BIOL358 Cancer Biology Spring 2016
INSTRUCTOR: Dr. Anastasia Thévenin
MEETING TIME: Tuesdays and Thursdays 11-­‐12:15, Kunkel 215
INSTRUCTOR CONTACT INFORMATION: thevenia@lafayette.edu x5464 (Kunkel 109)
OFFICE HOURS: Mondays 3-­‐4 pm, Fridays 11-­‐noon, and by appointment.
COURSE CONTENT: Biol358 is a special topics discussion-­‐based course that will focus on understanding numerous causes of cancer at the cellular and molecular levels. It will consist of an overview of several cell biology topics and then delve into cancer-­‐speciRic topics such as viruses and oncogenes, tumor suppressors, tumorigenesis, angiogenesis, metastasis and cancer treatments.
REQUIRED TEXT: The Biology of Cancer (2nd ed) 2014, Robert A. Weinberg, Garland Science.
RECOMMENDED: Immortal Life of Henrietta Lacks, Rebecca Skloot, 2010
COURSE OBJECTIVES AND EXPECTATIONS: This course is a discussion, research and presentation based. Through through lectures from the instructor, independent research of the literature by the students, class discussions and individual presentations, students will gain knowledge of enzymes and proteins involved in cancer cause and progression. This will be a fast-­‐paced course and to be successful, students will have to keep up with all assigned reading materials, including the textbook, case studies and all research articles (even if they are not the ones presenting it); in depth reading, by everyone, of every assignment is key to a fruitful class discussion. Reading primary literature takes a lot of practice (just like learning a new language). My biggest goal this semester is for you to walk out having made the connections and understanding the big picture of how mis-­‐regulation of molecules in cells leads to cancer, what are major hallmarks of tumors and what are the most advanced and current cancer treatments available for various types of cancers.
CONTACTING ME: The best way to reach me is by email. I will do my best to respond within 24 hours at the latest. If you are struggling early in in the semester, do not hesitate to get help early, rather than waiting until things get to be unmanageable. I am here to help, both inside and outside of the classroom. If you are struggling with researching your topic/putting together your presentation, I will be happy to sit down with you and guide you in the right direction. STUDENT LEARNING OUTCOMES
By the end of the semester, students will gain the ability to:
-­‐outline steps of the scientiRic method for each paper, identify hypotheses, as well as the control and test conditions for each experiment.
-­‐ effectively read and understand primary research articles.
-­‐ search journal databases and to effectively research a topic in question.
-­‐ break down difRicult concepts; students will learn and practice to give clear and organized talks and to lead/moderate/participate in group discussions.
-­‐ gain a clear understanding of connections between mis-­‐regulation of major cellular players and how this causes cancer progression.
-­‐ become knowledgeable on the current cancer treatment approaches.
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CLASSROOM POLICIES
• Arrive on time and stay for the entire time. It is disrespectful to your classmates (and me) for you to arrive late or start packing up early.
• Your attendance is required -­‐ you will be permitted one unexcused absence (if you have to miss one class discussion, please choose a day when you are NOT a presenter. Only a Dean’s Excuse will be sufRicient for the absence to be considered excused (see next section).
• 5% will be subtracted from the participation grade for every unexcused absence. Habitual tardiness will be treated as unexcused absences.
• If you know you will miss class due to sickness or family obligations, e-­‐mail me BEFORE the scheduled meeting time. I will do my best to accommodate those with well-­‐founded, non-­‐
habitual reasons for absences. A Dean’s Excuse is necessary for any make-­‐up work. • Turn in all assignments on time. Late assignments will incur 10% off your grade for each day it is late. Assignments turned in after 5 days will not be accepted.
• Respect one another’s ideas and sensitivities. For collaborative environments to be successful, all individuals must feel comfortable participating. • No cell phone or non-­‐class-­‐related internet use (see Electronic Devices Use section below). • Grades will be discussed during ofRice hours or by appointment only, NOT during class. Please be sure to meet with me regarding a particular grade within one week. If you would like to dispute a grade, you will need to do so in writing, with references to reputable sources, and within one week of having received your assignment back. • Please see me immediately if you have a diagnosed learning disability or suspect that you have one (see Statement on Learning Disabilities below).
