sciences at North Carolina State University. Zhejiang University,
Hangzhou, P.R., China, November 8‐15, 2006.
15. IXth International Fungal Biology Conference & 16th New Phytologist Symposium,
Structural and functional analysis of fungal pathogenesis: the rice blast fungus genome
project. Nancy, France, September 17‐20, 2006.
Gary Payne
Dr. Payne has given 22 invited presentations on his research over the past 5 years, of which 13 were
invited international talks.
Page | 26
1. Genomics of Aspergillus flavus pathogenesis. International Society of Mycotoxicology.
Mendosa, Argentina. November 11-17, 2011.
2. Mycotoxins: chemistry, biology and risk evaluation. International Union of Mircrobiological
Societies. September 6-10, 2011, in Sapporo, Japan. (unable to attend).
3. Potential Effects Shifting Climatic Conditions on Infection and Mycotoxin Production by
Aspergillus flavus. American Phytopathological Society. Hawaii. August 6-9, 2011.
4. Advances in Genomics for Reducing Aflatoxin Contamination. World Mycotoxin Forum.
Noordwijkerhout, The Netherlands. November 8-10, 2010
5. Genomic analysis provides new insights into mycotoxin production by Aspergillus flavus. II
International Symposium on Algal and Fungal Toxins for Industry June 27 to July 1, 2010
Merida Yucatan
6. Genomic analysis of pathogenesis and mycotoxin production by Aspergillus flavus.
International Society of Mycotoxicology. Tulln, Austria. September 9-12, 2009.
7. Virulence factors differentially expressed in Aspergillus flavus during infection. Fungal
Genetics Conference. Asilomar Conference Grounds, Pacific Grove, CA. March 14-21, 2009.
8. Genomics, gene expression, and the control of aflatoxin contamination Torino, Italy
International Congress of Plant Protection August 24-29, 2008.
9. Genomics is providing a glimpse into the lifestyle of the opportunistic pathogen Aspergillus
flavus. Plant Research International B.V., Wageningen, The Netherlands. April 16, 2007.
10. Comparative genomics of Aspergillus flavus and A. oryzae: an early view. Aspergillus
Systematics in the Genomic Era –An International Workshop. Centraalbureau voor
Schimmelcultures, Utrecht, The Netherlands. April, 12 – 14, 2007.
11. Large inter-institutional project for whole genome sequencing of Aspergillus flavus.
International Conference on Advances in genomics, biodiversity and rapid systems for
detection of toxigenic fungi and mycotoxins. Bari, Italy. September 27-29, 2006.
12. Aspergillus flavus genome sequence and comparative analysis with Aspergillus oryzae.
European Congress on Fungal Genetics. Vienna, Austria. April 6-10, 2006.
13. Whole genome comparison of A. flavus and A. oryzae. Advances Against Aspergillosis.
Athens, Greece. February 22 – 25, 2006.
Margo Daub
Dr. Daub has given 2 invited presentations on her research over the past 5 years, of which 1 was an
invited international talk.
1. Zhejiang University, ―Research programs in the Department of Plant Biology at NC State
University‖, May 2010
Marc Cubeta
Dr. Cubeta has given 23 invited presentations on his research over the past 5 years, of which 14 were
invited international talks.
1. Bielefeld University, Center for Biotechnology, Bielefeld, Germany, March 2011. Spring
Colloquium Invited Speaker, Beyond genomic investigation of the soil fungus Rhizoctonia
solani.
2. Institute for Vegetable and Horticultural Research, Grossbeeren, Germany, March 2011.
Invited Speaker, The Rhizoctonia solani genome initiative.
3. 10th European Conference on Fungal Genetics, 2010. Unraveling the complex dikaryotic
genome of the soil fungus Rhizoctonia solani. Leiden, The Netherlands.
4. Swiss Federal Institute of Technology 2010. The Rhizoctonia solani genome sequencing
project, providing insight into beneficial and plant parasitic fungi, Zurich, Switzerland.
5. Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre 2010. The Rhizoctonia
solani genome sequencing project, clues for understanding the ecology and systematics of
beneficial and plant parasitic fungi, Utrecht, The Netherlands.
Page | 27
6. Seventh World Potato Congress Soilborne Potato Disease Workshop 2009. The role of
phenyl acetic acid metabolic complex in the parasitic and saprobic behavior of Rhizoctonia
solani AG-3, Christchurch, New Zealand.
7. Seventh World Potato Congress. Keynote address in Crop management, Rhizoctonia disease
of potato; genomics, novel biocontrol and practical disease management, Christchurch, New
Zealand, followed by NZ Radio interview with Carla Gray.
8. Fourth International Rhizoctonia Symposium, 2008. Whole genome sequencing of the soil
fungus Rhizoctonia solani AG-3, Berlin, Germany.
9. Fourth International Rhizoctonia Symposium, 2008. Carbon metabolism and plant growth
regulation: the influence of quinic acid on phenylacetic acid production and pathogenic
activity of Rhizoctonia solani AG-3, Berlin, Germany.
10. Fourth International Rhizoctonia Symposium, 2008. Evolutionary history and population
genetics of the M2 double-stranded RNA of Rhizoctonia solani anastomosis group 3, Berlin,
Germany.
11. Conference on the Population and Evolutionary Biology of Fungal Symbionts Meeting, 2007.
The role of dsRNA in the parasitic and saprophytic behavior of the soil fungus Rhizoctonia
solani, Ascona, Switzerland.
12. Conference on the Population and Evolutionary Biology of Fungal Symbionts Meeting, 2007.
The influence of quinic acid on phenylacetic acid production and pathogenic activity of
Rhizoctonia solani AG-3, Ascona, Switzerland.
13. McGill University, 2007, Department of Biology, The evolutionary dynamics of fungal
viruses and their potential for managing Rhizoctonia diseases, Montreal, Canada. Also
provide a lecture on fungal genetics in the Fungal Biology class
14. Centro Internacional de la Papa, 2006. The role of dsRNA in the parasitic and saprobic
behavior of the soil fungus Rhizoctonia solani, Lima, Peru.
Ignazio Carbone
Dr. Carbone has given 12 invited presentations on his research over the past 5 years, of which 6 were
invited international talks.
1. The evolution of mycotoxin diversity in natural and experimental populations of Aspergillus
flavus and Aspergillus parasiticus. Forestry and Agricultural Biotechnology Institute (FABI),
South Africa; Nov 5-14, 2010.
2. The population genetics of aflatoxin diversity in Aspergillus flavus and Aspergillus
parasiticus. French CNRS Conferences Jacques Monod on ‗New and Emerging Fungal
Diseases of Animals and Plants: evolutionary aspects in the context of global changes‘.
Roscoff in Brittany. April 17 – 21, 2010.
3. The population dynamics of agriculturally important Aspergillus species. Symposium on
Biodiversity. Centro de Investigación Científica - CICY, Mérida, Yucatán, Mexico, Oct 19-
23, 2009.
