Share

PPEM 416: Plant Virology: Molecules to Populations (Spring 2018)

This will be the departmental foundation course for plant viruses, one of the four major pathogen groups.

Department(s)

  • Plant Pathology and Environmental Microbiology

Description

Plant viruses are one of the major groups of microorganisms that cause severe diseases impacting crops; at the same time some viruses coexist in wild plants without causing any apparent damage. How do plant viruses cause symptoms in plants? How can we control viruses and attenuate their symptoms? Many plant viruses evolved to be transmitted by vectors, such as insects. Why? How do plants and vectors respond when they are infected by viruses? How do plants become resistant to viruses, and how do viruses evade plant defenses? The goal of PPEM 416 Plant Virology: Molecules to Populations is to explain how plant viruses function. This understanding is fundamental to plan efficacious viral control strategies and, as a consequence, is necessary to improve the well-being of human populations that rely on crops for feed, fiber, and fuel production.

Course Logistics

Dates: 16 weeks, January 8 – April 27, 2018
Day and Time: M W F | 11:15-12:05 p.m.
Location: 103 Buckhout Lab

Prerequisites: BIOL 110, BIOL 120
No. of Credits: 3

Instructor: Dr. Cristina Rosa, Asst. Prof. Plant Virology, Department of Plant Pathology and Environmental Microbiology
Office: 321 Buckhout Lab
Email:
Phone: 814-867-5372
Office Hours: by appointment and at the end of each class.

Course Objectives

In this course, you will learn:

  • to define what is a plant virus and what is a virus species;
  • how plant viruses replicate and spread throughout a plant and from plant to plant;
  • how plant viruses modulate plant and vector responses and interactions;
  • the mechanisms of plant resistance to viruses and how viruses evade plant defenses;
  • to read scientific literature, understand it, apply the laboratory techniques used in molecular biology to plant virology and vice versa, to analyze the results found by other researchers, to evaluate them, and to create your own experimental plans.

Recommended Textbook

The recommended textbook is Comparative Plant Virology by R. Hull, 2nd Edition, Academic Press, publisher. The book is available for consultation in The Albert C. Hildebrandt Plant Pathology Library, located in 222 Buckhout Lab. Access to the library is restricted by a card reader; please ask Christina Dorsey (221 Buckhout Lab) for assistance. Plant virology papers identified by the instructor and later by the class will be extensively employed. The papers will be posted on Canvas or will be delivered in class by the instructor, or will be freely available on the internet via Google Scholar.

Class Attendance

Regular class attendance is one of the most important ways that students learn and understand course materials. It is a critical element of student success. Accordingly, it is the policy of the university that class attendance is expected and that students should follow the attendance policy of the instructor, as outlined in the syllabus. A student should attend every scheduled class and should be held responsible for all work covered in the courses taken.

Class attendance is expected regardless of the format of the course. It is the student’s responsibility to complete work early or make alternate arrangements with the course instructor, if due dates or required work will be missed because of a university-approved absence as described in this policy.

Instructors should provide, within reason, the opportunity to make up work for students who miss class for regularly scheduled, university-approved curricular and extracurricular activities (such as Martin Luther King Jr. Day of Service, field trips, debate trips, choir trips, and athletic contests). In addition, instructors should provide, within reason, the opportunity to make up work for students who miss class for post-graduate, career-related interviews when there is no opportunity for students to reschedule these opportunities (such as employment and graduate school final interviews.) In both cases, students should inform instructors in advance and discuss the implications of any absence. Missing class, even for a legitimate purpose, may mean that there is work that cannot be made up, hurting the student’s grade in the class. Likewise, students should be prepared to provide documentation for participation in university-approved activities, as well as for career-related interviews, when requested by the instructor.

Instructors also should provide, within reason, the opportunity to make up work for students who miss classes for other legitimate but unavoidable reasons. Legitimate, unavoidable reasons are those such as illness, injury, military service, family emergency, or religious observance. Again, it should be recognized that not all work can be “made-up” and that absences can affect student performance in a class.

Instructors can determine when irregular attendance negatively affects a student’s scholastic achievement, and thus grade, in the course, even to the point of failure. If class absence constitutes a danger to the student’s scholastic attainment, the instructor should make this fact known to the student at once. The student may appeal this decision to the head of the department in which the course is offered.

If an evaluative event will be missed due to an unavoidable absence, the student should contact the instructor as soon as the unavoidable absence is known to discuss ways to make up the work. An instructor might not consider an unavoidable absence legitimate if the student does not contact the instructor before the evaluative event. Students will be held responsible for using only legitimate, unavoidable reasons for requesting a make-up in the event of a missed class or evaluative event. (Conflicts with non-final examinations are covered in Policy 44-35.) Requests for missing class or an evaluative event due to reasons that are based on false claims may be considered violations of the policy on Academic Integrity (Policy 49-20).