•
To keep organized, I would recommend each student to have a three-­‐ring binder with all the printed reading material with extra blank pages for taking notes. GRADE DISTRIBUTION: A, 90-­‐100%; B, 80-­‐89%, C, 70-­‐79%, D, 60-­‐69%, F, 59 % and below. Pluses (except for A+) and minuses will be distributed within each range.
FEDERAL CREDIT HOUR POLICY AND GUIDELINES
The student work in this course is in full compliance with the federal deRinition of a four credit hour course (a total of 180 hours or 12 hours/week over ~ 15 weeks, with 2.5 hours spent in class and the rest of the time spent on researching, reading and preparing presentations/summaries). Please see the Registrar’s OfRice web site (http://registrar.lafayette.edu/Riles/2013/04/Federal-­‐
Credit-­‐Hour-­‐Policy-­‐Web-­‐Statement.doc) for the full policy and practice statement.
GRADE BREAKDOWN
Class Discussion participation/attendance (15%)
Facilitation of article discussion (15%)
Article summaries (10%)
Take home exams (2) (15% each)
Case Studies (10%)
Final exam: (20%)
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GRADED MATERIAL IN MORE DETAIL
Discussion participation. You are expected to be an active participant in your own learning process. Showing up unprepared (either by not reading the material/only skimming through the material/being unclear and entirely uneducated regarding your presentation topic) will make everyone else absolutely crazy (not just me). You are expected to be able to discuss any part of the article, Rigure, etc. Any time a primary literature article is assigned, students are asked to come to class with a summary/critique of the article, as well as two questions that you would like to discuss with the rest of the class. Summaries should be turned in at the start of class as a hard copy. Summaries are not simply a paraphrased version of the abstract. They are supposed to help you synthesize the important ideas that were in the paper and are critical in helping you prepare for the group discussion. At minimum, the summary should address the following:
-­‐ What is the point of the paper -­‐ what question was the paper asking (2-­‐3 sentences)? What general principles or big ideas are illustrated in the paper
-­‐ Write 2-­‐4 sentences for each Rigure, telling yourself what each experiment tries to accomplish, overall result and does it go along with the author’s hypothesis.
-­‐ What was the most convincing piece of data? Least convincing (if any) data?
-­‐ What is the logical extension of the work (e.g. new questions, future experiments).
-­‐ Two questions you would like to discuss with the class (can be more than two, of course) and any additional comments you’d like to make. Do not just write (for example): “What is Figure 2B about?” Your questions should be speciRic.
When reading the articles, make it a habit to highlight, underline, make notes on the margins, add extra labels to Rigures to help make them clear to you. If you encounter a word, abbreviation, technique you don’t know, google it and write in what you discover. All this preparation will make class discussions not only easy, but interesting and productive for all of us.
It is ok to be confused about a concept, experiment or a Rigure. We will work through it together to try to Rigure it out. Sometimes, I won’t have all the answers, either. However, it is not ok to come to class only having skimmed through the article. I will immediately be able to tell who read the paper closely and who did not. Please don’t let your participation grade suffer.
Case Studies: There will be 2-­‐3 case studies assigned throughout the semester. Students are responsible to do all assigned readings of the case study and to hand in answers to case study questions as a hard copy at the start of class.
Main presentation/Facilitation of your article discussion: Each pair of students will choose from the list of provided articles and will spend a full class period for their presentation. Please begin by giving a brief introduction on the system at hand, review any relevant signaling pathway(s) before moving into presenting and discussing the actual research article. Some articles may have an insane number of Rigures and data -­‐ it is the students’ job to select Rigures that drive the main point of the paper. Some Rigures should be mentioned only brieRly. We will practice the skill of choosing what should be presented and what to omit, early in the semester. Students will be provided with a more detailed rubric a few weeks before we begin these main presentations. You may need to read extra background materials in addition to your article and will be responsible for preparing and asking questions of the class, clarifying points and Biol358 Spring 2016 Dr. Anastasia Thévenin page 3
summarizing the topic. In addition, the discussion leaders/presenters should integrate any material from previous presentations (if relevant), to help us see the bigger picture and issues. Please make sure that your slides are formatted properly for a Mac. To be safe, I recommend that you have a copy of your presentation in a pdf format, in case you have issues with power point or keynote. You and your partner will have 40 minutes designated towards the article discussion.
Take home exams: There will be two take home exams during the semester. You are allowed to use your textbook, your notes and the internet. However, you are not allowed to collaborate with your class mates or any other individuals.
