Syllabus – Eukaryotic Gene Regulation (BIOLOGICAL SCIENCES 565),
Spring 2016 DRAFT
Instructor:
Dr. Ava J. Udvadia
Office:
Lapham Hall--LAP SB80
Class Hours:
TR 9:30-10:45am LAP 250
Office Hours:
TR 3:00 pm- 5:00 pm LAP SB80 (or by appointment)
Phone (emergencies only): 414-229-3404
Email:
audvadia@uwm.edu
Purpose of Course
It is expected that students participating in the course are comfortable with the basic concepts in
cell and molecular biology that are covered in a 300 level college Genetics or Cell Biology
course. The goal of this course is to provide students with a comprehensive understanding of
transcriptional and post-transcriptional regulation of eukaryotic genes. This goal will be achieved
using a combination of lecture, textbook readings, reviews articles, and readings from the
current literature. The course will cover the process and analysis of gene regulation in
eukaryotes including the roles of chromatin remodeling, noncoding RNA, DNA sequence
regulatory elements, and transcription factors in mediating transcriptional regulation. Finally, the
course will explore how differential gene regulation is involved in the processes of cell signaling,
development, and disease.
Format
The course is divided into 2 parts: lecture and literature review – both require active participation
in group discussions. The lecture component of the course will be based on material from the
textbook and discussion will be based on assigned homework problems. In the literature review
portion, students will have the opportunity to display their comprehension of the material by
participating in classroom discussions on current articles from the primary literature. The
discussions will be led by students and moderated by the instructor. Students are expected to
spend a minimum of 6 hours each week completing homework assignments in order to
effectively participate in the group discussions that will be a part of each class.
Prerequisite
BioSci 325 (P), or BioSci 315 (P)
Required Materials
Required Text:
 Gene Control, by David Latchman; Garland Science (January 21, 2010) (ISBN: 0815365136)
Optional Text:
 Molecular Biology 4th ed, by Robert F. Weaver; McGraw Hill 2007 (ISBN: 0073319945)
Online Materials:

https://uwm.courses.wisconsin.edu/
Access course materials through course D2L site
Time Investment
On average, students are expected to spend 48 hours per credit per semester on in-class
activities and activities outside of the classroom. The following is a workload estimate and
should be used as a guideline. Time spent on any given assignment as well as total time
required to adequately learn the material will vary from individual to individual. Students are
assessed on their performance on graded assignments and not on the time put into the course.
Total hours: 3 credits x 48 hours = 144 hours
In Class: 1.25 hours x 30 = 37.5 hours
Reading/homework assignments: 3 hours x 25 = 75 hours
Preparation of Journal Article Presentations (U): 32 hours
Preparation of Term Paper (G): 27 hours
Preparation of Lecture (G): 5 hours
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Reading Assignments
Date
Activity
Lecture 1
Topic
Introduction to Eukaryotic Gene
Regulation and the Toolbox
Readings
Latchman: Ch. 1, lecture 1
goals
Lecture 2, quiz1
Structure of Chromatin
Latchman: Ch. 2, lecture 2
goals
Lecture 3, quiz 2
Chromatin Regulation
Latchman: Ch. 3, lecture 3
goals
Lecture 4, quiz 3
Chromatin Regulation (continued)
Latchman: Ch. 3, lecture 4
goals
Lecture 5, quiz 4
The process of transcription
Latchman: Ch. 4, lecture 5
goals
Lecture 6, quiz 5
Regulatory cis-acting elements
Latchman: Ch. 4, lecture 6
goals
Lecture 7, quiz 6
Transcription Factors: DNA
binding motifs
Latchman: Ch. 5, lecture 7
goals
Lecture 8, quiz 7
Transcription Factors:
Transactivation domains
Latchman: Ch. 5, lecture 8
goals
Lecture 9, quiz 8
Post-transcriptional Processes
Latchman: Ch. 6, lecture 9
goals
Lecture 10, quiz
9
Post-transcriptional Regulation
Latchman: Ch. 7, lecture 10
goals
Lecture 11, quiz
10
Gene control and cellular
signaling pathways
Latchman Ch. 8, lecture 11
goals
Lecture 12, quiz
11
Noncoding RNAs
TBA
Exam Review,
Eukaryotic Gene Regulation
Latchman chapters 1-8;
lecture goals, your notes
Midterm Exam
Material from Lectures 1-11
Discussion
Answers to Midterm Exam
Tutorial
1. PubMed literature search
Latchman chapters 1-8;
lecture goals, your notes
Manual for PubMed
2. Critical reading of primary
research articles
Deadline for GSHow to read a
paper topic paper
approval
Nucleosome eviction and
activated transcription require
p300 acetylation of histone H3
lysine 14.