Class Participation

Participation is necessary in this class! You should arrive at each class on time and be prepared to fully participate in the class activities. If you must miss a class, you must notify the instructor before the absence.

You will be responsible for:

  • attending classes;
  • reading the assigned material;
  • completing the assignments;
  • making-up missed assignments;
  • participating in in-class activities;
  • evaluating your peers;
  • following the instructor's guidance;
  • actively engaging the instructor if problems arise;
  • checking daily for postings by the instructor on personal email and Canvas.

Course Delivery and Grading

This course was developed following a revised Bloom’s taxonomy (1956) with activities structured on six levels of thinking: remembering, understanding, applying, analyzing, evaluating, and creating (Anderson 2001). These levels will be approached sequentially and will be often reiterated. Each level will be assessed by the instructor as well as by your peers sitting in your same class. The assessments will be performed on the assigned literature, in class and at home, individual and group activities. A take-home final exam will be assigned during the last week of instruction.

The methods of course delivery will be through instructional lectures and by student-centered activities. The course structure, content, and assessment will be adjusted based on your input and as needed.

Grades will be based on the following assessments:

AssessmentPointsGrade %
Each week 50 75%
Take-home final exam 250 25%
TOTAL 1,000 100%

Weekly Assessment

Fifty points will be available each week and will be given on home assignments, in class short assessments and group activities and performance.

Make-Up Work

If you must miss work, please make arrangements ahead of time to reschedule with the instructor.

Extra Points

One percent of the grade will be given to each of you if all SRTEs are turned in before the end of instruction.

Final assessment

250 points will be assigned as grade for the final comprehensive examination.

Lecture Schedule

This schedule is tentative; the instructor will inform you of any changes.

WeekLectureDateTitleAssessment
1 1 Jan 8 Introduction Take home reading
2 Jan 10 Economics of plant viruses
The case of ACMV, MSV, geminiviruses
3 Jan 12 Economics of plant viruses In-class discussion
2 4 Jan 15 Holiday - No class Holiday - No class
5 Jan 17 Plant viral genomes Take home readings/work in class
6 Jan 19 Viral architecture In-class discussion
3 7 Jan 22 Virus replication
Pick your own virus/select reading
8 Jan 24 Work on your virus replication Work on reading
9 Jan 26 In class discussion In-class discussion
4 10 Jan 29 Viral expression Pick your own virus/select reading
11 Jan 31 Work on your virus expression Work on reading
12 Feb 2 In class discussion Class assessment: remembering
5 13 Feb 5 Virus movement: local Pick your own virus/select reading
14 Feb 7 Virus movement: systemic Work on reading
15 Feb 9 In class discussion In-class discussion
6 16 Feb 12 RNAi/silencing suppressors Pick your own virus/select reading
17 Feb 14 RNAi/silencing suppressors Work on reading
18 Feb 16 In class discussion In-class discussion
7 19 Feb 19 Other plant defenses against viruses Pick your own virus/select reading
20 Feb 21 Other plant defenses against viruses Work on reading
21 Feb 23 In class discussion In-class assessment: understanding
8 22 Feb 26 Molecular biology of viral symptomatology Pick your own virus/select reading
23 Feb 28 Molecular biology of viral symptomatology Work on reading
24 Mar 2 In class discussion In-class discussion
9 25 Mar 5 Spring break-no class Holiday-no class
26 Mar 7 Spring break-no class Holiday-no class
27 Mar 9 Spring break-no class Holiday-no class
10 28 Mar 12 Type of transmission Pick your own virus/select reading
29 Mar 14 Type of transmission Work on reading
30 Mar 16 In class discussion Class assessment: Analyzing
11 31 Mar 19 Viral disease management The case of PRSV and PPV/select reading
32 Mar 21 Viral disease management Work on reading
33 Mar 23 In class discussion In-class discussion
12 34 Mar 26 Plant virus origin Nature paper
35 Mar 28 Plant virus origin Work on reading
36 Mar 30 In class discussion In-class discussion
13 37 Apr 2 Virus evolution/quasispecies Pick your own virus/select reading
38 Apr 4 Virus evolution/quasispecies Work on reading
39 Apr 6 In class discussion Class assessment: applying
14 40 Apr 9 not-viral agents: satellite viruses Pick your own satellite virus/select reading
41 Apr 11 not-viral agents: satellite viruses
Work on reading
42 Apr 13 In class discussion Class assessment
15 43 Apr 16 not-viral agents: viroids Pick your own viroid/select reading
44 Apr 18 not-viral agents: viroids Work on reading
45 Apr 20 In class discussion Class assessment: Evaluating
16 46 Apr 23
Animal viruses
Animal viruses/select reading
47 Apr 25
Animal viruses
Animal viruses/select reading
48 Apr 27 In class review session Class assessment: Creating
17 Apr 30-May 4 Final comprehensive exam (TBA) Class assessment Final: creating (25% grading)