4. Bifurcation, reticulation and trans-species evolution in the aflatoxin gene cluster of
Aspergillus. Departamento de Fitopatologia, Universidade Federal de Vicosa, Vicosa, MG,
Brazil, Feb 24-29, 2008.
5. The evolution of aflatoxin biosynthesis. International Meeting on Fungal Symbiosis focusing
on the population and evolutionary biology of fungal symbionts. Ascona, Switzerland, Apr
29- May 4, 2007.
6. The evolution of aflatoxigenicity. The World Mycotoxin Forum. The Fourth Conference.
An international networking conference for the food and feed industry, Cincinnati, Ohio, Nov
6-8, 2006.
Page | 28
Paola Veronese
Dr. Veronese has given 11 invited presentations on her research over the past 5 years, of which 4 were
invited international talks.
1. X International Verticillium Symposium, ―How phytopathogenic Verticillium spp. manipulate
host-denfense secondary metabolism‖, Corfu Island, Greece, November 16-20, 2009 (keynote
speaker).
2. Departamento de Fitopatologia, Universidade Federal de Viçosa (UFV) ―Arabidopsis-
Verticillium Interaction As a Model Disease System‖, Viçosa, MG, Brazil, September 4,
2009.
3. International Meeting on ―Signal exchange between roots and microorganisms” ―Molecular
Genetics of plant Responses to Verticillium spp.”, organized by Dr. Christiane Gatz,
Albrecht-von-Haller-Institut, Georg-August-Universitata, Gottigen (Germany), March 7-9,
2007 (keynote speaker).
4. Southern Crop Protection and Food Research Centre (SCPFRC) ―Uncovering New
Mechanisms of Plant Disease Resistance‖, Agriculture & Agri-food Canada, London,
Ontario, Canada, August 23, 2006.
Peter Ojiambo
In the short time Dr. Ojiambo has been with CIFR he has given 4 invited presentations on his research
over the past 5 years, none internationally.
Page | 29
CIFR Publications
Peer Reviewed Journal Articles
1. Abbas, H. K., M. A. Weaver, B. W. Horn, I. Carbone, J. T. Monacell, and W. T. Shier.
2011. Selection of Aspergillus flavus isolates for biological control of aflatoxins in corn.
Toxin Reviews 30: 59-70.
2. Adomas, A., Heller, G., Li G., Olson, A., Chu, T.-M., Osborne, J., Craig, D., Van Zyl, L.,
Wolfinger, R., Sederoff, R., Dean, R.A., Stenlid, J., Finlay, R., Asiegbu, F. 2007.
Transcript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to
pathogen (Heterobasidion annosumn) invasion. Tree Physiology 27:1441-1458.
3. Aliferis, K.A., Jabaji, S., and Cubeta, M.A. 2011. Chemotaxonomy of fungi in the
Rhizoctonia solani species complex using GC/MS metabolic profiling. Metabolomics (In
Press).
4. Altunay, M., Byrd, G.T., Brown, D., Dean, R.A. 2008. An interaction-based access
control model (IBAC) for collaborative services. Workshop on Collaboration and
Security (COLSEC). Femilab Computing Division.
5. Amnuaykanjanasin, A., and Daub, M. E. 2009. The ABC transporter ATR1 is necessary
for efflux of the toxin cercosporin in the fungus Cercospora nicotianae. Fung. Genet.
Biol. 46:146-158.
6. Andrews, G.L., Dean, R.A., Hawkridge, A.M., and Muddiman, D.C. 2011. Improving
Proteome Coverage on a LTQ-Orbitrap Using Design of Experiments. J Am Soc Mass
Spectrom 22(4):773-83. Epub 2011 Feb 15.
7. Arauz, L.F., Neufeld, K.N., Lloyd, A.L., and Ojiambo, P.S. 2010. Quantitative models for
germination and infection of Pseudoperonospora cubensis in response to temperature and
duration of leaf wetness. Phytopathology 100:959-967.
8. Aylor, D. L., Price, E.W. and I. Carbone. 2006. SNAP: Combine and Map modules for
multilocus population genetic analysis. Bioinformatics 22: 1399-1401.
9. Bartz, F.E., Cubeta, M.A., Toda, T., Naito, S., and Ivors, K. 2010. An in planta method
for assessing the role of basidiospores in Rhizoctonia foliar disease of tomato. Plant
Disease 94:515-520.
10. Bartz, F.E., Danehower, D.A., Glassbrook, N., and Cubeta, M.A. 2011. Elucidating the
role of phenylacetic acid and hydroxy- and methoxy- phenylacetic acid derivatives in the
pathogenic activity of Rhizoctonia solani AG-3. Mycologia 103: (In Press).
11. Betts, M., Tucker, S., Galadima, N., Meng, Y., Patel, G., Li, L., Donofrio, N., Floyd, A.,
Nolin, S., Brown, D., Mandel, M., Mitchell, T., Xu, J-R., Dean, R.A., Farman, M.,
Orbach, M. 2007. Development of a high throughput transformation system for
insectional mutagenesis in Magnaporthe oryzae. Fungal Genetics and Biology 44:1035-
1049.
12. Brown, D.E., Powell, A.J., Carbone, I., Dean, R.A. 2008. GT-Miner: a graph-theoretic
data miner, viewer, and model processor. Bioinformation 3:235-237.
13. Carbone, I., Jakobek, J. L., Ramirez-Prado, J. H. and B. W. Horn. 2007. Recombination,
balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus
parasiticus. Molecular Ecology 16: 4401-4417. (recommended by Faculty of 1000
Biology).
Page | 30
14. Carbone, I., Ramirez-Prado, J. H., Jakobek, J. L., and B. W. Horn. 2007. Gene
duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster. BMC
Evolutionary Biology 7:111.
15. Cary, J. W., OBrian, G. R., Nielsen, D.M., Nierman, W., Harris-Coward, P., Yu, J.,
Bhatnagar, D., Cleveland, T. E., Payne, G. A., Calvo, A. M. 2007. Elucidation of veA-
dependent genes associated with aflatoxin and sclerotial production in Aspergillus flavus
by functional genomics. Applied Microbiology and Biotechnology 76: 1107-1118.
16. Ceresini, P.C., Shew, H.D. Vilgalys, R., T.Y. James, and Cubeta, M.A. 2007. Molecular
diversity and phylogeography of Rhizoctonia solani AG-3 based on sequence analysis of
two nuclear loci. BMC Evolutionary Biology 7:163-184. doi:10.1186/1471-2148-7-163.
17. Chang KY, Georgianna DR, Heber S, Payne, G. A., and Muddiman, DC. 2010. Detection
of alternative splice variants at the proteome level in Aspergillus flavus. Journal of
proteome research. 9: 1209-1217.
18. Charlton, N. D., Carbone, I., Tavantzis, S. M., and M. A. Cubeta. 2008. Phylogenetic
relatedness of the M2 double-stranded RNA in Rhizoctonia fungi. Mycologia 100: 555-
564.