Luebben, W.R., Sharma, N.,
and Nyborg, J.K. (2010).
Proc Natl Acad Sci U S A
107: 19254-19259.
Paper preview:
TBA
TBA
Paper
discussion:
TBA
TBA
Paper preview:
TBA
TBA
3
GS paper
outline due
GS review
papers due
May 16
Paper
discussion:
TBA
TBA
Paper preview:
TBA
TBA
Paper
discussion:
TBA
TBA
Paper preview:
TBA
TBA
Paper
discussion:
TBA
TBA
Paper preview:
TBA
TBA
Paper
discussion:
TBA
TBA
Graduate
Student Lectures
TBA
TBA
Graduate
Student Lectures
TBA
TBA
Graduate
Student Lectures
TBA
TBA
Graduate
Student Lectures
TBA
TBA
FINAL EXAM
Lapham 250, 10am - noon
Class Objectives
1. Learn the different mechanisms that regulate eukaryotic gene expression.
2. Apply this knowledge to understanding articles from the current primary literature.
3. Understand the methods that are used to study the regulation of eukaryotic gene expression.
4. Critically read, discuss, and present scientific findings even when they are outside your primary field of
interest.
5. Learn how to give and receive constructive criticism on scientific communications.
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Requirements
1. Complete reading assignments as noted on the syllabus prior to each class.
2. Complete written homework assignments as specified in directions prior to each class. See specific
directions on D2L under heading ”Assignments”.
3. Participate in classroom discussions of homework questions or reading assignments from the current
primary literature.
4. Lead discussion of an assigned primary research paper. See specific directions on D2L under heading
”Assignments”.
5. Graduate students only: 5000-8000 word term paper on topic of choice approved by instructor. 30
minute lecture on the topic. See specific directions on D2L under heading ”Assignments”.
6. Complete peer reviews of graduate student papers. See specific directions on D2L under heading
”Assignments”.
7. Take midterm and final exams.
Homework Policy
Homework is assigned to help direct your reading of the chapters or articles and to facilitate “active
learning” and meaningful classroom discussions. Completion of homework and participation in subsequent
classroom discussions is essential for the successful completion of the course. Be prepared to spend, on
average, 3 hours per assignment. Homework assignments are described in detail in the D2L handout
“Daily Assignments”. In order to receive credit for homework, you must make a good faith effort to
correctly answer all homework questions in your own words (e.g. “I don’t know” or “I didn’t understand” or
copying from the text are not acceptable answers). Incomplete homework is worth 0 points. Answers to
homework will be part of the classroom discussion. You must participate in the class discussion in order to
receive full credit for the homework. If you are absent from class, but submitted the homework on time you
will receive 2 points for the homework. Since answers are discussed in class, homework submitted after
class is not accepted. Homework that is submitted late, but before class will receive half credit if you are in
class. Because preparation for class is essential for effective classroom discussion, a minimum of 75% of
total homework points is required. Averaging less than 75% in homework points will result in a 5 point
deduction from your overall weighted average grade. Students with at least 95% in homework points at the
time of the midterm will earn 5 bonus points toward the midterm exam. Students with at least 95% in
homework points between the midterm and final exams will earn 5 bonus points toward the final exam.
Examination Policy
There will be 1 midterm and a final examination. Exams will be in “blue book” format and consist of essay
and/or short answer questions. Partial credit will be given for partially correct answers. Students will be
examined on their ability to apply their knowledge of eukaryotic gene regulation to a given research
problem. Students are expected to know how to form testable hypotheses, propose appropriate
approaches, and be able to articulate possible outcomes and interpretations that could result from their
proposed approaches. Requests for make-up exams in the event of an emergency should be made as
soon as possible and must be supported by documentation (e.g. physician’s order, accident report). Makeup exams will be oral or written, at the discretion of the instructor. In order to qualify for a make-up exam
for religious observances or other unavoidable absences (e.g. scientific conference attendance or
graduate school interview), you must notify Dr. Udvadia at least 2 weeks before the scheduled
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examination time and provide appropriate documentation for absence. The final exam will be given on the
date found in the schedule of classes.
Exam
Date
Midterm Exam
Final Exam
May 16, 2016
Time
Place___
9:30 – 10:45 am
LAP250
10 am- noon
LAP250
Grading Policy
Grades will be calculated on the basis of 2 exams, participation (homework and class discussion), and
journal article presentations (undergrads) or term papers & lectures (grad students only). Your final grade
will be weighted as follows.
