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Course Descriptions

A comprehensive list of undergraduate- and graduate-level courses taught by the Dept. of Plant Pathology and Environmental Microbiology (PPEM) faculty.

Course descriptions are stored in LionPATH, the university-wide student information system, and can be accessed via the Browse Course Catalog link in the lower left corner of the LionPATH home page. Most PPEM undergraduate courses can be found under the PPEM abbreviation and graduate courses under the PPEM and PPATH abbreviations. Please see below for comprehensive information.

Agroecology (AGECO)

AGECO 121 (GN) Plant Stress: It's Not Easy Being Green (3)
The many hazards faced by plants and the dynamic ways that plants respond to these problems are examined. Offered Fall Semester

AGECO 122 (METEO 122) (GN) Atmospheric Environment: Growing in the Wind (3)
Students will learn about the effect of weather on plants, animals, and humans. Offered Fall Semester

This course is for first-year students who are interested in learning about the atmospheric environment and its influence on animals, plants, and humans. It is about how processes at the ground surface and in the air govern weather conditions on Earth. Growing in the Wind focuses on five major weather elements: energy, temperature, moisture, pressure, and wind and how these factors govern ecosystems and habitation of Earth. Emphasis is also given to human impacts on weather and climate. The lectures (one-hour lecture twice weekly) are organized around the central theme that the unequal distribution of incoming solar energy (both spatially and temporally) produces temperature and pressure contrast at the Earth's surface and in the atmosphere that in turn cause storms and control the weather and climate. Computer lab exercises (two-hour lab once weekly) will reinforce concepts learned in lecture. No prerequisites are required. A sincere interest in the environment helps.

AGECO 457 (ENT 457) Principles of Integrated Pest Management (3)
Integrated study of pest complexes and their management, emphasizing ecological principles drawing on examples from a range of agricultural, forestry and urban systems. This course is designed for sixth, seventh, and eighth semester students and graduate students. Prerequisites: two or more of the following: ENT 313, HORT 238, PPEM 318, or PPEM 405 | Offered Fall Semester

The goal of this course is to introduce upper-level undergraduates and graduate students to the principles and practices of integrated pest management (IPM). This course addresses IPM issues concerning insects, plant diseases, and weeds in agriculture, natural systems and urban environments. Rooted in ecology, IPM also addresses the influence of human social, economic, and regulatory systems in pest management. Emphasis is placed on the basic tactics and tools of IPM including biological, cultural, legal, mechanical, and chemical controls, host-plant resistance, pest monitoring, and decision making. The overarching goals of environmental protection, economic viability, and social welfare are considered throughout the course. In addition, students will learn about IPM program implementation both domestically and internationally, including pest population modeling and the use of internet resources to inform decision makers. Several projects will provide real-world examples. These may include field trips and a semester-long project where students research and solve an actual pest management problem.

ENT 457 (See AGECO 457)

METEO 122 (See AGECO 122)

Plant Pathology (PPEM)

BIOL 425 (See PPEM 425)

E R M 430 (See PPEM 430)

PPEM 120 (GN) The Fungal Jungle: A Mycological Safari from Truffles to Slime Molds (3)
This course is an introduction to the world of fungi and their impact on humans and the environment around us. Offered Fall Semester

Fungi are a fascinating group of organisms that we encounter in everyday life. Apart from the mushrooms on our pizza or mold in our bathtub, fungi are important plant pathogens that severely interfere with agricultural production, cause diseases in humans and insects, and have a major role in ecosystems. The aim of this course is to introduce students to the world of fungi and review the important functions of fungi in human society, to educate students in basic concepts of fungal biology that are scientifically interesting and important to human society, and to train students to understand both basic and current topics in science. Topics to be covered include the structure and classification of fungi, the ways in which fungi interact with other organisms as pathogens or beneficial partners, the contributions fungi make to ecosystem functioning, and the ways in which humans use fungi and products derived from them. We will discuss examples that students are familiar with and encounter in their everyday life. The course also has an informal lab section that includes several class activities and visits. Class activities are designed to be done in small teams and promote teamwork learning, problem solving, and critical thinking skills. Students will learn how to isolate, grow, and identify fungi, among other activities, culminating in a fungal feast. For example, students will keep a journal on fungi, take quizzes, and deliver a presentation on their favorite fungus, among other assignments. This course is intended to be an introductory science course to non-science majors and will provide important general science knowledge as well as specific details about fungal biology.