19. Charlton, N.D. and Cubeta, M.A. 2007. Transmission of the M2 double-stranded RNA
virus in Rhizoctonia solani anastomosis group 3 (AG-3). Mycologia 99:859-867.
20. Chen, H., Lee, M. H., Daub, M. E., and Chung, K. R. 2007. Molecular analysis of the
cercosporin biosynthetic gene cluster in Cercospora nicotianae. Molec. Microbiol.
64:755-770.
21. Clark, C. M. and I. Carbone. 2008. Chloroplast DNA phylogeography in long lived Huon
Pine (Lagarostrobos franklinii), a Tasmanian rainforest conifer. Canadian Journal of
Forest Research 38: 1576-1589.
22. Collier, T. S., Hawkridge, A. M., Georgianna, D. R., Payne, G. A., and Muddiman, D. C.
2008. Top-down identification and quantification of stable isotope labeled proteins from
Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled
to a LTQ-FTICR mass spectrometer. Analytical Chemistry 80:4994-5001.
23. Collier, T.S., Sarkar, P., Franck, W.L., Rao, B.M., Dean, R.A., Muddiman, D.C. 2010.
Direct Comparison of Stable Isotope Labeling by Amino Acids in Cell Culture and
Spectral Counting for Quantitative Proteomics. Analytical Chemistry.
24. Copes, W., Rodriguez-Carres, M., Toda, T., and Cubeta, M.A. 2011. Seasonal prevalence
of species of binucleate Rhizoctonia fungi in growing medium, leaf litter, and stems of
container grown azalea. Plant Dis. 95:705-711.
25. Daub, M. E., and Chung, K. R. 2009. Photoactivated perylenequinone toxins in plant
pathogenesis. Chapt. 11 in: The Mycota V, Plant Relationships, 2nd Edition. H. Deising,
Ed. Springer-Verlag, Berlin Heidelberg
26. Daub, M. E., Herrero, S., and Taylor, T. V. 2010. Strategies for the development of
resistance to cercosporin, a toxin produced by Cercospora species. pp. 157 -172 In:
Cercospora Leaf Spot of Sugar Beet and Related Species. R. T. Lartey, J. J. Weiland, L.
Panella, P. W. Crous, and C. E. Windels, eds. APS Press, St. Paul, MN.
27. Dean, R.A. 2007. Fungal gene clusters. Nature Biotechnology 25:67.
Page | 31
28. Deng, J., Carbone, I., Dean, R.A. 2007. The evolutionary history of Cytochrome P450
genes in four filamentous ascomycetes. BMC Evolutionary Biology 7:30.
29. Deng, J., Dean, R.A. 2008. Characterization of adenylate cyclase interacting protein ACI1
in the rice blast fungus, Magnaporthe oryzae. The Open Mycology Journal 2:74-81.
30. Denslow, S. A., Rueschhoff, E. E., and Daub, M. E. 2007. Regulation of the Arabidopsis
thaliana vitamin B6 biosynthesis genes by abiotic stress. Plant Physiol. Biochem. 45:152-
161.
31. Diedhiou, P. M., Bandyopadhyay, R., Atehnkeng, J. and Ojiambo, P.S. 2011. Aspergillus
colonization and aflatoxin contamination of maize and sesame kernels in two agro-
ecological zones in Senegal. Journal of Phytopathology 159:268-275.
32. Donofrio, N.M., Oh, Y., Lundy, R., Pan, H., Brown, D.E., Jeong, J.S., Coughlan, S.,
Mitchell, T.K., Dean, R.A. (2006). Global gene expression during nitrogen starvation in
the rice blast fungus, Magnaporthe grisea. Fungal Genetics and Biology 43:605-617.
33. Du, W., OBrian, G.R., and Payne, G. A. 2007. Function and regulation of aflJ in the
accumulation of aflatoxin early pathway intermediate in Aspergillus flavus. Food
Additives and Contaminants 24: 1043-1050 2007.
34. Eller, M.S., Payne, G.A., and Holland, J.B. 2010. Selection for reduced fusarium ear rot
and fumonisin content in advanced backcross maize lines and their topcross hybrids.
Crop Science. Crop Sci. 50:2249–2260.
35. Ferrucho, R.L., Zala, M., Zhang, Z., Cubeta, M.A., Garcia-Dominguez, C., and Ceresini,
P.C. 2009. Highly polymorphic in silico-derived microsatellite loci in the potato-infecting
fungal pathogen Rhizoctonia solani anastomosis group 3 from the Colombian Andes.
Molecular Ecology Resources 9:1013-1016.
36. Georgianna, D.G., Fedorova, N.D., Burroughs, J. L, Dolezal, A.L, Bok, J., Horowitz-
Brown, S., Woloshuk, C. P., Yu, J. Keller, N.P., and Payne, G.A. 2009. Beyond aflatoxin:
four distinct expression patterns and functional roles associated with Aspergillus flavus
secondary metabolism gene clusters. Molecular Plant Pathology 11:213-226.
37. Georgianna, D.R., Hawkridge, A.M. Muddiman, D.C., and Payne, G.A. 2008.
Temperature dependent regulation of Proteins in Aspergillus flavus: Whole Organism
Stable Isotope Labeling by Amino Acids. Journal of Proteome Research 7:2973-2979.
38. Gokce, E., Andrews, G.L., Dean, R.A., and Muddiman, D.C. 2011. Increasing Proteome
Coverage with Offline RP HPLC Coupled to Online RP NanoLC-MS. Journal of
Chromatography B, 879(9-10):610-4. (Epub ahead of print)
39. Gómez-Alpizar, L., I. Carbone, and J. B. Ristaino. 2007. An Andean origin of
Phytophthora infestans inferred from nuclear and mitochondrial gene genealogies. Proc
Nat. Acad. Sci. 104: 3306-3311.
40. Gonzalez, E., Danehower, D., and Daub, M. E. 2007. Vitamer levels, stress response,
enzyme activity, and gene regulation of Arabidopsis lines mutant in the
pyridoxine/pyridoxamine 5‘-phosphate oxidase (PDX3) and the pyridoxal kinase (SOS4)
genes involved in the vitamin B6 salvage pathway. Plant Physiol. 145:985-996.
41. Gonzalez-Hernandez, D., Cubeta, M.A. and Vilgalys, R. 2006. Phylogenetic utility of
indels within sequences of ribosomal and beta-tubulin genes in fungi belonging to the
Rhizoctonia species complex. Mol. Phylogen. Evol. 40:459-470.
Page | 32
42. Goss, E. M., Carbone, I., and N. J. Grünwald. 2009. Ancient isolation and independent
evolution of the three clonal lineages of the exotic sudden oak death pathogen
Phytophthora ramorum. Molecular Ecology 18: 1161-1174.
43. Gowda, M., Nunes, C.C., Sailsbery, J., Xue, M., Chen, F., Nelson, C.A., Brown, D.E., Oh,
Y., Meng, S., Mitchell, T., Hagedorn, C.H., Dean, R.A. 2010. Genome-wide
characterization of methylguanosine-capped and polyadenylated small RNAs in the rice
blast fungus Magnaporthe oryzae. Nucleic Acids Research 38(21):7558-69.