Penn State Statements

The Penn State Principles

The Pennsylvania State University is a community dedicated to personal and academic excellence. The Penn State Principles were developed to embody the values that we hope our students, faculty, staff, administration, and alumni possess. At the same time, the University is strongly committed to freedom of expression. Consequently, these Principles do not constitute University policy and are not intended to interfere in any way with an individual's academic or personal freedoms. We hope, however, that individuals will voluntarily endorse these common principles, thereby contributing to the traditions and scholarly heritage left by those who preceded them, and will thus leave Penn State a better place for those who follow.

Academic Integrity

Penn State and the College of Agricultural Sciences take violations of academic integrity very seriously. Faculty, alumni, staff and fellow students expect each student to uphold the University's standards of academic integrity both in and outside of the classroom. Academic integrity is the pursuit of scholarly activity in an open, honest and responsible manner. Academic integrity is a basic guiding principle for all academic activity at The Pennsylvania State University, and all members of the University community are expected to act in accordance with this principle. Consistent with this expectation, students should act with personal integrity, respect other students' dignity, rights and property, and help create and maintain an environment in which all can succeed through the fruits of their efforts. Academic integrity includes a commitment not to engage in or tolerate acts of falsification, plagiarism, misrepresentation or deception. Such acts of dishonesty violate the fundamental ethical principles of the University community and compromise the worth of work completed by others (see Faculty Senate Policy 49‐20 and G‐9 Procedures.)

Code of Conduct and Student Conduct Procedures

Academic Integrity Guidelines for the College of Agricultural Sciences

A lack of knowledge or understanding of the University's Academic Integrity policy and the types of actions it prohibits and/or requires does not excuse one from complying with the policy.

Nondiscrimination Statement

The University is committed to equal access to programs, facilities, admission and employment for all persons. It is the policy of the University to maintain an environment free of harassment and free of discrimination against any person because of age, race, color, ancestry, national origin, religion, creed, service in the uniformed services (as defined in state and federal law), veteran status, sex, sexual orientation, marital or family status, pregnancy, pregnancy-related conditions, physical or mental disability, gender, perceived gender, gender identity, genetic information or political ideas. Discriminatory conduct and harassment, as well as sexual misconduct and relationship violence, violates the dignity of individuals, impedes the realization of the University's educational mission, and will not be tolerated. Direct all inquiries regarding the nondiscrimination policy to Dr. Kenneth Lehrman III, Vice Provost for Affirmative Action, Affirmative Action Office, The Pennsylvania State University, 328 Boucke Building, University Park, PA 16802-5901, Email: kfl2@psu.edu, Tel (814) 863-0471.

Disability

Penn State welcomes students with disabilities into the University's educational programs. Every Penn State campus has an office for students with disabilities. The Office for Disability Services (ODS) Web site provides contact information for every Penn State campus. For further information, please visit the Office for Disability Services Web site.

In order to receive consideration for reasonable accommodations, you must contact the appropriate disability services office at the campus where you are officially enrolled, participate in an intake interview, and provide documentation. If the documentation supports your request for reasonable accommodations, your campus's disability services office will provide you with an accommodation letter. Please share this letter with your instructors and discuss the accommodations with them as early in your courses as possible. You must follow this process for every semester that you request accommodations.

Mental Health Services

Many students at Penn State face personal challenges or have psychological needs that may interfere with their academic progress, social development, or emotional wellbeing. The university offers a variety of confidential services to help you through difficult times, including individual and group counseling, crisis intervention, consultations, online chats, and mental health screenings. These services are provided by staff who welcome all students and embrace a philosophy respectful of clients' cultural and religious backgrounds, and sensitive to differences in race, ability, gender identity and sexual orientation.

Counseling and Psychological Services at University Park (CAPS)
814-863-0395

Counseling and Psychological Services at Commonwealth Campuses

Penn State Crisis Line (24 hours/7 days/week): 877-229-6400
Crisis Text Line (24 hours/7 days/week): Text LIONS to 741741

Educational Equity/Report Bias

Consistent with University Policy AD29, students who believe they have experienced or observed a hate crime, an act of intolerance, discrimination, or harassment that occurs at Penn State are urged to report these incidents as outlined on the University's Report Bias webpage

Contact one of the following offices:

  • University Police Services, University Park: 814-863-1111
  • Multicultural Resource Center, Diversity Advocate for Students: 814-865-1773
  • Office of the Vice Provost for Educational Equity: 814-865-5906
  • Office of the Vice President for Student Affairs: 814-865-0909
  • Affirmative Action Office: 814-863-0471