Download Introduction to Bioinformatics - University of Texas Rio Grande Valley

Introduction to Plant Pathology
BIOL 5408
Instructor: Erin Schuenzel
Email: [email protected] – preferred contact method
Office: Science 1.332
Office Phone: 956-381-2229
Office Hours: M 10-11, T 8-9, W 10-11
Course Description
The aim of this course is to familiarize the student with a general introduction to plant pathology.
Students will be introduced to the major viral, bacterial and fungal pathogens with focus on those found
in the Lower Rio Grande Valley. Students will also understand how plants can respond to the microbes
on a cellular and organismal level. The disease triangle and current means of molecular identification
will be explored in the lab.
Texts
Essential Plant Pathology 2nd Ed. (2009) by G.L. Schumann and C.J. D’Arcy, APS Press ISBN 978-0-89054318-8 – Required
Plant Pathology 5th Ed. (2005) by G. N. Agrios, Academic Press, Inc. – Required (will be provided)
Course Requirements
Presentations: All powerpoint presentations will be available before class in the Content folder on the
class Blackboard site.
Lecture Quizzes: All quizzes will involve two-parts, an individual portion and a group portion. The
individual portion of the quiz will take in the first 15 minutes of class. The second part of the quiz is to
answer the same five questions as a group within a 10 minute time period. Each quiz will have five
multiple-choice questions. The individual portion is 10 points and the group portion is 30 points for a
total quiz grade of 20 points. Your nine highest quiz grades will be used for the final grade. Because this
is a group quiz – NO MAKE-UPS POSSIBLE. All quizzes are scheduled in advanced. Topics are listed
below in the calendar portion of the syllabus. There are eight quizzes, your seven highest are kept for
grading.
Term Paper: Each student will choose a plant disease to explore that is affecting or could affect plants in
the Rio Grande Valley. This paper will essentially be a literature review on the pathogen. The paper is
expected to include general information on the pathogen (taxonomy, economic impact), how the
disease spreads, the infection process, how the disease is diagnosed and what control methods are
currently being employed. The paper is due the last day of class, May 2nd, at 11pm through blackboard.
The term paper will be graded for content, clarity, accuracy and grammar.
Outside Essay Exams: The two exam essays will be posted on-line throughout the semester and will be
turned in through the classroom management system. Students will have a week (7 days) to turn-in
their essay. An official rubric for grading will be posting with the essay. In general, these essays cover
broad topics and should typically run 3-5 typed pages. All essays will be graded for content, clarity,
accuracy and grammar.
Laboratory: Each student must be enrolled in an appropriate laboratory section. The laboratory grade
will count for 35% of the final grade. The laboratory syllabus will be available on Blackboard.
Group Work: At the beginning of the semester, you will form groups. These groups will be used for the
group portion of the quizzes and group work done during class.
Class Policies
Grading Scale:
Grade
A
B
C
D
F
Percentage
x  90.0
89.9  x  80.0
79.9  x  70.0
69.9  x  60.0
59.9  x
Point Totals:
Quizzes (8 Lecture & 6 Lab)
Outside Essay Exams
Lab Reports
Lab Notebooks
Participation
Term Paper (Graduate)
30%
20%
10%
16%
10%
14%
(7 @ 30 points and 6 @ 15 points or 300 points)
(2 @ 100 points each or 200 points)
(2 @ 50 points each or 100 points)
(1 @ 16% each or 160 points)
(100 pints)
(1 @ 14% or 140 points)
Re-grades
The focus of the class is to learn the material; not force you to remember all the facts in a timed format.
Each outside essay exam and lab report, except the final lab report, can be turned in again to earn up to
10% of the points (for example full credit on the re-grade can result in a grade change from 65% to 75%).
You cannot earn more points than possible for the quiz or exam (for example you score a 29/30 on a
quiz, the highest you can earn is a 30/30 despite 2 points being available). The re-grade must be turned
by Friday May 6th by 11pm to be considered.
Late Essay Exams and Reports
Late essay exams and reports will be penalized 10% each day for 5 days. After 5 days the exam or report
will earn a 0.
Students with Disabilities
If you have a documented disability (physical, psychological, learning, or other disability which affects
your academic performance) and would like to receive academic accommodations, please inform your
instructor and contact Student Accessibility Services to schedule an appointment to initiate services. It is
recommended that you schedule an appointment with Student Accessibility Services before classes
start. However, accommodations can be provided at any time. Brownsville Campus: Student
Accessibility Services is located in Cortez Hall Room 129 and can be contacted by phone at (956) 8827374 (Voice) or via email at [email protected]. Edinburg Campus: Student Accessibility Services is
located in 108 University Center and can be contacted by phone at (956) 665-7005 (Voice), (956) 6653840 (Fax), or via email at [email protected].
Mandatory Course Evaluation Period
Students are required to complete an ONLINE evaluation of this course, accessed through your UTRGV
account (http://my.utrgv.edu); you will be contacted through email with further instructions. Online
evaluations will be available when notified. Students who complete their evaluations will have priority
access to their grades.
Attendance
Students are expected to attend all scheduled classes and may be dropped from the course for excessive
absences. UTRGV’s attendance policy excuses students from attending class if they are participating in
officially sponsored university activities, such as athletics; for observance of religious holy days; or for
military service. Students should contact the instructor in advance of the excused absence and arrange
to make up missed work or examinations.