44. He, Zhu-Mei, Price, M.S., OBrian, G.R., Georgianna, D.R. and Payne, G.A. 2007.
Improved protocols for functional analysis in the pathogenic fungus Aspergillus flavus.
BMC Microbiology 7:104.
45. Herrero, S. and Daub, M. E. 2007. Genetic manipulation of vitamin B6 biosynthesis in
tobacco and fungi uncovers limitations to up-regulation of the pathway. Plant Sci.
172:609-620.
46. Herrero, S., Amnuaykanjanasin, A., and Daub, M. E. 2007. Identification of genes
differentially expressed in the phytopathogenic fungus Cercospora nicotianae between
cercosporin toxin-resistant and -susceptible strains. FEMS Microbiol. Lett. 275:326-337.
47. Herrero, S., Gonzalez, E., Gillikin, J. W., Velez, H., and Daub, M. E. 2011. Identification
and characterization of a pyridoxal reductase involved in the vitamin B6 salvage pathway
in Arabidopsis. Plant Mol. Biol. 76:157 - 169.
48. Hind, S. R., Pulliam, S. E., Veronese, P., Shantharaj, D., Nazir, A., Jacobs, N. S. and
Stratmann, J. W. 2011. The COP9 signalosome controls jasmonic acid synthesis and
plant responses to herbivory and pathogens. The Plant Journal, 65(3):480-91.
49. Horn, B. W., Moore, G. G. and I. Carbone. 2009. Sexual reproduction in Aspergillus
flavus. Mycologia 101: 423-429.
50. Horn, B. W., Moore, G. G. and I. Carbone. 2011. Sexual reproduction in aflatoxin-
producing Aspergillus nomius. Mycologia 103: 174–183. DOI: 10.3852/10-115.
51. Horn, B. W., Ramirez-Prado, J. H. and I. Carbone. 2009. Sexual reproduction and
recombination in the aflatoxin-producing fungus Aspergillus parasiticus. Fungal
Genetics and Biology 46: 169-175. (cover page) (recommended by Faculty of 1000
Biology)
52. Horn, B. W., Ramirez-Prado, J. H. and I. Carbone. 2009. The sexual state of Aspergillus
parasiticus. Mycologia 101: 275-280.
53. Jeong, J-S., Mitchell, T., Dean, R.A. 2007. The Magnaporthe grisea snodport1 homolog,
MSP1, is required for virulence. FEMS Microbiology Letters 273:157-165.
54. Johansson, A. S., Whitaker, T. B., Hagler, W. M., Bowman, D. T., Slate, A. B., Payne, G.
2006. Predicting aflatoxin and fumonisin in shelled corn lots using poor-quality grade
components. Journal of AOAC international, 89(2), 433-440.
55. Johnson, D. N., Egner, P. A., Obrian, G., Glassbrook, N., Roebuck, B. D., Sutter, T. R.,
Payne, G. A., Kensler, T. W., and Groopman, J. D. 2008. Quantification of urinary
aflatoxin B-1 dialdehyde metabolites formed by aflatoxin aldehyde reductase using
isotope dilution tandem mass spectrometry. Chemical Research in Toxicology 21:752-
760.
Page | 33
56. Joobeur, T., Gusmini, G., Zhang, X., Levi, A., Xu, Y., Wehner, T.C., Oliver, M., Dean,
R.A. 2006. Construction of a watermelon BAC library and identification of SSRs
anchored to melon or Arabidopsis genomes. Theoretical and Applied Genetics 112:1543-
1457.
57. Kanetis, L., Holmes, G.J., and Ojiambo, P.S. 2010. Survival of Pseudoperonospora
cubensis sporangia exposed to solar radiation. Plant Pathology 59: 313-323.
58. Kanetis, L., Wang, X., Wadl, P.A., Neufeld, K., Holmes, G.A., Ojiambo, P.S, Cubeta,
M.A., and Trigiano, R.T. 2009. Development of simple sequence repeat markers for the
cucurbit downy mildew pathogen, Pseudoperonospora cubensis. Molecular Ecology
Resources 9:1460-1559
59. Kanetis, L., Wang, X., Wadl, P.A., Neufeld, K., Holmes, G.A., Ojiambo, P.S, Cubeta,
M.A., and Trigiano, R.T. 2009. Microsatellite loci in the downy mildew pathogen,
Pseudoperonospora cubensis. Molecular Ecology Resources 9:1460-1466.
60. Kaye, A.C., Moyer, J.W., Parks, E.J., Carbone, I., and Cubeta, M.A. 2011. Population
genetic analysis of Tomato spotted wilt virus on peanut in North Carolina and Virginia.
Phytopathology 101:147-153.
61. Kim, S., Hu, J., Oh, Y., Park, J., Choi, J., Lee, Y.H., Dean, R.A., Mitchell, T.K. 2010.
Combining ChIP-chip and expression profiling to model the MoCRZ1 mediated circuit
for Ca/calcineurin signaling in the rice blast fungus. PLoS Pathogens 6(5):e1000909.
62. Klosterman, S.J., Subbarao, K.V., Kang, S., Veronese, P., Gold, S.E., Thomma, B.P.,
Chen, Z., Henrissat, B., Lee, Y., Park, J., Garcia-Pedrajas, M.D., Barbara, D., Anchieta,
A., de Jonge, R., Santhanam, P., Maruthachalam, K., Atallah, Z. K., Amyotte, S., Paz, Z.,
Inderbitzen, P., Heiman, D., Young, S., Zeng, Q., Engels, R., Koehrsen, M., Galagan, J.,
Birren, B., Cuomo, C., Dobinson, K.F., Ma, L. Verticillium comparative genomics yields
insights into niche adaptation by plant vascular pathogens (submitted to PLoS Pathogens;
under revision)
63. Litvintseva, A. P., Carbone, I., Rossouw, J., Thakur, R., Govender, N. P., and T. G.
Mitchell. 2011. Evidence that the human pathogenic fungus Cryptococcus neoformans
var. grubii may have evolved in Africa. PLoS One 6(5): e19688.
64. Lourenço Jr., V., Moya, A., González-Candelas, F., Carbone, I., Maffia, L. A. and E. S.
G. Mizubuti. 2009. Molecular diversity and evolutionary processes of Alternaria solani
in Brazil inferred using genealogical and coalescent approaches. Phytopathology 99: 765-
774.
65. Luo, H., Laluk, K., Lai, Z., Veronese, P., Song, F., and Mengiste, T. 2010. The
Arabidopsis Botrytis Susceptible1 interactor defines a subclass of RING E3 ligases that
regulate pathogen and stress responses. Plant Physiology 154(4):1766-82. Epub 2010 Oct
4.
66. Malvárez, G, Carbone, I., Grünwald N. J., Subbarao, K. V., Schafer, M. and L. M. Kohn.
2007. New populations of Sclerotinia sclerotiorum from lettuce in California and peas and
lentils in Washington. Phytopathology 97: 512-525.