Graduate students:
Homework/Discussion*
Midterm Exam
Paper Preview Presentation
Journal Club Presentation
Lecture
Term Paper
Final Exam
5%
20%
20%
20%
35%
Undergraduate students:
5%
20%
20%
20%
35%
* Students must have points in each category to pass the course. Students completing less than 75% of
the homework points will be penalized 5 points from the total weighted average grade of the course.
Grading Scale
93-100
A
90-92
A87-89
B+
83-86
B
80-82
B77-79
C+
70-76
C
60-69
D
Expectations of students in Bio Sci 565
1. I expect you to have an adult level of maturity, self-motivation, and a strong desire to
learn the material in this course.
2. I expect you to have passed the pre-requisite courses with a C or better and to have
college level writing and speaking skills.
3. I expect you to show up for every lecture, on time.
4. I expect that you will prepare for lecture by completing the reading assignments before
class.
5. I expect you to upload written assignments to D2L on time.
6. I expect you to take notes during lecture.
7. I expect you to utilize the study materials provided to you on the D2L site.
8. I expect that you will spend at least 6 hours/week outside of class studying the material
for this class.
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a. Reading assignments should be completed ahead of lecture.
b. Lecture notes and reading assignments should be reviewed with a study partner
or group at least once/week.
c. Any concepts that are unclear to you after reading and reviewing should be
discussed with the professor at office hours (schedule alternative appointment if
you have a class/work conflict with office hours).
9. I expect you to ask questions when you are confused and to volunteer to answer
questions I ask at the beginning of and during the lectures.
10. I expect you to prepare for exam reviews by studying the material ahead of time and by
asking specific questions at the review session.
I am here to guide you in studying Mechanisms of Eukaryotic Gene Regulation. Meeting the
expectations outlined above will ensure that you learn the material to the best of your ability.
Registration Policy
Last day to drop class without “W” appearing on academic record is Feb 19, 2016. No drops will be
allowed after March 25, 2015, except for exceptional non-academic reasons. This course may not be
taken with an audit or credit/no credit status. In the event of excess enrollment, priority will be given to
students who are registering for the course for the first time.
Attendance Policy: This success of this course is heavily dependent on student participation
and interaction therefore attendance is required.
Cell Phone Policy: Please refrain from texting or talking on the phone during lectures and
discussions.
Academic Conduct Policy: There is absolutely no tolerance for any kind of cheating or
plagiarism on any of the assignments (including homework) in this class. The University has a
responsibility to promote academic honesty and integrity and to develop procedures to deal
effectively with instances of academic dishonesty. Students are responsible for the honest
completion and representation of their work, for the appropriate citation of sources, and for
respect of others’ academic endeavors. Students caught plagiarizing will receive a reprimand
and a zero for the assignment at a minimum and may be subject to more serious sanctions by
the University. This course follows the guidelines and procedures detailed in the description of
Student Academic Disciplinary Procedures found in Regents Policy Statements, UWS Chapter
14 and UWM Faculty Document #1686 and can be found online at
http://www.uwm.edu/Dept/Acad_Aff/policy/academicmisconduct.html.
Accommodations for Students with Disabilities: If you need special accommodations to
meet the requirements of this course, please contact the Accessibility Resource Center (Mitchell
Hall Room 112, 229-6287, https://uwm.edu/arc/) and inform the instructor
Firearms Policy:
A. No Firearms or Dangerous Weapons in UWM Buildings Individuals are prohibited from
carrying firearms and dangerous weapons into buildings or portions of buildings that are owned,
occupied, or controlled by UWM. UWM shall place signs in prominent places near all of the
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entrances to UWM buildings notifying the UWM community and visitors of this ban. This ban on
firearms and dangerous weapons inside UWM buildings applies equally to Licensees. This ban
does not apply to firearms or dangerous weapons carried solely within motor vehicles that might
be parked in UWM parking facilities except as provided in IV.B of this Policy (below).
B. No Firearms within 1000 Feet of Schools Individuals are prohibited from possessing
firearms, except for a handgun carried in a concealed manner by a Licensee, outside of UWM
buildings, on any portion of UWM buildings or grounds that falls within 1,000 feet of any school
(defined above) (e.g. Hartford Elementary School), including within vehicles parked in UWM
parking facilities within this zone. These areas are known as “Gun-Free School Zones.” Maps
showing the Gun-Free School Zone surrounding Hartford Elementary School and other schools
nearby UWM buildings are attached as Appendix A. UWM shall place signs in prominent places
on UWM grounds falling within these zones notifying the campus community and visitors of the
ban.
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