Five Year Report - 2014 Accreditation · PDF fileFive Year Report 2006 ... plant interactions...

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

http://www.nescent.org/

http://www.nescent.org/

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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

[email protected]

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

mailto:[email protected]

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Gary A. Payne North Carolina State University




Phone: (919) 515-6994 Fax: (919) 513-0024

[email protected]


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.


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


Department of Plant Biology


Phone: (919) 513-3807 Fax: (919) 515-6986

[email protected]


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.


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




Phone: (919) 513-1227 Fax: (919) 513-0024

[email protected]


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.


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




Phone: (919) 513-4866 Fax: (919) 513-0024

[email protected]


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).


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

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Paola Veronese North Carolina State University




Phone: (919) 513-8219 Fax: (919) 513-0024

[email protected]


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


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Peter Ojiambo North Carolina State University




Phone: (919) 513-2188 Fax: (919) 513-0024

[email protected]


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)


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

http://www.hopkinsmedicine.org/institute_basic_biomedical_sciences/

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


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


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


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


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


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


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).

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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.

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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.

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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.

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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


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


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

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