67. Mathioni, S.M., Belo, A., Rizzo, C.J., Dean, R.A., Donofrio, N.M. 2011. Transcriptome
profiling of the rice blast fungus during invasive plant infection and in vitro stresses. BMC
Genomics. 19;12(1):49. [Epub ahead of print]
Page | 34
68. Meng, S., Brown, D.E., Ebbole, D.J., Torto-Alalibo, T., Oh, Y. Y., Deng, J., Mitchell T.
K., Dean, R.A. 2009. Gene ontology annotation of the rice blast fungus, Magnaporthe
oryzae. BMC Microbial 9(Suppl 1):S8.
69. Meng, S., Torto-Alalibo, T., Chibucos, M., Tyler, B., Dean, R.A. 2009. Common
processes in pathogenesis by fungal and oomycete plant pathogens described with Gene
Ontology terms. BMC Microbiology 9(Suppl 1):S7.
70. Meng, Y., Patel, G., Crawford, M., Donofrio, N., Brown, D., Mitchell, T., Xu-J-R.,
Orbach, M., Thon, M., Dean, R.A., Farman, M. 2007. A systematic analysis of T-DNA
insertion events in Magnaporthe oryzae. Fungal Genetics and Biology 44:1050-1064.
71. Moore, G. G., Singh, R., Horn, B. W., and I. Carbone. 2009. Recombination and lineage-
specific gene loss in the aflatoxin gene cluster of Aspergillus flavus. Molecular Ecology
18: 4870-4887.
72. Moser, J. M., Carbone, I., Arasu, P. and G. Gibson. 2007. Impact of population structure
on genetic diversity of a potential vaccine target in the canine hookworm (Ancyclostoma
caninum). Journal of Parasitology 93: 796-805.
73. Neufeld, K. N., and Ojiambo, P.S. 2012. Interactive effects of temperature and leaf
wetness duration on sporangia germination and infection of cucurbit host types by
Pseudoperonospora cubensis. Plant Disease 96: (in press).
74. Nicholson, M.J., Koulman, A., Monahan, B. J., Pritchard, B.L., Payne, G.A. and Scott,
Barry. 2009. Identification of two aflatrem biosynthesis gene loci in Aspergillus flavus
and A. oryzae and metabolic engineering of Penicillium paxilli to elucidate their function.
Applied and Environmental Microbiology.75:7469-7481.
75. Nunes, C. C., Gowda, M., Sailsbery, J., Xue, M., Chen, F., Brown, D. E., Oh, Y. Y.,
Mitchell, T. K., Dean, R. A. 2011. Diverse and tissue-enriched small RNAs in the plant
pathogenic fungus, Magnaporthe oryzae. BMC Genomics, 12:288.
76. Nyankanga, R.O., Olanya, O.M., Ojiambo, P.S., Wien, H.C., Honeycutt, C.W., and Kirk.
W.W. 2011. Validation of tuber blight (Phytophthora infestans) prediction model. Crop
Protection 30: 547-553.
77. OBrian, G.R., Georgianna, D., Wilkinson, J., Yu, J., Abbas, H., Bhatnagar, D., Cleveland,
T. E., Nierman, W., and Payne, G. A. 2007. The effect of elevated temperature on gene
transcription and aflatoxin biosynthesis. Mycologia 99: 232-239.
78. Oh, Y., Donofrio, N., Pan, H., Coughlan, S., Brown, D.E., Meng, S., Mitchell, T., Dean,
R.A. 2008. Transcriptome analysis reveals new insight into appressorium formation and
function in the rice blast fungus Magnaporthe oryzae. Genome Biology 9:R85.
79. Ojiambo P.S., and Scherm, H. 2010. Efficiency of adaptive cluster sampling in estimating
plant disease incidence. Phytopathology 100: 663-670.
80. Ojiambo, P.S. and Holmes, G.J. 2011. Spatio-temporal spread of cucurbit downy mildew
in the eastern United States. Phytopathology 101:451-461.
Page | 35
81. Ojiambo, P.S., Holmes, G.J., Britton, W., Keever, T., Adams, M.L., Babadoost, M., Bost,
S.C., Boyles, R., Brooks, M., Damicone, J., Draper, M.A., Egel, D.S., Everts, K.L.,
Ferrin, D.M., Gevens, A.J., Gugino, B.K., Hausbeck, M.K., Ingram, D.M., Isakeit, T.,
Keinath, A.P., Koike, S.T., Langston, D., McGrath, M.T., Miller, S.A., Mulrooney, R.,
Rideout, S., Roddy, E., Seebold, K.W., Sikora, E.J., Thornton, A., Wick, R.L., Wyenandt,
C.A., and Zhang, S. 2011. Cucurbit downy mildew ipmPIPE: a next generation web-based
interactive tool for disease management and extension outreach. Online. Plant Health
Progress.
82. Ojiambo, P.S., Paul, P.A., and Holmes, G.J. 2010. A quantitative review of fungicide
efficacy for managing downy mildew in cucurbits. Phytopathology 100: 1066-1076.
83. Olanya, O.M., Ojiambo, P.S., Nyankanga, R.O., Honeycutt, C.W., and Kirk, W.W. 2009.
Recent developments in managing tuber blight of potato (Solanum tuberosum) caused by
Phytophthora infestans. Canadian Journal of Plant Pathology 31: 280-289.
84. Olson, H., I. Carbone, and M. Benson. 2011. Phylogenetic history of Phytophthora
cryptogea and Phytophthora drechsleri isolates from floriculture crops in North Carolina
greenhouses. Phytopathology In Press.
85. Parks, R., Carbone, I. Murphy, J. P., Marshall, D. S. and C. Cowger. 2008. Virulence
structure of the Eastern U.S. wheat powdery mildew population. Plant Disease 92: 1074-
1082.
86. Parks, R., Carbone, I., Murphy, P and C. Cowger. 2009. Population genetic analysis of an
eastern U.S. wheat powdery mildew population reveals geographic subdivision and recent
common ancestry with U.K. and Israeli populations. Phytopathology 99: 840-849.
87. Payne, G.A., Nierman, W.C., Wortman, J.R., Pritchard, B.L., Brown, D. Dean, R.A.,
Bhatnagar, D., Cleveland, T.E., Machida, M. and Yu, J.J. 2006. Whole genome
comparison of Aspergillus flavus and A. oryzae. Medical Mycology. 44:S9-S11.
88. Powell, A.J., Conant, G.C., Brown, D.E., Carbone, I., Dean, R.A. 2008. Altered patterns
of gene duplication and differential gene gain and loss in fungal pathogens. BMC Central
Genomics 9: Article Number 147.
89. Price, M. S., J. Yu, W. C. Nierman, H. S. Kim, B. Pritchard, C. A. Jacobus, D. Bhatnagar,
T. E. Cleveland, and G. A. Payne. 2006. The aflatoxin pathway regulator AflR induces
gene transcription inside and outside of the aflatoxin biosynthetic cluster. FEMS
Microbiology Letters 255:275-9.