SCHEDULE OF TOPICS
Please note, this schedule is tentative: topics or exact dates may be subject to change as semester progresses, especially around the drop/add period -­‐ you will be notiRied as soon as possible.
WEEK
TOPICS
Assigned reading
1
1/26 Introduction to the course. Review of macromolecules.
1/28 Cell biology review.
2
2/2 Cell Biology Review
2/4 What is Cancer
Ch.1
3
2/9 What is Cancer
2/11 Case study 1
Ch. 2
Moodle
4
2/16 Viruses
Ch. 3
2/18 Discussion on HeLa Cells Rebecca Skloot, Immortal Life of Moodle
Henrietta Lacks, pages 1-­‐66
5
6
7
8
2/23 Article Discussion
Moodle
2/25 Oncogenes Ch. 4
3/1 Article Discussion
Moodle
3/3 Case Study 2 Cell Signaling in cancer
Moodle
Ch. 5
3/8 Cell Signaling in Cancer
Ch. 6
3/10 Article Discussion EXAM I DUE Moodle
3/15 Tumor Suppressor Genes
Ch. 7
3/17 Article Discussion
Moodle
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9
3/22 NO CLASS -­‐ Spring Break
3/24 NO CLASS -­‐ Spring Break
10
11
12
13
3/29 Cell Cycle Control/p53 and apoptosis
Ch. 8 and 9
3/31 Article Discussion
Moodle
4/5 Tumorigenesis
Ch. 10
4/7 Case Study 3 -­‐ Risk Assessment
Moodle
4/12 Tumorigenesis
Ch. 11
4/14 Article Discussion
Moodle
4/19 Angiogenesis
Ch. 13
4/21 Article Discussion EXAM II DUE
14
4/26 Metastasis Ch 14
4/28 Article Discussion
15
5/3 Cancer Treatments
Ch. 15/16
5/5 Cancer Treatments
*Final exam -­‐ in class (day and time to be announced)
ACADEMIC HONESTY
Per Student Code of Conduct (Student Handbook, p. 7): “ To maintain the scholarly standards of the College and, equally important, the personal ethical standards of our students, it is essential that written assignments be of student’s own work, just as is expected in examinations and class participation. A student who commits academic dishonesty is subject to a range of penalties, including suspension or expulsion. Finally, the underlying principle is one of intellectual honesty. If a person is to have self-­‐respect and the respect of others, all work must be his/her own.” ELECTRONIC DEVICES USE
Please put away your cell phones for the duration of class. Cell phone use is only permitted in emergencies only and you will be expected to leave the classroom to use your phones. Do not allow your cell phones to ring during class time -­‐ 5 points will be taken off your participation grade each time your phone rings and you will be asked to leave. I would really prefer if you did not use personal laptops in class -­‐ if you feel very strongly about taking notes using your laptop, you may do so, but if it becomes a distraction, I reserve the right to tell you to discontinue note-­‐
taking on a laptop. If you choose to use your laptop/iPad for note-­‐taking, please sit at the back of the room, rather than at the front. Points will also be taken off if I see you using your computer for class-­‐unrelated activities.
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ACCOMMODATIONS FOR STUDENTS WITH DISABILITIES
In compliance with Lafayette College policy and equal access laws, I am available to discuss appropriate academic accommodations that you may require as a student with a disability. Requests for academic accommodations need to be made during the Rirst two weeks of the semester, except for unusual circumstances, so arrangements can be made. Students must register with the OfRice of the Dean of the College for disability veriRication and for determination of reasonable academic accommodations.
PRIVACY STATEMENT
Moodle contains student information that is protected by the Family Educational Right to Privacy Act (FERPA). Disclosure to unauthorized parties violates federal privacy laws. Courses using Moodle will make student information visible to other students in this class. Please remember that this information is protected by these federal privacy laws and must not be shared with anyone outside the class. Questions can be referred to the Registrar's OfRice.
CLASS CANCELLATION POLICY
It is Lafayette’s practice to remain open for classes regardless of the weather conditions, but classes are to be held at the instructor’s discretion. Therefore, in the event of inclement weather, if hazardous road conditions preclude me from being at the College on time, class may be cancelled. Should I need to cancel class, I will send an email message through Moodle to the entire class.
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