PPEM 225 Mushroom Cultivation (3)
Students will learn about commercial production of edible mushrooms and how to cultivate them on both a small and commercial scale. Prerequisite: BIOL 110 or equivalent | Offered Spring Semester

Pennsylvania’s growers account for nearly two thirds of the U.S. total mushroom production. The production of the button mushroom, Agaricus bisporus, is a technically challenging process that requires a thorough understanding of substrate preparation and pasteurization (Phase I and Phase II composting) to be successful. The class will follow an Agaricus bisporus crop at the Mushroom Research Center on campus for the 11-week cropping cycle, participating in all aspects of button mushroom production. The course will also cover specialty mushroom production (including shiitake, oyster, maitake, enoki), which can be achieved on a small scale with some basic training and understanding of the different nutritional and substrate preparation techniques. Because cultivation of many specialty mushrooms is easier than button mushroom production, we will cultivate shiitake mushrooms both on sawdust logs as well as traditional oak logs. The class will have the opportunity to cultivate at least one other specialty mushroom, such as the oyster or lion’s mane, in the lab. We will schedule one Saturday field trip to visit several commercial mushroom farms in southeast Pennsylvania. Though this trip is not mandatory, it will be a good chance to view all aspects of commercial mushroom farming.

PPEM 296 Independent Studies (1-18)
Creative projects, including research and design, which are supervised on an individual basis and which fall outside the scope of formal courses. Offered Fall and Spring Semesters

PPEM 297 Special Topics (1-9)
Formal courses given infrequently to explore, in depth, a comparatively narrow subject which may be topical or of special interest. May be offered Fall and Spring Semesters

PPEM 300 (GN) Horticultural Crop Diseases (3)
Diseases of horticultural crops are examined, stressing their cause, diagnosis, management, and national and international importance. Prerequisite: 3 credits in a biological science | Online course | Offered Fall Semester

Diseases of horticultural crops are examined stressing their cause, diagnosis, management, and understanding the roles they play in national and international trade and bio-security concerns. The biology of plant diseases involving a broad range of biotic and abiotic plant pathogens will be discussed. The student who completes the course will:

  1. Be able to describe the causes of plant diseases in general and horticultural crop diseases in particular;
  2. Be able to explain the interactions that occur among the plant, the environment, and biotic and abiotic agents during disease development;
  3. Have the ability to diagnose and explain the management of key diseases of horticultural crops;
  4. Be able to describe the economic and social impact that plant diseases have on horticultural crops, including how the world trade of these crops can result in the global spread of pathogens important to other agricultural crops and native plants in the environment.

The course is recommended for majors in horticulture and urban forestry but is appropriate for everyone interested in growing plants for enjoyment or profit or in maintaining the health of horticultural crops. This course provides an introduction to plant pathology in general and can be followed by more in-depth courses in plant-microbe interactions, mycology, nematology, phytobacteriology, air pollution impacts on terrestrial ecology, or forest pathology.

PPEM 318 Diseases of Forest and Shade Trees (2)
Introduction to diagnosis and management of forest and shade tree diseases. Offered Spring Semester

Diseases of Forest and Shade Trees is a practical, hands-on lab and lecture course designed primarily for forestry and landscape-contracting students. However, the course is also appropriate for any student interested in tree diseases or for any student who simply wants to know “What is wrong with my tree?” The course content covers the important tree diseases of Pennsylvania, with emphasis on tree diseases that also have national and international implications. New and emerging tree diseases are discussed during the last two weeks of the semester.

PPEM 405 Microbe-Plant Interactions: Plant Disease and Biological Control (3)
Survey of microbe-plant interactions causing plant disease, mechanisms of pathogenesis, disease management, and microbial and molecular biological control strategies. Prerequisite: BIOL 110 | Offered Fall Semester

Plant health in both natural and agricultural ecosystems is essential for sustaining human society and all other life forms on earth. Plant disease epidemics are common and diverse and can have devastating effects on our population and economy by debilitating the ecosystems on which we depend. This course focuses on biological and environmental factors that influence microbe-plant interactions which in turn determine plant health and initiate plant disease epidemics. Developing strategies for maintaining healthy plants in both natural and agricultural ecosystems requires an understanding of pathogen and host biology, as well as the role of the environment in disease epidemiology. Students will learn about the survival and spread of important plant-infecting fungi, bacteria, phytoplasma, and viruses, and how mechanisms for microbial pathogenicity are influenced by the environment. The final section of the course will focus on the use of beneficial microorganisms to maintain and improve plant health. Grades will be based on student performance on a wide variety of activities including labs, quizzes, seminar reports, and exams.