90. Ramirez-Prado, J. H., Moore, G. G., Horn, B. W. and I. Carbone. 2008. Characterization
and population analysis of the mating-type genes in Aspergillus flavus and Aspergillus
parasiticus. Fungal Genetics and Biology 45: 1292-1299.
91. Reese, B. N. Payne, G. A., Nielsen, D. M., and Woloshuk, C. P. 2011. Gene Expression
profile and response to maize kernels by Aspergillus flavus. Phytopathology 101:797-804.
92. Rehmeyer, C., Li, W., Kusaba, M., Kim Y., Brown, D., Staben, C., Dean, R.A., Farman,
M. 2006. Organization of chromosome ends in the rice blast fungus, Magnaporthe
oryzae. Nucleic Acids Research 34:4685-4701.
93. Rinehart, T., Copes, W., Toda, T. and Cubeta, M.A. 2007. Genetic characterization of
binucleate Rhizoctonia species causing web blight on azalea in Mississippi and Alabama.
Plant Dis. 91:616-623.
Page | 36
94. Robertson, L. A., Jines, M.P., Balint-Kurti, P. J., Kleinschmidt, C. E., White, D. G.,
Payne, G. A., Maragos, C. M., Molnár, T. L. and Holland. J. B. 2006. QTL mapping for
Fusarium ear rot and fumonisin contamination resistance in two populations of maize
(Zea mays). Crop Science 46:1734-1743.
95. Robertson-Hoyt, L.A., Betran, J., Payne, G.A., White, D. G., Isakeit, T., Maragos, C. M.,
Molnar, T.L., and Holland, J. B. 2007. Relationships among resistances to Fusarium and
Aspergillus ear rots and contamination by fumonisin and aflatoxin in maize.
Phytopathology 97:311-17.
96. Robertson-Hoyt, L.A., Kleinschmidt, C.E., White, D.G., Payne, G.A. Maragos, C.M., and
Holland, J. B. 2007. Relationships of resistance to fusarium ear rot and fumonisin
contamination with agronomic performance of maize Crop Sci. 47:1770-1778
97. Rokas, A., Payne, G., Fedorova, N., Baker, S., Machida, M., Yu, J., Georgianna, D.,
Dean, R.A., Bhatnager, D., Cleveland, T., Wortman, J., Joardar, V., Amedeo, P., Denning,
D., Nierman, W. 2007. What can comparative genomics tell us about species concepts in
the genus Aspergillus? Studies in Mycology 59:11-17.
98. Samuels, G., Ismaiel, A., McMahon, P., Guest, D., Rosmana, A., Junaid, M., Rodriguez-
Carres, M., and Cubeta, M.A. 2011. Vascular streak dieback of cacao in Southeast Asia
and Melanesia: in planta detection of the pathogen and a new taxonomy. Fungal Biology.
(In Press).
99. Shao, M., Wang, J., Dean, R.A., Lin, Y., Gao, X., Hu, S. 2007. Expression of a harpin-
encoding gene in rice confers durable nonspecific resistance to Magnaporthe grisea.
Plant Biotechnology Journal 6:73-81.
100. Shi, J., Sharma-Shivappa, R., Chinn, M., Dean, R.A., Shivappa, R. 2007. Challenges in
quantification of ligninolytic enzymes from Phanerochaete Chrysosporium cultivation for
pretreatment of cotton stalks. American Society of Agricultural and Biological Engineers
50:2347-2354.
101. Smith, C. A., Woloshuk, C. P., Robertson, D. and Payne, G. A. 2007. Silencing of the
Aflatoxin Gene Cluster in a Diploid Strain of Aspergillus flavus is Suppressed by Ectopic
aflR Expression. Genetics 179:1-10.
102. Smith, C.A, Robertson, D. Pritchard, B., Nielsen, D. M., Brown, D. Dean, R.A. and
Payne, G.A. 2008. The effect of temperature on Natural Antisense Transcript (NAT)
expression in Aspergillus flavus. Current Genetics 54:241-269.
103. Soderlund, C., Pampanwar, V., Haller, K., Ebbole, D., Farman, M., Mitchell, T., Orbach,
M., Wang, G-L., Wing, R., Xu, J-R, Dean, R.A. (2006). MGOS: a resource for studying
Magnaporthe grisea and Oryza sativa interactions. Molecular Plant-Microbe Interaction:
19: 1055-1061.
104. Starr, M.R., Robertson-Hoyt, L.A., Payne, G.A., and Holland, J. B. 2006. Improving
resistance to fumonisin contamination in maize. Illinois Breeding School. p. 83-92.
105. Sullivan, M. J., Parks, E. J., Cubeta, M. A., Gallup, C. A., Moyer, J.W., and Shew, H.D.
2010. Assessment of genetic diversity from a field population of Phytophthora nicotianae
with a changing race structure. Plant Disease 94:455-460. (cited as Editor‘s pick, April
2010).
106. Taylor, T. V., Mitchell, T. K., and Daub, M. E. 2006. An oxidoreductase is involved in
cercosporin degradation by the bacterium Xanthomonas campestris pv. zinniae. Appl.
Environ. Microbiol. 72:6070-6078.
Page | 37
107. Thon, M., Pan, H., Diener, S., Papalas, J., Taro, A., Mitchell, T., Dean, R.A. (2006). The
role of transposable element clusters in genome evolution and loss of synteny in the rice
blast fungus Magnaporthe oryzae. Genome Biology 7:R16.
108. Toda, T., Strausbaugh, C., Rodriguez-Carres, M., and Cubeta, M.A. 2011.
Characterization of a basidiomycete fungus from sugarbeet. Mycologia 103:(In Press).
109. Torto-Alalibo, T., Collmer, C.W., Gwinn-Giglio, M., Lindeberg, M., Meng, S., Chibucos,
M.C., Tseng, T.T., Lomax, J., Biehl, B., Ireland, A., Bird, D., Dean, R.A., Glasner, J.D.,
Perna, N., Setubal, J.C. Collmer, A., Tyler, B.M.. 2010. Unifying Themes in Microbial
Associations With Animal and Plant Hosts Described Using The Gene Ontology.
Microbiology and Molecular Biology Reviews 74(4):479-503.
110. Torto-Alalibo, T., Meng, S., Dean, R.A. . 2009. Infection strategies of filamentous
microbes described with the gene ontology. Trends Microbial 17(7):320-7.
111. Twizeyimana, M., Ojiambo, P.S., Hartman, G.L., and Bandyopadhyay, R. 2011.
Dynamics of soybean rust epidemics from sequential plantings of soybean cultivars in
Nigeria. Plant Disease 95:43-50.
112. Twizeyimana, M., Ojiambo, P.S., Haudenshield, J. S., Caetano-Anollés, G., Pedley, K. F.,
Bandyopadhyay, R., and Hartman, G. L. 2011. Genetic diversity and structure of the
Phakopsora pachyrhizi populations on soybean. Plant Pathology 60:719-729.