Scholastic Integrity
As members of a community dedicated to Honesty, Integrity and Respect, students are reminded that
those who engage in scholastic dishonesty are subject to disciplinary penalties, including the possibility
of failure in the course and expulsion from the University. Scholastic dishonesty includes but is not
limited to: cheating, plagiarism, and collusion; submission for credit of any work or materials that are
attributable in whole or in part to another person; taking an examination for another person; any act
designed to give unfair advantage to a student; or the attempt to commit such acts. Since scholastic
dishonesty harms the individual, all students and the integrity of the University, policies on scholastic
dishonesty will be strictly enforced (Board of Regents Rules and Regulations and UTRGV Academic
Integrity Guidelines). All scholastic dishonesty incidents will be reported to the Dean of Students.
Sexual Harassment, Discrimination and Violence
In accordance with UT System regulations, your instructor is a “responsible employee” for reporting
purposes under Title IX regulations and so must report any instance, occurring during a student’s time in
college, of sexual assault, stalking, dating violence, domestic violence, or sexual harassment about which
she/he becomes aware during this course through writing, discussion, or personal disclosure. More
information can be found at www.utrgv.edu/equity, including confidential resources available on
campus. The faculty and staff of UTRGV actively strive to provide a learning, working, and living
environment that promotes personal integrity, civility, and mutual respect in an environment free from
sexual misconduct and discrimination.
Course Drops
According to UTRGV policy, students may drop any class without penalty earning a grade of DR until the
official drop date. Following that date, students must be assigned a letter grade and can no longer drop
the class. Students considering dropping the class should be aware of the “3-peat rule” and the “6-drop”
rule so they can recognize how dropped classes may affect their academic success. The 6-drop rule
refers to Texas law that dictates that undergraduate students may not drop more than six courses
during their undergraduate career. Courses dropped at other Texas public higher education institutions
will count toward the six-course drop limit. The 3-peat rule refers to additional fees charged to students
who take the same class for the third time.
Week
Date
Subject
Readings
Quiz/Essay
Week 1
Jan-21
Introduction to Plant Pathology
Plant Taxonomy,
Plant Morphology & Physiology
Schumann & D’Arcy Ch. 1
On BB Learn
On BB Learn
Week 2
Jan-28
Plant Morphology & Physiology
Plant Immunology
General Microbiology
On BB Learn
On BB Learn
Quiz 1
Week 3
Feb-4
Viruses
Bacteria
S & A Ch. 5; Agrios – pages 724-733
S & A Ch. 3; Agrios – pages 618-626, 687-691
Quiz 2
Week 4
Feb-11
Fungi
Bacteria & Viruses
S & A Ch. 2; Agrios – pages 386-404
Undergraduate Student Presentations
Week 5
Feb-18
Oomycetes
Other Eukaryotes
Fungi
Agrios – pages 404-432
S & A Ch. 4 & 6; Agrios – pages 705-719, 826-835
Undergraduate Student Presentations
Week 6
Feb-25
Abiotic Factors
Plant Disease and Disease Cycles
Eukaryotes
S & A Ch. 7; Agrios – pages 251-262, 358-383
S& A Ch. 8; Agrios – pages 77-102
Undergraduate Student Presentations
Week 7
Mar-3
Epidemiology
Disease Cycles
S & A Ch. 10 & 11; Agrios – pages 266-273
Undergraduate Student Presentations
Quiz 3
Week 8
Mar-10
Ecological Interactions
Physiological Interaction
S & A Ch. 9A
S & A Ch. 9B
Essay 1 Assigned
Week 9
Mar-17
SPRING BREAK
Week 10
Mar-24
Pathogen Genetics
S & A Ch. 9C; Agrios – pages 125-165
Quiz 4
Week 11
Mar-31
Host Genetics
S & A Ch. 9C; Agrios – pages 125-165
Quiz 5
Week 12
Apr-7
Pathogenicity
Agrios – pages 139-165
Quiz 6
Week 13
Apr-14
Plant Response: Disease
Agrios – pages 177-203
Week 14
Apr-21
Plant Response: Resistance
Agrios – pages 208-246
Week 15
Apr-28
Graduate Presentations
Term Paper Due
SCHEDULE SUBJECT TO CHANGE
Essay 1 Due
Quiz 7, Essay 2 Assigned
Essay 2 Due
Lab Schedule
Jan-21
Microscopy (Fungi & Bacteria)
Jan-28
Media Preparation
Feb-4
Serial Dilution, Field Trip
Feb-11
Immunoassay Diagnostics (Viruses)
Quiz 2 – ELISA & CTV
Feb-18
PCR and Sequence based Diagnostics (Bacteria)
Quiz 3 – PCR, MLST, PSA, HLB
Feb-25
RT-PCR based Diagnostics (Bacteria)
Quiz 4 – RT-PCR & HLB
Mar-3
Next Generation Sequencing
Quiz 5 - Sequencing
Mar-10
Sequence Analysis, Pathogenicity Test
Quiz 6 – Pathogenicity & PST
Mar-17
SPRING BREAK
Mar-24
Pathogenicity Test
Mar-31
Pathogenicity Test
Apr-7
Unknown Pathogen
Apr-14
Unknown Pathogen
Apr-21
Unknown Pathogen
Apr-28
Graduate Student Presentations
May-5
Lab Notebook Due
May-9
Lab Report – Unknown Pathogen Due
Quiz 1 – Media & Microscopy
Lab Report – Pathogenicity Due