PPEM 412 Turfgrass Disease Management (3)
Introduction to biology of turfgrass pathogens and management of cool- and warm-season turfgrass disease. Prerequisite: TURF 230, TURF 235, CHEM 101 or CHEM 110, BIOL 127 | Offered Fall Semester

This course will provide an introduction to concepts of disease processes in plants and biology of plant pathogens, principles of turfgrass disease diagnosis based on symptom development, recognition of signs and microscopic structures of the pathogens, environmental and cultural management factors influencing disease development, significance of pathogen life cycle in disease epidemic development, and integrated turfgrass disease management practices for root and foliar disease. Disease of various turf types for golf courses, residential lawns, landscapes, and athletic fields will be discussed. Disease topics will include diseases that commonly occur in winter, disease that develop in spring and persist into summer, and diseases that initiate in summer and remain active until late fall in most regions of North America. A number of non-infectious disorders of turf caused by extreme environmental conditions and improper cultural practices will also be discussed.

PPEM 416 Plant Virology: Molecules to Populations (3)
An exploration of the molecular biology and population dynamics of the virus-plant interaction. Prerequisite: BIOL 110, BIOL 120 | Offered Spring Semester

This will be the departmental foundation course for plant viruses, one of the four major pathogen groups. The course will entail an exploration of the history, nature, cause, socioeconomics, symptomatology, physiology, diagnosis, ecology, epidemiology, and control of viral diseases on plants. Special emphases will be placed on replication and evolution of plant viruses, molecular biology of the virus-plant interaction, replication, virus-like agents (viroids & prions), natural and genetically-engineered disease resistance, virus-vector relationship, and population dynamics.

PPEM 417 Phytobacteriology (3)
How bacterial pathogens infect plants and evade plant immune responses. Prerequisite: BIOL 110; BIOL 222 or BIOL 322; B M B 211 or MICRB 201 or MICRB 251 or B M B 251 | Offered every other Spring Semester

This lecture and lab course covers the genetic, molecular, physical, and physiological mechanisms of bacterial pathogenesis in plants. We will examine how the tools of microbiology are used to deduce the pathogenic mechanisms behind various plant diseases caused by bacteria. Topics include: motility; attachment; evasion of host defense; toxins; enzymes and proteins; biofilms; and bacterial communication. Readings include research and review articles. The course includes weekly, hands-on laboratory activities that cover handling bacteria, isolating bacteria from plants, monitoring bacterial growth in plants, monitoring plant symptoms development, and the genetic control of bacterial and plant interactions.

PPEM 425 (BIOL 425) Biology of Fungi (4)
A survey of the biological diversity of fungi, stressing evolution, ecology, disease, morphology, life histories, and importance to humans. Prerequisite: fifth-semester or graduate standing in a biological science major with six credits completed in the major | Offered Fall Semester

This course is a hands-on survey of fungal diversity, covering a wide variety of topics in fungal biology: phylogenetics, morphology, ecology, evolution, population biology, fungi as food, fungi as sources of toxins, ethnomycology, fungi as agents of plant and animal disease, fungi as sources of pharmaceuticals, and industrial uses. All fungi will be discussed, from mushrooms and other fleshy fungi to molds to slime molds. The laboratory portion of the course will center mostly around handling and manipulating freshly collected and living fungi and microscopic analysis of their major features. There will be approximately four or five required field trips to local forests during the laboratory period to observe fungi in their natural habits and collect them for further analysis in the laboratory. Students will come out of the course with a broad base of knowledge about fungi and their diversity and the ability to handle them in the laboratory and observe them using the microscope.

PPEM 430 (E R M 430) Air Pollution Impacts to Terrestrial Ecosystems (3)
An overview of direct and indirect effects of air pollution on terrestrial plants and ecosystems. Prerequisite: BIOL 220W, FOR 308 | Offered Spring Semester

Pollutant sources, transport, meteorology, and temporal and spatial trends of pollution dispersion and deposition are introduced. An overview is presented of the direct and indirect effects of air pollutants on terrestrial ecosystems with an emphasis on plant life. The effects of ozone, sulfur dioxide, nitrogen oxides, particulate matter, halogens, and combined pollutants leading to acidic atmospheric depositions are presented. Emphasis is placed on air pollutants as plant pathogens leading to symptoms and eventual long-term accumulative effects to entire ecosystems. Methods of diagnostics, factors affecting plant response, ecosystem decline and resiliency, pest interactions, assessment of loss and cost/benefit analysis leading to abatement follows. Final parts of the course include perspectives of public awareness, development of National Ambient Air Quality Standards, compliance prevention of significant deterioration, and the Clean Air Act reforms of 1990.