113. Twizeyimana, M., Ojiambo, P.S., Sonder, K., Ikotun, T., Hartman, G.L., and
Bandyopadhyay, R. 2009. Pathogenic variation in rust pathogen Phakopsora pachyrhizi
infecting soybean in Nigeria. Phytopathology 99: 353-361.
114. Velez, H., Glassbrook, N. J., and Daub, M. E. 2007. Mannitol metabolism in the
phytopathogenic fungus Alternaria alternata. Fungal Genet. Biol. 44:258-268.
115. Velez, H., Glassbrook, N. J., and Daub, M. E. 2008. Mannitol biosynthesis is required for
pathogenicity of Alternaria alternata . FEMS Microbiol. Lett. 285-122-129.
116. Veronese, P., Nakagami, H., Bluhm, B., AbuQamar, S., Chen, X., Salmeron, J., Dietrich,
R., Hirt, H., Mengiste, T. 2006. The membrane-anchored Botrytis-Induced Kinase 1 plays
distinct roles in Arabidopsis resistance to necrotrophic and biotrophic pathogens. Plant
Cell 18, 257-273
117. Woodhall, J.W., Webb, K.M., Harper, G., Peters, J.C., Rodriguez-Carres, M., and Cubeta,
M.A. 2011. First report of a new binucelate Rhizoctonia in UK potato tubers. New
Disease Reports 23:31.
118. Wu, F., Bhatnagar, D., Bui-Klimke, T., Carbone, I., Hellmich, R., Munkvold, G., Paul, P.,
Payne, G., Takle, E. 2011. Climate Change Impacts on Mycotoxin Risks in US Maize.
World Mycotoxin Journal 4: 79-93.
119. Yin, J., Koné, D., Rodriguez-Carres, M. Cubeta, M.A., Burpee, L.L., Fonash, E.G.
Csinos, A.S., and Ji, P. 2011. First report of root rot caused by binucleate Rhizoctonia
anastomosis group F on Musa spp. Plant Disease 94:490.Disease 94:515-520.
120. Yu, J., Payne, G.A., Nierman, W.C., Machida, M., Bennett, J.W., Campell, B.C., Robens,
J.F., Bhatnagar, D., Dean, R.A., Cleveland, T.E. 2008. Aspergillus flavus genomics as a
tool for studying the mechanism of aflatoxin formation. Food Additives and
Contaminants 25 (9): 1152-1157.
Page | 38
121. Yu, J.J., Ronning, C. M., Wilkinson, J.R., Campbell, B.C., Payne, G. A., Bhatnagar, D.,
Cleveland, T.E. and Nierman, W. C. 2007. Gene profiling for studying the mechanism of
aflatoxin biosynthesis in Aspergillus flavus and A. parasiticus. Food Additives and
Contaminants 24:1035-1042.
122. Zandjanakou-Tachin, M., Vroh-Bi, I., Ojiambo, P.S., Tenkouano, A., Gumedzoe, M., and
Bandyopadhyay, R. 2009. Identification and genetic diversity of Mycosphaerella species
of banana and plantain in Nigeria. Plant Pathology 58: 536-546.
123. Zearfoss, A.D., Cowger, C., and Ojiambo, P.S. 2011. A degree-day model for the latent
period of Stagonospora nodorum blotch on winter wheat. Plant Disease 95:561-567.
124. Charlton, N.D., Tavantzis, S.M. and Cubeta, M.A. 2008. Detection of double stranded
RNA viruses in the soil fungus Rhizoctonia solani, In Plant Pathology Techniques and
Procedures, Chapter 14, pp. 171-182. Eds. R. Burns, Humana Press, 2nd Edition, Tocawa,
NJ.
125. Cubeta, M.A., Mozley, S.E., and Porter, D. 2007. Laboratory Exercises with Zoosporic
Fungi. In Plant Pathology Laboratory Exercises and Concepts. CRC Press, eds. Trigiano
and Windham, pp. 99-110. (Revised from 2003).
126. Ivors, K., Bartz. F.E., and Cubeta, M.A. 2010. Rhizoctonia foliar blight of tomato. In
Compendium of Tomato Diseases, 2nd Ed., eds. S. Miller and J. Jones, APS Press, St.
Paul, MN.
127. Keinath, A.P., Cubeta, M.A., and Langston, D.B., Jr. 2006. Cabbage Diseases, Ecology
and Control. In Encyclopedia of Pest Management, ed., David Pimentel, Taylor &Francis,
New York, NY .
128. Mozley, S.E., Leander, C.E., Porter, D, and Cubeta, M.A. 2007. Concepts: Zoosporic
Fungi. In Plant Pathology Laboratory Exercises and Concepts. CRC Press, eds. Trigiano
and Windham, pp. 91-98. (Revised from 2003 with concept examples).
129. Payne, G.A. and Cubeta, M.A. 2006. Biology and Detection of Human and Plant
Pathogenic Fungi. In Microbial Forensics, pp. 109-130. Eds. R.G. Breeze, B. Budowle
and S.E. Schutzer, Elsevier, London, UK. 425 pp.
Page | 39
CIFR Grant Support
CIFR Research Project Record (Last 5
years)
ID Investigators Co-Investigator(s) Year Funding Agency Period Amount Project Title
1 Carbone, I.
Arnold, A. E.,
Lutzoni, F., May,
G.
2010 NSF 2011-2015 $449,849
An interdisciplinary
study of hyperdiverse
fungal endophytes and
their function in boreal
forests
2 Carbone, I. 2005 USDA/NRI 2005-2008 $347,395
Evolution of
aflatoxigenicity in
Aspergillus
3 Carbone, I. Ristaino, J.B.,
Ivors, K. 2005 USDA/NRI 2005-2008 $312,000
Population migrations
of Phytophthora
infestans in organic and
conventional
agricultural production
systems program.
4 Cubeta, M.A. Grand, L.F. 2009 NSF 2009-2011 $252,062
Research and
Educational Use of
North Carolina State
University Mycological
Herbarium Through
Improved
Computerization and
Internet Presence
5 Cubeta, M. Dean, R.A. 2007 USDA 2007-2011 $369,061
Whole genome
sequencing of the soil
fungus Rhizoctonia
solani anastomosis
group (AG-3)
6 Cubeta, M.
Ojiambo, P.S.,
Cline, W., Barros,
J., Gurganus, K
2011 NCDA 2011-2012 $85,000
Improving Blueberry
Fruit Quality and
Marketability
7.1 Daub, M.E. Ibrahim, N. 2011 USDA/US-Egypt
Joint Board 2011-2014 $248,893
Development of disease
resistance to Cercospora
diseases of crops
7.2 Daub, M.E. Herrero, S. 2011 Syngenta Seeds
AB 2011-2012 $29,400
Expression of a
cercosporin resistance
gene and analysis of
resistance to Cercospora
disease
7.3 Daub, M.E. Ristaino, Jean 2010 Dole Corporation 2010-2013 $150,000
Dole Graduate Research
Fellowship for Black
Sigatoka Research
8 Daub, M.E. Ristaino, Jean 2010 NSF 2010-2013 $149,908 IRES in Tropical Plant
Pathology
9 Daub, M.E.
Gumpertz, M.L.,
Wyer, M.B.,
Solomon, D.,
Severin, L.R.
