Draft Syllabus – Eukaryotic Gene Regulation (BIOLOGICAL SCIENCES 565), Fall 2017
(last updated April 26, 2017)
Instructor: Dr. Ava J. Udvadia
Office: Lapham Hall--LAP N521
Class Hours: TR 3:30-4:45pm KEN 1140
Office Hours: Tuesday 1:30-3:30 pm LAP N521 (or by appointment)
Phone: 414-229-3404 (use only for emergency cancelation of scheduled appointment)
Email:
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.
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.
Format
The course is divided into 2 parts: lecture and literature review – both require students to actively participate 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, 2nd edition, by David Latchman; Garland Science (2015) (ISBN: 978-0-8153-4503-9)
Optional Text: If you need a reference text to brush up on gene regulation basics, I suggest Molecular Biology 2nd Ed., by David P. Clark and Nanette J. Pazdernik; Elsevier, 2012 (ISBN: 9780123785954). You can access through UWM libraries online for free
Online Materials: 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
Reading Assignments
Date / Activity / Topic / ReadingsSep 5 / Lecture 1 / Introduction to Eukaryotic Gene Regulation and the Toolbox / Latchman: pg 1-21, lecture 1 goals
Sep 7 / Lecture 2, quiz1 / Structure of Chromatin / Latchman: pg 35-65, lecture 2 goals
Sep 12 / Lecture 3, quiz 2 / The Epigenome: DNA methylation / Latchman: pg. 67-79, lecture 3 goals
Sep 14 / Lecture 4, quiz 3 / The Epigenome: Histone modifications / Latchman: pg. 79-111, lecture 4 goals
Sep 19 / Lecture 5, quiz 4 / The process of transcription / Latchman: pg. 115-133; 194-202, lecture 5 goals
Sep 21 / Lecture 6, quiz 5 / Regulatory cis-acting elements / Latchman: pg. 134-157, lecture 6 goals
Sep 26 / Lecture 7, quiz 6 / Transcription Factors: DNA binding / Latchman: pg. 159-181, lecture 7 goals
Sep 28 / Lecture 8, quiz 7 / Transcription Factors: Transactivation / Latchman: pg. 181-194, lecture 8 goals
Date / Activity / Topic / Readings
Oct 3 / Lecture 9, quiz 8 / Post-transcriptional Processes / Latchman: pg. 205-231, lecture 9 goals
Oct 5 / Exam Review
QUIZ / Eukaryotic Gene Regulation / REVIEW ALL READINGS, CLASS NOTES, AND HOMEWORK – complete practice exam
Oct 10 / Midterm Exam
Oct 12 / Tutorial / 1. PubMed literature search / Please view the webinar on PubMed linked to below, and sign up for an NCBI account before class:
https://www.nlm.nih.gov/bsd/disted/video/scientists.html
Oct 17 / Midterm Postmortem / Group discussion of exam answers
Research Topic Assignment Due October 17
Oct 19 / Paper preview / Reprogramming for regeneration / Umansky et al 2015_Runx1 transcription factor is required for myoblasts proliferation during muscle regeneration
PRESENTER:Dr. Udvadia
Oct 24 / Paper discussion
Oct 26 / Paper preview / Pioneer transcription factors / Raposo et al 2015_Ascl1 coordinately regulates gene expression and the chromatin landscape during neurogenesis
PRESENTERS:
Oct 31 / Paper discussion
Nov 2 / Paper preview / TF and histone modification / Josefowicz et al 2016_Chromatin kinases act on transcription factors and histone tails in regulation of inducible transcription
PRESENTERS:
Nov 7 / Paper discussion
Nov 9 / Paper preview / Stem cell programming / Velasco et al 2017_A multistep transcriptional and chromatin state cascade underlies motor neuron programming from embryonic stem cells
PRESENTERS:
Nov 14 / Paper discussion
Nov 16 / Paper preview / Enhancer RNAs / Bose et al 2017_RNA binding to CBP stimulates histone acetylation and transcription
PRESENTERS:
Nov 21 / Paper discussion
Nov. 21 / GRAD STUDENT REVIEW ARTICLES DUE NOVEMBE 21
Nov 22-26 THANKSGIVING RECESS
Nov 28 / Gr. Stud lect / TBA
Nov 30 / Gr. Stud lect / TBA
Dec 5 / Gr. Stud lect / TBA
Dec 7 / Gr. Stud lect / TBA
Dec 12 / Exam Review
Dec 18 / FINAL EXAM MONDAY DECEMBER 18, 12:30-2:30
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. Complete Research Topic Assignment. See specific directions on D2L under heading ”Assignments”.
5. Lead discussion of an assigned primary research paper. See specific directions on D2L under heading ”Assignments”.
6. Graduate students only: 5000-8000 word term paper on topic of choice approved by instructor. 60 minute lecture on the topic. See specific directions on D2L under heading ”Assignments”.
7. Complete peer reviews of graduate student papers. See specific directions on D2L under heading ”Assignments”.
8. 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. 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.
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). Make-up 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 examination time and provide appropriate documentation for absence. The final exam will be given on the date found in the schedule of classes – NO EXCEPTIONS.
Exam Date Time Place
Midterm Exam OCT 10, 2017 3:30-4:45 KEN 1140
Final Exam DEC 18, 2017 12:30-2:30 KEN 1140
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: Undergraduate students:
Homework/Discussion* 5% 5%
Midterm Exam 20% 20%
Paper Preview Assignment - 20%
Journal Club Presentation - 20%
Review Article Assignment 20% -
Lecture 20% -
Final Exam 35% 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.
Extra credit opportunities
1. Students with at least 95% in homework points at the time of the midterm will earn 5 bonus points toward the midterm exam.
2. Students with at least 95% in homework points between the midterm and final exams will earn 5 bonus points toward the final exam.
3. Students completing an in class peer evaluation of graduate student lectures can receive up to 2 points/review toward their homework grade
4. Students completing peer evaluations of graduate student lectures will receive 1 point/review toward their Paper preview presentation (U) or Lecture (G) grades.
Grading Scale
93-100 A
90-92 A-
87-89 B+
83-86 B
80-82 B-
77-79 C+
70-76 C
67-69 C-
60-66 D
2
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.
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 Oct 2, 2017. No drops are allowed after Oct 27, 2017, except for exceptional non-academic reasons (this must be arranged with your advisor). 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://uwm.edu/academicaffairs/facultystaff/policies/academic-misconduct/