PPEM 454 Virus Ecology (3)
Virus ecology describes how viruses interact with their hosts, and how those interactions modulate the hosts' interactions with their environment. Prerequisite: BIOL 110 or equivalent | Offered Fall Semester

In this course students will learn about the interplay among viruses, hosts, and the environment. The diversity of viruses, which infect all known life forms, will be explored. The important role viruses play in the ecology of the planet, including carbon cycles, host adaptation to extreme environments, host health or disease, and host evolution will be discussed in depth using specific examples. Students also will learn to critically read the scientific literature. Learning will be assessed through a combination of written and oral assignments and exams.

PPEM 496 Independent Studies (1-18)
Creative projects, including research and design, which are supervised on an individual basis and which fall outside the scope of formal courses. Offered Fall and Spring Semesters

PPEM 497 Special Topics (1-9)
Formal courses given infrequently to explore, in depth, a comparatively narrow subject which may be topical or of special interest. May be offered Fall and Spring Semesters

Plant Pathology (PPATH)

AGBIO 802 (See PPATH 802)

PPATH 502 Plant Disease Diagnosis (3)
Field and laboratory techniques used in diagnosing plant diseases caused by various types of pathogens with emphasis on fungi. Offered Fall Semester

PPATH 505 Fundamentals of Phytopathology (2)
An in-depth tutorial of the fundamental theories and concepts of plant pathology. Offered Spring Semester

Using the primary literature of the discipline, students will explore, in-depth, the knowledge base of plant pathology. Students will write a three- to five-page paper each week summarizing the major points of the topic covered in the primary literature assigned as related to four pathogens/diseases chosen by each student from an approved list. Students will also answer, in writing, one or two specific questions posed by the instructor each week. These writings constitute 90 percent of the grade. Five percent of the grade is based upon a written final exam and 5 percent on oral participation in class.

PPATH 522 Professional Development and Ethics in Plant Pathology (1)
Graduate students will develop key professional skills and ethics through a combination of lectures, discussions, and assignments. Offered Fall Semester

This course is designed to help graduate students acquire key professional skills and ethics through a combination of lectures, case study discussions on various ethics and professionalism issues, dialogs with invited guests about their professional experience, and mock exercises of paper and proposal reviews. Topics to be covered include:

  • the process and ethics of publishing;
  • how peer review of papers and grant proposals works;
  • plagiarism;
  • scientific misconduct;
  • oral and poster presentation skills;
  • successful strategies in grant proposal writing and proposal review.

PPATH 533 Molecular Genetics of Plant-Pathogen Interactions (3)
In-depth discussion/review of the primary literature on the mechanisms of plant-pathogen interactions at the molecular and cellular levels. Prerequisite: B M B 400 or equivalent | Offered Fall Semester in even-numbered years

The main objective of this course is to help students gain:

  • first-hand knowledge of various techniques used in studying the molecular basis of plant-pathogen interactions;
  • knowledge of the current concepts and theories on the nature and mechanisms of the plant-pathogen interactions;
  • an ability to integrate and synthesize various areas of knowledge in solving plant health related problems.

This course will serve the needs of students in Plant Pathology and other departments/programs who require an in-depth understanding of the molecular basis of plant-pathogen interactions for their program of study. This course's expected enrollment is 8-10. Grading will be based on class participation, paper presentations, assignments, and a mid-term exam.

PPATH 542 Epidemiology of Plant Diseases (3)
Disease development in populations of plants, with emphasis on the impact of environment and control practices on rate of development. Offered Spring Semester

PPATH 543 Pathogen Variation and Host Resistance (3)
Mechanisms and implications of genetic variation in plant pathogens related to breeding for disease resistance in plants by genetic means. Offered every other Spring Semester

PPATH 544 Fungal Genetics (4)
Fungal breeding systems, mating types, asexual restrictions and recombination, tetrad analysis, gene conversion, and extra genetic elements. Prerequisite: 3 credits of mycology and introductory genetics | Offered every other Spring Semester even years