2008 NSF 2008-2012 $495,983 Developing diverse
departments at NC State
Page | 40
10 Daub, M.E. Herrero, S. 2006 USDA/NRI 2005-2009 $280,450
Cercosporin-resistance
genes regulated by the
zinc cluster
transcription factor
CRG1
11 Daub, M.E. 2006 NSF 2005-2007 $405,000
Vitamin B6
biosynthesis in plants
and its role in stress
responses
12 Dean, R.A. Mitchell, T., Zhu,
H., Xu, J.R. 2006 USDA 2006-2010 $773,060
Characterization of the
transcription circuitry
regulating pathogenicity
in the rice blast fungus
13 Dean, R.A.
Tyler, B., Coller,
A., Perna, N.,
White, O., Collmer,
C., Gwinn-Giglio,
M. Bird, D.,
Setubal, J., Torto-
Alalibo, T.,
Chibucos, M.,
Mitchell, T.,
Glasner, J.
2006 NSF/USDA 2005-2008 $239,978
Gene ontology terms
for standardized
annotation of plant-
associated microbe
genes
14 Dean, R.A. 2006
Burroughs
Wellcome
Foundation
2006-2009 $180,000 Summer College in
Biotechnology
15 Dean, R.A.
Ebbole, D., Yang,
Y., Mitchell, T.,
Wang, G.
2006 NSF 2006-2011 $2,133,020
TRPGR: A high
throughput protoplast
system for rice
functional genomics
and proteomics:
Protein-protein
interactions at the host-
pathogen interface
16 Dean, R.A.
Ma, L.J., Mitchell,
T., Okubara, P.,
Kohn, L.
2007 NSF 2007-2011 $1,009,625
Comparative genome
analysis of foliar and
root infecting members
of the Magnaportheceae
17 Dean, R.A. Muddiman, D. 2009 NSF 2009-2012 $529,420
Global proteome and
signal pathway
phosphoproteome
dynamics during
appressorium formation
in the rice blast fungus,
Magnaporthe Oryzae
18 Dean, R.A. Co-PI 2010 NIH 2010-2013 $150,000
Molecular Mycology
and Pathogenesis
Training Program
19 Payne, G.A. Nielsen, D.M. 2009
National Institute
for Food &
Agriculture-AFRI
2009-2012 $398,000
Pathogenesis of
Aspergillus flavus on
developing maize seeds
20 Payne, G.A. Woloshuk, C.P. 2009
National Institute
for Food &
Agriculture-AFRI
2009-2011 $365,595
Understanding the
response of Fusarium
verticillioides to a
maize kernel
environment
Page | 41
21 Payne, G.A. Holland, J.B. 2009 Corn Growers
Association of NC 2009-2010 $5,000
Breeding for Resistance
to Fusarium Ear Rot
and Fumonisin
Accumulation
22 Payne, G. A. 2006
USDA/ARS
Cooperative
Agreement
2006-2011 $177,036
Development of genetic
markers for resistance
to aflatoxin
accumulation
23 Payne, G. A. Dean, R.A. 2006 USDA 2003-2008 $649,999
Whole genome
sequence and assembly
of Aspergillus flavus
24 Payne, G. A.
Keller, N.P.,
Woloshuk, C. P.,
and Yu, J.J.
2006 USDA/NRI/CGP 2006-2009 $700,000
Gene networks
controlling
development,
pathogenicity, and
secondary metabolism
in Aspergillus
25 Payne, G. A. Holland, J.B. 2006 Corn Growers
Association of NC 2005-2006 $5,000
Breeding strategies for
the control of Fusarum
ear rot and fumonisin
accumulation
26 Payne, G. A. 2006 USDA/NIR/CGP 2002-2006 $300,000
Characterization of
novel genes in aflatoxin
biosynthesis
27 Ojiambo, P.S. Louws, F. and
McGrath, M.T. 2010 USDA-NIFA 2010-2011 $136,150
Enhancing the Cucurbit
Downy Mildew
Forecasting System
28 Ojiambo, P.S. Adams, M.L. 2010 Pickle Packers
International 2010 $5,000
Validation of Findings
from the Meta-analysis
of Fungicide Efficacy in
Managing Downy
Mildew in Cucurbits
29 Ojiambo, P.S.
Jester, W. Gunter,
C., and Jennings,
K.
2010 Golden Leaf
Foundation 2010 $75,000
Development of a
Lettuce Industry in
North Carolina Phase
III
30 Ojiambo, P.S. Holmes, G. 2010 Pickle Packers
International 2010-2011 $15,000
Validating Downy
Mildew Forecasts using
Sentinel Plots and
Spore Traps
31 Ojiambo, P.S. Payne, G.A. 2009 Corn Growers
Association of NC 2009-2010 $18,000
Selecting Resistance to
Aflatoxin Accumulation
32 Ojiambo, P.S. Cowger, C. 2009
NC Small Grain
Growers
Association
2009-2010 $20,550
Optimizing fungicide
decisions for
management of Septoria
wheat leaf and glume
blotch
33 Veronese, P. Heber, steffen 2010 NSF-EAGER 2009-2011 $299,420
Role of alternative
splicing in plant
immune response
Page | 42
34 Veronese, P. Ma, L.J. (PI)
multiple co-PIs 2006
NSF&CSREES/U
SDA 2006-2008 $650,000
Verticillium
comparative genomics-
understanding
pathogenicity and
diversity of soil-borne
fungal pathogens
35 Veronese, P. Dole, J. (PI)
multiple co-PIs 2006
Dole Food
Company, Inc. 2007-2008 $1,000,000
Partnering with Dole
Food to extend cut
flower postharvest life
CIFR Group Grants
36 Dean, R.A.
Mitchell, T.K.,
Veronese, P.,
Daub, M., Payne,
G.A., Cubeta, M.,
Carbone, I.
2006 USDA/CSRS 2006-2011 $229,500
Graduate Training in
the application of
genomic and
bioinformatic
technologies to fungi
37 Payne, G.A.
Dean, R.A.,
Cubeta, M.A.,
Carbone, I.
2010 USDA Special
Grant 2010-2011 $209,400
Fungal genomics and
biosecurity
38 Payne, G.A.
Dean, R.A.,
Cubeta, M.A.,
Carbone, I.
2008 USDA Special
Grant 2008-2010 $209,765
Fungal genomics and
biosecurity
39 Payne, G.A.
Dean, R.A.,
Cubeta, M.A.,
Carbone, I.
2006 USDA Special
Grant 2006-2007 $300,372
Fungal genomics and
biosecurity
40 Payne, G.A.
Dean, R.A.,
Cubeta, M.A.,
Carbone, I.
2005 USDA Special
Grant 2005-2006 $243,275
Fungal genomics and
biosecurity