Fungal genetics will focus on the classical genetics of fungi starting with the expected inheritance ratios and patterns for single gene and multiple genes on various fungal traits. The methods of establishing crosses and obtaining progeny will be covered in the examples provided. Mating type and breeding systems are an important trait for obtaining the sexual phase, therefore an emphasis will be placed on the genetic determination of breeding methods and mating type, and what is known of mating type switching. There are several unique phenotypes associated only with fungi (pokey, senescent fungi, killer character and others) inherited by mitochondrial DNA and induced by plasmids or transposons. The determination of inheritance and the importance will be examined. Fungi provide the unique opportunity to conduct tetrad analysis in determination of inheritance and mapping of traits. In the laboratory, crosses will be set up by students to obtain data to conduct tetrad analysis and to visualize unusual tetrads brought about by gene conversion. Exchange of genetic material occurs without the sexual cycle though heterokaryosis and the parasexual cycle but may be limited by vegetative incompatibility. These difficult concepts will be discussed as well as visualized by conducting experiments in the laboratory. In discussions, an emphasis will be placed on plant pathogenic fungi and inheritance of virulence which is an important plant pathogen trait. Finally topics on population genetics of fungi including determination of genetic diversity, allele frequencies, genotype frequencies will be studied. Evaluation of student performance will be based on problems sets provided throughout the semester, laboratory reports, student projects and presentations, and a final examination. The problem sets are designed to help students solve genetic problems based on the concepts learned in lecture. The laboratory experiments are designed to complement the lectures and allow students to visualize difficult concepts from lecture. Students will be assigned a plant pathogenic fungus and will explore the literature especially any relevant genetic information on that fungus. The final examination will focus on short answer questions requiring the student to synthesize information. Expected enrollment is ten students.

PPATH 590 Colloquium (1-3)
Continuing seminars which consist of a series of individual lectures by faculty, students, or outside speakers. Offered Fall and Spring Semesters

PPATH 596 Individual Studies (1-9)
Creative projects, including non-thesis research, which are supervised on an individual basis and which fall outside the scope of formal courses. Offered Fall and Spring Semesters

PPATH 597 Special Topics (1-9)
Formal courses given on a topical or special interest subject which may be offered infrequently; several different topics may be taught in one year or term. Offered Fall and Spring Semesters

PPATH 600 Thesis Research (1-15)
Offered Fall and Spring Semesters

PPATH 601 Ph.D. Dissertation Full-Time (0)
Offered Fall and Spring Semesters

PPATH 602 Supervised Experience in College Teaching (1-3 per semester/maximum of 6)
Supervised preparation and presentation of materials in lectures and laboratories, preparation and supervision of exams, and student consultation and evaluation. Offered Fall and Spring Semesters

PPATH 802 (AGBIO 802) Plant Protection: Responding to Introductions of Threatening Pests and Pathogens (3)
This course provides knowledge of plant biosecurity, plant disease, regulations, and technologies using case study examples. World Campus | Offered Spring Semester

This course covers agricultural biosecurity issues relevant to plant-based agriculture. Topics include the size and scope of plant-based agriculture domestically and globally, the concept of plant disease, the nature of threats to plant health, modes of transmission of pests and pathogens, and the role of government and other public institutions in protecting the nation’s agricultural and forest systems. Information on the regulatory component of plant protection and how they function will be included.

Case studies of introductions of major pests and pathogens will be reviewed in depth and comprise the majority of the course. These cases are selected to represent different means of introduction and different types of pests or pathogens. Various strategies and technologies developed for prevention, detection, response, and recovery will be considered and compared. The intended and unintended influences that governmental regulations, industry practices, and international agreements can have on the spread of plant pathogens and pests will also be discussed. Finally, an assessment of readiness for future pathogen/pest introductions will be synthesized and presented.

PPATH 853 (TURF 853) Interpreting Turfgrass Science Literature (3)
Introduction to turfgrass research publications, interpretation of the data, and discussion of the significance of the results. World Campus | Offered Fall Semester

This course will provide an introduction to literature search in turfgrass management, identification of most pertinent peer-reviewed journals for each area of interest/specialty in turfgrass management, and utilization of other resources such as technical journals, trade journals, online and resident educational material resources, and extension bulletins/circulars from various institutions/organizations that address various topics on turfgrass management. This course will prepare the students for analyzing research questions or rationale formulated by an investigator, for understanding how the study was devised to address the objectives adequately and the results were obtained and presented in the publication, and for identifying the take-home message in the publication. Emphasis will be made on the criteria used for data collection, the significance of methods employed in statistical analyses of the data, and presentation of results in the publications to effectively convey the information to readers.

TURF 853 (See PPATH 853)

Contact Information

Carolyn K. Boring
  • Graduate Program Coordinator
Phone: 814-865-7069